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Environmental Microbiology. Talaro Chapter 26. Environmental Microbiology Study of microbes in their natural habitats Microbial Diversity – study of the different types of microbes in an environment Microbial Ecology Studies the interactions between microbes & their environments

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Environmental Microbiology
    • Study of microbes in their natural habitats
    • Microbial Diversity – study of the different types of microbes in an environment
  • Microbial Ecology
    • Studies the interactions between microbes & their environments
    • Involving biotic & abiotic components
    • Distribution
    • Abundance – numbers of bacteria
microbes comprise approximately half of all the biomass on earth

Microbes comprise approximately half of all the biomass on Earth

Prokaryotes exist in all of the habitats on Earth

Extreme cold

Extreme heat

Low O2

Extreme pressure – “barophiles”

now called piezophiles

High salt (low aw)

Prokaryotes exits in environments that are too

extreme or inhospitable for eukaryotic cells – Extremophiles!!

Limits of life on Earth are defined by the presence of prokaryotes

which tells us what to look for when looking for life on

extraterrestrial bodies

the primary role of microorganisms is to serve as catalysts of biogeochemical cycles

The primary role of microorganisms is to serve as catalysts of biogeochemical cycles



Microbial catalysts interact on a much smaller spatial scale, but affect the biosphere over a long period of time

Nanometers to micrometers

Bacteria on the tip of a plant root

Bacteria living in specialized organs of invertebrates

Geologic Time

Production of O2

Millions to billions of years

microorganism have a greater metabolic versatility than do macroorganisms

Microorganism have a greater metabolic versatility than do macroorganisms






Prokaryotes do not Exist in Isolation

Plant and animals are dependent upon the actions of prokaryotes

Archaea and Bacteria participate in mutualistic relationships that benefit both organisms

Only a small number of bacteria are pathogenic!

And there are bacteria that are pathogens of animals and plants


Examples of Mutualism

  • Sheep and cattle (ruminants) live off grass
    • Lack the digestive enzymes to break down cellulose
    • Bacteria in intestinal tract break down cellulose
      • Products of cellulose degradation are converted to carbon
      • sources that the ruminants can use
      • CH4 is also produced in high amounts (belching!)
    • Sugars absorbed by animal and used for energy
  • Plants unable to fix atmospheric N2
    • Symbiotic bacteria infect roots
    • Plant requires nitrogen for proteins

Antarctica glaciers

Hot springs

  • Complex aggregation
    • Bacteria, archaea, protozoa, algae
    • Microbial Mat
      • Free floating organism
      • Attached organism
    • Highly structured
  • Extracellular polysaccharide
    • Protective & adhesive matrix
      • Protection from the environment
      • Protection from protozoans
      • Protection from antibiotics & chemicals

Antarctic Sun February 12, 2006

Grows by cell division & recruitment
  • Industrial biofilms
    • Pipe corrosion
    • Ship corrosion
  • Infections
    • Dental plaque
    • Contact lenses
    • Heart valves
    • Artificial hip joints
Physiologically Integrated
    • Each group performs a specialized metabolic function
  • Lateral gene transfer
    • Conjugation between different species
    • Transduction between different species
  • Cell to cell communication
    • Quorum sensing

1. Initial attachment

4. Maturation of Biofilm Architecture

2. Production of EPS

5. Dispersion

3. Early Biofilm Architecture


Microbial mat

Cyanobacteria & purple bacteria

Lake Cadagno, Switzerland

White area is precipitated sulfur



Cyanobacterial mat in run-off from

a hot springs at Yellowstone National Park


winogradsky column

Nutrient Cycling

Winogradsky Column
  • A glass column that simulates the complex interactions of microbial biofilms in an aqueous environment
    • Upper aerobic zone
    • Microaerophilic zone
    • Lower anaerobic zone

Environmental Technology Consortium at Clark Atlanta University and Northern Arizona University 

Algae, cyanobacteria, aerobic heterotrophs
    • CO2 + H2O  CH2O + O2
      • Oxygenic photosynthesis
      • H2O is a source of electrons
    • CH2O + O2 CO2 + H2O
      • Aerobic respiration
  • H2S oxidizers
    • CO2 + H2S  CH2O + S + H2O
      • Anoxygenic photosynthesis
      • H2S is a source of electrons

More on anoxygenic and oxygenic photosynthesis is few moments

Purple nonsulfur photoheterotrophs
    • May exist as photoheterotrophs, photoautotrophs or chemoheterotrophs
    • Freely alternate between these metabolic modes depending on environmental conditions
      • Degree of anaerobiosis
      • Availability and types of carbon sources
        • CO2 for autotrophic growth
        • Organic compounds for heterotrophic growth
      • Availability of light for phototrophic growth
      • The “non-sulfur” label was used since it was originally thought that these bacteria could not use H2S as an electron donor
      • Can use H2S in low concentrations
Purple non-sulfur bacteria
    • CH2O + O2 CO2 + H2O (Chemoheterotrophs)
    • CH2O + O2CO2 + H2O (Photoheterotrophs)
    • CO2 + H2O  CH2O + O2 (Photoautotrophs)
  • Purple & Green sulfur bacteria
    • Anoxygenic photosynthesis
    • H2, H2S or So  SO42-
  • Sulfate reducers
    • SO42- S2- compound (H2S or FeS)
quorum sensing
Quorum Sensing
  • Cell-cell communication in bacteria
  • Coordinate behavior/activities between bacterial cells of the same species
  • Autoinducers trigger a change when cells are in high concentration
    • Specific receptor for the inducer
    • Extracellular concentration of autoinducer increases with population
    • Threshold is reached
    • The population responds with an alteration in gene expression
      • Bioluminescence
      • Secretion of virulence factors
      • Biofilm formation
      • Sporulation
      • Competence
energy nutrient flow
Energy & Nutrient Flow

It is likely that most of the Earth's atmospheric oxygen was produced by bacterial cells.

Plant cell chloroplast and oxygenic photosynthesis are originated in prokaryotes.

Anoxygenic Photosynthesis
  • Anaerobic bacterial photosynthesis that does not produce O2
  • CO2 + H2S  (CH2O)n + S + H2O
    • H2, H2S or So or organic compounds serves as a source of electrons
      • Need electrons to make fix C and make ATP
  • Purple and green photosynthetic sulfur bacteria
    • Aquatic & anaerobic
    • Pigments that absorb different l
    • Bacteriochlorophyll (800 - 1000 nm [far red])
    • Carotenoids (400 - 550 nm)
      • Phycobilins are not present
    • Only 1 photosystem
  • Rhodobacter
    • Oxidize succinate or butyrate during CO2 fixation
    • Hypothesized to be have become an endosymbiont of eucaryotes
    • Mitochondrion 16S rRNA sequences

Cyanobacteria & purple bacteria

Lake Cadagno, Switzerland




Tremendous ecological importance in the C, O and N cycles

Evolutionary relationship to plants

Cyanobacteria have chlorophyll a, carotenoids and phycobilins

Same chlorophyll a in plants and algae

Chlorophyll a absorbs light at 450 nm & 650 - 750 nm

Pycobilins absorb at 550 and 650 nm


Some cyanobacteria fix nitrogen in specialized cellsHETEROCYSTS.

  • Provide anaerobic environment required for nitrogenase.

Cyanobacteria have membranes that resemble photosynthetic thylakoids in plant chloroplasts.

Hypothesized that cyanobacteria were the progenitors of eucaryotic chloroplasts via endosymbiosis.

Cyanobacteria are very similar to the chloroplasts of red algae (Rhodophyta).


Several species of cyanobacteria are symbionts of liverworts, ferns, cycads, flagellated protozoa, and algae.

The photosynthetic partners of lichens are commonly cyanobacteria.

There is also an example of a cyanobacterium as endosymbionts of plant cells.

A cyanobacterial endophyte (Anabaena spp.) fixes nitrogen that becomes available to the water fern, Azolla.




Several thousand cyanobacteria species.

  • Many are symbionts.
  • 200 species are free-living, nonsymbiotic procaryotes.

Cyanobacteria often are isolated from extreme environments.

Hot springs of the Yellowstone National Park Antarctica lakes

Copious mats 2 to 4 cm thick in water beneath more than 5 m of permanent ice.

Cyanobacteria are not found in acidic waters where algae (euckaryotic) predominate.



Green alga

Figure 17. The distribution of photosynthetic pigments among photosynthetic microorganisms.

Red alga


Green bacterium

Purple bacterium



Anoxygenic bacterial photosynthesis

Photosystem I

Cyclic Photophosphorylation

Cyanobacteria, algae and plants, also have Photosystem II

iron sulfur protein

ATP is generated during photophosphorylation

bacterial chlorophyll

cyclic photophosphorylation


Anoxygenic bacterial photosynthesis

Photosystem I

Electrons from H2S are passed to ferredoxin

NADP is reduced

Autotrophic CO2 fixation

CO2 (CH2O)n

CO2 + H2S  (CH2O)n + S + H2O

Oxidation of H2S is linked to PS1


anoxygenic photosynthesis

Anoxygenic photosynthesis

Limitations on the amount of C that can be fixed

Need more electrons to fix more C


Oxygenic Photosynthesis

Plants, algae and cyanobacteria

Electrons lost here must be replenished

PS2 ensures a constant supply of electrons

ATP is generate by noncyclic photophosphorylation

CO2 (CH2O)n

Calvin Cycle

Electrons from PS1 reduce ferredoxin Ferredoxin passes the electrons to NADP

H2O is source of electrons



Table 6. Differences between plant and bacterial photosynthesis