microbial ecology 2012 pp t
TRANSCRIPT
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Microbial Ecology
Microbial Ecology:
Microorganisms in soil, water, and other
environments and how microorganisms act to
chemically change their environments.
Microbial ecologists study:
the biodiversity of microorganisms in nature
and how different guilds interact in microbialcommunities;
The activities of microorganisms in nature
and monitor their effects on ecosystems.
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Microbial Ecology Microorganisms in Nature
Methods in Microbial Ecology
Enrichment and Isolation Methods
Identification and Quantification:
Nucleic acid Probes, Fluorescent Antibodies, and
Viable Counts Measurements of Microbial Activity in Nature
Stable Isotopes and Their Use in Microbial Biogeochemistry
Aquatic Habitats
Terrestrial Environments Deep Sea Microbiology
Hydrothermal Vents
Carbon Cycle
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Microorganisms in Nature
A microbial communitystructure in a lake
ecosystem
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The microorganisms and the microenvironment
Contour
map of
O2
concentrationin a soil particle
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The microorganisms and the
microenvironment
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Surface and Biofilms
On surfaces microbial numbers and activityare usually much greater than in free water
because of adsorption effects.
Bacteria grown on a glass slide immersed in a small river
Fluorescence photomicrograph of a natural microbial
community colonizing plant roots in soil.
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Biofilm Biofilms are encased microcolonies of bacterial cells
attached to a surface by way of adhesivepolysaccharides excreted by the cells;
Functions: trap nutrients for growth of the enclosed
microbial population and help prevent detachment of
cells on surfaces in flowing systems; Significance:
in the human body, bacterial cells within a biofilm are made
unavailable for attack by the immune system;
dental plaque, a typical biofilm, contains acid-producingbacteria responsible for dental caries;
In industry, biofilms can slow the flow of water or oil through
pipelines, accelerate the corrosion of the pipes themselves.
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Other factors affecting
microbial ecology
Nutrient levels and growth rates
microbial competition and cooperation
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Methods in Microbial Ecology
Study biodiversity: isolation, identification
and quantification of microorganisms in
various habitats.
Study microbial activity:
Radioisotopes
Microelectrodes
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Enrichment and Isolation Methods
Enrichment culture technique: a medium and a
set of incubation conditions are used that are
selective for the desired organism and are
counterselective for the undesired organisms.
The Winogradsky column: for isolation of
purple and green phototrophic bacteria and
other anaerobes.
From enrichments to pure cultures: Steak plate
and agar shake tube method.
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The Winogradsky column
The column is filled with organic-rich, preferably sulfide-containing, mud. Hay,
shredded newsprint, sawdust, shredded leaves or roots, ground meats, hard boildedeggs, and even dead animals are added. CaCO3 and CaSO4 as buffer are added too.
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Agar shake tube method:
Isolation of anaerobic bactetia in pure culture
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Identification and Quantification:
Nucleic Acid Probes, Fluorescent Antibodies,
and Viable Counts
Microautoradiographs of single cells ofBacil lus megater iumhybridized with 16S
rRNA of bacteria (left) and to the 18S
rRNA of Eukatya (right)
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Identification and Quantification:
Nucleic Acid Probes, Fluorescent Antibodies,
and Viable Counts
Fluorescently labeled rRNA probes. Left, phase contrast
photomicrograph ofB. Megaterium and the yeast Saccharomyces
cerevisiae (no probe). Center, same field, cells stained with universal
rRNA probe. Right, same field, cells stained with eukaryal probe.
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Identification and Quantification:
Nucleic Acid Probes, Fluorescent Antibodies,
and Viable Counts
Differentiation of closely related gram-negative bacteria. Left, phase micrograph of mixture ofProteus vulgaris and a related bacterium
isolated from wasps;
Center, same field stained with the bacterial probe;
Right, same field stained with a probe specific for the bacterium from wasps.
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Identification and Quantification:
Nucleic Acid Probes, Fluorescent
Antibodies, and Viable Counts
Fluorescent antibody
staining is a method for
identifying a single
species in soil samples. Fluorescent antibodies
are therefore most
useful for tracking a
single microbial speciesin soil or other habitats.
Fluorescent dyes such as
acridine orange can
stain DNA and RNA.
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Phylogenetic nucleic acid probes for
analysis of microbial community
In almost all cases
phylogenetic analyses of
microbial communities
have shown them to
contain phylogeneticallydistinct organisms that
had not been previously
cultured.
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Measurements of
Microbial Activity in
Nature
Use of radioisotopes to
measure microbial activity in
nature
(a) Photosynthesis measured in
natural seawater with 14CO2
(b) Sulfate reduction in mud
measured with 35SO42-
Methanogenesis measured in
mud with acetate labeled in
either the methyl (14CH3COO-)
or the carboxyl (CH314COO-)
carbon.
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Measurements of Microbial Activity in Nature
using Microelectrodes
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Measurements of Microbial Activity in
Nature using Microelectrodes
Microbial mats and the use of microelectrodes
to study them.
Upper layers contain cyanobacteria, beneath
which are several layers of anoxygenic phototrophicbacteria
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Stable Isotopes and Their Use in Microbial
Biogeochemistry Stable isotopes: 13C and 34S
In nature, 13C:12C=1:19, enzymes prefer 12C, resulting in being
enriched in 12C and depleted in 13C in fixed carbon , the degree of13C depletion is calculated as an isotopic fractionation.
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Use of Isotopic Fractionation in
Microbial Ecology
d 13C(0/00)=(13C/12C sample- 13C/12C standard)/ 13C/12C standard X 1000
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Use of Isotopic Fractionation in
Microbial Ecologyd 34S(0/00)=(34S/32S sample- 34S/32S standard)/ 34S/32S standard X 1000
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Use of Isotopic Fractionation in
Microbial Ecology
Carbon isotopic analyses have been used to
distinguish biogenic from abiogenic organic
matter
Sulfur isotopes have been used to distinguishbetween biogenic and abiogenic ores (Iron
sulfides) and elemental sulfur deposits
Oxygen isotopic analyses (18O/16O) have been
used to trace the earths transition from an
anoxic to an oxic environment (the earths
molecular oxygen originated from oxygenic
photosynthesis by cyanobacteria).
A ti H bit t
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Aquatic Habitats
Phytoplankton (): Algae floating orsuspended freely in the water
Benthic algae (): Algae attached to the
bottom or sides
Primary producers: Phototrophic organisms
utilize energy from light in the initial production
of organic matter.
Open oceans are very low in primary productivity;
Inshore ocean areas are high, with lakes and
springs being highest of all in primary productivity
i bi
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Aquatic Habitats
Distribution of
chlorophyll in thewestern North
Atlantic Ocean as
recorded by satellite.
The Great LakesRed: rich in phytoplankton
Chesapeake Bay in FloridaRed: rich in phytoplankton
Offshore has blue and purple
color, has lower chlorophyll
concentration
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Aquatic Habitats
Oxygen Relationships in Lakes and Rivers
n a temperate
climate lake
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Aquatic Habitats
Oxygen Relationships in Lakes and Rivers
Effect of input of sewage or other organic-rich waste waters into a river
Oxygen depletion in a body of water is undesirable
as aquatic animals require O2, furthermore,
conversion to anoxia results in the production by
anaerobic bacteria of odoriferous compounds
A ti H bit t
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Aquatic Habitats
Biochemical Oxygen Demand
Biochemical Oxygen Demand (BOD): determined by taking a sample of water,
aerating it well, placing it in a sealed bottle,
incubating for a standard period of time
(usually 5 days at 20oC), and determining the
residual oxygen in the water at the end of
incubation.
Sanitary engineers term oxygen-consumingproperty of a body of water its BOD.
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Terrestrial Environments
A soil aggregate composed of
mineral and organic components
Profile of a mature soil
Mineral Soils: the weathering of rock,
Organic Soils: Sedimentation in bogs
and marshes
Soils are microbial habitats, water
availability limits microbial activity
i i i f i i
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Visualization of microorganisms on the
surface of soil particles by use of SEM
Left: Rod-shape bacteria Center: Actinomycete spores
Right: Fungus hyphae
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Deep Sea Microbiology
Deep sea microorganisms must stand:
Low temperature (100m, 2-3oC);
High pressure (1 atm every 10 m); Low nutrient levels
Water at depths greater than 1000 m is
relatively biologically inactive and hascome to be known as the deep sea.
D S Mi bi l
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Deep Sea Microbiology:
barotolerant and barophilic bacteria
Deep Sea Microbiology
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Deep Sea Microbiology
Physiology of barophiles
Relatively few proteins are controlled bypressure in barophiles as many proteins seem
to be the same in cells grown at both high and
low pressure.
Cell wall and related structural proteins and
transport proteins seem to be the major
variable components.
Pressure acts selectively to turn on or off thetranscription of specific genes coding for
proteins needed for growth at high pressure.
Hydrothermal Vents
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Hydrothermal Vents
A i l li i h l
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Animals living at thermal vents
Invertebrates from habitats neardeep-sea thermal vents are
dependent on the activities of
chemolithotrophic bacteria which
grown at the expense of inorganic
energy sources emitted from the
vents, such as H2S, Mn2+, CO,
CO32- and HCO3-.Tube Worms
Mussel
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Microorganisms in hydrothermal vents
Nutrition of animals living near
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Nutrition of animals living near
hydrothermal vents
Chemolithotrophic sulfur-oxidizing bacteria associated with the
trophosome tissue of tube worms from hydrothermal vents, the
bacteria supply the worm with its nourishments, the animal living
off the excretory products and dead cells of its symbiont bacteria.
Black
Bl k S k
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Black
SmokersBlack Smokers:
suggested the upper limit for microbial cells
is under 150oC
Carbon C cle
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Carbon Cycle
The most rapid means of global transfer of
carbon is via CO2 of the atmosphere.
CO2 is removed from the atmosphere
primarily by photosynthesis of land plants
and is returned to the atmosphere byrespiration of animals and
chemoorganotrophic microorganisms.
The single most important contribution ofCO2 to the atmosphere is via microbial
decomposition of dead organic material,
including humus.
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Importance of photosynthesis in
the carbon cycle
Oxygenic photosynthesis:
CO2 + H2O (CH2O) + O2
Respiration:
(CH2O) + O2 CO2 + H2O
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The Carbon Cycle
Decomposition
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Decomposition