Natronoflexus

Na.tro.no.fle’xus; N.L. neut. n. natron (arbitrarily derived from the Arabic n. natrun or natron) soda, sodium carbonate; N.L. pref. natrono-, pertaining to soda; L. masc. n. flexus, a bending, N.L. masc. n. Natronoflexus, bending/flexible cells living in soda. The genus Natronoflexus is a member of the family Marinilabiliaceae, order Bacteroidales, class Bacteroidia, and phylum Bacteroidota. It is an obligately anaerobic fermentative saccharolytic bacterium with the ability to utilize polygalacturonates and xylan as carbon and energy sources. The only species of the genus, N. pectinivorans, is a moderately salt-tolerant, chloride-independent obligate alkaliphile found in soda lakes in Central Asia. The DNA G+C content is 39.6mol% (genome). DNA G +C content (%): 39.6 (genome). Type species: Natronoflexus pectinivorans Sorokin et al. 2011, VL144.Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.BT/Environmental Biotechnolog

Dethiobacteraceae fam. nov.

De.thi’o.bac.ter.a.ce.a.e. N.L. masc. n. Dethiobacter, the type genus of the family; L. fem. pl. n. suff. -aceae, ending to denote a family; N.L. fem. pl. n. Dethiobacteraceae, the family of the genus Dethiobacter. The family Dethiobacteraceae includes obligately anaerobic, moderately salt-tolerant, and obligately alkaliphilic bacteria able to grow chemolithoautotrophically by elemental sulfur disproportionation and fixingCO2 by the Wood–Ljungdahl pathway. The two strains currently known in pure culture are both isolated from saline soda lakes. H2 can serve as an additionalelectron donor for sulfur and thiosulfate reduction. The family consists of a single genus Dethiobacter with the type species Dethiobacter alkaliphilus. DNA G +C content (%): 48.3–48.5 (genomes of two isolates). Type genus: Dethiobacter Sorokin et al. 2008, VL123.Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work publicBT/Environmental Biotechnolog

Dethiobacterales ord. nov.

De.thi’o.bac.ter.a.les. N.L.masc. n. Dethiobacter, the type genus of the order; L. fem. pl. n. suff. -ales, ending to denote an order; N.L. fem. pl. n. Dethiobacterales, the order of the genus Dethiobacter. The order Dethiobacterales is the only order of the class Dethiobacteria, which forms a deep-branching phylogenetic lineage within the phylum “Firmicutes D.” It consists of a single family Dethiobacteraceae and genus Dethiobacter, whose members are haloalkaliphilic anaerobes with a respiratory metabolism.Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work publicBT/Environmental Biotechnolog

Natronospira

Na.tro.no.spi’ra. N.L. neut. n. natron (arbitrarily derived from the Arabic n. natrun or natron), soda; L. fem. n. spira, coil; N.L. fem. n. Natronospira, a soda-loving coil-shaped bacterium.The genus Natronospira was originally classified as a member of the family Ectothiorhodospiraceae, order Chromatiales, and class Gammaproteobacteria, according to the 16S rRNA-based gene sequence comparison, while according to the phylogenomic analysis it forms a separate order-level branch within the Gammaproteobacteria unrelated to the Chromatiales members. It is an aerobic heterotroph that preferably utilizes proteins and peptides for growth. Natronospira is an extremely salt-tolerant, chloride-independent obligate alkaliphile. It inhabits oxic brines of hypersaline soda lakes, particularly in southwestern Siberia. The genus currently includes a single (type) species:N. proteinivora. DNA G +C content (%): 59.8 (genome). Type species: Natronospira proteinivora Sorokin et al. 2017VP.Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work publicBT/Environmental Biotechnolog

Dethiobacteria class nov.

De.thi’o.bac.ter.i.a. N.L. masc. n. Dethiobacter, type genus of the type order of the class Dethiobacterales; N.L. neut. pl. n. suff. -ia, ending to denote a class; N.L. neut. pl. n. Dethiobacteria, class of the order Dethiobacterales.The class Dethiobacteria forms a deep-branching phylogenetic lineage in the phylum “Firmicutes D” (according to the GDTB classification) and includesobligately anaerobic haloalkaliphilic bacteria with respiratory metabolism from soda lakes. It consists of a single order Dethiobacterales, family Dethiobacteraceae,and genus Dethiobacter.Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.BT/Environmental Biotechnolog

‘Candidatus Desulfonatronobulbus propionicus’: a first haloalkaliphilic member of the order Syntrophobacterales from soda lakes

Propionate can be directly oxidized anaerobically with sulfate as e-acceptor at haloalkaline conditions either incompletely to acetate (an example is Desulfobulbus alkaliphilus), or completely (for example by the members of genus Desulfonatronobacter). An enrichment with propionate at methanogenic conditions (without sulfate) inoculated with mixed sediments from hypersaline soda lakes in Kulunda Steppe (Altai, Russia) resulted in a domination of a new member of Syntrophobacteraceae (Deltaproteobacteria) in a consortium with the haloalkaliphilic lithotrophic methanogen Methanocalculus alkaliphilus. Transfer of this culture to a medium containing propionate as e-donor and sulfate as e-acceptor resulted in a disappearance of the methanogen and sulfide formation by the bacterial component, finally isolated into a pure culture at these conditions. Strain APr1 formed a distinct phylogenetic lineage within the family Syntrophobacteraceae, being equally distant from its members at the genus level. Phenotypically, strain APr1 resembled the species of the genus Syntrophobacter with substrate spectrum restricted to propionate and propanol utilized with sulfate, sulfite and thiosulfate as the e-acceptors. Propionate is oxidized incompletely to acetate. It is a moderately salt-tolerant (max. 1.2 M Na+) obligate alkaliphile (pH opt. 10). The isolate is proposed to be classified as a new candidate genus and species ‘Candidatus Desulfonatronobulbus propionicus’.Accepted Author ManuscriptBT/Environmental Biotechnolog

Desulfonatronospira sulfatiphila sp. Nov., and Desulfitispora elongata sp. nov., two novel haloalkaliphilic sulfidogenic bacteria from soda lakes

Two novel haloalkaliphilic bacteria with dissimilatory sulfidogenic metabolism were recovered from syntrophic associations obtained from anaerobic sediments of hypersaline soda lakes in Kulunda Steppe (Altai, Russia). Strain ASO3-2T was a member of a sulfidogenic syntrophic association oxidizing acetate at extremely haloalkaline conditions, and was isolated in pure culture using formate as electron donor and sulfate as electron acceptor. It was identified as representing a novel member of the genus Desulfonatronospira within the Deltaproteobacteria. In contrast to the two known species of this genus, the novel isolate was able to grow with formate as electron donor and sulfate, as well as with sulfite, as electron acceptor. Strain Acr1T was a minor component in a soda lake syntrophic association converting benzoate to methane and acetate. It became dominant in a subculture fed with crotonate. While growing on crotonate, strain Acr1T formed unusually long cells filled with polyhydroxyalkanoate-like granules. Its metabolism was limited to fermentation of crotonate and pyruvate and the ability to utilize thiosulfate and sulfur/polysulfide as electron acceptor. Strain Acr1T was identified as representing a novel member of the genus Desulfitispora in the class Clostridia. Both isolates were obligately haloalkaliphilic with extreme salt tolerance. On the basis of phenotypic and phylogenetic analyses, the novel sulfidogenic isolates from soda lakes are proposed to represent two novel species: Desulfonatronospira sulfatiphila sp. nov. (ASO3-2T=DSM 100427=UNIQEM U993T) and Desulfitispora elongata sp. nov. (Acr1T=DSM 29990=UNIQEM U994T).Accepted Author ManuscriptBT/Environmental Biotechnolog

Ecology of Methanonatronarchaeia

Methanonatronarchaeia represents a deep-branching phylogenetic lineage of extremely halo(alkali)philic and moderately thermophilic methyl-reducing methanogens belonging to the phylum Halobacteriota. It includes two genera, the alkaliphilic Methanonatronarchaeum and the neutrophilic Ca. Methanohalarchaeum. The former is represented by multiple closely related pure culture isolates from hypersaline soda lakes, while the knowledge about the latter is limited to a few mixed cultures with anaerobic haloarchaea. To get more insight into the distribution and ecophysiology of this enigmatic group of extremophilic methanogens, potential activity tests and enrichment cultivation with different substrates and at different conditions were performed with anaerobic sediment slurries from various hypersaline lakes in Russia. Methanonatronarchaeum proliferated exclusively in hypersaline soda lake samples mostly at elevated temperature, while at mesophilic conditions it coexisted with the extremely salt-tolerant methylotroph Methanosalsum natronophilum. Methanonatronarchaeum was also able to serve as a methylotrophic or hydrogenotrophic partner in several thermophilic enrichment cultures with fermentative bacteria. Ca. Methanohalarchaeum did not proliferate at mesophilic conditions and at thermophilic conditions it competed with extremely halophilic and moderately thermophilic methylotroph Methanohalobium, which it outcompeted at a combination of elevated temperature and methyl-reducing conditions. Overall, the results demonstrated that Methanonatronarchaeia are specialized extremophiles specifically proliferating in conditions of elevated temperature coupled with extreme salinity and simultaneous availability of a wide range of C1-methylated compounds and H2/formate.BT/Environmental Biotechnolog

<i>Natronolimnohabitans</i>

Na.tro.no.lim.no.ha’bi.tans. Arabic n. natrun or natron, soda, sodium carbonate; Gr. fem. n. limne, lake; L. masc. n. habitans, an inhabitant; N.L. masc. n. Natronolimnohabitans, an organism living in soda lakes.The genus Natronolimnohabitans represents a currently monospecies alkaliphilic haloarchaeon inhabiting hypersaline soda lakes. Initially, the type species was placed in the genus Natronolimnobius mainly based on the phylogenetic relatedness inferred from the 16S rRNA gene sequence similarities. However, later on, it was reclassified to the current genus, Natronolimnohabitans, based on the results of more advanced phylogenomic analyses. Cells are rod-shaped and nonmotile. Gram-stain-negative, and red-pigmented. Obligate aerobic, and oxidase- and catalase-positive. Extremely halophilic with a growth Na+ range between 2.5 and 4.5M (optimum at 3.5 M). Cells lyse in less than 0.5M NaCl. Obligately alkaliphilic with a growth pH range between 7.5 to 10.0 (optimum at 9.5). Mesophilic or thermotolerant (optimal growth at 45∘C). Chemoorgano-trophic, utilizing mostly organic acids as carbon and energy source. The major polar lipids are diphytanyl (C20:C20) and phytanyl-sesterterpanyl (C20:C25) diether derivatives of phosphatidylglycerol (PG) and phosphatidylglycero-phosphate methyl ester (PGP-Me). The major respiratory quinones are MK-8 and MK-8(H2). Isolates have been obtained from soda lakes. DNA G+C content (mol%): 63.1 (HPLC), 64.3 (genome). Type species: Sorokin et al. 2020VP (basonym: Natronolimnobius innermongolicus Itoh et al. 2005, VL105).Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work publicBT/Environmental Biotechnolog

Process of energy conservation in the extremely haloalkaliphilic methyl-reducing methanogen Methanonatronarchaeum thermophilum

The recently isolated methanogen Methanonatronarchaeum thermophilum is an extremely haloalkaliphilic and moderately thermophilic archaeon and belongs to the novel class Methanonatronarchaeia in the phylum Halobacteriota. The knowledge about the physiology and biochemistry of members of the class Methanonatronarchaeia is still limited. It is known that M. thermophilum performs hydrogen or formate-dependent methyl-reducing methanogenesis. Here, we show that the organism was able to grow on all tested C1-methylated substrates (methanol, trimethylamine, dimethylamine, monomethylamine) in combination with formate or molecular hydrogen. A temporary accumulation of intermediates (dimethylamine or/and monomethylamine) in the medium occurred during the consumption of trimethylamine or dimethylamine. The energy conservation of M. thermophilum was dependent on a respiratory chain consisting of a hydrogenase (VhoGAC), a formate dehydrogenase (FdhGHI), and a heterodisulfide reductase (HdrDE) that were well adapted to the harsh physicochemical conditions in the natural habitat. The experiments revealed the presence of two variants of energy-conserving oxidoreductase systems in the membrane. These included the H2: heterodisulfide oxidoreductase system, which has already been described in Methanosarcina species, as well as the novel formate: heterodisulfide oxidoreductase system. The latter electron transport chain, which was experimentally proven for the first time, distinguishes the organism from all other known methanogenic archaea and represents a unique feature of the class Methanonatronarchaeia. Experiments with 2-hydroxyphenazine and the inhibitor diphenyleneiodonium chloride indicated that a methanophenazine-like cofactor might function as an electron carrier between the hydrogenase/ formate dehydrogenase and the heterodisulfide reductase.BT/Environmental Biotechnolog