Open AccessSensitive and substrate‐specific detection of metabolically active microorganisms in natural microbial consortia using community isotope arrays
Author(s) -
Tourlousse Dieter M.,
Kurisu Futoshi,
Tobino Tomohiro,
Furumai Hiroaki
Publication year - 2013
Publication title -
fems microbiology letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.899
H-Index - 151
eISSN - 1574-6968
pISSN - 0378-1097
DOI - 10.1111/1574-6968.12112
Subject(s) - stable isotope probing , fosmid , microorganism , gammaproteobacteria , biology , metagenomics , environmental chemistry , library , bacteria , microbiology and biotechnology , chemistry , biochemistry , 16s ribosomal rna , gene , genetics
The goal of this study was to develop and validate a novel fosmid‐clone‐based metagenome isotope array approach – termed the community isotope array ( CIA rray) – for sensitive detection and identification of microorganisms assimilating a radiolabeled substrate within complex microbial communities. More specifically, a sample‐specific CIA rray was used to identify anoxic phenol‐degrading microorganisms in activated sludge treating synthetic coke‐oven wastewater in a single‐sludge predenitrification–nitrification process. Hybridization of the CIA rray with DNA from the 14 C‐phenol‐amended sample indicated that bacteria assimilating 14 C‐atoms, presumably directly from phenol, under nitrate‐reducing conditions were abundant in the reactor, and taxonomic assignment of the fosmid clone end sequences suggested that they belonged to the G ammaproteobacteria . The specificity of the CIA rray was validated by quantification of fosmid‐clone‐specific DNA in density‐resolved DNA fractions from samples incubated with 13 C‐phenol, which verified that all CIA rray‐positive probes stemmed from microorganisms that assimilated isotopically labeled carbon. This also demonstrated that the CIA rray was more sensitive than DNA ‐ SIP , as the former enabled positive detection at a phenol concentration that failed to yield a ‘heavy’ DNA fraction. Finally, two operational taxonomic units distantly related to marine G ammaproteobacteria were identified to account for more than half of 16S r RNA gene clones in the ‘heavy’ DNA library, corroborating the CIArray‐based identification.