BayCEER Workshop 2019

Tracing functions within groundwater microbiomes by means of stable isotope probing

O 2.4 in Stable isotopes in environmental research - bridging disciplines, organisms and processes

10.10.2019, 15:15-15:30, H36, NW III

Stable isotope probing (SIP) has become a state-of-the-art technology in environmental microbiology, allowing for the targeted detection and identification of organisms, metabolic pathways, and organismic interactions involved in specific biodegradation processes within complex microbial communities. While the labelling of different biomarkers such as membrane lipids, DNA, rRNA and proteins have been intensively employed over the last decade, the detection of labelled transcriptomes of pollutant-degrading microbial communities remains mostly untapped. Via a targeted approach to process-relevant gene expression in complex microbiomes, it can alleviate some of the major limitations of current non-target environmental ‘omics. Here, we demonstrate the feasibility of total RNA-SIP in experiments where microbes from a hydrocarbon-contaminated aquifer were studied in microcosms with ¹³C-labelled-toluene to understand their adaptation to the simultaneous availability of low levels of different electron acceptors. SIP successfully resolved the involvement of microaerobic vs. aerobic and anaerobic populations. Under microoxic, nitrate-amended conditions hydrocarbon degradation was actually stimulated, but transcripts of denitrification showed no signs of ¹³C-labelling. The expression of distinct oxygenase-based catabolic pathways for toluene degradation was clearly apparent in ¹³C-labelled mRNA. We discuss how these direct insights into the gene expression and adaptation mechanisms within complex degrader communities can guide more integrated approaches in monitoring and restoration of contaminated sites.

Keywords: Stable isotope labelling Environmental microbiology Groundwater Pollutant degradation

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