Discovery of functional gene markers of bacteria for monitoring hydrocarbon pollution in the marine environment - a metatranscriptomics approach

Abstract

The use of natural marine bacteria as "oil sensors" for the detection of pollution events can be suggested as a novel way of monitoring oil occurrence at sea. Nucleic acid-based devices generically called genosensors are emerging as potentially promising tools for in situ detection of specific microbial marker genes suited for that purpose. Functional marker genes are particularly interesting as targets for oil-related genosensing but their identification remains a challenge. Here, seawater samples, collected in tanks with oil addition mimicking a realistic oil spill scenario, were filtered and archived by the Environmental Sample Processor (ESP), a fully robotized genosensor, and the samples were then used for post-retrieval metatranscriptomic analysis. After extraction, RNA from ESP-archived samples at start, day 4 and day 7 of the experiment was used for sequencing. Metatranscriptomics revealed that several KEGG pathways were significantly enriched in samples exposed to oil. However, these pathways were highly expressed also in the non-oil-exposed water samples, most likely as a result of the release of natural organic matter from decaying phytoplankton. Temporary peaks of aliphatic alcohol and aldehyde dehydrogenases and monoaromatic ringdegrading enzymes (e.g. ben, box, and dmp clusters) were observed on day 4 in both control and oil tanks. Few alkane 1-monooxygenase genes were upregulated on oil, mostly transcribed by families Porticoccaceae and Rhodobacteraceae, together with aromatic ring-hydroxylating dioxygenases, mostly transcribed by Rhodobacteraceae. Few transcripts from obligate hydrocarbonoclastic genera of Alcanivorax, Oleispira and Cycloclasticus, were significantly enriched in the oil-treated tank in comparison to control, and these were mostly transporters and genes involved in nitrogen and phosphorous acquisition. This study highlights the importance of seasonality, i.e., phytoplankton occurrence and senescence leading to organic compound release which can be used preferentially by bacteria over oil compounds, delaying the latter process. As a result, such seasonal effect can reduce the sensitivity of genosensing tools employing bacterial functional genes to sense oil. A better understanding of the use of natural organic matter by bacteria involved in oil-biodegradation is needed to develop an array of functional markers enabling the rapid and specific in situ detection of anthropogenic pollution.

Beyond taxonomy: Validating functional inference approaches in the context of fish‐farm impact assessments

“…Metagenomics, herein defined as the study of the entire DNA material recovered from environmental samples, and metatranscriptomics, as the study of gene expression from mRNA recovered from environmental samples, have also received considerable attention in the last few years (Bourlat et al, 2013; Grossart et al, 2020; Knapik et al, 2019; Semmouri et al, 2020). While amplicon‐based eDNA metabarcoding provides information on which organisms are present, metagenomics and metatranscriptomics enable insights into the functions they possess, and in the latter instance, the activity of these functions.…”