Microbial Ecology 2012 Pp t

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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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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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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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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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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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Microbial Ecologyd 34S(0/00)=(34S/32S sample- 34S/32S standard)/ 34S/32S standard X 1000


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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



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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

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Microbial Ecology 2012 Pp t