title: Reconstruction of Transformation Processes Catalyzed by the Soil Microbiome Using Metagenomic Approaches.
abstract: Microorganisms are central players in the turnover of nutrients in soil and drive the decomposition of complex organic materials into simpler forms that can be utilized by other biota. Therefore microbes strongly drive soil quality and ecosystem services provided by soils, including plant yield and quality. Thus it is one of the major goals of soil sciences to describe the most relevant enzymes that are involved in nutrient mobilization and to understand the regulation of gene expression of the corresponding genes. This task is however impeded by the enormous microbial diversity in soils. Indeed, we are far to appreciate the number of species present in 1 g of soil, as well as the major functional traits they carry. Here, also most next-generation sequencing (NGS) approaches fail as immense sequencing efforts are needed to fully uncover the functional diversity of soils. Thus even if a gene of interest can be identified by BLAST similarity analysis, the obtained number of reads by NGS is too low for a quantitative assessment of the gene or for a description of its taxonomic diversity. Here we present an integrated approach, which we termed the second-generation full cycle approach, to quantify the abundance and diversity of key enzymes involved in nutrient mobilization. This approach involves the functional annotation of metagenomic data with a relative low coverage (5 Gbases or less) and the design of highly targeted primer systems to assess the abundance or diversity of enzyme-coding genes that are drivers for a particular transformation step in nutrient turnover.
authors.affiliation: Research Unit for Environmental Genomics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany. Anne.schoeler@helmholtz-muenchen.de.
authors.forename: Anne
authors.initials: A
authors.lastname: Schöler
authors.affiliation: Research Unit for Environmental Genomics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
authors.forename: Maria
authors.initials: M
authors.lastname: de Vries
authors.affiliation: Research Unit for Environmental Genomics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
authors.forename: Gisle
authors.initials: G
authors.lastname: Vestergaard
authors.affiliation: Research Unit for Environmental Genomics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Schloter
mesh_terms: D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D056186:Metagenomics / Q000379:methods*; D064307:Microbiota / Q000235:genetics; D010944:Plants / Q000235:genetics / Q000382:microbiology; D012988:Soil Microbiology; D014169:Transformation, Bacterial / Q000235:genetics*
keywords: Amplicon libraries; Bioinformatics; Ecosystem service; Metagenomics; Next-generation sequencing; Nutrient cycles; Primer design; Quantitative real-time PCR; Soil microbiome