Abstract
Deep sediments host many archaeal lineages, including the Asgard superphylum which contains lineages predicted to require syntrophic partnerships. Our knowledge about sedimentary archaeal diversity and their metabolic pathways and syntrophic partners is still very limited. We present here new genomes of Helarchaeota and the co-occurring sulfate-reducing bacteria (SRB) recovered from organic-rich sediments off Costa Rica Margin. Phylogenetic analyses revealed three new metagenome-assembled genomes (MAGs) affiliating with Helarchaeota, each of which has three variants of the methyl-CoM reductase-like (MCR-like) complex that may enable them to oxidize short-chain alkanes anaerobically. These Helarchaeota have no multi-heme cytochromes but have Group 3b and Group 3c [NiFe] hydrogenases, and formate dehydrogenase, and therefore have the capacity to transfer the reducing equivalents (in the forms of hydrogen and formate) generated from alkane oxidation to external partners. We also recovered five MAGs of SRB affiliated with the class of Desulfobacteria, two of which showed relative abundances (represented by genome coverages) positively correlated with those of the three Helarchaeota. Genome analysis suggested that these SRB bacteria have the capacity of H2 and formate utilization and could facilitate electron transfers from other organisms by means of these reduced substances. Their co-occurrence and metabolic features suggest that Helarchaeota may metabolize synergistically with some SRB, and together exert an important influence on the carbon cycle by mitigating the hydrocarbon emission from sediments to the overlying ocean.
Highlights
Many of the total microbial cells in the marine environment are estimated to be present in marine sediments [1], of which a considerable fraction are archaea [2,3,4]
Marine sediment is the natural habitat of the only cultured Asgard archaeon Candidatus Prometheoarchaeum syntrophicum MK-D1 [18] and the vast majority of known Asgard archaea discovered via metagenomic analysis [13, 14], so further exploration of marine sediment is promising to increase our understanding about this fascinating branch of life by recovering more novel lineages
This study revealed that the majority of Asgard archaeal cells in sulfate-reducing organic-rich shallow sediments co-occur with sulfate-reducing bacteria (SRB) in the subduction zone off Costa Rica
Summary
Many of the total microbial cells in the marine environment are estimated to be present in marine sediments [1], of which a considerable fraction are archaea [2,3,4]. Marine sediment is the natural habitat of the only cultured Asgard archaeon Candidatus Prometheoarchaeum syntrophicum MK-D1 [18] and the vast majority of known Asgard archaea discovered via metagenomic analysis [13, 14], so further exploration of marine sediment is promising to increase our understanding about this fascinating branch of life by recovering more novel lineages. This speculation is supported by the recent discovery of new Asgard lineages, such as Helarchaeota [19] in hydrothermal sediments in the Guaymas Basin (GB) and Sifarchaetoa in organic-rich sediments of the Costa Rica Margin [20]
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