Fungal Communities in Soils: Soil Organic Matter Degradation
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.
Key wordsStable isotope probing Microbial communities Soil ecology Organic matter decomposition Metagenomics Metatranscriptomics Cellulose
This work was supported by the Czech Science Foundation grant 13-06763S and by the Institute of Microbiology of the Czech Academy of Sciences (RVO61388971).
- 1.Berg B, Laskowski R (2006) Litter decomposition: a guide to carbon and nutrient turnover. Academic, AmsterdamGoogle Scholar
- 7.Baldrian P, Kolařík M, Štursová M, Kopecký J, Valášková V, Větrovský T, Žifčáková L, Šnajdr J, Rídl J, Vlček Č, Voříšková J (2012) Active and total microbial communities in forest soil are largely different and highly stratified during decomposition. ISME J 6:248–258PubMedPubMedCentralCrossRefGoogle Scholar