What is Microbial Ecology?

What is Microbial?
of or referring to a minute life form; a
microorganism, especially a bacterium that
causes disease. Not in technical use.

What is Ecology?
the study of the interactions between organisms
and their environment

Microbial ecology = The study of interactions between

microorganisms and their environment (chemical, physical, and
biological environment!)

More terms
Community: an area where organisms can
interact with each other and the nonliving
environment; often called an ecosystem
Ecological niche: the role an organism
plays within a particular ecosystem
Microenvironments: small environments
within a larger ecosystem relevant to
microbes

Nutrient aquistion
Primary producers: autotrophs produce which convert
CO2 into organic materials (these include
photoautotrophs and chemilithotrophsoxidize inorganic
chemicals for E); serve as food for consumers and
decomposers
Consumer/heterotrophs: utilize organic cmpds and rely
on primary producers; food chain involves primary
consumers (herbivores) secondary consumers
(carnivores that eat herbivores) and tertiary consumers
(carnivores that eat other carnivores
Decomposers: digest the remains of primary producers
and all consumers; bacteria and fungi are involved in the
process of minerilization (the complete breakdown of
organic molecules into inorganic molecules)

Living styles of Microorganisms

The term microbial ecology really wasnt in

common
use until the late 1960s
Why?

Microbial ecology has its roots in microbiology,

rather than ecology
The history of the field is largely a transition
from laboratory pure cultures to studying
organisms in nature

Microbial communities/ Microbial

mat
Thick, dense, highly
organized structure
of distinct layers
Green (top layer
cyanobacteria)
Pink layer (sulfur
bacteria)
Black layer on the
bottom (sulfate
reducers H2S
production)

Nutrient Cycling: CNS and P

Definition: (Element Cycling, Nutrient Cycling)

- the physical movement and chemical transformation of
material by biochemical activities throughout the
atmosphere, hydrosphere, and lithosphere
C, H, O, N, S, P, Fe, Mo, Mn, etc
Major roles of microorganisms in most element cycles
because of diverse metabolic capabilities
ubiquity high rates of enzymatic activity
Reservoirs/ pools stores of elements (mass) e.g.
atmosphere, soil, biomass, oceans all are reservoirs of
C
Transfer rates/Fluxes rates of movement of elements
between reservoirs (mass per time)

Nutrient Cycles
Nutrient cycles and energy flow are
related.
C cycling is most directly related to energy
flow.
CO2 + H2O + light nrg CHO + O2
CHO + O2 released nrg + H2O + CO2.

Food Chain Energetics

Aautotrophs: CO2org. C
higher plants (H2O split; nrg from sun)
algae (H2O split; nrg from sun)
bacteria (H2O, H2 or H2S split; nrg from sun or chemical oxidations)
Heterotrophs: org. C org. C
consumers
primary = herbivores
secondary = feed on herbivores
tertiary = feed on secondary
omnivores = feed on combination of producers/ consumers
Decomposers (detritivores): org. C less complex org. C CO2
bacteria, fungi

Elemental Cycling: definitions

Assimilatory processes: builds biomass constituents.
Dissimilatory process: reduction coupled to nrg-yielding
oxidation.
Mineralization: Conversion from organic to inorganic
state.
Oxidation: loss of electrons; releases energy.
Reduction: gain of electrons; requires energy input.
Redox couple: coupling of oxidation and reduction. The
net difference in the oxidation and reduction halfreactions provides energy for cell function.

The Carbon Cycle

1. Fast Cycle decades or less
a. reservoirs: atmosphere, surface oceans, biota, soils
b. transfers: photosynthesis, respiration, fossil fuel burning
c. Biological processes dominate

2. Slow Cycle millenia

a. reservoirs: deep oceans, sediments, fossil fuels
b. transfers: sediment burial, volcanoes
c. Geological processes dominate

The Carbon Cycle/4 main types of

processes:
1) dissolution and precipitation
2) physical-chemical exchange of carbon
between environmental compartments
3) assimilation and dissimilation
[photosynthesis, respiration, trophic
transfer]
4) conversions between methane and CO 2

and bacteria

The Nitrogen Cycle

Nitrogen has numerous oxidation states and is involved
in complex chemical pathways, some manners of microbial
energy production, and the cycling of other elements.
How to figure oxidation states of a key atom?
Each O = -2, Each H = +1, Each Cl = -1
Set up equation with overall charge on one side,
individual atoms on other.

Key nitrogen conversions

Nitrogen fixation - Conversion of dinitrogen gas to ammonium.

Nitrification - Conversion of ammonium to nitrate - aerobic bacteria; different
species responsible for 2 specific steps in the process.
Dissimilatory nitrate reduction Anaerobic conversion of nitrate to nitrite;
bacteria. Nitrate used as electron acceptor to drive energy production. First
step in denitrification.
Denitrification - Multistep reduction of nitrate to gaseous dinitrogen.
Performed by nitrate reductase enzyme system - different bacteria may
perform different steps. Numerous intermediates. Nitrate used as electron
acceptor to drive energy production.
Nitrogen incorporation - Uptake of nitrate or ammonium and incorporation
into protein and other cellular constituents. Plants, animals and
microorganisms - different organisms prefer nitrate or ammonium. Use of
nitrate is called assimilatory nitrate reduction.
Mineralization / Ammonification - Release of ammonium from organic
nitrogen or nitrate - performed by fungi, bacteria.

Ammonification the conversion of organic nitrogen (proteins,

amino sugars, nucleic acids, chitin) to ammonium (NH4+)
heterotrophic bacteria and fungi decomposers
generic equation:

Nitrification the oxidation of ammonia (NH3) to

nitrite (NO2-) and nitrate (NO3-)

Two steps, two organisms (autotrophic)

NH3 oxidizers = Nitroso- (Nitrosomonas, Nitrosolobus,
Nitrosospira)
NO2- oxidizers = Nitro (Nitrobacter, Nitrospira, Nitrospina
Nitrococcus)
Phylogenetically, fairly narrow group of bacteria

Denitrification the reduction of nitrate to dinitrogen gas

and nitrous oxide

Anaerobic process NO3- is used as terminal electron

acceptor
Many denitrifiers are facultative anaerobes aerobes that
are capable of anaerobic metabolism when O2 is
unavailable

Nitrification, Ecosystem Significance:

converts relatively immobile form (NH3/NH4+) to very mobile
form (NO3-); provides substrate for denitrification

Global/Regional Significance: Nitrification is leaky,

producing both N2O (a major greenhouse gas 190 times
more potent than CO2) and NO (contributes to acid rain)

Dentirification Ecosystem significance

converts available NO3- to inert gases unavailable for
plant uptake. Can form basis for NO3- bioremediation
Global significance: major source of N2O (potent
greenhouse gas)

Environmental aspects of
nitrogen cycle
Nitrogen fertilizer application, livestock farm
drainage, and human sewage system leakage
contribute to nitrate contamination of surface
and waters (blue baby syndrome).
NOx gas formation contributes to greenhouse
effect.
Denitrification / ammonium volatilization can
deplete agricultural fields of natural nitrogen
stores.

Plant: microbe symbiosis

N2 fixation

The Sulfur Cycle

S is the 10th most abundant element in the
Earths crust.
S makes up about 1% of microbial biomass dry
weight.
S is required for amino acid synthesis, vitamins,
hormones, coenzymes, connective tissues, plant
lipids,
S is not usually a limiting nutrient.
S is intensively cycled through the biosphere.
Some important similarities to N cycle.

Why is S so intensely cycled:

Sulfur has a wide range of oxidation states:
S2- inorganic sulfides, organic mercaptans
S0
elemental sulfur
S2O32thiosulfate
SO42-

sulfate

Various forms of S have oxidation states that vary by a total of 8

electrons.

(P is not vigorously cycled; it does not have many different

biologically relevant oxidation states).

Phosphorous cycling

Biologically important nutrient

Cycle is largely geochemically driven
Few oxidation states
Most P in the form of organic or inorganic
phosphate

Major contributor to global N2

fixation

Enzyme = nitrogenase
Only bacteria produce nitrogenase
Nitrogenase is extremely oxygen sensitive
Major N2 fixers (symbiotic and free-living)
are aerobic (Cyanobacteria, Rhizobium,
Bradyrhizobium)

Symbiotic interactions between

plants and microorganisms
Consistent theme of root exudate
importance
Continuum between mutualism and
parasitism
Extensive coevolutionary history
Critical importance for nutrient cycling, soil
fertility and human economy

Mycorrhizae (red) on root hairs

(yellow and green)
Mycorrhizae are fungi
growing in symbiotic
relationships with plant
roots
They help plants take
up phosphorous, while
they gain nutrients
through rot secretions
~85% of vascular
plants have
mycorrhizae

Rhizobiumsymbiotic bacteria
Rhizobium lives free in soil but only fixes N2 when inside the
root nodules of its host plant, in a strictly controlled
microaerophilic environment.
Oxygen is required to generate sufficient respiratory energy to
drive N2 fixation. But too much oxygen inactivates nitrogenase.
In root nodules the O2 level is regulated by a special hemoglobin
- leghemoglobin. The globin protein is encoded by plant genes
but the heme cofactor is made by the symbiotic bacteria. This is
produced only when the plant is infected with Rhizobium. Root
cells convert sugar to organic acids which they supply to the
bacteroids. In exchange, the plant receives amino-acids (rather
than free ammonia).

Rhizobium continued
Legume plants secrete specific flavonoids, which are detected by
interaction with bacterial NodD proteins. When NodD binds a
flavonoid it activates other nodulation genes. Some of the nod
genes code for enzymes that make Nod factors, which are
recognized by the plant. There are many different flavonoids and
Nod factors and lots of variety in the host specificity between
plants and Rhizobia.
the bacteria to move to the root. The bacteria enter the outer root
tissue and produce cytokinins (plant hormones) which cause
division of plant cells to form nodules. The bacteria lose their
outer membranes and become irregular in shape - "bacteroids".

Root nodule of plants by

bacterial Rhizoium species

Microorganisms and ruminants

Another mutualistic relationship exists between
microorganisms and the various herbivores
called ruminants
bacteria live in their rumen which proceeds their
true stomach facilitating breakdown of cellulose
(the most abundant C-sources of food that most
animals can not digest)
Each mL of rumen contains 1010 bacteria flora
The plethora of gas produced is released when
the animal belches

Current trends in microbial ecology:

space exploration microbes in extreme environments

(hot springs, thermal vents, lithosphere)
Climatic change interactions with microbial
communities
molecular techniques diversity of microorganisms
new methods to assess presence/abundance
of individual species in situ
We can now culture <1% of all environmental
prokaryotes
Does microbial diversity matter?
What roles do any specific cells play in a community?