Asgard archaea capable of anaerobic hydrocarbon cycling

Abstract

Large reservoirs of natural gas in the oceanic subsurface sustain complex communities of anaerobic microbes, including archaeal lineages with potential to mediate oxidation of hydrocarbons such as methane and butane. Here we describe a previously unknown archaeal phylum, Helarchaeota, belonging to the Asgard superphylum and with the potential for hydrocarbon oxidation. We reconstruct Helarchaeota genomes from metagenomic data derived from hydrothermal deep-sea sediments in the hydrocarbon-rich Guaymas Basin. The genomes encode methyl-CoM reductase-like enzymes that are similar to those found in butane-oxidizing archaea, as well as several enzymes potentially involved in alkyl-CoA oxidation and the Wood-Ljungdahl pathway. We suggest that members of the Helarchaeota have the potential to activate and subsequently anaerobically oxidize hydrothermally generated short-chain hydrocarbons.

Genome Repository of Oiled Systems (GROS): an interactive and searchable database that expands the catalogued diversity of crude oil-associated microbes

“…The 2021 MAGs were 133 assignable to 63 different bacterial and archaeal phyla based on genome-aggregate amino acid 134 identity (gAAI) values ( Fig. 3), with over 40 of them affiliated with Candidate Phyla Radiation 135 (CPR) as well as the newly described Asgard superphylum 18,19 . Recent studies have shown that 136…”

“…This is likely attributable to the lack 162 of dissolved oxygen and the presence of gaseous hydrocarbons at the latter sites when compared 163 to the DWH-impacted sites, most of which were aerobic. Archaea are typically associated with 164 the presence of methane and other short-chain and gaseous hydrocarbons as is the case in natural 165 oil seeps where dissolved oxygen is often not detectable18 . In contrast, the deep sea DWH plume 166 at the seafloor was aerobic, presumably leading to enrichment of taxa that differed from those in 167 the sub-surface samples.…”

Lokiarchaeon exhibits homoacetogenesis

“…3b). Five of the six Lokiarchaeon populations also exhibited a 174 13 C-labeling pattern that was suggestive of mixotrophic activity, as they had similar labeling in 175 both the bicarbonate and dEPS incubations (Fig. 3b).…”

“…All OTUs affiliated with "Candidatus Lokiarchaeota" (n=6) were significantly enriched with 172 13 C in the bicarbonate incubations (CI > 90%), with 5-35% total carbon atoms per Lokiarchaeon 173 population being 13 C -labeled ( Fig. 3b).…”

“…The incomplete nature of Asgard archaea genomes together with the lower representation of 91 sequenced archaeal genomes compared to Bacteria 12 , make it likely that the high levels of archaeal 92 gene expression seen here are actually an underestimate. Indeed, after updating our database with 93 recently sequenced Lokiarchaeota MAGs 13,14 , the number of expressed ORFs in 94 metatranscriptomes with highest similarity to Lokiarchaeota MAGs increased nearly two fold 95 (from 522 to 982 ORFs). Lokiarchaeal MAGs comprise sequences from closely related strains 96 and do not exhibit evidence of significant contamination 15 , thus we interpret expressed genes in 97 our metatranscriptomes with highest similarity to Lokiarchaeon MAGs as being derived from the 98 Lokiarchaeon group.…”