Microbial Activities In Relation To Catabolism In Soil Systems

The principal "players" in the decomposition process are the micro-bial populations, (i.e., the bacteria, fungi, and viruses). The bacteria and fungi are as biochemically diverse as they are diverse in phylogeny. Bacteria, currently considered to encompass more than 35 phyla, are probably the most speciose array of organisms on earth (Tiedje et al., 2001; Torsvik and 0vreas, 2002). In addition, bacteria are undoubtedly the most numerous organisms, and have been estimated to total from 4

to 6 • 1030 cells on Earth. A sizable proportion (more than 90%) of bacteria are in the subsurface, which includes the earth's mantle to 4 kilometers (km) in depth (Whitman et al., 1998). Numbers of bacteria in soils of all biomes were estimated to be 2.5-1029 cells, with some of the larger quantities in desert scrub and savanna lands. The foregoing counts translate into 2 • 109 cells g-1 in the top meter, and 1 • 108 cells g-1 in the 1-to 8-m soil depth, with numbers in forest soils being markedly lower (Whitman et al., 1998).

In soils away from the rhizosphere, the environment for bacteria is usually stressful. Amajority of bacteria exist in this low-nutrient condition and may be starving (Morita, 1997). One should note that although some bacteria can double every 20 minutes or less in growth media in the laboratory, they may undergo only two to three divisions per year, on average, in soil under field conditions because of the extreme limitations of available reduced carbon substrates. This energetic limitation is considered in detail in Chapter 6. A pictorial representation of bacterial carbon flow is given in Figure 3.1 (Scow, 1997). Note the aforementioned flows to both biomass growth and maintenance respiration. The latter requirement becomes limiting to many bacteria under conditions of nutrient limitation. In anoxic or low-redox microsites within soil aggregates and faunal guts, decomposition via microbial fermentation or anaerobic respiration with nitrate or other electron acceptors can occur. Decomposition linked to aerobic respiration would occur in regions with higher levels of oxygen, such as on the exteriors of aggregates.

Many genera of prokaryotes, including both bacteria and archaea, have evolved the highly important biochemical trait of "fixing" (rupturing the triple covalent bonds of) dinitrogen, making it available as ammonium for plant or microbial uptake (Postgate, 1987). This has important ramifications for nitrogen and phosphorus cycling and interactions with soil organic matter (Stewart and Cole, 1983; Stewart et al., 1990; Giller, 2001).

Knowledge of the prokaryotes has increased greatly in the past decade, with numerous accounts of their phylogeny published (Bergey's manual at http://www.cme.msu.edu/bergeys; Torsvik and 0vreas, 2002). The principal concern of bacterial phylogeny is to trace both the extent of species of bacteria, as well as the archaea. Until recently, archaea were considered to be inhabitants of extreme environments, including deep sea trenches and vents and hot springs, but they have been found also in numerous other habitats, including fresh water lakes and forest and agricultural soils (Bintrim et al., 1997; Jurgens et al., 1997; Pace, 1997). For more information on soil prokaryote interactions in soils and rhizospheres, see the review by Kent and Triplett (2002).

A method often used to analyze bacterial populations is to amplify DNA extracted from environmental samples by polymerase chain

Carbon substrates

Carbon substrates

Metabolites and extracellular polysaccharides

Metabolites and extracellular polysaccharides

FIGURE 3.1. Flow of carbon in a bacterial cell (from Scow, 1997).

reaction (PCR), using primers universal to the 16S ribosomal RNA (rRNA) genes of bacteria and archaea (Lane, 1991; Prosser, 2002). In both tropical (Borneman and Triplett, 1997) and arid southwestern U.S. soils (Kuske et al., 1997), more than 50% of the prokaryotic DNA sequences of soil prokaryotes belonged to groups with no representatives in laboratory culture. This has marked implications for identifying prokaryotes involved in biogeochemical cycling and other environmental processes (see Chapter 7). Either DNA or RNA can be extracted from soils, but a majority of the studies have been based on DNA extraction, which is easier to accomplish efficiently because of the higher lability and turnover of RNA. The rRNA content in active cells is higher than in inactive ones, thus rRNA-based analyses are a better approach for characterizing active microbial populations in soils (Ogram and Sharma, 2002). Techniques are now available to analyze microbial community structure and function, by analyzing microbial rRNAand mRNA, respectively. Both types of RNA can be extracted from soils and converted to complementary DNA (cDNA) by the enzyme reverse transcriptase for subsequent PCR amplification. Standard PCR analyses using "universal primers for rRNA genes" are not quantitative but do provide very useful qualitative information on dominant microbial populations. As long as suitable primers are available, microbial rRNA copies or mRNA copies can be quantified using quantitative, or "real-time," PCR. These latter approaches provide an important means for linking soil microbial community structure and function.

Perhaps the greatest difference between bacteria and fungi is to be found in their mode of growth. Fungi have long strands (hyphae) that can grow into and explore many small microhabitats, secreting any of a considerable array of enzymes, decomposing material there, imbibing the decomposed monomers, and translocating the carbon and other nutrients back into the hyphal network (Fig. 3.2). In contrast to bacteria, fungi can remain active in soils at very low water potential (-7200 kPa) and are better suited than bacteria to exist in interpore spaces (Shipton, 1986). Many genera of fungi are closely associated with plants (see Chapter 2) and animals. Studies of coevolution of fungi with other eukaryotes have been summarized by Pirozynski and Hawksworth (1988). For an extensive overview of the roles that fungi play in terrestrial ecosystems, see Dighton (2003).

Although not covered in detail in this book, there is a rapidly growing area of interest in effects of plant pathogens in ecosystems. Because plant pathogens play important roles in mediating plant competition and succession, and in the maintenance of plant species diversity, they can have important feedback effects on soil communities and ecosystem processes as well. For a good review of these processes, see Gilbert (2002). We discuss effects of microarthropod grazing on fungal plant pathogens in Chapter 4.

In contrast to fungi, bacteria are usually unicellular, or in clustered colonies, occupying discrete patches of soil measuring only a few cubic micrometers (|im3) in volume. Bacteria depend on many episodic events, such as rainfall and root growth or ingestion by various soil fauna, for passive movement to enable them to move about. When flagella are present, directed motility in the water-film is also possible.

Viruses may play significant roles in the microbial ecologies of soil environments because they can be a source of mortality, particularly for bacteria. Farrah and Bitton (1990) noted that lytic phages (viruses attacking bacteria) could act so as to restrict the growth of susceptible bacteria, and other phages could transmit genetic information between bacteria. The information on viral numbers and activities in soil in general is quite limited. Temperate phages (as distinct from virulent ones) in desert systems were inactivated on soil particles at acid pH (4.5-6). These phages had virtually no effect on populations of soil bacteria in Arizona soils, but persisted at low densities in their hosts (Pantastico-Caldas et al, 1992). This contrasts markedly with the often-cited deleterious impacts of virulent phages on Escherichia coli in liquid cultures

FIGURE 3.2. Extensive growth of fungal mycelium (arrow) was observed when crushed microaggregate (0.50-mm diameter) from native soil was stained with water-soluble aniline blue (a); smaller-sized (0.10-mm diameter) aggregates from a crushed macro-aggregate (1.0-mm diameter) were held together by fungal hyphae (b) (from Gupta, 1989).

FIGURE 3.2. Extensive growth of fungal mycelium (arrow) was observed when crushed microaggregate (0.50-mm diameter) from native soil was stained with water-soluble aniline blue (a); smaller-sized (0.10-mm diameter) aggregates from a crushed macro-aggregate (1.0-mm diameter) were held together by fungal hyphae (b) (from Gupta, 1989).

in the laboratory. For more information on bacteriophages and interactions with bacteria under starvation conditions, see Schrader et al. (1997).

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