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

Taiki Katayama,Susumu Sakata,Satoshi Yoshida,Hideyoshi Yoshioka,Miki Amo,Hiroshi A Takahashi,Masanori Kaneko,Tetsuya Fujii

doi:10.1038/s41396-021-01175-7

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.

Highlights

Natural gas hydrates are cage-like structures of water molecules that contain low-molecular-weight gases, such as methane, and occur in subseafloor sediments along continental margins [1]
The potential for methylotrophic methanogenesis remains elusive in the deep subseafloor sediments, its occurrence and contribution to biogenic methane formation have previously been suggested in the deep terrestrial subsurface [18,19,20]
The detection of methanol in sediment porewater, the methylotrophic methanogenic activity from methanol and the culturable obligatory methylotrophic methanogens from various sediment depths and from incubated sediment samples without any supplementation all indicate the potential for methylotrophic methanogenesis

Summary

Introduction

Natural gas hydrates are cage-like structures of water molecules that contain low-molecular-weight gases, such as methane, and occur in subseafloor sediments along continental margins [1]. Extensive studies have been performed to characterize the methanogenic activity and diversity in sediments at gas hydrate sites using various biogeochemical techniques. Previous studies often failed to recover the gene sequences of methanogens from sediments at hydrate sites [9,10,11,12], possibly due to the small proportions (0.1%) of archaeal communities [13, 14]. The potential for methylotrophic methanogenesis remains elusive in the deep subseafloor sediments, its occurrence and contribution to biogenic methane formation have previously been suggested in the deep terrestrial subsurface [18,19,20]. The concentrations of methylotrophic substrates such as methanol in sediment core samples are generally low [21], which hampers potential activity measurement using a radiotracer

Methods

Results

Conclusion