Chapter 17
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 microbial
communities;
? The activities of microorganisms in nature
and monitor their effects on ecosystems.
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
Microorganisms in Nature
A microbial community
structure in a lake
ecosystem
The microorganisms and the microenvironment
Contour
map of
O2
concentration
in a soil particle
The microorganisms and the
microenvironment
Surface and Biofilms
? On surfaces microbial numbers and activity
are 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.
Biofilm
? Biofilms are encased microcolonies of bacterial cells
attached to a surface by way of adhesive
polysaccharides 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-producing
bacteria responsible for dental caries;
? In industry,biofilms can slow the flow of water or oil through
pipelines,accelerate the corrosion of the pipes themselves,
Other factors affecting
microbial ecology
? Nutrient levels and growth rates
? microbial competition and cooperation
Methods in Microbial Ecology
? Study biodiversity,isolation,identification
and quantification of microorganisms in
various habitats.
? Study microbial activity,
? Radioisotopes
? Microelectrodes
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.
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 boilded
eggs,and even dead animals are added,CaCO3 and CaSO4 as buffer are added too.
Agar shake tube method:
Isolation of anaerobic bactetia in pure culture
Identification and Quantification:
Nucleic Acid Probes,Fluorescent Antibodies,
and Viable Counts
? Microautoradiographs of single cells of
Bacillus megaterium hybridized with 16S
rRNA of bacteria (left) and to the 18S
rRNA of Eukatya (right)
Identification and Quantification:
Nucleic Acid Probes,Fluorescent Antibodies,
and Viable Counts
? Fluorescently labeled rRNA probes,Left,phase contrast
photomicrograph of B,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.
Identification and Quantification:
Nucleic Acid Probes,Fluorescent Antibodies,
and Viable Counts
? Differentiation of closely related gram-negative bacteria,
? Left,phase micrograph of mixture of Proteus 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.
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 species
in soil or other habitats.
? Fluorescent dyes such as
acridine orange can
stain DNA and RNA.
Phylogenetic nucleic acid probes for
analysis of microbial community
? In almost all cases
phylogenetic analyses of
microbial communities
have shown them to
contain phylogenetically
distinct organisms that
had not been previously
cultured.
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.
Measurements of Microbial Activity in Nature
using Microelectrodes
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 phototrophic
bacteria
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 of
13C depletion is calculated as an isotopic fractionation.
Use of Isotopic Fractionation in
Microbial Ecology
d 13C(0/00)=(13C/12C sample- 13C/12C standard)/ 13C/12C standard X 1000
Use of Isotopic Fractionation in
Microbial Ecology
d 34S(0/00)=(34S/32S sample- 34S/32S standard)/ 34S/32S standard X 1000
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 distinguish
between biogenic and abiogenic ores (Iron
sulfides) and elemental sulfur deposits
? Oxygen isotopic analyses (18O/16O) have been
used to trace the earth’s transition from an
anoxic to an oxic environment (the earth’s
molecular oxygen originated from oxygenic
photosynthesis by cyanobacteria).
Aquatic Habitats
? Phytoplankton (浮游植物 ),Algae floating or
suspended freely in the water
? Benthic algae (水底藻类 ),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
Aquatic Habitats
? Distribution of
chlorophyll in the
western North
Atlantic Ocean as
recorded by satellite.
The Great Lakes
Red,rich in phytoplankton
Chesapeake Bay in Florida
Red,rich in phytoplankton
Offshore has blue and purple
color,has lower chlorophyll
concentration
Aquatic Habitats
Oxygen Relationships in Lakes and Rivers
（上温层）
（深水层，缺氧层）
（温水层）
In a temperate
climate lake
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
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-consuming
property of a body of water its BOD.
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
Visualization of microorganisms on the
surface of soil particles by use of SEM
? Left,Rod-shape bacteria
? Center,Actinomycete spores
? Right,Fungus hyphae
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 has
come to be known as the,deep sea”.
Deep Sea Microbiology,
barotolerant and barophilic bacteria
Deep Sea Microbiology
Physiology of barophiles
? Relatively few proteins are controlled by
pressure 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 the
transcription of specific genes coding for
proteins needed for growth at high pressure.
Hydrothermal Vents
Animals living at thermal vents
? Invertebrates from habitats near
deep-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
Microorganisms in hydrothermal vents
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
Smokers
Black Smokers:
suggested the upper limit for microbial cells
is under 150oC
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 by
respiration of animals and
chemoorganotrophic microorganisms.
? The single most important contribution of
CO2 to the atmosphere is via microbial
decomposition of dead organic material,
including humus.
Importance of photosynthesis in
the carbon cycle
? Oxygenic photosynthesis:
CO2 + H2O (CH2O) + O2
? Respiration:
(CH2O) + O2 CO2 + H2O
The Carbon Cycle
Decomposition
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 microbial
communities;
? The activities of microorganisms in nature
and monitor their effects on ecosystems.
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
Microorganisms in Nature
A microbial community
structure in a lake
ecosystem
The microorganisms and the microenvironment
Contour
map of
O2
concentration
in a soil particle
The microorganisms and the
microenvironment
Surface and Biofilms
? On surfaces microbial numbers and activity
are 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.
Biofilm
? Biofilms are encased microcolonies of bacterial cells
attached to a surface by way of adhesive
polysaccharides 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-producing
bacteria responsible for dental caries;
? In industry,biofilms can slow the flow of water or oil through
pipelines,accelerate the corrosion of the pipes themselves,
Other factors affecting
microbial ecology
? Nutrient levels and growth rates
? microbial competition and cooperation
Methods in Microbial Ecology
? Study biodiversity,isolation,identification
and quantification of microorganisms in
various habitats.
? Study microbial activity,
? Radioisotopes
? Microelectrodes
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.
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 boilded
eggs,and even dead animals are added,CaCO3 and CaSO4 as buffer are added too.
Agar shake tube method:
Isolation of anaerobic bactetia in pure culture
Identification and Quantification:
Nucleic Acid Probes,Fluorescent Antibodies,
and Viable Counts
? Microautoradiographs of single cells of
Bacillus megaterium hybridized with 16S
rRNA of bacteria (left) and to the 18S
rRNA of Eukatya (right)
Identification and Quantification:
Nucleic Acid Probes,Fluorescent Antibodies,
and Viable Counts
? Fluorescently labeled rRNA probes,Left,phase contrast
photomicrograph of B,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.
Identification and Quantification:
Nucleic Acid Probes,Fluorescent Antibodies,
and Viable Counts
? Differentiation of closely related gram-negative bacteria,
? Left,phase micrograph of mixture of Proteus 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.
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 species
in soil or other habitats.
? Fluorescent dyes such as
acridine orange can
stain DNA and RNA.
Phylogenetic nucleic acid probes for
analysis of microbial community
? In almost all cases
phylogenetic analyses of
microbial communities
have shown them to
contain phylogenetically
distinct organisms that
had not been previously
cultured.
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.
Measurements of Microbial Activity in Nature
using Microelectrodes
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 phototrophic
bacteria
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 of
13C depletion is calculated as an isotopic fractionation.
Use of Isotopic Fractionation in
Microbial Ecology
d 13C(0/00)=(13C/12C sample- 13C/12C standard)/ 13C/12C standard X 1000
Use of Isotopic Fractionation in
Microbial Ecology
d 34S(0/00)=(34S/32S sample- 34S/32S standard)/ 34S/32S standard X 1000
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 distinguish
between biogenic and abiogenic ores (Iron
sulfides) and elemental sulfur deposits
? Oxygen isotopic analyses (18O/16O) have been
used to trace the earth’s transition from an
anoxic to an oxic environment (the earth’s
molecular oxygen originated from oxygenic
photosynthesis by cyanobacteria).
Aquatic Habitats
? Phytoplankton (浮游植物 ),Algae floating or
suspended freely in the water
? Benthic algae (水底藻类 ),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
Aquatic Habitats
? Distribution of
chlorophyll in the
western North
Atlantic Ocean as
recorded by satellite.
The Great Lakes
Red,rich in phytoplankton
Chesapeake Bay in Florida
Red,rich in phytoplankton
Offshore has blue and purple
color,has lower chlorophyll
concentration
Aquatic Habitats
Oxygen Relationships in Lakes and Rivers
（上温层）
（深水层，缺氧层）
（温水层）
In a temperate
climate lake
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
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-consuming
property of a body of water its BOD.
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
Visualization of microorganisms on the
surface of soil particles by use of SEM
? Left,Rod-shape bacteria
? Center,Actinomycete spores
? Right,Fungus hyphae
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 has
come to be known as the,deep sea”.
Deep Sea Microbiology,
barotolerant and barophilic bacteria
Deep Sea Microbiology
Physiology of barophiles
? Relatively few proteins are controlled by
pressure 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 the
transcription of specific genes coding for
proteins needed for growth at high pressure.
Hydrothermal Vents
Animals living at thermal vents
? Invertebrates from habitats near
deep-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
Microorganisms in hydrothermal vents
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
Smokers
Black Smokers:
suggested the upper limit for microbial cells
is under 150oC
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 by
respiration of animals and
chemoorganotrophic microorganisms.
? The single most important contribution of
CO2 to the atmosphere is via microbial
decomposition of dead organic material,
including humus.
Importance of photosynthesis in
the carbon cycle
? Oxygenic photosynthesis:
CO2 + H2O (CH2O) + O2
? Respiration:
(CH2O) + O2 CO2 + H2O
The Carbon Cycle
Decomposition
