Na.tro.no.ar.chae.a.ce’ae. N.L. neut. n. Natronoarchaeum, the type genus of the family; L. fem. pl. n. suff. -aceae, ending to denote a family; N.L. fem. pl. n. Natronoarchaeaceae, the family of the genus Natronoarchaeum.
The family Natronoarchaeaceae is a member of the order Halobacteriales, class Halobacteria, and is formed on the basis of phylogenomic analyses. It includes extremely halophilic and either aerobic or facultatively anaerobic archaea with variable key functionality, such as anaerobic sulfur respiration and potential to utilize various polysaccharides as growth substrates. The family currently contains four genera: the type genus Natronoarchaeum and the genera Salinarchaeum, Halostella, and Natranaeroarchaeum from various hypersaline
habitats.
DNA G+C content (mol%): 60.8–68.2 (whole genome sequences).
Type genus: Natronoarchaeum Shimane et al. 2010VP emend. Qui et al. 2014.@en

Members of the Aeromonas genus are commonly found in natural aquatic ecosystems. However, they are also frequently present in non-chlorinated drinking water distribution systems. High densities of these bacteria indicate favorable conditions for microbial regrowth, which is considered undesirable. Studies have indicated that the presence of Aeromonas is associated with loose deposits and the presence of invertebrates, specifically Asellus aquaticus. Therefore, a potential source of energy in these nutrient poor environments is chitin, the structural shell component in these invertebrates. In this study, we demonstrate the ability of two Aeromonas strains, commonly encountered in drinking water distribution systems, to effectively degrade and utilize chitin as a sole carbon and nitrogen source. We conducted a quantitative proteomics study on the cell biomass and secretome from pure strain cultures when switching the nutrient source from glucose to chitin, uncovering a diverse array of hydrolytic enzymes and metabolic pathways specifically dedicated to the utilization of chitin. Additionally, a genomic analysis of different Aeromonas species suggests the general ability of this genus to degrade and utilize a variety of carbohydrate biopolymers. This study indicates the relation between the utilization of chitin by Aeromonas and their association with invertebrates such as A. aquaticus in loose deposits in drinking water distribution systems.@en

Natr.an.aer.o.vir.ga’ce.ae N.L. fem. n. Natranaerovirga, the type genus of the family, -aceae ending to denote a family; N.L. fem. pl. n. Natranaerovirgaceae, the Natranaerovirga family. The family Natranaerovirgaceae includes obligately
anaerobic fermentative bacteria from soda lakes. They are highly salt-tolerant alkaliphiles utilizing carbohydrates as energy and carbon source. The family belongs to the order “Lachnospirales,” class Clostridia, and consists of a single genus Natranaerovirga. The family-level status was established by phylogenomic
analysis based on the Genome Taxonomy Database classification (GDTB).
DNA G +C content (mol%): 31.3–32.3 (whole-genome sequence).
Type genus: Natranaerovirga Sorokin et al. 2012,  VL145.
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Beta-mannans are insoluble plant polysaccharides with beta-1,4-linked mannose as the backbone. We used three forms of this polysaccharide, namely, pure mannan, glucomannan, and galactomannan, to enrich haloarchaea, which have the ability to utilize mannans for growth. Four mannan-utilizing strains obtained in pure cultures were closely related to each other on the level of the same species. Furthermore, another strain selected from the same habitats with a soluble beta-1,4-glucan (xyloglucan) was also able to grow with mannan. The
phylogenomic analysis placed the isolates into a separate lineage of the new genus level within the family Natrialbaceae of the class Halobacteria. The strains are moderate alkaliphiles, extremely halophilic, and aerobic saccharolytics. In addition to the three beta-mannan forms, they can also grow with cellulose, xylan, and xyloglucan. Functional genome analysis of two representative strains demonstrated the presence of several genes coding for extracellular endo-beta-1,4-mannanase from the GH5_7 and 5_8 subfamilies and the GH26 family of glycosyl hydrolases. Furthermore, a large spectrum of genes encoding other glycoside hydrolases that were potentially involved in the hydrolysis of cellulose and xylan were also identified in the genomes. A comparative genomics analysis also showed the presence of similar endo-beta-1,4-mannanase homologs in the cellulotrophic genera Natronobiforma and Halococcoides. Based on the unique physiological properties and the results of phylogenomic analysis, the novel mannan-utilizing halolarchaea are proposed to be classified into a new genus and species Natronoglomus mannanivorans gen. nov., sp. nov. with the type strain AArc-m2/3/4 (=JCM 34861=UQM 41565).@en

A variety of lakes located in the dry steppe area of southwestern Siberia are exposed to rapid climatic changes, including intra-century cycles with alternating dry and wet phases driven by solar activity. As a result, the salt lakes of that region experience significant fluctuations in water level and salinity, which have an essential impact on the indigenous microbial communities. But there are few microbiological studies that have analyzed this impact, despite its importance for understanding the functioning of regional water ecosystems. This work is a retrospective study aimed at analyzing how solar activity-related changes in hydrological regime affect phototrophic microbial communities using the example of the shallow soda lake Tanatar VI, located in the Kulunda steppe (Altai Region, Russia, southwestern Siberia). The main approach used in this study was the comparison of hydrochemical and microscopic data obtained during annual field work with satellite and solar activity data for the 12-year observation period (2011–2022). The occurrence of 33 morphotypes of cyanobacteria, two key morphotypes of chlorophytes, and four morphotypes of anoxygenic phototrophic bacteria was analyzed due to their easily recognizable morphology. During the study period, the lake surface changed threefold and the salinity changed by more than an order of magnitude, which strongly correlated with the phases of the solar activity cycles. The periods of high (2011–2014; 100–250 g/L), medium (2015–2016; 60 g/L), extremely low (2017–2020; 13–16 g/L), and low (2021–2022; 23–34 g/L) salinity with unique biodiversity of phototrophic communities were distinguished. This study shows that solar activity cycles determine the dynamics of the total salinity of a southwestern Siberian soda lake, which in turn determines the communities and microorganisms that will occur in the lake, ultimately leading to cyclical changes in alternative states of the ecosystem (dynamic stability).

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The author regrets that there were errors in the JCM collection numbers in the Abstract and the protologue Table 3 of the paper by Sorokin et al. (Syst. Appl. Microbiol. 2024, 47, 126519). The correct JCM collection numbers should be: JCM 35396 and JCM 35397 instead of JCM 335396 and JCM 335397.@en

Na.tro.no.cal’cu.lus N.L. neut. n. natron, arbitrarily derived from the Arabic natrun or natron, soda; L. masc. n. calculus, pebble, gravel; N.L. masc. n. Natronocalculus, soda-loving pebble-shaped cells. The genus Natronocalculus is a member of the family Halorubraceae, order Haloferacales, and class Halobacteria, according to the NCBI classification, while recent
changes in the taxonomy of the Halobacteria based on the Genome Taxonomy Database phylogenomic classification place Natronocalculus into the family Haloferacaceae, order Halobacteriales. The genus members are aerobic, extremely halophilic and moderately
alkaliphilic, and saccharolytic archaea, utilizing various alpha-glucans and sugars as carbon and energy sources. The genus currently includes a single species Natronocalculus amylovorans inhabiting hypersaline soda lakes. The genus three-letter abbreviation is Ncl.
DNA G +C content (mol%): 51.5 (whole-genome sequence of the type strain).
Type species: Natronocalculus amylovorans Sorokin et al. 2022, VL211.
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Natr.an.aer.o.ar.chae’um N.L. neut. n. natron, soda; from Arabic n. natrun, soda, sodium carbonate; Gr. pref. an-, not (here: inseparable prefix); Gr. masc. n. aêr air; Gr. masc. adj. archaîos, ancient; N.L. neut. n. Natranaeroarchaeum, anaerobic natronophilic
archaeon. The genus Natranaeroarchaeum is classified as a member of the family Natronoarchaeaceae, order Halobacteriales, and class Halobacteria, according to phylogenomic analyses. It includes extremely halophilic and facultatively aerobic, obligately alkaliphilic, and saccharolytic archaea, capable of anaerobic sulfur respiration with sugars and starch as carbon and energy sources. The genus currently includes two species, the type species Natranaeroarchaeum sulfidigenes and Natranaeroarchaeum aerophilum, originating from hypersaline soda lakes. The DNA G+C content is 60.8–61.0 (whole-genome sequences). The genus three-letter abbreviation is Naa.
DNA G +C content (%): 60.8–61.0 (whole-genome sequences of type strains).
Type species: Natranaeroarchaeum sulfidigenes Sorokin et al. 2022a, VL211.
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The genus Natranaerovirga is a member of the class Clostridia. It includes obligately anaerobic, fermentative heterotrophs which whose key metabolic property is the ability to utilizes polygalacturonates as growth substrates. The species of the genus are highly salt-tolerant, chloride-independent, obligate alkaliphiles found in saline soda lakes and soils in Central Asia. The genus currently includes two species: N. pectinivora, the type species of the genus, and N. hydrolytica. The DNA G+C content is 31.3-32.3 % (whole genome sequences). @en

Use of curldlan, an insoluble β-1,3-glucan, as an enrichment substrate under aerobic conditions resulted in the selection from hypersaline soda lakes of a single natronarchaeon, strain AArc-curdl1. This organism is an obligately aerobic saccharolytic, possessing a poorly explored (in Archaea) potential to utilize beta-1–3 glucans, being only a second example of a haloarchaeon with this ability known in pure culture. The main phenotypic property of the isolate is the ability to grow with insoluble β-1,3-backboned glucans, i.e. curdlan and pachyman. Furthermore, the strain utilized starch family α-glucans, beta-fructan inulin and a limited spectrum of sugars. The major ether-bound membrane polar phospholipids included PGP-Me and PG. The glyco- and sulfolipids were absent. The major respiratory menaquinone is MK-8:8. According to phylogenomic analysis, AArc-curdl1 represents a separate species in the recently described genus Natronosalvus within the family Natrialbaceae. The closest related species is Natronosalvus amylolyticus (ANI, AAI and DDH values of 90.2, 91.6 and 44 %, respectively). On the basis of its unique physiological properties and phylogenomic distance, strain AArc-curdl1T is classified as a novel species Natronosalvus hydrolyticus sp. nov. (=JCM 34865 = UQM 41566).@en

Cy.clo.na.tro’num. Gr. masc. n. kyklos, a circle; N.L.neut. n. natron, soda; N.L. neut. n. Cyclonatronum,circle-shaped and soda-loving.
The genus Cyclonatronum is a member of theclass Rhodothermia of the phylum Bacteroidota. Itincludes obligately aerobic organoheterotrophs that mostly utilize proteins and peptides, and possess an active sodium-pumping proteorhodopsin. The genus currently includes a single species, Cyclonatronum proteinivorum, which is represented by a mesophilic, moderately salt-tolerant, chloride-independent, and obligate alkaliphile found in saline soda lakes in Central Asia.
DNA G +C content (mol%): 51.5 (genome sequence).
Type species: Cyclonatronum proteinivorum Zhilina et al. 2023, VL211.@en

Soda lakes are unique double-extreme habitats characterized by high salinity and soluble carbonate alkalinity, yet harboring rich prokaryotic life. Despite intensive microbiology studies, little is known about the identity of the soda lake hydrolytic bacteria responsible for the primary degradation of the biomass organic matter, in particular cellulose. In this study, aerobic and anaerobic enrichment cultures with three forms of native insoluble cellulose inoculated with sediments from five soda lakes in south-western Siberia resulted in the isolation of four cellulotrophic haloalkaliphilic bacteria and their four saccharolytic satellites. The final aerobic enrichment included a cellulotrophic bacteroidetes (strain ABcell3) related to Sporocytophaga accompanied by a hemicellulolytic Marinimicrobium strain ABcell2.
The anaerobic enrichments resolved in three primary cellulotrophic bacteria and their three saccharolytic bacteroidetes satellites. The culture selected on amorphous cellulose (ac) included a new cellulotrophic member of the Chitinispirillaceae (Fibrobacterota)—strain ANBcel5, and two different saccharolytic satellites from the Marinilabiliales and Balneolales orders. The final enrichment selected on Sigma 101 cellulose consisted of an endospore-forming cellulotrophic strain ANBcel31 belonging to the genus Herbivorax (Acetivibrionales) and its saccharolytic satellite from the Balneolales order. The anaerobic enrichment on a filter paper yielded a binary consortium with the cellulotrophic endospore-forming Halanaerobiales strain ANBcel28 in obligate syntrophy with a cellobiose-utilizing Natronincola. A functional genome analysis of the cellulotrophic isolates confirmed the presence of a large repertoire of genes encoding excreted cellulases, mostly from the GH9 and GH5 families, and indicated that in the endospore-forming anaerobic strains, ANBcel28 and ANBcel31 most of their endo-glucanases are assembled in cellulosomes. Overall, this study showed that cellulose can be mineralized in soda lakes at moderately saline and highly alkaline conditions either by aerobic or fermentative haloalkaliphilic bacteria.@en

The family Desulfurivibrionaceae includes obligately anaerobic, moderately salt-tolerant, obligately alkaliphilic chemolithoautotrophic bacteria with a unique energy metabolism consisting of elemental sulfur disproportionation. H₂ or formate can also serve as additional electron donors for sulfur reduction, while nitrate can be ammonified with either sulfide or formate as the electron donors. The cultured representatives are found exclusively in saline soda lakes. The family consists of a single genus Desulfurivibrio with the type species D. alkaliphilus and a second yet undescribed species “D. dismutans” DNA G+C content (%): 60.0-60.3 (whole genome sequences)
Type genus : Desulfurivibrio Sorokin et al. 2008, VL123

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The genus Natronospira is represented by a single species of extremely salt-tolerant aerobic alkaliphilic proteolytic bacterium, isolated from hypersaline soda lakes. When cells of Gram-positive cocci were used as a substrate instead of proteins at extremely haloalkaline conditions, two new members of this genus were enriched and isolated in pure culture from the same sites. Strains AB-CW1 and AB-CW4 are obligate aerobic heterotrophic proteolytic bacteria able to feed on both live and dead cells of staphylococci and a range of proteins and peptides. Similar to the type species, N. proteinivora, the isolates are extremely salt-tolerant obligate alkaliphiles. However, N. proteinivora was unable to use bacterial cells as a substrate. Electron microscopy showed direct contact between the prey and predator cells. Functional analysis of the AB-CW1 and AB-CW4 genomes identified two sets of genes coding for extracellular enzymes potentially involved in the predation and proteolysis, respectively. The first set includes several copies of lysozyme-like GH23 peptidoglycan-lyase and murein-specific M23 [Zn]-di-peptidase enabling the cell wall degradation. The second set features multiple copies of secreted serine and metallopeptidases apparently allowing for the strong proteolytic phenotype. Phylogenomic analysis placed the isolates into the genus Natronospira as two novel species members, and furthermore indicated that this genus forms a deep-branching lineage of a new family (Natronospiraceae) and order (Natronospirales) within the class Gammaproteobacteria. On the basis of distinct phenotypic and genomic properties, strain AB-CW1T (JCM 335396 = UQM 41579) is proposed to be classified as Natronospira elongata sp. nov., and AB-CW4T (JCM 335397 = UQM 41580) as Natronospira bacteriovora sp. nov.@en

Cy.clo.na.tron.a’ce.ae N.L. neut. n. Cyclonatronum, type genus of the family; L. fem. pl. n. suff. -aceae, ending to denote a family; N.L. fem. pl. n. Cyclonatronaceae, the Cyclonatronum family.
The family Cyclonatronaceae is amember of the order Balneolales, class Rhodothermia, and phylum Bacteroidota. It includes heterotrophic bacteria with either aerobic or fermentative metabolism that utilize peptides or sugars as growth substrates. The known members of the family are mesophilic, moderately salt-tolerant, chloride-independent, and obligate alkaliphiles found in saline soda lakes in Central Asia. The family currently includes two genera, the type genus Cyclonatronum and the genus Natronogracilivirga, both represented by a single species.
DNA G+C content (mol%): 49.7–51.5 (whole genome sequences).
Type genus: Cyclonatronum Zhilina et al. 2023, VL211.
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Dissimilatory nitrate reduction to ammonia (DNRA) is a common biochemical process in the nitrogen cycle in natural and man-made habitats, but its significance in wastewater treatment plants is not well understood. Several ammonifying Trichlorobacter strains (former Geobacter) were previously enriched from activated sludge in nitrate-limited chemostats with acetate as electron (e) donor, demonstrating their presence in these systems. Here, we isolated and characterized the new species Trichlorobacter ammonificans strain G1 using a combination of low redox potential and copper-depleted conditions. This allowed purification of this DNRA organism from competing denitrifiers. T. ammonificans is an extremely specialized ammonifier, actively growing only with acetate as e-donor and carbon source and nitrate as e-acceptor, but H₂ can be used as an additional e-donor. The genome of G1 does not encode the classical ammonifying modules NrfAH/NrfABCD. Instead, we identified a locus encoding a periplasmic nitrate reductase immediately followed by an octaheme cytochrome c that is conserved in many Geobacteraceae species. We purified this octaheme cytochrome c protein (TaNiR), which is a highly active dissimilatory ammonifying nitrite reductase loosely associated with the cytoplasmic membrane. It presumably interacts with two ferredoxin subunits (NapGH) that donate electrons from the menaquinol pool to the periplasmic nitrate reductase (NapAB) and TaNiR. Thus, the Nap-TaNiR complex represents a novel type of highly functional DNRA module. Our results indicate that DNRA catalyzed by octaheme nitrite reductases is a metabolic feature of many Geobacteraceae, representing important community members in various anaerobic systems, such as rice paddy soil and wastewater treatment facilities.

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Proteomics has greatly advanced the understanding of the cellular biochemistry of microorganisms. The thermoalkaliphile Caldalkalibacillus thermarum TA2.A1 is an organism of interest for studies into how alkaliphiles adapt to their extreme lifestyles, as it can grow from pH 7.5 to pH 11. Within most classes of microbes, the membrane-bound electron transport chain (ETC) enables a great degree of adaptability and is a key part of metabolic adaptation. Knowing what membrane proteins are generally expressed is crucial as a benchmark for further studies. Unfortunately, membrane proteins are the category of proteins hardest to detect using conventional cellular proteomics protocols. In part, this is due to the hydrophobicity of membrane proteins as well as their general lower absolute abundance, which hinders detection. Here, we performed a combination of whole cell lysate proteomics and proteomics of membrane extracts solubilised with either SDS or FOS-choline-12 at various temperatures. The combined methods led to the detection of 158 membrane proteins containing at least a single transmembrane helix (TMH). Within this data set we revealed a full oxidative phosphorylation pathway as well as an alternative NADH dehydrogenase type II (Ndh-2) and a microaerophilic cytochrome oxidase ba₃. We also observed C. thermarum TA2.A1 expressing transporters for ectoine and glycine betaine, compounds that are known osmolytes that may assist in maintaining a near neutral internal pH when the external pH is highly alkaline.

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Me.thy.lo.ha.lo.mo.nad.a.ce’ae N.L. fem. n. Methylohalomonas, the type genus of the family, -aceae ending to denote a family; N.L. fem. pl. n. Methylohalomonadaceae the Methylohalomonas family.
The family Methylohalomonadaceae includes obligately methylotrophic, aerobic bacteria from hypersaline salt lakes. They are moderate halophiles utilizing C1 compounds as the energy and carbon source via the serine cycle. The family is a member of the order Methylohalomonadales in the Gammaproteobacteria
and consists of a single genus Methylohalomonas. The family-level status was established by phylogenomic analysis based on the Genome Taxonomy DataBase
classification. DNA G + C content (%): 59.4 (genome sequence). Type genus: Methylohalomonas Sorokin et al. 2007VP.@en

Thi.o.ha.lo.spir.al’es N.L. fem. n. Thiohalospira, the type genus of the order; L. fem. pl. n. suff. -ales, ending to denote an order; N.L. fem. pl. n. Thiohalospirales, the order of the genus Thiohalospira.
The order Thiohalospirales accommodates aerobic, chemolithoautotrophic, sulfur-oxidizing halophilic bacteria from hypersaline habitats which assimilate
CO₂ via the Calvin–Benson-Bassham cycle. The order is a deeply branching lineage of the Gammaproteobacteria and consists of a single family Thiohalospiraceae and genus Thiohalospira. The order-level status was established by phylogenomic analysis based on the Genome Taxonomy DataBase classification. Type genus: Thiohalospira Sorokin et al. 2008^VP.@en

Climate change, desertification, salinisation of soils and the changing hydrology of the Earth are creating or modifying microbial habitats at all scales including the oceans, saline groundwaters and brine lakes. In environments that are saline or hypersaline, the biodegradation of recalcitrant plant and animal polysaccharides can be inhibited by salt-induced microbial stress and/or by limitation of the metabolic capabilities of halophilic microbes. We recently demonstrated that the chitinolytic haloarchaeon Halomicrobium can serve as the host for an ectosymbiont, nanohaloarchaeon ‘Candidatus Nanohalobium constans’. Here, we consider whether nanohaloarchaea can benefit from the haloarchaea-mediated degradation of xylan, a major hemicellulose component of wood. Using samples of natural evaporitic brines and anthropogenic solar salterns, we describe genome-inferred trophic relations in two extremely halophilic xylan-degrading three-member consortia. We succeeded in genome assembly and closure for all members of both xylan-degrading cultures and elucidated the respective food chains within these consortia. We provide evidence that ectosymbiontic nanohaloarchaea is an active ecophysiological component of extremely halophilic xylan-degrading communities (although by proxy) in hypersaline environments. In each consortium, nanohaloarchaea occur as ectosymbionts of Haloferax, which in turn act as scavenger of oligosaccharides produced by xylan-hydrolysing Halorhabdus. We further obtained and characterised the nanohaloarchaea–host associations using microscopy, multi-omics and cultivation approaches. The current study also doubled culturable nanohaloarchaeal symbionts and demonstrated that these enigmatic nano-sized archaea can be readily isolated in binary co-cultures using an appropriate enrichment strategy. We discuss the implications of xylan degradation by halophiles in biotechnology and for the United Nation's Sustainable Development Goals.

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