Symbiosis is an association of two or more different species
Interactions of organisms with each other and with their physical environment
contribute to the functioning of ecosystems
Populations-assemblages of similar organisms within an ecosystem
Communities-mixtures of different populations within an ecosystem
Ecosystems-self-regulating biological communities and their physical
environment
A major problem in understanding microbial ecology is that most microscopically
observable microorganisms cannot be cultured in the lab; however, recent
advances in molecular techniques are providing information on the still
uncultured microorganisms in ecosystems
Microbial Interactions
Microorganisms can be physically associated with other organisms in a
number of ways
Ectosymbiosis-microorganism remains outside the other organism
Endosymbiosis-microorganism is found within the other organism
Ecto/endosymbiosis-microorganism lives both on the inside and the
outside of the other organism
Physical associations can be intermittent and cyclic or permanent
Mutualism
An obligatory association that provides some reciprocal benefit to
both partners (some examples are given below)
Protozoan-termite relationship-protozoa live in the guts of insects
that ingest but cannot metabolize cellulose; the protozoa secrete cellulases,
which metabolize cellulose, releasing nutrients that the insects can
use
Lichens-an association between a fungus (ascomycetes) and an alga
(green algae) or cyanobacterium
Fungal partner (mycobiont) obtains nutrients from alga by hyphal
projections (haustoria) that penetrate the algal cell wall as well
as oxygen for respiration
Algal partner (phycobiont) is protected from excess light intensity
and is provided with water, minerals, and a firm substratum in which
it can grow protected from environmental stress
Zooxanthellae-algae harbored by marine invertebrates; reef-building
(hermatypic) corals use zooxanthellae to satisfy most of their energy
needs; the coral pigments protect the algae from ultraviolet radiation
Tube worm-bacterial relationships occur in hydrothermal vent
communities where vent fluids are anoxic, have high concentrations
of hydrogen sulfide, and can reach temperatures of 350°C
Endosymbiotic chemolithotrophic bacteria provide the main energy
source in the community through the oxidation of hydrogen sulfide
The endosymbiotic bacteria are maintained in specialized cells
(trophosome) of the tube worm
The tube worm binds hydrogen sulfide to hemoglobin and transports
it to the bacteria; the bacteria use the energy from hydrogen sulfide
oxidation to synthesize reduced organic material that is supplied
to the tube worm
Methane-based mutualisms-methanotrophs are intracellular symbionts
of methane-vent mussels and sponges, which use the bacteria to support
their nutritional needs
Microorganism-insect mutualisms-bacterial endosymbionts provide essential
vitamins and amino acids to host insects; insect provides a secure physical
habitat and ample nutrients to the bacteria
The rumen ecosystem-bacteria in the rumen anaerobically metabolize
cellulose to smaller molecules that can be digested by the ruminant;
microorganisms produce the majority of vitamins that are needed by the
ruminant; methane is also produced in the process
Syntrophism-a mutually beneficial relationship in which each organism
provides one or more growth factors, nutrients, or substrates for the
other organism; also referred to as cross-feeding or the satellite phenomenon;
an important example is interspecies hydrogen transfer, which occurs
in anaerobic environments (described below)
Fermentative bacteria produce low molecular weight fatty acids
Anaerobes such as Syntrophobacter degrade fatty acids, producing
hydrogen gas; however, in order for this to provide sufficient energy
for Syntrophobacter, the hydrogen produced must be consumed
Methanogens consume the hydrogen gas during methanogenesis; this
promotes further production of fatty acids and hydrogen gas
Protocooperation-a mutually beneficial relationship that is not obligatory
(some examples are given below)
Degradation of 3-chlorobenzoate by three different microorganisms
Linkage of the carbon cycle and the sulfur cycle by the relationship
of sulfide-oxidizing autotrophic bacteria and heterotrophic organisms
Growth of sulfide-oxidizing bacteria on surface of nematodes; nematodes
live at interface of aerobic and anaerobic sulfide-containing sediments,
thus providing an appropriate habitat for the bacterial symbionts; bacteria
decrease the levels of toxic sulfides and serve as food supply for host
Hydrothermal vent communities and cave communities where sulfur-oxidizing
bacteria serve as food source for sponges, gastropods, and other organisms
Quorum sensing allows microorganisms to communicate as they form
associations with plants and animals
Commensalism
The microorganism (commensal) benefits, while the host is neither
harmed nor helped; often the microorganism shares the same food source
with the host
Occurs in situations in which waste products of one microorganism
serves as the substrate for another; also occurs in situations where
one microorganism modifies the environment making it better suited for
another microorganism (some examples are given below)
Nitrification-requires the activity of two different species;
one oxidizes ammonia to nitrite and the other oxidizes nitrite to
nitrate
The common nonpathogenic strain of Escherichia coli lives in
the human colon; this facultative anaerobe uses oxygen creating
an anaerobic environment in which obligate anaerobes (e.g., Bacteroides)
can grow;
coli derives no obvious benefit or harm
Succession of microorganisms in an environment-during milk spoilage
synthesis of acidic fermentation products by one population stimulates
proliferation of acid-tolerant microorganisms; during biofilm formation,
the first colonizer makes it possible for others to colonize
Colonization of surfaces of plants and animals by normal flora-plant
or animal produces organic substances, which are used by the normal
flora of the host organism
Predation
Predator organism engulfs or attacks a prey organism; prey can be
larger or smaller than predator; normally results in death of prey
Predatory bacteria are known (e.g., Bdellovibrio, Vampirococcus,
and Daptobacter); may cause lysis of prey, release of cell contents
while attached to surface of prey, or penetrate cytoplasm of prey
Ciliates are important microbial predators in aquatic environments
and in wastewater treatment facilities
Positive outcomes of predation
Microbial loop-microbial predators mineralize the organic matter
produced by autotrophs (primary producers) before it reaches the
higher consumers; this returns nutrients to the primary producers
and promotes their activity
Ingestion of prey provides protective environment for the prey
Predatory fungi are known (e.g., fungi that trap nematodes)
Parasitism
One organism (parasite) benefits from another (host); there is a
degree of coexistence between the host and parasite that can shift to
a pathogenic relationship (a type of predation)
Examples:
Parasitic fungi and an algal host
Biocontrol-use of one microorganism to control activity of another
Human diseases (discussed in chapters 38 through 40)
Ammensalism-organism releases a specific compound that harms another
organism
Antibiotics
Bacteriocins
Antibacterial peptides (e.g., cecropins and defensins produced by
insects and mammals, respectively)
Acidic fermentation products
Competition
Different organisms within a population or community try to acquire
the same resources (e.g., nutrients, location, etc)
Competitive exclusion principle-if two populations overlap too much
in terms of their resource use, then one of the populations is excluded
Symbioses in complex systems-interactions between two populations lead
to the occurrence of feedback responses in the larger biotic community;
these feedback responses impact all other parts of the ecosystem and lead
to equilibrium of all populations within the community
Nutrient Cycling Interactions
Biogeochemical cycling (nutrient cycling) involves both biological and
chemical processes; oxidation-reduction reactions change the chemical and
physical properties of the nutrient
Carbon cycle
Carbon can be interconverted between methane, complex organic matter,
carbon monoxide, and carbon dioxide
Methane is produced by methanogens; carbon fixation can occur by
the activities of cyanobacteria, the green algae, photosynthetic bacteria,
and chemolithoautotrophs
Degradation of organic matter
Organic matter varies in terms of elemental composition, structure
of basic repeating units, linkages between repeating units, and
physical and chemical characteristics
Degradation of organic matter is influenced by nutrients present
in the environment, abiotic conditions (pH, oxidation-reduction
potential, O2, osmotic conditions), and the microbial
community present
Microbial degradation of complex organic material occurs when
microbes use these molecules for growth
Chitin, protein, microbial biomass, and nucleic acids contain
large amounts of nitrogen; the excess nitrogen is released by
a process called mineralization
Molecules containing only hydrogen, carbon, and oxygen cannot
support the growth of microbes; microbes acquire the other nutrients
they need for biomass synthesis in a process called immobilization
Most organic substrates can be degraded in the presence or absence
of oxygen; however, hydrocarbons and lignin degradation usually
occurs aerobically
Hydrocarbon degradation usually requires oxygen because the
first step involves addition of molecular oxygen to the molecule;
recently however, slow anaerobic digestion in the presence of
sulfate or nitrate has been observed
Filamentous fungi are major lignin degraders and they require
oxygen; the need for oxygen has practical implications-wood
pilings can be used below the water table where anaerobic conditions
are maintained; however, if the water table drops, degradation
can take place, thereby weakening the structure
Presence or absence of oxygen affects the final products that
accumulate when organic substances are degraded
Aerobic conditions-oxidized products are made (e.g., nitrate,
sulfate)
Anaerobic conditions-reduced end products are formed
If end products remain in the environment in which they were
formed, they can only serve as sources of nutrients; if they
are moved to other environments, then they can be involved in
further energy-yielding reactions
Sulfur cycle-sulfur can be interconverted between elemental sulfur, sulfide,
and sulfate forms by the actions of various microorganisms
Dissimilatory sulfate reduction produces sulfide, which accumulates
in the environment
Assimilatory sulfate reduction results in the reduction of sulfate
for use in amino acid biosynthesis
Nitrogen cycle
Nitrification-aerobic oxidation of ammonium ion to nitrite and ultimately
to nitrate
Denitrification-reduction of nitrate to nitrite, nitrous oxide, and
gaseous molecular nitrogen
Nitrogen assimilation-utilization of inorganic nitrogen and its incorporation
into new microbial biomass
Nitrogen fixation
A series of sequential reduction steps to convert gaseous nitrogen
to ammonia
Requires an expenditure of energy
Can be carried out by aerobes or anaerobes; the actual reduction
process must be done anaerobically, even by aerobic microorganisms
Physical barriers, O2-scavenging molecules, and high
rates of metabolic activity are used to maintain the anaerobic conditions
required for nitrogen fixation
Anoxic ammonia oxidation (anammox)-oxidation of ammonia is coupled
with the reduction of nitrite to nitrogen gas
Iron Cycle-iron can be interconverted between ferric iron, ferrous iron,
and magnetite
Iron oxidation from ferrous iron to ferric iron is carried out by
a number of genera under aerobic conditions; some microorganisms can
carry out the process under anaerobic conditions using nitrate as the
electron acceptor
Iron reduction from ferric iron to ferrous iron occurs under anaerobic
conditions and is carried out by bacteria that use ferric iron as a
final electron acceptor
Magneto-aerotactic bacteria reduce iron to magnetite, which is used
to construct intracellular magnetic compasses; these bacteria use magnetic
fields to migrate to a position in a bog or swamp where the oxygen level
is optimal for their functioning
Manganese cycle-transformation of manganous ion to MnO2; occurs
in hydrothermal vents and bogs
Other cycles and cycle links
The reduction of a wide variety of metals can decrease toxicity of
these metals
Microbial transformations of phosphorous primarily involve transformation
of phosphorous (+5 valence) to other forms, including polyphosphates
Many cycles are linked by using commonly shared oxidants and reductants
Microorganisms and metal toxicity-metals have varied toxic effects on
microorganisms and homeothermic animals; microorganisms modify this toxicity
Noble metals (silver, gold, platinum, etc.)-cannot cross the blood-brain
barrier of vertebrates, but have distinct effects on microorganisms
Metals and metalloids that can be methylated (e.g., mercury, arsenic,
lead, selenium, and tin)-methylation enables them to cross the blood-brain
barrier and affect the central nervous system of higher organisms; also
affect microorganisms; methylated mercury can be concentrated in the
food chain (a process known as biomagnification)
Metals that occur in ionic forms (copper, zinc, cobalt, etc.) can
be directly toxic to microorganisms and more complex organisms; often
required as trace elements, but excess is toxic
The Physical Environment
The microenvironment and niche
Microenvironment-specific physical location of a microorganism
The fluxes and gradients of oxidants, reductants, nutrients, and
waste products create a unique niche (the microorganism, the physical
habitat, the time of resource use, and resources available for growth
and function)
Biofilms and microbial mats
Biofilms-organized microbial systems consisting of layers of microbial
cells associated with surfaces
Biofilms can be observed using confocal scanning laser microscopy
Biofilms on living surfaces usually play a role in causing disease;
there are numerous advantages to forming biofilms in this situation
The surface releases nutrients
The biofilm provides protection from disinfectants
The biofilm creates a focus for later occurrence of disease
Release of microbial cells or products from the biofilm can affect
the immune system of the host
Microbial mats-large biofilms that have macroscopic dimensions; found
in many freshwater and marine habitats
Microorganisms and ecosystems-organisms function as primary producers,
consumers, and decomposers; microbes usually function in ecosystems in the
following ways:
Function as primary producers-synthesize organic matter through photosynthetic
and chemosynthetic processes
Decompose organic matter, often with the release of inorganic compounds
(mineralization)
Serve as nutrient rich food sources for chemoheterotrophic microorganisms
and animals
Modify substrates and nutrients used in symbiotic growth processes
and interactions, thus contributing to biogeochemical cycling
Change the amounts of materials in soluble and gaseous forms
Produce inhibitory compounds that decrease microbial activity or
limit the survival and functioning of plants and animals
Contribute to the functioning of plants and animals through positive
and negative symbiotic interactions
Microorganism movement between ecosystems
Microorganisms are constantly moving and being moved between ecosystems
by a variety of mechanisms
Fate of microorganisms when moved to another ecosystem is of theoretical
and practical importance (e.g., what happens to an animal endosymbiont
when it is moved to an aquatic environment)
When microorganisms are moved out of their normal environment, they
usually eventually die; the reasons for this are not clear
Stress and ecosystems
Factors such as pH, temperature, pressure, salinity, water availability,
and ionizing radiation can act as stress factors
If one or more of these factors is extremely high or low, it
creates an extreme environment
Extremophiles are organisms that survive in extreme environments
Salinity-favors extreme halophiles
High barometric pressure (e.g., deep sea environments) favor barotolerant,
moderately barophilic, and extremely barophilic bacteria
Acidity-acidophiles maintain a high internal pH relative to the environment
Alkalinity-alkalophiles maintain a low internal pH relative to the
environment
High temperature (up to 113°C) favors thermophiles and extreme thermophiles
Methods Used in Microbial Ecology
Methods in microbial ecology are used to evaluate presence, types, and
activities of microorganisms in ecosystems; measurements must span a range
of time scales and physical dimensions; methods used include:
Microscopic examination
Viable cell counting
Measurement of nutrient cycling
Measurement of organic carbon by biochemical oxygen demand (BOD),
chemical oxygen demand (COD), or total organic carbon (TOC)
A major problem for the microbial ecologist is to identify the microorganisms
in an ecosystem, especially those that are nonculturable; assessment of
microbial community diversity is often done using nucleic acid-based techniques
Nucleic acid probe technology can be used to look for specific organisms
Gel array microchips (genosensors) containing a mixture of probes
can detect small subunit (ssu) rRNA in mixed populations
Recently, techniques for examining single cells in complex microbial
communities have been developed (e.g., optical tweezers and micromanipulation)
A summary of methods and their uses in various environments is given
in Table 28.8 of the textbook
