Cultivation and biogeochemical analyses reveal insights into methanogenesis in deep subseafloor sediment at a biogenic gas hydrate site

Abstract

Gas hydrates deposited in subseafloor sediments are considered to primarily consist of biogenic methane. However, little evidence for the occurrence of living methanogens in subseafloor sediments has been provided. This study investigated viable methanogen diversity, population, physiology and potential activity in hydrate-bearing sediments (1–307 m below the seafloor) from the eastern Nankai Trough. Radiotracer experiments, the quantification of coenzyme F430 and molecular sequencing analysis indicated the occurrence of potential methanogenic activity and living methanogens in the sediments and the predominance of hydrogenotrophic methanogens followed by methylotrophic methanogens. Ten isolates and nine representative culture clones of hydrogenotrophic, methylotrophic and acetoclastic methanogens were obtained from the batch incubation of sediments and accounted for 0.5–76% of the total methanogenic sequences directly recovered from each sediment. The hydrogenotrophic methanogen isolates of Methanocalculus and Methanoculleus that dominated the sediment methanogen communities produced methane at temperatures from 4 to 55 °C, with an abrupt decline in the methane production rate at temperatures above 40 °C, which is consistent with the depth profiles of potential methanogenic activity in the Nankai Trough sediments in this and previous studies. Our results reveal the previously overlooked phylogenetic and metabolic diversity of living methanogens, including methylotrophic methanogenesis.

Revisiting Microbial Diversity in Hypersaline Microbial Mats from Guerrero Negro for a Better Understanding of Methanogenic Archaeal Communities

“…These findings highlight the necessity of using a variety of marker genes to characterise a broader spectrum of the methanogenic diversity residing in this ecosystem. Similar results have been reported for anaerobic digesters [ 66 ], but studies in extreme environments are scarce [ 67 ].…”

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

“…Although the condition in the subseafloor was considered to be suitable for hydrogenotrophic or acetoclastic methanogenesis, we only detected H 2 -dependent methylotrophic methanogens (Methanomassiliicoccales and Methanofastidiosales), which produce methane using hydrogen, C1 substrates and synthesize biomass using acetate [63]. Similarly, in other reports about the sediments of JiaoLong, Shenhu and Haima methane seep from the South China Sea as well as hydrate-bearing sediments from eastern Nankai Trough, the H 2 -dependent methylotrophic methanogenesis was found to be a major methanogenic pathway [64][65][66][67]. The methylotrophic methanogenesis were reported to be able to unitize non-competitive substrates (methanol, methylamines, or methyl sulfide and so on) originated from the degradation of organic macromolecules such as lignin and pectin [68].…”

Vertically stratified methane, nitrogen and sulphur cycling and coupling mechanisms in mangrove sediment microbiomes

“…Previous studies showed that the abundance of methanogenesis genes increased with the mudflat sediment depth [ 66 ], and the composition of methanogens showed obvious variations in different ecosystems [ 6 , 67 ]. For example, hydrogenotrophic methanogenesis was dominated in a subseafloor sediment [ 68 ], peatlands [ 69 ] and mangrove sediments [ 70 ]. In this study, we observed a relatively high abundance of mcrA gene and an increasing trend along the sediment depth, suggesting a possibly more active methanogenesis in the deep sediment.…”