title: Soil-specific limitations for access and analysis of soil microbial communities by metagenomics.
abstract: Metagenomics approaches represent an important way to acquire information on the microbial communities present in complex environments like soil. However, to what extent do these approaches provide us with a true picture of soil microbial diversity? Soil is a challenging environment to work with. Its physicochemical properties affect microbial distributions inside the soil matrix, metagenome extraction and its subsequent analyses. To better understand the bias inherent to soil metagenome 'processing', we focus on soil physicochemical properties and their effects on the perceived bacterial distribution. In the light of this information, each step of soil metagenome processing is then discussed, with an emphasis on strategies for optimal soil sampling. Then, the interaction of cells and DNA with the soil matrix and the consequences for microbial DNA extraction are examined. Soil DNA extraction methods are compared and the veracity of the microbial profiles obtained is discussed. Finally, soil metagenomic sequence analysis and exploitation methods are reviewed.
authors.affiliation: Department of Marine Biotechnology, Institute of Marine Environmental Technology, University of Maryland Baltimore County, Baltimore, MD 21202, USA. nlombard@umbc.edu
authors.forename: Nathalie
authors.initials: N
authors.lastname: Lombard
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Prestat
authors.forename: Jan Dirk
authors.initials: JD
authors.lastname: van Elsas
authors.forename: Pascal
authors.initials: P
authors.lastname: Simonet
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000254:growth & development; D044822:Biodiversity; D004269:DNA, Bacterial / Q000032:analysis*; D004271:DNA, Fungal / Q000032:analysis*; D017753:Ecosystem; D005658:Fungi / Q000145:classification / Q000235:genetics / Q000254:growth & development; D014644:Genetic Variation; D056186:Metagenomics / Q000379:methods*; D017422:Sequence Analysis, DNA; D012987:Soil / Q000737:chemistry; D012988:Soil Microbiology
chemical_list: D004269:DNA, Bacterial; D004271:DNA, Fungal; D012987:Soil