Effect of microbes on the global cycles of elements: The most significant effect that the microbes have on their environment is their underlying ability to recycle the essential elements needed to build biological systems. Earth is a closed system with limited amounts of carbon, O2, and nitrogen to support life. These essential elements of living systems must be converted from one form to another and shared among all living organisms.
In the global environment, procaryotes are absolutely essential to drive the cycles of elements that make up living systems, i.e., the carbon, oxygen, nitrogen and sulfur cycles.
Organic compounds are used as carbon source by HETEROTROPHS (by definition). As is also the case for the Nitrogen and Sulfur Cycles (below), organic compounds are converted from one to another within plants, animals and microorganisms – also animals eating plants, microorganisms decomposing plants and animals, microorganisms undergoing fermentation, etc.
CO2 + H2O -----------------> CH2O (cell material) + O2 (oxygenic phototrophy)
CH2O (cell material) + O2 -----------------> CO2 + H2O (aerobic respiration)
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 various lithotrophic bacteria and the methanogens are huge groups of autotrophs that account for a correspondingly huge amount of CO2 fixation during the global Carbon cycle.
The lithotrophic procaryotes (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) may indicate an important role of these procaryotes as primary producers of organic carbon on Earth.
There are lithotrophic bacteria that can oxidize CO (carbon monoxide) to CO2, but their significance in the biological carbon cycle is not known.
monomers----------------->fatty acids + CO2 + H2 (fermentation)
monomers + O2 ----------------->CO2 + H2O (aerobic respiration)
Biodegradation is where the microorganisms get most of their credit for participation in the Carbon cycle. Biodegradation is the decomposition (by organotrophs/heterotrophs) of organic material (CH2O) back to CO2 and H2O. 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 polymer 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/autotrophs for recycling. Procaryotes which play an important role in biodegradation in nature include the Actinomycetes (including Streptomyces), Pseudomonas (and other pseudomonads), Clostridium, Bacillus and Arthrobacter.
The importance of microbes in biodegradation is embodied in the adage that "there is no known natural compound that cannot be degraded by some 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 4 billion years. Actually, we are up to our ears in cellulose and lignin, which is better than concrete, and some places are getting up to their ears in Teflon, plastic, styrofoam, insecticides, pesticides and poisons that are degraded slowly by microbes, or not at all.
CO2 + H2 -----------------> CH2O (cell material) + CH4 (methanogenesis)
The methanogens play a dual role in the carbon cycle. The methanogens 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. (Generally, for convenience, we have included the methanogens among the anaerobic respirers.) 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 + H2O-----------------> CH2O + O2 (oxygenic photosynthesis)
CH2O +O2-----------------> CO2 + H2O (aerobic respiration)
Basically, O2 is derived from the photolysis of H2O during plant-type (oxygenic) photosynthesis, and it is converted back to H2O during aerobic respiration. Given that the procaryotic cyanobacteria existed for millions of years before the evolution of eukaryotic algae and plants, and that contemporary cyanobacteria are the photosynthetic "grass of the sea", it is inferred that these procaryotes are the source of a lot of the O2 in the earth's atmosphere that is required by aerobic organisms from all domains of life. This establishes a relationship between autotrophs and heterotrophs that has a counterpart in the carbon cycle wherein autotrophs fix carbon needed by heterotrophs, and heterotrophs produce CO2 used by the autotrophs. Of course, plants and algae conduct a significant amount of CO2 fixation and O2 production in this metabolic relationship between O2-producing autotrophs and O2-consuming heterotrophs. Since CO2 is the most prevalent Greenhouse gas in the atmosphere, it isn't good if these two equations to get out of balance.
N2 ----------------> 2 NH3 (nitrogen fixation)
NH3 ----------------> NO2– (Nitrosomonas)
NO2– ----------------> NO3– (Nitrobacter)
This process 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.
NO3– ----------------> NO2– ----------------> N2 (denitrification)
H2S----------> S ----------> SO42– (chemo- or photolithotrophic sulfur oxidation)
SO42–---------------------------------------------------->H2S (sulfate reduction)
Two unrelated groups of procaryotes oxidize H2S to S and S to SO42–. 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 so 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 SO42–.
Sulfur-oxidizing bacteria 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 SO42– 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 SO42– 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.
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 SO42– 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 SO42–.
The text of this page was essentially a handout/essay written by Ken Todar which was used in pre-2001 Farm Microbiology sessions with some additions (including the figures with the hand-drawn cycles) and rearranging to fit the present outline.
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