Meta-omics-aided isolation of an elusive anaerobic arsenic-methylating soil bacterium.

Viacava, Karen; Qiao, Jiangtao; Janowczyk, Andrew; Poudel, Suresh; Jacquemin, Nicolas; Meibom, Karin Lederballe; Shrestha, Him K; Reid, Matthew C; Hettich, Robert L; Bernier-Latmani, Rizlan (2022). Meta-omics-aided isolation of an elusive anaerobic arsenic-methylating soil bacterium. The ISME journal, 16(7), pp. 1740-1749. Springer Nature 10.1038/s41396-022-01220-z

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Soil microbiomes harbour unparalleled functional and phylogenetic diversity. However, extracting isolates with a targeted function from complex microbiomes is not straightforward, particularly if the associated phenotype does not lend itself to high-throughput screening. Here, we tackle the methylation of arsenic (As) in anoxic soils. As methylation was proposed to be catalysed by sulfate-reducing bacteria. However, to date, there are no available anaerobic isolates capable of As methylation, whether sulfate-reducing or otherwise. The isolation of such a microorganism has been thwarted by the fact that the anaerobic bacteria harbouring a functional arsenite S-adenosylmethionine methyltransferase (ArsM) tested to date did not methylate As in pure culture. Additionally, fortuitous As methylation can result from the release of non-specific methyltransferases upon lysis. Thus, we combined metagenomics, metatranscriptomics, and metaproteomics to identify the microorganisms actively methylating As in anoxic soil-derived microbial cultures. Based on the metagenome-assembled genomes of microorganisms expressing ArsM, we isolated Paraclostridium sp. strain EML, which was confirmed to actively methylate As anaerobically. This work is an example of the application of meta-omics to the isolation of elusive microorganisms.

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