Oren, A. Diversity of halophilic microorganisms: environments, phylogeny, physiology, and applications. J. Ind. Microbiol. Biotechnol. 28, 56–63 (2002).

Article  CAS  PubMed  Google Scholar 

Oren, A. Molecular ecology of extremely halophilic Archaea and Bacteria. FEMS Microbiol. Ecol. 39, 1–7 (2002).

Article  CAS  PubMed  Google Scholar 

Narasingarao, P. et al. De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME J. 6, 81–93 (2012).

Article  CAS  PubMed  Google Scholar 

Ghai, R. et al. New abundant microbial groups in aquatic hypersaline environments. Sci. Rep. 1, 135 (2011).

Article  PubMed  PubMed Central  Google Scholar 

Zhao, D. et al. Comparative genomic insights into the evolution of Halobacteria-associated ‘Candidatus Nanohaloarchaeota’. mSystems 7, e0066922 (2022).

Article  PubMed  Google Scholar 

Rinke, C. et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431–437 (2013).

Article  ADS  CAS  PubMed  Google Scholar 

Sorokin, D. Y. et al. Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis. Nat. Microbiol. 2, 17081 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Aouad, M., Borrel, G., Brochier-Armanet, C. & Gribaldo, S. Evolutionary placement of Methanonatronarchaeia. Nat. Microbiol. 4, 558–559 (2019).

Article  CAS  PubMed  Google Scholar 

Feng, Y. et al. The evolutionary origins of extreme halophilic archaeal lineages. Genome Biol. Evol. 13, evab166 (2021).

Article  PubMed  PubMed Central  Google Scholar 

Martijn, J. et al. Hikarchaeia demonstrate an intermediate stage in the methanogen-to-halophile transition. Nat. Commun. 11, 5490 (2020).

Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

Sorokin, D. Y. et al. Reply to ‘Evolutionary placement of Methanonatronarchaeia’. Nat. Microbiol. 4, 560–561 (2019).

Article  CAS  PubMed  Google Scholar 

Zhou, H. et al. Metagenomic insights into the environmental adaptation and metabolism of Candidatus Haloplasmatales, one archaeal order thriving in saline lakes. Environ. Microbiol. 24, 2239–2258 (2022).

Article  CAS  PubMed  Google Scholar 

Oren, A. Microbial life at high salt concentrations: phylogenetic and metabolic diversity. Saline Syst. 4, 2 (2008).

Article  PubMed  PubMed Central  Google Scholar 

Fukuchi, S., Yoshimune, K., Wakayama, M., Moriguchi, M. & Nishikawa, K. Unique amino acid composition of proteins in halophilic bacteria. J. Mol. Biol. 327, 347–357 (2003).

Article  CAS  PubMed  Google Scholar 

Lanyi, J. K. Salt-dependent properties of proteins from extremely halophilic bacteria. Bacteriol. Rev. 38, 272–290 (1974).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Madern, D., Ebel, C. & Zaccai, G. Halophilic adaptation of enzymes. Extremophiles 4, 91–98 (2000).

Article  CAS  PubMed  Google Scholar 

Tadeo, X. et al. Structural basis for the amino acid composition of proteins from halophilic archea. PLoS Biol. 7, e1000257 (2009).

Article  PubMed  PubMed Central  Google Scholar 

Petitjean, C., Deschamps, P., López-García, P., Moreira, D. & Brochier-Armanet, C. Extending the conserved phylogenetic core of Archaea disentangles the evolution of the third domain of life. Mol. Biol. Evol. 32, 1242–1254 (2015).

Article  CAS  PubMed  Google Scholar 

Dombrowski, N., Lee, J.-H., Williams, T. A., Offre, P. & Spang, A. Genomic diversity, lifestyles and evolutionary origins of DPANN archaea. FEMS Microbiol. Lett. 366, fnz008 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Belilla, J. et al. Archaeal overdominance close to life-limiting conditions in geothermally influenced hypersaline lakes at the Danakil Depression, Ethiopia. Environ. Microbiol. 23, 7168–7182 (2021).

Article  CAS  PubMed  Google Scholar 

Belilla, J. et al. Hyperdiverse archaea near life limits at the polyextreme geothermal Dallol area. Nat. Ecol. Evol. 3, 1552–1561 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M. & Tanabe, M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 44, D457–D462 (2016).

Article  CAS  PubMed  Google Scholar 

Falb, M. et al. Metabolism of halophilic archaea. Extremophiles 12, 177–196 (2008).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Albers, S.-V. & Jarrell, K. F. The archaellum: how Archaea swim. Front. Microbiol. 6, 23 (2015).

Article  PubMed  PubMed Central  Google Scholar 

Sasaki, J. & Spudich, J. L. Signal transfer in haloarchaeal sensory rhodopsin – transducer complexes. Photochem. Photobiol. 84, 863–868 (2008).

Article  CAS  PubMed  Google Scholar 

Dassarma, S. et al. Genomic perspective on the photobiology of Halobacterium species NRC-1, a phototrophic, phototactic, and UV-tolerant haloarchaeon. Photosynth. Res. 70, 3–17 (2001).

Article  CAS  PubMed  Google Scholar 

Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 36, 1925–1927 (2020).

Article  CAS  Google Scholar 

Chklovski, A., Parks, D. H., Woodcroft, B. J. & Tyson, G. W. CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nat. Methods 20, 1203–1212 (2023).

Article  CAS  PubMed  Google Scholar 

Castelle, C. J. et al. Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations. Nat. Rev. Microbiol. 16, 629–645 (2018).

Article  CAS  PubMed  Google Scholar 

Hamm, J. N. et al. Unexpected host dependency of Antarctic Nanohaloarchaeota. Proc. Natl Acad. Sci. USA 116, 14661–14670 (2019).

Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

La Cono, V. et al. Symbiosis between nanohaloarchaeon and haloarchaeon is based on utilization of different polysaccharides. Proc. Natl Acad. Sci. USA 117, 20223–20234 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Pruitt, K. D., Tatusova, T. & Maglott, D. R. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35, D61–D65 (2007).

Article  CAS  PubMed  Google Scholar 

Mistry, J. et al. Pfam: the protein families database in 2021. Nucleic Acids Res. 49, D412–D419 (2021).

Article  CAS  PubMed  Google Scholar 

Cantalapiedra, C. P., Hernández-Plaza, A., Letunic, I., Bork, P. & Huerta-Cepas, J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol. Biol. Evol. 38, 5825–5829 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rodríguez del Río, Á. et al. Functional and evolutionary significance of unknown genes from uncultivated taxa. Nature 626, 377–384 (2024).

Cabello-Yeves, P. J. & Rodriguez-Valera, F. Marine–freshwater prokaryotic transitions require extensive changes in the predicted proteome. Microbiome 7, 117 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Rasmussen, T. How do mechanosensitive channels sense membrane tension? Biochem. Soc. Trans. 44, 1019–1025 (2016).

Article  CAS  PubMed  Google Scholar 

Petitjean, C., Deschamps, P., López-García, P. & Moreira, D. Rooting the Domain Archaea by phylogenomic analysis supports the foundation of the new Kingdom Proteoarchaeota. Genome Biol. Evol. 7, 191–204 (2015).

Article