Metagenomic insight into methanogenic pathways in seagrass sediments

Methanogenesis is important to the net carbon burial capacity in seagrass sediments. This microbially driven biogeochemical process can be fulfilled via three main pathways: hydrogenotrophic, acetoclastic and methylotrophic methanogenesis. However, the relative importance of each methanogenic pathway in seagrass meadows is poorly reported. In marine sediments where sulfate is abundant (15-43 mmol/L), hydrogenotrophic and acetoclastic methanogenesis are usually inhibited because of the competition for methanogenic substrates including hydrogen and acetate by sulfate-reducing bacteria. Thus, methylotrophic methanogenesis is hypothesized to play a crucial but yet-underappreciated role in the carbon cycle. In this study, culture-independent metagenomic approaches were used to profile the methanogenic pathways in seagrass sediments. Based on the functional potential analysis, methylotrophic methanogenesis is revealed as the dominant pathway in the seagrass sediments. Based on the metagenome-assembled genome analysis, Methanococcoides, which harbors known methylotrophic methanogens, is the only detected genus of methanogens in the seagrass meadow metagenomes. In the bare sediment, the abundance of Methanococcoides in the bottom was 41% higher than that in the surface due to the low oxygen in the bottom. While in the sediment covered by seagrasses, the abundance of Methanococcoides in the surface was 43-82% higher because of the higher fresh organic carbon content, which provides abundant substrates for methanogens. These findings reveal the methylotrophic methanogenesis is the main methanogenic pathway in both bare sediments and sediments covered by seagrasses. The hydrochemical analysis further suggested that in bare sediments, the methanogenesis was mainly controlled by oxygen content. However, in seagrass sediments, the availability of substrates was the dominated factor.