The majority of microorganisms in gas hydrate-bearing subseafloor sediments ferment macromolecules

Abstract

Background Gas hydrate-bearing subseafloor sediments harbor a large number of microorganisms. Within these sediments, organic matter and upward-migrating methane are important carbon and energy sources fueling a light-independent biosphere. However, the type of metabolism that dominates the deep subseafloor of the gas hydrate zone is poorly constrained. Here we studied the microbial communities in gas hydrate-rich sediments up to 49 m below the seafloor recovered by drilling in the South China Sea. We focused on distinct geochemical conditions and performed metagenomic and metatranscriptomic analyses to characterize microbial communities and their role in carbon mineralization. Results Comparative microbial community analysis revealed that samples above and in sulfate-methane interface (SMI) zones were clearly distinguished from those below the SMI. Chloroflexota were most abundant above the SMI, whereas Caldatribacteriota dominated below the SMI. Verrucomicrobiota, Bathyarchaeia, and Hadarchaeota were similarly present in both types of sediment. The genomic inventory and transcriptional activity suggest an important role in the fermentation of macromolecules. In contrast, sulfate reducers and methanogens that catalyze the consumption or production of commonly observed chemical compounds in sediments are rare. Methanotrophs and alkanotrophs that anaerobically grow on alkanes were also identified to be at low abundances. The ANME-1 group actively thrived in or slightly below the current SMI. Members from Heimdallarchaeia were found to encode the potential for anaerobic oxidation of short-chain hydrocarbons. Conclusions These findings indicate that the fermentation of macromolecules is the predominant energy source for microorganisms in deep subseafloor sediments that are experiencing upward methane fluxes.

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

“…The sites include: 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). Additionally, 33 metatranscriptomic data were obtained from our previous publications 51, 77, 79, 81 , including those from South China Sea cold seeps in Jiaolong, Haima, Qiongdongnan Basin, and the Shenhu area. The detailed information of the metagenomic and metatranscriptomic datasets used in this study were described in our previous cold seep gene catalog publication 82 .…”

“…Additionally, 33 metatranscriptomic data were obtained from our previous publications ( Supplementary Fig. 1 ) 50, 64, 75, 78 , including those from South China Sea cold seeps in Jiaolong, Haima, Qiongdongnan Basin, and the Shenhu area. The detailed information of the metagenomic and metatranscriptomic datasets used in this study were described in our previous cold seep gene catalog publication 40 .…”

“…Fermentation is the main process transforming organic carbon in cold seep environments 1,51 , which produces significant amounts of hydrogen (H 2 ) and various organic acids, both of which are key electron donors for organohalide reducers 41,48,52,11 . Consistently, 288 organohalide reducers were found to encode 495 hydrogenases.…”

“…These samples were collected from 16 geographically diverse cold seep sites from around the world (Supplementary Fig. 1) 1,3,40,50,64,[67][68][69][70][71][72][73][74][75][76][77] , encompassing various types of cold seeps such as oil and gas seeps, methane seeps, gas hydrates, asphalt volcanoes, and mud volcanoes. The sites include: 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).…”

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

“…1 ). Among them, 65 metagenomes and 10 metatranscriptomes were compiled from our previous publications 8 , 59 , and other 22 metagenomes were downloaded from NCBI Sequencing Read Archive (SRA). A detailed description of sampling locations and sequencing information for metagenomic and metatranscriptomic data is given in Supplementary Data 1 .…”