+ + + + +

+ +

Nucleic acids

Purine and pyrimidine bases, sugars, phosphate

Phosphodiester and A-glycosidic bonds

+ + + + +


Carbon fixation occurs through the activities of cyanobacte-ria and green algae, photosynthetic bacteria (e.g., Chromatium and Chlorobium), and aerobic chemolithoautotrophs.

In the carbon cycle depicted in figure 28.19, no distinction is made between different types of organic matter that are formed and degraded. This is a marked oversimplification because organic matter varies widely in physical characteristics and in the biochemistry of its synthesis and degradation. Organic matter varies in terms of elemental composition, structure of basic repeating units, linkages between repeating units, and physical and chemical characteristics.

The formation of organic matter is discussed in chapters 10 through 12. The degradation of this organic matter, once formed, is influenced by a series of factors. These include (1) nutrients present in the environment; (2) abiotic conditions (pH, oxidation-reduction potential, O2, osmotic conditions), and (3) the micro-bial community present.

The major complex organic substrates used by microorganisms are summarized in table 28.5. Of these, only previously grown microbial biomass contains all of the nutrients required for microbial growth. Chitin, protein, microbial biomass, and nucleic acids contain nitrogen in large amounts. If these substrates are used for growth, the excess nitrogen and other minerals that are not used in the formation of new microbial biomass will be released to the environment, in the process of mineralization. This is the process in which organic matter is decomposed to release simpler, inorganic compounds (e.g., CO2, NH4+, CH4, H2).

The other complex substrates in table 28.5 contain only carbon, hydrogen, and oxygen. If microorganisms are to grow by using these substrates, they must acquire the remaining nutrients they need for biomass synthesis from the environment; in the process of immobilization.

The oxygen relationships for the use of these substrates also are of interest, because most of them can be degraded easily with or without oxygen present. The exceptions are hydrocarbons and lignin. Hydrocarbons are unique in that microbial degradation, especially of straight-chained and branched forms, involves the initial addition of molecular O2. Recently, anaerobic degradation of hydrocarbons with sulfate or nitrate as oxidants has been observed. With sulfate present, organisms of the genus Desulfovib-rio are active. This occurs only slowly and with microbial communities that have been exposed to these compounds for extended periods. Such degradation may have resulted in the sulfides that are present in "sour gases" associated with petroleum.

Lignin, an important structural component in mature plant materials, is a complex amorphous polymer based on a phenylpropane building block, linked by carbon-carbon and carbon-ether bonds. It makes up approximately 1/3 of the weight of wood. This is a special case in which biodegradability is dependent on O2 availability. There often is no significant degradation because most filamentous fungi that degrade native lignin in situ can function only under aerobic conditions where oxidases can act by the release of active oxygen species. Lignin's lack of biodegradability under anaerobic conditions results in accumulation of lignified materials, including the formation of peat bogs and muck soils. This absence of lignin degradation under anaerobic conditions also is important in construction. Large masonry structures often are built on swampy sites by driving in wood pilings below the water table and placing the building footings on the pilings. As long as the foundations remain water-saturated and anaerobic, the structure is stable. If the water table drops, however, the pilings will begin to rot and the structure will be threatened. Similarly, the cleanup of harbors can lead to decomposition of costly docks built with wooden pilings due to increased aerobic degradation of wood by filamentous fungi. Rumen function provides a final example of the relationship between

614 Chapter 28 Microorganism Interactions and Microbial Ecology

Aerobic carbon use

Carbon use with mineral release

Complex organic matter

Carbon use with mineral release

Complex organic matter



Oxidation of reduced products

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