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Microbial Ecology
Chapter 30
Principles of Microbial Ecology,
Definitions

Ecology


Ecosystem


The study of relationships among organisms and their
environment.
Includes all of the biotic (living) components and the
abiotic (physical and chemical) components of an
environment.
Biosphere

That region of the earth that is inhibited by living
organisms.
Principles of Microbial Ecology

Definitions

Biodiversity


Biomass


Evenness of distribution of the # of species present
Weight of all organisms present
Ecological Community

Comprised of a variety of different species in a given
environment; more stable than an environment with
fewer organisms.
Principles of Microbial Ecology

Ecological Niche


The role that an organism
plays in its particular
ecosystem as well as the
physical space it occupies.
Microenvironment


Environment immediately
surrounding an individual
cell
Biofilm (Fig. 30.1, pg. 766)
Principles of Microbial Ecology

Indigenous


Native organisms
Nonindigenous

Temporary inhabitants
Principles of Microbial Ecology

Nutrient Acquisition

Primary Producers

Autotrophs





Convert CO2
organic material
Photoautotrophs – plants, algae, cyanobacteria
Anoxygenic phototrophs
 Use sunlight for energy
Chemolithoautotrophs
 Oxidize inorganic compounds for energy
Food source for consumers and decomposers
Principles of Microbial Ecology

Consumers

Heterotrophs



Utilize organic material
Food chain
 Herbivores – primary consumers
 Carnivores – secondary consumers
 Carnivores – tertiary consumers
Food web
 Interacting food chains
Principles of Microbial Ecology

Decomposers

Heterotrophs




Primarily bacteria and fungi
Digest remains or primary producers and consumers
 Detritus - Fresh or partially decomposed organic matter
Specialize in digesting complex materials
Mineralization

Complete breakdown of organic matter into inorganic
molecules such as ammonia, sulfates, phosphates & CO2
Principles of Microbial Ecology

Low Nutrient Environments

Common in nature

Dilute aqueous solutions



Lakes, rivers, streams
Distilled water reservoirs
Respiratory equipment
Principles of Microbial Ecology

Microbial Competition

Ability of microbes to
compete successfully for
a habitat generally
related to


Rate at which organism
multiples
Ability to withstand
adverse environmental
conditions
Principles of Microbial Ecology

Antagonism

Promotes biodiversity through competition

Bactericins
 Proteins produced by some soil microbes that kill closely
related strains of bacteria
Principles of Microbial Ecology

Microbes and Environmental Change

Examples

Enzyme induction




Inactivates mercury
Only formed when mercury is present
Antibiotic resistant bacteria
Growth and metabolism of organism can change
environment.

Figure 30..4, pg. 768
Principles of Microbial Ecology

Microbial Communities

Biofilms (discussed in ch. 4)

Microbial Mat

A thick, dense, highly organized structure composed of
distinctive layers (fig. 30.5, pg. 769)
Principles of Microbial Ecology

Microbial Ecology Studies

Traditional



Cultures
Microscopy
Molecular Techniques

Microscopy


Dyes that made are fluorescent by metabolic activities
Fluorescence in situ hybridization (FISH)
 Nucleic acid probes to observe only cells with specific
nucleotide sequences
Principles of Microbial Ecology



Confocal scanning laser microscopes
 To observe sectional views of a 3-dimensional specimen
(biofilm)
Polymerase chain reaction (PCR)
 To detect only certain organisms
 Denaturing gradient gel electrophoresis (DGGE)
 PCR & DGGE studies conform that standard cultures
techniques can be poor indicators of natural microbial
population composition
Genomics
 Sequence information can apply to more than one group of
microbes
Aquatic Habitats

Water


Extremely efficient solvent
Can absorb various wavelengths of light

Important aspect relating to photosynthesis
Aquatic Habitats

Marine Environment

Oceans




Cover more than 70% of earth’s surface
Most abundant aquatic habitat
Represent 95% of global water
Fresh Water Environment

Lakes, Rivers


Fraction of global water source
Important source of fresh water
Aquatic Habitats

Oceans and lakes

Characteristic zones influence distribution of
microbial populations

Upper layers


Sufficient light penetration - photosynthetic microorganisms
Oligotrophic waters


Nutrient poor
Growth of photosynthetic organisms & autotrophs
limited by lack of phosphate, nitrate and iron
Aquatic Habitats

Eutrophic waters

Nutrient rich (fig. 30.6, pg. 770)



Photosynthetic activities in upper layers produce organic
compounds
Organic compounds permit growth of heterotrophs in lower
layers
Heterotrophs consume dissolved O2 during metabolism
 O2 consumption can outpace slow rate of atmospheric O2
diffusion into water
 Can create a hypoxic environment
Aquatic Habitats

Definitions

Eutrophic

A body of water rich in nutrients


Oligotrophic


A body of water low in nutrients
Eutrophication


swamps, bog lakes, etc.
Natural nutrient enrichment of waters
Accelerated Eutrophication

Rapid loading of nutrients
Aquatic Habitats

Potable Water


Safe for drinking
Rainwater

Distillate


Ground Water


contaminated by air pollutants
aquifers, underground lakes & rivers
Surface Waters

Creeks, rivers, ponds, lakes
Aquatic Habitats

Factors Affecting Presence of Organisms

Nutrients

Oceans typically oligotrophic

Inshore areas not as stable as deep ocean
 Dramatically affected by run-off
 Dead zone in Gulf of Mexico every spring
Aquatic Habitats

Oxygen (limiting factor)





low solubility in water, quantities limited
well mixed cold water ~8-9mg/l
warm water ~ 5mg/l
Deep marine water is O2 saturated due to mixing
associated with tides, currents and wind
Temperature - Worldwide 0oC to ~100oC
Aquatic Habitats

Freshwater environments

Oligotrophic lakes may have anaerobic layers due to
thermal stratification

Epilimmion




Hypolimmion




Colder deeper layers (~5o-4oC)
May be anaerobic due consumption of O2 by heterotrophs
Water most dense at 4oC (39oF)
Thermocline (~20o-10oC)


Warm upper layer (25o-22oC)
Generally oxygen rich due to photosynthetic organisms
Generally aerobic
Zone (layer) of rapid temperature change
As weather cools, water mixes oxygenating deep water
Aquatic Habitats

Freshwater Environments

Rivers and Streams

Usually shallow and turbulent




Facilitates O2 circulation
Generally aerobic
Generally good sunlight penetration for photosynthesis
Sheathed bacteria adhere to stable structures to allow
utilization of nutrients flowing pass
 Examples: Sphaerotilus & Leptothrix
Aquatic Habitats

Factors Affecting Presence of Organisms

Sunlight Penetration (Photic Zone)




depth of sunlight penetration
algae & cyanobacteria
photosynthesis provides nutrients & oxygen for other
organisms
pH Range 2 - 9

fish hypersensitive to bacterial parasites at pH 5.5,
usually die if pH drops below 4.5
Aquatic Habitats

Specialized Aquatic Environments

Salt lakes – no outlets



Iron springs


Water evaporates, concentrates salt
Halophilic organisms
Contain large quantities of ferrous ions
Sulfur Springs

Support both photosynthetic and non-photosynthetic
sulfur bacteria
Aquatic Habitats

Lake Zones

Littoral Zone



Limnetic Zone


Extending from shore to the limit of occupancy of rooted
plants
Part of the photic zone
Region of open water bounded by zone of emergent
(rooted) vegetation
Benthic Zone

Sediment (regardless of depth)
Aquatic Habitats

Freshwater

Composition of the water reflects its source


Stagnant ponds to free flowing rivers and lakes
Ground water


Surface water



Normally relatively free of nutrients and toxins
Affected by surface runoff of materials
Organics, fertilizers, herbicides, pesticides, etc.
Inshore Marine

Affected by freshwater runoff and pollutants
Aquatic Habitats

Marine Environment

Factors affecting presence of miroorganisms


Same Factors as Fresh Water plus
Barometric pressure (hydrostatic pressure)




1 atm / 33 feet of seawater
ocean 35,750 feet (11,000 meters) deep, hydrostatic pressure 1,083 atm
Organisms are barophilic (barophiles)
Salinity


Marine averages 3.5% (fresh averages ~0.5%)
Organisms are halophilic (halophiles) or halotolerant
Aquatic Habitats

Microbial Flora

Dictated by Available Nutrients

Bulk of Microbial Mass


Aerobic Chemoheterotrophic Bacteria



algae, cyanobacteria & protozoa
degrade organic materials
Cytophaga, Caulobacter
Chemoautotrophic Bacteria

obtain energy from aerobic oxidation of reduced inorganic
compounds
Aquatic Habitats

Sulfur Oxidizers - Thiobacillus


Nitrifiers



oxidize H2S dissolved in water to inorganic sulfur or sulfate
more important in marine environments
oxidize ammonia - nitrite - nitrate
Sediment

Methanogenic Bacteria

Foraminiferans & Radiolarians (oil and gas markers)
Aquatic Habitats

Marine Waters

Microbial Flora

Most bacteria are found



Deep ocean vents



In association with organic particles (often less than 0.1mm in
size) near the surface
In association with skin or gut of fish
Chemoautotrophic bacteria
Some Vibrios are of major importance as fish pathogens
Some microbes cause human-like diseases in fish


Pasteuralla piscicida (like tularemia)
Mycobacterium marinum (TB like disease)
Aquatic Habitats

Major Functions of Freshwater and Marine
Bacteria

Decompose Organic Matter


Transform Essential Minerals


liberate mineral nutrients
cycling them through forms other organisms can use
Release Dissolved Organic Compounds

into the food web to support growth of other organisms
Aquatic Habitats

Determining Microbial Flora

Epifluorescence Counting


Stain with acridine orange (stains DNA)
view slide under UV light


tedious and can be inaccurate, counts DNA from living and
dead organisms
Luciferin-luciferase Enzyme System


Gives estimate of the number of viable organisms in a
given volume of water
Based on carbon:ATP ratio (~250 for most microbes)
Terrestrial Habitats

Characteristics of Soil

Composed of


Pulverized rocks, decaying organic material, air & water
Life


Bacteria, fungi, algae, protozoa, worms, insects, and
plants roots
May contain



More than 4,000 different species per gram of soil
More than 2 tons of bacteria and fungi per acre
Can be a rapidly and dramatically changing
environment
Terrestrial Habitats

Soil Layers (Horizons)

Topsoil (A Horizon)




Subsoil (B Horizon)


Accumulation of clays, salts & various nutrients
C Horizon


Dark, nutrient-rich
Supports plant growth
Depth – few inches to several feet
Partially weathered bedrock
R Horizon

Unweathered bedrock
Terrestrial Habitats

Microorganisms in Soil

Composition affected by environmental conditions

Moisture



Finely textured soils (clay) tend to be waterlogged and
anaerobic
Sandy soils (dry quickly) tend to be aerobic
Acidity


Suppresses bacterial growth
Fungi thrive with less competition for nutrients
Terrestrial Habitats

Temperature



Mesophiles comprise the bulk of the soil bacteria, they grow
best between 20oC and 50oC
Thermophiles occur in compost piles where they generate heat
Available Nutrients

The size of the microbial population in soil is limited by on the
amount of organic matter available
Terrestrial Habitats

Soil Organisms

Prokaryotes


Most numerous soil inhabitants
Most common genera



Nocardia, Arthrobacter, Streptomyces
Streptomyces
 Produce conidia (dessication resistant spore)
 Produce geosmins (give soil musty odor)
 Produce many medically useful antibiotics
Gram (+) bacteria more abundant than Gram (-) bacteria
Terrestrial Habitats

Not all Soil Organisms are Beneficial

Human Bacterial Pathogens


Clostridium and Norcardia
Human Fungal Pathogens

Coccidioides, Histoplasma, and Blastomyces
Terrestrial Habitats

Fungi


Make up bulk of soil biomass
Most are aerobic




Some are free-living
Some occur in symbiotic relationship with plant roots


Usually found in top 10 cm of soil
Crucial in decomposing plant matter
Mycorrhizae
Algae

Live mostly on or near surface
Terrestrial Habitats

Algae



Dependent on sunlight and photosynthesis to provide energy needs.
Sensitive to environmental conditions of drought and low
temperature
Major nutrient source for


Earthworms and nematodes
Protozoa



Aerobic - generally found near the surface
Found in moist soils at a density of ~104 to 105 organisms per gram
of soil
Predators of soil bacteria and algae
Terrestrial Habitats

Rhizosphere


Zone of soil that adheres to plant roots
Roots cells extract organic molecules


Sugars, amino acids and vitamins
Fosters growth of microorganisms


Gram (-) more prevalent than surrounding soil
Certain grasses – enriched with Azospirillum species
Biochemical Cycling & Energy Flow

Biochemical Cycles


Cyclical paths elements take as they flow through
living (biotic) and non-living (abiotic) components
of ecosystem
Fixed and limited amount of elements available

Carbon and nitrogen particularly important



Stable gaseous forms CO2 and N gas enter atmosphere
Global impacts
Elements continually cycle in ecosystem

Energy does not, must be continually added to fuel life
Biochemical Cycling

Elements - three general purposes

Biomass production

Incorporated into cell material


All organisms require nitrogen to produce amino acids
Energy source


Reduced form of element is used to generate energy –
ATP
Energy yielding reactions oxidize the energy source


Chemoorganotrophs use reduced carbon compounds – sugar,
lipids and amino acids
Chemolithotrophs use reduced inorganic molecules – H2S,
ammonia (NH3) and hydrogen gas (H4)
Biochemical Cycling

Terminal electron acceptor

Electrons from energy source transferred to an oxidized
form of element during respiration



Aerobic conditions
 O2 is terminal electron acceptor
Anaerobic conditions some prokaryotes use
 Nitrate (NO3), nitrite (NO2), sulfate (SO4)and CO2
The following pages will review cycling
processes for oxygen, carbon, nitrogen,
phosphorus and sulfur
Oxygen Cycle

During photosynthesis
cyanobacteria, algae and
green plants produce oxygen
from water. The oxygen is
utilized via respiration.

The level of oxygen in the
atmosphere is maintained by
chemical reactions in the
upper atmosphere, aerobic
respiration and photosynthesis
Carbon Cycle

Carbon



Carbon enters producers during photosynthesis or
chemosynthesis
In turn enters consumers via consumption of the producers.
Carbon returned to the atmosphere in the form of CO2 by
respiration and the actions of decomposers consuming dead
or decaying waste.

Oxygen has profound influence on cycle





Allows degradation of certain compounds
Helps determine the types of carbon containing gases produced
Aerobic decomposition
Great deal of OC2 formed through aerobic respiration
(CH2O)n + (O2)n
CO2 + H2O
Carbon Cycle

Low oxygen (wet soils, marshes, swamps, etc.)
 Degradation is incomplete
 Generate CO2 and other gases
 Some CO2 used by methanogens (ex: Archaea) as terminal
electron acceptor generating methane (CH4)
 4H2 + CO2
CH4 + H2O
 Methane entering atmosphere is oxidized by UV light and
chemical ions to CO and CO2
Nitrogen Cycle

Nitrogen (Fig. 30.11; pg. 775)


Most important constituent of proteins and nucleic
acids
Consumers obtain required nitrogen from ingested
plants and animals and use it to build biomass

Prokaryotes – diverse in use of nitrogen compounds



Some use oxidized compounds like nitrate and nitrite
Some use reduced nitrogen compounds like ammonium
All of these metabolic activities represent steps in the N
cycle
Nitrogen Cycle

Nitrogen Fixation

Nitrogen gas reduced to form ammonium



Ammonium can be incorporated into cellular material
Atmosphere 79% N2
 Relatively few organisms use atmospheric (gaseous)
nitrogen – rely on prokaryotes to convert atmospheric
nitrogen into a useable form
Nitrogenase
 Enzyme complex that mediates nitrogen fixation and is
readily inactivated by oxygen
 Nitrogen fixing aerobes must have a mechanism for
protection
Nitrogen Cycle

Nitrogen fixing prokaryotes (diazotrophs)

Free living




Symbiotic - significant in benefiting plant growth



Azotobacter - chief suppliers of fixed nitrogen in grasslands &
similar ecosystems
Cyanobacteria - most significant nitrogen fixer in aquatic
environments
Clostridium spp. - dominant free-living anaerobes in soils
Found in association with all leguminous plants including
alfalfa, clover, peas, beans, peanuts and vetch
Rhizobium
Synthetic nitrogen compounds
Nitrogen Cycle

Ammonification

The decomposition of organic nitrogen into ammonia



Occurs when extracellular proteolytic enzymes convert
proteins into amino acids.
Other enzymes then decompose amino acids into ammonium
(NH4+) and sulfate ions.
Ammonium ions in turn can be oxidized to nitrite (NO2-) and
nitrate (NO3-) through Nitrification
Nitrogen Cycle

Nitrification


Oxidation of ammonium to nitrite
Nitrifiers - encompass two groups of chemolithotrophic bacteria




Ammonia oxidizers  Nitrosomonas - (NH4+ to NO2-) (ammonium to nitrite)
Nitrite oxidizers
 Nitrobacter & Nitrospira (NO2- to NO3-) (nitrite to nitrate)
Obligate aerobes – use molecular O2 as final electron acceptor
 Nitrification does not occur in waterlogged soils or anaerobic
aquatic environments
Important because it supplies plants with nitrates which is the most
useable form of nitrogen for plant metabolism
Nitrogen Cycle

Denitification


Process to convert nitrate to gaseous nitrogen
Nitrate represents fully oxidized nitrogen





Pseudomonas spp. can use nitrate as terminal electron acceptor
 Anaerobic respiration
Nitrate reduced to gaseous nitrogen compounds – nitrous oxide and
molecular nitrogen
Release to atmosphere represents a loss of nitrogen and contributes to
global warming
Benefit – waste water treatment processes to remove nitrate
Anammox


Brocadia anamoxidans oxidizes ammonium anaerobically
Potential benefit in waste water treatment
Sulfur Cycle

Sulfur



Occurs in all living things
Chiefly a compound of amino acids methioine &
cysteine
Key steps of cycle rely on prokaryotes




Some use reduced form of H2S, some elemental S
Others use sulfate
Most plants and microbes assimulate sulfur as sulfate
(SO42-)
Is present in the soil (like nitrogen) chiefly as a part of
proteins
Sulfur Cycle

Hydrogen sulfide is toxic to lining things



Under aerobic conditions, H2S oxidizes spontaneously to
sulfur and is then converted to sulfate (SO42-) (its most readily
utilized form) by sulfur bacteria
Under anaerobic conditions sulfate-reducing bacteria reduce
sulfate to hydrogen sulfide
Oxidation of hydrogen sulfide to sulfate carried out
principally by nonphotosynthetic autotrophs,
Thiobacillus, Thiothrix and Beggiatoa and less
commonly by photosynthetic autotrophs (green and
purple sulfur bacteria)
Sulfur Cycle

Sulfur Reduction

Reduction of sulfate to sulfide


Carried out by anaerobic bacteria that are capable of utilizing
sulfate as the final electron acceptor in their anaerobic
respiration
Include Desulfovibrio and Desulfomonas
Phosphorus Cycle

Involves movement of phosphorus between
inorganic and organic forms

Microorganisms play three major roles in
phosphorus transformations



Mineralize organic phosphorus
Convert insoluble forms of inorganic phosphorus to
soluble forms
Immobilize inorganic phosphorus
Phosphorus Cycle

Overall Transformations of Phosphorus

Soil Organisms


Break down organic phosphate into to inorganic
phosphates
Then convert inorganic phosphates to orthophosphate
(PO43-)



Orthophosphate is water soluble and readily used by most
plants and microorganisms
When plants & animals die decomposers convert
organic phosphate back into inorganic phosphate
Phosphorus is often the limiting nutrient in many
environments