Chapter 23

Microbial Ecosystems
Ecosystem
Sum total of all of the organisms and abiotic factors in a particular environment
Freshwater, soil, plant, and marine microbial ecosystems

Habitat
Portions of the ecosystem best suited to one or a small number of microbial populations

Symbiosis
A relationship between two or more organisms that share a particular ecosystem
1) Parasitism
Symbiosis in which one member in the relationship is harmed in the process
2) Mutualism
Symbiotic relationship in which both species benefit
3) Commensalism
Symbiotic relationship in which one species benefits while the other in neither harmed nor helped
Diversity of microbial species in an ecosystem can be expressed in two ways
1) Species richness
The total number of different species present
2) Species abundance
The proportion of each species in the ecosystem
Microbial species richness and abundance is determined by the amounts and kinds
of nutrients available
Figure 23.1 (Madigan et al. 2009)
Guild
Metabolically related microbial populations
Microbial community
Sets of guilds

Population

Guild

Community

Ecosystem
Figure 23.2 (Madigan et al. 2009)
Biogeochemistry
Study of the biologically mediated chemical transformations
Carbon, sulfur, nitrogen, and iron
Biogeochemical cycle
The transformations of a key element that is catalyzed by either biological or chemical agents
Usually proceed by oxidation-reduction reactions
Example

H
2
S S
0
and or SO
4
2-
H
2
S

1)Microorganisms (phototrophic or chemolithotrophic) oxidize H
2
S
2)Sulfate reduced to sulfide by sulfate-reducing bacteria
Niche
Differences in the type and quantity of resources and the physiochemical conditions of the habitat
Ecological theory states that for every organism there exists at least one niche (the prime niche) in
which that organism is most successful
Organisms that share a niche and a particular resource are termed ecotypes
Microenvironment
Describes the niche where a microorganism actually lives and metabolizes
Extended periods of exponential microbial growth are rare in nature
Nutrients exist in low supply
Nonuniform distribution of nutrients
Competition for nutrients
Surfaces are important microbial habitats
1) Nutrients adsorb to surfaces and often contain more resources than are available to free-floating cells
2) Surfaces are areas to which microbial cells can attach and remain in a favorable habitat
Biofilm
Assemblages of bacterial cells attached to a surface and enclosed in an adhesive matrix (mixture of
polysaccharides and proteins/nucleic acids) excreted by the cells
Contain several porous layers
Figure 23.5c (Madigan et al. 2009)
1) Attachment of a few cells to a surface
Causes expression of biofilm-specific genes which encode proteins that
1) Synthesize intercellular signaling molecules
2) Initiate matrix formation
2) Colonization
3) Development

Figure 23.6 (Madigan et al. 2009)
Why are biofilms advantageous for bacteria?
1) Biofilms are a means of microbial self-defense
2) Biofilm formation allows cells to remain in a favorable niche
3) Allow bacterial cells to live in close association with each other
4) Seem to be the typical way bacterial cells grow in nature (default mode of growth)

Why is controlling growth of biofilms important?
1) Biofilms form in the body (periodontal disease, kidney stones, tuberculosis, and Staphylococcus
infections) and can resist attacks by the immune system and antibiotics
2) Biofilms slow the flow of water, oil, and other liquids through pipelines
3) Accelerate degradation of submerged objects

Freshwater environments are highly variable in the resources and conditions
available for microbial growth
Primary producer
An organism that uses light to synthesize new organic material from CO
2
and produces O
2
1) Phytoplankton suspended freely in water
2) Benthic species organisms attached to the bottom or sides of a freshwater environment

Rivers and streams
Oxygen levels in rivers are extremely important due to the requirement of oxygen for aquatic animals
Input of organic material from sewage and/or agricultural and industrial pollution will severely deplete
oxygen levels
Lakes
Stratification of lakes, especially during summer, due to unconsumed organic matter sinking to deeper
waters
1) Epilimnion
Warmer, less dense surface layers
Strictly aerobic organisms (includes higher plants and
animals)
2) Hypolimnion
Colder, denser bottom layers
Anaerobic chemoorganotrophs and methanogens
***Thermocline is the transition zone from
epilimnion to hypolimnion
Figure 23.8 (Madigan et al. 2009)
Biochemical oxygen demand (BOD)
microbial oxygen consuming property of a water
sample
To determine BOD
1) Acquire water sample
2) Aerate it to saturation
3) Seal bottle
4) Incubate 5 days at 20
o
C in the dark
5) Determine residual oxygen after incubation
Measure of amount of organic matter that can be
oxidized by microorganisms
Drop in BOD usually signals recovery from
contamination
Figure 23.9 (Madigan et al. 2009)
Soil
Loose outer material of Earths surface, distinct from the underlying bedrock
1) Mineral soils derived from weathering of rock and other inorganic materials
2) Organic soils sedimentation in bogs and marshes

Soil components
1) Inorganic mineral matter (40%)
2) Organic matter (5%)
3) Air and water (50%)
4) Living organisms, both micro and macro

Soil particles (classified based on size)
1) Sand (between 0.1 2 mm)
2) Silt (between 0.002 0.1 mm)
3) Clay (less than 0.002 mm)
4) Loam ( no one particle size dominates)
Figure 23.11 (Madigan et al. 2009)
Soil formation
Combination of physical, chemical, and biological processes
1) Phototrophs (algae, lichens, or mosses) produce organic material
2) Organic material supports chemoorganotrophic bacteria and fungi
3) Chemoorganotrophic bacteria increase in number as plant cover increases
4) CO
2
produced during respiration becomes dissolved in water to form H
2
CO
3
(carbonic acid)
5) Dissolves more inorganic rock material
***Freezing and thawing creates cracks and allows pioneer plants to develop

Factors affecting microbial activity in soil
1) Availability of water
2) Availability of oxygen
3) Availability or resources
Figure 23.10 (Madigan et al. 2009)
Rhizosphere
Region immediately outside the root
Zone where microbial activity is high
Rhizoplane
Surface of the root
Phyllosphere
Surface of the plant leaf
Phytopathogens
Plant pathogens, including bacteria, fungi, viruses, and microscopic worms
Examples: Pseudomonas, Xanthamonas, Erwinia, etc.
Open ocean (pelagic zone) has very low nutrient levels
Water temperatures are much cooler and more constant than in freshwater
environments
Marine microbial communities because of their roles in CO
2
sequestration and O
2

production influence everything from food chains to global climate
Primary productivity
Prochlorophytes
Phototrophic organisms that are phylogenetically related to cyanobacteria
Contain chlorophylls a and b or a and d
Example: Prochlorococcus
Trichodesmium
Filamentous, nitrogen-fixing cyanobacterium
Contain phycobilins
Figure 23.19 (Madigan et al. 2009)
Visible light penetrates no further than ~300 m (photic zone)
Deep sea
Water at depths greater than 1,000 m
Greater than 75% of all ocean water is deep sea
Mariana Trench in Pacific Ocean is greater than 10,000 m in depth
Three environmental extremes in deep sea
1) Low temperature
2) High pressure
3) Low nutrient levels
***Deep sea is also completely dark
Barotolerant organism
Able to grow under elevated
pressures but growing best at 1 atm
Barophile
Grows best under pressure greater
than 1 atm
Extreme barophile
Organism unable to grow at a
pressure of 1 atm and typically
requiring several hundred atms of
pressure for growth
Figure 23.20 (Madigan et al. 2009)