title: Fungal Communities in Soils: Soil Organic Matter Degradation.
abstract: Stable isotope probing (SIP) provides the opportunity to label decomposer microorganisms that build their biomass on a specific substrate. In combination with high-throughput sequencing, SIP allows for the identification of fungal community members involved in a particular decomposition process. Further information can be gained through gene-targeted metagenomics and metatranscriptomics, opening the possibility to describe the pool of genes catalyzing specific decomposition reactions in situ and to identify the diversity of genes that are expressed. When combined with gene descriptions of fungal isolates from the same environment, specific biochemical reactions involved in decomposition can be linked to individual fungal taxa. Here we describe the use of these methods to explore the cellulolytic fungal community in forest litter and soil.
authors.affiliation: Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic. vetrovsky@biomed.cas.cz.
authors.forename: Tomáš
authors.initials: T
authors.lastname: Větrovský
authors.affiliation: Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic. stursova@biomed.cas.cz.
authors.forename: Martina
authors.initials: M
authors.lastname: Štursová
authors.affiliation: Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic. baldrian@biomed.cas.cz.
authors.forename: Petr
authors.initials: P
authors.lastname: Baldrian
mesh_terms: D002482:Cellulose / Q000378:metabolism; D004271:DNA, Fungal / Q000235:genetics*; D005658:Fungi; D015966:Gene Expression Regulation, Fungal; D007553:Isotope Labeling / Q000379:methods*; D056186:Metagenomics; D010802:Phylogeny; D012988:Soil Microbiology; D013379:Substrate Specificity
chemical_list: D004271:DNA, Fungal; D002482:Cellulose
keywords: Cellulose; Metagenomics; Metatranscriptomics; Microbial communities; Organic matter decomposition; Soil ecology; Stable isotope probing