Asgard archaea in the haima cold seep: Spatial distribution and genomic insights

Lu, Rui; Gao, Zhaoming; Li, Wenli; Wei, Zhanfei; Wei, Tao-Shu; Huang, Junzhe; Li, Meng; Tao, Jun; Hong-bin, Wang; Wang, Yong

doi:10.1016/j.dsr.2021.103489

Cited by 15 publications

(12 citation statements)

References 58 publications

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“…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%

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: Methodsmentioning

confidence: 99%

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

et al. 2023

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“…Samples of SY5, SY6 and S11 were obtained from sediments of Haima cold seep areas 59 and raw sequencing data were deposited in NCBI SRA (PRJNA739036 and PRJNA738468). For other samples, sample collection and DNA sequencing were detailed previously 7, 8, 60–62 . The 68 sediment samples were catalogued into eight groups according to depth below the seafloor ( Supplementary Figure 2 ): 0-0.05 mbsf (n = 11); 0.05-0.1 mbsf (n = 14); 0.1-0.2 mbsf (n = 16); 0.2-0.3 mbsf (n = 8); 0.3-1.0 mbsf (n = 6);1.0-2.0 mbsf (n = 4); 2.0-3.0 mbsf (n = 4); 3.0-4.5 mbsf (n = 5).…”

Section: Methodsmentioning

confidence: 99%

Section: Metagenomes For Deep-sea Cold Seep Sedimentsmentioning

confidence: 99%

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

Dong

Peng

Wang

et al. 2022

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Deep sea cold seep sediments host abundant and diverse bacterial and archaeal populations that significantly influence biogeochemical cycles. While numerous studies have revealed the community structure and functional capabilities of cold seep microbiomes, little is known about their genetic heterogeneity within species. Here, we examined intraspecies diversity patterns of 39 abundant species identified in sediment layers down to 4.3 mbsf across six cold seep sites from around the world. These species were predicted to participate in methane oxidation and sulfate reduction, and based on their metabolic capabilities, grouped as aerobic methane-oxidizing bacteria (MOB), anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB). These physiologically and phylogenetically diverse MOB, ANME and SRB display different degrees of intrapopulation sequence divergence and different evolutionary trajectories. Populations were in general characterized by low rates of homologous recombination and strong purifying selection with most of the nucleotide variation being synonymous. Functional genes related to methane (pmoAandmcrA) and sulfate (dsrA) metabolisms were found to be under strong purifying selection in the vast majority of species investigated, although examples of active positive selection were also observed. These genes differed in evolutionary trajectories across phylogenetic clades but are functionally conserved across cold seep sites. Intrapopulation diversification of MOB, ANME and SRB species as well as theirmcrAanddsrAgenes was observed to be depth-dependent and undergo divergent selection pressures throughout the sediment column. These results highlight the role of the interplay between ecological processes and the evolution of key bacteria and archaea in deep sea cold seep sediments and shed light on how microbial populations adapt in the subseafloor biosphere.

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“…Part of these metagenomes were downloaded from NCBI's Sequence Read Archive, including datasets derived from Haakon Mosby mud volcano, Eastern North Pacific ODP site 1244, Mediterranean Sea Amon mud volcano, Santa Monica Mounds, and Gulf of Mexico 66,[82][83][84][85] . Other data were obtained from our previous publications described in detail Article https://doi.org/10.1038/s41467-022-32503-w elsewhere 11,40,71,86,87 , including a Scotian Basin cold seep in the northwest Atlantic Ocean, and the South China Sea cold seeps Jiaolong, Haiyang4, Site F and Haima (Supplementary Data 1).…”

Section: Metagenomic Datasets For Deep-sea Cold Seep Sedimentsmentioning

confidence: 99%

Phylogenetically and catabolically diverse diazotrophs reside in deep-sea cold seep sediments

et al. 2022

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Microbially mediated nitrogen cycling in carbon-dominated cold seep environments remains poorly understood. So far anaerobic methanotrophic archaea (ANME-2) and their sulfate-reducing bacterial partners (SEEP-SRB1 clade) have been identified as diazotrophs in deep sea cold seep sediments. However, it is unclear whether other microbial groups can perform nitrogen fixation in such ecosystems. To fill this gap, we analyzed 61 metagenomes, 1428 metagenome-assembled genomes, and six metatranscriptomes derived from 11 globally distributed cold seeps. These sediments contain phylogenetically diverse nitrogenase genes corresponding to an expanded diversity of diazotrophic lineages. Diverse catabolic pathways were predicted to provide ATP for nitrogen fixation, suggesting diazotrophy in cold seeps is not necessarily associated with sulfate-dependent anaerobic oxidation of methane. Nitrogen fixation genes among various diazotrophic groups in cold seeps were inferred to be genetically mobile and subject to purifying selection. Our findings extend the capacity for diazotrophy to five candidate phyla (Altarchaeia, Omnitrophota, FCPU426, Caldatribacteriota and UBA6262), and suggest that cold seep diazotrophs might contribute substantially to the global nitrogen balance.

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Asgard archaea in the haima cold seep: Spatial distribution and genomic insights

Cited by 15 publications

References 58 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

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

Phylogenetically and catabolically diverse diazotrophs reside in deep-sea cold seep sediments

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