Identification of Cellulose-Responsive Bacterial and Fungal Communities in Geographically and Edaphically Different Soils by Using Stable Isotope Probing

Abstract

ABSTRACTMany bacteria and fungi are known to degrade cellulose in culture, but their combined response to cellulose in different soils is unknown. Replicate soil microcosms amended with [13C]cellulose were used to identify bacterial and fungal communities responsive to cellulose in five geographically and edaphically different soils. The diversity and composition of the cellulose-responsive communities were assessed by DNA-stable isotope probing combined with Sanger sequencing of small-subunit and large-subunit rRNA genes for the bacterial and fungal communities, respectively. In each soil, the13C-enriched, cellulose-responsive communities were of distinct composition compared to the original soil community or12C-nonenriched communities. The composition of cellulose-responsive taxa, as identified by sequence operational taxonomic unit (OTU) similarity, differed in each soil. When OTUs were grouped at the bacterial order level, we found that members of theBurkholderiales,Caulobacteriales,Rhizobiales,Sphingobacteriales,Xanthomonadales, and the subdivision 1Acidobacteriawere prevalent in the13C-enriched DNA in at least three of the soils. The cellulose-responsive fungi were identified as members of theTrichocladium,Chaetomium,Dactylaria, andArthrobotrysgenera, along with two novelAscomycotaclusters, unique to one soil. Although similarities were identified in higher-level taxa among some soils, the composition of cellulose-responsive bacteria and fungi was generally unique to a certain soil type, suggesting a strong potential influence of multiple edaphic factors in shaping the community.