Carbon Metabolism of Methylotrophic Methanogens and Asgard Archaea in Marine Sediments

Abstract

Carbon is the central element of life, as it is involved in building up of biological constituents and energy metabolisms in the cell. Archaea, - the most recently recognized domain of life - hold a crucial phylogenetic position in the evolution of life, but for most archaeal phyla, little is known about their role and activity in carbon metabolism. Archaea inhabit a variety of environments such as soils, sediments, sea water, and the guts of animals. Specifically in marine sediments, Thaumarchaeota, Euryarchaeota, Bathyarchaeota, Woesearchaeota and Asgard archaea are commonly found in archaeal communities. Methanogens affiliated to Euryarchaeota are well-known players in carbon metabolism, i.e., acetoclastic, hydrogenotrophic, and methylotrophic methanogenesis. Based on pure culture studies and genomic evidence, significant amounts of the biomass of methylotrophic methanogens growing on methyl substrates is derived from inorganic carbon. However, the in situ activity of these methanogens in carbon assimilation is unclear as the large inorganic carbon pool in marine sediment potentially affects carbon utilization patterns. To address this hypothesis, we initially applied nucleic acid stable isotope probing (SIP) to detect methylotrophic methanogens in marine sediment incubations. SIP results showed that 13C-labeled dissolved inorganic carbon (DIC) is necessary to identify methylotrophic methanogens, as illustrated by the nucleic acid synthesis pathway in these methanogens that 70-80% of carbon stems from DIC rather than methanol. In parallel, lipid-SIP suggested that DIC contributed to more than 60% from incubations with sediment from the sulfate reduction zone (SRZ), i.e., 20% higher than expected from lipid synthesis pathway. We further unexpectedly found that up to 12% methane was formed from DIC in autoclaved slurry incubations inoculated with the marine methylotrophic methanogen Methanococcoides methylutens. Similarly, methane formation from CO2 during methylotrophic methanogenesis was also observed with SRZ sediment incubations. In the same sediment incubations a higher amount of inorganic carbon was incorporated into lipids than expected, indicating that more DIC was assimilated into biomass than expected. Thus, the CO2 conversion to methane and biomass may play an important role in marine sediments. In the most recently discovered super phylum of the Archaea, the Asgard archaea might hold the key to understand the evolutionary origin of eukaryotes. Unlike methanogens, however, the diversity, carbon metabolism and the activity of Asgard archaea in marine sediments are still unknown. In this study, five new groups of Asgard archaea namely Kariarchaeota, Balderarchaeota, Hodarchaeota, Lagarchaeota and Gerdarchaeota are reported. In experiments with 13C-DIC, potential electron donors and electron acceptors, subgroup of Asgard archaea i.e., Lokiarchaeota was detected in the heavy SIP fractions from the incubations amended with organic polymers or sulfur, suggesting their activities of carbon fixation, organic polymers (cellulose, lignin and humic acid) degradation and sulfur metabolism. Furthermore, metagenomes were sequenced from heavy fractions of DNA-SIP samples obtained in the aforementioned experiments and from DNA extracted from mangrove sediments in the southeast coast of China. These metagenomes indicate that Asgard archaea harbor pathways of inorganic carbon fixation and degradation of cellulose, protein, short-chain and medium-chain alkane as well as assimilatory sulfate reduction. Crucially, the methyl coenzyme M reductase genes found in Helarchaeota have extended the potential of short-chain hydrocarbon oxidation to the Asgard archaea in this study. Overall, these findings illustrate that Asgard archaea actively utilize organic and inorganic carbon at the same time in mixotrophic fashion, which might play critical roles in carbon cycling of marine sediments. In particular, the successful detection of methylotrophic methanogens and Asgard archaea in marine sediments by nucleic acid-SIP with 13C-DIC suggested a crucial role of inorganic carbon in carbon metabolisms of these archaea. Given that many archaea harbor the acetyl-CoA associated carbon fixation pathway, my findings indicate that inorganic carbon assimilation might be ubiquitous in archaea when supply or availability of organic carbon are not sufficient in marine sediments.