Unexpected genetic and microbial diversity for arsenic cycling in deep sea cold seep sediments

Abstract

Cold seeps, where cold hydrocarbon-rich fluid escapes from the seafloor, showed strong enrichment of toxic metalloid arsenic (As). The toxicity and mobility of As can be greatly altered by microbial processes that play an important role in global As biogeochemical cycling. However, a global overview of genes and microbes involved in As transformation at seeps remains to be fully unveiled. Using 87 sediment metagenomes and 33 metatranscriptomes derived from 13 globally distributed cold seeps, we show that As resistance genes (arsM, arsP, arsC1/arsC2, acr3) were prevalent at seeps and more phylogenetically diverse than previously expected. Asgardarchaeota and a variety of unidentified bacterial phyla (e.g. 4484-113, AABM5-125-24 and RBG-13-66-14) may also function as the key players in As transformation. The abundances of As-cycling genes and the compositions of As-associated microbiome shifted across different sediment depths or types of cold seep. The energy-conserving arsenate reduction or arsenite oxidation could impact biogeochemical cycling of carbon and nitrogen, via supporting carbon fixation, hydrocarbon degradation and nitrogen fixation. Overall, this study provides a comprehensive overview of As-cycling genes and microbes at As-enriched cold seeps, laying a solid foundation for further studies of As cycling in deep sea microbiome at the enzymatic and processual levels.

Phylogenetically and structurally diverse reductive dehalogenases link biogeochemical cycles in deep-sea cold seeps

“…Sulfate reduction and anaerobic methane oxidation, associated with dsrA and mcrA gene activities, respectively, are two important metabolic processes in cold seeps 44, 45 . The observed positive correlation between the abundances of rdhA and dsrA genes indicates that reductive dehalogenation and sulfate reduction processes likely occur simultaneously in cold seeps ( Fig.…”

“…Sulfate reduction and anaerobic methane oxidation, associated with dsrA and mcrA gene activities, respectively, are two important metabolic processes in cold seeps 43,44 .…”

Component specific responses of the microbiomes to common chemical stressors in the human food chain

“…Minor changes were found in the sediment microbiomes, where it mildly increased or decreased according to treatment type. Individual studies of individual components (water 57 , sediments 63 , soils 19 , plants 35 and animals 26 ) may have suggested such heterogeneous changes in beta diversity in response to different stressors. Here, by comparing three stressors on five microbial communities, we demonstrate that the same stressors, in terms of chemical quality and quantity, have differential influence on different microbiomes.…”

“…Minor changes were found in the sediment microbiomes, where it mildly increased or decreased according to treatment type. Individual studies of individual components (water 57 , sediments 63 , soils 19 , plants 35 and animals 26 ) may have suggested such heterogeneous changes in beta diversity in response to different stressors.…”

A vast repertoire of secondary metabolites potentially influences community dynamics and biogeochemical processes in cold seeps

“…For metabolomic studies, seven depth samples from the Qiongdongnan Basin were selected, which also underwent nearly full-length 16S ribosomal RNA (rRNA) gene amplicon sequencing. Detailed descriptions of the sampling sites, depths, cores, and sequencing information for the metagenomic and metatranscriptomic data can be found in table S1 and our previous work (7,48,64,84).…”