New Preprint: Targeting microbial arsenic resistance genes: a new bioinformatic toolkit informs arse

Taylor, Susanna, and Ashley have a new preprint out on the biorxiv this week!

Here's the link.

Targeting microbial arsenic resistance genes: a new bioinformatic toolkit informs arsenic ecology and evolution in soil genomes and metagenomes.

Microbial communities impact the biogeochemical cycling of arsenic, a ubiquitous and toxic metalloid that impacts human and animal health. The ecology of arsenic resistance genes in the environment is not well understood, especially within the context of diverse microbial communities. We developed an open-access bioinformatic toolkit for testing different sequencing datasets for nine arsenic resistance genes: acr3, aioA, arsB, arsC (grx), arsC (trx), arsD, arsM, arrA, and arxA. Our toolkit includes BLAST databases, hidden markov models and resources for gene-targeted assembly of arsenic resistance genes. We used this toolkit to examine the phylogenetic diversity, genomic location (chromosome or plasmid), and biogeography of arsenic resistance genes in genomes and metagenomes from soil, providing a synthesis of arsenic resistance from the most microbially diverse and complex environment. We found that arsenic resistance genes were common, though not universally detected, in genomes and metagenomes from soils, contradicting the common conjecture that all organisms have arsenic resistance genes. From soil genomes, we defined major clades and explored the potential for horizontal and vertical transfer of each gene family, informing their evolutionary histories. Microbial communities differed in their potential to impact arsenic biogeochemical cycling because different types of resistances were detected in different proportions, in different soils. Arsenic resistance genes were globally distributed but particular sequence variants were highly endemic (e.g., acr3), suggesting dispersal limitation. The gene encoding arsenic methylation arsM was abundant in soil metagenomes (median 48%), suggesting that it plays a previously understated and prominent role in arsenic biogeochemistry globally. Use of this flexible toolkit to understand arsenic resistance in a variety of environments will inform the foundations of microbial arsenic ecology and evolution, and provide insights into environmental potentials for arsenic biogeochemical cycling and bioremediation.