Abstract
Soil microbiomes harbor unparalleled functional and phylogenetic diversity and are sources of novel metabolisms. 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. By analogy to mercury, As methylation was proposed to be catalyzed by sulfate-reducing bacteria. However, to date, there are no 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 harboring 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.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Competing Interests Statement: The authors declare there are no competing financial interests in relation to the work described. The work was funded by the Swiss National Science Foundation (SNSF) grant 310030_176146-1 and the SNSF NCCR Microbiomes (grant # 51NF40_180575). The work at ORNL was conducted under the Plant-Microbe Interface Science Focus Area, as supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomic Science Program.
This is the version originally submitted to the ISME journal.