Soil, defined as the superficial layer on the surface of the Earth, at the interface between the lithosphere and the atmosphere, supports and sustains life on earth. The world grows 95% of its food in the uppermost layer of soil, making topsoil one of the most important components of our food system. Soils are also described as the skin of the living world, vital but thin and fragile, and easily damaged by intensive farming, forest destruction, pollution and global heating. Microorganisms give life to soil by serving as a critical transition point between biology and geology. Microbial activities at this interphase drives the dynamics of soil ecosystem and determines its health. Apart from their key role in biogeochemical cycles, they are also involved in the first step of the formation of soil by the alteration of the parent rock, and in structuring of the soil (Paul and Clark, 1989). In structuring soil, the mineral components (sand, silt and clay) are organized into aggregates differing in size, shape and stability. The cohesion between the mineral particles is ensured by organic cements such as microbial exopolysaccharides (Oades et al., 1991 & Foster, 1990). The other two important players in influencing soil structure are plant root systems and soil animals. Thus, this three way network of soil microbes, plant root systems and soil organisms such as earthworms and termites play a crucial role in maintaining soil structure and its suitability as a growth medium for plants and for organic matter turn over. It is estimated that a quarter of all animal species on Earth live in soil and provide the nutrients for all sources of food. Soils also store as much carbon as all plants above ground and are therefore critical in tackling climate change. USDA’s Natural Resources Conservation Service estimates that natural processes takes about 500 years to form one inch of top soil and less than a century to degrade due to improper management.
Soil structure is the result of assemblage between minerals and organic components present in soil. For a deeper understanding, soils are defined as a complex three-dimensional structure consisting of packed aggregates and pore spaces (Wilpiszeski et al. 2019). Aggregates can be classified based on their size, macroaggregates have a diameter in excess of 250 µm and up to 2 mm, and anything less than this are classified as microaggregates (Fen and Jones, 1982). Macroaggregates are formed by the tangling of roots and fungal hyphae around coarse particles while microaggregates are the result of aggregation of fine particles such as silt and clay caused by microbial exopolysaccharides (Balkwill et al. 1975). This heterogeneous structure created by the positioning of irregularly shaped aggregates formed by particle packaging results in soil pores (Young et al. 1998). These aggregates form create networks of particles and cavities that are periodically connected during wetting events, which in turn create a variable flow of water and nutrients that can be accessed by soil organisms (Wilpiszeski et al. 2019). Organic waste recycling and turn over in soil is very much a function of soil pores and the amount of gaseous exchange that takes place through these pores, determines the metabolic nature of decomposition, whether it is anaerobic or aerobic decomposition. This rate is also influenced by substrate location and soil moisture conditions (Focht, 1992; Young and Ritz, 1998), and microfaunal grazers on microflora (Wardle et al. this volume). Thus aggregates interiors can exhibit properties distinct from the surrounding matrix which in turn can produce distinct microbial communities that are influenced and shaped by these abiotic factors, resulting in distinct metabolic activities (Sexstone et al. 1985).
Plant root systems play a key role in holding soil structure. A root can exert a force of up to 9 bars on soils resulting in a zone of compaction around the root in which the minerals are reoriented with their basal surface tangential to the root surface (Loutit and Miles, 1978). The pH of rhizosphere soil may differ by up to 2 pH units from the pH of the bulk soil (Smiley, 1979). Roots secrete chemicals, based on the nutrient status of soils. Roots, growing in soils deficient in Fe or Mn, secrete carboxylic acids, phenolics and chelating agents (Gardner et al. 1982). These compounds, along with microbial exudates, induce the breakdown of soil minerals and the formation of secondary minerals (Berthelin, 1984). Transpiration causes ions to move towards the root surface, where they are selectively adsorbed by the roots. Those that are left out, accumulate at the root surface. These, along with microbial exudates causes rhizosphere soil to differ chemically from the surrounding bulk soil. Studies have shown the accumulation of C, Ca, P, Mg, Si, etc. at the root surface (Sarkar et al. 1979).
Nutrient availability in soils is also mediated by both, roots and rhizosphere microorganisms. Organic acids have been implicated in the release of phosphorous from insoluble minerals such apatite. Up to 60% of the soil phosphorous is organic, and root and/or microbial enzymes may be involved in the release of inorganic phosphorus from organics (Berthelin, 1984). Phosphatases have been demonstrated in roots and rhizospheres using histochemical methods and Transmission Electron Microscopy (TEM) (Foster, 1986; Foster, 1983; Foster et al. 1983; Martin and Foster, 1985). Even under submerged conditions, there is a structured rhizosphere. The roots are mainly surrounded by decomposing organic matters in various stages of decay (Foster, 1978; Foster et al. 1983). Biesboer (1984) showed the rich rhizosphere of Typha, including the presence of nitrogen-fixing bacteria, in the grooves between the epidermal cells. In rice plants grown under water logged conditions, Heritage and Foster (1984) demonstrated the symbiotic relationship between sulfur bacteria and rice roots. The sulfur bacteria present in rhizosphere of rice plants are characterized by their angular granules of sulfur and their solubility in carbon disulfide. Joshi and Hollis (1977) demonstrated that absence of sulfur bacteria resulted in the accumulation of hydrogen sulfide (H2S) causing “White head” disease in rice. In the presence of sulfur bacteria, H2S is reduced to elemental sulfur, but the process resulted in the release of hydrogen peroxide, which is toxic to sulfur bacteria. Heritage and Foster (1984) showed the release of peroxidase from roots and other rice root rhizosphere bacteria, which were absorbed in the capsule material of sulfur bacteria (Heritage and Foster, 1984).
Understanding soil structure through spatial arrangements of micro and macroaggregates is a critical component is the study of functional microbial ecology. Soil’s bulk properties, including organic carbon content and water content are influenced by the distribution and relative abundance of micro and macroaggregates (Wilpiszeski et al. 2019). Approximately 90% of soil bacteria associate with macroaggregates, while 70% live within microaggregates (Ranjard et al. 2000). Less than 1% of the available soil surface area is typically colonized by soil microbes (Young and Crawford, 2004), while the distribution is both, within aggregates and on the surface of the aggregates. Some cells become trapped within the mineral matrix during aggregate formation, while others colonize the aggregate exterior during subsequent wetting events (Rilling et al. 2017). The porosity and connectivity of aggregates are influenced by the diversity of bacteria and fungi during formation (Crawford et al. 2012). Thus aggregates are critical in the study of soil microbial ecology and assessing cell clusters within soil aggregates will ensure proper representation of soil microbiome.
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