Messina, Enzo

Summary Halorhodospira halophila , one of the most‐xerophilic halophiles, inhabits biophysically stressful and energetically expensive, salt‐saturated alkaline brines. Here, we report an additional stress factor that is biotic: a diminutive Candidate‐Phyla‐Radiation bacterium, that we named ‘ Ca . Absconditicoccus praedator’ M39‐6, which predates H . halophila M39‐5, an obligately photosynthetic, anaerobic purple‐sulfur bacterium. We cultivated this association (isolated from the hypersaline alkaline Lake Hotontyn Nur, Mongolia) and characterized their biology. ‘Ca . Absconditicoccus praedator’ is the first stably cultivated species from the candidate class‐level lineage Gracilibacteria (order‐level lineage Absconditabacterales). Its closed‐and‐curated genome lacks genes for the glycolytic, pentose phosphate‐ and Entner–Doudoroff pathways which would generate energy/reducing equivalents and produce central carbon currencies. Therefore, ‘Ca . Absconditicoccus praedator’ is dependent on host‐derived building blocks for nucleic acid‐, protein‐, and peptidoglycan synthesis. It shares traits with (the uncultured) ‘ Ca . Vampirococcus lugosii’, which is also of the Gracilibacteria lineage. These are obligate parasitic lifestyle, feeding on photosynthetic anoxygenic Gammaproteobacteria, and absorption of host cytoplasm. Commonalities in their genomic composition and structure suggest that the entire Absconditabacterales lineage consists of predatory species which act to cull the populations of their respective host bacteria. Cultivation of vampire : host associations can shed light on unresolved aspects of their metabolism and ecosystem dynamics at life‐limiting extremes.

Abstract Na.no.ha.lo'bi.um. Gr. masc. n. nanos a dwarf; Gr. masc. n. hals , halos salt; Gr. masc. n. bios life; N.L. neut. n. Nanohalobium small organism living in salt. The genus Candidatus Nanohalobium was established based on a genome sequence found after the enrichment, cultivation, and characterization of a binary association with its chitinolytic host, obtained from a crystallizer pond brine collected in the marine solar saltern Saline della Laguna of Trapani, Italy. Ca . Nanohalobium is phylogenetically affiliated with members of the Ca . Nanohaloarchaeota ( Candidatus Haloredivivus, Candidatus Nanosalina, and Candidatus Nanosalinicola) of the archaeal DPANN superphylum. Cultivation experiments and analysis of the 0.97 Mb genome of Ca . Nanohalobium constans LC1Nh revealed that the organism has an organoheterotrophic, sugar‐fermenting lifestyle, lacking key anabolic machinery and any respiratory complexes. Additionally, the cultivation experiments revealed a remarkable mutualism of a nanohaloarchaeon–haloarchaeon association, namely the nanohaloarchaeon's ability to hydrolyze glycogen and starch to glucose, enabling the growth of Halomicrobium sp. LC1Hm in the absence of chitin. The low‐median isoelectric point for the predicted proteins suggests a “salt‐in” strategy used by the nanohaloarchaeon for osmotic balance. 16S rRNA gene sequences affiliated with Ca . Nanohalobium were recovered from other saltern ponds and hypersaline lakes worldwide. DNA G + C content (mol%) : 43.2 (genome). Type species : Candidatus Nanohalobium constans , La Cono et al. 2020. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Nanohalobium is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Nanobdellati / Candidatus Nanohalarchaeota / Candidatus Nanohalobiia / Candidatus Nanohalobiales / Candidatus Nanohalobiaceae / Candidatus Nanohalobium The genus Candidatus Nanohalobium can also be recovered in the Genome Taxonomy Database (GTDB) as g__Nanohalobium (version v220) ** . GTDB classification: d__Archaea / p__Nanohaloarchaeota / c__Nanosalinia / o__Nanosalinales / f__Nanosalinaceae / g__Nanohalobium * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776

Significance We report on cultivation and characterization of an association between Candidatus Nanohalobium constans and its host, the chitinotrophic haloarchaeon Halomicrobium LC1Hm, obtained from a crystallizer pond of marine solar salterns. High-quality nanohaloarchael genome sequence in conjunction with electron- and fluorescence microscopy, growth analysis, and proteomic and metabolomic data revealed mutually beneficial interactions between two archaea, and allowed dissection of the mechanisms for these interactions. Owing to their ubiquity in hypersaline environments, Nanohaloarchaeota may play a role in carbon turnover and ecosystem functioning, yet insights into the nature of this have been lacking. Here, we provide evidence that nanohaloarchaea can expand the range of available substrates for the haloarchaeon, suggesting that the ectosymbiont increases the metabolic capacity of the host.