Biogeochemical Activity of Methane-Related Microbial Communities in Bottom Sediments of Cold Seeps of the Laptev Sea

Abstract

Bottom sediments at methane discharge sites of the Laptev Sea shelf were investigated. The rates of microbial methanogenesis and methane oxidation were measured, and the communities responsible for these processes were analyzed. Methane content in the sediments varied from 0.9 to 37 µmol CH4 dm−3. Methane carbon isotopic composition (δ13C-CH4) varied from −98.9 to −77.6‰, indicating its biogenic origin. The rates of hydrogenotrophic methanogenesis were low (0.4–5.0 nmol dm−3 day−1). Methane oxidation rates varied from 0.4 to 1.2 µmol dm−3 day−1 at the seep stations. Four ANME methanotrophic lineages (1, 2a–2b, 2c, and 3) (Methanosarciniales, phylum Halobacterota) were predominant (up to 46.3% of the whole community). Aerobic ammonium-oxidizing Crenarchaeota (family Nitrosopumilaceae) predominated in the upper sediments. Most archaea (up to 8%) were represented by new lineages, for which the metabolic pathways are presently unknown. Predominant bacteria in the upper sediments were heterotrophic Actinobacteriota and Bacteroidota. Members of the genera Sulfurovum and Sulfurimonas occurred in the sediments of the seep stations. Mehtanotrophs of the classes Alphaproteobacteria (Methyloceanibacter) and Gammaproteobacteria (families Methylophilaceae and Methylomonadaceae) occurred in the sediments of all stations. The microbial community composition was similar to that of methane seep sediments from geographically remote areas of the global ocean.

A comprehensive genomic catalog from global cold seeps

“…These sites are as follows: Eastern North Pacific (ENP), Santa Monica Mounds (SMM), Western Gulf of Mexico (WGM), Eastern Gulf of Mexico (EGM), Northwestern Gulf of Mexico (NGM), Scotian Basin (SB), Haakon Mosby mud volcano (HM), Mediterranean Sea (MS), Laptev Sea (LS), Jiaolong cold seep (JL), Shenhu area (SH), Haiyang4 (HY4), Qiongdongnan Basin (QDN), Xisha Trough (XST), Haima seep (HM1, HM3, HM5, HM_SQ, S11, SY5, and SY6) and site F cold seep (RS, SF, FR, and SF_SQ). Paired-end sequencing data from ENP, SMM, WGM, NGM, HM, MS, LS and part of site F (RS and FR) were downloaded from the National Center for Biotechnology Information-Sequence Read Archive (NCBI-SRA) and European Bioinformatics Institute-European Nucleotide Archive (EBI-ENA) according to the accession numbers published in each study 8 – 10 , 22 – 26 . The remaining 106 metagenomic datasets used in this study were obtained from our previous publications 7 , 14 , 27 – 34 .…”

“…Culture-independent metagenomic techniques are the key to unraveling the genetic diversity and metabolic potential of uncharacterized microbes and have been applied to identify thousands of microorganisms and their metabolic versatility. Recently, the microbial community and function of cold seep sediments have been increasingly studied with metagenomes obtained from different sea areas 7 – 10 . However, there are no large-scale gene and genome catalogs available for the microbiome of global cold seeps.…”

Opportunistic consumption of marine pelagic, terrestrial, and chemosynthetic organic matter by macrofauna on the Arctic shelf: a stable isotope approach

“…Contrary, small-scale heterogeneity was expected at the “Seep” habitat (stations 5625, 6939, 6947, 6952, 6953, 6992) as there is evidence that chemosynthetic production is distributed very locally, e.g ., patches of white microbial mats ( Baranov et al, 2020 ; Vedenin et al, 2020 ). The “Background” station (6950) was located outside of the influence of the Lena River runoff but close to the “Seep” stations so that they would be similar in terms of bentho-pelagic coupling and fluxes of organic matter to the seafloor but differ in the sediment biogeochemical processes associated with microbial activities ( Savvichev et al, 2018 ; Savvichev et al, 2023 ). Although the “Background” and “Delta” had only one location sampled, we consider the number of animals sampled from each of these habitats to be sufficient to represent the isotopic niche of respective communities ( Table 1 ; Table S1 ).…”

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

“…Culture-independent metagenomic techniques are the key to unraveling genetic diversity and metabolic potential of uncharacterized microbes, and have been applied to identify thousands of microorganisms and their metabolic versatility. Recently, the microbial community and function of cold seep sediments are increasingly studied with metagenomes obtained from different sea areas [7][8][9][10] . However, there are no large-scale gene and genome catalogs available for the microbiome of global cold seeps.…”

“…1a; Supplementary Table 1). 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] .…”