Active Anaerobic Archaeal Methanotrophs in Recently Emerged Cold Seeps of Northern South China Sea

Abstract

Cold seep ecosystems are developed from methane-rich fluids in organic rich continental slopes, which are the source of various dense microbial and faunal populations. Extensive studies have been conducted on microbial populations in this unique environment; most of them were based on DNA, which could not resolve the activity of extant organisms. In this study, RNA and DNA analyses were performed to evaluate the active archaeal and bacterial communities and their network correlations, particularly those participating in the methane cycle at three sites of newly developed cold seeps in the northern South China Sea (nSCS). The results showed that both archaeal and bacterial communities were significantly different at the RNA and DNA levels, revealing a higher abundance of methane-metabolizing archaea and sulfate-reducing bacteria in RNA sequencing libraries. Site ROV07-01, which exhibited extensive accumulation of deceased Calyptogena clam shells, was highly developed, and showed diverse and active anaerobic archaeal methanotrophs (ANME)-2a/b and sulfate-reducing bacteria from RNA libraries. Site ROV07-02, located near carbonate crusts with few clam shell debris, appeared to be poorly developed, less anaerobic and less active. Site ROV05-02, colonized by living Calyptogena clams, could likely be intermediary between ROV07-01 and ROV07-02, showing abundant ANME-2dI and sulfate-reducing bacteria in RNA libraries. The high-proportions of ANME-2dI, with respect to ANME-2dII in the site ROV07-01 was the first report from nSCS, which could be associated with recently developed cold seeps. Both ANME-2dI and ANME-2a/b showed close networked relationships with sulfate-reducing bacteria; however, they were not associated with the same microbial operational taxonomic units (OTUs). Based on the geochemical gradients and the megafaunal settlements as well as the niche specificities and syntrophic relationships, ANMEs appeared to change in community structure with the evolution of cold seeps, which may be associated with the heterogeneity of their geochemical processes. This study enriched our understanding of more active sulfate-dependent anaerobic oxidation of methane (AOM) in poorly developed and active cold seep sediments by contrasting DNA- and RNA-derived community structure and activity indicators.

Horizontal and vertical heterogeneity of sediment microbial community in Site F cold seep, the South China Sea

“…Our result of co-occurrence network showed that ANME-1b was associated strongly with SEEP-SRB2, which was consistent with the finding conducted in Haima cold seep (Zhang et al, 2020). In addition, there were proportional abundances of SEEP-SRB1, ANME-2, and Methanosarcinales in NRS.…”

“…HS − + HCO − 3 + H 2 O, which is usually performed by a consortium of anaerobic methanotrophic archaea (ANME) and SRB (Hoehler et al, 1994;Cui et al, 2019). ANME, which could be classified into ANME-1, ANME-2, and ANME-3, are found widely distributed in cold seep sediments (Knittel et al, 2005;Vigneron et al, 2013;McKay et al, 2016;Niu et al, 2017;Wu et al, 2018;Cui et al, 2019;Zhang et al, 2020). ANME-1 are divided into ANME-1a and ANME-1b subgroups, whereas ANME-2 are most widely distributed and divided into ANME-2a, ANME-2b, ANME-2c, and ANME-2d subgroups (Orphan et al, 2002;Mills et al, 2003;Knittel et al, 2005).…”

“…In general, the syntrophic partners of ANME-1 and ANME-2 are SRB affiliated with Desulfosarcina/Desulfococcus (DSS; within the Desulfobacteraceae) or Desulfobulbus (DBB; within the Desulfobulbaceae) (Orphan et al, 2001a;Orphan et al, 2001b;Orphan et al, 2002;Boetius et al, 2000;Jørgensen and Boetius, 2007;Zhang et al, 2020). It was found that ANME-1 were associated to SEEP-SRB2 (within the Desulfuribacteraceae) (Ruff et al, 2016); ANME-2 were associated to SEEP-SRB1 (members of DSS), SEEP-SRB2, and SEEP-DBB (members of DBB) (Orphan et al, 2001a;Pernthaler et al, 2008;Kleindienst et al, 2012;Green-Saxena et al, 2014;Ruff et al, 2016); and ANME-3 were associated with DBB and SEEP-SRB1 (Niemann et al, 2006;Lösekann et al, 2007;Schreiber et al, 2010).…”

Diversity of Anaerobic Methane Oxidizers in the Cold Seep Sediments of the Okinawa Trough

“…Methyl coenzyme M reductase A genes in the seep sediments of the OT from the surface to bottom layers were between 10 5 and 10 8 genes g −1 (wet weight), which was higher than the abundances observed in the Haima cold seep (10 3 –10 7 genes g −1 ; Niu et al, 2017 ), northern continental slope of South China Sea (10 3 –10 5 genes g −1 ; Fan et al, 2017 ), and cold seeps of the Northern South China Sea (10 5 genes g −1 ; Zhang et al, 2020 ). In addition, we used 16S rRNA and mcrA genes to investigate the diversity of methane metabolic microbes.…”

Metal-driven anaerobic oxidation of methane as an important methane sink in methanic cold seep sediments

“…Tables S1, S6 and S7), the results of the reaction-transport modeling predict the model-derived rates for Fe-AOM of up ∼0.02 μmol CH 4 cm −3 d −1 in the methanic zone (Figure 4 and Table 1). These rates are more than 20 times as big as the estimated potential Fe-AOM rates from in situ marine methanic sediments with much higher Fe 2+ concentration (180~800 µM) [20][21][22][23] (Table 1), but much lower than those derived from stimulated microbial communities in laboratory incubation studies 5,24,25,49 .…”