Fungal Communities in Soils: Soil Organic Matter Degradation

  • Tomáš Větrovský
  • Martina Štursová
  • Petr Baldrian
Part of the Methods in Molecular Biology book series (MIMB, volume 1399)


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 words

Stable 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. 1.
    Berg B, Laskowski R (2006) Litter decomposition: a guide to carbon and nutrient turnover. Academic, AmsterdamGoogle Scholar
  2. 2.
    Clemmensen KE, Bahr A, Ovaskainen O, Dahlberg A, Ekblad A, Wallander H, Stenlid J, Finlay RD, Wardle DA, Lindahl BD (2013) Roots and associated fungi drive long-term carbon sequestration in boreal forest. Science 339:1615–1618PubMedCrossRefGoogle Scholar
  3. 3.
    Baldrian P, Valášková V (2008) Degradation of cellulose by basidiomycetous fungi. FEMS Microbiol Rev 32:501–521PubMedCrossRefGoogle Scholar
  4. 4.
    Berlemont R, Martiny AC (2013) Phylogenetic distribution of potential cellulases in bacteria. Appl Environ Microbiol 79:1545–1554PubMedPubMedCentralCrossRefGoogle Scholar
  5. 5.
    de Boer W, Folman LB, Summerbell RC, Boddy L (2005) Living in a fungal world: impact of fungi on soil bacterial niche development. FEMS Microbiol Rev 29:795–811PubMedCrossRefGoogle Scholar
  6. 6.
    Baldrian P, López-Mondéjar R (2014) Microbial genomics, transcriptomics and proteomics: new discoveries in decomposition research using complementary methods. Appl Microbiol Biotechnol 98:1531–1537PubMedCrossRefGoogle Scholar
  7. 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
  8. 8.
    Edwards IP, Upchurch RA, Zak DR (2008) Isolation of fungal cellobiohydrolase I genes from sporocarps and forest soils by PCR. Appl Environ Microbiol 74:3481–3489PubMedPubMedCentralCrossRefGoogle Scholar
  9. 9.
    Štursová M, Žifčáková L, Leigh MB, Burgess R, Baldrian P (2012) Cellulose utilization in forest litter and soil: identification of bacterial and fungal decomposers. FEMS Microbiol Ecol 80:735–746PubMedCrossRefGoogle Scholar
  10. 10.
    Šnajdr J, Dobiášová P, Větrovský T, Valášková V, Alawi A, Boddy L, Baldrian P (2011) Saprotrophic basidiomycete mycelia and their interspecific interactions affect the spatial distribution of extracellular enzymes in soil. FEMS Microbiol Ecol 78:80–90PubMedCrossRefGoogle Scholar
  11. 11.
    Větrovský T, Baldrian P (2013) Analysis of soil fungal communities by amplicon pyrosequencing: current approaches to data analysis and the introduction of the pipeline SEED. Biol Fertil Soils 49:1027–1037CrossRefGoogle Scholar
  12. 12.
    Lindahl BD, Nilsson RH, Tedersoo L, Abarenkov K, Carlsen T, Kjøller R, Kõljalg U, Pennanen T, Rosendahl S, Stenlid J, Kauserud H (2013) Fungal community analysis by high-throughput sequencing of amplified markers—a user’s guide. New Phytol 199:288–299PubMedPubMedCentralCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Tomáš Větrovský
    • 1
  • Martina Štursová
    • 1
  • Petr Baldrian
    • 1
  1. 1.Laboratory of Environmental MicrobiologyInstitute of Microbiology of the CASPraha 4Czech Republic

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