Transcript Vectors for Even Larger Genomic DNA Inserts

General Microbiology (Micr300)
Lecture 12
Environmental Microbiology
(Text Chapters: 19.1-19.8; 19.16-19.20; 19.22)
Populations, Guilds and
Communities
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In nature, individual microbial cells grow to
form populations.
Metabolically related populations are called
guilds
Set of guilds interact in microbial communities
Microbial communities in turn interact with
communities of macroorganisms and the
environment to define the entire ecosystem
Biogeochemical Cycles
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Microorganisms play major roles in
energy transformations and
biogeochemical processes that result in
the recycling of elements essential to
living systems. The study of these
chemical transformations is called
biogeochemistry.
Environments and
Microenvironments
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Microorganisms are very small, and their
habitats are likewise small. The
microenvironment is the place where
the microorganism actually lives.
For example, the outer zones of a small
soil particle may be fully oxic, meaning
that O2 is present, whereas the center,
only a very short distance away, can
remain completely anoxic (O2-free)
Competition and Cooperation
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Microorganisms in nature often live a
feast-or-famine existence such that only
the best-adapted species thrive in a given
niche. Cooperation among microorganisms is also important in many
microbial interrelationships.
Microbial Growth on Surfaces and
Biofilms
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Biofilms are bacterial assemblages,
encased in slime, that form on surfaces.
Biofilms can lead to the destruction of
inert and living surfaces as a result of the
products excreted by the bacterial cells.
Biofilm formation is a complex process
involving cell-to-cell communication
(Figure 19.5).
Microbial Habitats
Terrestrial Environments
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The soil is a complex habitat with
numerous microenvironments and niches
(Figure 19.6).
Microorganisms are present in the soil
primarily attached to soil particles. The
most important factor influencing
microbial activity in surface soil is the
availability of water, whereas in deep soil
(the subsurface environment), nutrient
availability plays a major role.
Diagram of a Soil Aggregate
Freshwater Environments
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In aquatic ecosystems, the main primary
producers are usually phototrophic
microorganisms.
Bacteria consume most of the organic
matter produced, which can lead to
depletion of oxygen in the environment.
The biochemical oxygen demand
(BOD) is a measure of the oxygenconsuming properties of a water sample.
Freshwater Environments
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In many lakes in temperate climates, the water
mass becomes stratified during the summer,
with the warmer and less dense surface layers
separated from the colder and denser bottom
layers (Figure 19.9).
Even though a river may be well mixed because
of rapid water flow and turbulence, large
amounts of added organic matter can lead to a
marked oxygen deficit from bacterial respiration
(Figure 19.10).
Marine Habitats
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Marine waters have less nutrients than many
freshwaters, yet substantial numbers of
microorganisms exist there. Many of these use
light to drive ATP synthesis.
The form of rhodopsin (called
proteorhodopsin) found in open ocean
prokaryotes is very similar to bacteriorhodopsin
but is present in cells that are phylogenetically
Bacteria, not Archaea.
Marine Habitats
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In terms of
prokaryotes,
species of the
domain Bacteria
tend to
predominate in
oceanic surface
waters, whereas
Archaea are more
prevalent in deeper
waters
Deep-Sea Microbiology
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The deep sea is a cold, dark habitat
where high hydrostatic pressure and low
nutrient availability prevail.
Barophiles grow best under pressure;
barotolerants can grow under elevated
pressures but grow best at atmospheric
pressures; and extreme barophiles,
obtained from the greatest depths,
require high pressure for growth (Figure
19.14).
Hydrothermal Vents
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Hydrothermal vents are deep-sea hot
springs where volcanic activity generates
fluids containing large amounts of
inorganic energy sources that can be
used by chemolithotrophic bacteria
(Figure 19.16).
These bacteria fix CO2 into organic
carbon, some of which is then used by
the deep-sea animals.
Hydrothermal Vents
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There are two major types of vents, hot
vents, or black smokers, and warm
vents.
Deep-sea hydrothermal vents are habitats
where the primary producers are
chemolithotrophic rather than
phototrophic
http://www.pmel.noaa.gov/vents/marianas/multimedia04.html#videos
Biotransformation
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A major toxic form of mercury is
methylmercury. This form of mercury can
yield Hg2+, which bacteria reduce to Hg0.
The ability of bacteria to resist the toxicity
of heavy metals often results from the
presence of specific plasmids that encode
enzymes capable of detoxifying or
pumping out the metals (Figure 19.41).
Petroleum Biodegradation
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Hydrocarbons are subject to microbial attack.
Hydrocarbon-oxidizing microorganisms are used
for bioremediation of spilled oil, and their
activities are assisted by addition of inorganic
nutrients to balance the influx of carbon from
the oil.
A wide variety of bacteria, several molds and
yeasts, and certain cyanobacteria and green
algae can oxidize petroleum products
aerobically.
Biodegradation of Xenobiotics
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Many chemically synthesized
compounds—such as insecticides,
herbicides, and plastics (collectively called
xenobiotics)—are completely foreign to
microorganisms.
Nonetheless, xenobiotics can often be
degraded by one or another prokaryote.
Both aerobic and anaerobic mechanisms
are known.
Biodegradation of Xenobiotics
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Although the aerobic breakdown of chlorinated
xenobiotics is undoubtedly of ecological
importance, reductive dechlorination is of
particular environmental interest because of
how rapidly anoxic conditions can develop in
polluted microbial habitats in nature.
Some compounds may be degraded either
partially or totally provided that some other
organic material is present as the primary
energy source. This phenomenon is called
cometabolism.
Microbial Interactions with Plants
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Key microbial habitats on plants include the
rhizoplane/rhizosphere and the phyllosphere.
Lichens are symbiotic associations between a
fungus and an alga or cyanobacterium.
Mycorrhizae are formed from fungi that
associate with plant roots and improve their
ability to absorb nutrients. Mycorrhizae have a
great beneficial effect on plant health and
competitiveness.
Root Nodule Bacteria and
Symbiosis with Legumes
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One of the most widespread and important
plant-microbial symbioses is that between
legumes and certain nitrogen-fixing bacteria.
The plant provides the energy source needed
by the root nodule bacteria, and the bacteria
provide fixed nitrogen for the growth of the
plant.
The bacteria induce the formation of root
nodules within which the nitrogen-fixing
process occurs. In the nodule, precise levels are
controlled by the O2-binding protein
leghemoglobin.
Stages in the
infection and
development
of root nodules