Chapter 28 - Microbial Ecology

other environmental influences that affect soil microbes include...

acidity, temperature, and nutrient supply - acidity suppresses bacterial growth, allowing fungi to thrive with less competition > this is why mushrooms often appear in lawn fertilized with acid producing fertilizer such as ammonium chloride

community

all of the different organisms in the location

biosphere

all of the ecosystems on Earth

genomics

allows comparisons of species to others

carbon fixation

carbon fixation is funds,mental aspect of carbon cycle - without primary producers, no other organisms could exist - we spend on them to generate the organic carbon compounds we use as an energy source and for biosynthesis

anammox

certain bacteria oxidize ammonium under anaerobic conditions, using nitrite as a terminal electron acceptor - reaction is called anammox (anoxic ammonia oxidation) -> forms N2 and might provide economical means of removing nitrogen compounds during wastewater treatment

food chain

chain of consumption - interacting food chains form a food web

living organisms interact with each other in symbiotic relationships...

commensalism, mutualism, and parasitism

mineralization

complete breakdown of organic molecules into inorganic molecules such as ammonia, sulfates, phosphates, and carbon dioxide

ecosystem

consists of a community of organisms and the non living environment with which they interact - major ecosystems include oceans, rivers and lakes, deserts, marshes, grasslands, forests, and tundra

metagenomics

cultivation independent study of communities or their members by analyzing genetic material taken directly from an environment

ectomycorrhizae

fungi grow around plant cells, forming a sheath around the root - mainly associate with certain trees, including conifers, beeches, and oaks - over 5,000 species of fungi involved

mycorrhizas

fungi growing in symbiotic relationships with plant roots - help plants take up phosphorus and nutrients from the soil, and in turn the fungi gain nutrients from root secretions - estimated that over 85% of vascular plants (plants with specialized water and food conducting tissues) have mycorrhizas

endomycorrhizae

fungi penetrate root cells, growing as coils or tight, ugh like masses within the cells; most common mycorrhizal relationship - about 100 species of fungi involved, and most appear to be obligate symbionts, as do some plants

oligotrophic

(nutrient poor) waters limit growth of autotrophs due to lack of inorganic nutrients - especially phosphate, nitrate, and iron

eutrophic

(nutrient rich) waters encourage growth of autotrophs, which produce organic compounds that foster growth of heterotrophs in lower layers - heterotrophs consume dissolved O2, which can deplete and leave water hypoxic, leading to death of aquatic animals

the texture of the soil influences...

how much air and water can flow through it - finely textured soils (clay soils) are more likely to become waterlogged and anaerobic - sandy soils dry quickly and are generally aerobic

sulfur oxidation

hydrogen sulfide (H2S) and elemental sulfur (S0) can serve as energy source for certain chemolithotrophs - Beggiatoa, Thiothrix, and Thiobacillus oxidize molecules to sulfate (SO4^2-) - anaerobic marine prokaryotes, Thioploca and Thiomargarita namibiensis, use energy source and terminal electron acceptor found in two different environments - photosynthetic green and purple sulfur bacteria anaerobically oxidize to produce sulfate

nutrient acquisition

organisms are categorized according to their trophic level (source of food), which is intimately related to the cycling of nutrients - three general trophic levels: primary producers, consumers, and decomposers

population

organisms of the same type in a given location

less than 1% of microorganisms...

have been successfully grown in culture - even if all microorganisms could be cultivated in the laboratory, their behavior might not accurately reflect their role in the environment > grown in pure cultures under controlled conditions > in nature, organisms grow as members of mixed communities under often changing conditions > nutrients usually in short supply

microbial mat

thick, dense, highly organized structure composed of distinct layers - colors frequently correspond with microbial groups: > photosynthetic cyanobacteria (green) > anoxygenic phototrophic purple sulfur bacteria (pink) > obligate anaerobic sulfate reducers (black) - microbial mats found in many locations, but those in hot springs near Yellowstone National Park are extensively studied

we depend on microbes to...

- cycle nutrients - maintain fertile soil - decompose wastes and other pollutants

algae and protozoa also found in most soils

- algae depend on sunlight for energy, so they mostly live on or near the soil surface - most protozoa require O2, so they are found near the soil surface, typically where microbes on which they feed are plentiful

primary producers

- autotrophs that convert CO2 into organic materials > photoautotrophs use sunlight for energy > chemolithoautotrophs oxidize inorganic chemicals for energy - primary producers serve as food source for consumers and decomposers

biochemical cycling and energy flow

- biochemical cycles are paths that elements take as they flow through (biotic) and non living (abiotic) components of ecosystems - important in recycling because a limited amount of elements that make up living cells exists on the Earth and in the atmosphere > carbon and nitrogen cycles particularly important because they involve stable gaseous forms (carbon dioxide and nitrogen gas), which enter the atmosphere and thus have global impacts - elements continually cycle, but energy does not > energy must be continually added to ecosystem to fuel life - human activities have major impact > example: industrial processes that convert N2 (nitrogen gas) into ammonia containing fertilizers have increased food production, but also alters the nitrogen cycle by increasing the amount of nitrogen available in organic compounds + leads to pollution of lakes and coastal areas > example: release of CO2 and other carbon containing gases raises global temperatures - elements have three purposes in metabolism: > biosynthesis (biomass production) -> required by all organisms; many different pathways > energy source -> + reduced carbon compounds such as sugars, lipids, and amino acids are used as energy sources by chemoorganotrophs + chemolithotrophs can use reduced inorganic molecules such as hydrogen sulfide (H2S), ammonia (NH3), and hydrogen gas (H2) > terminal electron acceptor -> + in aerobic conditions, O2 is used as terminal electron acceptor in respiration + in anaerobic conditions, some prokaryotes can use nitrate (NO3-), nitrite (NO2-), sulfate (SO4-), or carbon dioxide (CO2) as a terminal electron acceptor

energy sources for ecosystems

- chemotrophs harvest energy trapped in chemical binds to generate ATP > this energy cannot be totally recycled, because a portion is always lost as heat when bonds ar broken > energy continuously lost from biological systems + to compensate, energy must be replaced - photosynthesis converts radiant energy (sunlight) to chemical energy in the form of organic compounds > available for chemoorganotrophs - requirement for radiant energy traditionally explained why life not equally abundant everywhere > discovery of different types of communities far removed from sunlight, including near hydrothermal vents and within rocks, has dramatically altered this idea > these communities rely on chemolithoautotrophs, which harvest the energy of reduced inorganic compounds and use it to form organic compounds - hydrothermal vents release H2S > bacteria and archaea oxidize H2S, and use energy to fix CO2. providing the animals with both a carbon and energy source - microbial populations have been found 1-3 km underground > these organisms gain energy from H2 9hydrogen) produced in the subsurface > could be as much as 2 * 10^14 tons of underground microbes (equivalent to 1.5 meters thick over the entire land surface of the earth (highly speculative))

microbes in low nutrient environments

- common in nature, includes lakes, rivers, and streams, so microorganisms that can grow in dilute aqueous solutions are widespread > most microbial growth in these settings is in biofilms, and the cells are shed from the biofilm into the aqueous solution - microbes can even grow in distilled water reservoirs, such as in research laboratories and pulmonary mist therapy units in hospitals > the microbes extract the trace amounts of nutrients absorbed by the water from the air or collected on the surface of the biofilm > growth is slow but can reach concentrations as high as 10^7 per milliliter; not high enough to result in cloudy solution, so goes unnoticed > can have serious health consequences and can impact success of laboratory experiments that depend on water purity - organisms that grow in dilute environments contain highly efficient transport systems for moving nutrients inside the cell

characteristics of soil

- composed of pulverized rock, decaying organic material, air, and water - teems with life, including bacteria, fungi, algae, protozoa, worms, insects, and plant roots - soil communities may contain more than 4,000 different species per gram of soil - top 6 inches of fertile soil may harbor more than 2 tons of bacteria and fungi per acre - soil environment can fluctuate abruptly and dramatically > heavy rains can cause soil to rapidly become waterlogged > trees dropping dropping leaves can suddenly enrich the soil with organic nutrients > farmers and gardeners change the nutrient mix by adding fertilizers

the rhizosphere

- concentration of microbes, especially Gram- bacteria, generally much greater in the rhizosphere (the zone of soil that adheres to plant roots) than in surrounding soil > this is because the root cells secrete organic molecules, enriching the region > particular bacterial species appear to preferentially interact with certain plants + example: rhizosphere of certain grasses can have high concentrations of Azospirillum species, which fix nitrogen

seawater...

- contains ~3.5% salt vs. ~0.05 in freshwater > seawater supports growth of halophilic organisms > temperatures vary widely at the surface, but generally decrease with depth to about 2 degrees C in deeper waters - ocean waters are typically oligotrophic, limiting the growth of microorganisms > the limited organic material produced by photosynthetic organisms is quickly consumed as it descends, so few nutrients reach sediments below > even in the deep sea, marine water O2-saturated due to mixing with tides, currents, and wind action

microorganisms in soil

- density and composition of soil microbiota dramatically affected by environmental conditions - wet soils unfavorable for aerobic microbes because the spaces in soil fill with water, diminishing the amount of air in the soil - when water content of soil drops to low levels (drought or in desert), metabolic activities may decrease > many species produce survival forms (endospores and cysts) resistant to drying

microorganisms and environmental changes

- environmental changes often alter communities > organisms adapted to live in one environment likely not well suited to a different one > external sources of environment can change > growth and metabolism of organisms can also alter the environment dramatically + nutrients may become depleted and waste products accumulate - changing conditions can bring about succession of bacterial species > example: succession in raw milk

consumers

- heterotrophs (use organic carbon for growth/relies on activities of autotrophs) that eat primary producers or other consumers > herbivores, which eat plants or algae, are primary consumers > carnivores that eat herbivores are secondary consumers; those that eat other carnivores are tertiary consumers

decomposers

- heterotrophs that digest the waste products and remains of primary producers and consumers > fresh or partially decomposed organic matter (including carcasses, excreta, plant litter) is detritus - specialize in digesting complex materials such as cellulose, converting them into small molecules that can more easily be used by other organisms - microorganisms, especially bacteria and fungi, play a major role in decomposition due to ubiquity and unique metabolic capabilities

terrestrial habitats

- human interest in soil microbiology stems partly from useful chemicals synthesized by microbes > example: over 500 different antibiotic substances produced by species of Streptomyces + >50 of which have applications in medicine, agriculture, and industry + pharmaceutical industry has tested many thousands of soil microorganisms looking for useful antibiotics + soil microbes are being investigated for ability to degrade toxic chemicals (bioremediation) + soil probably has greatest range of biosynthetic and biodegradative capabilities

methanogenesis and methane oxidation

- in aerobic environments, CO2 is used by methanogens > these archaea obtain energy by oxidizing hydrogen gas, using CO2 as terminal electron acceptor, and generating methane (CH4) - methane that enters the atmosphere is oxidized by ultraviolet light and chemical ions, forming carbon monoxide (CO) and CO2 - microorganisms called methylotrophs can use methane as an energy source, oxidizing it to produce CO2

specialized aquatic environments

- include salt lakes such as the Great Salt Lake in Utah, which have no outlets > as water evaporates, salt concentrations become much higher than that of seawater + extreme halophiles thrive in this environment - other specialized habitats include iron springs that contain large quantities of ferrous ions > habitats for species of Gallionella and Sphaerotilus - sulfur springs support growth of both photosynthetic and non photosynthetic sulfur bacteria - other aquatic environments include groundwater, stagnant ponds, swimming pools, and drainage ditches > each offering its own opportunity for microbial growth

aquatic environments

- marine environments such as the oceans cover >70% of Earth's surface > most abundant aquatic habitat, representing ~95% of global water > freshwater environments (lakes and rivers) represent only a small fraction of total water - deep lakes and oceans have characteristic zones that influence the distribution of microbial populations > uppermost layer (where sufficient light penetrates) supports growth of photosynthetic microorganisms, including algae and cyanobacteria + organic material synthesized by these primary producers gradually descends and is metabolized by heterotrophs - number of microbes in waters is influenced by the nutrient content > oligotrophic and eutrophic

rhizobia

- members of diverse group of genera, including Rhizobium, Bradyrhizobium, Sinorhizobium, and Azorhizobium -> collectively referred to as rhizobia > most agriculturally important symbiotic nitrogen fixers > grow within nodules on roots of legumes (plants that bear seeds in pods) including alfalfa, clover, peas, beans, and peanuts > their input of soil nitrogen may be ~10 times the annual rate of nitrogen fixation by non symbiotic organisms > to foster plant growth, farmers often add appropriate symbionts to seed of certain legumes - plant cells foster the nitrogen fixation by synthesizing a protein called leghemoglobin, which binds to O2, protecting the O2 sensitive nitrogenase > the plant also provides various nutrients to the endosymbionts > meanwhile, the endosymbionts provide fixed nitrogen to the plant - nodule formation involves extensive chemical communication between rhizobia and legume partners > plant root secretions attract appropriate rhizobial species, which then colonizes the roots - relationship between plant and bacterium not obligate, but offers competitive advantages to both partners > the rhizobia compete poorly in soils lacking legumes, and legumes compete poorly in heavily fertilized soils

microorganisms and herbivores

- microbes inhabit specialized digestive compartment and digest cellulose and hemicellulose - in ruminants such as cattle, sheep, and deer, the digestive compartment is called a rumen > precedes the true stomach; over 200 species inhabit > functions as anaerobic fermentation vessel > microbes have first chance to use ingested nutrients > digested materials are degraded into sugars, which are fermented to produce organic acids > animal uses metabolic end products and microbial cells - in non ruminants such as horses and rabbits, the digestive compartment is called a cecum > lies between small and large intestines > microbes not used as food source since after stomach > animal can digest and absorb available nutrients without competition from microbes

sulfur assimilation and decomposition

- most plants and microbes assimilate sulfur as sulfate (SO4^2-), reducing it to form biomass - decomposition releases hydrogen sulfide (H2S), a gas

respiration and fermentation

- organic material consumed by heterotrophs for energy source and biosynthesis > CO2 produced - rapidly multiplying bacteria often play dominant role in degrading sugars, amino acids, and proteins - in contrast, only certain fungi degrade lignin > aerobic conditions required for this degradation, so wood at bottom or marshes resists decay - O2 supply strongly affects carbon cycle > allows degradation of certain compounds, and helps determine the types of carbon containing gases produced

microbial competition

- perhaps nowhere in the living world is competition more quickly evident than among microorganisms > ability to compete successfully for a habitat is related to rate of multiplication, and its ability to withstand adverse environmental conditions > because of logarithmic growth, any small differences in generation times will result in a very large difference in the total number of cells of each species after a relatively short time - antagonistic strategies also helps determine community makeup > some microbes resort to chemical warfare and produce antimicrobial compounds > bacteriocins, proteins produced by bacteria that kill closely related strains, are an example of antagonistic chemicals

phosphorus cycle and other cycles

- phosphorus is component of nucleic acids, phospholipids, and ATP - most plants and microbes take up phosphorus as orthophosphate (PO4^3-) - algae and cyanobacteria (primary producers) limited in many aquatic environments by low concentrations of phosphorus > addition of phosphates from other sources such as agricultural runoff, phosphate containing detergents, and wastewater, can result in eutrophication - other important elements including iron, calcium, zinc, manganese, cobalt, and mercury also recycled by microorganisms > many prokaryotes have plasmids coding for enzymes that carry out oxidation of metallic ions

nitrogen fixation

- process in which N2 (nitrogen gas) is reduced to form ammonia (NH3), which can then be incorporated into cellular material > the process, catalyzed by enzyme complex nitrogenase, requires a tremendous amount of energy since N2 has very stable triple covalent bond - atmosphere consists of ~80% nitrogen gas > relatively few organisms can fix nitrogen - some nitrogen fixing prokaryotes, diazotrophs, are free living, whereas others form symbiotic associations with higher organisms, particularly certain plants such as members of Azotobacter > heterotrophic, aerobic, Gram- rods may be main suppliers of fixed nitrogen in ecosystems such as grasslands that lack plants with nitrogen fixing symbionts > dominant free living, anaerobic, soil diazotrophs are members of genus Clostridium > certain cyanobacteria are diazotrophs; use both nitrogen and carbon from atmosphere

denitrification

- process that reduces nitrate (NO3-), converting it to gaseous forms such as nitrous oxide (N2O) and molecular nitrogen (N2) > happens when prokaryotes anaerobically respire, using nitrate as terminal electron acceptor - denitrification can have negative environmental and economic impacts: > under anaerobic conditions in wet soils, denitrifying bacteria will reduce the oxidized nitrogen compounds of fertilizers, releasing gaseous nitrogen into the atmosphere > in some areas, this process may represent 80% of nitrogen lost from fertilized soils > nitrous oxide contributes to global warming - can be useful in wastewater treatment as a means to remove nitrate

other nitrogen fixing symbionts

- several genera of non leguminous trees, including alder and gingko, have nitrogen fixing root nodules at some stages of their life cycle > the bacteria involved are members of genus Frankia - in aquatic environments, cyanobacteria are most significant nitrogen fixers > especially important in flooded soils such as rice paddies + rice has been cultivated for centuries without the addition of nitrogen containing fertilizer + cyanobacterium Anabaena azollae grow in specialized same of aquatic fern Azolla + farmer allows the flooded rice paddy to overgrow with Azolla ferns; then, as rice grows, it crowds out the ferns, which die and release their nitrogen into the water

freshwater environments

- types and numbers of microbes inhabiting freshwater depend on multiple factors including light, concentration of dissolved O2 and nutrients, and temperature - oligotrophic lakes in temperate climates may have anaerobic layers due to thermal stratification resulting from seasonal temperature changes > surface water warmed in summer months, which forms a layer that does not mix with the cooler, denser water below + upper layer, called epilimnion, is usually O2 rich + lower layer, called hypolimnion, may be anaerobic + separating these two layers is the thermocline, a zone of rapid temperature change + as weather cools, water mixes, providing O2 to the deep water - rapidly moving waters, such as rivers and stream, generally aerobic due to mixing of O2

sulfur reduction

- under anaerobic conditions, sulfate generated by the sulfur oxidizers can then be used as a terminal electron acceptor by certain organisms - the sulfur and sulfate reducing bacteria and archaea use sulfate in the process of anaerobic respiration, reducing it to hydrogen sulfide (H2S) > results in unpleasant odor and reaction with metals, causing corrosion

soil forms as rock weathers...

- water, temperature changes, windblown particles, and other physical forces gradually cause rock to crack and break - photosynthetic organisms including algae, mosses, and lichens growing on the surfaces of rocks synthesize organic compounds - bacteria and fungi use these compounds as carbon and energy sources, producing acids and other chemicals that gradually decompose the rocks - as soil slowly forms, some plants begin to grow - when these die and decay, the residual organic material functions as a sponge, retaining water and thus allowing more plants to grow - over time, organic material accumulates, forming a slowly degrading complex polymeric substance called humus

ammonification

decomposition process that converts organic nitrogen into ammonia (NH3) - in alkaline environments, gaseous ammonia may enter the atmosphere > in neutral environments, ammonium (NH4+) is formed > this positively charged ion adheres to negatively charged particles - wide variety of microbes degrade proteins, which are among the most common nitrogen containing compounds > the microbes secrete proteolytic enzymes to break proteins into short peptides or amino acids > products are then transported into the cell of the decomposer > amino groups are removed, releasing ammonium

inshore areas...

ecology is not as stable as the deep sea and can be dramatically affected by nutrient rich runoff - example: dead zone, a region devoid of fish and other marine life that forms in the Gulf of Mexico > Mississippi River carries nutrients accumulated from agricultural, industrial, and urbanized regions into the Gulf > as a consequence, populations of algae and cyanobacteria flourish in spring and summer > heterotrophs metabolize the organic compounds, consuming dissolved O2, turning a region in the Gulf hypoxic

within the biosphere...

ecosystems vary both in biodiversity (number and variety of species present and their evenness of distribution) and biomass (weight of all organisms present) - microorganisms play a major role in most ecosystems, and many ecosystems host microbes unique to themselves - the role an organism plays in a particular ecosystem is its ecological niche

microbial communities

microorganisms most often grow as biofilms attached to solid surfaces or at air-water interfaces

studying microbial ecology

molecular techniques useful in studying - dyes made fluorescent by metabolic activities carried out only by living cells used to observe viable cells - fluorescence in situ hybridization (FISH) uses fluorescently labeled nucleic acid probes to determine if a specific species or group is present in a sample - scanning laser microscopes allow observation of sections of three dimensional specimens such as biofilms - PCR reactions can detect individual organisms, or assess population characteristics via total 16s rRNA amplification > can separate via denaturing gradient gel electrophoresis (DGGE) to resolve differences; individual fragments can also be cloned and studied

macroenvironment

more easily measured gross environment, but may be very different from the microenvironment - consider bacterial cells living within a biofilm: > growth of aerobic organisms can deplete O2, creating tiny zones where obligate anaerobes can grow > fermenters can produce organic acids that may then be metabolized by other organisms > in addition, various growth factors can be transferred between organisms > thus, microbes that might be unexpected in a macroenvironment might thrive there within specialized microenvironments

nitrogen cycle

nitrogen is a component of proteins and nucleic acids

nitrification

process that oxidizes ammonium (NH4+) to nitrate (NO3-) - group of obligate aerobic bacteria known as nitrifiers accomplish this in a cooperative two step process > use ammonium and nitrite (NO2-) as energy sources > nitrification does not occur in anaerobic environments - nitrification has important consequences with respect to agriculture and pollution: > farmers often apply ammonium containing compounds as fertilizers; positive charge adheres to negatively charged soil particles > nitrification converts the ammonium to nitrate, a form of nitrogen more readily used by plants, but leached from soil by rainwater, which contaminates water > nitrite is toxic because it can combine with hemoglobin of blood, reducing bloods O2 carrying capacity

without microorganisms, we would...

quickly become buried by the tons of wastes we generate, and nutrients would be depleted, halting growth and reproduction

marine environments

ranges from deep sea, where nutrients are scarce, to the shallower coastal regions, where nutrients may be abundant due to runoff from the land

prokaryotes are most numerous...

soil inhabitants - physiological diversity allows colonization of all soil types - Gram+ bacteria generally more abundant in soils than Gram- bacteria > among most common Gram+ bacteria are Bacillus, which form endospores that allow survival during adversity > Streptomyces species produce desiccation resistant conidia, metabolites called geosmins, and antibiotics > others include myxobacteria and species of Clostridium, Azotobacter, Agrobacterium, and Rhizobium

ecology

study of interactions of organisms with one another and with their physical environment

sulfur cycle

sulfur found in all living matter, mainly in amino acids methionine and cysteine - key steps of sulfur cycle depend on activities of prokaryotes

symbiotic nitrogen fixers and plants

symbiotic nitrogen fixing organisms are far more significant in benefiting plant growth and crop production than free living nitrogen fixers

although prokaryotes are the most numerous soil microbes...

the biomass of fungi is much greater - most are aerobes, so they usually grow in the top 10 cm of soil - they degrade complex macromolecules including lignin (major component of cell walls of woody plants) and cellulose - some are free living and others live symbiotically > mycorrhizae are fungi growing in a symbiotic relationship with plant roots

carbon cycle

the carbon travels through the food chain as primary producers are eaten by primary consumers, which are then eaten by secondary consumers - decomposers then use organic molecules in the remains of primary producers and consumers

microenvironment

the environment immediately surrounding an individual microbe is most relevant to that cell, but because microorganisms are so small, the microenvironment is difficult to identify and measure