A global survey of arsenic-related genes in soil microbiomes

BMC Biol. 2019 May 30;17(1):45. doi: 10.1186/s12915-019-0661-5.

Abstract

Background: Environmental resistomes include transferable microbial genes. One important resistome component is resistance to arsenic, a ubiquitous and toxic metalloid that can have negative and chronic consequences for human and animal health. The distribution of arsenic resistance and metabolism genes in the environment is not well understood. However, microbial communities and their resistomes mediate key transformations of arsenic that are expected to impact both biogeochemistry and local toxicity.

Results: We examined the phylogenetic diversity, genomic location (chromosome or plasmid), and biogeography of arsenic resistance and metabolism genes in 922 soil genomes and 38 metagenomes. To do so, we developed a bioinformatic toolkit that includes BLAST databases, hidden Markov models and resources for gene-targeted assembly of nine arsenic resistance and metabolism genes: acr3, aioA, arsB, arsC (grx), arsC (trx), arsD, arsM, arrA, and arxA. Though arsenic-related genes were common, they were not universally detected, contradicting the common conjecture that all organisms have them. From major clades of arsenic-related genes, we inferred their potential for horizontal and vertical transfer. Different types and proportions of genes were detected across soils, suggesting microbial community composition will, in part, determine local arsenic toxicity and biogeochemistry. While arsenic-related genes were globally distributed, particular sequence variants were highly endemic (e.g., acr3), suggesting dispersal limitation. The gene encoding arsenic methylase arsM was unexpectedly abundant in soil metagenomes (median 48%), suggesting that it plays a prominent role in global arsenic biogeochemistry.

Conclusions: Our analysis advances understanding of arsenic resistance, metabolism, and biogeochemistry, and our approach provides a roadmap for the ecological investigation of environmental resistomes.

Keywords: Arsenic; Biogeography; Bioinformatics; Functional gene; Horizontal gene transfer; Phylogenetic diversity; Phylogeny; Plasmid; Resistome; Targeted gene assembly.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Access to Information
  • Arsenic / adverse effects*
  • Arsenic / metabolism
  • Bacteria / drug effects*
  • Bacteria / genetics
  • Bacteria / metabolism
  • Drug Resistance, Bacterial / genetics*
  • Microbiota / drug effects*
  • Microbiota / genetics
  • Soil Microbiology*
  • Soil Pollutants / adverse effects*

Substances

  • Soil Pollutants
  • Arsenic