Bacteriology at UW- Madison
The most significant effect that microbes, especially procaryotes,
have on their
is their underlying ability to recycle the essential elements that make
up cells. The earth is a closed system with limited amounts of certain
elements in forms that are utilized by cells. These element
are generally acted upon first by microbes to assimilate them into
living matter. The total biomass of microbial cells in the biosphere,
metabolic diversity, and their persistence in all habitats that support
life, guarantee that microbes will play crucial roles in the
and recycling of these elements among all forms of life.
The table below lists the major elements that make up a typical procaryotic cell (in this case, E. coli). As expected, over 90 percent of the elemental analysis consists of carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur. These are the elements that become combined to form all the biochemicals and macromolecules that comprise living systems. C, H, O, N, P and S are the constituents of organic material (An organic compound is a chemical that contains a carbon to hydrogen bond. Organic compounds on earth are evidence of life. Organic compounds may be symbolized as CH2O, which is the empirical formula for a sugar such as glucose.) H and O are the constituents of water (H2O), that makes up over 95 percent of the cell composition. Calcium (Ca++), iron (Fe++), magnesium (Mg++) and potassium (K+) are present as inorganic salts in the cytoplasm of cells.
Table 1. Major elements, their sources and functions in cells.
|Element||% of dry weight||Source||Function|
|Carbon||50||organic compounds or CO2||Main constituent of cellular material|
|Oxygen||20||H2O, organic compounds, CO2, and O2||Constituent of cell material and cell water; O2 is electron acceptor in aerobic respiration|
|Nitrogen||14||NH3, NO3, organic compounds, N2||Constituent of amino acids, nucleic acids nucleotides, and coenzymes|
|Hydrogen||8||H2O, organic compounds, H2||Main constituent of organic compounds and cell water|
|Phosphorus||3||inorganic phosphates (PO4)||Constituent of nucleic acids, nucleotides, phospholipids, LPS, teichoic acids|
|Sulfur||1||SO4, H2S, S, organic sulfur compounds||Constituent of cysteine, methionine, glutathione, several coenzymes|
|Potassium||1||Potassium salts||Main cellular inorganic cation and cofactor for certain enzymes|
|Magnesium||0.5||Magnesium salts||Inorganic cellular cation, cofactor for certain enzymatic reactions|
|Calcium||0.5||Calcium salts||Inorganic cellular cation, cofactor for certain enzymes and a component of endospores|
|Iron||0.2||Iron salts||Component of cytochromes and certain nonheme iron-proteins and a cofactor for some enzymatic reactions|
and the Cycles of Elements
Of course, all living organisms play a role in the cycles of elements, but for the most part, it is the procaryotes that play major and sometimes unique roles. Herein, we discuss total microbial contribution to the cycles of the major elements, but major emphasis is placed on procaryotes.
The fungi (molds and yeasts). The molds are aerobic organisms that utilize organic compounds for growth. They play an important role in decomposition or biodegradation of organic matter, particularly in soil. Yeasts can grow anaerobically (without oxygen) through the process of fermentation. They play a role in fermentations in environments high in sugar. The prominent role of fungi in the environment is in the carbon cycle, during the process of decomposition, especially in the soil.
The algae are also an important part of the carbon cycle. They are the predominant photosynthetic organisms in many aquatic environments. The algae are autotrophs, which means they use carbon dioxide (CO2) as a source of carbon for growth. Hence they convert atmospheric CO2 into organic material (i.e., algal cells). Algae also play a role in the oxygen (O2) cycle since their style of photosynthesis, similar to plants, produces O2 in the atmosphere. The cyanobacteria are a group of procaryotic microbes, as prevalent as algae, that have this type of metabolism. Photosynthetic algae and cyanobacteria can be found in most environments where there is moisture and light. They are a major component of marine plankton which the basis of the food chain in the oceans.
Protozoans are heterotrophic organisms that have to catch or trap their own food. Therefore, they have developed elaborate mechanisms for movement and acquiring organic food which they can digest. Their food usually turns out to be bacterial cells, so one might argue that they are ecological predators that keep bacterial populations under control in soil, aquatic environments, intestinal tracts of animals, and many other environments.
The procaryotic bacteria and archaea, as a result of their diversity and unique types of metabolism, are involved in the cycles of virtually all essential elements. In two cases, methanogenesis (conversion of carbon dioxide into methane) and nitrogen fixation (conversion of nitrogen in the atmosphere into biological nitrogen) are unique to procaryotes and earns them their "essential role" in the carbon and nitrogen cycles.
There are other metabolic processes that are unique, or nearly so, in the procaryotes that bear significantly on the cycles of elements. For example, procaryotes called lithotrophs use inorganic compounds like ammonia and hydrogen sulfide as a source of energy, and others called anaerobic respirers use nitrate (NO3) or sulfate (SO4) in the place of oxygen, so they can respire without air. Most of the archaea are lithotrophs that use hydrogen (H2) or hydrogen sulfide (H2S) as a source of energy, while many soil bacteria are anaerobic respirers that can use their efficient respiratory metabolism in the absence of O2.
The basic processes of heterotrophy are spread throughout the bacteria. Most of the bacteria in the soil and water, and in associations with animals and plants, are heterotrophs. Heterotrophy means living off of dead organic matter, usually by some means of respiration (same as animals) or fermentation (same as yeast or lactic acid bacteria). Bacterial heterotrophs in the carbon chain are important in the processes of biodegradation and decomposition under aerobic and anaerobic conditions.
In bacteria, there is a unique type of photosynthesis that does not use H2O or produce O2 which impacts on the carbon and sulfur cycles.
Meanwhile, the cyanobacteria (mentioned above) fix CO2 and produce O2 during photosynthesis, and they make a very large contribution to the carbon and oxygen cycles.
The list of examples of microbial involvement in the cycles of
that make up living systems is endless, and probably every microbe in
web is involved in an intimate and unique way.
The Oxygen Cycle
Basically, O2 is derived from the photolysis of H2O during plant (oxygenic) photosynthesis. Two major groups of microorganisms are involved in this process, the eucaryotic algae, and the procaryotic cyanobacteria (formerly known as "blue-green algae"). The cyanobacteria and algae are the source of much of the O2 in the earth's atmosphere. Of course, plants account for some O2 production as well, but the microbes predominate in marine habitats which cover the majority of the planet.
Since most aerobic organisms need the O2 that results from plant photosynthesis, this establishes a relationship between plant photosynthesis and aerobic respiration, two prominent types of metabolism on earth. Photosynthesis produces O2 needed for aerobic respiration. Respiration produces CO2 needed for autotrophic growth.
CO2 + H2O-----------------> CH2O (organic material) + O2 plant (oxygenic) photosynthesis
CH2O + O2-----------------> CO2 + H2O aerobic respiration
Since these photosynthetic microbes are also autotrophic (meaning
convert CO2 to organic material during growth) they have a
impact on the carbon cycle (below).
The Carbon Cycle
Carbon is the backbone of all organic molecules and is the most prevalent element in cellular (organic) material. In its most oxidized form, CO2, it can be viewed as an "inorganic" molecule (no C - H bond). Autotrophs, which include plants, algae, photosynthetic bacteria, lithotrophs, and methanogens, use CO2 as a sole source of carbon for growth, which reduces the molecule to organic cell material (CH2O). Heterotrophs require organic carbon for growth, and ultimately convert it back to CO2.
Thus, a relationship between autotrophs and heterotrophs is established wherein autotrophs fix carbon needed by heterotrophs, and heterotrophs produce CO2 used by the autotrophs.
CO2 + H2O-----------------> CH2O (organic material) autotrophy
CH2O + O2-----------------> CO2 + H2O heterotrophy
Since CO2 is the most prevalent greenhouse gas in the atmosphere, it isn't good if these two equations to get out of balance (i.e. heterotrophy predominating over autotrophy, as when rain forests are destroyed and replaced with cattle).
Autotrophs are referred to as primary producers at the "bottom of the food chain" because they convert carbon to a form required by heterotrophs. Among procaryotes, the cyanobacteria, the lithotrophs and the methanogens are a formidable biomass of autotrophs that account for a corresponding amount of CO2 fixation in the global carbon cycle.
The lithotrophic bacteria and archaea that oxidize reduced N and S compounds and play important roles in the natural cycles of N and S (discussed below), are virtually all autotrophs. The prevalence of these organisms in sulfur-rich environments (marine sediments, thermal vents, hot springs, endosymbionts, etc. may indicate an unappreciated role of these procaryotes as primary producers of organic carbon on earth.
The methanogens play a dual role in the carbon cycle. These archaea are inhabitants of virtually all anaerobic environments in nature where CO2 and H2 (hydrogen gas) occur. They use CO2 in their metabolism in two distinct ways. About 5 percent of CO2 taken up is reduced to cell material during autotrophic growth; the remaining 95 percent is reduced to CH4 (methane gas) during a unique process of generating cellular energy. Hence, methane accumulates in rocks as fossil fuel ("natural gas"), in the rumen of cows and guts of termites, in sediments, swamps, landfills and sewage digesters. Since CH4 is the second-most prevalent of the greenhouse gases, it is best to discourage processes that lead to its accumulation in the atmosphere.
CO2 + H2 -----------------> CH2O (cell material) + CH4 methanogenesis
Under aerobic conditions, methane and its derivatives (methanol, formaldehyde, etc.) can be oxidized as energy sources by bacteria called methylotrophs. Metabolically this is a version of decomposition or biodegradation during the carbon cycle which is discussed below.
Biodegradation is the process in the carbon cycle for which microbes get most credit (or blame). Biodegradation is the decomposition of organic material (CH2O) back to CO2 + H2O and H2. In soil habitats, the fungi play a significant role in biodegradation, but the procaryotes are equally important. The typical decomposition scenario involves the initial degradation of biopolymers (cellulose, lignin, proteins, polysaccharides) by extracellular enzymes, followed by oxidation (fermentation or respiration) of the monomeric subunits. The ultimate end products are CO2, H2O and H2, perhaps some NH3 (ammonia) and sulfide (H2S), depending on how one views the overall process. These products are scarfed up by lithotrophs and autotrophs for recycling. Procaryotes which play an important role in biodegradation in nature include the actinomycetes, clostridia, bacilli, arthrobacters and pseudomonads.
Overall Process of Biodegradation (Decomposition)
polymers (e.g. cellulose)-----------------> monomers (e.g. glucose) depolymerization
monomers-----------------> fatty acids (e.g. lactic acid, acetic acid, propionic acid) + CO2 + H2 fermentation
monomers + O2 -----------------> CO2 + H2O aerobic respiration
The importance of microbes in biodegradation is embodied in the
that "there is no known natural compound that cannot be degraded by
microorganism." The proof of the adage is that we aren't up to our ears
in whatever it is that couldn't be degraded in the last 3.5 billion
Actually, we are up to our ears in cellulose and lignin, which is
than concrete, and some places are getting up to their ears in teflon,
plastic, styrofoam, insecticides, pesticides and poisons that are
slowly by microbes, or not at all.
Figure 1. The Carbon Cycle. Organic matter (CH2O) derived from photosynthesis (plants, algae and cyanobacteria) provides nutrition for heterotrophs (e.g. animals and associated bacteria), which convert it back to CO2. Organic wastes, as well as dead organic matter in the soil and water, are ultimately broken down to CO2 by microbial processes of biodegradation.
The figure above mostly ignores the role of methanogenesis in the carbon cycle. Since methanogens have the potential to remove CO2 from the atmosphere, converting it to cell material and CH4, these procaryotes not only influence the carbon cycle, but their metabolism also affects the concentration of major greenhouse gases in earth's atmosphere.
Recently, I asked a colleague, Professor Paul Weimer of the University of Wisconsin Department of Bacteriology, whether mathanogenesis which utilizes CO2 while producing CH4 was better or worse on the greenhouse effect. This is his response.
"Worse. For methanogenesis by CO2 reduction, the stoichiometry is 4H2 + CO2 --> CH4 + 2 H2O, so one mole of a greenhouse gas is exchanged for another. But methane is about 15 times more potent than is CO2 in terms of heat absorption capability on a per-molecule basis, so the net effect is a functional increase in heat absorption by the atmosphere. Remember also that in most natural environments, around two-thirds of the methane is produced by aceticlastic methanogenesis (CH3COOH --> CH4 + CO2) - an even less welcome situation, as BOTH products are greenhouse gases.
Even though methane
concentrations in the atmosphere
are two orders of magnitude below those of CO2, methane is
to account for about 15% of the anthropogenic climate forcing, compared
to about 60% from CO2. Most of the rest of the contribution
is from nitrous oxide (N2O, a respiratory denitrification
that has something like 300 times the heat absorbing capacity as CO2)
and the old chlorofluorocarbons (CFCs), even stronger heat absorbers
but more famous and dangerous as stratospheric ozone-depleters."
The Nitrogen Cycle
The nitrogen cycle is the most complex of the cycles of elements that make up biological systems. This is due to the importance and prevalence of N in cellular metabolism, the diversity of types of nitrogen metabolism, and the existence of the element in so many forms. Procaryotes are essentially involved in the biological nitrogen cycle in three unique processes.
Nitrogen Fixation: this process converts N2 in the atmosphere into NH3 (ammonia), which is assimilated into amino acids and proteins. Nitrogen fixation occurs in many free-living bacteria such as clostridia, azotobacters and cyanobacteria, and in symbiotic bacteria such as Rhizobium and Frankia, which associate with plant roots to form characteristic nodules. Biological nitrogen fixation is the most important way that N2 from the air enters into biological systems.
N2 ----------------> 2 NH3 nitrogen fixation
Anaerobic Respiration: this relates to the use of oxidized forms of nitrogen (NO3 and NO2) as final electron acceptors for respiration. Anaerobic respirers such as Bacillus and Pseudomonads are common soil inhabitants that will use nitrate (NO3) as an electron acceptor. NO3 is reduced to NO2 (nitrite) and then to a gaseous form of nitrogen such as N2 or N2O (nitrous oxide). The process is called denitrification. (A related process conducted by some Bacillus species, called dissimilatory nitrate reduction reduces NO3 to ammonia (NH3), but this is not considered denitrification.) Denitrifying bacteria are typically facultative microbes that respire whenever oxygen is available by aerobic respiration. If O2 is unavailable for respiration, they will turn to the alternative anaerobic respiration which uses NO3. Since NO3 is a common and expensive form of fertilizer in soils, denitrification may not be so good for agriculture, and one rationale for tilling the soil is to keep it aerobic, thereby preserving nitrate fertilizer in the soil.
NO3 ----------------> NO2
The overall reactions of denitrification shown above proceed through the formation of nitrous oxide (N2O). A recent article by Wunsch an Zumft in Journal of Bacteriology, vol. 187 (2005), sheds new light on the process of denitrification. N2O is a bacterial metabolite in the REVERSAL of Nitrogen fixation. The anthropogenic atmospheric increase of N2O is a cause for concern, as noted above (as a greenhouse gas, N2O has 300 times the heat absorbing capacity as CO2). Denitrifying bacteria respire using N2O as an electron acceptor yielding N2 and the thereby provide a sink for N2O. This article provides new insight into this process by identifying a membrane-bound protein in denitrifying bacteria called NosR, that is necessary for the expression of N2O reductase from the nosZ gene. The NosR protein has redox centers positioned on opposite sides of the cytoplasmic membrane, which allows it to sustain whole-cell N2O respiration by acting on N2O reductase.
Nitrification is a form of lithotrophic metabolism that is chemically the opposite of denitrification. Nitrifying bacteria such as Nitrosomonas utilize NH3 as an energy source, oxidizing it to NO2, while Nitrobacter will oxidize NO2 to NO3. Nitrifying bacteria generally occur in aquatic environments and their significance in soil fertility and the global nitrogen cycle is not well understood.
The Overall process of Nitrification
NH3 ----------------> NO2 (Nitrosomonas)
NO2 ----------------> NO3 (Nitrobacter)
A final important aspect of the nitrogen cycle that involves procaryotes, though not exclusively, is decomposition of nitrogen-containing compounds. Most organic nitrogen (in protein, for example) yields ammonia (NH3) during the process of deamination. Fungi are involved in decomposition, as well.
Plants, animals and protista, as well as the procaryotes, complete
nitrogen cycle during the uptake of the element for their own
Nitrogen assimilation is usually in the form of nitrate, an
group, or ammonia.
Figure 2. The Nitrogen Cycle
The Sulfur Cycle
Sulfur is a component of a couple of vitamins and essential metabolites and it occurs in two amino acids, cysteine and methionine. In spite of its paucity in cells, it is an absolutely essential element for living systems. Like nitrogen and carbon, the microbes can transform sulfur from its most oxidized form (sulfate or SO4) to its most reduced state (sulfide or H2S). The sulfur cycle, in particular, involves some unique groups of procaryotes and procaryotic processes. Two unrelated groups of procaryotes oxidize H2S to S and S to SO4. The first is the anoxygenic photosynthetic purple and green sulfur bacteria that oxidize H2S as a source of electrons for cyclic photophosphorylation. The second is the "colorless sulfur bacteria" (now a misnomer because the group contains many Archaea) which oxidize H2S and S as sources of energy. In either case, the organisms can usually mediate the complete oxidation of H2S to SO4.
H2S----------------> S ----------------> SO4 litho or phototrophic sulfur oxidation
Sulfur-oxidizing procaryotes are frequently thermophiles found in hot (volcanic) springs and near deep sea thermal vents that are rich in H2S. They may be acidophiles, as well, since they acidify their own environment by the production of sulfuric acid.
Since SO4 and S may be used as electron acceptors for respiration, sulfate reducing bacteria produce H2S during a process of anaerobic respiration analogous to denitrification. The use of SO4 as an electron acceptor is an obligatory process that takes place only in anaerobic environments. The process results in the distinctive odor of H2S in anaerobic bogs, soils and sediments where it occurs.
Sulfur is assimilated by bacteria and plants as SO4 for use and reduction to sulfide. Animals and bacteria can remove the sulfide group from proteins as a source of S during decomposition. These processes complete the sulfur cycle.
Figure 3. The Sulfur Cycle
The Phosphorus cycle
The phosphorus cycle is comparatively simple. Inorganic phosphate exists in only one form. It is interconverted from an inorganic to an organic form and back again, and there is no gaseous intermediate.
Phosphorus is an essential element in biological systems because it is a constituent of nucleic acids, (DNA and RNA) and it occurs in the phospholipids of cell membranes. Phosphate is also a constituent of ADP and ATP which are universally involved in energy exchange in biological systems.
Dissolved phosphate (PO4) inevitably ends up in the oceans. It is returned to land by shore animals and birds that feed on phosphorus containing sea creatures and then deposit their feces on land. Dissolved PO4 is also returned to land by a geological process, the uplift of ocean floors to form land masses, but the process is very slow. However, the figure below considers how PO4 is recycled among land-based groups of organisms.
Figure 4. The Phosphorus Cycle. Plants, algae and photosynthetic bacteria can absorb phosphate (PO4) dissolved in water, or if it washes out of rocks and soils. They incorporate the PO4 into various organic forms, including such molecules as DNA, RNA, ATP, and phospholipid. The plants are consumed by animals wherein the organic phosphate in the plant becomes organic phosphate in the animal and in the bacteria that live with the animal. Animal waste returns inorganic PO4 to the environment and also organic phosphate in the form of microbial cells. Dead plants and animals, as well as animal waste, are decomposed by microbes in the soil. The phosphate eventually is mineralized to the soluble PO4 form in water and soil, to be taken up again by photosynthetic organisms.
Ecology of a Stratified Lake
The role of microbes in the global cycle of elements (described above) can be visited on a smaller scale, in a lake, for example, like Lake Mendota, which may become stratified as illustrated in Figure 5. The surface of the lake is well-lighted by the sun and is aerobic. The bottom of the lake and its sediments are dark and anaerobic. Generally there is less O2 and less light as the water column is penetrated from the surface. Assuming that the nutrient supply is stable and there is no mixing between layers of lake water, we should, for the time being, have a stable ecosystem with recycling of essential elements among the living systems. Here is how it would work.
At the surface, light and O2 are plentiful, CO2 is fixed and O2 is produced. Photosynthetic plants, algae and cyanobacteria produce O2, cyanobacteria can even fix N2; aerobic bacteria, insects, animals and plants live here.
At the bottom of the lake and in the sediments, conditions are dark and anaerobic. Fermentative bacteria produce fatty acids, H2 and CO2, which are used by methanogens to produce CH4. Anaerobic respiring bacteria use NO3 and SO4 as electron acceptors, producing NH3 and H2S. Several soluble gases are in the water: H2, CO2, CH4, NH3 and H2S.
The biological activity at the surface of the lake and at the bottom of the lake may have a lot to do with what will be going on in the middle of the water column, especially near the interface of the aerobic and anaerobic zones. This area, called the thermocline, is biologically very active. Bacterial photosynthesis, which is anaerobic, occurs here, using longer wave lengths of light that will penetrate the water column and are not absorbed by all the plant chlorophyll above. The methanotrophs will stay just within the aerobic area taking up the CH4 from the sediments as a carbon source, and returning it as CO2. Lithotrophic nitrogen and sulfur utilizing bacteria do something analogous: they are aerobes that use NH3 and H2S from the sediments, returning them to NO3 and SO4.