So far, there have been no reports of trimethylamine (TMA)-utilizing extremely halophilic microorganisms in hypersaline habitats. Our aerobic enrichments at 4 M total Na+ with 5 mM TMA inoculated with surface sediments from hypersaline soda (at pH 9.5) or chloride-sulfate (at pH 7) lakes in southwestern Siberia were successful only for the latter. The initial enrichment included both bacteria and haloarchaea but only the bacterial component was able to grow as a pure culture with TMA. Strain Cl-TMA forms a new-species lineage within the genus Thiohalorhabdus which includes extremely halophilic and obligate lithoautotrophic sulfur-oxidizing gammaproteobacteria. Cl-TMA can grow methyloautotrophically utilizing TMA, dimethylamine (DMA) and methanol (MeOH) as the electron donors or chemolithoauto-trophically with thiosulfate. Mixotrophic growth was also observed with the three methyl compounds and thiosulfate. Carbon is assimilated autotrophically via the Calvin- Benson-Basham pathway. Unlike the type species of Thiohalorhabdus, T. denitrificans, Cl-TMA was incapable of anaerobic growth via denitrification. The isolate belongs to extreme halophiles growing between 2.5 and 5 M NaCl with an optimum at 3–3.5 M. Genome analysis identified two gene clusters coding for PQQ-dependent methanol dehydrogenases (MxaFI and XoxF), four homologues of the formaldehyde activating enzymes (Faes), a TMA/DMA oxidation locus, and two cluster of genes encoding an N-methylglutamate dehydrogenase pathway (NMGP) for methylamine oxidation. The first steps of C1-subtrate conversions are followed by the tetrahydrofolate (THF)-linked and tetrahydromethanopterin (H4MPT)-linked formaldehyde oxidation pathways and two formate dehydrogenases. All of those signatures of methylotrophy were absent in T. denitrificans. In contrast, genes for two key sulfur oxidation enzymes, thiosulfate dehydrogenase TsdAB and sulfide dehydrogenase FccAB, that are present in the type species are missing in Cl-TMA. Thiosulfate is oxidized to sulfate by a combination of
an incomplete Sox cycle and an sHdr system. Strain Cl-TMAT (JCM 35977 = UQM 41915) is proposed to be classified as Thiohalorhabdus methylotrophus sp. nov.@en

The role of high-pH conditions in anaerobic digestion (AD) has traditionally been confined to it's use in pre-treatment processes. However, operating AD at elevated pH and alkalinity offers significant advantages, including in-situ upgrading of biogas to biomethane. This study examines the potential and scalability of AD under these conditions (pH ∼ 9.3; alkalinity ∼ 0.5 eq/L). The substrate used was the alkaline waste generated from the extraction of extracellular polymeric substances (EPS) from aerobic granular sludge (AGS), and the inoculum used was a haloalkaliphile microbial community from soda lake sediments. To evaluate the system’s performance, the organic loading rate (OLR) was incrementally increased. The highest methane production obtained was 8.4 ± 0.1 mL/day/gVSadded at a hydraulic retention time (HRT) of 15 days and an OLR of 1 kgVS/day/m3. At this loading rate, methanogenesis became the rate limiting conversion. The maximum volatile solids conversion was 48.1 ± 1.1 %. Throughout the reactor operation, methane purity in the biogas consistently exceeded 90 % peaking at 96.0 ± 0.2 %, showcasing the potential for in-situ biogas purification under these conditions. In addition, no ammonia inhibition was observed, even with free-ammonia (NH3) concentrations reaching up to 14 mM. This study underscores the potential of high-pH anaerobic digestion as a sustainable method for both waste treatment and energy recovery.@en

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

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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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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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

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 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

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

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

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

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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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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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 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

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

Thi.o.ha.lo.mo.nad.a.ce’ae N.L. fem. n. Thiohalomonas, the type genus of the family, -aceae ending to denote a family; N.L. fem. pl. n. Thiohalomonadaceae the Thiohalomonas family. The family Thiohalomonadaceae accommodates facultatively anaerobic, chemolithoautotrophic sulfur-oxidizing bacteria. They utilize reduced sulfur compounds as the energy source and either oxygen or NOx as the electron acceptors. CO₂ is assimilated via the Calvin–Benson–Bassham cycle. The family
is a member of the order Thiohalomonadales in the Gammaproteobacteria and consists of the genera Thiohalomonas and Sulfurivermis. The family-level status was established by phylogenomic analysis based on 120 single-copy conserved protein markers. DNA G + C content (mol%): 58–65 (Tm of 3 species).Type genus: Thiohalomonas Sorokin et al. 2007^VP.@en

Thi.o.ha.lo.bac.ter.a.ce’ae N.L. masc. n. Thiohalobacter, the type genus of the family, -aceae ending to denote a family; N.L. fem. pl. n. Thiohalobacteraceae the
Thiohalobacter family. The family Thiohalobacteraceae consists of aerobic, chemolithoautotrophic, sulfur-oxidizing bacteria from hypersaline salt lakes. They are moderately halophilic aerobic, bacteria utilizing reduced sulfur compounds as the energy source and assimilating CO₂ via the Calvin–Benson–Bassham cycle. The family is a member of the order Thiohalobacterales within the Gammaproteobacteria and consists of a single genus Thiohalobacter. The family-level status was established by phylogenomic analysis based on the Genome Taxonomy DataBase classification. DNA G + C content (%): 64.2 (genome sequence). Type genus: Thiohalobacter Sorokin et al. 2010^VP.@en

A spiral-shaped, highly motile bacterium was isolated from freshwater sulfidic sediment. Strain J10 ^T is a facultative autotroph utilizing sulfide, thiosulfate, and sulfur as the electron donors in microoxic conditions. Despite high 16S rRNA gene sequence sequence identity to Magnetospirillum gryphiswaldense MSR-1 ^T (99.6 %), digital DNA-DNA hybridisation homology and average nucleotide identity between the two strains was of the different species level (25 % and 83 %, respectively). Strain J10 ^T is not magnetotactic. The DNA G + C content of strain J10 ^T is 61.9 %. The predominant phospholipid ester-linked fatty acids are C18:1ω7, C16:1ω7, and C16:0. Strain J10 ^T (=DSM 23205 ^T = VKM B-3486 ^T) is the first strain of the genus Magnetospirillum showing lithoautotrophic growth and is proposed here as a novel species, Magnetospirillum sulfuroxidans sp. nov. In addition, we propose to establish a framework for distinguishing genera and families within the order Rhodospirillales based on phylogenomic analysis using the threshold values for average amino acid identity at ̴ 72 % for genera and ̴ 60 % for families. According to this, we propose to divide the existing genus Magnetospirillum into three genera: Magnetospirillum, Paramagnetospirillum, and Phaeospirillum, constituting a separate family Magnetospirillaceae fam. nov. in the order Rhodospirillales. Furthermore, phylogenomic data suggest that this order should accomodate six more new family level groups including Magnetospiraceae fam. nov., Magnetovibrionaceae fam. nov., Dongiaceae fam. nov., Niveispirillaceae fam. nov., Fodinicurvataceae fam. nov., and Oceanibaculaceae fam. nov.

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