biostudies-literatureMartijn JVetenskapsrådetEuropean Research CouncilDutch Research Council (NWO)5490https://www.ebi.ac.uk/biostudies/studies/S-EPMC7599335biostudies-literatureUnknown11(1)Halobacteria (henceforth: Haloarchaea) are predominantly aerobic halophiles that are thought to have evolved from anaerobic methanogens. This remarkable transformation most likely involved an extensive influx of bacterial genes. Whether it entailed a single massive transfer event or a gradual stream of transfers remains a matter of debate. To address this, genomes that descend from methanogen-to-halophile intermediates are necessary. Here, we present five such near-complete genomes of Marine Group IV archaea (Hikarchaeia), the closest known relatives of Haloarchaea. Their inclusion in gene tree-aware ancestral reconstructions reveals an intermediate stage that had already lost a large number of genes, including nearly all of those involved in methanogenesis and the Wood-Ljungdahl pathway. Nature communicationsHikarchaeia demonstrate an intermediate stage in the methanogen-to-halophile transition.PMC75993358178342016-035593100392018-06727WISE fellowshipSchon MESpang AWilliams TALind AEEttema TJGMartijn JVosseberg JfalseHikarchaeia demonstrate an intermediate stage in the methanogen-to-halophile transition.Halobacteria (henceforth: Haloarchaea) are predominantly aerobic halophiles that are thought to have evolved from anaerobic methanogens. This remarkable transformation most likely involved an extensive influx of bacterial genes. Whether it entailed a single massive transfer event or a gradual stream of transfers remains a matter of debate. To address this, genomes that descend from methanogen-to-halophile intermediates are necessary. Here, we present five such near-complete genomes of Marine Group IV archaea (Hikarchaeia), the closest known relatives of Haloarchaea. Their inclusion in gene tree-aware ancestral reconstructions reveals an intermediate stage that had already lost a large number of genes, including nearly all of those involved in methanogenesis and the Wood-Ljungdahl pathway. 2020-01-01T00:00:00Z2020 Oct2025-04-26T16:48:44.619Z2020-11-19T11:32:13ZS-EPMC75993353312790910.1038/s41467-020-19200-2