title: Diversification and niche adaptations of Nitrospina-like bacteria in the polyextreme interfaces of Red Sea brines.
abstract: Nitrite-oxidizing bacteria (NOB) of the genus Nitrospina have exclusively been found in marine environments. In the brine-seawater interface layer of Atlantis II Deep (Red Sea), Nitrospina-like bacteria constitute up to one-third of the bacterial 16S ribosomal RNA (rRNA) gene sequences. This is much higher compared with that reported in other marine habitats (~10% of all bacteria), and was unexpected because no NOB culture has been observed to grow above 4.0% salinity, presumably due to the low net energy gained from their metabolism that is insufficient for both growth and osmoregulation. Using phylogenetics, single-cell genomics and metagenomic fragment recruitment approaches, we document here that these Nitrospina-like bacteria, designated as Candidatus Nitromaritima RS, are not only highly diverged from the type species Nitrospina gracilis (pairwise genome identity of 69%) but are also ubiquitous in the deeper, highly saline interface layers (up to 11.2% salinity) with temperatures of up to 52 °C. Comparative pan-genome analyses revealed that less than half of the predicted proteome of Ca. Nitromaritima RS is shared with N. gracilis. Interestingly, the capacity for nitrite oxidation is also conserved in both genomes. Although both lack acidic proteomes synonymous with extreme halophiles, the pangenome of Ca. Nitromaritima RS specifically encodes enzymes with osmoregulatory and thermoprotective roles (i.e., ectoine/hydroxyectoine biosynthesis) and of thermodynamic importance (i.e., nitrate and nitrite reductases). Ca. Nitromaritima RS also possesses many hallmark traits of microaerophiles and high-affinity NOB. The abundance of the uncultured Ca. Nitromaritima lineage in marine oxyclines suggests their unrecognized ecological significance in deoxygenated areas of the global ocean.
authors.affiliation: Red Sea Research Centre, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
authors.forename: David Kamanda
authors.identifier: 0000-0002-0442-4279
authors.initials: DK
authors.lastname: Ngugi
authors.affiliation: Bioinformatics and Systems Biology, Justus Liebig University Giessen, Germany.
authors.forename: Jochen
authors.initials: J
authors.lastname: Blom
authors.affiliation: Bigelow Laboratories for Ocean Sciences, East Boothbay, ME 04544-0380, USA.
authors.forename: Ramunas
authors.identifier: 0000-0003-4458-3108
authors.initials: R
authors.lastname: Stepanauskas
authors.affiliation: Red Sea Research Centre, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
authors.forename: Ulrich
authors.identifier: 0000-0002-0684-2597
authors.initials: U
authors.lastname: Stingl
mesh_terms: D000222:Adaptation, Physiological; D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D017753:Ecosystem; D019156:Indian Ocean; D053858:Metabolic Networks and Pathways; D056186:Metagenomics; D009573:Nitrites / Q000378:metabolism; D010084:Oxidation-Reduction; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D054712:Salinity; D012492:Salts; D012623:Seawater / Q000382:microbiology; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D009573:Nitrites; D012336:RNA, Ribosomal, 16S; D012492:Salts; C017082:brine