Environmental Ecology

Lecture 1 – Introduction
It’s important to study environmental biology mainly due to climate change (Warming stripes,
an illustration that shows the annual deviation of temperatures from 1850 to 2017). However,
climate change is not the only issue that we are facing, but there are a range of interlinked
processes that lead to environmental degradation, loss of biodiversity and to a change and
potential collapse of ecological systems as we know them.

The module will provide a foundation of knowledge about the natural and managed
environment, highlight the importance of the environment to human society and well-being,
and illustrate the basic principles of ecology through which living organisms interact with the
environment.

To do so it will Introduce the evolutionary and bio-geochemical principles underlying

Environmental Biology, discuss the evidence for and drivers of environmental degradation
and climate change and assess how society can respond to the environmental challenges and
the climate emergency.

So some questions this module will answer are: How does the Earth System work and how do
major biological processes affect this system? How do organisms interact with one another
and the environment? How is human activity perturbing environmental and ecological
processes? Can we adapt/mitigate/restore and live more sustainably?

1. Global scale
In these previous years we spent a lot of time and effort exploring the space, however, the
concept of colonizing other planets to ensure the survival of our species is unrealistic. There is
no planet B.

In the last years (2020 and 2021), there had been floods (China, UK, Kenia…), droughts and
wildfires (Siberia, UK, Amazon…), and extreme temperatures (NW USA, Texas…).

All these extreme events mean the loss of life, people displaced, destruction of infrastructure…
the estimated costs are $40 billion for Germany alone.

All of these is caused mainly by human activity (pollution, plastics, oil spills, carbon emission…).
Climate change also has effects like eutrophication, leading to a plague of jellyfish in Japan and
the Mediterranean Sea.

Lecture 2 – The environment and the individual

Part I: What do humans get from the environment?

Resources like air, water, food, shelter, medicines, clothing, culture all come from the
environment. The human species has developed an ability to modify the environment to
enhance all of these resources. This has led to a triplication of the population in the last 100
years. Other species thrive when good conditions (mice plague), but humans manage to adapt
and persist even in bad conditions.

Part II: How do humans interact with, and modify, the environment?

In the beginning, our ancestors were hunters and gatherers due to the lack of technology and
agriculture. Nowadays, the only form of this is fishing, because now we have the technology to
capture water and food.

The environment provides a wide range of ‘goods’ and ‘services’ to human beings. It’s
important to identify these ‘goods’ and ‘services’, understand how they function and their
‘value’ to humans whilst there is still time to do something about it.

 Natural Capital: World’s stocks of natural assets which include geology, soil, air, water,
and all living things. It is from this Natural Capital that humans derive a wide range of
goods and services which make human life possible. These are often delivered by
ecosystems, which has led to them being called ecosystem goods and services.
 Ecosystem: A community of plants, animals, and microorganisms, along with their
environment, that function together as a unit. An ecosystem can be as large as a rain
forest or as small as a rotting log. The whole globe is an ecosystem too.
1. Typology/Classification of Ecosystem Goods and Services
 Supporting. Ecological services that go in the background but are essential for the
production of all other services. E.g. Soil formation, photosynthesis, primary production,
nutrient cycling…
 Regulating. Benefits obtained from the regulation of the environment. E.g. air quality,
climate, water quality, erosion, pest and disease, pollination.
 Provisioning. Material benefits obtained from the environment. E.g: food, fibre, fuel,
ornamentals, genetic resources, fresh water…
 Cultural. Non-material benefits obtained from the environment. E.g: spiritual value,
educational value, inspirational value, aesthetic value, recreational value…
These categories can be related to the constituents of well-being. The arrows indicate the
linkages there are.

Part III: Is this anthropocentric approach the best one?

 Ecosystem Approach: the comprehensive integrated management of human activities,

based on best available scientific knowledge about the ecosystem and its dynamics…and
aims to achieve sustainable use of ecosystem goods and services and maintenance of
ecosystem integrity.
1. Supporting services
One good example of this is nutrient cycling (biogeochemical cycles). Approximately 20
chemical nutrients (elements) essential for life are cycled through ecosystems and maintained
at different concentrations in different parts of ecosystems. Ecosystems regulate the flows
and concentrations of nutrients through complex processes that allow the elements to be
extracted from their mineral sources or recycled from dead organisms. This service is provided
by a diversity of different species, mostly microorganisms. These species differ between
ecosystems.
2. Regulating Services
 Climate regulation. Ecosystems influence climate both locally and globally. At local scale,
changes in land cover can affect both temperature and precipitation (e.g. forests can affect
regional rainfall levels). At global scale, ecosystems play important role in climate by either
sequestering or emitting greenhouse gases (e.g. forests capture and store carbon dioxide).
 Natural hazard regulation. Ecosystems can play important roles in modulating the effects
of extreme events such as floods and landslides, affecting the probability and severity of
events: Soils store large amounts of water, facilitate transfer of surface water to
groundwater, and prevent or reduce flooding. Also, barrier beaches, wetlands, and lakes
attenuate floods by absorbing runoff peaks and storm surges.
 Regulation of pests and disease. Intact forests reduce occurrence of standing water
(breeding ground for mosquitoes) and therefore can reduce prevalence of malaria.
Ecosystem modifications like dam building and expansion of agricultural irrigation have
sometimes increased local incidence of infectious diseases such as malaria,
schistosomiasis, and arbovirus infections, especially in the tropics. Other modifications to
ecosystems have reduced incidence of infectious disease.
On one occasion in Lake Malawi, overfishing led to an increase in Schistosomiasis (parasitic
worm). Fish predation reduces numbers of the intermediate host (snail) of the parasite
which causes the disease.
3. Provisioning Services
 Food. Food is essential to human life and is provided by natural ecosystems and through
agriculture. Food production (agriculture) and the capture of wild fish to feed such a large
population is having a huge adverse impact on the environment.
 Timber, fibre, and fuel. Timber is used in building, manufacturing, fuel, and other needs.
Forests (providing fuel and charcoal), agricultural crops, and manure are all used as
sources of biomass energy. Wide variety of crops and livestock used for fibre production
(Cotton, flax, hemp, jute, silk, wool…).
4. Cultural Services
Human cultures, knowledge systems, religions, social interactions, and amenity services have
been influenced and shaped by the nature of ecosystems. At the same time, humans have
influenced and shaped their environment to enhance the availability of certain valued
services. Ecosystems contribute to cultural diversity and identity, cultural landscapes and
heritage values, spiritual services, inspiration (such as for arts and folklore), aesthetics,
recreation, and tourism.
5. Water
Water belongs to all 4 classifications: is required for life, supporting ecosystems, it quality and
quantity regulates the environment. Its supply is used by people (provisioning) and it has
landscape and recreational value.
 Part IV: The Millennium Ecosystem Assessment

This assessment was called for by UN Secretary General in 2000 and completed in 2005 and
was undertaken by a lot of experts so has the value of peer reviewed.

It’s a critical evaluation of information concerning the consequences of ecosystem changes for
human well-being. It’s intended to be used to guide decisions on complex public issues.

Its conclusion states that, mainly due to population increase, over the past 50 years, humans
have changed ecosystems more rapidly and extensively than in any comparable period of time
in human history. This has resulted in a substantial and largely irreversible loss in the diversity
of life on Earth.

1. Unprecedented change
 Structure and function of ecosystems . More land was converted to crop land in the 30
years after 1950 than in the 150 years between 1700 and 1850. In 2000, cultivated systems
(areas where at least 30% of the landscape is in crop land, shifting cultivation, confined
livestock production, or freshwater aquaculture) covered 25% of Earth’s terrestrial surface.


Biomes. A biome is a major ecological community, classified according to the predominant

vegetation and characterized by adaptations of organisms to that particular environment.
Some biomes have loss up to 70% of the area, being converted into a cultivated system.
Ecosystems in some regions are returning to conditions similar to their pre-conversion
states. However, rates of ecosystem conversion remain high or are increasing for specific
ecosystems and regions.
 Species diversity. Humans have increased the species extinction rate by as much as 1,000
times over background rates typical over the planet’s history. This is known by fossil
record. 10–30% of mammal, bird, and amphibian species are currently threatened with
extinction.
 Ecosystems. 20% of the world’s coral reefs were lost and 20% degraded in the last several
decades. 35% of mangrove area has been lost in the last several decades. The amount of
water in reservoirs quadrupled since 1960 and withdrawals from rivers and lakes doubled
since 1960.
Mangrove ecosystem provide protection against tides, winds, storm surges and habitat for
fish (physical barrier). Climate change have effects on stability and health through sea
level rise and variable rainfall: Reduced water flows in dry season increase salinity and
intense rainfall reduces salinity. Also, under pressure from pollution, deforestation and
overfishing this ecosystems are damaged.
2. Status of services from MEA
There is no data for the supporting service 😊
 Status of Regulating Services (C cycle). Since about
1750, the atmospheric concentration of CO 2 increased
by about 34%. Approximately 60% of that increase
occurred since 1959. Terrestrial ecosystems were, on
average, a net source of CO2 during the 19th and early
20th centuries. Primarily due to deforestation, but
with contributions from degradation of agricultural
land, pasture, and forests. They became a net sink
around middle of last century (although carbon losses
from land use change continue at high levels). Factors
contributing to growth of role of ecosystems in carbon sequestration include afforestation,
reforestation, and forest management in North America, Europe, China, and other regions.
 Status of Provisioning Services (fishing). We can see how over time the unsustainable
fishing is increasing, this can lead to phenomena similar to what happened with the North
Atlantic Cod. After 50 years of heavy harvesting in late 20th century, Canadian cod fishery
collapsed in early 1990s. Total bans ensued, and recovery was expected. However, this has
been a slow process.

 Status of Cultural Services. ‘Rapid loss of culturally valued ecosystems and landscapes lead
to social disruptions and societal marginalization, now occurring in many parts of the
world’ / ‘people display, in general, a strong preference for natural over built
environments’ / ‘numerous studies have demonstrated that contact with nature may
enhance restoration from stress and increase health and well-being’
Part V: Does it matter?
 1. UK issue
UK had its own National Ecosystem Assessment. It was the first analysis of UK’s natural
environment in terms of benefits provides to society and continuing economic prosperity. Part
of it belongs to the Living With Environmental Change (LWEC) initiative. It began in mid-2009
and reported in June 2011. Inclusive process involving many government, academic, NGO and
private sector institutions.

Due to increasing of population, UK house construction increased a lot. Also, there has been
several floods. Brexit meant that the UK was no longer part of the EU Common Agricultural
Policy (CAP), so it had to make its own. In this new CAP, farming will be more environmentally
friendly.

The fate of the environment and ecosystems (nationally and globally) is influenced enormously
by ‘political’ decisions.

Lecture 3 – Systems ecology

ECOLOGY: The scientific study of (i) the distribution and abundance of organisms, and the
interactions that determine their distribution and abundance; (ii) the relationships between
organisms and their environment. It has a descriptive component and a understanding
component.

1. Evolution
The theoretical basis for understanding all life on Earth is evolution by natural selection.
Natural selection is the differential success (survival and reproduction) of individuals within
the population that results from their interaction with the environment: Heritable variation in
characteristics and variation results in differential success.

Natural selection results in changes in the properties of populations of organisms over multiple
generations: evolution. Adaptation is a product of evolution by natural selection: Any heritable
behavioural, morphological, or physiological trait that has evolved by natural selection such
that it maintains the fitness of an organisms under a given set of environmental conditions.
Fitness = long term reproductive success.

2. Resources
All living things require resources, and they can only survive, grow, and reproduce under
certain sets of physical conditions.

 Resources are biotic or abiotic components of the environment that are consumed or used
by an organism. E.g. Sources of energy (autotrophs, heterotrophs), nutrients for
maintenance, growth and reproduction or oxygen, CO2, water, space.

 Conditions are physicochemical features of the environment: temperature, humidity,

salinity, pH, physical effects of tides, wind etc. They are not consumed by organisms.
Organisms are adapted to – and have requirements for - particular sets of conditions. They
also have a range of tolerances. Conditions can change in space and time and affect the
abundance and distribution of individuals and populations. Organisms can also alter the
conditions in their environment. (E.g. The rain in a rainforest is caused by all the
vegetation).
Through natural selection, species have evolved to optimize the acquisition of resources and to
be adapted to the physical conditions.
 3. No species lives in isolation
 Community: assemblage of species populations that occur together in space and time.
 Ecosystem: the biological community plus the abiotic environment in which it is set.
A community can be defined at any scale within a hierarchy. A forest or a puddle.
4. Biodiversity
"The variability among living organisms … and the ecological complexes of which they are part;
this includes diversity within species, between species and of ecosystems“. Results from the
interactions between organisms & their environment (biotic & abiotic).

A community is not a random collection of species, it is characterized by its structure &

dynamics.

• Community structure: (i) species richness, relative abundance; (ii) types of species: their
functions & how they relate to each other.
• The structure is affected by: Conditions & resources present, interactions within &
between species: competition, predation, mutualism. The action of foundation species and
keystone species (if you remove that specie, the ecosystem collapses). Frequency of
disturbances or disruptive events.
Other factors that determine the abundance and distribution of a population are Ability to
disperse to new areas. Geographical barriers to dispersal
(mountain ranges, ocean, desert etc.). Evolutionary /
geological history, continental drift (geological time scale)
e.g. kangaroos.

5. Food web
The community consists of a series of interconnected
trophic interactions. Species within the community can be
classified into functional groups according to the way they
acquire energy.

Energy flows in a food web from one part of the ecosystem

to another (trophic dynamics). Energy is fixed and released
through metabolic processes that drive all the living
components of the biosphere.

Species within the community can be classified into functional groups according to the way
they acquire energy:
 Herbivores: plants are abundant as food, but it is poor quality, taking a large investment in
time and energy to digest.
 Carnivores: High energy food but incurs high costs in catching and killing (higher costs than
foraging costs of herbivory).
A generalized food chain – the transfer of energy through a sequence of trophic levels:

Note how short this chain is – most food chains tend to have 3 or 4 levels. Chains with 5 links
are very rare.

The laws of thermodynamics govern energy flow. Potential energy: stored energy. Kinetic
energy: performs work at the expense of potential energy. Energy is neither created nor
destroyed. It can change from one form to another and move from place to place.
 Part II: Ecological energetics

Energy is fixed and released through metabolic processes that drive all the living components
of the biosphere. Energy is transformed between potential and kinetic forms when it is fixed or
released, and it is lost from the food web with each transformation.

The standard units of energy are the joule (energy used in moving 1kg through 1m) or the
calorie (heat required to raise 1g of water by 1 oC). (Note: 1 joule = 4.3 calories)

The first ecosystems probably comprised unicellular chemosynthetic bacteria releasing energy
from inorganic molecules. But since 3 billion years ago, oxygenic photosynthetic organisms
have supported the majority of ecological communities that have developed on Earth since the
oxidation event, which willed all the anaerobic bacteria since oxygen is toxic.

Energy enters the biosphere mainly as sunlight. Radiant energy on earth = 5 x 10 10 J m-2 per
year. Both chemosynthetic and photosynthetic organisms are autotrophs (literally ‘self-
nourishers’).

Primary producers: the base of food chains and fix energy in the process of photosynthesis

1. Primary producers
Photosynthetic organisms utilize the radiant energy of sunlight, and water as an electron
source, to synthesize carbohydrates.
6CO2 + 6H2O  C6H12O6 + 6O2
carbon dioxide water radiant energy glucose oxygen

Only 44% of light is at wavelengths used by photosynthetic pigments. Typically, around 2% of

the energy that strikes the leaf surface is fixed in sugars, so it’s
not very efficient. Nevertheless, the biomass of
photoautotrophs is the principal source of energy for all major
ecosystems.

• Productivity. The fixing of energy in tissues or gametes.

• Gross Primary Productivity (GPP). Total amount of energy
assimilated from photosynthesis. NPP = GPP - R
• Respiration (R). Energy used in metabolism.
• Net Primary Productivity (NPP). Energy available for
growth or reproduction after that used in respiration.

2. Primary production
Temperature, water, and nutrients control primary production
in terrestrial ecosystems. NPP is constrained by water,
temperature, nutrients…

Here we have some measures of NPP for different ecosystems

plotted against precipitation and temperature. And the higher
the precipitation and temperature, the higher the productivity.

The increasing mean of annual temperature is directly related

to annual intercepted solar radiation at the site, which is the
key factor, although temperature also matters as it affects
enzyme activity. Sites with high mean temperature typically support higher rates of
photosynthesis.
This is a graph
showing NPP
against length of
photosynthetic
period in days in
forests of North
America.

As the length of the

photosynthetic period increases, NPP also increases.

3. Evapotranspiration and productivity (the wetter

the better)
A combination of warm temperatures and good water supply
for transpiration give higher primary productivity.

Transpiration is the evaporation of water from plants through

the stomata while they are photosynthesizing.
Evapotranspiration is the combined value of land surface
evaporation and transpiration from plants.

It reflects the demand and supply of water of the ecosystem.

The demand of water of an ecosystem is a function of
incoming radiation and temperature. The supply is a function
of precipitation.

In this graph it shows the production against

evapotranspiration of different ecosystems. The ecosystems
where the evapotranspiration is higher (high supply and
demand of water) have the most productivity.

4. Aquatic ecosystems
Temperature, light, and nutrients control primary production
in aquatic ecosystems.

• Photosynthetic organisms can only grow when GPP > R.

• Compensation point: light intensity is such that GPP = R.

With depth comes the gradual loss of light which

implies the less energy available for photosynthesis.

The demand for respiration from a plant is always

constant, but the productivity declines with depth until
it reaches the compensation depth/point where below
it no plant can grow.

The most productive waters are coastal. Shallow waters

allow greater transport of nutrients from bottom
sediments to surface waters, aided by wave action and tides and also coastal waters receive
larger nutrient inputs from rivers.

Ocean systems are crucial for global productivity. Some people say that the oxygen you take
one every two breaths (or two every three) comes from the sea. (Mt=million metric tons).

In this table we can see the importance of both marine systems

and tropical rainforests for both oxygen production and CO 2
sequestration.

Part III: Nutrient cycling

Energy moves from primary producers to the rest of the food

chain. The key principle is that primary productivity limits

secondary production. Secondary production depends on primary

production for energy. So primary production acts as a constraint.
E.g. grass biomass determines cow biomass.

In both figures, secondary production increases with primary

production.
Some energy in the form of NPP, once consumed by herbivores, is passed from the body as
waste (faeces, urine). Of the energy assimilated, part is lost as heat for metabolism. The
remainder is available for maintenance and is eventually lost to the environment as heat.

The energy left over goes into growth and product of young. This net energy of production is
secondary production.

So energy is used in metabolism, reproduction, and growth. The efficiencies of these

transformations are expressed as percentages.

• Assimilation efficiency = Energy assimilated (A)/Energy consumed (C). Measures the

efficiency of energy transfers between consumers and consumed. Carnivores have
higher efficiencies because it is easier to digest animal tissues than plant material.
• Production efficiency = Energy fixed in tissues (P)/Energy consumed (C). Measures the
proportion of energy consumed that eventually becomes fixed within tissues of a
consumer.
• Growth efficiency = Energy fixed in tissues (P)/Energy
assimilated (A). Measures the efficiency with which new
tissues are produced, allowing for losses due to
respiration and gamete production. -

1. Production efficiencies of animal groups

Endotherms have lower efficiencies because they have higher
metabolic costs, associated with maintaining a constant body
temperature.

Ectotherms have lower metabolic costs, and this is reflected in

their production efficiencies. The adaptive advantage of the
maintained body temperature, of course, is that endotherms can
remain active when temperatures are too low for ectotherms.

As the production efficiency of insect is really high, people are starting to think in farming
insects as a source of food.

2. Energy flow through the food chain

0.01% of the NPP ends up in mouse tissue (population of mice is kept low by predators so

primary producers don’t disappear).

2.5% of the energy within the mouse is

incorporated into the weasel. Overall, the
weasel receives 0.0003% of the net primary productivity. The energy attenuates as it
passes along the chain and most finds its way to the decomposer community.

Food chains have a set number of links, but rarely extend beyond 5 links. The rapid
decline in energy up the chain was thought to limit the number of links, but we actually
don’t see longer chains in those dominated by more efficient ectotherms.

Chain length is not controlled by primary productivity (i.e. no difference high vs low
productive biomes), but by other factors.

 Consumers get larger and fewer with each link. Large carnivores need large territories,
which limits the number of links.
 ‘Top-down’ control: Predators control the abundance of prey populations. This Not to scale!
affects abundance of organisms at all levels below in the chain, either
decreasing or increasing it. (A lot of birds, few fish 1, a lot of fish 2, few fish 3, a
lot of shrimp).
Food chains are not that simple, they’re actually food webs.

3. Decomposition
Ecosystems have 2 major food chains: the grazing food chain and the detrital food
chain, which are linked.

The distinction is the source of energy for first level consumers – the herbivores. The grazing
food chain is driven by primary producers (photosynthetic organisms) and the detrital food
chain is driven by detritus (dead organic matter).

All organisms end up as detritus. There are herbivores that eat living plants and others that eat
decomposing plants. Carnivores eat all types of herbivores.

In most ecosystems the bulk of the energy fixed by primary producers pass straight to the
decomposer community as
herbivores are kept in check
by the carnivores. This fuels
the productivity of the
decomposers whilst also
driving the recycling of
nutrients.
The decomposer community is essential for
ecosystem survival: Most essential nutrients are
recycled within the ecosystem. Decomposition
and nutrient recycling are complex processes
involving a wide variety of organisms (Leaching,
fragmentation, changes in physical and chemical
structure, ingestion, excretion).

Bacteria are the dominant decomposers of dead

animal matter, while fungi are the major
decomposers of plant material.

The rate of decay is related to:

• The quality of plant litter as a substrate.

• Features of the physical environment

that directly affect soil organisms (soil
texture, pH; temperature, precipitation).

Decomposition proceeds as plant litter is

converted into soil organic matter (Nutrients in
organic matter are mineralized during
decomposition).

4. Biogeochemical cycles

The shading, width and direction of the arrows

indicates the scale of energy flow between
producers, consumers, and reducers.
Not every nutrient transformation is biologically mediated. All nutrients flow from the
nonliving to the living, and back to the nonliving components of the ecosystem. This cyclic path
is known as a biogeochemical cycle.

5. Human appropriation of net primary

productivity, HANPP
As usual, the humans come along and take

everything for themselves. Humans appropriate

the Earth’s NPP by growing plants for food, fiber,
fuel, timber… Converting land to less productive
forms: tropical forest to pastures, growth of cities,
desertification through over grazing.

Population and per capita consumption

interact to determine regional scale
impact. East and south Asia, with half the
world’s population, appropriates 72% of its
regional NPP but has the lowest per capita
consumption of any region.

The average HANPP of industrialized

countries is double that of developing
nations, which comprise 83% of the world
population.

What does this mean for a sustainable world?

Less consumption of NPP per capita in industrialized countries.

And for developing countries? Future agriculture (agroecology) – efficient production for
people & leave room aside for nature.

Lecture 4 – The Climate System

Part I: Introduction to weather, climate, and trends

 Weather. The condition of the

atmosphere at a particular time and
place, with regard to the temperature,
moisture, rainfall, cloudiness, etc. Single
event given in a single day.
 Climate. The general condition of the
atmosphere at a particular location over
a long period of time, generally 30 years.
Long term trend.
With the climate information of different
location we can create climate maps.

1. Temperature trends
This very famous plot is known as
the ‘hockey stick graph’, and it

It was made with a lot of sources

of information (e.g. coral rings or
tree rings), and the redder the

Relative to the baseline (0), the

average temperature of the last
hundred years was 1 degree below 0. We can see how during that years there is a lot of

In the last years, the overall trend is increasing over the baseline. The rate of change is also
increasing over time. This was calculated using instrumental data (black line in the plot), which
correlates completely with the previous information.

This change in temperature has resulted in a plethora of observations:

• Precipitation patterns, (flood, drought).

• Retreat of land bound ice, (Greenland).
• Thawing of permafrost.
• Loss of sea ice.
• Increased occurrence of extreme weather events (flooding, wildfires).
• Shifting habitat ranges.
• Phenological shifts (shift in timing of life events e.g. flowering time, mating season…).
Part II: Earth’s energy balance

The Sun is emitting a vast amount of radiation. 64 million W/m 2 (J/m/s) is produced at surface
of the sun but only 1370 W/m2 is emitted directed at the earth. However, due to the Coriolis
effect, the average over the whole Earth at the top of the atmosphere is 342W/m 2 (incident
radiation). The Earth absorbs and radiates that energy. The balance of the input and output of
the radiation is the radiative equilibrium.

It’s estimated that without atmosphere the average temperature would be -18ºC and not the
actual 15ºC. This is due to the greenhouse effect, when the re-radiated energy reflected from
the Earth id captured by the atmosphere and reflected back or scattered.

1. Planetary neighbours
 Venus. 154,000 times as much carbon dioxide in its atmosphere as Earth, so its
atmosphere has a super-greenhouse effect (460ºC average).
It was thought that early in the history of the solar system it was covered in oceans, but
now it has lost all the water, so all of that water is now water vapor in the atmosphere (a
very potent greenhouse gas). Over time, the H in water was lost, and the oxygen combined
with carbon to make CO2 (now 96.5% of atmosphere is CO2).
 Mars. Thin atmosphere, so it has a very weak greenhouse effect (-60 ºC average).
2. Earth’s energy budget
From all the incoming radiation, 30% is already reflected by clouds, upper atmosphere, shiny
surfaces… The other 70% is absorbed by the atmosphere and the land.

The Earth then re-emits this radiation at a much longer wavelength. 40% of this re-emitted
energy passes through the atmospheric window, the rest is recaptured by the atmosphere.

There is a disparity between the radiation that’s absorbed and the radiation that’s re-radiated.
This due to the cycle of ‘back radiation’ that the atmosphere recaptures and holds on for a
little bit longer. This is driven by the greenhouse gasses, altering our weather.

The total radiation input and output are quite balanced in both the surface and the
atmosphere. There’s still a slight of difference which means warming in this case.

3. Factors that can alter energy flow and balance

 Solar input. Lauded by climate change deniers.
 Atmosphere’s composition. E.g. increase of greenhouse gasses.
 Hydrological cycle. E.g. increase in clouds leads to increase in albedo.
 Ocean. 70% of the planets surface are ocean. Changes in the circulation or absorption.
 Land surface. Land use changes Earth’s reflectivity.
 Cryosphere. Frozen stuff.
4. Radiative Forcing
So we have seen that the earth absorbs radiation from the sun and re-radiates energy into
space and these processes are near equilibrium. Any factor that changes the energy impinging
on the earth or being re-radiated will alter the equilibrium.

Such effects are called radiative forcing and they can be positive or negative. Equally
important, they provide a basis for quantification. Defined as Wm 2. 2 definitions:

 Radiative forcing is a measure of how the energy balance of the Earth-atmosphere system
is influenced when factors that affect climate are altered (IPCC – Intergovernmental Panel
on Climate Change 4th Assessment).
 The change in average net radiation at
the top of the troposphere which
occurs because the concentration of a
greenhouse gas or some other change
in the overall climate system.
(Houghton).

In this plot the have the changes in W/m2

driven by different factors.

There are natural and anthropogenic

factors and cooling and warming factors.

CO2 is not the most potent greenhouse gas,

but it has the biggest impact due to its quantity in the atmosphere.

Here we can find all those factors previously listed that could alter the energy flow and
balance.

5. Greenhouse gases
All greenhouse gasses are
multiatom molecules (they
have 3 atoms or more). This
characteristic allows them to
have 2 different
behMethylococcus
capsulatuaviours: stretching
and bending. The asymmetric
stretching and the bending-
twisting create a dipole that
vibrates in different
frequencies, so they can
interact with energy of lots of
different frequencies.

Water vapor, nitrous oxide

(N2O), methane (CH4), CO2…

The solid lines show the

radiation emitted from the sun
and reradiated from the Earth.

The solid blocks show what actually passes through the atmosphere. The lines show what it is
expected to emit, but the solid blocks show what
actually happens. The difference is due to things that
are in the atmosphere.

CO2 and water vapour captures some energy that’s

emitted from the Earth, making the difference between
what’s expected and what’s observed. With the Sun’s energy happens the same, but this time
with ozone.

The importance of this plot is how much of this interaction has an anthropogenic origin.

Part III: Summary

 Climate is the condition of the atmosphere over the long term.

 Many changes in natural systems and phenomena point to a changing climate
 Earth temperature is a consequence of an equilibrium between solar input and re-
radiation
 Changes in the energy flow will influence the radiation balance and hence earth
temperature.
 Greenhouse gases absorb re-radiated energy warming the planet
Lecture 5 – Hydrological cycle
Water can be stored in different locations (atmosphere, clouds, lakes, rivers, snow and ice,
underground…) but it is always continually moving. Some of the water is salt and some fresh
(2.5%).

1. Infiltration
Key physical process. Some water from rain and snow infiltrates into subsurface soil and rock.
Some will remain in shallow soil layer, where it gradually moves vertically and horizontally
through soil and sub-surface material. Eventually, it might enter a stream by seepage into
stream bank. Much of the water moves vertically downwards and ends up as ground water.

2. Ground water storage

Large amounts water is stored in the ground. Water still moving, possibly very slowly, and is
still part of water cycle. Upper layer of soil is
unsaturated zone, where water is present in
varying amounts that change over time but does
not saturate soil. Below this layer is saturated
zone, where all pores, cracks, and spaces between
rock particles are saturated with water. Term
‘ground water’ is used to describe this area. Top of
surface where ground water occurs is called water
table.

Aquifer is another term for ground water.

Although usually used to describe water-bearing
formations capable of yielding enough water to
supply people. After entering an aquifer, water
moves slowly, usually following gravity, toward lower lying
places and eventually is discharged from aquifer from
springs, seeps into streams, or is withdrawn from ground by
wells. Water may travel long distances and remain in ground
water storage for long periods.

Groundwater is one of most important natural resources

globally. For example, provides much of public and
domestic water supply in USA, supports agricultural and
industrial economies, and contributes flow to rivers, lakes, and wetlands. About 40% of public
water supply in USA is from groundwater in principal aquifers. More than 40 million people,
including most of rural population, obtain drinking water from wells.

Part I: Regulation of water quality and quantity

It is determined mainly by physical processes, but ecosystems also play a key role. The ability
of ecosystems to regulate water is strongly influenced by changes in land cover, for example
replacement of forests with crop land. In recent years we have allowed a lot of additional
pollutants to enter water environment.

1. Water quantity
It is important to balance needs of society (industry, agriculture, and people) and environment
(rivers, lakes, wildlife, and habitats), including the need to dilute pollutants.

Water quantity has a very major impact in many parts of world on humans (including
agriculture) and ecosystems. It has impact on distribution of human population (e.g. some
parts of Australia, due to climate change, are becoming less habitable for humans). Supply is
also affected by climate change by how we use the land and the rate of extraction/use.

Millennium Ecosystem Assessment:

 5 to possibly 25% of global freshwater use exceeded long-term accessible supplies.

 15 - 35% of irrigation withdrawals exceeded supply rates and were therefore
unsustainable. zone of uncertaintyThis map shows how unsustainable is irrigation in
different parts of the world. Asia, USA, South Africa, and ESPAÑÑÑA.

There have been several important droughts all over the world this last years: in 2009, Kenya
suffered a drought that killed even elephants. In Australia, camels destroyed air conditioners to
access moisture. California the main vegetable producer of the country, however, it’s
susceptible to droughts, and last years it suffered a worst drought than the year before (fires).
Different event, but same
extremity: floods. Capacity of
ecosystems to buffer from extreme
events has been reduced through
loss of wetlands, forests,
mangroves… People are
increasingly occupying regions
exposed to extreme events due to
the increase of population.

In England, flood damage costs are around £1.1 billion per year. Around one in six properties is
at risk of flooding. Over 2.4 million properties are at risk of flooding from rivers or the sea, of
which nearly half a million are at significant risk. One million of these are also vulnerable to
surface water flooding with a further 2.8 million properties susceptible to surface water
flooding alone. There are other ‘human’ costs.

Another extreme precipitation event is avalanches caused by heavy snowfall.

2. Water quality
Globally, water quality is declining, although in most industrialised countries pathogen and
organic pollution of surface waters has decreased over last 20 years.

Cultivated systems can have negative impacts on freshwater quality through pollutants
contained in drainage water, runoff, and effluents. Agriculture can also concentrate pollutants
by extracting water from environment for irrigation.

Pollutants can be: inorganic (soil particles), organic

sediments or particulate matter, plant nutrients (which
lead to eutrophication), especially nitrogen, phosphorus
(principal cause of blue-green algae blooms, which lead
to anoxia), pesticides… Nitrate concentration has grown
rapidly in last decades as a result of intensive
agriculture.

Eutrophication is the phenomenon in which fertilizer

compounds (usually N and P) enter water bodies
increasing the phytoplankton population (algal bloom).
This increase in the phytoplankton blocks sunlight,
depleting the environment from oxygen. This affects the phytoplankton itself but also all of the
other species that lives in the ecosystem.

Cryptosporidium is protozoan parasite that causes a severe diarrhoeal disease known as

cryptosporidiosis. Its spread is easy by contaminated food and water. While rare, there have
been outbreaks of water-borne cryptosporidiosis in both UK and US. Generally, these have
been caused by inadequate water treatment or breaches of integrity of distribution systems.

Plastics are an obvious consequence of human activity.

Salinisation is the excessive increase of water-soluble salts in soil. It’s often associated with
irrigated areas where low rainfall, high evapotranspiration rates or soil textural characteristics
impede washing out of salts which subsequently build-up in soil surface layers. Irrigation with
water with high salt content worsens problem. Natural disasters in coastal areas, such as
tsunamis, can cause severe salinisation problems with several years of low fertility of affected
soil before recovery. De-icing of roads with salts can lead to localised salinisation.

Part II: The importance of wetland ecosystems

Wetland ecosystems (including lakes, rivers, marshes, and coastal regions to a depth of 6
meters at low tide) estimated to cover more than 1,280 million hectares, an area 33% larger
than United States and 50% larger than Brazil.

Wetlands are “areas of marsh, fen, peatland or water, whether natural or artificial, permanent
or temporary, with water that is static or flowing, fresh, brackish or salt, including areas of
marine water the depth of which at low tide does not exceed six metres” (Ramsar Convention
on Wetlands).

The Ramsar Convention is intergovernmental treaty that provides framework for national
action and international cooperation for conservation and wise use of wetlands and their
resources.

1. Wetland ecosystems services

 Hydrological regimes. Groundwater recharge and discharge, water storage for agriculture
and industry.
 Pollution control and detoxification. Retention, recovery and removal of excess nutrients
and pollutants. Some wetlands reduce concentration of nitrate by >80%.
 Erosion protection. Retention of soils and prevention of structural change (coastal erosion,
bank slumping).
 Natural hazards. Flood control, storm protection.
 Soil formation. Sediment retention, accumulation of organic matter.
 Nutrient cycling. Storage, recycling, processing, acquisition of nutrients .
 Biodiversity. Habitats for resident and transient species.

One of most important roles may be in regulation of climate change through sequestering and
releasing major proportion of fixed carbon in biosphere. Although covering only 3–4% of
world’s land area, peatlands estimated to hold 25–30% of global carbon contained in
terrestrial vegetation and soils.

Part III: How are humans trying to improve the situation?

1. EU Directives
They lay down certain end results that must be achieved in every Member State. National
authorities have to adapt laws to meet these goals but are free to decide how to do so.

Each directive specifies date by which national laws must be adapted. Directives bring different
national laws into line with each other and are particularly common in matters affecting
operation of single market (e.g. product safety standards).

Water Framework Directive. It’s a framework for the protection of all waters including rivers,
lakes, estuaries, coastMethylococcus capsulatual waters and groundwater, and their
dependent wildlife/habitats under one piece of environmental legislation. Aims to:
Protect/enhance all waters (surface, ground, and coastal waters), achieve "good status" for all
waters by December 2015, manage water bodies based on river basins or catchments and
involve the public.
In the UK there is the Catchment Abstraction
Management Strategies (CAMS), that
manages how much water businesses, etc.
can take out of the system. We have the
Warwickshire Avon abstraction licensing
strategy.

2. Potential flood regulating actions

 Provide vegetative cover. Will slow and
filter flow. Vegetation traps organic and
mineral particles that are then
incorporated into soil, while plants take
up any nutrients.
 Manage drainage.
 Maintain rivers. By increasing channel
conveyance (flow) or where appropriate,
restoring meanders.
 Install infiltration devices. Work by
enhancing natural capacity of ground to
store and drain water.
 Dry basins. Designed to promote infiltration of
surface water to ground.
 Ponds. Permanently wet basin designed to
retain storm water and permit settlement of
suspended solids and biological removal of
pollutants.
 Slowing the Flow at Pickering.

3. Artificial recharge
Practice of increasing amount of water that enters
a groundwater reservoir by artificial means aka
putting water back to the ground.

Includes, for example, direction of water to land

surface through canals (as redirecting a river in a
flood so it settles in a land area and infiltrates slowly), irrigation furrows or sprinkler systems,
and injection of water into sub-surface through wells.

4. Nitrates
Nitrates Directive, adopted by EU 1991, aims to reduce water pollution caused by nitrogen
from agricultural sources and to prevent pollution in future. Requires Member States to:

 Designate as Nitrate Vulnerable Zones (NVZs) all land draining to waters that are affected
by nitrate pollution.
 Establish a voluntary code of good agricultural practice to be followed by all farmers
throughout country.
 Establish a mandatory Action Programme of measures for purposes of tackling nitrate loss
from agriculture.
 Review extent of their NVZs and effectiveness of their Action Programmes at least every
four years and to make amendments if necessary.
Lecture 6 - Soil Systems
Soil is really important as it is involved in water purification, climate regulation (reducing CO2
and other GH gasses levels by C fixation), biogeochemical cycling,
storing pollutants, and even in human health (some antibiotics are
made with microorganisms found in the soil).

Part I: The Structure of Soil Systems

1. What is soil?

 A dynamic natural body composed of mineral and organic

materials and living forms in which plants grow.
 Weathered end-product of action of climate and living
organisms on soil parent material with a particular topography,
over time.
The soil dynamism come from the Five Soil
Formation Factors: Organisms, Topography, Time,
Climate and Parent Material.

2. Components of soil

 Solids. Organic matter plus minerals (42-47%)

which are mostly silicon and oxygen, which
combine with other elements to create
minerals like silicon dioxide or quartz (primary
mineral derived from the weathering of parent
material).
 Liquids (water) and Gases (N2, O2, CO2…). They
fill up the pore space of soil (50%). Water displaces air and vice versa (in a rainy day, water
displaces air, and in dry season the opposite), so the % of each other vary depending on
the amount of water.
 Living organisms. They make less than 1% of the size, but they’re really numerous. There
are more microorganisms in 1 grain of sand than humans on Earth. This also includes plats
roots, fungus, insects, earthworms…

3. Soil horizons

The process of soil weathering leads to the formation

of soil layers/horizons.

 O horizon (organic layer). The layer right

underneath the atmosphere. It’s mostly
composed of loose and decaying organic matter.
 A horizon. Mineral matter mixed with humus
(decaying organic matter).
 E horizon. Composed of light-coloured mineral
particles. This is the zone of eluviation (The
transport of soil material from upper layers of
soil to lower levels by downward percolation of
water across soil horizons) and leaching.
 B horizon. Area of accumulation of clay
transported from above. This process is known as
illuviation: Accumulation of dissolved or
suspended soil materials in one area or layer as a
 result of leaching (percolation) from another. Usually clay, iron, or humus wash out and
form a line with a different consistency and colour.
 C horizon. Partially unweathered parent material.

 Parent material. Bedrock. Unweathered material.

There are 5 horizons (5 of above), but that doesn’t mean that each soil is going to have each of
those soil horizons. We can see these two types of soils, both from Arizona, not too far away
one of each other:

The left soil has marked O, A, E and B

horizons. In B horizon we can see
illuviation as there is accumulated clay.
The red colour is due to oxidised iron.

However, the right soil, which is a desert-

soil dominated by shrub-like vegetation,
only has two horizons, A and C. It doesn’t
have O horizon due to the lack of plants.

4. Sizes of soil constituents

As a reference, the thickness of a nail is

400 µm.

Sand is the largest of the inorganic

constituents and ranges between 50 and 2000 µm of diameter. Silt is smaller than sand but
bigger than clay. Clay is the smallest, it is referred as a fine compound.

The inorganic compounds tend to be larger than microbes, and in some cases this is true, but
fungi are very variable.

5. Soil structure

Aggregates: Grouping of soil particles that cohere to each other more strongly than to other
surrounding particles. The formation of this aggregates is a function of biology (microbes and
roots products), chemistry (soil particle chemistry), and physics.
Inside a soil aggregate we find
pore spaces with bacterial
colonies. This bacteria can
secrete polysaccharide
derived compounds that act
as a glue, binding particle
together. They can also
secrete humic-like substances
creating hydrophobic regions.

Fungi can also secrete those

kind of substances and their
hyphae can act as a physical
mean of forming aggregates,
pushing, or holding particles
in place, leading to a physical
entanglement.

When looking at a cross-section of the

hyphae, we can see how out of the cell
wall there is a secretion of polysaccharides
that traps clay particles.

The formation of these aggregates results

in microsites, interaggregate and
intraaggregate pores, and preferential
flow.

This pores allow the movement of water,

air, and microbes through the soil. The
pores that exist between aggregates are
known as interaggregate pore, while the
pores found within an aggregate are
intraagregate pores, much smaller (nm to
µm).

Microsites are pores with an accumulation

of microorganisms due to a different chemical condition such as low oxygen level (?).

The pores can also be classified between their size:

 Macropores (>75 µm)

 Mesopores (30-75 µm)
 Micropores (5-30 µm)
 Ultramicropores (0.1-5 µm)
 Cryptopores (<0.1 µm)

This pore sizes can be increased by the action of invertebrates, plat roots, earthworms, small
mammals… crating macropores, resulting in a significant aeration of the soil as well as the
preferential flow of water.

6. Soil texture
Texture can be defined as the coarseness or
fineness of a soil. It depends on the content of
sand, silt, and clay. Those soils predominated by
sand are considered coarse textured, while those
with more clay and silt are known as fine
textured soils. It is a fixed property of the soil.

Texture determines the ease with which a soil is

worked (agricultural sense), the aeriation of the
soil, moisture relations, and biological activity.

For example, soils with much clay are not easy to work with, don’t aerate very well, hold
moisture and all this inhibits biological activity. However, a sandy soil can’t hold as much
organic matter, being an issue for accumulating nutrients for plant growth. A well-
proportioned soil with sand, clay, and silt is the best soil for plant growth.

The soil texture triangle is a tool to know the type of soil just by
knowing two out of the three types of particles.

For example, a soil with 30% clay and 30% silt is clay loam. Clay
loam could also be identified if we knew the 40% of sand.

Soil texture impacts porosity and infiltration.

The average pore size of a clay textured soil is quite small, but the overall number of pores is
quite high, resulting in grater overall pore space. Small pores do not transmit water as fast as
large pores, so a high clay soil will slow the movement of any material moving through it
(water, air, microbes…). This means that clay and silt soils are more prone to floods.

7. Bulk density

Bulk density is the weight of a soil in a given volume calculated as:

Bulk density = Dry Mass of Solids / Total Volume

8. Cation Exchange Capacity (CEC)

CEC is the total exchangeable cations that a soil can absorb. This influences the soils ability to
hold on to nutrients as well as provide a buffer against soil acidification. Soils with higher
amounts of clay or organic matter tend to have high CEC.

This parameter arises due to the negative charges associated with clay and organic matter’s
particles. Clay is negatively charged for one of two reasons:
 Isomorphic substitution (clays). The replacement of one atom by another of similar size in
a crystal lattice without disrupting or changing the crystal structure of the mineral.
In the picture is the example of a substitution of an aluminium ion (trivalent) for a
magnesium or iron ion (divalent). One positive charge is lost, so the net negative charge is -
1.
 Ionization (pH dependent). Clays (kaolinite), organic matter, Fe and Al hydroxides, where
hydroxyl groups (OH) at the edge of a lattice can ionize: Al – OH = Al – O - + H+
Here we have Al bonded to a hydroxyl group. This group can ionize, giving O- and a loosely
associated proton. This process is also known as broken edge bonds. This process increases
as pH increases.

Organic matter has hydroxyl, carboxyl… groups that help with CEC.

Clay and organic matter particles that participate in CEC have to be very small (they are
referred as colloids). These colloids, as they are very small, they have a high surface area for
cation exchange capacity to occur.

9. Sorption in soil

Sorption is a major process that influences the movement and bioavailability of essential
compounds in pollutants and soil. The broad definition is the association of organic or
inorganic molecules with the solid phase of soil, especially clay.

For inorganic charged molecules, cation exchange is

the primary mechanism of sorption. In general,
positively charged ions (Ca2+) participate in cation
exchange. Since sorped forms of these metals are in
equilibrium with the soil solution, they can serve as a
long-term reservoir of essential nutrients (Ca onto
clay particle) or pollutants. These can be slowly
released back into the soil solution as the soil
solution concentration cation decreases with time.

Attachment of microbes can also be mediated by this

sorption property, specifically due to the numerous
functional groups of clay. However, both clay and bacteria are negatively charged. They don’t
repel each other thanks to cation bridges, formed due to the accumulation of cations.

10. Revision
1. Name the 5 major components of a typical moist surface soil (mineral soil) and give the
approximate percentage of each component by volume. How would you define “organic
soil”?

2. Identify the most reactive fraction of the three soil solids (i.e., the sand, silt, or clay
fraction). Explain why this fraction is most reactive. Why is desirable to have some clay in a
soil?

3. Discuss the relationship between particle size and surface area of sand, silt, and clay. How
does particle size affect the pore space in a soil? How does it affect water retention by a soil?
The movement of gases within the soil?

4. What is the role of soil microbes in the formation and maintenance of waterstable soil
aggregates? Identify three mechanisms through which soil microbes contribute to the
formation and stabilization of such aggregates

Lecture 7 – Biogeochemical cycling

Part I: Introduction to biogeochemical cycling
‘Bio-geo-chemical’ has the biological component (microbial metabolism, primary/secondary
production…), the geological component (Formation of crust, spreading zones at mid-ocean
ridges, hydrothermal fields, subduction and recycling of crust, volcanism, formation and
metamorphosis of rocks and minerals, diagenesis of fossilized carbon…)
 Tectonics. Not all of the ocean floor has the same age due to tectonics. Earth’s crust is
constantly renewing/recycling. Earth is more than 4 billion years old, but the older ocean
floor is about 280 million years, being fairly young.

There is also the chemical component (Reactions and behaviour of chemicals in the
environment, e.g., partitioning, solubility, reaction kinetics in different compartments
(atmosphere, soil, hydrosphere, etc.).

1. Biological component

We’re going to see the atmospheric gases and their link to metabolism.

Atmospheric gas Biological process

Dinitrogen – N2 Nitrogen fixation, denitrification, annamox,
commamox
Oxygen – O2 Oxygenic photosynthesis, respiration, …
Carbon dioxide – CO2 Carbon fixation, organic matter oxidation
Methane – CH4 Methanogenesis, methanotrophy…
Nitrous oxide – N2O Denitrification (and other processes)
Chloromethane – CH3Cl Production by plants and fungi, degradation
by bacteria
Bromoform – CHBr3 Biological production by phytoplankton, …
2. Methane
• Biological methane production. Produced and degraded by methanogenic
microorganisms.

• Geological. Contained and

produced in hydrothermal
fluids (Eternal Flame Falls,
New York). Released by
volcanism, at hydrothermal
vents, or natural gas seeps.

• Chemical. Produced by
reduction of CO2 in H2-rich
fluids (due to
serpentinization) in earth’s
crust (e.g. at hydrothermal
vents). Degraded by
hydroxylation in the
atmosphere (yielding
methanol).

3. Why understand
biogeochemical cycles

• Basis for understanding

physicochemical conditions
on Earth. Important to
understand the past, present
and future of the Earth
system.

• Knowledge of microbial
activities (metabolism) on
modern Earth and
integration with geochemical record allows to unravel How biogeochemistry of Earth has
evolved, how life may have evolved, and whether and where we may find extraterrestrial
life.

• Biogeochemical cycles are not static. They have changed during Earth’s history and
they’re currently changing due to human activities. Understanding the cycles allows to
model how changes will affect global ecosystem(s) and Earth system.

Part II: Origin of life

1. When did life originate?

The Earth originated around 4.6 billion years ago, and it is generally accepted that the first life,
in form of bacteria, originated 3.8 billion years ago, in the Archaean period. The evidence for
this statement comes from fossil evidence. Microbial life can be observed in rocks found in
Western Australia and South Africa dated to about 3.5 billion years ago.
So there is evidence that suggests that life was present at the beginning of the Archaean
(3.8-2.5 Gya). The temperature in this period is debated, suggestions range from range from
26-35°C to 50-70°C.

However, more recent ‘evidence’ suggests life

already present in the Hadean.

The Hadean is the first period of Earth’s history

(4.6 Gya to 3.8 Gya). This period is known to have
seas of magma with a few rocks and rain of
meteorites, but now it is thought that at the end
of the period this conditions could have been
mitigated. There wasn’t any oxygen in the
atmosphere, but due to the crust formation,
there could have had relatively cool conditions,
and everything could be reduced in a chemical
sense.

One of the ways that organic Carbon could

potentially be preserved in the geological record
is in zircon minerals (refractory materials that are
hard to metamorphose) that can be older that
the rocks that contain them.

In Jack Hills, Western Australia, there are large abundance of zircon minerals older than 4.4
billion years old. After investigating around 10.000 zircons, one was discovered to have
primary graphite inclusions. They think this graphite are microorganisms that were
transformed into graphite through temperature and pressure. They think this because the
isotopic signature suggests that this graphite has a biological origin.

99% of the natural carbon is C12 and about 1% is C13, a little bit heavier. Enzymes discriminate
between C12 and C13, Methylococcus capsulatu they have a higher rate of reaction with C12.
This means that the products that are formed through biological processes are going to be
lighter than the natural abundance of isotopes.
If you compare the isotopic signature of the zone of uncertaintygraphite inclusions of the
zircon, they are relatively light and in the range of organic carbon. This is geochemical evidence
that suggests that 4.1 billion years old zircon contains carbon of probably biological origin.

There is another paper that, using a molecular clock reconstruction of integrated genomic
sequences of living organisms, suggested that LUCA must have been present in the Hadean
probably around 4.5 billion years ago.

2. Earliest metabolism

It is challenging to determine the precise nature of early metabolism on Earth. Early metabolic
strategies probably included:

 Methanogenesis (based on CO2 and H2), early Archaea

 Acetogenesis (based on CO2 and H2), early Bacteria
 Sulfur based metabolism (reduced S as energy source)
 Anoxygenic photosynthesis (using H2S as e- donor)
All of these metabolic strategies, used to generate ATP, are still represented in
extant and evolutionary deep-rooting (i.e. ‘old’) microbial phyla.

3. Where did life originate?

There is the little pond hypothesis, which theorises that life originated in a
warm little pond with electrical discharges that caused clay minerals to
transform into organic compounds.

Then there is the hydrothermal vent hypothesis, which states that

hydrothermal vents provided relatively stable and protected conditions under
which life could evolve based on reduced inorganic compounds that came up
from the seafloor. These vents also have incredible temperature gradients.

This hypothesis suggests that prebiotic chemistry was H 2-dependent of

transition-metal sulphide catalysts at a hydrothermal-vent setting.
Similar to the CO2-reducing biochemistry of modern microorganisms (bacteria and archaea)
that use the Wood–Ljungdahl acetyl-coenzyme A (acetyl-CoA) pathway. This pathway leads to
acetyl-CoA, an energy-rich thioester that could be the most central carbon backbone in
microbial metabolism. The synthesis of acetate and CH 4 from H2 and CO2 releases energy that
could be packaged into some cellular structure, going from prebiotic chemistry to life.

The key features of the transition of prebiotic chemistry to life are Self-replicating RNA (RNA
world, ribozymes)Enzymatic activity of proteinsDNA - genetic coding functionEvolution
of biochemical pathwaysDivergence of lipid biosynthesisDivergence of cell wallsLUCA

4. Summary

• Microbial life on Earth drives important processes that are part of biogeochemistry

• Microorganisms have evolved probably over more than 4 billion years ago
• As well as shaping current conditions on Earth,
they have changed the chemistry of the
environment over geological time scales

• Conditions for the emergence of life may exist

elsewhere in the universe (see slides at end of
powerpoint)

Part III: How life changed the Earth system

One of the most important events of the Earth’s

history is the great oxygenation event.

In the Hadean, the first cellular life would probably

be methanogens. After some evolution, the first
photosynthetic organisms appeared, but they
were anoxic, using H2S as an electron donor.

At some point in evolution, one of those

anoxygenic photosynthetic organisms evolved to
use water instead of H2S, liberating O2 as a waste
product. They were oxygenic photosynthetic
organisms.

Oxygen started to accumulate in the atmosphere relatively slowly because the ocean was full
of reduced compounds, which cleared the oxygen up.

The oxidation event, which lasted more than 1 billion years (until 10%), led to the formation of
the ozone layer, with blocked UV radiation, protecting the DNA of the organisms of Earth of
mutations.

1. Stromatolites

Stromatolites are “living fossils” (mineral structures) thought to contain ancestors of

cyanobacteria. These precursors of chloroplasts and primitive forms of plant life were present
in archaeal oceans 3.5 billion years ago. Oxygenic (O 2-evolving) photosynthesis altered the
chemistry of the oceans and atmosphere.

Oxygenic photosynthesis probably evolved hundreds of millions of years before the

atmosphere became significantly oxygenated. This makes sense as it would have taken eons to
oxidize the continued production of reduced volcanic gases, hydrothermal fluids, and crustal
minerals.

The great oxygenic event was most likely driven by ancestors of cyanobacteria (Betts et al.,
2018) as cyanobacteria evolved later (1947–1023 Ma) than GOE (2400 Ma).

Part III: Biogeochemical cycles

Cycling of elements that are part of the biomass of living organisms or that are transformed
during energy generating dissimilatory metabolism. The main elements in biomass are C, N,
P, and S, but other essential elements occur in small amounts (e.g. metals in enzymes).
 Energy gaining transformations in (microbial) metabolism, e.g. O 2, nitrogen, sulphur, iron,
manganese etc. Undergo reduction and oxidation processes, and these elements will also be
assimilated and liberated again when biomass decays.

Biogeochemical cycling is the transformation of matter from inorganic form to organic form
and back and the movement of matter from non-living to living compartments and back.

Some forms of specific elements may also be cycled due to energy yielding reactions, without
becoming assimilated into biomass. Examples are the electron acceptors of respiratory
metabolism, e.g. O2, NO3-, SO42-, Fe3+ or inorganic electron donors of energy metabolism such
as NH4+, Fe2+, HS-

Major proportion of biogeochemical cycling usually driven by microbes, some conversions

exclusively by microorganisms

1. Metabolic groups of microorganisms

Metabolic guild Process Relevance to biogeochemistry Example organisms

(genera)

Methanogens CH4 formation Ancient metabolism, still relevant on modern Methanococcus

Earth; greenhouse gas; anaerobic digestion Methanosarcina

Acetogens Acetate formation Ancient metabolism, modern day acetogens are Moorella
versatile, use range of C1 compounds Acetobacterium

Phototrophic Phototrophic, H2S oxidation to First phototrophs, exploited reduced sulfur in early Chlorobium
sulfur bacteria sulfur and sulfate, fixation of CO2 Earth; still relevant in anoxic habitats (microbial Chromatium
mats, anoxic/oxic interfaces in lake ecosystems)

Oxygenic Phototrophic oxidation of H2O to First O2 producers in biosphere, stromatolites, Synechococcus

phototrophs oxygen, fixation of CO2 progenitor of chloroplasts, responsible for Nostoc
oxygenation of the atmosphere and the oceans;
2. Summary

Early prebiotic chemistry may have existed in a wide range of settings and the circumstances
for the origin of life remain uncertain

One of the potential geological settings that has been suggested are hydrothermal sites

Metabolic by- and end products have had major effects in changing chemistry of atmosphere
and oceans

• Oxygenation of atmosphere and oceans

• Weathering of rocks, dissolution of minerals, formation of soils

• CH4 formation, greenhouse

Knowledge of modern-day biogeochemical processes is vital for understanding dynamics of

climate system

Part IV: Life in the universe

Present day life on Earth includes evolutionarily ancient microorganisms at hydrothermal vent
sites. Planetary objects with water, internal heat and geological activity may have similar sites
where life may arise/persist.

It is conceivable that conditions suitable to evolve life exist elsewhere in the Universe, based
on the large number of objects and their diversity.

1. Titan

Saturn moon. Subsurface ocean with liquid water. Cryovolcanoes identified as potential
sources of geological methane. Surface lakes/seas of hydrocarbons. Methane and ammonia
present as potential energy sources for microbial life

2. Enceladus

Saturn moon. Covered by ice, subsurface liquid water. Internal heat and geologically active.
Cryovolcanoes near South Pole ejecting water and hydrogen

3. Mars

Some ‘pockets’ of water ice near poles, & potentially

subsurface. Atmospheric methane detected previously, but
currently controversial whether signals are ‘real’. Methane
traces could be a sign of microbial subsurface life, as methane
can be generated by microbial metabolism.

Lecture 8 – Carbon cycle

Part I: Conceptual models of
biogeochemical cycles

This simple model shows in boxes

the reservoirs (Pg) and represents
fluxes with arrows (Pg/year). All
the numbers are estimated.

There is a minor disequilibrium

between the atmosphere and the
terrestrial biosphere, showing that
there is less assimilation of carbon
from the atmosphere and there is
more going from the terrestrial
biosphere to the atmosphere. The
ocean is a huge reservoir of
carbon. But these numbers have been changing slowly, mainly the atmosphere due to
greenhouse gasses emissions.

1. Flux disequilibrium
If we look more closely into this disequilibrium we can see a lot of anthropogenic changes in
the carbon cycle (red arrows).

One of the major changes is the use of fossil fuels (organic carbon). This carbon would
normally be locked away from the carbon cycle.

Other anthropogenic
change is land-use change
and land sink. A change in
land use affects the
carbon cycle when you
change, for example, from
a forest to a pasture. This
changes the amount of
carbon fixation that the forest would do, and also how the carbon is processed within the soil
is changed (often there’s an increase in
mineralisation of organic C which leads to CO 2
emissions, meaning a loss of organic carbon).
On the other hand, this increase in CO 2 leads to
the carbon fertilization effect, making
photosynthesis more effective, so land sink
increases.

Another part where we see this disequilibrium

is between the sea and the atmosphere. This
shows how the oceans are taking up a lot of
the CO2 that we emit into the atmosphere.
There is also the fact that oceans are emitting
more carbon to the atmosphere, maybe
because they’re getting warmer or because
there is more degradation of organic carbon.
The intake flux outweighs the flux out (of the ocean), leading to ocean acidification.

We must try to put 0 in all of the red arrows in order to stop the emission of greenhouse
gasses. Knowing which processes affect this issue allows us to do that.

2. Terrestrial carbon cycle

The carbon cycle in the ocean works in two parts: the upper layers and the deeper layers.

The surface layer, which is in contact with the atmosphere, exchanges carbon with it. This DIC
(dissolved inorganic carbon) is used by photosynthetic organisms (50 Pg of net primary
production) to create POC (particulate organic C) and DOC (dissolved organic C). However, 37
Pg of carbon is returned to DIC through respiration.

The deeper layers of the ocean receive C from the upper layers in two different ways: sinking
of POC and DOC (relatively small amount of C is fixed and even less amount reaches the
bottom ocean’s sediments where it’s buried) and deep-water formation (when water cools
and increases its density, it goes down creating a circulatory system that drives ocean’s
currents and sinks DIC).

Part II: Biochemistry of the carbon cycle

CO2 is the central metabolite for the carbon cycle. Depending in the conditions of oxygen we
get different processes in which carbon is used by

organisms (red arrows indicate exclusive to

microbes).

Methane can be produced directly from CO2 with H by methanogens or by degradation of

organic compounds and acetate under anoxic conditions.

1. Metabolic diversity of microorganisms

2. Primary production/autotrophic carbon fixation

The generation of organic matter from CO 2 by photoautotrophs and chemolithoautotrophic

organisms is called primary production. Primary producers are the basis of all heterotrophic
life

Significant primary producers are Plants in the terrestrial environment, Phytoplankton

(microscopic algae) in the marine environment, Chemoautotrophic microorganisms
in hydrothermal vent systems (e.g. sulfur oxidisers).

Carbon fixation is the process of

assimilation of CO2 by autotrophic
organisms. There are five known
metabolic pathways for fixing CO 2,
best known is the Calvin cycle with
the enzyme Rubisco. During fixation,
CO2 is combined with an acceptor
molecule and reduced to the level of
(CH2O)n, oxidation state changes
from +4 to 0, and the energy
liberated can be used to create
molecules such as glucose.
The energy for reducing CO2 is derived from Light reactions of photosynthesis in plants and
cyanobacteria and Oxidation of energy rich reduced inorganic molecules (e.g. NH4+, HS-, Fe2+)
in chemolithoautotrophic microorganisms.

3. Groups of autotrophic microorganisms

Sulfur-oxidizing bacteria
 Oxidize H2S, S, S2O32- or other reduced sulfur species to gain energy
 Fix CO2 into biomass

Iron-oxidizing bacteria
 Oxidize Fe2+ to Fe3+ (energy)
 Fix CO2

Nitrifying bacteria / ammonia-oxidizing bacteria/archaea

 Oxidize NH3 to NO2-; oxidize NO2- to NO3-
 Fix CO2

Cyanobacteria / phytoplankton
 Oxidize H2O
 Fix CO2
3. Marine phytoplankton

This includes diverse photosynthetic microorganisms including eukaryotic algae and

cyanobacteria. They contribute approx. 50% of global net primary production.

Two globally distributed groups of marine cyanobacteria, Prochlorococcus & Synechococcus,

are responsible for 25% of global oxygen production.

See oceobio for more info.

4. Hydrothermal vent ecosystems

Until the 70s, it was thought that all life was light dependent. However. There are organisms
inhabiting these vents systems nourishing only with chemical energy which is ultimately
geothermal energy.

In these ecosystem, water is entrained into the crust and interacts with hot basalt leading to a
lot of chemical reactions that lead to the production of reduced organic compounds that flow
out to the surface.
 The fluid vent is over 350 ºC, but within the chimney wall there is a gradient of temperature.
The most thermophilic organisms (bacteria and archaea) thrive at a temperature of about
110ºC, creating a chemosynthetic microbial ecosystems independent of photosynthetically
produced biomass (use reduced organic compounds as energy source to fix CO 2).

There are also higher organisms (Giant tubeworm Riftia pachyptila) that depend on
chemolithoautotrophic microorganisms. These Sulfur-oxidizing endosymbionts fix carbon
inside worm tissues, oxidizing a range of energy-rich, reduced sulfur compounds, (e.g. H 2S, S2-n,
S0, S2O32-) and providing the host with organic carbon. The host
in exchange gives the microorganisms inorganic material from
the surrounding water.

5. Summary 1

• Different types of conceptual models

– Help to visualize fluxes, processes, and reservoir sizes
– Substructure of specific compartments, e.g. sunlit ocean/deep ocean
– Highlight metabolic groups involved in

redox cycles
• Carbon fixation by primary producers
– Photolithoautotrophs
Chemolithoautotrophs independent of sunlight
Part III: Major organic carbon pools
The most abundant organic compounds in the
environment is plant matter (cellulose, hemicellulose,
lignin, starch…). Another considerable amount is in
chitin (fungi, insects, zooplankton) and other cellular
compounds (peptidoglycan from prokaryotes, lipids,
protein, nucleic acids, humics derived from soil, hydrocarbons formed by diagenesis and used
as fossil fuels).

1. Respiration/fermentation

All of that organic C must go back to CO 2, and it is done by respiration and fermentation.

Dissimilation of organic carbon (e.g. sugars), to CO 2 and or organic acids and hydrogen and
coupling that to generation of ATP as an energy storage (in respiration, via membrane
potential and proton motive force). Oxidation of organic matter to CO 2 can be coupled to both
aerobic and anaerobic respiration

• Aerobic respiration: O2 electron acceptor

• Anaerobic respiration: various e- acceptors, e.g.
– NO3- (dissimilatory denitrification)
– SO42- (dissimilatory sulphate reduction)
– Fe3+ (dissimilatory iron reduction)
– CO2 (methanogenesis)

There is a difference in how much energy these different electron acceptors allow an
organism to extract from the organic carbon that it’s being oxidized. The highest yield of
energy achieved is using oxygen as electron acceptor. The next best electron acceptor is
nitrates, followed by manganese, then iron, sulphates, sulphur, methane and finally acetate.

In a sediment, in the first layers are inhabited by use oxygen for respiration, in the next layer
(anoxic, as all oxygen was used) will be inhabited by bacteria that use nitrate, and so on.

In this flow of carbon there is also some cooperation, as organic polymers are hydrolysed so
the oligo/monomers can be utilized by respirating organisms but also by fermentative bacteria.
Fermentation is a way of organisms that do not respire to gains just a few electrons and make
energy. The products of fermentation are H 2, organic acids, alcohols, and CO2. All of these
products are really important type of intermediates that can also feed all the different anoxic
respirations.

2. Aerobic heterotrophic bacteria

There is a huge diversity and a wide range of phylogenetic groups. All of them respire organic
carbon to CO2 using O2 as electron acceptor. There are, however, differences in substrate
range and specialization (e.g. polymer degradation, preference of specific substrates)
 A notable group are the SAR11 bacteria, believed to be the
most abundant heterotrophs in the oceans; long considered uncultivable, but some cultures
now available.

3. Dissimilatory sulphate reduction

Marine environment is rich in sulphate (28mM). Sulphate reduction is dominant process for
organic matter degradation (accounting for an estimated 50% of organic matter degradation),
producing sulphide. Precipitation of iron sulphide in anoxic layer gives black sediment
colouration.

Lecture 9 – Nitrogen cycle

Part I: Overview of the Nitrogen cycle
Nitrogen is an extremely important element for organic molecules, it’s a key building block of
proteins, an indispensable component of the protoplasm of all
organisms, a nutrient that plants require in greatest quantity…

It’s however an element which is very susceptible to microbial

transformations and one of the few nutrients that is lost by both
volatilization and leaching. Some nitrogen compounds can be
pollutants. Nitrogen requires conservation and maintenance.

A tera-gram is 1 trillion grams. Almost 80% of N is stored in the

atmosphere, becoming the biggest N pool o Earth. The smallest pools
are the ones that are actively cycled.

1. Important Inorganic-N Compounds

Compound Valence Form in env. Attributes

Ammonium (NH4+) or -3 Fixed in clay lattice, dissolved as Cationic - rather immobile. Can be volatilized as
ammonia (NH3) gaseous ammonia (NH3) NH3 at high pH. Assimilated by plants and
microbes. Substrate for autotrophic nitrification
(NH3 oxidation)
Hydroxylamine, NH2OH -1 Not easily detected Intermediate in NH3 oxidation
Dinitrogen N2 0 Gas Largest pool of N. Relatively insoluble. Substrate
for N2 fixation. End-product of denitrification.
Nitrous Oxide N2O +1 Gas, dissolved A greenhouse gas and implicated in ozone
destruction, very soluble. Intermediate in
denitrification. By-product of nitrification.
Nitric Oxide NO +2 Gas Chemically reactive intermediate in
denitrification. Byproduct of nitrification
Nitrite NO2- +3 Aqueous, dissolved Normally present at very low concentration.
Toxic byproduct of NH3 oxidation. Substrate for
NO2- oxidation. Intermediate in denitrification
Nitrate NO3- +5 Aqueous, dissolved Anionic  mobile. Readily leached. Assimilated
by plants and microbes. End-product of
 nitrification. Substrate for denitrification.
2. N cycle

N2, the largest N pool, is not in a usable format for plants or microbes, so it has to be converted
into a usable form. Some microbes can do this through N fixation. This process’ products are
ammonia and ammonium (this process can be done artificially by the Haber-Bosch process).

Ammonium can be assimilated (N assimilation) turning from an inorganic form to organic

matter biomass. The rest of this biologically produced ammonium can be subjected to
subsequent microbial processing, nitrification, producing nitrate. This compound can be
utilized by plants, but if there is too much, as it is anionic, it solubilizes in water producing
leaching, leading to eutrophication.

Nitrate can also be subjected to denitrification, where under anaerobic conditions, it is used as
a terminal electron acceptor and reduced to nitrite, nitric oxide, nitrous oxide (a potent
greenhouse gas), and ultimately, dinitrogen.

Ultimately, organic nitrogen can be decomposed by microbes releasing ammonium/ammonia

by a process known as mineralization or decomposition.

This nitrogen cycle can be greatly affected by human interactions (anthropogenic forcing). In
this image, the fluxes indicate tera-grams of N per year.

The number in parenthesis are preindustrial averages (1831-1860), while the number not in
parenthesis are contemporary values (1991-2005). We can see how the amount of N taken
from the atmosphere into the terrestrial systems is almost doubled, mainly due to increases
of agricultural precision (crops that are good at N fixation).

Soil emissions has quadrupled due to a lot of different processes (land degradation,
agriculture…). Harvest agriculture has tripled the amount of N released, mainly due to
combustion of agricultural equipment. The amount of fertilizer went from 0 to 114 (Haber-
bosh process). Atmospheric depositions (N in a reactive form in aerosols floating in the
atmosphere), freshwater emissions and N released from rivers to oceans have increased.

3. Major transformations of Nitrogen

4. Energy yields

Microbes can process nitrogen compound to produce energy.

Denitrification has a couple mechanisms by which microbes can gain energy.

Nitrogen fixation has a negative yield, but this is complemented by the supplements from
symbiotic plants.

5. Aerobic vs. anaerobic!!!

Nitrogen fixation (dinitrogen gas to ammonium) is neither aerobic nor anaerobic (even
though the enzyme is degraded in aerobic conditions).

Ammonium can then be converted into nitrate by nitrification, a strictly aerobic process. Each
arrow is an enzymatic step, so it can be done by two different

Nitrogen Mineralization
Organic matter decomposition
RNH2 --> NH4+, NO3-

Nitrogen Immobilization
Microbial uptake into cells
NH4+ --> RNH2

Nitrification
For energy production
NH --> NO2- --> NO3-
4
+

Denitrification
Anaerobic respiration
NO3- --> N2O, N2

Dinitrogen fixation Cell growth

N2 --> 2NH3 Symbiotic & nonsymbiotic

groups of microbes (NH3  NH2OH  NO2-,

two enzymatic steps and then NO2-  NO3-,
one enzymatic step) or by just one
(commamox = complete ammonia oxidation).

Nitrate (NO3-) can be reduced in an

assimilatory manner (taken into the microbial
cell) forming an organic amino compound. This
amino compound can be mineralized (broken
down back into ammonium) and then
ammonium can be assimilated back to an amino compound. These processes are neither
anaerobic nor aerobic.

Going back to nitrate, it can be reduced in a

dissimilatory process (N is not taken into the
cell) into nitrite, an anaerobic process
instead of oxygen, N is used as a terminal
electron acceptor).

Nitrite (NO2-) can go back to ammonia

through DNRA (dissimilatory nitrate
reduction to ammonia). Just as dissimilatory
nitrate reduction, it happens extracellularly,
and N is not taken into the cell. Nitrite can
also suffer a denitrification process
(anaerobic) in which each intermediate is used as a terminal electron acceptor in place of
oxygen.

Anammox (anaerobic ammonia oxidation) is the process by which ammonia and nitrate oxide
react to form hydrazine, which can be further reduced into dinitrogen gas.

Part II:
Mineralization and immobilization
Nitrogen in organic matter or added as fertilizer is available to plant and microbes. If the N is
“assimilated” by a microbe or plant, it is said to be “immobilized” and is no longer available to
plants or other microbes until the cell die and is “mineralized” back to inorganic, plant-
available forms of N.

An addition of N in a system can be done via fertilizers or organic matter. These inputs can be
mineralized, broken down into inorganic nitrogen (ammonium and nitrate).

Those inorganic N compounds can be assimilated either by plants or microorganisms. When

the N is in a cell, it can’t be assimilated by any other cell until the first one dies, leaving the
organic nitrogen free so it can be mineralized into ammonium and assimilated or further

nitrification can turn it into nitrate and then be assimilated.

1. Ammonification

Nitrogen mineralization is the transformation of organic nitrogen into inorganic nitrogen (NH 3,
NH4+, NOX-.) It is a form of regeneration of N in a form that it is usable for plant development.

However, there is a form of N mineralization: Ammonification. It consists in the specific

transformation of an organic amino group (RNH2) into ammonia or ammonium. It is mediated
by a vast array of microbes. Ammonia accumulation represents “waste product” overflow on
the part of the microbe (e.g. excess N over microbial demand).

2. Proteolysis

Microbes produce extracellular enzymes (proteases, peptidases…) in order to facilitate the

liberation of inorganic N. Proteins are broken down into CO 2, NH4+, SO42-, H2O, amines, H2S,
organic acids, mercaptans (volatile, odoriferous organic S compounds).

Putrefaction is the anaerobic decomposition of proteins with the production of very foul-
smelling intermediates such as mercaptans and specialized amines such as cadaverine and
putrescine.

Substrate Enzymes Products

Proteins Proteinases, Proteases Peptides, aa
Peptides Peptidases Aa
Chitin See below Chitobiose N-acetylglucosamine
Peptidoglycan Lysozyme N-acetylglucosamine and N-acetylmuramic acid
DNA/RNA Endo/Exonucleases Nucleotides
Urea Urease NH3 and CO2
This polymer can be broken down by its first monomer, by its second, or wherever in the
middle.
3. Nucleic acid metabolism
Second only to proteins in importance as nitrogenous substrates for microbes. DNA/RNA are
polynucleotides composed by purine (A, G) and pyrimidine (C, T, U) bases, (deoxy)ribose, and
phosphate.

Deoxyribonuclease degrades DNA into deoxyribonucleotides, and ribonuclease degrades RNA

into ribonucleotides. Both of them are nucleases.

4. Urea metabolism

Urea is a product of the destruction of the nitrogenous bases contained in nucleic acids. It’s an
important fertilizer, so it also enters the environment via animal excretions. The position of
urea as an intermediate in microbial metabolism, an animal excretory product, and a fertilizer
makes it a key compound in the N cycle.

Urease degrades urea into CO 2 and 2NH3. Urea is readily metabolized in the environment
(especially soil) in a short period of time, as many microbes (bacteria, fungi, actinomycetes…
103 to > 106 per g-soil) possess this enzyme (urease).

There is an intermediate compound in the decomposition of urea: ammonium carbonate. This

compound can be further hydrolysed releasing another ammonia mole.

This process tends to be anaerobic, and obligate anaerobes are hard to isolate. This means
that the microbes that can decompose urea in anaerobic conditions are facultative anaerobes
(they can do it in aerobic or anaerobic conditions).

5. Ammonia volatilization from urea

This is a big problem. When urea is broken down, pH tends to rise readily as high as 8 or 9. At
these high pH’s the product is NH 3 (not NH4+) which can lead to volatilization leading to loss of
nitrogen and potential air pollution. This initial phase may remove as much as 10-70% of the
urea-N.

Controlling loss of urea-N through ammonia volatilization lies in:

1. Sub-surface rather than surface application.
2. Application to low pH soils – not high (locking N in ammonium, not ammonia).
3. Adequate soil moisture, so water dissolves NH 3 particles rather than having them volatilized.
6. Environmental Factors Affecting N-Mineralization

 Total N content of soil. Soils rich in N liberate greater quantities of N. 1-4% is the quantity
of soil organic N that is made available during the growing season in temperate latitudes.
 Moisture. Mineralization happens at high moisture levels (in arid regions onset of rainfall is
followed by a rapid onset of mineralisation). The optimum moisture is 50-75% volumetric
water content. Mineralisation is not affected by submergence in water, it’s rapid in paddy
soils. Alternate wetting and drying enhances mineralization.
 pH. Mineralization is greater in neutral than acid soils. Liming (increasing pH) stimulates
mineralization. Organic N accumulates in acidic soils.
 Temperature. Optimum = 40-60 °C (above mesophilic range).
 Available N. Addition of inorganic-N sometimes stimulate mineralization – this is referred
to as “priming”.
Part III: Nitrification and denitrification

We can think of both nitrification and denitrification as a leaky pipe.

For

nitrification the process should be form ammonium/ammonia to nitrate. However, there is

some N leaking in forms of N2O and NO production. The product of nitrification, nitrate, can
also be lost through leaching.

For denitrification, the process should be form nitrite to N 2. However, there is some N leaking
in forms of N2O and NO production.

There is one difference, for denitrification, those gaseous metabolites can be brought back into
the pipe reactants.

1. Nitrification

It’s the chemoautotrophic (this microbes obtain C from CO 2 and obtain energy from inorganic
metabolites) oxidation of NH3/NH4+ to nitrite (NO2- ) and nitrate (NO3-).

There are two main steps:

 Ammonia oxidation. Nitrosomonas (bacteria), Thaumarchaeota (archaea), etc.

 Nitrite oxidation. Nitrobacter, Nitrospina, Nitrococcus (bacteria).

However, this can be done directly by

Commamox (COMplete AMMOnia
OXidation): Nitrospira (bacteria).

2. Environmental Factors Influencing

Nitrification

 pH. Nitrification proceeds slowly in acidic

environments, even when much NH4+ is
available. Rates of nitrification are
reduced markedly below pH 6.0 and it is
negligible below pH 5.0. Nitrification in
acidic soils is usually enhanced by liming. High pH can lead to accumulation of NO2 - due to
inhibition of nitrite oxidizers by free NH3.
 Aeriation. O2 is an obligate requirement. Soil structure can affect rates of nitrification
through its influence on reaeration of soil pores. Nitrification does occur even in
submerged soils, as there is usually and oxidized layer, due to the O2 in the water column,
overlying reduced soil below.
 Moisture. Waterlogging reduces nitrification rates due to low O2. Under arid conditions –
H2O may be insufficient for growth. The optimum moisture is about 50-66% VWC.
 Temperature. Optimum = 30-35 °C (these microbes are mesophiles).
 3. Undesirable Consequences of Nitrification

 Increased leaching of NO3- .

This is due to its anionic
chemistry, making it much
more susceptible to leaching
– can escape the root zone
quickly.
 May contribute to water
contamination. In surface
waters leads to
eutrophication, in
groundwater, by drinking
water contamination,
there’s chance of
methemoglobinemia (blue-
baby syndrome)
 NO3- can be converted,
through denitrification, to
gaseous end products (NO, N2O, N2). Climate change implications.

4. Denitrification

The microbial reduction of NO3 - and NO2 - with the liberation of gaseous end products such
as nitric oxide (NO), nitrous oxide (N2O), and ultimately dinitrogen (N2). NO3-  NO2-  NO
 N2O  N2.

Nitrate Assimilation is a reductive process in which nitrate is used as a nutrient source.

Nitrogen remains in the environment and is not removed from the realm of potential
availability as a plant nutrient. Both are reductive processes, but the end products differ.

The main microbes capable of denitrification are pseudomonas, but there is a plethora of
other microbes. All of them are aerobes that use NO3- as an alternate O2 electron receptor.
Denitrifires account for 0.1-5% of soil bacterial. Some fungi and actinomycetes have been
implicated in N2O production via incomplete denitrification.

5. Environmental Influences on Denitrification

 Nature and amount of organic matter. Slow in soils low in organic matter. Stimulated by
carbon-rich materials: Sugars > cellulose > lignin.
 Aeriation. Rough 0.2 ppm of O2 is the upper limit. Occurs when O2 supply is insufficient.
Can occur in anaerobic microsites. Favoured by aerobic-anaerobic cycles (e.g., intertidal
areas, submerged soils).
 Moisture. H2O generally above 60% VWC. Effect of moisture attributed to its role in
governing O2 diffusion. Maximal when more than 80% of pores are water-filled.
 pH. Many denitrifires are sensitive to acidic conditions. Affects amounts of N2O or N2
produced due to sensitivity of nitrous oxide reductase to low pH.
 Nitrate concentration. Probably more limiting than carbon in most soils. Influences the
final products of denitrification. High NO3 - favors N2 production.
 Temperature. Wide range: 2 – 65 °C , Optimum = 25 °C, None above 70 °C
Part IV: Full circle

High levels of fertilizer, especially urea, and microbes mineralize that urea to ammonia.
Ammonia can either be taken up by plants when water is added and converted to ammonium
or the excess can be subjected to nitrification, so ammonia transforms in nitrate, which can
also be taken up by plants, but it can also be leached into water sources causing
eutrophication.

Nitrate is also subjected to denitrification, considering the amounts of water added that turn
the soil in an anaerobic environment. This causes compounds that pollute the air by
volatilization.

How to curb N pollution and greenhouse gases coming from this system? First, not add so
much fertilizer, just the optimal amount for plant growth. You could also add nitrification
inhibitors. You also modify the efficiency of N uptake of plants or make a more
environmentally friendly fertilizer.

1. Guided Revision: N-Cycle Lecture

1. Draw a schematic diagram of the nitrogen cycle and label the pools of nitrogen and the
transformations that occur between them.
2. Identify which N transformations require energy and which release energy.
3. Which transformations are assimilatory, and which are dissimilatory?
4. Which transformations are oxidative, and which are reductive?
5. Understand the basic steps in the mineralization of proteins, nucleic acids, and urea
6. What are the products of nitrification? Are they harmful to plants or humans?
7. What conditions stimulate nitrification?
8. Describe the environmental conditions that enhance rates of denitrification
9. What are the environmental implications of denitrification?
Lecture 10 – Methanotrophy and analysis of communities
Part I: Methanotrophy

Methane is originated biologically by methanogenesis by methanogenic archaea in anaerobic

conditions (cellulose digestion in ruminants, landfill, peat bogs, anoxic soils such as rice
paddies…). It is also produced in geothermal/volcanic methane formations in Erath’s crust.
One important methane sink is the atmosphere, where it is oxidised by hydroxyl radicals.
Aerobic oxidation by bacteria (soils and sediments) and anaerobic respiration by archaea
compose the most important biological sink.

** methanotrophs
1. Methanotrophs

Methanotrophic microorganisms are present in most environments and affect the net flux of
methane to the atmosphere. They also take up methane from the atmosphere, mitigating
methane emissions.

Aerobic methanotrophs use methane as a C source and an energy source. By oxidizing it with
O2 they transform it into CO2 and H2O + energy (biomass).

Anaerobic methanotrophs utilize methane with either sulphate or nitrate to produce CO 2 and
either hydrogen sulphide or dinitrogen.

2. Why/how study methanotrophs?

 Why? They are an important natural sink for GH gas

methane. They could be used for enhancing mitigation of
methane flux from landfills. Identifying methanotrophs in
various environments will help to study their response to
climate change. Methanotrophs also co-metabolically
degrade wide range of pollutants
 How? By cultivation-dependent (enrichment
and isolation, characterization) or cultivation-
independent (DNA/RNA based approaches)
approaches.
Part II: Cultivation of methanotrophs

1. Traditional isolation and

characterization of microorganisms

This culture helps us to make cultures that we can

study in the lab and allow us to find out about biochemistry, physiology, genetics, and
taxonomy of the sample.

The inoculum is the

material sample from
where you’ll study the
microorganisms that are
there (e.g. soil). To this
inoculum, we can inject
some specific nutrient
(methane) to enhance
growth of target
microorganisms. Then we
check if there is activity of
methane degradation (gas
chromatograph). If
methane goes down (or
even up) we can then isolate the microorganism. It would be a good idea to do a control
without enrichment to test that methane is not being degraded by an abiotic process. We can
then do cultures with the isolated bacteria and do different tests to characterize them.

2. Enrichment (of
methanotrophs)

A minimal media with methane as sole

carbon and energy source must be
defined and then inoculated with the
environmental sample (e.g., soil,
sediment, water samples). Then we can
monitor CH4 in headspace by gas
chromatography and also monitor for
growth by measuring optical density.

3. Methylococcus capsulatus
(Bath)

It is the best studied methanotroph model organism. It was firstly isolated from geothermal
waters of Roman Baths (Bath, UK) which have a geothermal source and are enriched with
methane.

4. Diversity of methanotrophs

 ‘Type I’ Gammaproteobacteria. Ribulose monophosphate (RuMP) pathway of

formaldehyde assimilation. Possess bundles of intracytoplasmic membranes
 ‘Type II’ Alphaproteobacteria. Serine pathway of formaldehyde assimilation. Possess
intracytoplasmic membranes arrayed around the periphery of the cell
 Other. Crenothrix polyspora (filamentous bacterium; Bacteroidetes): recently discovered
but never isolated as a pure culture (discovered 2006).
Methylacidiphilum infernorum (acidophilic Verrucomicrobia): Discovered in 2007
There are 9 recognized genera of methanotrophs. Based on their 16S ribosomal RNA (rRNA)
phylogeny, the major carbon
assimilation pathway used to
metabolize methane and the
arrangement of
intracytoplasmic membranes,
methanotrophic bacteria can
be divided into two groups :

Type I methanotrophs
belong to the gamma
subdivision of the
Proteobacteria. They use the
ribulose monophosphate
(RuMP) pathway to
assimilate formaldehyde into
cell carbon and possess
bundles of intracytoplasmic
membranes.
Type II methanotrophs belong to the α-subdivision of the Proteobacteria. They use the serine
pathway for the assimilation of formaldehyde and possess intracytoplasmic membranes
arrayed around the periphery of the cell.

There are 6 genera belonging to Type I and 3 genera belong to type II.

5. Summary of aerobic methanotrophy

• Microbial process in which bacteria degrade methane as carbon and energy source,
producing CO2
• Diverse organisms, isolated from a wide range of environments
• Metabolic pathway characterized, enzymology and genetics relatively well-understood
• Other interesting aspects
– Co-oxidize a wide range of compounds (e.g. trichloroethylene TCE…)
– Biotechnological interest for bioremediation
– Environmental impact on CH4 fluxes
Part III: Microbial community analysis

The visual characterization of microbial communities under the microscope (after fluorescent
dyeing) is uninformative, as morphological diversity is limited (so different communities look
similar), and visually you can’t identify the microorganism or their physiology.

There are 107-109 bacteria (10

million-1 billion) in a gram of
soil. They could count up to
10,000 different species and
have other diverse eukaryotic
microbes (algae, amoeba,
ciliates, flagellates…). There are also 1 million microbes in 1 mL of
seawater (thousand of species). However, only a small fraction of
microorganisms have been cultivated (1%).

1. Cultivation biases

Countless studies have shown that it’s not possible to analyze microbial
diversity in environmental samples using cultivation. Cultivable bacterial
diversity is not matched by the diversity obtained by using cultivation-
independent approaches. This is why the vast majority of environmental
microorganisms are often said to be ‘unculturable’. Common statement
(overly simplified): 99% of bacteria and archaea have not been cultured.

2. Counts

Plate counts. The number of colony-forming units (cfu) of a

sample is determined by plating serial dilutions onto solidified
media. The cfu is related back to the sample volume and gives
the total viable count (e.g. 106 cfu g-1 soil).

Direct counts. A fluorescent dye that interacts with DNA is used. These counts are higher than
cfu. This is due to some reasons: the medium used is too specific and cannot be used to all of
the variety of microorganisms that exist in the sample. This count can also disrupt the
consortia and also include dead/dormant cells.
 3. RNA

RNA is present in all organisms (small subunit of

ribosomes, 16S in bacteria and 18S in eukaryotes). This
rRNA is a highly conserved region (while also having
variable regions), so it is used as a
taxonomic/phylogenetic marker. In most bacteria it has
1550bp approximately.

The phylogenetic identification of microorganisms can be

done on single bacterial isolates but also be used for
complex microbial communities.

Part IV: Cultivation independent molecular approaches

1. Retrieval of the environmental sample (e.g. soil,

seawater…)
2. Extraction of nucleic acids (DNA and/or RNA) from
sample
3. PCR amplification of marker genes
– 16S rRNA for ‘taxonomic diversity’
– Functional marker genes for studying ‘functional diversity’
4. Analysis of diversity of marker genes by high throughput sequencing (or clone libraries)
5. Statistical comparison of communities from different samples, time points, etc.
Hug et al. (2015) published a new tree of life using this cultivation-independent molecular
approach, proving that there was a lot of diversity that wasn’t discovered.

Ribosomal RNA gene surveys of environmental sequences show that large numbers (even
complete phylogenetic groups of bacteria and archaea) have remained uncultivated. Red
dots = candidate phyla without cultivated representatives.

1. Problems

Microbial Communities Are Taxonomically and Functionally Diverse. If rRNA sequence is similar
to another, that doesn’t mean that both have even similar metabolisms or physiology. rRNA
genes do not indicate the ‘function’ (metabolic potential) of uncultivated microbial taxa.

2. Functional genetic marker

Genes that encode key enzymes of metabolic pathways, can be used to test the metabolism of
microorganisms in a sample. The presence of the functional marker gene indicates metabolic
potential (function). Diversity of functional genes can be analysed using PCR amplification,
cloning and sequencing analogous to rRNA approach or even using sequencing community
genomes (metagenomics).

In fact, the pmoA gene was used to define groups of methanotrophs. Since 1997, using of
primers amplifying pmoA has revolutionized understanding of methanotroph diversity. The
vast majority of pmoA genes represent uncultivated groups of microorganisms that are not
closely related to isolated methanotrophs. As of Feb 2021, there are ~32,000 pmoA sequences
in public sequence databases. Primers for mmoX (encoding a subunit of soluble methane
monooxygenase) have also been developed.

• Hundreds of studies using pmoA, mxaF and mmoX have increased understanding of
diversity and ecology of methanotrophs (and continuing)
• Example of methanotrophs in environment for community analysis, can be applied to
other functional guilds
• More recent approaches for microbial community analyses are based on metagenomics,
metatranscriptomics and metaproteomics and other more advanced techniques based
on high throughput sequence data
– See recommended articles on moodle for more information
3. Summary

• Methanotrophic bacteria are an important sink for CH 4

– Pathway of methane oxidation well understood through study of model isolates
– Key enzymes and genes characterised
– Most environmental microorganisms are difficult to isolate
– Cultivation biases
– majority ‘unculturable’ (need to try harder?)
– Molecular microbial ecology approaches used to characterise communities and
specific populations
• Study of cultivated ‘model’ organisms essential to facilitate identification of genes involved
in metabolism for used as functional markers for environmental detection
Lecture 11 – Biodiversity
1. Definitions

 The diversity of plant and animal life in a particular habitat (or in the world as a whole)
 The variety of plant and animal life found in an ecosystem and the variation in their genetic
makeup
 The variety of life forms, the different plants, animals and microorganisms, the genes they
contain and the ecosystems they form
 All hereditarily based variation at all levels of organisation, from the genes within a single
local population or species, to the species composing all or part of a local community, and
finally to the communities themselves that compose the living parts of the multifarious
ecosystems of the world. E O Wilson
Around 2 million species of animals, plants, and fungi have been described, but there may be
5-15 million. We have identified and named a greater proportion of vertebrates and plants
than insects and fungi. 6,399 species of mammals have been described (2018).

Some species appear when somebody realized that what is was thought to be one species is
actually two, this happened to the Tapanuli orangutan. Morphometric, behavioural, and
genomic evidence led to the conclusion, that the isolated population at the southern range
limit of Sumatran orangutans is distinct from both northern Sumatran and Bornean species.
Genomic evidence suggests that while northern Sumatra and Borneo species separated about
674,000 years ago, this species diverged much earlier, about 3.38 million years ago. Now the
most endangered great ape in the
world. About 800 left in fragmented
habitat spread over about 1,000 km2 ,
with densest populations in primary
forest.

Part I: Contribution of biodiversity

1. Nutrient cycle

A supporting service by the way. Yellow

boxes reflect the processes that are
mediated by microorganisms. They are
present in the soil, water, dead
organisms, in symbiosis (legumes)… This
cycle depends on a wide range of
organisms, and in different parts of the world, these species will be different but with the same
functions.

2. Pollination

Pollinators include bees, butterflies, birds, moths, flies, beetles, bats… They have a crucial role,
but pollination is not mediated entirely by animals. Interactions are generalized i.e. there are
few interactions where one species of plant depends on only one species of animal. Usually,
the same animal can pollinate several different types of plants, and these interactions change
with time and space. A study made in ESPAÑA showed how a lavender flower was visited by 85
species of dipteran, hymenopteran, and lepidopteran pollinators. However, the quality of
pollination does vary with the species.

3. Agricultural products.

Include both plants and animals, which some of them we have selectively bred with time to
provide the characteristic we want. Even though there still exist differences.

 Brassicaceae. The Mustard family (Brassicaceae or Cruciferae) consists of 338 genera

and approximately 3,700 species. They are very important to agriculture and the
environment, accounting for approximately 10% of the world's vegetable crop
production and serving as a major source of edible oil and biofuel.
Over time, we have selected features of these plants and we domesticated these
plants, enhancing the chosen genes with the cost of losing others. We can get those
lost genes from the wild species or another close relative.
At Warwick University, genetic variation investigated for: Nitrogen and phosphorus use
efficiency, water use efficiency, resistance to pests and diseases, broccoli shelf life…
 Brazil. They were looking for a pest-resistant plant to tackle the froghopper (insect)
that was attacking their cattle’s food.

4. Medicine

 For centuries, bark extract was sued to relieve pain. Salicylic acid was synthesised in
1850s from this tree, but the compound damaged mucous membranes. In 1893, Bayer
company obtained a patent on acetylsalicylic acid (aspirin).
 Discovery of penicillin attributed to Alexander Fleming in 1928. He showed that, if
Penicillium notatum was grown in the appropriate substrate, it would exude a
substance with antibiotic properties, which he called penicillin. Could be synthesised in
1957 opening the way to the development of particular penicillin to combat particular
bacteria. By the early 1960's, researchers started producing hundreds of kinds of
experimental penicillin.
 Galantamine used for the treatment of mild to moderate Alzheimer’s disease and
other memory impairments.
 Docetaxel (taxane drug) is a man-made drug that was first made from yew tree
needles. It works by stopping cancer cells from replicating, so blocks the growth of
cancer.
5. Cultural services.

6. Bioremediation

Many bacteria found in soils and ground water are able to biodegrade organic compounds.
They can be useful for a number of processes for remediating contaminated soils and ground
water. These microorganisms could convert contaminants to less hazardous substances:
carbon dioxide and water. Processes for addressing metals are under development.

Part II: What causes changes in biodiversity?

1. Habitat change/destruction

Building a new road or a city can completely destroy a habitat. However, sometimes what it
does is fragmentate it, reducing the population in each part increasing genetic drift, inbreeding
depression, and increasing the risk of extinction if population becomes very small.
Genetic drift: change in the relative
frequency with which an allele occurs
in a population due to random
variation.

Urbanization is changing animals and

plants, which are adapting to these
new habitats. This changes include
body size, shifts in behavioural
patterns, and adjustments in
reproduction.

Fishing techniques also homogenizes three-dimensional benthic habitats, dramatically

reducing biodiversity.

2. Invasive species

An invasive species is a species that did not live in a particular place before but was introduced
accidentally or by human interaction. Invasive species can cause abrupt changes in populations
in coastal ecosystems, for example, the introduction of the invasive, carnivorous ctenophore
Mnemiopsis leidyi (a jellyfish-like animal) in the Black Sea. This animal eats eggs and larvae of
fish and caused rapid loss of 26 major fisheries species and has been implicated (along with
other factors) in the continued growth of the oxygen-deprived “dead” zone. The species was
subsequently introduced into the Caspian and Aral Seas, where it had similar impacts.

Introduction of non-native bumblebees sometimes has negative effects. Non-native Bombus

terrestris introduced into Japan to pollinate greenhouse tomatoes but escaped and
naturalised. Queens competitive and take over nest sites of native bumblebees.

3. Pollution

Pollution can come from nutrients (fertilizers), pesticides, or other pollutant activities such as
mining and industrial waste.

In a pesticide-free situation, predators consume pests (ladybirds eat aphids, frogs consume
invertebrates…). In many agricultural areas, pest control provided by natural enemies has been
replaced by the use of pesticides. Such pesticide use has itself degraded the capacity of
agroecosystems to provide pest control.

Veterinary products also can pollute an ecosystem. Gyps vultures of India and South Asia were
some of the most abundant large raptors in the world. Within 10 years, 3 species became
endangered due to a drug used to treat livestock. Vultures feeding on carcasses had renal
failure and died. Vultures provide vital ecosystem service through the disposal of livestock
carcasses, their loss has huge socio-economic impacts. Carcasses were left to rot, posing a risk
to human health (diseases, including anthrax, and species such as rats). Also resulted in
explosion in feral dogs (common cause of human rabies). In 2006, India, Pakistan and Nepal
banned manufacture of drug and pharmaceutical firms encouraged to promote a safe
alternative and vulture numbers have stabilised.

4. Climate change
Climate change is likely to affect the distribution of many species, both animals and plants. It’s
also likely to affect their phenology (e.g. flowering time of plants and emergence time of
insects) so that they become desynchronized.

Climate change will reduce climate space, also reducing species locations. This would mean
that animals and plants would have to move, for some species, this is impossible and habitat
fragmentation and natural barriers (such as the sea) will limit the capacity of some other
species to disperse.

Part III: Things about biodiversity to be concerned now and in the future
 Will the loss of biodiversity have an impact on the Earth and human well-being?
 Is ‘quantity’ or ‘quality’ important?
 Are there some species that we just can’t afford to lose?
 How do we value biodiversity against other activities?
 How do we maintain biodiversity in the face of increasing pressures from human
development and climate change?
Lecture 12 – Ecological interactions: competition and predation
All living things require resources, and they can only survive,
grow, and reproduce under certain sets of physical
conditions. Each species has a set of conditions and
tolerances under which they can survive, grow, and
reproduce.

Species don’t live in isolation, they share the space and

resources with other species.
• Community: an assemblage of species populations that
occur together in space and time.
• Ecosystem: the biological community plus the abiotic
environment in which it is set.

1. Community
The community consists of a series of interconnected trophic interactions: a food web. Species
within the community can be classified into functional groups according to the way they
acquire energy.
Energy flows in a food web from one part of the ecosystem to another (trophic dynamics).

A community is not a random collection of species. It is characterized by its structure and

dynamics.
• Community structure: (i) species richness (number of species that occur within the
community), and their relative abundance (numbers that they have in relationship
with each other); (ii) types of species: their functions and how they relate to each
other.

The structure is affected by (dynamics) conditions and resources present, the interactions
within and between species: competition, predation, mutualism; The action of foundation
species and keystone species, and the frequency of disturbances or disruptive events.

Competition and predation both concern the requirement for individuals to obtain resources
for survival, growth, and reproduction. Competition occurs where common resources are
limited. Predation concerns the acquisition of food by herbivore and carnivore heterotrophs in
a food web.
Part I: Competition
It is defined by the interaction between organisms in which the fitness of one or both is
lowered by the presence of another when they have a shared resource. Competition can be:

• Intraspecific competition – between members of the same species.

• Interspecific competition – between different species with similar ecological
requirements.

Competition may be asymmetric, but in many cases both competitors suffer a fitness
reduction even though one organism get all the resource due to the expense of energy on
the competitive process.

All organisms require resources to grow and reproduce successfully.

These resources can be biotic (food) or abiotic (water, sunlight, space…).
In doing so they interact with their own and/or other species.
Understanding these interactions is important for issues such as
management of fisheries, pests, conservation of wildlife etc.

In nature, resources are limited. Intraspecific competition, in crowded

environments, restricts population development.

The Whooping crane (Grus americana) was an endangered species recovering from near
extinction. It breeds in Canada, overwinters in Texas. Was protected in 1916 (15 birds alive in
1941).

This plot shows an exponential increase in numbers on wintering grounds. This happens in an
environment with no limited resources and uncrowded (a weird case). This curve is
exponential, Births > deaths.

In real populations, growth is not exponential. It has been estimated that one cabbage aphid
could (in principle) produce 250 million tonnes of offspring in a year (by asexual reproduction).
But in nature, resources are limited (e.g. food) and the environment functions to slow down
population growth through intraspecific competition for limited resources.
Population regulation involves density dependence (negative feedback gets bigger with the
population):
• Rate of population growth is slowed with increasing population density.
• Population is affected in proportion to its size.
• Density-dependent mortality; density-dependent fecundity.

The more the population, the more competition there is. Eventually, the population can’t grow
more because everything is balancing itself, resulting in a logistic curve of population growth
(S-shaped). When the population grows, births > deaths. When it is constant, births = deaths.
a) Population growth of Lactobacillus sakei in nutrient broth.
b) Population of shoots of the annual plant Juncus gerardi in salt marsh.
c) Population of willow trees in an area where myxomatosis disease had prevented rabbit grazing.

The same basic idea of density dependence applies to intra- and inter-specific competition.
Interspecific competition can result in the
co-existence or exclusion of 1 species
population by another, depending on
resource availability and conditions. Again,
this is important for the conservation of
biodiversity.

1. Mechanisms of competition

• Interference competition. Individuals

interact directly (e.g. via aggression).
They can interfere with foraging,
reproduction, or directly prevent
physical establishment. Plants
sometimes engage in chemical
warfare by volatile chemicals that
act as herbicides.
• Exploitation competition.
Individuals do not interact
directly, rather one individual is
affected by the amount of resource that remains after it has been exploited by others (i.e.
consumption of food depletes the amount available to others).

Part II: Predation

Predation is the second type of inter-species interaction. It is defined as the consumption of

one organism (the prey) by another (the predator). The prey is alive when the predator attacks
it.

Ecologically, predation is not just about the consumption of animals as food, herbivores (and
omnivores) are also predators, as they consume live organisms (plants, in this case).
Decomposers are not predators, as when they eat an organism it is already dead.

Predators can be divided into 3 functional categories:

• True predators. Kill prey straight after an attack, consume several or many preys in a
lifetime.
 • Grazers. Consume only part of each prey, not usually lethal,
attack several or many preys in a lifetime (e.g. cow, giraffe,
mosquito).
• Parasites. Consume only part of prey, may not be lethal, attack
one or very few hosts, intimate association.

Predation is not just a

transfer of energy,
predators are agents
of mortality and
regulate prey
populations. The prey
is a resource and
regulates the predator population. This results in coupled density dependence: reduces large
populations and increases small populations. This could be seen in nature in a few cases: Wolf-
moose on Isle Royale, Michigan

Part III: Ecology: competition, predation, and environmental management

If 1 predator has 2 prey species, then an increase in either one of prey species may cause an
increase in the predator. But an increase in the predator may harm both prey species.

Each prey species is indirectly having a negative effect on the other via their positive effect on
the predator.

By increasing predator abundance, each prey species is indirectly decreasing the abundance of
the other prey species. This process is called apparent competition.

1. Bighorn sheep in Sierra Nevada USA

There were only 360 bighorn sheep Ovis canadensis sierra remaining in the Sierra Nevada
(California & Nevada USA). Pumas, Puma concolor, prey on the sheep but their primary prey is
a population of 19000 mule deer Odiocoileus hemionus.

Researchers radio collared 162 sheep, and found them soon after
death, ascribing a cause of death to 39 animals, of which 22 were
caused by cougar predation. Sheep mortality caused by cougars was
correlated with % overlap of range of sheep and mule deer.

• Mono basin: no mule deer, no cougar mortality

• Baxter: 67% overlap of sheep and mule deer population, had

greatest cougar predation of sheep.

Apparent competition was affecting sheep conservation.

 Part IV: Invasive exotic species

Non-native species are accidentally or deliberately

introduced to an area outside of their natural range, which
establishes and spreads and causes economic,
environmental/ecological damage.

They cause damage because they compete so successfully in

new ecosystems that they displace native species, provoking
damaging effects through predation. Some also transmit
pathogens to native species. They are the second biggest
cause of biodiversity loss.

1. Characteristics of invasive species

They are able to tolerate a variety of habitat conditions and

grow and reproduce rapidly while competing aggressively for
resources (like food, water, and nesting sites). They lack
natural enemies in the new ecosystem. This allows them to
proliferate.

These things may be linked: lack of natural enemies may

allow a species to be more competitive because it is more
abundant.

2. Squirrels

In the UK, the native species of squirrel is the red squirrel (Sciurus vulgaris). However, in 1876
the grey squirrel (Sciurus carolinensis) was introduced from N America.

Grey is able to digest a wider range of food resources in mixed woodland and remains active
throughout the year. It was also a carrier of the parapox virus which has a major impact on the
native red squirrel.

3. Himalayan balsam (Impatiens glandulifera)

It’s native to the west and the central Himalayas. Introduced in GB as a garden plant the early
1800s. Out competes the native UK species in ecologically sensitive areas, particularly
riverbanks.

4. Burmese python, Florida Everglades

Burmese pythons (Python molurus bivittatus) are large (up to 6m) constrictors native to
Southeast Asia. They have established across thousands of square kilometers in southern
Florida, including all of Everglades National Park (ENP) since 2000.

Pythons in Florida consume a wide range of mammals and birds, including species classified as
threatened or endangered.

The effects were researched using surveys of mammal

roadkill from 2003 – 2011 and compared against baseline
surveys done in 1996 – 1997. This showed substantial
decreases in encounter rates of several mammal species:
• No rabbits or foxes observed between 2003 – 2011.
 • 99% reduction in racoons, 99% reduction in opossums, 94% for white-tailed deer, 88%
for bobcats.
At peripheral locations in the park where pythons are less common, mammal encounter rates
were intermediate.

A. Temporal variation in mammal-encounter rates in ENP from road survey counts

before (1996–1997) and after (2003–2011) pythons became common. The numbers below
bars represent the change in the number of observations/100 km for each species or group.

B. Current (2008–2011) spatial variation in mammal-encounter rates in core (southern

ENP), peripheral, and extralimital regions of python range.

5. Varroa mite, Varroa destructor

Host shift from Asian bee Apis cerana to European honeybee Apis mellifera in the 1950s.
Arrived UK 1992. Parasitic mite on bee brood transmits a highly damaging virus. Resistant to
chemical pesticides

Part V: Classical control of invasive species

The intentional introduction of an exotic predator as a biological control agent for permanent
establishment and long-term pest control.

Based on the ‘natural enemy release hypothesis’. An organism invades a new geographic area
(usually moved accidentally by people). In so doing, it escapes its “natural enemies”. Its
population is no longer controlled, and it becomes a pest. This is a major reason for the
success of invasive species.

1. Cottony cushion scale

In 1868, Cottony cushion scale, Icerya purchasi, accidentally was introduced to California citrus
orchards. By 1886 it nearly destroyed citrus farming. The scale came from Australia, so 2
natural enemies imported:
• A true predator, the vedalia beetle Rodolia cardinalis (500 released). Beetle spread
rapidly, controlled the scale by 1890. Still working now.
• A parasitoid wasp Cryptochaetum (12,000 released) took longer to establish. Effective
on the coast.

2. Safety testing
Classical control is generally safe. Around 2000 natural enemy species released, with
permanent suppression of 165 arthropod pest species (especially effective against arthropods).

130 species release for arthropod control in Europe. Few apparent problems … but if it goes
wrong the consequences can be severe! Strict safety testing – host range.

3. Altering the competitive balance

The pine marten (Martes martes): mustelid, inhabits forests. Feeds on small mammals, birds,
carrion. Extinct in England, rare in Wales, expanding in Scotland. Recovering and spreading in
Ireland.

Where range of pine marten meets grey squirrel:

• Grey squirrel retreats, red squirrel

expands.

Greys spend more time on ground than reds,

making them more vulnerable to predator. Has
resulted in reducing grey squirrel population size
in Ireland.

• Ireland: Grey squirrel population has now

started to decline in 9,000km 2 of former
range. Red squirrel now common after 30
years.

However, some invasive species may be

impossible to control (Burmese python).

Lecture 13 – Populations and communities

Part I: General patterns
In most cases, the patterns of population growth are more complex than competition-
predation patterns.

There are multiple determinants of population dynamics. Fluctuations in abundance are

caused by a wide variety of biotic (density-dependent) and abiotic (density-independent, e.g.
weather, climate) factors.

Competition and predation are density-dependent processes and tend to be stabilizing for
populations over the long term. Other factors that affect population size are chance variation
in births and deaths, environmental changes, genetic drift, and catastrophes (volcano, forest
fire).

In the real world, population change is complex and can be hard to

predict, simply because of the number and type of processes in the
ecosystem that affect the population in question, as well as chance
effects. Some populations remain stable over many years, others
fluctuate significantly.

• (top) Population dynamics of sand dune plant Androsace

septentrionalis over 8 years in Poland. The population is (more
or less) stable over time and has complex underlying dynamics
(within years). Herbivores cause nº to go down.

• (bottom) Irregular irruptions of house mice (Mus domesticus) in

farmland in Australia. These irruptions cause serious crop
damage and only occur when good conditions (unpredictable)
arrive.
4 idealized diagrams of population dynamics:

• (a) phases of population growth after

disasters.

• (b) stable dynamics controlled by

environment carrying capacity (k): k =
high.

• (c) as (b) but k = low, maybe due to

resource availability

• (d) opposite to (a), habitable site

dominated by population decay after
sudden episodes of colonization.

1. Determinants of population change: Key factor analysis (Colorado potato beetle,

Leptinotarsa decemlineata)

An intense investigation of population levels and the factors that affect them. Identifies what
regulates and determines the abundance of a population

Spring Colorado potato beetle adults emerge from hibernation in mid-June when potato
plants are emerging through the ground. They start laying eggs within 3 days, for 1 month.
Eggs are laid in clusters on the lower leaf surface. Larvae crawl up the plant. Pupate in the soil.
Summer adults emerge in early August, feed, re-enter soil in September to hibernate.

To conserve plants and animals, a

good way to do it is to understand
the forces that cause their pests to
die (key factor analysis). Colorado
potato beetles eat potato leaves
which are poisonous, so they also
have developed a resistance to
pesticides. However, they have other
causes of mortality.

The table shows the number of

beetle death causes counted on 96 potato hills. Mortality factor: what was believed to be the
main cause of death in each phase of the life cycle. We can see how 12000 eggs are laid but
only 14 reach adulthood. With the logN factor (logarithm of number at the start of each phase)
a k-value can be calculated (differences in successive values in the previous column, i.e. deaths
in one of the phases).

2. Conservation: the problems of protecting endangered species, MVP and MDA

Land-use change through human activities affects other organisms through loss or degradation
of their habitat, usually by fragmentation of their habitats caused by turning wild areas into
farmland. Some populations are now restricted to protected areas. How do you decide how
large these protected areas must be to keep a population viable?
To conserve species, you need to understand the factors that determine their population size.
The number must be large enough to withstand chance variations in births and deaths,
environmental changes, genetic drift, and catastrophic events.

The minimum viable population (MVP) is the

number of individuals necessary to ensure the long-
term survival of a species: a 99 % chance of survival
for 1000 years despite the foreseeable effects of
demographic and environmental stochasticity
(random) and natural catastrophes.

MVP depends on the life history the species and the

ability of individuals to disperse among habitat
patches. Genetic models suggest that vertebrates
with populations of an actual size less than 1000 are
highly vulnerable to extinction. For species that have
large fluctuations in population size (many
invertebrates and annual plants), the estimated MVP
is 10,000.

Once the MVP for a species has been determined, the area needed to support the population
must be estimated. This is the minimum dynamic area (MDA). To calculate this you need to
understand the carrying capacity of the habitat and the home range size of individuals, family
groups, or colonies. This gives an estimate of the area requirement per individual.

Figure. Large parks contain larger populations of each species than small parks; only the largest
parks may contain long-term viable populations of many large vertebrate species. Each symbol
represents an animal population in a park. If the minimum viable population (MVP) of a
species is 1000 (dashed line), parks of at least 100 ha will be needed to protect small
herbivores. Parks of more than 10,000 hectares will be needed to support populations of large
herbivores, and parks of at least 1 million hectares will be needed to protect populations of
large carnivores.

With an estimate for both MDA and MVP, the area needed to
maintain a viable population can be determined. For large
carnivores, this area can be enormous, e.g. the estimate for a
population of 1000 grizzly bears is 2 million km 2. This is why
most large carnivore populations are endangered and only
found in very large public land areas and nature reserves.

A study on bighorn sheep populations by Joe Berger at

University of Montana provides one of the best-documented
cases of MVP size. 120 populations were examined, and all populations with fewer than 50
individuals became extinct within 50 years. All populations with 100 or more individuals
survived over that same time period.

Part II: Metapopulations

Migration is a vital factor that influences abundance. Landscapes are usually

heterogeneous: areas of suitable habitat are interspersed between unsuitable areas. A
patch is a relatively homogeneous area of suitable habitat that differs from its
surroundings. Many populations are fragmented and patchy. Dispersal between patches
affects the overall population dynamics.

Key features are: ‘habitable site’ (size, number, life span) and ‘dispersal
distance’.

1. Silver-studded blue butterfly Plebejus argus

This butterflies’ larvae feed on small number of heathland plant

species (gorse, heather) that have patchy distribution. Adults lay eggs
only on this host plants.

This butterfly can colonize all habitable sites of less than 1km from
where it emerged. As it can only fly up to that distance. Any habitable
site more far away than 1 km remains uninhabited (beyond dispersal
power).

A metapopulation consists of a collection of sub-populations. Each sub-population has a

chance of going extinct and appearing again through colonization. Metapopulation dynamics is
a balance between extinction and colonisation.

Metapopulation dynamics can change over time due

to migration between different patches. The plot
shows Sub-population sizes of Glanville fritillary
(Melitaea cinxea) in different patches on Aland Island,
Finland, which has a persistent, highly fragmented
metapopulation. Even large sub-populations had a
high chance of declining to extinction within 2 years.

2. Lince ibérico vivaspaña

The Iberian lynx (Lynx pardinus) is the most

endangered felid in the world. In 1900 it was found in
much of Spain and Portugal, now it’s restricted to
Iberian Peninsula.

Their world population is below 1000 individuals distributed among 9 spatially and
genetically isolated populations. Understanding that the lynx functions as a metapopulation
is central to its conservation. Its existence depends upon maintaining genetic exchange
among the local populations, so the priority would be to link the patches so the population
would be more than the MVP.

Part III: Keystone species

A keystone species has a disproportionate effect on the community and ecosystem it

inhabits because of its activities. If you remove a keystone species, the ecosystem collapses.
Beavers are a keystone species
because they created damps that form
lakes which are highly valuable for
biodiversity. Wolfs (apex predators) are other keystone species, as they instigate trophic
cascades:

In Banff National Park, Alberta, gray wolves

moved back in 1980s after hunting was
banned, starting a trophic cascade: Wolfs
predate elk, which previously had
consumed aspen and willow trees on
riverbanks and caused large scale
deforestation. Increasing trees led to
increasing beaver population. Beaver
lakes created new habitats for a wide
range of other species. Same thing
happening in Yellowstone, Wyoming (31
wolves reintroduced 1995 -6).

Part IV: Ecological succession

An ecological succession is the process of

change in the species structure of an
ecological community over time.

1. Primary succession

It’s the development of a community on newly exposed substrate. The site has never
supported a community before.

Early colonizing pioneer species tolerate the novel conditions and initiate ecological processes.
Later species grow more slowly but are able to outcompete the colonizers after the pioneer
species change the soil by depositing organic matter, as the new species are highly
competitive. Reasonably predictable sequence of species: pioneer  mid-succession 
climax. (Hypothetical, dominance controlled succession.

2. Secondary succession

The re-colonization of a community after disturbance. This site supported a community that
doesn’t exist anymore

3. Founder controlled communities

This is typical of coral reefs, where most reef fish are active by day and need hiding places to
shelter from predators (sharks) at night.

Suitable territories (with good hiding places) are patchy. When one becomes vacant,
individuals of different fish species have an equal chance of occupying it. All species are good
colonists of a gap and equal competitors. Species equivalent in ability to invade gaps.

Part V: Summary
Understanding meta-populations, patchiness and community structure is important for
conservation.

How can human society provide for its own needs and allow nature to thrive at the same time?
Ecosystem services & right to life.

We are undergoing the 6th mass extinction event on Earth: changes in land and sea use
(industrial farming); direct exploitation of organisms; climate change; pollution; invasive alien
species…

We need a new, sustainable, and fair society. It requires knowledge and vision to imagine what
it will be and to make it a reality.

1. How to save the planet?

• Produce more food on less land: but do so in an environmentally sustainable way.

• Stop over exploitation of wild organisms.
• Put significant areas over to wildlife.
• Improve connectivity & join up patches.
• Make landscape multifunctional – farming and wildlife together.
• ‘Joined up’ policies: inclusive, enabling politics, economic reform etc.

One example: Suitable habitat patches need to be connected to allow wildlife to move freely.

Banff national park, Alberta. Parks Canada is installing 7 overpasses and 41 underpasses on the
section bisected by the Trans-Canada Highway. A 2014 study found that fencing off the road
and installing wildlife passes had maintained high genetic diversity in black and grizzly bear
populations. “When habitat is isolated, we can have impact on individual animals where they
might not be able to find water or food. We can also have impact on the genetic diversity of
populations,” says Mark Benson, a member of the human-wildlife coexistence team for Parks
Canada (Guardian newspaper 23.1.2021.)

In the UK, wildlife bridges are likely to form part of the government’s nature recovery network
which aims to link together biodiverse areas under a 25-year environment plan

2. Changing society’s mind-set

• The importance of maintaining viable ecosystems, and the mechanisms by which

ecological communities function, are not widely appreciated.
• All communities are connected, directly or indirectly, as part of the biosphere.
• The planet is essentially one giant food web?
• Anthropogenic change in 1 part of the system can affect multiple other parts.

We shall look at examples later.

Lecture 14 – The Anthropocene

Anthropocene: unofficial unit of geologic time, used to describe the most recent period in
Earth's history when the human activity started to have a significant impact on the planet’s
climate and ecosystems. This concept attempts to capture the sense of human domination on
natural earth cycles.
The term was created by Paul Crutzen (1933-2021) who received a Nobel prize for
understanding the ozone layer and its degradation. He made a paper “Geology of mankind” in
which he argued that humans had such an impact on the Erath’s systems that the effects can
be seen in the geological record, facilitating a new geological epoch. He proposed that it
started in the late 18th century with the industrial revolution. This paper was more an opinion,
as it was short and had very little supporting evidence.

After this, a few more article started to appear focusing on this new term. In 2007, Paul Kurtz,
Will Steffen and John McNeill publish a more robust paper arguing the Anthropocene.

1. Key Arguments that Define the Anthropocene:

 Humans have a substantial effect on Earth functioning

 Impacts are multifaceted including climate change, resource extraction, waste production,
overharvesting, and land cover change.
 These impacts are breaching planetary boundaries and lead to fundamental shifts in Earth
procezone of uncertaintysses.
 Human activity is interwound with planetary feedbacks.
 The effects of human activity are leaving distinct stratigraphic record - hence the use of a
geological epoch.
They suggested that this new geological period started in the 1950s, when modern industry
increased in size and scale, rather than in the 18 th century.

2. The great acceleration

The 1950s was the date proposed for the start of this period due to the great acceleration. In
2015, this was revised, and the great acceleratioMethylococcus capsulatusn was defined as a
distinct phase shift in the mid-20 th century. This affects Earth’s systems and also socio-
economic trends.

3. Planetary boundaries

There are fundamental limits to the amount of human disruption that can occur before we
observe widescale changes in Earth system processes.
The same 2015 paper showed different
variables that are approaching this limit to
where they cannot recover to pre-
anthropogenic levels. This includes climate
change, biogeochemical cycling (P, N), land-
system degradation and conversion, genetic
diversity…

Some people argue that some of these

processes (e.g. N cycle) are more localized
than globalized. Nevertheless, it is clear that
the Anthropocene and planetary boundaries
are intrinsically linked.

4. Geological perspective

In 2008, geologists published a paper asking

the question of whether there is geological
evidence of the Anthropocene.

Now, in theory, we are in the Holocene epoch (Cenozoic) which started 11,700 years ago with
the end of the last major ice age. In this interglacial period humans developed agriculture, so it
is already defined by human activity.

Other argue that the shift we are currently seeing is so robust that an epoch is too low of a
categorization of time, so we should be talking about an “Anthropozoic era”.

5. Formally defining the Anthropocene

AWG (Anthropocene Working Group) was established in 2009, reporting to the International
Commission on Stratigraphy, within the International Union of Geological Sciences.

In May 2019, the AWG completed a binding vote determining two major research questions:
 "Should the Anthropocene be treated as a formal chrono-stratigraphic unit?"
 "Should the primary guide for the base of the Anthropocene be one of the stratigraphic
signals around the mid-twentieth century of the Common Era?".

Both questions received a positive

response, with 29 votes in favour, 4
votes against, and no abstention (33
votes received out of 34 potential
voting members).
The challenge is that this epoch is not solely a
geological issue, it’s also social, historical…

AWG published a paper in 2015 (before the

previous voting) that proposes exactly July 16 th,
1945, as the start date of the Anthropocene,
which was the first atmospheric detonation of a
nuclear device. This detonation could be observed
in the atmospheric and geological record as a shift
towards modernization.

The graph includes annual concentration of

radioactive C averages from 1940 to 1954 of
samples harvested from a Douglas Fir on the
Olympic Peninsula (Stuiver et al. 1998b), monthly
averages for the mid-latitudes of the Northern Hemisphere (Hua and Barbetti 2004), and
approximately biweekly sampling of sites in Europe (Levin and Kromer 2004).

6. Anthropocene critiques

Many recent papers argue that there is a large range of geological evidence to support the
Anthropocene epoch (plastics and changes in biogeochemical cycles in sediments and soils,
radioactive signals, paleogeographic distribution of species around Earth).

The problem is that the mid 20 century is so recent that many of these strata are still forming
so it’s difficult to match the strict guidelines set by the International Union of Geological
Sciences, so some still argue that the proposed Anthropocene is unjustified: “It is too recent a
time period to be suited for geological definition” - “It is a political statement” - “It is valuable
as an informal concept but there is no need to formalize it” – “Human civilization is an event,
not an epoch” – “Anthropocene is a joke” – “Anthropocene is not an issue of stratigraphy but
rather pop culture”.
It's not certain that the recommendation of the AWG will be approved, leading to the
Anthropocene possibly not being declared an epoch.

Some others argue that AWG doesn’t have social scientists or historians and that geologists are
taking too much of a lead in defining the Anthropocene and the discussion should be much
more interdisciplinary.

Social scientists argue that geological thinking is leading the charge for qualifying the
Anthropocene. “The Anthropocene resembles an attempt to conceptually traverse the gap
between the natural and the social…through the construction of a bridge from one side only
(the geological), leading traffic in one direction opposite the actual process…”

7. Biosphere perspective

This perspective differs from the Earth’s systems perspective, as biosphere may be altered
while not necessarily altering
Earth’s system function. E.g. a
forest can lose biodiversity but
still retaining the properties that
makes it a forest as C
sequestration or the hydrological
cycle.

A key point is the idea of mass

extinction. Currently there are a
large proportion of endangered
species either by direct or
indirect anthropogenic
pressures. If this extinctions
come to fruition, we would have
lost some level of species
richness to the Earth. A paper
estimated that over 200,000
populations of species that are on the brink of extinction have vanished since 1900.

Even in the absence of extinction, there have been human-induced mixing of species, being a
change in the biosphere. Some people consider this as the second coming of Pangea, where all
physical boundaries that normally keep species separated have been removed due to human
interference. Some others consider the Earth as a large global scale archipelago where all
islands can be reached by all species.

This means that if in a million years someone check the paleontological record of Earth, they
would notice that new species appear in areas were they were not found before, being this a
strong anthropogenic signal.

8. Historical perspective

People have been proposing different starting dates of the Anthropocene, some being a lot of
years prior to the 1945 proposed date. Another discussion is whether the Anthropocene is a
new phenomenon or something that humans have been doing or inducing for millennia.

Malhi. 2017. Annual Review of Environment and Resources 42: 77-104

 Discovery of fire and starting of cooking of meat by some Homo species.
 Some megafauna extinction due to homo sapiens activity
 Discovery of agriculture
 Large-scale mining operations
 European conquest of America
 Great acceleration in mid-20th century
 A critical planetary boundary

Ellis et al. 2016. Nature. This paper made a case that Anthropocene has deep roots in human
history. These roots are localized further back in history, but their effects eventually led to the
global scale perturbations we see today.

 Megafauna hunting and extinction (10,000-50,000 years BP): This led to the increase of
human population and size.
Denominator: number of species in the same weight class present 50,000 years ago.
Numerator: present species. Large megafauna has the major differences

 Crop domestication (5,000-10,000 years BP). Development of corn, bananas, sorghum, and
other modified plants.
Ruddiman argued that this should be the starting point because it wasn’t a localized event.
The development of flooded agriculture of rice in Asia emitted enough CO 2 to delay the
next ice age. According to his estimations, we should now be in the midst of another ice
age, but due to the emissions to the atmosphere, Earth’s temperature is rising instead of
declining.
Some disagree with this argument because ice ages are difficult to predict.
 Colonization of America (1500 AD). It is estimated that 90% of native Americans died due
to slavery and disease. Some argue that this led to a regrowth of American forests which
coincides with a reduction of CO2, around the year 1650.
 When 2ºC warming reached (future). Another planetary boundary that is discussed is
where the biosphere shifts from being a sink to a source of CO 2.
9. Cultural perspective

The Anthropocene has come to mean different things to different people – not necessarily
related to the natural sciences. There are a lot of books dedicated entirely to this concept,
which shows the flexibility of the concept. The Anthropocene concept has notably influenced
art and architecture.

The Anthropocene has become somewhat synonymous with a large-scale capitalistic,

technocentric worldview, common in western society. What do we mean by “anthropo”? Who
is included in this collective?
 10. Responding to the Anthropocene

Some argue we should work within planetary boundaries to

manage the effects that humans have already caused.

Others state we should utilize human ingenuity to profit from

the Anthropocene with technology and engineering. Some
take a much darker viewpoint and consider the
Anthropocene as an unrecoverable catastrophe.

11. Summary

The Anthropocene…

 Captures the magnitude of human domination on the

Earth system.
 Emphasizes the multifaceted nature of contemporary environmental change – not just
climate change.
 Has catalysed new and innovative multidisciplinary thinking.
 Has become a cultural phenomenon that allows us to explore what it means to be human.
 Is a motivator for action by emphasizing the global nature of environmental change.
Looking Forward, The Anthropocene Lecture Series: Anthropogenic Impacts on Biodiversity,
Agriculture, Food, and Health Drivers of Climate Change Climate Change Future Scenarios
Future Agriculture Mitigation Adaptation

Guided Revision: The Anthropocene

1. Read Malhi (2017) – Posted on Moodle.
2. Understand the concept of Planetary Boundaries and the Great Acceleration.
3. Define where the proposed Anthropocene fits in geological time.
4. Understand different hypotheses as to when the Anthropocene begins.

Lecture 15 - Anthropogenic changes to ecosystems

Part I: Recap

An ecological community consists of a series of interconnected trophic interactions: a food

web. Species within the community can be classified into functional groups according to the
way they acquire energy. Energy flows in a food web from one part of the ecosystem to
another (trophic dynamics).

A community is not a random collection of species, it is characterized by its structure and

dynamics.

• Community structure: (i) species richness, relative abundance; (ii) types of species:
their functions & how they relate to each other.

• The structure is affected by: Conditions and resources present, Interactions within and
between species: competition, predation, mutualism… The action of foundation species
and keystone species and the frequency of disturbances or disruptive events.

It follows that disturbance/disruption caused by human activity can alter community structure,
dynamics & ecosystem services. This can occur by:
• Habitat destruction.
 • Altering conditions (e.g. climate change).
• Altering the availability of resources.
• Reducing the abundance of keystone species.
• Disrupting interactions within / between species.

Multiple causal factors can occur at the same time. These

factors interact in non-linear, complex ways. Some ecological
processes will be more sensitive than others to anthropogenic
disturbance or will have greater effects on community structure
and function when disrupted.

So, key factors are:

• Type of disturbance.
• Magnitude of disturbance.
• Sensitivity of species recipients.
• Abundance and spatial distribution of recipients.
• Ecosystem function of recipients.
• Interacting effects of different types of disturbance.
• Community structure.

2. Changing society’s mind-set

The importance of maintaining viable ecosystems, and the mechanisms by which ecological
communities’ function, are not widely appreciated.

All communities are connected, directly or indirectly, as part of the biosphere. The planet is
essentially one giant food web.

Anthropogenic change in 1 part of the system can affect multiple other parts.

3. Earth’s 6th mass extinction

The global rate of species extinction is 10x, possibly 100x higher than the average rate over the
last 10 million years. Around ¼ of animal and plant species under threat of extinction now. 1
million species face extinction within decades.

The extent and condition of natural ecosystems declined by 50%. Since 1970, 68% decline in
population size of mammals, birds, fish, amphibians, and reptiles.
IPBES (2019), Summary for policymakers of
40% of amphibians, 33% of reef forming corals, >33% of the global assessment report on biodiversity
mammals and 10% of insects are threatened with extinction. and ecosystem services

Extinctions are irreversible, so it’s crucial that we manage to stop

this as species are links in an ecosystem: the loss of 1 species leads to the loss of others.

Part II: Drivers of biodiversity loss

1. 5 main drivers

 Changes in land and sea use. This is the most important driver. Humans have altered 75%
of land and 66% of marine environments since pre-industrial times.
 Direct exploitation of organisms. In 2015, a third of marine stocks were being fished at
unsustainable levels.
 Climate change. Global warming has already impacted almost half of threatened mammals
and one quarter of birds.
 Pollution. Marine plastic pollution has
increased tenfold since 1980, with an
average 300-400M tons of waste dumped
annually into the world’s waters. N and
phosphate inputs also pollute
environments.
 Invasive alien species. The numbers of
invasive alien species per country have
risen by about 70% since 1970.

IPBES (2019), Summary for policymakers of the global assessment report on

Part III: Ex1, Human disturbance: Land use change for farming

The majority of Earth’s ice-free land surface is used to obtain food, mainly to produce meat.

12% of Earth’s surface is cropland, 37% is pastures, and 22% are forests used for timber,
managed by and for human activity. That’s 71% of Earth’s ice-free surface.

This usage of land is caused by food production, which has had an effect on global biomass of
mammals and birds.
2. Remaining areas of wilderness
 3. Land use change and climate change

Human destruction of the Amazon rainforest, combined with climate change, has significantly
reduced rainfall in the region, which is essential for tree growth and survival. As we have seen,
it is the evapotranspiration of the trees that causes the rain, so without trees, the rainforest
ceases to exist at some point.

40% of the Amazon Forest is at a tipping point where it could transition to savannah, a total
ecosystem change that would lead to a precipitous reduction in carbon capture and
biodiversity.

4. Reforming our food system: 3 ‘levels’

Global diets should be much more plant-based, because of the disproportionate effect of
animal farming on biodiversity, land use and the environment.

More land needs to be protected and set aside for

nature.

• At least 30%, probably 50% of land surface.

Farm in a way that supports and enhances

biodiversity, limiting inputs and replacing
monoculture with polyculture.

Part IV: Ex2, biodiversity loss, climate change and

emerging infectious disease

The major threats from zoonotic diseases are Covid-

19, Ebola, and SARS. The majority of emerging
infectious diseases come from wild or farmed animals.

The expansion of agricultural land into natural ecosystems results in mixing of wilds animals,
their pathogens, and farmed animals and humans. Increases risk of disease species jump.

Climate change causes changes in abundance and distribution of wild species animal hosts.
Alters risks of species jumps to humans. Most people now live in high-density towns and
cities, with global travel, increasing the rate at which zoonotic disease spread among human
society.
The transformation of wild area into crop land has
also resulted in human communities being bigger,
instead of sporadic villages. If people live in small
communities, the emerging infectious disease (such as
Ebola) would kill probably the entire village, but it
wouldn’t spread to the next villages.

Jones et al. Global trends in emerging infectious

diseases. Nature 451, 990–993 (2008).

Global trends of EID have been increasing over time in the last decades.
a zoonotic pathogens from wildlife b zoonotic, non-wildlife c drug resistant pathogens d vector
borne diseases (green low, red high)

Jones et al. Global trends in emerging infectious diseases. Nature 451, 990–993 (2008).

1. Climate change, bats, and COVID 19

Bats carry the highest proportion of zoonotic viruses of all mammalian orders. The world’s bats
carry >3000 coronaviruses (CoV). CoV strains in bats from Yunnan (China) most closely
resemble SARS-CoV-1 and SARS-CoV-2. Yunan, Laos, Myanmar are plausible places of origin for
these pathogens.

These areas are also the habitat of masked civets (Paguma larvata) and Sunda pangolins
(Manis javanica) which are thought to be intermediate hosts that transmitted SARS-CoV-1 and
SARS-CoV-2 to humans from wild animal markets. The number of CoVs in an area is correlated
with bat species richness.

Species richness is affected by climate change: it alters suitability of habitats and changes
spatial distribution (range shift). Range shifts result in changes in species composition in the
community.

A climate-vegetation model, combined with data on bat occurrence and habitat requirements,
was used to study effect of climate change on bat range shift. Climate-change driven increase
in bat richness in the region that is the likely origin of SARS-CoV-1 and SARS-CoV-2. A global
hotspot. Mechanistic link between climate change and emergence of SARS and COVID.

Estimated increase in the local number of bat species due to shifts in their geographical ranges
driven by climate change between the 1901-1930 and 1990-2019 period. The zoomed-in area
represents the likely spatial origin of the bat-borne ancestors of SARS-CoV-1 and 2. (Beyer,
Manica & Mora (2021). Shifts in global bat diversity suggest a possible role of climate change in
the emergence of SARS-CoV-1 and SARS-CoV-2. Science of the Total Environment, 767, 145413.)
 Part V: Ex3, Keystone species impact - climate change disrupts a trophic cascade

1. Sea otters, kelp, and sharks

Sea otters are a keystone species in the North Pacific. They eat sea urchins, the main predators
of kelp. If sea otters are abundant, kelp is abundant because they predate on sea urchins, this

is the trophic cascade of sea otters.

Kelp is a foundational species. Kelp forest in the pacific north provides a habitat for many
marine species. Sea otters (Representative
Concentration PathwayEnhydra lutis) predate

White sharks show a developmental shift at 3

– 4 years (2.5 – 3 m body length). Juveniles
eat fish in warmer coastal waters, while adults

Climate change has caused a northwards shift

in range of juvenile white sharks (Carcharodon

a Available juvenile white shark habitat

b – d changes in 3 latitude regions (north, central, south)

This dramatic increase in juvenile white sharks in Monterey Bay, a critical area for sea otters,
caused a significant increase in sea otter mortality from white shark bites year-round. This is a
huge risk to the trophic cascade and ecosystem benefits (of kelp forests).

2. Whale pump

Baleen whales feed on krill at depth. Their faeces deposition in surface waters (it floats)
provides nitrogen for phytoplankton growth. Surface waters have low nutrient concentration,
so it’s a very important nitrogen pump for the ecosystem.
The plankton capture CO2 and are the base of the food chain for fish stocks. This nutrient
pump may be more important for marine productivity in coastal sees than nutrient input from
rivers.

Large scale
whale losses

through hunting is likely to have significantly reduced the effect of the pump. Conserving
whales should lead to an increase in fish stocks while previously, fishers have viewed whales as
competitors.
 Part VI: How to save the planet and learning outcomes

• Human population stabilization: stop poverty, invest in education and women’s rights.
• Reduce our impact by focusing on 4 goals:
– Replace fossil fuels with renewables
– Upgrade to efficient food production and
reduce meat consumption.
– Manage the ocean – a global network of
no fish zones.
– Rewild the world – encourage nature
wherever we can.

Knowledge of ecology and environmental science will

help us understand how to solve the planetary
emergency.

But it requires a wholescale change in the forces that

form the modern world:

– Politics, culture, commerce, industry, science.

It sounds daunting but it is all possible.

Lecture 16 – Climate change and its drivers

– Appreciate the difference between short and long
term climate trends
– Gain an appreciation for the inputs that may be
affecting our climate system
– Become familiar with how scientists study our climate and the evidence
supporting anthropogenic climate change
Part I: Climate trends

Hockey stick graph by Michael Mann.

It shows historical data from a number of centuries showing the relatively stable global
temperatures for the past thousand years or so. However, in recent history, since the start
of the industrial revolution (where instrumentation data starts  black line) there is a
rapid increase of global temperature. All of these temperatures are relative to a baseline
between 1960 and 1990.

Focusing just on instrumentation data: it shows a lot of variability. The g lobal mean surface
temperatures have risen by about 1.2oC since the beginning of the last century. The rate of
warming over the last 50 years is almost double that over the last 100 years.

We can average out some of that noise (variability) by looking at averages of temperatures by
decades. We can still see the general upward trend.

1. Non-anthropogenic drivers

These data are collected from ice scores.

There are several locations in Greenland and
Antarctica. At Vostok, Antarctica, the drilling
has gone on for more than 25 years; Longest core 3.5 Km
(the deeper the ancient the data is).

Snow falls, and is compressed, trapping air bubbles and

dust particles (carbon dating), showing how the
atmosphere was like at that time. Oxygen isotope ratios
allow temperatures to be estimated. It also provides
atmosphere samples for CO2 and CH4.
18
O measurements can give estimates of temperature.
Water can have 2 isotopes of oxygen (O16 or O18).

The ratio heavy:light O isotopes in seawater = 0 so there is

the same quantity of both. However, when water
evaporates, O16 is preferentially evaporated, so O 18 is lost,

altering the ratio.

Further cycles of rain and

evaporation as the water vapor
heads to poles depletes 18O more.
In warmer conditions the greater
the depletion of O18 through
multi evaporative cycles.

 Milankovitch cycles (planetary movements) (long-term)

Earth’s more recent warming has taken place over time scales of decades to centuries.
However, in last 150 years, Milankovitch cycles have not changed the amount of solar energy
input.

 Sunspots (short-term)
Eruptions of the surface of the sun which increase temporarily
increase the radiative output, affecting the incident radiation coming
into the Earth.

Periods of time with no sunspots are correlated with cold periods of

time (in 1600 people could ice-skate on the Thames).

Over the last 40 years we have had fewer sunspots.

 Volcanoes (short-term)
A natural event that puts a lot of ash and particulate matter in
the sky, blocking the radiation from the sun, making
temperatures decrease.
  Teleconnections (short-term)
Fluctuations of global climate that happens in a cyclical
regular basis (El Niño Southern Oscillation ENSO).
Tradewinds in the Pacific, which normally take water,
heat and moisture into South America suddenly shift
and take all that into the Pacific.

Even though El Niño years affect global climate change,

it is not driving it, and still the
temperatures are going upwards.

Overall we still cannot explain the recent

global warming. This steady rise over
recent decades is too fast or out of sync
with Milankovitch cycles and it is too
persistent for short-term factors of
sunspots or oceanic oscillations.

2. Anthropogenic drivers
(greenhouse gasses)

 CO2
It is the most important greenhouse gas
(because its abundance), but not most
potent. Half-life in the atmosphere of ~31
years.

It is highly efficient at absorbing

wavelengths of energy re-radiated by the earth.

Captures and scatters these, ensuring not

all is lost to space.

How did we incriminate CO2 for being responsible for this global warming?

The culprit CO2 became clear while we were investigating what effect would nuclear bombs
have in the isotopes of the atmosphere. Charles Keeling decided to monitor CO 2, and those
monitor stations have been monitoring CO2 levels until today for climate change purposes.

Mauna Loa is a very good place to monitor CO 2 because it is in the Pacific, so it is not
surrounded by other CO2 sources.

The temperature data is derived from 18O measurements. The CO2 concentration of air trapped
in the core. Carbon isotopes are used for dating.

CO2 changes (red) linked to temperature changes (blue) of Milankovitch cycles – feedback
loops!
Right now, CO2 levels are way off the graph, in a historical record. This shows how the amount
of CO2 that is in the atmosphere is not associated with natural origins or natural cycles. There
is some additional input going on.

The other, more close-up graph shows how it is easy to think that the origin of this increase is
due to anthropogenic effects.

If we plot the amount of CO2 in the atmosphere over time and altitude, we can see how there
are large peaks in the Northern Hemisphere driving this global trend.

There is also some variability with seasons. The driving force behind this seasonality is
photosynthesis.

The Northern Hemisphere is responsible due to its higher landmass and more people living in
it. Furthermore, it has been proven the relationship between fossil fuel burning (fossil fuel
emissions are increasing at the same rate as CO 2). With the increase of CO 2 we can also find a
decrease in O2 concentrations in the atmosphere, which would be
gone by burning fossil fuels.

And why fossil fuels? Why couldn’t it be wildfires? There is less C 13

than C12 in fossil fuels, while in the atmosphere the ratio is different
but known. When this fossil fuels are burned, the ratio of C 12 and C13
change in the atmosphere.

‘Anthropogenic CO2’ refers to the additional burden of CO 2 added

to the atmosphere by human activities. ‘Anthropogenic emissions’
consist of two fractions:

• CO2 from fossil fuel burning and cement

production, released from hundreds of
millions of years of geological storage

• CO2 from deforestation and agricultural

development, which has been stored for
decades to centuries

The main carbon reservoirs in gigatonnes (GtC) are

the atmosphere (750), the oceans and ocean biota
(39,000), soil (1,580) and land biota (610). So the
ocean and soil are the major reservoirs, not the
atmosphere. Over time, the carbon that is in the
atmosphere will sink in those other reservoirs, but
this exchange is very slow, so we can’t rely on that to
get rid of the CO2 excess. What we are doing when
we burn fossil fuels is removing carbon from reservoirs
and putting them into the atmosphere.

 Methane CH4
It’s the 2nd most important greenhouse gas in case of
radiative forcing after CO2. Short half-life in the
atmosphere of ~10 years. Molecule for molecule 25 times
as efficient as CO2 at absorbing re-radiated energy
If we look at the concentrations in Mauna Loa (in parts per billion, ppb) we can see a clear
upward trend. However, we can see a plateau in early 2000, maybe due to its short life. If
there is a reduction in methane production, we can see how the curve flattens.

The concentration of methane has been stable over a long period of time, over the past 10,000
years (data from ice scores). In the last 100 years, there has been a rapid increase. Cows
produce a lot of methane.

Atmospheric CH4 originates from both non-biogenic and biogenic sources.

BIOGENIC SOURCES. Accounts for more than 70% of the global total. It’s based on methane
biogenesis (primary fermentation to acetic acid). Anaerobic environments
• CH3COOH  CH4 + CO2
• CO2 + 4H2  CH4 + 2H2O
Sources include wetlands, rice agriculture (including associated trees), livestock, enteric
fermentation (inside guts of livestock) and slurries, 37% anthropogenic methane. (FAO figures).
Also landfills, forests, oceans. Also termites.

NON-BIOGENIC SOURCES. Emissions from fossil fuel mining and burning (natural gas,
petroleum, and coal). Biomass burning. Waste treatment. Geological sources (fossil CH 4 from
natural gas seepage in sedimentary basins and geothermal/volcanic CH 4).

Some of both biogenic and non-biogenic can be anthropogenic.

Methane sinks are:

 The Atmosphere. (OH), the hydroxyl free radical is the

major oxidizing chemical in the atmosphere. Each year, it
destroys approx. 3.7 Gt of greenhouse gases, including CH 4,
HFCs and HCFCs.
Levels inferred from reactive trace gases. These include 14CO
(half life of 2 months; regional or short –term changes) or
methyl chloroform (half life of 4.9 years; long term trends).
Relatively stable long term but subject to short –term
variations.
 The soil. CH4 is oxidised in dry soil
 The stratosphere. CH4 lost from the troposphere by
diffusion
 Nitrogen compounds
Nitrous oxide (N2O) is the most important nitrogenous gas for radiative forcing. Joint 3rd most
important gas with respect to radiative forcing. Molecule for molecule is 230 times more
efficient than CO2 as a greenhouse gas, but it concentration is much lower, that’s why it’s the
3rd most important. Is long-lived in the atmosphere though, unlike NH 3 and NOx (NO and NO2):
110 years vs 50 days.

Concentrations of N2O have risen from about 270ppb in pre-industrial times. Current levels are
about 326ppb (20% increase). Annual emissions have increased by 40-50% over that period,
due to human activity.

N2O is originated from natural sources (decaying

organic matter and animal waste) or industrial
sources and fertilizers.
 Halocarbons

They lead to the destruction of stratospheric ozone layer, so now

they have been strongly limited by the Montreal Protocol. But
also potent greenhouse gases in their own right – x1000 more
efficient than CO2 as a greenhouse gas.

Overall, are the 3rd most significant for radiative forcing,

contributing 12% of that due to Long Lived GHGs. The most
significant are CFC-11, CFC-113 which are decreasing and CFC-
12 which has plateaued. Long – lived in the atmosphere (45 –
100 years for the major species), so we don’t produce them
anymore, but their effect it’s still there.

 Combined effect of GHGs

Overall, all the GHGs, mostly CO2 even though it is the weakest, are adding up to an additional
3 watts per square meter of radiative forcing. A sunspot adds half a watt per square meter.
 Aerosols
Aerosols are small particles (typically 0.001 - 0.01
mm diameter) suspended in the atmosphere.
Industrial haze is an obvious example of them.
These absorb radiation and scatter it back into
space. The effect on radiative forcing can be positive
or negative but overall cause global cooling. Examples include Sulphates, Black Carbon from
Fossil Fuels, Biomass Burning, Mineral Dust.

 Sulphate aerosols
Most important source of aerosols. They originate from
natural sources e.g. Volcanoes, marine bacteria, and
anthropogenic sources e.g. Power stations burning coal which
is rich in sulphur. Sulphates can also be produced by chemical
action on sulphur dioxide. Short lifetime of particles (5 days)
so effects limited to close to sources.

If the effects of Sulphur aerosol of the year 2000 were removed, global temperature would rise
due to the loose of cooling effect.
 3. Anthropogenic drivers (albedo and
land use)

Albedo is the fraction of solar energy

(shortwave radiation) reflected from
the Earth back into space.

Snow, ice, and deserts are good

reflecting solar radiation whereas
vegetation and oceans are good
absorbing it.

Albedo is totally dependent on how

we are using our land and what the
land cover is like. With human activity
came the change in the type of
vegetation that has been used
throughout the world, loosing forests
and ice cover. This could have cooling
or warming effects.

If you have particular pollution in the

atmosphere, this could contribute to
the composition of clouds, making them much more
reflective to incident radiation. Higher albedo, less
precipitation, and less radiation and heat at surface.

So now an effort to summarise all of the gasses and

effects we have discussed .

Here summarised by relative radiative forcing of each

component measured a plus (warming) or neg
(cooling) effect relative to 1750.

• Considering the strength of linked feedback

loops and levels of confidence for each effect we’ve discussed today.

So can look and compare all factors.

• CO2 = 1.5-2Wm2 – biggest, with high confidence

 • CH4 = 1Wm2… etc
• Down to mixed and negative effects
• Solar irradiance – minimal effect
• Overall when added all together – still very much a
positive warming force
• Shifting the energy balance of what comes
in/out has shifted.
4. Summary

 Climate trends: Records going back over 1000s years show

a sharp recent increase in global temperature.
 Climate changes in response to factors that alter the
earth’s energy balance – Radiative Forcing.
 Causes and effect: Long- and short-term changes in natural
phenomena cannot explain the recent rise.
 The forcing due to GHGs is far greater than forcing due
to natural phenomena such as changes in solar
irradiance.
 Role of humans: Increased greenhouse gas levels are
from anthropogenic sources, consistent with man-made
global warming.
For the exam:
 You should be able to demonstrate understanding
of:
 Radiative forcing
 Long and short term factors that influence
climate
 Contribution to warming and cooling by different atmospheric gasses.
 Contribution of factors that affect warming via absorbing or reflecting
radiation (albedo).

Lecture 17 – Climate change, future scenarios

Part I: Temperature and other climatic factors

The global average mean temperature has increased over the last 200 years. This change can
also be seen in the global average minimum and maximum temperatures during the day. We
can see how the temperature increase is faster during the night than during the day, so the
temperature difference between the two is smaller (blue graph).

This may occur because heat is absorbed by land and oceans during the day, which dampens
the effect of the heat accumulated during the day but contributes to the release of heat during
the night.

The global temperature shift can also differ by location. This pattern is not uniform. Bigger
landmasses are heated up more rapidly. The cooler part is due to the ice melting into the
ocean, meaning a loss of ice surface.

1. Precipitation trends
All of the climate inputs have an influence on the other, and once energy is put into the
system, it has knock-on effects for all of the components, that is why the climate system is so
complex. One of the effects is on the hydrological cycle, more heat means more evaporation,
having an impact on clouds and precipitations, intensifying the water cycle.

We can plot the rate of change of precipitation trends and see how in the last 100 years there
is not much change but in the last 50 years there is a lot of change, with areas becoming
wetter and other dryer.

Extreme weather events are increasing in number, which could explain how the increase in
precipitation is affecting the weather: the extra precipitation is not spread over the whole
year, but it is increasing the intensity of rainfall.

2. Climate feedback

Climate feedbacks: processes that can either amplify or diminish the effects of radiative
forcing. Precipitation, clouds, greening of forests, ice albedo…

Climate tipping points: When Earth’s climate abruptly moves between relatively stable states.
Ice loss, thawing permafrost and methane release, ocean circulations…

The climate has undergone rapid changes over the last 100 years and this trend has
accelerated. These changes are expected to continue BUT impacts of warming are multiple and
interconnected. Positive and negative feedbacks. Tipping points

Part II: Predicting the future

In order to predict the future’s climate we need 4 things:

 Good climate model

 Understand how past changes in anthropogenic
activity have influenced climate
 Predict how anthropogenic activities may change
in the future
 Fit these together

Climate models need to incorporate the prediction

of several steps from emissions to climate
response. Multiple steps contribute to the overall
uncertainty of a climate model projection, as
shown by CIs.

1. Climate predictions

Won’t go into detail about climate model

development but in principle how they work:

They contain multiple components, representative of local and global weather patterns and
feedback loops.

Key principles
• Take climate system from surface, up through troposphere to stratosphere
• Partition into series of boxes
• Model flow of energy between boxes
 o i.e. heat from sea, and lateral movement to surrounding boxes over time
o Dynamic processes over range of scales.
• Huge amount of computing power needed for this
o Boxes have become smaller as computing power has increased
o More detail of energy flows is always improving.
It is interesting to see if as models become more complex and detailed, the predictions change.

Atmosphere-Ocean General Circulation Models (AOGCMs). Earth models of intermediate

complexity (EMICs). Simple climate models (SCMs)

Part III: IPCC future scenarios

The Intergovernmental Panel on Climate Change (IPCC) was established jointly by the World
Meteorological Organisation (WMO) and the United Nations Environment Programme (UNEP).
Its purpose is to predict what future risks would be and to provide global and country level
policies.

The long-term nature and uncertainty of climate change and its driving forces require
scenarios that extend to the end of the 21st century.

The 1996 Plenary of the IPCC requested a “Special Report on Emissions Scenarios” (SRES).
Defined by 2000. These SRES scenarios are used up to and including IPCC 4 th assessment.

New scenarios framework developed in 2008, for use in 5 th assessment onwards.

1. Special Report on Emissions Scenarios (SRES)

SRES involves four narrative scenarios "storylines" to describe alternative futures depending
on different emissions and global patterns.

They cover a wide range of key "future" characteristics such as demographic change, economic
development, and technological change.

Together they describe divergent futures that encompass a significant portion of the
underlying uncertainties in the main driving forces.

Developed 4 major scenario families – A1B most extreme. None included mitigation policies.
SRES was superseded by RCPs.

2. Representative Concentration Pathways (RCPs)

The 5th Assessment Report of IPCC has defined a set of 4 new scenarios (RCPs) from which
uncertainties in socio-eco and climate can be explored.

RCPs consist of the components of radiative forcing which serve as input for climate
modelling.

Identified by their total radiative forcing increase (Wm 2) in the year 2100 relative to 1750:

• 2.6 Wm2 for RCP2.6 - mitigation leading to peak and decline in emission ➔ low forcing
• 4.5 Wm2 for RCP4.5 – stabilization by 2100
• 6.0 Wm2 for RCP6.0 - stabilization after 2100 (closest scenario)
• 8.5 Wm2 for RCP8.5 – growth in
greenhouse gas emissions, which peak
after 2100 ➔ very high forcing
(extreme scenario, 98th percentile)

The RCPs represent a range of 21st century mitigation policies, as compared with baseline
trajectories SRES used in the 3rd and 4th IPCC Assessment Reports.

RCPs span a wide range of total forcing values BUT

• do not cover the full range of impacts from albedo

change and aerosols.
• do not guarantee boundaries for emissions change.
• do not represent specific futures or policy actions –
socio-economic drivers developed separately explore
range of approaches that can lead to each.

3. RCP projections

If we take the two extreme scenarios (RCP2.6 and

RCP8.5) we can see how they differ trajectories over the
next 100 years.

Global surface temperature change for the end of the

21st century is likely to exceed 1.5 ℃ relative to 1850 to
1900 for all RCP scenarios except RCP 2.6.

It is likely to exceed 2℃ for RCP 6.0 and RCP 8.5, and more likely than not to exceed 2℃ for
RCP 4.5.

4. Common trajectories

Global mean surface temperature increases as a

function of cumulative total global CO2.

All models on same trajectory with CO 2 increase but

achieve atmospheric concentrations over different
timescales.

The difference is where it plateaus.

Part VI: Impact projections for global patterns of change

1. Future global surface temperature

Depending on whether we are talking about RCP2.6 or RCP8.5 the intensity of the change
varies. In both scenarios, the greatest temperature increase is over land and in the high
northern latitudes. The Arctic regions are going to
suffer the most.

There is less warming over the Southern oceans and

North Atlantic. Continues trends in 20th century.
 2. Future global precipitation

Greatest increases over the high northern temperate regions and the
equator.

Decrease around tropics and sub tropics. Continues trends in 20th century.

3. Future weather extremes

Changes in temperature and precipitation have implication for extreme

weather. Changes in extremes based on multi-model simulations for
2081-2100 compared to 1980-1999.

Precipitation
intensity increases
(max. 5 days of
rain), particularly in
tropical and high
latitudes, and it gets
really extreme in
RCP8.5. There is a
tendency to drying
of mid–continental
areas ➔ greater risk of drought  wildfires.

This has a cascade of effects, affecting: a decrease in frost days, very likely that heatwaves will
become more intense, and the minimum temperatures will rise faster than maximum. Also,
increase in growing season, which could be beneficial, but taking into account all factors, it is
not.

4. Short-term prediction and model testing

To test how confident those models are, we could test these models by predicting backwards,
into the past, and see if they fit correctly.

Blue line, forward, red line, backwards.

These models fit in generally good, but there is a lot of noise, so an accurate annual prediction
still difficult.

Another way to test models is by predicting short term

changes and then wait to see if it is correct. The model
correctly predicted the areas of change, but it didn’t
predict at all the intensity of the changes but still in the
confidence intervals of the estimate for those models.

Part V: Impact on oceans

Oceans cover ¾ of the earth’s surface and they are
major components of the earth weather system.
They are also affected by climate change.
Predicted changes include temperature, sea levels,
and acidification.

1. Ocean temperature

Temperature varies with location and season due to currents and depth. In fact, that depth can
be a sink of all of that surface heat,
acting like a buffer. In reality, it’s
more complicated, as average surface
temperature has increase by ~0.4-0.8
in past 100 years and they will
continue to store that heat and then
release it for decades.

Data on heat content is collected

from range of sources (satellites,
machines, and put sensors on animals). Surface temperature is closely
related to heat content between 0 and 700 m
depth. Trends are consistent in both.

Averaged over the full depth of the ocean,

the 1993–2018 heat-gain rates are 0.57-0.81
watts per square meter. Joules (unit of energy)
allow for comparison with energy in other
parts of earth climate system.

The greatest surface temperature increases is

predicted over land and in the high northern
latitudes. Less warming over the Southern
oceans and North Atlantic. But this obscures
the accumulation of heat in deeper waters.

In fact, land and the atmosphere absorb the smallest amount of

heat, and surface water is what most heat absorbs, being a very
big buffer. Some heat also makes it to the lower columns of water.
And we need to understand these deeper layers of the ocean as it
can then release all of this heat just as land does (absorbing during
the day and releasing during the night) but with much slower
timescales being able to commit future warming.

2. Impact on sea level

The implication of all of this heat content is the thermal expansion of water, not because
changes in the hydrological cycle.

Even if we stopped the emissions now, thermal expansion is a reality, and it would still happen.

3. Impact on sea ice

Ice is only likely to be retained
over long term under RCP 2.6
mitigation scenario. Every other
scenario is heading towards 0.

Ice loss would improve navigation

around polar regions but a cost of
major ecological changes e.g.
species dependent on sea ice and
albedo.

Positive feedback to climate

change.

4. Coral reefs

Scleractinian corals have calcium carbonate

skeletons. They have an obligate symbiotic relationship with zooxanthellaea, a single celled
photosynthetic algae.

Corals become sequestered into the reef framework when the coral polyp dies. The greatest
abundance close to the equator. They are highly biodiverse ecosystems, an estimated 1 million
species in 400,000 Km2 (a 632km square) of reef. However, they are highly sensitive to climate
change.

Thermal threshold for coral bleaching is only 1-2℃ above summer maxima for 3-5 weeks. is
more common with warming. Thermal thresholds vary with latitude and sea temperatures –
corals highly adapted.

A bleached coral has no algae. It is not dead but very vulnerable. Corals can be recovered if the
bleach is mild, but it can produce major damage to entire coral reefs.

Corals are highly adapted and grow very slow, so they cannot respond to these changes and
shift their habitat range of individuals.

In this map is shown the maximum surface water temperatures and the major bleaching
events. In 1998 there was one of the worst bleaching events, also linked to El Niño years.

In the past 20 years there has been more bleaching events (great coral reef) linked to episodic
increases in ocean surface temperatures. Progressive bleaching events make recovery almost
impossible.

5. Impact on ocean’s CO2

By increasing CO2 in the atmosphere, some of it (1/4) is

absorbed into the ocean. As a net result of adding CO2
there is an increase of availability of hydrogen ions and
a decrease of carbonate (CO 32-) because it becomes
bound up in bicarbonate as equilibrium shifts. This
carbonate decrease will reduce production of
calcareous shells (inc. corals) and enhance dissolution.
The increased H+ will result in a slow increase in ocean acidity. Oceanic pH has decreased by 0.1
unit since 1750.

CO2 binds to water to make bicarbonate and H + ions. H+ increases the acidity, but also binds
free carbonate in solution, so carbonate unavailable to make calcium carbonate in shells.
Different emission scenarios show different changes in ocean acidification. There is also some
variability in location but it’s very uniform. We are looking at a change in sort of 0.3 units over
the next 60 years, a really significant change.

Rising in CO2 levels are likely to result in declining calcification which is linked to decrease in
ocean pH (more acid). It is calculated that doubling CO 2 would decrease calcification in
aragonite corals by 20 – 60 %. Warming temperatures put corals at risk of bleaching and death.
The reduction in coral cover would increase erosion.

Part VI: Summary

 Projecting changes in the climate requires
– Good climate models
– A plausible projection of greenhouse gas emissions
 Projections are probabilistic – outcomes given as a a range
 All models predict continued warming through the 21 st century
 Precipitation could increase or decrease depending on location.
 Probability of extreme weather is likely to increase.
Impacts on oceans:
 Likely major environmental impacts are not limited to land
 Deep ocean temperatures are also expected to increase

  Some changes already built in

 Absorbance of CO2 from atmosphere is also expected to cause acidification of the oceans
 BUT its not all doom and gloom! It is our power to change our actions and behavior.
1. For exam
• Demonstrate understanding of:
• How scientists approach climate prediction and model confidence.
• IPCC future scenarios.
• Expected patterns of change based on IPCC scenarios.
• Demonstrate understanding of impact of climate change and emissions on global climate –
Ocean case study.
 Lecture 18 – Future agriculture
1. Agriculture Bill

A Bill to authorise expenditure for certain agricultural and other purposes:

 To make provision about direct payments following the United Kingdom’s departure from
the European Union and about payments in response to exceptional market conditions
affecting agricultural markets.
 To confer power to modify retained direct EU legislation relating to agricultural and rural
development payments and public market intervention and private storage aid.
 To make provision about reports on food security; to make provision about the acquisition
and use of information connected with food supply chains.
 To confer powers to make regulations about the imposition of obligations on business
purchasers of agricultural products, marketing standards, organic products and the
classification of carcasses.
 To make provision for the recognition of associations of agricultural producers which may
benefit from certain exemptions from competition law.
 To make provision about fertilisers.
 To make provision about the identification and traceability of animals; to make provision
about red meat levy in Great Britain.
 To make provision about agricultural tenancies.
 To confer power to make regulations about securing compliance with the WTO Agreement
on Agriculture, and for connected purposes.
2. Environmental bill

A Bill to make provision about targets, plans and policies for improving the natural
environment.
 For statements and reports about environmental protection; for the Office for
Environmental Protection.
 About waste and resource efficiency.
 About air quality.
 For the recall of products that fail to meet environmental standards, about water.
 About nature and biodiversity.
 For conservation covenants.
 About the regulation of chemicals; and for connected purposes.

3. Some of the future challenges for agriculture

 Increasing population
 Shortages/increased costs of: – Land – Water – Energy – Phosphate (fertiliser)
 Reduction in fertiliser input (pollution, availability, cost)
 Constraints on pesticide use (pollution, human concerns)
 Effects of climate change other than water availability
 Food versus fuel crops
 Increased/decreased demand for animal products
 Other ‘human’ factors – labour, food prices etc
4. ‘Choice’ of production systems

In the 21st century, farmers have many tools available to them to increase yield and quality.
However, some of the tools can have an adverse effect on the environment and possibly on
human health (e.g. pesticides). The use of tools depends on what is available to individual
farmers and costs versus benefits, so choosing is on them. In some circumstances some or all
of these tools are not available for economic (e.g. developing countries) or political reasons
(e.g. Cuba in the late 20th century).

 Cuba. Until end 1980s agriculture heavily subsidised by Soviet bloc as they were a
communist country. They imported >50% calories consumed and 80-95% of wheat, beans,
fertilisers, pesticides, animal feed. In 1990, the trade with Soviet bloc collapsed leading to
shortages and limited access to petrol, pesticides, fertilisers…
Government policy had to adopt an alternative model using local knowledge, skills, and
resources. They used oxen instead of tractors, Integrated Pest Management, and farmer
cooperation. Taken time to work – intensive organic gardens in urban areas. Sustainable
agriculture in rural areas, biological control, rotation, compost production, polyculture,
intercropping, green manures. Still problems but population now fed much better than in
mid 1990s and now Cuba is opening up to the world…
5. Different farming systems

 Conventional. It uses all available tools to maximise yield and quality. It changes over time.
 Organic. Production system which avoids or largely excludes the use of synthetically
compounded fertilizers, pesticides, growth regulators, and livestock feed additives. To the
maximum extent feasible, organic farming systems rely upon crop rotations, crop residues,
animal manMethylococcus capsulatusures, legumes, green manures, off-farm organic
wastes, mechanical cultivation, mineral-bearing rocks, and aspects of biological pest
control to maintain soil productivity and tilth, to supply plant nutrients, and to control
insects, weeds, and other pests (USDA, 1980).
 Low-Input agriculture - has been defined as a production activity that uses synthetic
fertilizers or pesticides below rates commonly recommended. It does not mean
elimination of these materials. Yields are maintained through greater emphasis on cultural
practices, Integrated Pest Management, and utilization of on-farm resources and
management.

The environmental impact of these different farming systems can be assessed by LCA. LCA (life-
cycle analysis) is a technique to assess the environmental aspects and potential impacts
associated with a product, process, or service, by compiling an inventory of relevant energy
and material inputs and environmental releases, evaluating the potential environmental
impacts associated with the identified inputs and releases, and interpreting the results to help
make a more informed decision.

One thing you can measure is global warming potential (t CO2) over 100 years per ton of food.

6. Organic production

Doesn’t use synthetic inputs like pesticides and fertilisers and doesn’t provide much pollution
from those types of inputs. This has been suggested that might contribute to reducing our
impact on the environment.
Organic production is likely to use more land to produce the same yield and it may use less
energy per unit area (by not using synthetic fertilisers) but not necessarily per ton because
the yield per area is still decreased. It uses more fuel (tractors) but generates less pollution by
pesticides.

In the graph organic and conventional productions are compared by calculating the ratio of
organic impact divided by non-organic impact. Different food commodities are compared by a
number of environmental impacts.

If the ratio is 1 it means that organic and

non-organic are equivalent, but if it is
above 1, organic is worse. So organic
uses more land and less pesticides, but
regarding the other impacts, it is not
always as simple as some people might
think.

7. Changing our diet

On average, 10g of vegetable protein are

needed to generate 1g of animal protein, so changing our diet to vegetarianism or veganism is
on the table to reduce environmental impact.

There have been studies comparing the environmental impact of vegetable protein
(soyabeans) with meat production. Meat production has much more impact comparing with
soyabeans.
8. Intensification versus extensification

Is it better to use more land to grow crops but

reduce ‘pressure’ from fertilisers and pesticides
or to use less land, but grow crops more
intensively? Similarly is it better to farm animals
intensively in a way that reduces environmental
impact – rather than farm them extensively (e.g.
for animal welfare)?

A land-sparing scenario (B & C) is one in which farmland is higher yielding (and therefore often
less biodiverse), but since high farm productivity means that less land is needed to achieve a
given level of output, this could allow more non-farmland to be spared for nature. In a land
sharing scenario (A), farmland is less high yielding (measured in terms of e.g. cereal output)
but more biodiverse. However, for the same level of food output, as compared with a land
sparing scenario, less land is available solely for nature conservation. Is used in organic
production.

Re-wilding. Large-scale restoration of ecosystems where nature can take care of itself. It can
be done in the space left in land-sparing scenarios.

9. Using science and technology

Using knowledge about crop, livestock, pest, weed, and disease biology we can manage
farming systems. The use of inputs must be optimised (precision farming). Using crop and
animal genetics to produce varieties and breeds that respond better to low input situations.
All of these approaches would reduce inputs.

 Using knowledge. Good crop rotation (not growing crops of the same plant family in the
same land in consecutive years) and soils management strategies. Matching fertiliser and
water requirements to the crop. Monitoring and forecasting pests and diseases (so
pesticides are only applied when it is absolutely necessary).
 Precision farming. Instead a field as one unit where everything is the same, you can treat
different parts of the land differently using yourMethylococcus capsulatu farm equipment.
Apply more fertilisers or more weed control in certain areas. This is possible due to new
sensors, remote GPS, and other tools. An example of this is a mechanical hoe that uses
vision guidance to reduce weeds without damaging the crops (lettuces). There is a lot of
potential with robots and drones.
o High precision positioning systems (like GPS) - accuracy when driving in the field.
o Automated steering systems: reduce human error and are the key to effective site
management.
o Geomapping: used to produce maps including soil type, nutrients levels etc in
layers and assign that information to the particular field location.
o Sensors and remote sensing: collect data from a distance to evaluating soil and
crop health (moisture, nutrients, compaction, crop diseases). Data sensors can be
mounted on moving machines.
o Integrated electronic communications between components in a system for
example, between tractor and farm office, tractor and dealer or spray can and
sprayer.
o Variable rate technology (VRT): ability to adapt parameters on a machine to
apply, for instance, seed or fertiliser according to the exact variations in plant
growth, or soil nutrients and type.
 Crops genetics. Varieties that are resistant to pests and disease. Varieties that use
nutrients and water more efficiently. Varieties that are more competitive against weeds.
This can be achieved through conventional plant breeding and genetic modification. Both
approaches require identification of genes for which molecular techniques are very useful.
Same idea applies to animals.
10. Ecosystem service provision by land managers

The land used for food, fibre, or fuel production (provisioning services) can also deliver a
number of other ecosystem services such as: Water regulation (quantity and quality) and
various services associated with biodiversity.
Land managers can reduce the pressure on existing services and manage the land in a way
that provides additional services.

11. LEAF

LEAF encourages farmers to adopt Integrated Farm Management (IFM), promote the benefits
of IFM to consumers, raise awareness of the way many farmers are responding to current
concerns. Includes crop rotation, managing hedgerows for wildlife, and using pesticides and
fertilisers only when necessary.

12. Conservation agriculture

Approach to managing agro-ecosystems for improved and sustained productivity, increased
profits and food security while preserving and enhancing the resource base and the
environment. Characterized by three linked principles: continuous minimum mechanical soil
disturbance, permanent organic soil cover, and diversification of crop species grown in
sequences and/or associations.

In 2018, an estimated 55.3 per cent of the world’s population lived in urban settlements. By
2030, urban areas are projected to house 60 per cent of people globally and one in every three
people will live in cities with at least half a million inhabitants. That is why urban, or peri urban
agriculture could be a need in the future. Rooftop farmers or vertical farming.

Insects can be food for humans or animals. They are a good source of proteins. Presentation of
the world's first cultured hamburger (synthetic meat) (unbaked here) at a news conference in
London on 5 August 2013. The cultured meat product was developed by a team of scientists
from Maastricht University led by Mark Post at a cost of €250,000.

Lecture 19 – Mitigation
The world changes even without mans influence (e.g. tectonic drift). However, mankind can
accelerate than process (Tuvalu island might be the first country to be wiped off the map by
global warming. Max height above see 4.5m).

We have problems with peak oil (extracting less than demanded, affecting climate), peak soil
(are we eliminating the limited agricultural land because we are not farming appropriately?),
peak water (due to rising population, more rainfall in form of floods or droughts), peak
biodiversity loss, peak population, and peak GDP (poverty and development).

1. Responding to climate change

Involves an iterative risk management process that includes both adaptation (learning how to
live with those problems) and mitigation (alleviate problems). It needs to consider climate
change damages, co-benefits, sustainability, and equity and attitudes to risk.

2. Mitigation potential

 Economic potential. Considers social costs and benefits and social discount rates assuming
that market efficiency is improved by policies and measures and barriers are removed. It
considers what is the impact of dealing with climate change in the economy.
 Market potential. Based on private costs and private discount rates. It is expected to occur
under forecast market conditions. It includes policies and measures currently in place. It
notes that barriers limit the actual uptake.
What do we do with fuel going forward? How are we going to heat our houses or run our cars?

One way of mitigation is putting a tax to businesses on carbon emissions. Mitigation potential
goes up with a big tax (100$ instead of 20$ per ton) so businesses avoid emitting GHGs. But is
this affordable?
 3. Great
green wall

There is a debate
about the impact of
growing trees on
climate change. If they are planted in the wrong place you could make the situation worse. We
are still seeing deforestation in Brazil despite the anti-deforestation policies.

The great green wall is a project in which local trees are being planted through the south
border of the Sahara Desert in order to mitigate its expansion.

4. Resource efficiency

Mitigation, through reducing greenhouse gas emissions, will primarily be addressed through
greater resource efficiency including:
• Improving energy efficiency performance of new and existing buildings and influencing
behaviour of occupants
• Reducing the need to travel and ensuring good accessibility to public and other
sustainable modes of transport
• Promoting land use that acts as carbon sinks
• Encouraging development and use of renewable energy (energy sector)
• Reducing the amount of biodegradable waste landfilled

5. Energy sector
This sector is probably one of the most important ones we have to target. All energy
originates from the sun (e.g. Wind, Solar, Oil, Gas etc) it is how we harvest that energy which
could be crucial. It is estimated that solar cells if efficient could supply all our energy
requirements.

Estoy hasta la puta polla

0.7

18 – 19.8

stunky