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

Abstract

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.

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

“…We investigated the biosynthetic potential of the cold seep microbiome at global scale by first analyzing 2,479 previous constructed metagenome-assembled genomes (MAGs; 1,992 bacterial, 487 archaeal) spanning 89 phyla 7,45 (Figure 1, Supplementary Figure 1 and Supplementary Table 2). A total of 2,865 BGCs (longer than 10 kb; 2,627 bacterial and 238 archaeal) were predicted (Figure 2a, b and Supplementary Table 3).…”

“…These sites are as follows: Eastern Gulf of Mexico (EGM), Northwestern Gulf of Mexico (GOM), Scotian Basin (SB), Haima seep (HM1, HM3, HM5, S11, SY5, SY6), Haiyang4 (HY4), Site F cold seep (SF), Qiongdongnan Basin (QDN), Shenhu area (SH), and Jiaolong cold seep (JL). Detailed descriptions of the sampling sites and sequencing information for the metagenomic and metatranscriptomic data can be found in our previous work 7,45,58,80 . Paired-end raw reads were quality-controlled by trimming primers and adapters and filtering out artifacts and low-quality reads using the Read_QC module within the metaWRAP pipeline (v1.3.2; -skip-bmtagger) 81 .…”