Recent advances and perspectives in metagenomic studies of soil microbial communities

Abstract

Metagenomics is a modern and rapidly growing field of molecular genetics and ecology that studies the collective genome of the microbial community and is based on the analysis of environmental DNA, extracted directly from a variety of natural habitats. The advent of high-throughput sequencing techniques had opened the principally new opportunities in studies of the genetic structure of microbial communities, but at the same time highlighted significant difficulties, arising particularly during the investigation of the soil metagenome. Soil is the most densely populated habitat on the planet, and can contain up to 1,000 Gbp of genetic information per gram suggesting the great misfortune during the analysis of the soil metagenome consisting in the preferential analysis of only a small fraction of the total soil metagenome with relatively low accuracy. We emphasize the necessity for structuring of the soil metagenome and identification of its main components. Considering that modern metagenomics should first be addressed to the eternal questions of soil microbiology, in this review we tried to identify the meaningful parts of soil metagenome primarily by the analysis of soil microbial communities. We discussed in detail the spatial organization of soil metagenome associated with micro- and macrostructure of the soil matrix, the structural organization of soil metagenome associated with the presence of heterogeneous pools of soil DNA, taxonomical and functional organization of the soil metagenome revealed from the investigation of global patterns of distribution of microbial communities in relation to the specific environmental factors. We demonstrated that soil microbial communities are characterized by a presence of a restricted number of taxonomic organization types, which are based on the most powerful ecological factors such as soil pH and moisture. Comparing to more or less labile taxonomic structure, the functional structure of the soil metagenome is rather conservative and is maintained primarily by two factors - the microbial co-operation and the maintenance of high levels of genetic diversity. Finally we come to a conclusion that the soil metagenome represents an integrative hereditary system for maintenance of the basic soil functions under the variable ecological conditions.