Chapter 23-Microbial Ecology

Microbial Ecosystems
Chapter 23

Ecological Concepts
Many microbes establish relationships with other organisms (symbioses)
Parasitism
One member is harmed and the other benefits
Mutualism
Both species benefit
Commensalism
One species benefits and the other is neither harmed nor helped

Ecological Concepts
The diversity of microbial species in an ecosystem can be expressed in two ways
Species richness: the total number of different species present
Species abundance: the proportion of each species in an ecosystem
Microbial species richness and abundance is a function of the kinds and amounts of nutrients available in a given habitat

Microbial Ecosystems and Biogeochemical Cycling
Guilds
Metabolically related microbial populations
Sets of guilds form microbial communities that interact with macroorganisms and abiotic factors in the ecosystem

Microbial Ecosystems and Biogeochemical Cycling
Biogeochemistry: the study of biologically mediated chemical transformations
A biogeochemical cycle defines the transformations of a key element that is catalyzed by biological or chemical agents
Typically proceed by oxidation-reduction reactions
Microbes play critical roles in energy transformations and biogeochemical processes that result in the recycling of elements to living systems

Environments and Microenvironments
Difference in the type and quantity of resources and the physiochemical conditions of a habitat define the niche for each microbe
For each organism there exists at least one niche in which that organism is most successful (prime niche)
Microenvironment
The immediate environmental surroundings of a microbial cell or group of cells

Environments and Microenvironments
Physiochemical conditions in a microenvironment are subject to rapid change, both spatially and temporally
Resources in natural environments are highly variable and many microbes in nature face a feast-or-famine existence
Growth rates of microbes in nature are usually well below maximum growth rates defined in the laboratory
Competition and cooperation occur between microbes in natural systems
Biofilms: Microbial Growth on Surfaces

Surfaces are important microbial habitats because
Nutrients adsorb to surfaces
Microbial cells can attach to surfaces

Biofilms: Microbial Growth on Surfaces
Biofilms
Assemblages of bacterial cells adhered to a surface and enclosed in an adhesive matrix excreted by the cells
The matrix is typically a mixture of polysaccharides
Biofilms trap nutrients for microbial growth and help prevent detachment of cells in flowing systems

Biofilms: Microbial Growth on Surfaces

Biofilm formation is initiated by attachment of a cell to a surface followed by expression of biofilm-specific genes

Genes encode proteins that synthesize intercellular signaling molecules and initiate matrix formation

Biofilms: Microbial Growth on Surfaces
Intracellular communication (quorum sensing) is critical in the development and maintenance of a biofilm
The major intracellular signaling molecules are acylated homoserine lactones
Both intra- and interspecies signaling likely occurs in biofilms

Biofilms: Advantages and Control
Bacteria form biofilms for several reasons
Self-defense
Biofilms resist physical forces that sweep away unattached cells, phagocytosis by immune system cells, and penetration of toxins (e.g., antibiotics)
Allows cells to remain in a favorable niche
Allows bacterial cells to live in close association with one another

Biofilms: Advantages and Control
Biofilms are important in human health and commerce
Biofilms have been implicated in several medical and dental conditions
Including periodontal disease, kidney stones, tuberculosis, Legionnaire’s disease, and Staphylococcus infections
In industrial settings, biofilms can slow the flow of liquids through pipelines and can accelerate corrosion of inert surfaces
Few highly effective antibiofilm agents are available
Freshwater Environments
Freshwater environments are highly variable in the resources and conditions available for microbial growth

The balance between photosynthesis and respiration controls the oxygen and carbon cycles

Phytoplankton: oxygenic phototrophs suspended freely in water; include algae and cyanobacteria

Benthic species are attached to the bottom or sides of a lake or stream
Freshwater Environments
The activity of heterotrophic microbes in aquatic systems is highly dependent upon activity of primary producers; oxygenic phototrophs produce organic material and oxygen

Oxygen has limited solubility in water; once consumed in freshwater lakes the deep layers can become anoxic

Oxygen concentrations in aquatic systems is dependent on the amount of organic matter present and the physical mixing of the system
Freshwater Environments

In many temperate lakes the water column becomes stratified during the summer

Freshwater Environments
Rivers
May be well mixed because of rapid water flow
Can still suffer from oxygen deficiencies due to high inputs of
Organic matter from sewage
Agricultural and industrial pollution

Freshwater Environments

Biochemical Oxygen Demand (BOD)
The microbial oxygen-consuming capacity of a body of water

Terrestrial Environments
Soil
The loose outer material of Earth’s surface
Distinct from bedrock
Soil can be divided into two broad groups
Mineral soils
Derived from rock weathering and other inorganic materials
Organic soils
Derived from sedimentation in bogs and marshes

Terrestrial Environments
Soils are composed of
Inorganic mineral matter (~40% of soil volume)
Organic matter (~5%)
Air and water (~50%)
Living organisms

Terrestrial Environments
Most microbial growth takes place on the surfaces of soil particles

Soil aggregates can contain many different microenvironments supporting the growth of several types of microbes





Terrestrial Environments

The availability of water is the most important factor in influencing microbial activity in surface soils
Nutrient availability is the most important factor in subsurface environments

Plants as Microbial Habitats
Rhizosphere
The region immediately outside the root
Zone where microbial activity is usually high
Phyllosphere
The surface of plant leaf
Microbial communities form in both the rhizosphere and phyllosphere of plants

Open Oceans
Compared with most freshwater environ-ments, the open ocean environment is
Saline
Low nutrient; especially with respect to nitrogen, phosphorus, and iron
Cooler
Due to the size of the oceans, the microbial activities taking place in them are major factors in the Earth’s carbon balance
Open Oceans

Nearshore marine waters typically contain higher microbial numbers than the open ocean because of higher nutrient levels

Open Oceans
Most of the primary productivity in the open oceans is due to photosynthesis by prochlorophyte
Prochlorococcus accounts for
> 40% of the biomass of marine phototrophs
~50% of the net primary production

Open Oceans

The planktonic filamentous cyanobacterium Trichodesmium is an abundant phototroph in tropical and subtropical oceans
Small phototrophic eukaryotes, such as Ostreococcus, inhabit coastal and marine waters and are likely important primary producers

Open Oceans
Small planktonic heterotrophic prokaryotes are abundant (105–106 cells/ml) in pelagic marine waters

The most abundant marine heterotroph is Pelagibacter, an oligotroph

Oligotroph: an organism that grows best at very low nutrient concentrations

Open Oceans
Pelagibacter and other marine heterotrophs contain proteorhodopsin, a form of rhodopsin that allows cells to use light energy to drive ATP synthesis
Aerobic anoxygenic phototrophs
Another class of marine microbes that use light energy but do not fix carbon dioxide
Light is used for ATP synthesis via photophosphorylation

Open Oceans
Prokaryote densities in the open ocean decrease with depth
Surface waters contain ~106 cells/ml; below 1,000 m cell numbers drop to 103–105/ml
Bacterial species tend to dominate in surface waters and Archaeal species dominate in deeper waters

Open Oceans
Viruses are the most abundant microorganisms in the oceans (107 virion particles/ml)

Viruses affect prokaryotic populations and are highly diverse

The Deep Sea and Barophilism
> 75% of all ocean water is deep sea, lying primarily between 1000 and 6000 m
Organisms that inhabit the deep sea must deal with
Low temperature
High pressure
Low nutrient levels
Absence of light energy

The Deep Sea and Barophilism

Deep sea microbes are
Psychrophilic (cold-loving) or psychrotolerant
Barophilic (pressure-loving) or barotolerant