1.

1
Foundations in Microbial Diversity and Ecology 27.4 Microbial Ecology and Its Methods: An Overview
a. Only about 1 % of the microorganisms that can be observed in complex a. Many approaches can be used to study microorganisms in the environment.
natural assemblages under a microscope have been grown at the present These include analyses of nutrient cycling. biomass. population size and
time. Molecular techniques are making it y»ssible to obtain information on activity. and community structure.
uncultured microorganisms. b. Methods presently being used make it possible to study presence. types. and
b. Microbial ecology is the study of microorganisms' interactiotb with their activities of microorganisms in their natural environments (including soils,
living and nonliving environments. waters. plants. and animals). Although the vast majority of microor• ganisms
that can be observed cannot yet be grown in the laboratory. mo• lecular
techniques make it possible to obtain information about these noncultured
27.2 Biogeochemical Cycling microorganisms.
a. Microorganisms—functioning with plants. animals. and the environment— c. The construction of DNA libraries from microbial communities from which
play important roles in nutrient cycling. which is also termed SSU rRNA genes or other genes of interest can be amplified by PCR and
biogeochemical cycling. Assimilatory processes involve incorporation of sequenced has re.•ealed that microbial populations and communities are
nutrients into the organism •s biomass during metabolism: dissimilatory more diverse and complex than traditionally thought (fig•re 27.17).
processes. in comparison. involve the release of nutrients to the
environment after metabolism. Optical tweezers and micromanipulators can be used to recover individual
cells or cell organelles from complex microbial communities. This makes it
b. Biogeochemical cycling involves oxidation and reduction and changes in possible to obtain genomic and phylogenetic information from specific
the concentrations of cycle components such carbon. nitrogen, phosphorus. individual microbial cells for use in studies of microbial (figure 27.19).
ami sulfur can result from microbial activity 27.2. 27.4-27.9).
Major Organic contB»unds used by microorganisms differ in Structure.
linkage. elemental composition. and susceptibility to degradation under
oxic and anoxic conditions. Lignin is degraded only under oxic conditions.
a fact that has important implications in terms of carbon retention in the
biosphere.
In terms ofeffects on humans. metals can considered in three broad groulB:
(1) the noble metals. which have antimicrobial properties tnJt which do
ru»t have negative effects on humans: (2) metals such mercury and lead.
from which toxic organometallic comm»unds can be formed: and (3)
certain other metals, which are antimicrobial in ionic form. such as copper
and zinc. The second of these groups is of particular concern (tabk 27.3).

27.3 The Physical Environment

a. A microorganism functions in a physical location that can be described its
microenvironment. The resources available in a and their
time of use by a microorganism describe the niche. pores are important
microenvironments that can protect bacteria from predation_
b. Biofilms. or organized layers of microorganisms. are widespread and are
formed on a wide variety of living and nonliving surfaces. Ihese are
important in occurrence and the survival ofpathogens. Biofilms can develop
to form complex layered communities called microbial mats 27.11).
c. Microorganisms serve as primary producers that accumulate organic matter.
sources include hydrogen, sulfide, and methane. In addition, many
chemoheterotrophs decompose the organic matter that primary producers
accumulate and carry out mineralization, the release of inorganic nutrients
from organic matter. The multiple and overlapping roles played by
microorganisms in nutrient cycling is called the microbial loop (figure
27.13).
d. Decreased species diversity usually occurs in extreme environments. and
many microorganisms that can function in such habitats. called
extremophiles. have specialized growth requirements. For them. extreme
environmental conditions can be required.
 2.1
Marine and Freshwater Environments
Most water on the Earth is marine (97%). The majority of this is cold (2 to
50C) and at high pressure. Fresh water is a minor but important part of
Earth's biosphere.
b. Oxygen solubility and diffusion rates in surface waters are limited: waters are
low oxygen diffusion rate environments, in comparison with soils. Carbon
dioxide, nitrogen, hydrogen. and methane are also important gases for
microbial activity in waters.
The carbonate equilibrium system keeps the oceans buffered at pH 7.6 to 8.3
(figure 282).
28.4 Microorganisms in Freshwater Environments
d. The penetration oflight into the surface water determines the depth ofthe
photic zone. Warming the surface waters can lead to the development of a
thermocline. The nutrient comp(vsition of the ocean influences the C:N:P ratio
of the phyto• plankton, which is called the Redfield ratio. This ratio is important
for predicting nutrient cycling in oceans. Atmospheric additions of minerals,
including iron and nitrogen, affect this ratio and global-level oceanic processes.
The microbial loop describes the transfer Of nutrients between trophic levels
while taking into account the multiple contributions of microbes to
recycling nutrients. Nutrients are recycled so efficiently. the majority
remain in the photic zone (figure 283).
major role in controlling cyanobacterial dev'elopment and nutrient
turnover (tig•rß m4 and 2815).
g. Sediments deep beneath the ocean's surface are home to about one-half of
the world •s procaryotic biomass.
h. Methane hydrates, the result Of psychrophilic archaeal methanogenesis
under extreme atmospheric pressure. may contain more natural gas than is
currently found in known reserves.
Deep sediment drilling reveals that microbes within this habitat may employ
unique energetic strategies (We 2816).
a. Glaciers and permanently frozfn lakes are sites ofactive microbial
communi• ties. 'Ille East Antarctic Ice Sheet and Lake Vostok, which lies
beneath it, are productive study sites (fig•re 2817).
b. Nutrient sources for streams and rivers may be autochthonous or
allochthonous. Often allochthonous inputs include urban. industrial. and
agricultural runoff (figure 2818).
Lakes can be oligotrophic or eutrophic. Eutrophication can cause
increased growth of chemoorganotrophic microbes and the system may
become anoxic (fWre 2820).

28.2 Microbial Adaptations to Marine and Freshwater Environments

a. The marine microbial community is dominated. in terms of numbers and
biomass, by ultramicrobacteria.
b. Many unusual microbial groups are found in waters, especially when
oxidants and reductants can be linked. These include Thioploca and
Thiomatgarita, both of which are found in coastal areas where nutrient
mixing occurs. Thiomargarita is the world's largest known bacterium (figure
28.4).
Aquatic fungi are important members of the aquatic microbial community.
These include the chytrids, with a motile zoosporic stage, and the Ingoldian
fungi, which often have tetraradiate structures. Both of these are uniquely
adapted to an aquatic existence, and the chytrids may contribute to disease
in amphibians (figure, 286 and 287).

28.3 Microorganisms in Marine Environments

a. Tidal mixing in estuaries, as characterized by a salt wedge, is osmotically
stressful to microbes in this habitat. Thus they have evolved mechanisms
to cope with rapid changes in salinity (fig.re 288).
b. Coastal regions like estuaries and salt marshes can the sites of harmful
algal blooms such as those caused by the diatom Pseudonitzchia and the
dinoflagellates Alexanderium and Ptiesteria 289).
c. Autotrophic microbes in the photic zone within the open ocean account
for about one-half of all the carbon fixation on Earth.
d. The carbon and nitrogen budgets of the open-ocean zone are intensely
studied because of their implications for controlling global warming
(figure 2812).
Two members of the a•proteobacteria—SARl I and Silicobacterpomemyi
— demonstrate unique adaptatioms to life in the oligotrophic open
ocean. SARI I is the most numerous organism on Earth.
Archaea are important components of the microbial community. Viruses
are present at high concentratioms in many waters. and (Xcur at ID-fold
higher leveLs than the bacteria. In marine systems they may play a
 3.1
Soils as an Environment for Microorganisms
a. Terrestrial environments are dominated by the solid phase. consisting of
organic and inorganic components.
b. In an ideal soil. microorganisms function in thin water films that have close
contact with air. Miniaquatic environments can form within soils (figure
29.1).
29.2 Soils, Plants, and Nutrients
a. Soil organic matter (SOM) helps retain nutrients and water and maintain
soil structure. It can be divided into humic and nonhumic material AZ).
b. Microbial degradation ofSOM occurs in three phases. starting with the
degradatinn and cmrsumpiion of soluble compounds. followed by the
extracellular attack of more resistant material such a cellulose, and finally
the slow degradation of structurally complex molecules such as lignin,
29.3 Microorganisms in the Soil Environment
a. Most microorganisms in these environments are associated with surfaces,
and these surfaces influence microbial use oi nutrients and interactiore; with
plants and other living organisms (figure 302),
b. Bacteria and fungi in soils have different functional strategies. Fungi tend to
develop on the surfaces of aggregates, whereas microcolonies of bacteria
are commonly associated with smaller pores,
Insects, earthworms, and Other soil animals are also important parts Of the
soil. These decomposer•reducers interact With the microorganisms to
influence trient cycling and Other processes.
2944 Microorganisms and the Formation Of Different Soils
a. Soils form under many conditiotß. In all cases organic matter accumulation
occuß through the direct activities of primary producers or by the import of
plvrormed organic materials. Soils can be formed in regions such as the
anta«iic where there are no vascular plants (figure 29.5).
29.5 Microorganism Associations with Vascular Plants
a. Plants develop associations with many twsof microorganisms. These
include important associations involving mycorrhizae, rhizobia. and
actinorhiz.ae,
b. Mycorrhizal relationships (plant-fungal associations) are varied and
complex. Six basic types can be observed including endomycorrhizal and
sheathed/ ectomycorrhizal types. Specialized monotropoid fungi make it
possible for
30.1 Microbial Interactions
a. Symbiotic interactions include mutualism (mutually beneficial and
obligatory), cooperation (mutually beneficial, not obligatory). and
commensalism (product of one organism can be used beneficially by
another organism). Predation involves one organism (the predator)
ingesting/killing a larger or smaller prey, parasitism (a longer-term internal
maintenance of another organism or acellular infectious agent). and
amensalism (a microbial product can inhibit another organism).
Competition involves organisms competing for space or a limiting
nutrient. This can lead to dominance Of one organism. or coexistence of
both at lower populations (figure 3(11).
achlorophyllous plants to survive using carbon fixed by green plants.
The hyphal network of the mycobiont can lead to the formation of a
mycorrhimsphere (figure 29.8: table 29.6).
c. The mycorrhizal relationship often is eståblished with the assistance of
mycorrhization helper bacteria. In addition. bacteria may occur inside of
the mycorrhizal fungus. These bacteria apparently contribute to the
nitrogen cycling of the plant-fungus complex.
d. The Rhizobium•legume symbiosis is one of the best•studied examples of
plant-microorganism interactions. This interaction is mediated by
complex chemicals that serve as communication signals (figum 29.13).
The actinomycete Frankia forms nitrogen-fixing symbioses with some
trees and shrubs.
f, Agmbacterium establishes a complex communication system with its plant
host into which it transfers a fragment of DNA. Genes on this DNA
encode proteins that result in the formation of plant tumors or galls
(fig.res 29.18 and 2019).
g, More complex microbe.plant interactions include tripartite and tetrapartite as.
socialions which often involve the plant, mycorrhizal fungi and bacteria.
29.6 Soil Microorganisms and the Atmosphere
a. Microorganisrns can play major roles In the dynamics of greenhouse
gases such as carbon dioxide, nitrous oxide, nitric oxide, and methane.
Microorganisms can to both the production and consumption of these
gases (figure 2020).
b. Fungi. especially can produce clietnicalsthat are normally considered as
ane thropogenic pollutants. These include chloromethane and !yanide.
29.7 The Subsurface Biosphere
a. The subsurface includes at least three zones; the shallow subsurface; the
zone Where gas. oil. and coal have accumulated: and the deep
subsurface, where methane synthesis occurs (fig•res 21.22..29.23 and
NE').
29.8 Soil Microorganisms and Human Health
a. Microorganisms. particularly the fungi. can develop in moist areas in
houses and cause major health problems for humans, including asthma. An
important fungus involved in these problems is Stachybotrys 29.25).
b. A consortium is a physical association of organisms that have a mutually
beneficial relationship based on positive interactions.
c. Mutual advantage is central to many organisnH)rganism interactions.
These interactions can be based on material transfers related to energetics.
 4.1
cell-tocell communication. or physical protection. With several important
mutualistic interactions. chemolithotrophic microorganisms play a critical
role in making organic matter available for use by an associated organism
(e.g.. endosymbionts in Rifiia).
d. The rumen is an excellent example of a mutualistic interaction between an
animal and a complex microbial community. In this microbial community.
corn-
 plex plant materials are broken down to simple organic compounds that
can be absorbed by the ruminant, as well as forming waste gases such as
methane that are released to the environment (figure 306).
Syntrophism simply means growth together. It does not require physical
contact and involves a mutually positive transfer of materials, such as
interspecies hydrogen transfer.
Cooperative interactions are beneficial for both organisms but are not
obligatory. Important examples are marine animals, including Alvinella.
Rimicat•us and Eubostrichus, that involve interactions with hydrogen
sulfide-oxidizing chemotrophs (fißrre O7).
g. Predation and parasitism are clcxsely related. Predation has many beneficial
effects on populations of predators and prey. These include the microbial
loop (returning minerals immobilized in organic matter to mineral forms
for reuse by chemotrophic and photcxsynthetic primary producers).
protection of prey from heat and damaging chemicals, and possibly aiding
pathogenicity, as with Legionella (figure 30.13).

30.2 Human-Microbe Interactions

a. Animals and environments that are germfree or have one or more known
microorganisms are termed gnotobiotic. Gnotobiotic animals and
techniques provide good experimental systems with which to investigate
the interactions of animals and specific species or microorganisms (figure
3016).
b. Various microbes have adapted to specific niches found on the human
host. These niches are uniquely able to support microbe growth by
maintaining a relatively constant environment.
30.3 Normal Microbiota Of the Human Body
Commensal microorganisms living on or in the skin can be characterized as
either transients or residents (figure 017).
b. The normal microbiota of the oral cavity is composed of those
microorganisnus able to resist mechanical removal.
The stomach contains very few microorganisms due to its acidic pH.
d. The distal portion Of the small intestine and the entire large intestine have
the largest microbial community in the body. Over 400 species have been
identifled. the vast majority of them anaerobic.
The upper genitourinary tract is usually free of microorganisms. In contrast.
the adult female genital tract has a complex microbiota.
In some instances. after a microorganism contacts or enters a host. a positive
mutually beneficial relationship occurs and becomes integral to the health
of the host. In other instances, the microorganism may produce disease or
even death of the host.
g. Many ofthe normal host microbiota compete with pathogenic
microorganisms. An opportunistic microorganism is generally harmless in
its normal environment but may become pathogenic when moved to a different
body location or in a compromised host.