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Cultivating microbial dark matter in benzene‐degrading methanogenic consortia
Author(s) -
Luo Fei,
Devine Cheryl E.,
Edwards Elizabeth A.
Publication year - 2016
Publication title -
environmental microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.954
H-Index - 188
eISSN - 1462-2920
pISSN - 1462-2912
DOI - 10.1111/1462-2920.13121
Subject(s) - biology , metagenomics , 16s ribosomal rna , pyrosequencing , population , microbiology and biotechnology , bacteria , biochemistry , genetics , gene , demography , sociology
Summary The microbes responsible for anaerobic benzene biodegradation remain poorly characterized. In this study, we identified and quantified microbial populations in a series of 16 distinct methanogenic, benzene‐degrading enrichment cultures using a combination of traditional 16 S rRNA clone libraries (four cultures), pyrotag 16 S rRNA amplicon sequencing (11 cultures), metagenome sequencing (1 culture) and quantitative polymerase chain reaction ( qPCR ; 12 cultures). An operational taxonomic unit ( OTU ) from the D eltaproteobacteria designated ORM 2 that is only 84% to 86% similar to S yntrophus or D esulfobacterium spp. was consistently identified in all enrichment cultures, and typically comprised more than half of the bacterial sequences. In addition to ORM 2, a sequence belonging to P arcubacteria (candidate division OD 1) identified from the metagenome data was the only other OTU common to all the cultures surveyed. Culture transfers (1% and 0.1%) were made in the presence and absence of benzene, and the abundance of ORM 2, OD 1 and other OTUs was tracked over 415 days using qPCR . ORM 2 sequence abundance increased only when benzene was present, while the abundance of OD 1 and other OTUs increased even in the absence of benzene. D eltaproteobacterium ORM 2 is unequivocally the benzene‐metabolizing population. This study also hints at laboratory cultivation conditions for a member of the widely distributed yet uncultivated P arcubacteria ( OD 1).