Dataset Information


Transcriptome-stable isotope probing provides targeted functional and taxonomic insights into hypoxic pollutant-degrading aquifer microbiota

ABSTRACT: We investigated a contaminant-degrading microbial community by sequencing total RNA (without rRNA depletion) from microcosms containing sediment from a hypoxic contaminated aquifer fed with isotopically labeled toluene. Overall design: Microcosms were made using sediment from a hypoxic, hydrocarbon-contaminated aquifer in Siklos, Hungary. They were incubated under hypoxic/microoxic conditions and provided with isotopically-labeled toluene as a substrate. RNA was extracted and subjected to isopycnic centrifugation to separated heavy (isotopically labeled) and light (unlabeled) RNA, representing microbes which did or did not metabolize toluene, respectively. Total RNA was sequenced to provide both taxonimic (16S) and functional (mRNA) data on this microbiota, the first instance of total-RNA-stable isotope probing used to investigate a contaminated environment.

INSTRUMENT(S): Illumina NextSeq 500 (aquifer metagenome)

SUBMITTER: Tillmann Lueders  

PROVIDER: GSE119644 | GEO | 2018-09-07


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Transcriptome-Stable Isotope Probing Provides Targeted Functional and Taxonomic Insights Into Microaerobic Pollutant-Degrading Aquifer Microbiota.

Bradford Lauren M LM   Vestergaard Gisle G   Táncsics András A   Zhu Baoli B   Schloter Michael M   Lueders Tillmann T  

Frontiers in microbiology 20181113

While most studies using RNA-stable isotope probing (SIP) to date have focused on ribosomal RNA, the detection of 13C-labeled mRNA has rarely been demonstrated. This approach could alleviate some of the major caveats of current non-target environmental "omics." Here, we demonstrate the feasibility of total RNA-SIP in an experiment where hydrocarbon-degrading microbes from a BTEX-contaminated aquifer were studied in microcosms with 13C-labeled toluene under microoxic conditions. From the total se  ...[more]

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