Groups of Soil Microorganisms

A teaspoon of soil contains between 100 million and 1 billion bacteria and thousands of bacterial species, making them the most numerous organisms in soil. They are prokaryotic (= without a nucleus), unicellular, and range in diameter from 0.5 to 1.0 pm (Figure 36.1). Bacteria can be autotrophic or het- erotrophic, with the latter using a wide range of natural and synthetic compound for C and energy. They are the most metabolically versatile members of the soil biota: they can use the whole range of TEAs, which allows them to live everywhere within the soil. Bacteria are aquatic and live in soil pore water or on the surface of soil particles that make up soil pores. They reproduce by fission, creating two cells from a single cell. Many bacteria can survive adverse environmental conditions, such as desiccation and temperature extremes, by reducing their metabolic requirements or by producing spores that are resistant to environmental stresses. They are the main drivers of biogeochemical cycles in soil (Table 36.1) and are responsible for symbiotic biological nitrogen fixation. A small number of soil bacteria are plant and animal pathogens, and a few are human pathogens, such as Bacillus anthracis, which causes anthrax. The size and composition of bacterial communities is generally constrained by the availability of organic C and electron acceptors, by predation by bacterivorous nematodes and protozoa, and by infection by bacteriophage—viruses that infect bacteria (Figure 36.2).

Archaea are prokaryotic, unicellular, aquatic microorganisms that resemble bacteria in size and morphology, which led to their misclassification until very recently. They differ from bacteria in the structure of the molecules that make up their cell membranes, which allows them to live in a broad range of extreme conditions. Like bacteria, archaea can be autotrophic or heterotrophic, and can use a range of TEAs. Relatively little is known about the ecology of archaea. Many species are extremophiles that thrive in extremes of temperature, pressure, pH, or salinity. In soil, a number of archaeal species are autotrophs that oxidize ammonium to nitrite for energy, like their bacterial counterpart. Although they carry out the same process, their niches are differentiated by a preference for environments with low ammonium concentrations by ammonia-oxidizing Archaea (Jia and Conrad, 2009). The size and composition of archaeal communities are likely controlled by the same factors that control bacterial communities.

Soil fungi are eukaryotic (= with a nucleus) and can be unicellular or multicellular, with dozens of species of fungi found in a gram of soil. Multicellular fungi form strands (hyphae), which together form filaments (mycelia) that are visible to the naked eye (Figure 36.1). Hyphae are between 2 and 10 pm in diameter, and unicellular species (yeasts) are ~4pm in diameter. Filamentous fungi live in larger soil pores or displace soil particles as they grow through the soil, whereas yeasts live in smaller, water-filled pores. Most fungi are saprophytic, feeding on organic detritus in soil. They are aerobes, although some unicellular species are facultative anaerobes. Fungi reproduce by budding, or through sexual or asexual spore production. In forest soils, fungal biomass is generally larger than that for bacteria, whereas in agricultural soils, it tends to be smaller than bacterial biomass, likely due to physical disruption of mycelia and lower C inputs in the latter. In contrast, filamentous fungi are less affected by lack of moisture than bacteria or archaea. Fungi play various roles in the soil ecosystem (Frqc et al., 2018), including (i) decomposition of detritus—especially polymers like cellulose and lignin—and consequent biogeochemical cycling of C, nutrients, and trace elements (Table 36.1); (ii) improving the ability of vascular plants to acquire water, phosphorus ,and other nutrients through mycorrhizal associations; and (iii) as pathogens of plants, including economically important crops, as well as insects and other animals. The availability and diversity of organic C substrates are important controls on the size and composition of soil fungal communities, as are predatory pressures from fungivorous nematodes, mites, and other soil fauna (Figure 36.2).

Viruses range in size from 20 to 400 nm, with 107—104 viral particles present in 1 g of soil (Emerson, 2019). They consist of a molecule of nucleic acid (DNA or RNA) covered in a protein coating (Figure 36.1). They do not carry out any of the metabolic processes that other microorganisms do, and cannot reproduce on their own. Instead, they use the reproductive machinery of their hosts to reproduce, lysing the host cell to release the viral particles. Viruses can live under oxic and anoxic conditions, and are susceptible to environmental stresses, including temperature, pH, and low moisture. They infect mammals, plants, insects, and bacteria, affecting their survival and thus population dynamics. Viruses that infect bacteria and archaea (bacteriophage) are important in controlling the size of their communities and in interspecies gene transfer, which in turn affects biogeochemical cycles (Armon, 2011).

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