CALS Farm and Industry Short Course Program: Farm Microbiology: Archived Lecture Notes

Soil Microbiology, Cycling of Elements and Biodegredation

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.

  1. 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. The essence of an organic molecule is the C-H bond, so organic forms of carbon, with the empirical formula of CH2O, are reduced forms of carbon.

    1. Use of CO2 as carbon source of AUTOTROPHS (by definition).

    2. Release of CO2 as an end product in respiration (and some fermentation) by CHEMOORGANOTROPHS.

    3. Methanogenesis.

    4. Methane oxidation.

    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.

    The Carbon Cycle.

    Another View of the Carbon Cycle.

    1. Exchange between Primary Producers (Autotrophs – including Cyanobacteria) and Biodegraders (Organotrophs). Autotrophs (by definition) use CO2 as the sole source of carbon for growth, thereby reducing it to cell material, and their form of catabolism is generally lithotrophic. Autotrophs include plants, algae, photosynthetic bacteria, methanogens and many kinds of lithotrophic bacteria. Heterotrophs require organic carbon for growth, and if their metabolism (which is generally organotrophic) proceeds far enough, they eventually convert the fixed carbon back to CO2.

      1. Interaction beween oxygenic photoautotrophs and aerobically respiring chemoheterotrophs.

        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.

      2. Overall process of biodegredation (decomposition).

        polymers----------------->monomers (depolymerization)

        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.

    2. Importance of Pseudomonas. The above adage regarding the degredation of natural compounds must have been coined to apply to members of the genus Pseudomonas, known for their ability to degrade hundreds of different organic compounds including insecticides, pesticides, herbicides, plastics, petroleum substances, hydrocarbons and other of the most refractory molecules in nature. However, they are usually unable to degrade biopolymers in their environment, such as cellulose and lignin, and their role in anaerobic decomposition is minimal.

    3. Importance of Streptomyces. Species of this genus have a world-wide distribution in soils. They are important in aerobic decomposition of organic compounds and have an important role in biodegradation and the carbon cycle. Also, products of metabolism called geosmins impart a characteristic earthy odor to soils. Certain species are major producers of commercially-available antibiotics such as tetracyclines, erythromycin, streptomycin, gentamicin, etc.

    4. Methanogenesis.

      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.

    5. Methane Oxidizers. These bacteria have a unique metabolism that converts methane to carbon dioxide.

    6. The Compost Pile. (See special lecture handout.)

    7. The Rumen. (See special lecture handout.)

  2. The Oxygen Cycle.


    2. O2 production by oxygenic PHOTOTROPHS.

    The Oxygen Cycle.

    1. Exchange between Respirers and Oxygenic Phototrophs (latter includes Cyanobacteria).

      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.

    2. Association of Oxygen with Other Elements. A simplified view of the O2-H2O cycle disregards the occurrence of radical forms of the oxygen molecule, and the persistent association of the oxygen atom with the other elements and molecules in living systems.

  3. The Nitrogen Cycle.

    1. Respiration of ammonium and nitrite by CHEMOLITHOTROPHS. This process is called nitrification.

    2. Dissimilatory nitrate reduction – a form of anaerobic respiration. This process is called denitrification when nitrate is reduced all the way to N2.

    3. Nitrogen-fixation by certain bacteria under aerobic (upper) and anaerobic (lower) conditions.

    4. Assimilatory nitrate reduction performed by plants and microorganisms.

    5. Assimilatory ammonium uptake performed by plants and microorganisms.

    6. Ammonification performed by microorganisms.

    The Nitrogen Cycle.

    Another View of the Nitrogen Cycle.

    1. Complexity. The Nitrogen cycle is the most complex of the cycles of elements in 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, nitrification and anaerobic respiration.

    2. Nitrogen-Fixation. This process converts N2 in the atmosphere into NH3 (ammonia), which is assimilated into amino acids and proteins. Nitrogen fixation occurs in a diverse assortment of free-living bacteria, and also in symbiotic bacteria 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.

      1. Process.

        N2 ----------------> 2 NH3 (nitrogen fixation)

      2. Symbiotic Nitrogen-Fixing Bacteria: Rhizobium is the most often-cited example. These organisms live in nodules on the roots of legumes (peas, beans, soybeans, trefoil, alfalfa, etc.) and fix atmospheric nitrogen. The plants benefit from the nitrogen compounds, and the bacteria benefit from the specialized environment provided by the plant.

      3. Non-Symbiotic (Free-Living) Nitrogen-Fixing Bacteria: Important examples are Azotobacter, most Cyanobacteria, Klebsiella (i.e., most strains of K. pneumoniae), Bacillus & Clostridium (some species of each). In the laboratory, one can add soil to a medium containing all of the required nutrients for growth of most bacteria – minus any nitrogen compounds – and the first organisms to start growing will be the nitrogen-fixers which are able to utilize the atmospheric nitrogen dissolved in the water.

    3. Nitrification.

      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.

    4. Anaerobic Respiration of Nitrate. This relates to the use of oxidized forms of nitrogen (NO3 and NO2) as final electron acceptors for respiration. Anaerobic respirers such as certain species of Pseudomonas and Bacillus 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 or NH3. The process is called denitrification. Denitrifying bacteria are typical aerobes 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.

      1. Process.

        NO3 ----------------> NO2 ----------------> N2 (denitrification)

      2. Problem in anaerobic soil with Pseudomonas. Some Pseudomonas species are anaerobic respirers, using nitrate in place of oxygen, and can deplete soil of expensive nitrate fertilizer (converting nitrate to nitrogen gas) if the soil is allowed to become anaerobic. One rationale for tilling the soil is to keep it aerobic, thereby preserving nitrate fertilizer in the soil. Effective drainage can prevent waterlogging of the soil – a cause of anaerobic conditions.

    5. Assimilation. Eucaryotes and procaryotes of all kinds take up the element for their own nutrition. Nitrogen assimilation is usually in the form of NO3, an amino group, or ammonia.

    6. Ammonification. 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.

  4. 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 SO42–) to its most reduced state (sulfide or H2S). The sulfur cycle, in particular, involves some unique groups of procaryotes and procaryotic processes.

    1. Oxidation of sulfide and sulfur by CHEMOLITHOTROPHS (by respiration) and PHOTOLITHOTROPHS.

    2. Dissimilatory sulfate reduction – a form of anaerobic respiration.

    3. Assimilatory sulfate reduction performed by plants and microorganisms.

    4. Desulfurylation performed by animals and microorganisms.

    The Sulfur Cycle.

    Another View of the Sulfur Cycle.

    1. Exchange between Lithotrophs (including the Purple and Green Sulfur Photosynthetic Bacteria) and Anaerobic Respirers.

      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.

    2. Assimilation and Desulfurylation. Sulfur is assimilated by bacteria and plants as SO42– 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.

  5. Overview of Elemental Cycles in a Typical Lake. The role of procaryotes in the global cycle (described above) can be visited on a smaller scale, in a lake, for example, like Lake Mendota, which may become stratified as illustrated in the figure below. The surface of the lake is well-lighted by the sun and 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.

    Ecology of a Stratified Lake.

    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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Page last modified on
3/14/05 at 3:45 PM, CST.
John Lindquist, Dept. of Bacteriology,
University of Wisconsin – Madison