Contrasting Pathways for Anaerobic Methane Oxidation in Gulf of Mexico Cold Seep Sediments

Abstract

Gulf of Mexico sediments harbor numerous hydrocarbon seeps associated with high sedimentation rates and thermal maturation of organic matter. These ecosystems host abundant and diverse microbial communities that directly or indirectly metabolize components of the emitted fluid. To investigate microbial function and activities in these ecosystems, metabolic potential (metagenomic) and gene expression (metatranscriptomic) analyses of two cold seep areas of the Gulf of Mexico were carried out. Seeps emitting biogenic methane harbored microbial communities dominated by archaeal anaerobic methane oxidizers of phylogenetic group 1 (ANME-1), whereas seeps producing fluids containing a complex mixture of thermogenic hydrocarbons were dominated by ANME-2 lineages. Metatranscriptome measurements in both communities indicated high levels of expression of genes for methane metabolism despite their distinct microbial communities and hydrocarbon composition. In contrast, the transcription level of sulfur cycle genes was quite different. In the thermogenic seep community, high levels of transcripts indicative of syntrophic anaerobic oxidation of methane (AOM) coupled to sulfate reduction were detected. This syntrophic partnership between the dominant ANME-2 and sulfate reducers potentially involves direct electron transfer through multiheme cytochromes. In the biogenic methane seep, genes from an ANME-1 lineage that are potentially involved in polysulfide reduction were highly expressed, suggesting a novel bacterium-independent anaerobic methane oxidation pathway coupled to polysulfide reduction. The observed divergence in AOM activities provides a new model for bacterium-independent AOM and emphasizes the variation that exists in AOM pathways between different ANME lineages.IMPORTANCECold seep sediments are complex and widespread marine ecosystems emitting large amounts of methane, a potent greenhouse gas, and other hydrocarbons. Within these sediments, microbial communities play crucial roles in production and degradation of hydrocarbons, modulating oil and gas emissions to seawater. Despite this ecological importance, our understanding of microbial functions and methane oxidation pathways in cold seep ecosystems is poor. Based on gene expression profiling of environmental seep sediment samples, the present work showed that (i) the composition of the emitted fluids shapes the microbial community in general and the anaerobic methanotroph community specifically and (ii) AOM by ANME-2 in this seep may be coupled to sulfate reduction byDeltaproteobacteriaby electron transfer through multiheme cytochromes, whereas AOM by ANME-1 lineages in this seep may involve a different, bacterium-independent pathway, coupling methane oxidation to elemental sulfur/polysulfide reduction.

Thermogenic hydrocarbons fuel a redox stratified subseafloor microbiome in deep sea cold seep sediments

“…These findings mirror those recently reported in the hot Guaymas Basin hydrothermal sediments 40 and thus reveal that recently discovered C 2+ short chain alkane metabolisms are not peculiar to hot hydrothermal settings and are likely much more widespread throughout the deep seabed at cold seeps. A notable difference from other cold seep sediments is that this Scotian Basin site is dominated by ANME-1 rather than ANME-2 lineages 10, 11 , with three distinct ANME-1 groups (S3_bin4, Co_bin174 and S3_bin12) being particularly abundant (27.47%, 7.33% and 4.69%, respectively) at the sulfate methane transition zone (Supplementary Table 2) , an observation supported by 16S rRNA gene amplicon sequencing (Supplementary Table 5) .…”

“…To gain more detailed insights into anaerobic short chain alkane degradation in this non-hydrothermal setting, metabolic pathways involved in the oxidation of methane and non-methane gaseous alkanes were reconstructed 17 (Figure 4) . Twelve MAGs harbour canonical mcrA genes that cluster with ANME-1 and ANME-2 methanotrophs, along with with fwd , ftr , mch , mtd , mer/metF/fae-hps and mtr that mediate subsequent steps in the tetrahydromethanopterin-dependent ‘reverse methanogenesis’ pathway 10, 41 for oxidation of methyl-CoM to CO 2 (Figure 4a and Supplementary Table 6) . Some MAGs lack specific genes in this pathway, likely reflecting variability in genome completeness (61% to 96%).…”

“…ANME-1 MAGs were 60 to 91% complete, so it cannot be ruled out that they harbour canonical or alternative reductases e.g. as in the recently proposed bacterium-independent anaerobic methane oxidation 10 whereby reverse methanogenesis is coupled to reduction of elemental sulfur and polysulfide. Consistent with this model, genes encoding sulfide:quinone oxidoreductase-like proteins in ANME-1 MAGs S3_bin4 and Co_bin174 were detected in deeper layers of the sediment where sulfate was depleted (e.g.…”

“…Multiple 16S rRNA gene surveys have revealed that cold seep sediments at or near the sediment-water interface host an extensive diversity of archaeal and bacterial lineages 5–9 . However, much less is known about metabolic versatility of this diverse microbiome, and how surface and subsurface populations are connected and differentiated in different redox zones within the sediment column 10, 11 . Most seep-associated microorganisms lack sequenced genomes, precluding meaningful predictions of relationships between microbial lineages and their biogeochemical functions 4, 8, 10–13 .…”

Lateral gene transfer drives metabolic flexibility in the anaerobic methane oxidising archaeal familyMethanoperedenaceae

“…This is the first genomic evidence suggesting that members of the Methanoperedenaceae may be involved in respiratory sulfur-dependent AOM and warrants further investigation. ANME-1 have been proposed to couple AOM to the reduction of polysulfide in a biogenic hydrocarbon seep sediment, but this was based on the annotation and high expression of a putative sulfide: quinone oxidoreductase (SQR)(67). Genes for dissimilatory sulfate reduction pathways were absent in the Methanoperedenaceae MAGs, consistent with other ANME lineages (68).…”