Linking Genes to Microbial Biogeochemical Cycling: Lessons from Arsenic

Abstract

The biotransformation of arsenic is highly relevant to the arsenic biogeochemical cycle. Identification of the molecular details of microbial pathways of arsenic biotransformation coupled with analyses of microbial communities by meta-omics can provide insights into detailed aspects of the complexities of this biocycle. Arsenic transformations couple to other biogeochemical cycles, and to the fate of both nutrients and other toxic environmental contaminants. Microbial redox metabolism of iron, carbon, sulfur, and nitrogen affects the redox and bioavailability of arsenic species. In this critical review we illustrate the biogeochemical processes and genes involved in arsenic biotransformations. We discuss how current and future metagenomic-, metatranscriptomic-, metaproteomic-, and metabolomic-based methods will help to decipher individual microbial arsenic transformation processes, and their connections to other biogeochemical cycle. These insights will allow future use of microbial metabolic capabilities for new biotechnological solutions to environmental problems. To understand the complex nature of inorganic and organic arsenic species and the fate of environmental arsenic will require integrating systematic approaches with biogeochemical modeling. Finally, from the lessons learned from these studies of arsenic biogeochemistry, we will be able to predict how the environment changes arsenic, and, in response, how arsenic biotransformations change the environment.

Evidence of differential adaptation to decreased temperature by anammox bacteria

“…Recently, mass spectrometry based metaproteomic approaches are attracting particular attention for discovering microbial functions in mixed culture systems (Barr et al, 2015;Mosier et al, 2015;de Almeida et al, 2016;Salerno et al, 2016). mRNA levels can respond rapidly and sensitively to environmental conditions changes, while changes in protein abundances can be comparatively much slower (Zhu et al, 2017). The correlation between mRNA and protein inventories in environmental microbial communities can be generally week (Zhu et al, 2017).…”

“…mRNA levels can respond rapidly and sensitively to environmental conditions changes, while changes in protein abundances can be comparatively much slower (Zhu et al, 2017). The correlation between mRNA and protein inventories in environmental microbial communities can be generally week (Zhu et al, 2017). It can be observed that mRNA levels do not always coincide with bacterial activities (Wang et al, 2016a,b).…”

Arsenic Methylation Dynamics in a Rice Paddy Soil Anaerobic Enrichment Culture

“…15 Methylation has traditionally been understood as a detoxification process, particularly in aerobic systems in which As(III) is converted into less toxic pentavalent methylated species, or into volatile arsines which are removed from environmental media via volatilization. 12,14,16,17 The formation of very toxic trivalent methylated species complicates this interpretation, however, particularly in anaerobic environments in which trivalent methylarsenicals are not oxidized to their pentavalent derivatives. 15 arsM genes are present in phylogenetically and functionally diverse microorganisms 8,9,11,18−20 and are widely distributed in soil, freshwater, and marine ecosystems.…”

Taxonomically and metabolically distinct microbial communities with depth and across a hillslope to riparian zone transect

“…The seed sequences for the HMMs were taken from Zhu et. al., [69] and references within. Seed sequences were added by searching for amino acid sequences of proteins with similar function and structure by searching NCBI's nr database with BLASTp to increase the taxonomic diversity.…”