Introduction

Soil has been defined as the upper weathered layer of the Earth's crust. It consists of a complex mixture of particulate materials derived from abiotic parent minerals, living biota and particulate organic detritus and humic substances. Soil formation is influenced by climate (temperature and moisture), parental material, time, topography, and organisms (Jenny 1994), and involves complex interactions between physical, chemical and biological processes. Soil texture (the relative proportion of particles of different sizes) and mineral constituents depend on the parent material (rocks) and transportation by water, ice, and wind. The soil structure is the distribution of pores of various sizes that occur between soil particles. The pore sizes depend on the level of aggregation of the particulate material in the soil, and the pores contain gases and water.

Soil is also defined as the surface layer of the Earth that is exploited by roots. This kind of definition is not the most appropriate one for introducing a chapter on soil microorganisms, as they are also found in soil compartments that are not colonized by roots. Microorganisms have been observed far below the rooting depth, and numerous bacteria and fungi colonize small pores and microaggregates that are not accessible to roots or even root hairs. According to another definition, soil genesis is a microbiologically driven process. In order to highlight the diversity that results from combining the interactions of very diverse and complex organism communities on different types of rock materials under variable climatic and topographic conditions and over different timescales, many soil scientists avoid using the term "soil," but prefer to speak of "soils."

Basically, soil is a combined mixture of organic matter (derived from living organisms) and unconsolidated minerals (composed of varying proportions of sand,

Amity Institute of Microbial Technology, Amity University, Uttar Pradesh,

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I. Sherameti and A. Varma (eds.), Soil Heavy Metals, Soil Biology, Vol 19, DOI 10.1007/978-3-642-02436-8_3, © Springer-Verlag Berlin Heidelberg 2010

silt and clay), and it provides habitats for thousands of soil-specific species. The habitat is the direct soil environment with which a particular species interacts. The soil habitat has edaphic properties; i.e., properties pertaining to the soil or determined by factors inherent to the soil. These properties are the result of interactions between the soil mineral composition, living organisms and their decomposition. The soil provides a porous three-dimensional matrix, with a large surface area, for soil-dwelling species. Thus, species that reside within the soil matrix are interstitial species.

The vegetation and soil biota affect soil development by weathering and controlling organic matter accumulation and mineralization. The recognition of close interactions between soils and vegetation is reflected in the division of soils into major types, which are associated with climatic vegetation zones. Microorganisms are able to modify and shape their physical and chemical environment. They dissolve and alter minerals derived from the parental material, contribute to and mineralize soil organic matter, and recycle nutrients. Microbes produce biopolymers (polysaccharides) as cell envelopes. Such polymers facilitate the formation and stabilization of soil aggregates, and thereby improve the soil's water-holding capacity. Together with colloidal clay particles and humus, the polymers create complex structures with extensive surfaces that adsorb minerals and organic molecules. Adsorption of proteins and nucleic acids to surfaces protect them from biodegradation and denaturation. Adsorbed DNA remains available for horizontal gene transfer through the transformation of competent cells (Lorenz and Wackernagel 1994). The activities of extracellular enzymes are maintained or even increased by adsorption on minerals, whereas adsorption to humic substances can either maintain or decrease their activities (Nannipieri et al. 1990; Allison 2006). Adsorption to soil colloids can strongly reduce the availability of organic molecules as nutrients for microorganisms; such soils can be oligotrophic environments.

Clay colloids of soil minerals serve as catalysts for abiotic chemical reactions. Due to their coatings of metal oxides and hydroxides and electronegative charges, they can mediate electron transfer reactions and catalyze the oxidation of phenols and polyphenols. In this way, they also contribute to humus formation through reactions like deamination, polymerization and condensation of organic molecules. It has been suggested that microbial processes like decomposition and the mineralization of organic substances prevail under moderate conditions, whereas abiotic reactions are more dominant under harsh conditions where microbial activities are hampered (Huang 1990; Ruggiero et al. 1996).

Soil habitats are different from aquatic habitats in that they are much more complex and heterogeneous, resulting in the formation of habitats that can support high microorganism abundance and diversity. A characteristic feature of soil habitats is their wide range of steep physicochemical gradients (e.g., of substrate concentrations, redox potential, pH, available water), which depend upon the size of the soil aggregate. Even small soil aggregate a few mm in size can offer many different microenvironments, resulting in different types of microorganism colonization (Standing and Killham 2006). Microhabitats are typically a few micrometers in size for unicellular prokaryotes, but may be much larger for filamentous actinomycetes and fungi. Microhabitats for prokaryotes exist either within or between aggregates. Intra-aggregate habitats typically have small pores that are often filled with water and anaerobic, whereas interaggregate habitats are more frequently aerobic. However, the living conditions in these habitats can show considerable changes across both space and time, and so soils are highly dynamic systems.

The distributions, activities and interactions of soil biota depend on soil properties such as texture, structure, available nutrients, and water. The best growth conditions are normally found on surfaces, and so most (80-90%) soil microorganisms attach themselves to surfaces (Hattori et al. 1997) using extracellular biopolymers that stick to particles. Specific soil habitats such as organic litter aggregates, biofilms, the rhizosphere, and animal droppings are rich in readily available organic nutrients and can have very high microbial activities. Hence, the distribution of soil microbes is generally localized, and the volume occupied by microorganisms may be less than 5% of the soil (Nannipieri et al. 2003). Microorganisms are by far the most active and functionally diverse part of the soil biota. It has been estimated that 90% of the soil processes are mediated by the microbiota, including prokaryotes and fungi. Generally, about one-third of the organic carbon of temperate soils is transformed into humus and microbial biomass, whereas about two-thirds of the carbon is respired by microorganisms to CO2 (Stotzky 1997).

Interestingly, deep subsurface terrestrial environments, which can extend for several hundreds of meters below the soil surface, have been shown to sustain ample microbial biomasses. Although the cell numbers are much lower than those found in the surface soil, a variety of microorganisms - primarily bacteria - are present in deep subsurface soils. These organisms most likely have access to organic nutrients present in the groundwater that percolates down the subsurface material and flows through their habitat. Studies on the microbial ecology of deep basalt aquifers have shown that both chemoorganotrophic and chemolithotrophic prokaryotes (see "Types of Microorganisms") are present, but that the chemolithotrophs dominate in these environments (Stevens and McKinley 1995).

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