ABSTRACT
Biodiversity is a general term referring to the total of all species in any habitat. Studies on biodiversity of soils have primarily focused on the microbial components of the food web with less attention to the meso-and macrofauna represented by micro-arthropods, nematodes, earthworms and many other larger organisms such as arthropods, crustaceans and small mammals. Rather than viewing microorganisms as individual entities or species, their presence in soils should be considered as communities consisting of millions to billions of individual species representing millions of different taxonomic groups. Interactions among groups within communities mediate numerous important functions including decomposition of natural and xenobiotic organic substances (including pesticides) and carbon cycling; nutrient mineralization and cycling; soil structure formation; plant growth promotion and soil organic matter formation (Whalen and Sampedro, 2010; Willey et al., 2008; Torsvick et al., 1990). When evaluating the impacts of environment and imposed land management on soils, we must, therefore, consider microbial diversity from standpoints of structural diversity – the species numbers or abundance and their distribution within a microbial community based on taxonomic characteristics – and functional diversity – the distribution and abundance of microbial groups based on metabolic functions, as described for communities above (Brown, 2014; Whalen and Sampedro, 2010). Recent developments in molecular methods have advanced the studies of soil microbial communities by expanding the concept of microbial diversity through detection of nonculturable microorganisms and functional genes that can be matched with soil biological processes and the microbial source of origin (Fierer et al., 2013). These studies have led to
recognition of the microbiome, defined as a multispecies community of microorganisms in a specific environment, including soil, derived using genome-enabled technology (Stulberg et al., 2016) that can be further characterized based on the total proteins of the community (proteomics) responsible for microbial activity and on the metabolites of the community (metabolomics) that identify the products of microbial activity (Bouchez et al., 2016).
