Deep sea cold seep is an atmospheric Hg sink and MeHg source

Li, Jiwei; Dong, Xiyang; Tang, Yongjie; Zhang, Chuwen; Yang, Yongheng; Zhang, Wei; Liu, Shanshan; Feng, Xinbin; Shang, Lihai; Peng, Xiaotong

doi:10.21203/rs.3.rs-2323106/v1

Cited by 6 publications

(11 citation statements)

References 49 publications

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“…Similar trends of microdiversity with depth for these populations were also observed within their mcrA and dsrA genes at some specific sites (Supplementary Data 9 ). Since differences between sites depend on seepage dynamics influencing redox zonation 4 , evolutionary metrics were also examined in relation to available sediment porewater geochemistry from SY and S11 sites 61 , 62 , including sulfate (SO 4 2− ), dissolved inorganic carbon (DIC) and methane (CH 4 ) levels. Two-tailed Pearson correlation tests (Supplementary Data 10 ) confirm that evolutionary metrics in several populations were significantly related to these three parameters, with DIC and CH 4 likely exerting strong selection pressure on microbial populations based on being negatively correlated with pN/pS values at the genome level.…”

Section: Resultsmentioning

confidence: 99%

“…For samples from the Northwestern Gulf of Mexico, metagenomic data sets along with metadata were downloaded from NCBI Sequencing Read Archive (SRA) and NCBI BioProject databases ( https://www.ncbi.nlm.nih.gov/bioproject/PRJNA553005 ) 63 . The other 63 metagenomic data sets used in this study were obtained from our previous publications 3 , 11 , 31 , 61 , 62 , 64 , 65 (details in Supplementary Data 1 ). Geochemical parameters (SO 4 2− , DIC, and CH 4 ) from SY and S11 sites and cell densities from the SB site were collected from our previous publications 3 , 61 , 62 .…”

Section: Methodsmentioning

confidence: 99%

“…The other 63 metagenomic data sets used in this study were obtained from our previous publications 3 , 11 , 31 , 61 , 62 , 64 , 65 (details in Supplementary Data 1 ). Geochemical parameters (SO 4 2− , DIC, and CH 4 ) from SY and S11 sites and cell densities from the SB site were collected from our previous publications 3 , 61 , 62 . The 68 sediment samples were cataloged into eight groups according to depth below the sea floor (Supplementary Fig.…”

Section: Methodsmentioning

confidence: 99%

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Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps

et al. 2023

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Deep sea cold seep sediments host abundant and diverse microbial populations that significantly influence biogeochemical cycles. While numerous studies have revealed their community structure and functional capabilities, little is known about genetic heterogeneity within species. Here, we examine intraspecies diversity patterns of 39 abundant species identified in sediment layers down to 430 cm below the sea floor across six cold seep sites. These populations are grouped as aerobic methane-oxidizing bacteria, anaerobic methanotrophic archaea and sulfate-reducing bacteria. Different evolutionary trajectories are observed at the genomic level among these physiologically and phylogenetically diverse populations, with generally low rates of homologous recombination and strong purifying selection. Functional genes related to methane (pmoA and mcrA) and sulfate (dsrA) metabolisms are under strong purifying selection in most species investigated. These genes differ in evolutionary trajectories across phylogenetic clades but are functionally conserved across sites. Intrapopulation diversification of genomes and their mcrA and dsrA genes is depth-dependent and subject to different selection pressure throughout the sediment column redox zones at different sites. These results highlight the interplay between ecological processes and the evolution of key bacteria and archaea in deep sea cold seep extreme environments, shedding light on microbial adaptation in the subseafloor biosphere.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps

et al. 2023

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“…Sediment cores penetrated 18 to 20 cm into the seabed. Details for DNA sequencing can be found elsewhere 28 and involved genomic DNA extraction with the MO BIO PowerSoil DNA Isolation Kit followed by sequencing on the MGI sequencing platforms DNBSEQ-T1 or BGISEQ500 (MGI Tech Co., Ltd., China) at BGI-Shenzhen (China).…”

Section: Sample Description Metagenomic Sequencing and Analysismentioning

confidence: 99%

Viruses in deep-sea cold seep sediments harbor diverse survival mechanisms and remain genetically conserved within species

Peng

Zhang

Pan

et al. 2023

Preprint

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Deep sea cold seep sediments have been discovered to harbor novel, abundant, and diverse bacterial and archaeal viruses. However, little is known about viral genetic features and evolutionary patterns in these environments. Here, we examined the evolutionary ecology of viruses across active and extinct seep stages in the area of Haima cold seeps in the South China Sea. Diverse antiviral defense systems in 487 microbial genomes spanning 43 families inform the dynamics of host-virus interactions. Accordingly, a total of 338 viral operational taxonomic units are identified and linked to 36 bacterial and archaeal phyla. Cold seep viruses are predicted to harbor diverse adaptive strategies to persist in this environment, including counter-defense systems, reverse transcriptases, auxiliary metabolic genes, and alternative genetic code assignments. Extremely low nucleotide diversity is observed in cold seep viral populations, being influenced by factors including microbial host, sediment depth and cold seep stage. Most cold seep viral genes are under strong purifying selection with trajectories that differ depending on whether cold seeps are active or extinct. This work sheds light on the understanding of environmental adaptation mechanisms and evolutionary patterns of viruses in the sub-seafloor biosphere.

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“…These sites are as follows: Eastern North Pacific (ENP), Santa Monica Mounds Bioinformatics Institute-European Nucleotide Archive (EBI-ENA) according to the accession numbers published in each study [8][9][10]35,[38][39][40][41] . The remaining 106 metagenomic datasets used in this study were obtained from our previous publications 7,12,[42][43][44][45][46][47][48][49] .…”

Section: Collection Of Metagenomesmentioning

confidence: 99%

A comprehensive catalog with 100 million genes and 3,000 metagenome-assembled genomes from global cold seep sediments

Han

Zhang

Zhao

et al. 2023

Preprint

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Cold seeps harbor abundant and diverse microbial microbes that represent a tremendous potential for biological applications and also have a significant influence on biogeochemical cycles. Though recent metagenomic studies have expanded our understanding of the microbial community and function of seep microorganisms, the knowledge of diversity and genetic repertoire of global seep microbes is lacking. Here, we collected a compilation of 165 metagenomic data from 16 cold seep sites across the globe to construct comprehensive gene and genome catalogs. The non-redundant gene catalog was comprised of 147 million genes (clustered at 95% amino acid identity), and 35.72% of them could not be assigned to a function with the currently available databases. A total of 3,164 species-level representative metagenome-assembled genomes (MAGs) are obtained, most of which (94.31%) belong to novel species. Of them, 81 ANME species are identified covering all subclades except ANME-2d, and 23 syntrophic SRB species spanning Seep-SRB1a Seep-SRB1g, and Seep-SRB2 clades. The non-redundant gene and MAGs catalogs are a valuable resource that enables expanded knowledge of the structure and functions of cold seep microbiomes.

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Deep sea cold seep is an atmospheric Hg sink and MeHg source

Cited by 6 publications

References 49 publications

Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps

Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps

Viruses in deep-sea cold seep sediments harbor diverse survival mechanisms and remain genetically conserved within species

A comprehensive catalog with 100 million genes and 3,000 metagenome-assembled genomes from global cold seep sediments

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