DS
D. Sorokin
info
Please Note
<p>This page displays the records of the person named above and is not linked to a unique person identifier. This record may need to be merged to a profile.</p>
195 records found
1
...
Biomethanation of alkaline waste sludge in haloalkaline conditions
Combined proof of concept experiments and technical economic evaluation
Journal article
(2026)
-
Ramon Zwaan, Dimitry Y. Sorokin, Gerben R. Stouten, Mark C.M. van Loosdrecht, Philipp Wilfert
A highly pure biomethane stream (≈97% CH4) was produced continuously under halo-alkaline conditions (pH > 9, 0.6 M Na+) from complex alkaline organic waste residue originating from biopolymer extraction from sewage sludge. During the proof-of-concept operation, the substrate was degraded with similar efficiency (40% of the volatile solids, VS) compared to neutral conditions (36% of the VS). Operational data was utilised in a technical evaluation to identify bottlenecks for full-scale implementation at an early stage of process development and for comparison to conventional biogas upgrading using pressure swing and membranes. Initially identified bottlenecks for alkaline fermentation were related to overcautious assumptions, while others could be technically solved. Alkaline fermentation offers an attractive method for supplying increasingly needed high-purity biomethane using various recalcitrant substrates that have undergone alkaline pre-treatment. This is more feasible than the conventional ex-situ biogas upgrading. Next, upscaling steps for alkaline fermentation should be pursued. Strategies for integrated CO2 sequestration and nutrient recovery are outlined, which will offer additional benefits in the future.
...
A highly pure biomethane stream (≈97% CH4) was produced continuously under halo-alkaline conditions (pH > 9, 0.6 M Na+) from complex alkaline organic waste residue originating from biopolymer extraction from sewage sludge. During the proof-of-concept operation, the substrate was degraded with similar efficiency (40% of the volatile solids, VS) compared to neutral conditions (36% of the VS). Operational data was utilised in a technical evaluation to identify bottlenecks for full-scale implementation at an early stage of process development and for comparison to conventional biogas upgrading using pressure swing and membranes. Initially identified bottlenecks for alkaline fermentation were related to overcautious assumptions, while others could be technically solved. Alkaline fermentation offers an attractive method for supplying increasingly needed high-purity biomethane using various recalcitrant substrates that have undergone alkaline pre-treatment. This is more feasible than the conventional ex-situ biogas upgrading. Next, upscaling steps for alkaline fermentation should be pursued. Strategies for integrated CO2 sequestration and nutrient recovery are outlined, which will offer additional benefits in the future.
Acetoclastic versus hydrogenotrophic methanogenesis
Defining how pH and alkalinity shape acetate metabolism in a haloalkaliphilic methanogenic community for biomethane production
Journal article
(2026)
-
Beatriz C. Diniz, Ben Abbas, Dimitry Y. Sorokin, Mark C.M. van Loosdrecht, Philipp Zantout-Wilfert
In methanogenic communities, two main pathways drive methanogenesis: acetoclastic methanogenesis, which converts acetate into CH4 and CO2, and hydrogenotrophic methanogenesis, which reduces CO2 with H2 to CH4. Under high-pH conditions, a shift in dominance from acetoclastic to hydrogenotrophic methanogenesis is often observed. The goal of this work was to identify the pH tipping point for this metabolic shift and to elucidate the influence of alkalinity on this transition in a haloalkaliphilic methanogenic community enriched from anaerobic soda lake sediments. To this end, a haloalkaliphilic microbial community was cultivated across a pH range (8.20–10.00) at three different alkalinities (0.1, 0.6, 1.2 eq/L). Specific qPCR probes were developed to quantify the two dominant methanogens for each catabolism: “Ca. Methanocrinis natronophilus” (acetoclastic) and Methanocalculus alkaliphilus (hydrogenotrophic). Results showed that the relative abundance of Methanocalculus increased with the rise of pH for all alkalinities, with alkalinity exerting a stronger influence than pH. At low alkalinity (0.1 eq/L), Methanocalculus abundance doubled from 5.14 ± 1.95% to 9.15 ± 0.77% (pH 8.40–10.35). At moderate alkalinity (0.6 eq/L), it increased from 8.33 ± 1.34% to 47.92 ± 3.76% (pH 8.41–10.00), and at the highest alkalinity (1.2 eq/L), it increased from 6.78 ± 1.06% to 60.25 ± 2.00% (pH 8.26–9.68). 16S rRNA gene amplicon sequencing further identified “Candidatus Contubernalis” as a putative syntrophic acetate-oxidizing bacterium likely partnering with Methanocalculus in indirect hydrogenotrophic methanogenesis. This work highlights that haloalkaliphilic hydrogenotrophic methanogens offer a promising strategy to integrate CO2 capture in alkaline solutions with biomethanation.
...
In methanogenic communities, two main pathways drive methanogenesis: acetoclastic methanogenesis, which converts acetate into CH4 and CO2, and hydrogenotrophic methanogenesis, which reduces CO2 with H2 to CH4. Under high-pH conditions, a shift in dominance from acetoclastic to hydrogenotrophic methanogenesis is often observed. The goal of this work was to identify the pH tipping point for this metabolic shift and to elucidate the influence of alkalinity on this transition in a haloalkaliphilic methanogenic community enriched from anaerobic soda lake sediments. To this end, a haloalkaliphilic microbial community was cultivated across a pH range (8.20–10.00) at three different alkalinities (0.1, 0.6, 1.2 eq/L). Specific qPCR probes were developed to quantify the two dominant methanogens for each catabolism: “Ca. Methanocrinis natronophilus” (acetoclastic) and Methanocalculus alkaliphilus (hydrogenotrophic). Results showed that the relative abundance of Methanocalculus increased with the rise of pH for all alkalinities, with alkalinity exerting a stronger influence than pH. At low alkalinity (0.1 eq/L), Methanocalculus abundance doubled from 5.14 ± 1.95% to 9.15 ± 0.77% (pH 8.40–10.35). At moderate alkalinity (0.6 eq/L), it increased from 8.33 ± 1.34% to 47.92 ± 3.76% (pH 8.41–10.00), and at the highest alkalinity (1.2 eq/L), it increased from 6.78 ± 1.06% to 60.25 ± 2.00% (pH 8.26–9.68). 16S rRNA gene amplicon sequencing further identified “Candidatus Contubernalis” as a putative syntrophic acetate-oxidizing bacterium likely partnering with Methanocalculus in indirect hydrogenotrophic methanogenesis. This work highlights that haloalkaliphilic hydrogenotrophic methanogens offer a promising strategy to integrate CO2 capture in alkaline solutions with biomethanation.
The draft genome of a chemolithoautotrophic ammonia-oxidizing bacterium of the genus Nitrosomonas is reported. Nitrosomonas sp. strain ANs5, previously classified as a strain of N. halophila, is an alkali-tolerant ammonia-oxidizing bacterium isolated from the soda lakes of northeast Mongolia.
...
The draft genome of a chemolithoautotrophic ammonia-oxidizing bacterium of the genus Nitrosomonas is reported. Nitrosomonas sp. strain ANs5, previously classified as a strain of N. halophila, is an alkali-tolerant ammonia-oxidizing bacterium isolated from the soda lakes of northeast Mongolia.
Journal article
(2025)
-
Dimitry Y. Sorokin, Alexander Y. Merkel, Nicole J. Bale, Michel Koenen, Jaap S. Sinninghe Damste, Laura Marturano, Enzo Messina, Violetta La Cono, Michail M. Yakimov
Despite intensive microbiological characterization of soda lake microbial communities, no culturable representatives from the phylum Planctomycetota have been isolated from these haloalkaline habitats. In the context of studying polysaccharide utilization by soda lake microbial communities, we used polysaccharide hyaluronic acid as enrichment substrate at aerobic, moderate haloalkaline conditions (1 M total Na+, pH 9.5). This resulted in a
selective enrichment and isolation in pure culture of a bacterial strain AB-hyl4 belonging to Planctomycetota. The cells are tiny motile cocci growing in large aggregates, with the Gram-negative type of ultrastructure and producing a yellow pigment. This obligate aerobic saccharolytic heterotroph has an extremely narrow growth substrate range including, besides hyaluronic acid, melezitose and glycerol. The membrane lipids consist of phosphatidylcholine and two types of neutral lipids, including hopanoids and monounsaturated C17 and C19 hydrocarbons. Phylogenomic analysis placed the isolate into the family Phycisphaeraceae, class Phycisphaerae, as a new genus-level lineage. Its genome contained a gene encoding a polysaccharide lyase from the PL8 family which is probably responsible for the degradation of hyaluronic acid to a dimer, followed by its transport and hydrolysis into monomers in periplasm and final glycolytic degradation in cytoplasm. On the basis of distinct phenotypic and genomic properties, strain AB-hyl4T (DSM 117794 = UQM 41914) is proposed to be classified as
Natronomicrosphaera hydrolytica gen. nov., sp. nov. ...
selective enrichment and isolation in pure culture of a bacterial strain AB-hyl4 belonging to Planctomycetota. The cells are tiny motile cocci growing in large aggregates, with the Gram-negative type of ultrastructure and producing a yellow pigment. This obligate aerobic saccharolytic heterotroph has an extremely narrow growth substrate range including, besides hyaluronic acid, melezitose and glycerol. The membrane lipids consist of phosphatidylcholine and two types of neutral lipids, including hopanoids and monounsaturated C17 and C19 hydrocarbons. Phylogenomic analysis placed the isolate into the family Phycisphaeraceae, class Phycisphaerae, as a new genus-level lineage. Its genome contained a gene encoding a polysaccharide lyase from the PL8 family which is probably responsible for the degradation of hyaluronic acid to a dimer, followed by its transport and hydrolysis into monomers in periplasm and final glycolytic degradation in cytoplasm. On the basis of distinct phenotypic and genomic properties, strain AB-hyl4T (DSM 117794 = UQM 41914) is proposed to be classified as
Natronomicrosphaera hydrolytica gen. nov., sp. nov. ...
Despite intensive microbiological characterization of soda lake microbial communities, no culturable representatives from the phylum Planctomycetota have been isolated from these haloalkaline habitats. In the context of studying polysaccharide utilization by soda lake microbial communities, we used polysaccharide hyaluronic acid as enrichment substrate at aerobic, moderate haloalkaline conditions (1 M total Na+, pH 9.5). This resulted in a
selective enrichment and isolation in pure culture of a bacterial strain AB-hyl4 belonging to Planctomycetota. The cells are tiny motile cocci growing in large aggregates, with the Gram-negative type of ultrastructure and producing a yellow pigment. This obligate aerobic saccharolytic heterotroph has an extremely narrow growth substrate range including, besides hyaluronic acid, melezitose and glycerol. The membrane lipids consist of phosphatidylcholine and two types of neutral lipids, including hopanoids and monounsaturated C17 and C19 hydrocarbons. Phylogenomic analysis placed the isolate into the family Phycisphaeraceae, class Phycisphaerae, as a new genus-level lineage. Its genome contained a gene encoding a polysaccharide lyase from the PL8 family which is probably responsible for the degradation of hyaluronic acid to a dimer, followed by its transport and hydrolysis into monomers in periplasm and final glycolytic degradation in cytoplasm. On the basis of distinct phenotypic and genomic properties, strain AB-hyl4T (DSM 117794 = UQM 41914) is proposed to be classified as
Natronomicrosphaera hydrolytica gen. nov., sp. nov.
selective enrichment and isolation in pure culture of a bacterial strain AB-hyl4 belonging to Planctomycetota. The cells are tiny motile cocci growing in large aggregates, with the Gram-negative type of ultrastructure and producing a yellow pigment. This obligate aerobic saccharolytic heterotroph has an extremely narrow growth substrate range including, besides hyaluronic acid, melezitose and glycerol. The membrane lipids consist of phosphatidylcholine and two types of neutral lipids, including hopanoids and monounsaturated C17 and C19 hydrocarbons. Phylogenomic analysis placed the isolate into the family Phycisphaeraceae, class Phycisphaerae, as a new genus-level lineage. Its genome contained a gene encoding a polysaccharide lyase from the PL8 family which is probably responsible for the degradation of hyaluronic acid to a dimer, followed by its transport and hydrolysis into monomers in periplasm and final glycolytic degradation in cytoplasm. On the basis of distinct phenotypic and genomic properties, strain AB-hyl4T (DSM 117794 = UQM 41914) is proposed to be classified as
Natronomicrosphaera hydrolytica gen. nov., sp. nov.
Intensive microbiology studies of the past several decades of soda lakes, uncovered a rich functional diversity of haloalkaliphilic microbes driving carbon, nitrogen and sulfur cycles in these unique double-extreme habitats. One of the unexpected finding was a discovery there of aerobic extremely halophilic cellulotrophic natronoarchaea. Yet, little is still known about the identity of the soda lake bacteria able to use native cellulose as growth substrate, except for a single case of an anaerobic clostridium. In this work we present results of phenotypic and functional genomic analysis of an anaerobic bacterium, strain ANBcel5T, enriched from hypersaline Siberian soda lakes with amorphous cellulose as growth substrate. Phylogenetic analysis placed the isolate into the family Chitinispirillaceae in the phylum Fibrobacterota as a new genus and species lineage with the 16S rRNA gene identity and Relative Evolutionary Divergence (RED) to its only known species Chitinispirillum alkaliphilum ACht6–1T of 95.2 % and 0.847, respectively. In contrast, despite obvious morphological resemblance to ACht6–1T, strain ANBcel5T is a narrow cellulose-utilizing fermentative anaerobe fermenting cellulose and cellobiose to acetate, H2 and succinate. It is a moderately salt-tolerant obligate alkaliphile growing optimally at 0.6 M total Na+ as carbonates and pH 9.5. Functional genome analysis of the isolate revealed the presence of multiple genes encoding extracellular endocellulases from the GH families 5 and 9, three sodium-translocating membrane complexes and osmolytes Nε-acetyl-β-lysine and glycine betaine biosynthesis. The bacterium is proposed to be classified as Cellulosispirillum alkaliphilum gen. nov., sp. nov. (DSM 113825 = UQM 41584).
...
Intensive microbiology studies of the past several decades of soda lakes, uncovered a rich functional diversity of haloalkaliphilic microbes driving carbon, nitrogen and sulfur cycles in these unique double-extreme habitats. One of the unexpected finding was a discovery there of aerobic extremely halophilic cellulotrophic natronoarchaea. Yet, little is still known about the identity of the soda lake bacteria able to use native cellulose as growth substrate, except for a single case of an anaerobic clostridium. In this work we present results of phenotypic and functional genomic analysis of an anaerobic bacterium, strain ANBcel5T, enriched from hypersaline Siberian soda lakes with amorphous cellulose as growth substrate. Phylogenetic analysis placed the isolate into the family Chitinispirillaceae in the phylum Fibrobacterota as a new genus and species lineage with the 16S rRNA gene identity and Relative Evolutionary Divergence (RED) to its only known species Chitinispirillum alkaliphilum ACht6–1T of 95.2 % and 0.847, respectively. In contrast, despite obvious morphological resemblance to ACht6–1T, strain ANBcel5T is a narrow cellulose-utilizing fermentative anaerobe fermenting cellulose and cellobiose to acetate, H2 and succinate. It is a moderately salt-tolerant obligate alkaliphile growing optimally at 0.6 M total Na+ as carbonates and pH 9.5. Functional genome analysis of the isolate revealed the presence of multiple genes encoding extracellular endocellulases from the GH families 5 and 9, three sodium-translocating membrane complexes and osmolytes Nε-acetyl-β-lysine and glycine betaine biosynthesis. The bacterium is proposed to be classified as Cellulosispirillum alkaliphilum gen. nov., sp. nov. (DSM 113825 = UQM 41584).
Journal article
(2025)
-
Dimitry Y. Sorokin, Alexander Y. Merkel, Rustam H. Ziganshin, Ilya V. Kublanov
Elemental sulfur disproportionation combined with obligate autotrophy is a unique type of sulfur-based anaerobic metabolism known in a limited number of bacteria, primarily found among the members of Desulfobacterota phylum. Until recently, the only characterized alkaliphilic representative of this group was Desulfurivibrio alkaliphilus, originally isolated as an H2-dependent sulfur reducer. In this study, we describe the properties of a novel species within this genus, Desulfurivibrio dismutans strain AMeS2, which was originally enriched and isolated from a soda lake sample as an autotrophic elemental sulfur disproportionating bacterium. Similar to D. alkaliphilus AHT 2T, D. dismutans AMeS2 is an obligately alkaliphilic and moderately salt-tolerant autotrophic bacterium. In contrast to known neutrophilic sulfur disproportionating bacteria, it is capable of disproportionating sulfur without Fe(III). It can also grow by dissimilatory sulfur reduction to sulfide or nitrate reduction to ammonium (DNRA) with formate (but not with H2) as the electron donor. The addition of formate to sulfur-disproportionating AMeS2 culture significantly increased the sulfur-reducing activity but did not completely abolish the oxidative branch of sulfur disproportionation. Genome analysis confirmed the presence of dissimilatory sulfur oxidation and dissimilatory sulfur and nitrate reduction machineries in the strain. S0 disproportionation occurs by means of cytoplasmic dissimilatory sulfite reductase (Dsr) donating electrons to, and periplasmic polysulfide reductase (PsrABC) receiving electrons from the menaquinone pool. Nitrate reduction to ammonium (DNRA) occurs by the combined action of a membrane formate dehydrogenase FdnGHI, periplasmic nitrate reductase, and octaheme c ammonifying nitrite reductase. Autotrophic growth is enabled by the Wood–Ljungdahl pathway (WLP). The genome also encodes proteins that presumably connect the oxidative branch of sulfur disproportionation with the carbon (WLP) cycle. Comparative proteomics of cells grown by sulfur disproportionation and formate-dependent DNRA demonstrated overexpression of the genes encoding Psr and rDSR at sulfur-disproportionating conditions, confirming their key role in this process. On the contrary, the genes encoding DNRA proteins are upregulated in the presence of nitrate. Thus, genomic and proteomic analyses revealed the pathways for energy conservation in a new representative of Desulfurivibrio growing at DNRA and under the thermodynamically challenging conditions of sulfur disproportionation.
...
Elemental sulfur disproportionation combined with obligate autotrophy is a unique type of sulfur-based anaerobic metabolism known in a limited number of bacteria, primarily found among the members of Desulfobacterota phylum. Until recently, the only characterized alkaliphilic representative of this group was Desulfurivibrio alkaliphilus, originally isolated as an H2-dependent sulfur reducer. In this study, we describe the properties of a novel species within this genus, Desulfurivibrio dismutans strain AMeS2, which was originally enriched and isolated from a soda lake sample as an autotrophic elemental sulfur disproportionating bacterium. Similar to D. alkaliphilus AHT 2T, D. dismutans AMeS2 is an obligately alkaliphilic and moderately salt-tolerant autotrophic bacterium. In contrast to known neutrophilic sulfur disproportionating bacteria, it is capable of disproportionating sulfur without Fe(III). It can also grow by dissimilatory sulfur reduction to sulfide or nitrate reduction to ammonium (DNRA) with formate (but not with H2) as the electron donor. The addition of formate to sulfur-disproportionating AMeS2 culture significantly increased the sulfur-reducing activity but did not completely abolish the oxidative branch of sulfur disproportionation. Genome analysis confirmed the presence of dissimilatory sulfur oxidation and dissimilatory sulfur and nitrate reduction machineries in the strain. S0 disproportionation occurs by means of cytoplasmic dissimilatory sulfite reductase (Dsr) donating electrons to, and periplasmic polysulfide reductase (PsrABC) receiving electrons from the menaquinone pool. Nitrate reduction to ammonium (DNRA) occurs by the combined action of a membrane formate dehydrogenase FdnGHI, periplasmic nitrate reductase, and octaheme c ammonifying nitrite reductase. Autotrophic growth is enabled by the Wood–Ljungdahl pathway (WLP). The genome also encodes proteins that presumably connect the oxidative branch of sulfur disproportionation with the carbon (WLP) cycle. Comparative proteomics of cells grown by sulfur disproportionation and formate-dependent DNRA demonstrated overexpression of the genes encoding Psr and rDSR at sulfur-disproportionating conditions, confirming their key role in this process. On the contrary, the genes encoding DNRA proteins are upregulated in the presence of nitrate. Thus, genomic and proteomic analyses revealed the pathways for energy conservation in a new representative of Desulfurivibrio growing at DNRA and under the thermodynamically challenging conditions of sulfur disproportionation.
Polysaccharide-degrading natronoarchaea have been poorly studied to date. However, over the past decade, significant progress has been made in understanding their diversity and metabolic potential. In this study, two natronoarchaeal strains, enriched from oxic sediment samples of the soda lakes of Wadi an Natrun in Egypt (AArcel7) and Kulunda steppe in Russia (A-rgal3), were characterized. Strain AArcel7 was enriched with amorphous cellulose, while strain A-rgal3 dominated anenrichment culture using rhamnogalacturonan. Cells of both strains are polymorphic,
from motile flat rods to nonmotile cocci. They are aerobic heterotrophs that are able to grow on chitin and several other carbohydrates. Both strains thrive within a salinity range of 2.5 to 4.5 M total Na+, with optimal growth at 3.5–4 M, and are moderately alkaliphilic with an optimum pH at 8.5–9.0 (AArcel7) and 9.2–9.5 (A-rgal3). Genome-based phylogenetic analysis demonstrated that these isolates form a new species lineage in the chitin-specialized genus Natrarchaeobius. An indepth
study of Natrarchaeobius genomes allowed us to identify several genes that potentially enable them to hydrolyze chitin and to metabolize N-acetylglucosamine (GlcNAc), which has not been investigated previously in the chitin-utilizing natronoarchaea. Based on physiological, phylogenetic, and genomic analyses, strains AArcel7 and A-rgal3 are suggested to form a novel species, Natrarchaeobius versutus sp. nov., with AArcel7T (DSM 119357 = UNIQEM U973) as the type strain.
Furthermore, strain AArcht7T, formerly classified as the type species of the genus Natrarchaeobius, is proposed to be reclassified as Natrarchaeobius oligotrophus (DSM 119677 = UNIQEM U967). ...
from motile flat rods to nonmotile cocci. They are aerobic heterotrophs that are able to grow on chitin and several other carbohydrates. Both strains thrive within a salinity range of 2.5 to 4.5 M total Na+, with optimal growth at 3.5–4 M, and are moderately alkaliphilic with an optimum pH at 8.5–9.0 (AArcel7) and 9.2–9.5 (A-rgal3). Genome-based phylogenetic analysis demonstrated that these isolates form a new species lineage in the chitin-specialized genus Natrarchaeobius. An indepth
study of Natrarchaeobius genomes allowed us to identify several genes that potentially enable them to hydrolyze chitin and to metabolize N-acetylglucosamine (GlcNAc), which has not been investigated previously in the chitin-utilizing natronoarchaea. Based on physiological, phylogenetic, and genomic analyses, strains AArcel7 and A-rgal3 are suggested to form a novel species, Natrarchaeobius versutus sp. nov., with AArcel7T (DSM 119357 = UNIQEM U973) as the type strain.
Furthermore, strain AArcht7T, formerly classified as the type species of the genus Natrarchaeobius, is proposed to be reclassified as Natrarchaeobius oligotrophus (DSM 119677 = UNIQEM U967). ...
Polysaccharide-degrading natronoarchaea have been poorly studied to date. However, over the past decade, significant progress has been made in understanding their diversity and metabolic potential. In this study, two natronoarchaeal strains, enriched from oxic sediment samples of the soda lakes of Wadi an Natrun in Egypt (AArcel7) and Kulunda steppe in Russia (A-rgal3), were characterized. Strain AArcel7 was enriched with amorphous cellulose, while strain A-rgal3 dominated anenrichment culture using rhamnogalacturonan. Cells of both strains are polymorphic,
from motile flat rods to nonmotile cocci. They are aerobic heterotrophs that are able to grow on chitin and several other carbohydrates. Both strains thrive within a salinity range of 2.5 to 4.5 M total Na+, with optimal growth at 3.5–4 M, and are moderately alkaliphilic with an optimum pH at 8.5–9.0 (AArcel7) and 9.2–9.5 (A-rgal3). Genome-based phylogenetic analysis demonstrated that these isolates form a new species lineage in the chitin-specialized genus Natrarchaeobius. An indepth
study of Natrarchaeobius genomes allowed us to identify several genes that potentially enable them to hydrolyze chitin and to metabolize N-acetylglucosamine (GlcNAc), which has not been investigated previously in the chitin-utilizing natronoarchaea. Based on physiological, phylogenetic, and genomic analyses, strains AArcel7 and A-rgal3 are suggested to form a novel species, Natrarchaeobius versutus sp. nov., with AArcel7T (DSM 119357 = UNIQEM U973) as the type strain.
Furthermore, strain AArcht7T, formerly classified as the type species of the genus Natrarchaeobius, is proposed to be reclassified as Natrarchaeobius oligotrophus (DSM 119677 = UNIQEM U967).
from motile flat rods to nonmotile cocci. They are aerobic heterotrophs that are able to grow on chitin and several other carbohydrates. Both strains thrive within a salinity range of 2.5 to 4.5 M total Na+, with optimal growth at 3.5–4 M, and are moderately alkaliphilic with an optimum pH at 8.5–9.0 (AArcel7) and 9.2–9.5 (A-rgal3). Genome-based phylogenetic analysis demonstrated that these isolates form a new species lineage in the chitin-specialized genus Natrarchaeobius. An indepth
study of Natrarchaeobius genomes allowed us to identify several genes that potentially enable them to hydrolyze chitin and to metabolize N-acetylglucosamine (GlcNAc), which has not been investigated previously in the chitin-utilizing natronoarchaea. Based on physiological, phylogenetic, and genomic analyses, strains AArcel7 and A-rgal3 are suggested to form a novel species, Natrarchaeobius versutus sp. nov., with AArcel7T (DSM 119357 = UNIQEM U973) as the type strain.
Furthermore, strain AArcht7T, formerly classified as the type species of the genus Natrarchaeobius, is proposed to be reclassified as Natrarchaeobius oligotrophus (DSM 119677 = UNIQEM U967).
Journal article
(2025)
-
Dimitry Y. Sorokin, Alexander Merkel, William Gebbie, Marina G. Kalyuzhnaya
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. ...
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. ...
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.
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.
Anaerobic digestion at high-pH and alkalinity for biomethane production
Insights into methane yield, biomethane purity, and process performance
Journal article
(2025)
-
Beatriz C. Diniz, Philipp Wilfert, Dimitry Y. Sorokin, Mark C.M. van Loosdrecht
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.
...
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.
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. ...
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. ...
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.
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.
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. ...
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. ...
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.
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.
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.
...
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.
...
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.
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.
Journal article
(2024)
-
Dimitry Y. Sorokin, Alexander G. Elcheninov, Nicole J. Bale, Jaap S. Sinninghe Damsté, Ilya V. Kublanov
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).
...
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).
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).
...
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).
Journal article
(2024)
-
Dimitry Y. Sorokin, Alexander Y. Merkel, Tatyana V. Kolganova, Nocile J. Bale, Jaap S. Sinninghe Damsté
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.
...
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.
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.
...
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.
...
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.
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.
Journal article
(2024)
-
Dimitry Y. Sorokin, Alexander G. Elcheninov, Nicol J. Bale, Jaap S. Sinnighe Damsté, Ilya V. Kublanov
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). ...
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). ...
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).
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).
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
...
Type genus : Desulfurivibrio Sorokin et al. 2008, VL123
...
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
Type genus : Desulfurivibrio Sorokin et al. 2008, VL123
Journal article
(2024)
-
G. Tugui, Dimitry Y. Sorokin, Wim Hijnen, Julia Wunderer, K.J.M.B. Bout, Mark C.M. van Loosdrecht, Martin Pabst
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.
...
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.
Journal article
(2024)
-
Dimitry Y. Sorokin, Alexander Y. Merkel, Tatyana V. Kolganova, Nicole J. Bale, Jaap S. Sinninghe Damsté
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.
...
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.