D. Sorokin
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195 records found
1
Acetoclastic versus hydrogenotrophic methanogenesis
Defining how pH and alkalinity shape acetate metabolism in a haloalkaliphilic methanogenic community for biomethane production
Biomethanation of alkaline waste sludge in haloalkaline conditions
Combined proof of concept experiments and technical economic evaluation
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.
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).
Anaerobic digestion at high-pH and alkalinity for biomethane production
Insights into methane yield, biomethane purity, and process performance
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.
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.
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).
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.
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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archaeon. The genus Natranaeroarchaeum is classified as a member of the family Natronoarchaeaceae, order Halobacteriales, and class Halobacteria, according to phylogenomic analyses. It includes extremely halophilic and facultatively aerobic, obligately alkaliphilic, and saccharolytic archaea, capable of anaerobic sulfur respiration with sugars and starch as carbon and energy sources. The genus currently includes two species, the type species Natranaeroarchaeum sulfidigenes and Natranaeroarchaeum aerophilum, originating from hypersaline soda lakes. The DNA G+C content is 60.8–61.0 (whole-genome sequences). The genus three-letter abbreviation is Naa.
DNA G +C content (%): 60.8–61.0 (whole-genome sequences of type strains).
Type species: Natranaeroarchaeum sulfidigenes Sorokin et al. 2022a, VL211.
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The genus 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. ...
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.
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 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.
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).
Type genus : Desulfurivibrio Sorokin et al. 2008, VL123
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Type genus : Desulfurivibrio Sorokin et al. 2008, VL123