Pub Date : 2025-05-01DOI: 10.1016/j.syapm.2025.126608
Dimitry Y. Sorokin , Alexander Y. Merkel , Nicole J. Bale , Michel Koenen , Jaap S. Sinninghe Damsté , 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.
{"title":"Natronomicrosphaera hydrolytica, gen. nov., sp. nov., a first representative of the phylum Planctomycetota from soda lakes","authors":"Dimitry Y. Sorokin , Alexander Y. Merkel , Nicole J. Bale , Michel Koenen , Jaap S. Sinninghe Damsté , Laura Marturano , Enzo Messina , Violetta La Cono , Michail M. Yakimov","doi":"10.1016/j.syapm.2025.126608","DOIUrl":"10.1016/j.syapm.2025.126608","url":null,"abstract":"<div><div>Despite intensive microbiological characterization of soda lake microbial communities, no culturable representatives from the phylum <em>Planctomycetota</em> 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<sup>+</sup>, pH 9.5). This resulted in a selective enrichment and isolation in pure culture of a bacterial strain AB-hyl4 belonging to <em>Planctomycetota</em>. 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 <em>Phycisphaeraceae</em>, class <em>Phycisphaerae,</em> 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-hyl4<sup>T</sup> (DSM 117794 = UQM 41914) is proposed to be classified as <em>Natronomicrosphaera hydrolytica</em> gen. nov., sp. nov.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 3","pages":"Article 126608"},"PeriodicalIF":3.3,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143902308","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-04-18DOI: 10.1016/j.syapm.2025.126607
Abdelaziz El Houari , Magali Ranchou-Peyruse , Elisabeth Carlier , Anthony Ranchou-Peyruse , Agnès Hirschler-Réa , Rhizlane Bennisse , Radia Bouterfas , James E. McDonald , Rémy Guyoneaud , Abdel-Illah Qatibi
Members of the phylum Synergistota are important but understudied components of microbial communities during anaerobic digestion. In this study, their diversity was assessed in full-scale anaerobic digester sludge samples from Marrakesh wastewater treatment plant (Morocco), using 16S rRNA gene community profiling, as well as targeted isolation, physiological characterization, and genome sequencing of novel Synergistaceae isolates. The 16S rRNA gene analysis identified 23 operational taxonomic units (OTUs) belonging to the family of Synergistaceae, representing 8.8 % of the total microbial community. 17 of these OTUs belonged to previously uncultured taxa. A dominant OTU19, presumably a new representative of the family of Synergistaceae was isolated in pure culture (strain DS-S4T) and subjected to both culture- and genome-based characterizations. Phylogenetic analysis revealed that strain DZ-S4T was related to Cloacibacillus porcorum CL-84T and Cloacibacillus evryensis 158T but with low sequence similarity of 89.94 % and 88.60 %, respectively. Based on genome relatedness, including Average Nucleotide Identity (ANI) and Amino Acid Identity (AAI), strain DZ-S4T is considered to represent a novel genus for which the name Caenicola gen.nov is proposed. Moreover, several phenotypic and eco-physiological properties differentiated the novel isolate from its related species, indicating that the strain represents a new species for which the name Caenicola nitritireducens sp. nov. is proposed, with strain DZ-S4T (=DSM 104940T = JCM 31897T) being the type strain. Additionally, this study investigates the ecological role of strain DZ-S4T, specifically the protein degradation, the bioconversion of carbohydrates, and the nitrite reduction during anaerobic digestion.
{"title":"Representatives of the Synergistaceae family, taxonomic description and genome sequence of Caenicola nitritireducens gen nov., sp. nov., a novel fermenting and amino-acid degrading bacterium isolated from a municipal anaerobic digester sludge","authors":"Abdelaziz El Houari , Magali Ranchou-Peyruse , Elisabeth Carlier , Anthony Ranchou-Peyruse , Agnès Hirschler-Réa , Rhizlane Bennisse , Radia Bouterfas , James E. McDonald , Rémy Guyoneaud , Abdel-Illah Qatibi","doi":"10.1016/j.syapm.2025.126607","DOIUrl":"10.1016/j.syapm.2025.126607","url":null,"abstract":"<div><div>Members of the phylum <em>Synergistota</em> are important but understudied components of microbial communities during anaerobic digestion. In this study, their diversity was assessed in full-scale anaerobic digester sludge samples from Marrakesh wastewater treatment plant (Morocco), using <em>16S rRNA</em> gene community profiling, as well as targeted isolation, physiological characterization, and genome sequencing of novel <em>Synergistaceae</em> isolates<em>.</em> The <em>16S rRNA</em> gene analysis identified 23 operational taxonomic units (OTUs) belonging to the family of <em>Synergistaceae</em>, representing 8.8 % of the total microbial community. 17 of these OTUs belonged to previously uncultured taxa. A dominant OTU19, presumably a new representative of the family of <em>Synergistaceae</em> was isolated in pure culture (strain DS-S4<sup>T</sup>) and subjected to both culture- and genome-based characterizations. Phylogenetic analysis revealed that strain DZ-S4<sup>T</sup> was related to <em>Cloacibacillus porcorum</em> CL-84<sup>T</sup> and <em>Cloacibacillus evryensis</em> 158<sup>T</sup> but with low sequence similarity of 89.94 % and 88.60 %, respectively. Based on genome relatedness, including Average Nucleotide Identity (ANI) and Amino Acid Identity (AAI), strain DZ-S4<sup>T</sup> is considered to represent a novel genus for which the name <em>Caenicola</em> gen.nov is proposed. Moreover, several phenotypic and eco-physiological properties differentiated the novel isolate from its related species, indicating that the strain represents a new species for which the name <em>Caenicola nitritireducens</em> sp. nov. is proposed, with strain DZ-S4<sup>T</sup> (=DSM 104940<sup>T</sup> = JCM 31897<sup>T</sup>) being the type strain. Additionally, this study investigates the ecological role of strain DZ-S4<sup>T</sup>, specifically the protein degradation, the bioconversion of carbohydrates, and the nitrite reduction during anaerobic digestion.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 3","pages":"Article 126607"},"PeriodicalIF":3.3,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143877548","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-04-12DOI: 10.1016/j.syapm.2025.126606
Undine S. Mies , Hao Zheng , Katja Platt , Renate Radek , Nicole Paczia , Sebastian C. Treitli , Andreas Brune
The tree of life comprises many deep-branching lineages with no or only very few cultured representatives. One such lineage is the phylum Elusimicrobiota, which contains only two described species and whose biology has been only poorly explored. We isolated three new species from this phylum from the intestinal tracts of cockroaches. Like their closest relative, Elusimicrobium minutum, the only member of the family Elusimicrobiaceae described to date, they are small, pleomorphic gram-negative rods characterized by a distinct cell cycle, and like all ultramicrobacteria, they pass through a 0.22-μm filter membrane. Physiological characterization of all isolates revealed that they are obligately anaerobic fermenters that lack catalase and cytochrome c oxidase activities but can remove oxygen from their environment in a non-respiratory manner. Their substrate range is limited to a few hexoses, such as d-glucose, d-galactose, and N-acetyl-d-glucosamine, which are fermented to lactate, acetate, ethanol, and hydrogen as major products. Comparative genome analysis, which included more than 100 MAGs of uncultured lineages of Elusimicrobiaceae, revealed the underlying metabolic pathways and outlined a new phylogenomic framework of the family. Based on phylogenomic, physiological, and morphological evidence, we describe the new isolates as Parelusimicrobium proximum gen. nov., sp. nov., Elusimicrobium posterum sp. nov., and Elusimicrobium simillimum sp. nov. under the rules of ICNP. Based on high-quality genomes of all uncultured representatives, we propose a comprehensive taxonomy of all lineages in the family under the rules of SeqCode, including the new genera Avelusimicrobium, Proelusimicrobium, and the candidate genus “Pseudelusimicrobium”.
{"title":"Comparative genomics of Elusimicrobiaceae (phylum Elusimicrobiota) and description of the isolates Elusimicrobium simillimum sp. nov., Elusimicrobium posterum sp. nov., and Parelusimicrobium proximum gen. nov. sp. nov.","authors":"Undine S. Mies , Hao Zheng , Katja Platt , Renate Radek , Nicole Paczia , Sebastian C. Treitli , Andreas Brune","doi":"10.1016/j.syapm.2025.126606","DOIUrl":"10.1016/j.syapm.2025.126606","url":null,"abstract":"<div><div>The tree of life comprises many deep-branching lineages with no or only very few cultured representatives. One such lineage is the phylum <em>Elusimicrobiota</em>, which contains only two described species and whose biology has been only poorly explored. We isolated three new species from this phylum from the intestinal tracts of cockroaches. Like their closest relative, <em>Elusimicrobium minutum</em>, the only member of the family <em>Elusimicrobiaceae</em> described to date, they are small, pleomorphic gram-negative rods characterized by a distinct cell cycle, and like all ultramicrobacteria, they pass through a 0.22-μm filter membrane. Physiological characterization of all isolates revealed that they are obligately anaerobic fermenters that lack catalase and cytochrome <em>c</em> oxidase activities but can remove oxygen from their environment in a non-respiratory manner. Their substrate range is limited to a few hexoses, such as <span>d</span>-glucose, <span>d</span>-galactose, and <em>N</em>-acetyl-<span>d</span>-glucosamine, which are fermented to lactate, acetate, ethanol, and hydrogen as major products. Comparative genome analysis, which included more than 100 MAGs of uncultured lineages of <em>Elusimicrobiaceae</em>, revealed the underlying metabolic pathways and outlined a new phylogenomic framework of the family. Based on phylogenomic, physiological, and morphological evidence, we describe the new isolates as <em>Parelusimicrobium proximum</em> gen. nov., sp. nov., <em>Elusimicrobium posterum</em> sp. nov., and <em>Elusimicrobium simillimum</em> sp. nov. under the rules of ICNP. Based on high-quality genomes of all uncultured representatives, we propose a comprehensive taxonomy of all lineages in the family under the rules of SeqCode, including the new genera <em>Avelusimicrobium</em>, <em>Proelusimicrobium</em>, and the candidate genus “<em>Pseudelusimicrobium</em>”.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 3","pages":"Article 126606"},"PeriodicalIF":3.3,"publicationDate":"2025-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143859501","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-03-17DOI: 10.1016/j.syapm.2025.126605
Pranami Goswami , Runjia Ji , Jianxun Shen , Andrew P. Roberts , Wei Lin
Magnetotactic bacteria (MTB) are recognised widely for their ability to synthesise intracellular magnetite (Fe3O4) and/or greigite (Fe3S4) nanocrystals and align with Earth's magnetic field. They are crucial for understanding prokaryotic organelle biogenesis. MTB members of the Nitrospirota phylum (previously known as the Nitrospirae phylum) are of interest due to their important ecological roles in the biogeochemical cycling of iron and sulphur. Here, we introduce Magnetominusculus dajiuhuensis DJH-1Ts, a newly discovered Nitrospirota MTB species that thrives in the acidic Dajiuhu Peatland of central China. By combining electron microscopy, 16S rRNA gene-based analysis and genome-resolved metagenomics, we elucidate its distinctive morphology, genomic features, and metabolic functions. The metagenome-assembled genome, assigned to the genus Magnetominusculus, family Magnetobacteriaceae, order Thermodesulfovibrionales, class Thermodesulfovibrionia according to the GTDB taxonomy, reveals an obligate anaerobe that lives in central China's largest wetland. We propose the formal name Magnetominusculus dajiuhuensis DJH-1Ts sp. nov., following the SeqCode system. Genomic and metabolic characterisation of this novel species suggests its potential role in nitrogen, sulphur, and carbon metabolism in aquatic biogeochemistry, particularly in peatlands. The genome of this novel strain indicates that it harnesses the Wood-Ljungdahl pathway for carbon fixation and acetate metabolism in anaerobic conditions, while its potential role in nitrogen cycling is characterised by denitrification and nitrogen fixation. It also participates in reduction of sulphate to sulphide, indicating a role in sulphur cycling in its ecological niche. Taken together, the discovery and characterisation of Magnetominusculus dajiuhuensis DJH-1Ts provide new insights into MTB diversity and ecological functions, particularly in peatland biogeochemistry.
{"title":"Genomic and metabolic characterisation of a novel species Magnetominusculus dajiuhuensis DJH-1Ts sp. nov. from an acidic peatland","authors":"Pranami Goswami , Runjia Ji , Jianxun Shen , Andrew P. Roberts , Wei Lin","doi":"10.1016/j.syapm.2025.126605","DOIUrl":"10.1016/j.syapm.2025.126605","url":null,"abstract":"<div><div>Magnetotactic bacteria (MTB) are recognised widely for their ability to synthesise intracellular magnetite (Fe<sub>3</sub>O<sub>4</sub>) and/or greigite (Fe<sub>3</sub>S<sub>4</sub>) nanocrystals and align with Earth's magnetic field. They are crucial for understanding prokaryotic organelle biogenesis. MTB members of the <em>Nitrospirota</em> phylum (previously known as the <em>Nitrospirae</em> phylum) are of interest due to their important ecological roles in the biogeochemical cycling of iron and sulphur. Here, we introduce <em>Magnetominusculus dajiuhuensis</em> DJH-1<sup>Ts</sup>, a newly discovered <em>Nitrospirota</em> MTB species that thrives in the acidic Dajiuhu Peatland of central China. By combining electron microscopy, 16S rRNA gene-based analysis and genome-resolved metagenomics, we elucidate its distinctive morphology, genomic features, and metabolic functions. The metagenome-assembled genome, assigned to the genus <em>Magnetominusculus</em>, family <em>Magnetobacteriaceae</em>, order <em>Thermodesulfovibrionales</em>, class <em>Thermodesulfovibrionia</em> according to the GTDB taxonomy, reveals an obligate anaerobe that lives in central China's largest wetland. We propose the formal name <em>Magnetominusculus dajiuhuensis</em> DJH-1<sup>Ts</sup> sp. nov., following the SeqCode system. Genomic and metabolic characterisation of this novel species suggests its potential role in nitrogen, sulphur, and carbon metabolism in aquatic biogeochemistry, particularly in peatlands. The genome of this novel strain indicates that it harnesses the Wood-Ljungdahl pathway for carbon fixation and acetate metabolism in anaerobic conditions, while its potential role in nitrogen cycling is characterised by denitrification and nitrogen fixation. It also participates in reduction of sulphate to sulphide, indicating a role in sulphur cycling in its ecological niche. Taken together, the discovery and characterisation of <em>Magnetominusculus dajiuhuensis</em> DJH-1<sup>Ts</sup> provide new insights into MTB diversity and ecological functions, particularly in peatland biogeochemistry.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 3","pages":"Article 126605"},"PeriodicalIF":3.3,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143698021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-03-17DOI: 10.1016/j.syapm.2025.126604
Olga A. Podosokorskaya , Anastasiia I. Maltseva , Alexander G. Elcheninov , Andrei A. Novikov , Kseniya S. Zayulina , Alexander Y. Merkel
A novel anaerobic moderately thermophilic bacterium, strain 38H-spT, was isolated from a hot spring located 12 m deep of the Kunashir Island shore. Gram-stain negative cells were non-sporeforming, motile, thin helices with regular coiling, occasionally forming bundles of cells. The strain grew at 30–60 °C and pH range of 5.5–8.4 with an optimum at 55 °C and pH 6.6–7.0. Strain 38H-spT required 0.5–5.5% NaCl (1.5% is an optimum) for growth. It was a chemoorganoheterotroph, growing on carbohydrates, including polymers (starch, pullulan, xylan, cellulose, arabinoxylan, xanthan gum, mannan, galactomannan, alginate and laminarin). Major products of glucose fermentation were acetate, ethanol, hydrogen, and carbon dioxide. Major cellular fatty acids were iso-C15:0, C14:0, C12:1 DMA. The size of complete genome of strain 38H-spT was 2.35 Mb; DNA G + C content was 40.1%. 93 CAZymes including 54 glycoside hydrolases were found to be encoded in the genome of the strain. According to 16S rRNA gene sequence and conserved protein sequences phylogenies strain 38H-spT with its closest relative Spirochaeta thermophila represented a deeply branched lineage of the class Spirochaetia. Based on phylogenetic analysis and phenotypic features these two bacteria were assigned to a novel family within a novel order for that the names Winmispiraceae fam. nov. and Winmispirales ord. nov. are proposed with Winmispira thermophila gen. nov., comb. nov. (previously known as Spirochaeta thermophila) as type species. Strain 38H-spT (=DSM 100344T = VKM B-2965T) represents the novel genus and species Rarispira pelagica gen. nov., sp. nov.
{"title":"Novel thermophilic hydrolytic bacterium Rarispira pelagica gen. nov., sp. nov., reclassification of Spirochaeta thermophila as Winmispira thermophila gen. nov., comb. nov., and proposal of Winmispiraceae fam. nov. and Winmispirales ord. nov. in the class Spirochaetia","authors":"Olga A. Podosokorskaya , Anastasiia I. Maltseva , Alexander G. Elcheninov , Andrei A. Novikov , Kseniya S. Zayulina , Alexander Y. Merkel","doi":"10.1016/j.syapm.2025.126604","DOIUrl":"10.1016/j.syapm.2025.126604","url":null,"abstract":"<div><div>A novel anaerobic moderately thermophilic bacterium, strain 38H-sp<sup>T</sup>, was isolated from a hot spring located 12 m deep of the Kunashir Island shore. Gram-stain negative cells were non-sporeforming, motile, thin helices with regular coiling, occasionally forming bundles of cells. The strain grew at 30–60 °C and pH range of 5.5–8.4 with an optimum at 55 °C and pH 6.6–7.0. Strain 38H-sp<sup>T</sup> required 0.5–5.5% NaCl (1.5% is an optimum) for growth. It was a chemoorganoheterotroph, growing on carbohydrates, including polymers (starch, pullulan, xylan, cellulose, arabinoxylan, xanthan gum, mannan, galactomannan, alginate and laminarin). Major products of glucose fermentation were acetate, ethanol, hydrogen, and carbon dioxide. Major cellular fatty acids were iso-C<sub>15:0</sub>, C<sub>14:0</sub>, C<sub>12:1</sub> DMA. The size of complete genome of strain 38H-sp<sup>T</sup> was 2.35 Mb; DNA G + C content was 40.1%. 93 CAZymes including 54 glycoside hydrolases were found to be encoded in the genome of the strain. According to 16S rRNA gene sequence and conserved protein sequences phylogenies strain 38H-sp<sup>T</sup> with its closest relative <em>Spirochaeta thermophila</em> represented a deeply branched lineage of the class <em>Spirochaetia.</em> Based on phylogenetic analysis and phenotypic features these two bacteria were assigned to a novel family within a novel order for that the names <em>Winmispiraceae</em> fam. nov. and <em>Winmispirales</em> ord. nov. are proposed with <em>Winmispira thermophila</em> gen. nov., comb. nov. (previously known as <em>Spirochaeta thermophila</em>) as type species. Strain 38H-sp<sup>T</sup> (=DSM 100344<sup>T</sup> = VKM B-2965<sup>T</sup>) represents the novel genus and species <em>Rarispira pelagica</em> gen. nov., sp. nov.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 3","pages":"Article 126604"},"PeriodicalIF":3.3,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143682041","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-03-14DOI: 10.1016/j.syapm.2025.126602
Dimitry Y. Sorokin , Alexander Y. Merkel , William Gebbe , 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 chemolithoautotrophically 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.
到目前为止，还没有报道三甲胺(TMA)-利用极端嗜盐微生物在高盐栖息地。我们在西伯利亚西南部的高盐苏打（pH值为9.5）或硫酸盐氯化物（pH值为7）湖泊的表层沉积物中接种了5 mM TMA，总Na+浓度为4 M的好氧富集，仅对后者成功。最初的富集包括细菌和盐古菌，但只有细菌成分能够作为TMA的纯培养物生长。菌株Cl-TMA在Thiohalorhabdus属中形成了一个新种谱系，其中包括极端嗜盐性和专性自养硫氧化γ变形菌。Cl-TMA可以利用TMA、二甲胺（DMA）和甲醇（MeOH）作为电子供体进行甲基自养生长，也可以利用硫代硫酸盐进行化能自养生长。三种甲基化合物和硫代硫酸盐也观察到混合营养生长。碳通过Calvin-Benson-Basham途径自养同化。与反硝化Thiohalorhabdus的模式物种不同，Cl-TMA不能通过反硝化进行厌氧生长。该分离物属于生长在2.5 ~ 5 M NaCl范围内的极端嗜盐菌，最佳生长条件为3 ~ 3.5 M NaCl。基因组分析鉴定出两个基因簇编码pqq依赖性甲醇脱氢酶（MxaFI和XoxF），四个甲醛激活酶（Faes）同源物，一个TMA/DMA氧化位点，以及两个编码甲胺氧化n -甲基谷氨酸脱氢酶途径（NMGP）的基因簇。c1 -底物转化的第一步是四氢叶酸（THF）连接和四氢甲烷蝶呤（H4MPT）连接的甲醛氧化途径和两种甲酸脱氢酶。所有这些甲基化特征在反硝化弓形虫中都不存在。相比之下，在模式物种中存在的两个关键硫氧化酶，硫代硫酸盐脱氢酶TsdAB和硫代硫酸盐脱氢酶FccAB的基因在Cl-TMA中缺失。硫代硫酸盐通过不完全Sox循环和sHdr系统的结合被氧化为硫酸盐。菌株Cl-TMAT （JCM 35977 = UQM 41915）拟归类为Thiohalorhabdus methylotrophus sp. nov。
{"title":"Thiohalorhabdus methylotropha sp. nov., an extremely halophilic autotrophic methylotiotroph from hypersaline lakes","authors":"Dimitry Y. Sorokin , Alexander Y. Merkel , William Gebbe , Marina G. Kalyuzhnaya","doi":"10.1016/j.syapm.2025.126602","DOIUrl":"10.1016/j.syapm.2025.126602","url":null,"abstract":"<div><div>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<sup>+</sup> 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 <em>Thiohalorhabdus</em> 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 chemolithoautotrophically 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 <em>Thiohalorhabdus</em>, <em>T. denitrificans</em>, 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 <em>N</em>-methylglutamate dehydrogenase pathway (NMGP) for methylamine oxidation. The first steps of C<sub>1</sub>-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 <em>T. denitrificans</em>. 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-TMA<sup>T</sup> (JCM 35977 = UQM 41915) is proposed to be classified as <em>Thiohalorhabdus methylotrophus</em> sp. nov.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 3","pages":"Article 126602"},"PeriodicalIF":3.3,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143636963","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-03-02DOI: 10.1016/j.syapm.2025.126600
Izzet Burcin Saticioglu , Nihed Ajmi , Orkid Coskuner-Weber , Semih Alpsoy , Hilal Ay , Fuat Aydin , Seçil Abay , Emre Karakaya , Tuba Kayman , Cem Dalyan , Fatih Doğan Koca , Gorkem Tasci , Doğancan Yarim , Danny Morick , Artun Yibar , Serdar Erdogan , Soner Altun , Muhammed Duman
Three bacterial strains, Mu-43T, Mu-80T, and Mu-86T, were isolated from the 2021 and 2022 mucilage event in the Marmara Sea and were taxonomically characterized. 16S rRNA gene sequence analysis confirmed that these strains belong to the genus Microbacterium. A polyphasic approach involving genomic and phenotypic analysis was employed to determine their taxonomic positions. A polyphasic approach integrating genomic and phenotypic analyses established their taxonomic positions. M. istanbulense Mu-43T showed 99.0 % 16S rRNA similarity to M. bandirmense Mu-80T, with digital DNA–DNA hybridization (dDDH) and average nucleotide identity using BLAST (ANIb) values of 22.3 % and 78.3 %, respectively. M. bandirmense Mu-80T exhibited 99.2 % similarity to M. esteraromaticum DSM 8609T, with dDDH and ANIb values of 23.6 % and 80 %. M. marmarense Mu-86T showed 97.4 % similarity to M. arthrosphaerae JCM 30492T, with dDDH and ANIb values of 20.1 % and 74.2 %. Metagenomic analysis highlighted their ecological relevance, with relative abundances of 1.43 %, 1.15 %, and 0.95 %, respectively. Further genomic analysis identified biosynthetic gene clusters associated with secondary metabolite production, including non-ribosomal peptide synthetases and terpenoid biosynthesis pathways, suggesting potential antimicrobial activity. Additionally, antibiotic resistance genes, such as ABC efflux pumps and Erm23S_rRNA methyltransferase, indicate adaptation to environmental stress. These findings indicate that these species contribute to nutrient cycling and organic matter decomposition in mucilage-affected environments. Based on genomic and phenotypic data, these strains are proposed as novel species: M. istanbulense sp. nov. Mu-43T (LMG 33297T = DSM 117065T), M. bandirmense sp. nov. Mu-80T (LMG 33295T = DSM 117210T), and M. marmarense sp. nov. Mu-86T (LMG 33293T = DSM 117066T).
{"title":"Three new Microbacterium species isolated from the Marmara Sea mucilage event: Microbacterium istanbulense sp. nov., Microbacterium bandirmense sp. nov., Microbacterium marmarense sp. nov","authors":"Izzet Burcin Saticioglu , Nihed Ajmi , Orkid Coskuner-Weber , Semih Alpsoy , Hilal Ay , Fuat Aydin , Seçil Abay , Emre Karakaya , Tuba Kayman , Cem Dalyan , Fatih Doğan Koca , Gorkem Tasci , Doğancan Yarim , Danny Morick , Artun Yibar , Serdar Erdogan , Soner Altun , Muhammed Duman","doi":"10.1016/j.syapm.2025.126600","DOIUrl":"10.1016/j.syapm.2025.126600","url":null,"abstract":"<div><div>Three bacterial strains, Mu-43<sup>T</sup>, Mu-80<sup>T</sup>, and Mu-86<sup>T</sup>, were isolated from the 2021 and 2022 mucilage event in the Marmara Sea and were taxonomically characterized. 16S rRNA gene sequence analysis confirmed that these strains belong to the genus <em>Microbacterium</em>. A polyphasic approach involving genomic and phenotypic analysis was employed to determine their taxonomic positions. A polyphasic approach integrating genomic and phenotypic analyses established their taxonomic positions. <em>M. istanbulense</em> Mu-43<sup>T</sup> showed 99.0 % 16S rRNA similarity to <em>M. bandirmense</em> Mu-80<sup>T</sup>, with digital DNA–DNA hybridization (dDDH) and average nucleotide identity using BLAST (ANIb) values of 22.3 % and 78.3 %, respectively. <em>M. bandirmense</em> Mu-80<sup>T</sup> exhibited 99.2 % similarity to <em>M. esteraromaticum</em> DSM 8609<sup>T</sup>, with dDDH and ANIb values of 23.6 % and 80 %. <em>M. marmarense</em> Mu-86<sup>T</sup> showed 97.4 % similarity to <em>M. arthrosphaerae</em> JCM 30492<sup>T</sup>, with dDDH and ANIb values of 20.1 % and 74.2 %. Metagenomic analysis highlighted their ecological relevance, with relative abundances of 1.43 %, 1.15 %, and 0.95 %, respectively. Further genomic analysis identified biosynthetic gene clusters associated with secondary metabolite production, including non-ribosomal peptide synthetases and terpenoid biosynthesis pathways, suggesting potential antimicrobial activity. Additionally, antibiotic resistance genes, such as ABC efflux pumps and Erm23S_rRNA methyltransferase, indicate adaptation to environmental stress. These findings indicate that these species contribute to nutrient cycling and organic matter decomposition in mucilage-affected environments. Based on genomic and phenotypic data, these strains are proposed as novel species: <em>M. istanbulense</em> sp. nov. Mu-43<sup>T</sup> (LMG 33297<sup>T</sup> = DSM 117065<sup>T</sup>), <em>M. bandirmense</em> sp. nov. Mu-80<sup>T</sup> (LMG 33295<sup>T</sup> = DSM 117210<sup>T</sup>), and <em>M. marmarense</em> sp. nov. Mu-86<sup>T</sup> (LMG 33293<sup>T</sup> = DSM 117066<sup>T</sup>).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 3","pages":"Article 126600"},"PeriodicalIF":3.3,"publicationDate":"2025-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143550595","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-27DOI: 10.1016/j.syapm.2025.126592
Ling-Rui Zhu, Ya-Ling Mao, Yao Hu, Ya-Ping Sun, Jing Hou, Heng-Lin Cui
A new family related to the family Haloarculaceae was proposed and the genus Actinarchaeum was merged into the genus Halocatena through phylogenetic, phylogenomic, and comparative genomic analyses. Four strains KK48T, YCN56T, SYNS191T, and SYNS196T with new taxonomic status were isolated from inland saline lakes and a marine solar saltern. According to the comparison of 16S rRNA gene and rpoB' gene sequences, strains KK48T, YCN56T, SYNS191T, and SYNS196T showed high sequence similarities to the genera Salinibaculum and Salinirubellus, respectively. The values of average nucleotide identity, digital DNA–DNA hybridization, and average amino acid identity between these strains and the species of Salinibaculum and Salinirubellus ranged from 75.3 to 77.7 %, 24.5–25.9 % and 66.3–73.4 %, respectively. These data were well below the threshold for species classification, supporting their placements in new taxa. The major polar lipids of these strains were phosphatidic acid, phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, sulfated mannosyl glucosyl diether, mannosyl glucosyl diether, and disulfated mannosyl glucosyl diether. Based on the phenotypic, chemotaxonomic, phylogenetic, and phylogenomic properties, strains KK48T (= CGMCC 1.19060T = JCM 35607T), YCN56T (= CGMCC 1.62603T = JCM 36493T), SYNS191T (= CGMCC 1.62607T = JCM 36494T), and SYNS196T (= CGMCC 1.62608T = JCM 36495T) represent four novel species of the genera Salinibaculum and Salinirubellus. And Salinibaculum rarum sp. nov., Salinibaculum salinum sp. nov., Salinibaculum marinum sp. nov., and Salinirubellus litoreus sp. nov. are proposed to accommodate these strains.
{"title":"Genome-based taxonomy of the family Haloarculaceae, proposal of Natronomonadaceae fam. nov., and description of four novel halophilic archaea from two saline lakes and a marine solar saltern","authors":"Ling-Rui Zhu, Ya-Ling Mao, Yao Hu, Ya-Ping Sun, Jing Hou, Heng-Lin Cui","doi":"10.1016/j.syapm.2025.126592","DOIUrl":"10.1016/j.syapm.2025.126592","url":null,"abstract":"<div><div>A new family related to the family <em>Haloarculaceae</em> was proposed and the genus <em>Actinarchaeum</em> was merged into the genus <em>Halocatena</em> through phylogenetic, phylogenomic, and comparative genomic analyses. Four strains KK48<sup>T</sup>, YCN56<sup>T</sup>, SYNS191<sup>T</sup>, and SYNS196<sup>T</sup> with new taxonomic status were isolated from inland saline lakes and a marine solar saltern. According to the comparison of 16S rRNA gene and <em>rpoB'</em> gene sequences, strains KK48<sup>T</sup>, YCN56<sup>T</sup>, SYNS191<sup>T</sup>, and SYNS196<sup>T</sup> showed high sequence similarities to the genera <em>Salinibaculum</em> and <em>Salinirubellus</em>, respectively. The values of average nucleotide identity, digital DNA–DNA hybridization, and average amino acid identity between these strains and the species of <em>Salinibaculum</em> and <em>Salinirubellus</em> ranged from 75.3 to 77.7 %, 24.5–25.9 % and 66.3–73.4 %, respectively. These data were well below the threshold for species classification, supporting their placements in new taxa. The major polar lipids of these strains were phosphatidic acid, phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, sulfated mannosyl glucosyl diether, mannosyl glucosyl diether, and disulfated mannosyl glucosyl diether. Based on the phenotypic, chemotaxonomic, phylogenetic, and phylogenomic properties, strains KK48<sup>T</sup> (= CGMCC 1.19060<sup>T</sup> = JCM 35607<sup>T</sup>), YCN56<sup>T</sup> (= CGMCC 1.62603<sup>T</sup> = JCM 36493<sup>T</sup>), SYNS191<sup>T</sup> (= CGMCC 1.62607<sup>T</sup> = JCM 36494<sup>T</sup>), and SYNS196<sup>T</sup> (= CGMCC 1.62608<sup>T</sup> = JCM 36495<sup>T</sup>) represent four novel species of the genera <em>Salinibaculum</em> and <em>Salinirubellus</em>. And <em>Salinibaculum rarum</em> sp. nov., <em>Salinibaculum salinum</em> sp. nov., <em>Salinibaculum marinum</em> sp. nov., and <em>Salinirubellus litoreus</em> sp. nov. are proposed to accommodate these strains.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 3","pages":"Article 126592"},"PeriodicalIF":3.3,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143534782","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-10DOI: 10.1016/j.syapm.2025.126591
Olga A. Podosokorskaya , Maria I. Prokofeva , Alexandra A. Kuchierskaya , Alexandra A. Klyukina , Alexander G. Elcheninov
A novel anaerobic moderately thermophilic bacterium, strain 4138-strT, was isolated from a thermal spring of North Ossetia (Russian Federation). Gram-negative cells were non-sporeforming, straight or curved filamentous rods, occasionally forming rosettes. The strain grew at 30–55 °C, pH range of 6.1–8.7, NaCl range of 0–4 %, with an optimum at 50 °C, pH 7.1–7.5 and 0.2–0.4 % NaCl. It was a chemoorganoheterotroph, growing on simple sugars (glucose, maltose, cellobiose, etc.) and carbohydrates (starch, pullulan, laminarin, xylan, lichenan, curdlan, pachyman) or proteinaceous substrates (peptone, tryptone, gelatin, casein). Sulfur was used as electron acceptor. Major products of glucose fermentation were acetate, hydrogen, and carbon dioxide. Major cellular fatty acids were iso-C15:0 and anteiso-C15:0. The quinone was MK-7. The size of the whole genome of strain 4138-strT was 3.275 Mbp; DNA G + C content was 42.1 %. Genome analysis allowed to identify genes encoding carbohydrate-active enzymes and extracellular proteases. In addition, central metabolism and fermentation pathways of strain 4138-strT were reconstructed. According to both phylogenetic analyses, based on 16S rRNA gene sequences and conserved protein sequences, as well as genome-based comparisons, strain 4138-strT formed a species-level lineage within Tenuifilum genus of Tenuifilaceae family (phylum Bacteroidota). Here we propose a novel species Tenuifilum osseticum sp. nov. with type strain 4138-strT(=KCTC 25386T = VKM B-3628T = UQM 41477T).
{"title":"Tenuifilum osseticum sp. nov., a novel thermophilic hydrolytic bacterium within the Tenuifilaceae isolated from a North Ossetian thermal spring, and emended description of the genus Tenuifilum","authors":"Olga A. Podosokorskaya , Maria I. Prokofeva , Alexandra A. Kuchierskaya , Alexandra A. Klyukina , Alexander G. Elcheninov","doi":"10.1016/j.syapm.2025.126591","DOIUrl":"10.1016/j.syapm.2025.126591","url":null,"abstract":"<div><div>A novel anaerobic moderately thermophilic bacterium, strain 4138-str<sup>T</sup>, was isolated from a thermal spring of North Ossetia (Russian Federation). Gram-negative cells were non-sporeforming, straight or curved filamentous rods, occasionally forming rosettes. The strain grew at 30–55 °C, pH range of 6.1–8.7, NaCl range of 0–4 %, with an optimum at 50 °C, pH 7.1–7.5 and 0.2–0.4 % NaCl. It was a chemoorganoheterotroph, growing on simple sugars (glucose, maltose, cellobiose, etc.) and carbohydrates (starch, pullulan, laminarin, xylan, lichenan, curdlan, pachyman) or proteinaceous substrates (peptone, tryptone, gelatin, casein). Sulfur was used as electron acceptor. Major products of glucose fermentation were acetate, hydrogen, and carbon dioxide. Major cellular fatty acids were iso-C<sub>15:0</sub> and anteiso-C<sub>15:0</sub>. The quinone was MK-7. The size of the whole genome of strain 4138-str<sup>T</sup> was 3.275 Mbp; DNA G + C content was 42.1 %. Genome analysis allowed to identify genes encoding carbohydrate-active enzymes and extracellular proteases. In addition, central metabolism and fermentation pathways of strain 4138-str<sup>T</sup> were reconstructed. According to both phylogenetic analyses, based on 16S rRNA gene sequences and conserved protein sequences, as well as genome-based comparisons, strain 4138-str<sup>T</sup> formed a species-level lineage within <em>Tenuifilum</em> genus of <em>Tenuifilaceae</em> family (phylum <em>Bacteroidota</em>). Here we propose a novel species <em>Tenuifilum osseticum</em> sp. nov. with type strain 4138-str<sup>T</sup>(=KCTC 25386<sup>T</sup> = VKM B-3628<sup>T</sup> = UQM 41477<sup>T</sup>).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 2","pages":"Article 126591"},"PeriodicalIF":3.3,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143402975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.syapm.2025.126590
Abdelaziz El Houari , Morgan Carpenter , Daniel Chaplin , Peter Golyshin , James E. McDonald
Bacteria responsible for the anaerobic decomposition of lignocellulosic waste biomass play key roles in the global carbon cycle and possess enzymes with potential industrial application. Here, a novel anaerobic, thermophilic, non-spore-forming bacterium, strain m5T, was isolated from methanogenic enrichment cultures obtained from a lab-scale methanogenic landfill bioreactor digesting anaerobic municipal solid waste. Cells were Gram-stain-negative, catalase-negative, oxidase-negative, rod-shaped, and non-motile. The genomic DNA G + C content was 40.92 mol%. The optimal NaCl concentration, temperature and pH for growth were 0.5–1 g.L−1, 45 °C, and at pH 7.0, respectively. The major fatty acids were C14:0, C16:0, C18:0, C18:1ω9c, and anteisoC15:0. Strain m5T was able to grow in the absence of yeast extract on glucose, fructose, arabinose, cellobiose, galactose, maltose, raffinose, sucrose, lactose, and pyruvate. In the presence of 0.2 % yeast extract, strain m5T grew on wide range of carbohydrates and amino acids, and was able to use complex substrates such cellulose and xylan. Major end products from cellulose and xylan degradation were valerate and propionate. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the new isolate was most closely related to Seramator thermalis SYSU GA16112T (94.42 % 16S rRNA gene sequence identity). Genome-based relatedness as well as both Average Nucleotide Identity (ANI), and Average Amino Acid Identity (AAI) strongly supported that strain m5T belongs to the Dysgonomonadaceae family. Metagenomic analysis of the landfill bioreactor community revealed that the Dysgonomonadaceae family was the most abundant in the constructed bioreactors. Based on its unique genomic features, strain m5T is considered to represent a novel genus, for which the name Anaerorudis is proposed. Moreover, several phenotypic, biochemical, and physiological properties differentiated the novel bacterial strain from related species, indicating that the strain represents a new species for which the name Anaerorudis cellulosivorans sp. nov. is proposed, with strain m5T (= DSM 112743T = ATCC TSD-267T) being the type of strain. This study highlights the biotechnological potential of strain m5T, specifically in the bioconversion of cellulose and xylan, a recalcitrant substrate within lignocellulosic plant biomass, to enhance biogas production.
{"title":"Taxonomic description and genome sequence of Anaerorudis cellulosivorans gen. Nov. sp. nov., a novel cellulose- and Xylan-degrading bacterium of the Bacteroidota phylum isolated from a lab-scale methanogenic landfill bioreactor digesting municipal solid waste","authors":"Abdelaziz El Houari , Morgan Carpenter , Daniel Chaplin , Peter Golyshin , James E. McDonald","doi":"10.1016/j.syapm.2025.126590","DOIUrl":"10.1016/j.syapm.2025.126590","url":null,"abstract":"<div><div>Bacteria responsible for the anaerobic decomposition of lignocellulosic waste biomass play key roles in the global carbon cycle and possess enzymes with potential industrial application. Here, a novel anaerobic, thermophilic, non-spore-forming bacterium, strain m5<sup>T</sup>, was isolated from methanogenic enrichment cultures obtained from a lab-scale methanogenic landfill bioreactor digesting anaerobic municipal solid waste. Cells were Gram-stain-negative, catalase-negative, oxidase-negative, rod-shaped, and non-motile. The genomic DNA G + C content was 40.92 mol%. The optimal NaCl concentration, temperature and pH for growth were 0.5–1 g.L<sup>−1</sup>, 45 °C, and at pH 7.0, respectively. The major fatty acids were C<sub>14:0</sub>, C<sub>16:0</sub>, C<sub>18:0</sub>, C<sub>18:1</sub> <em>ω</em>9<em>c</em>, and anteisoC<sub>15:0</sub>. Strain m5<sup>T</sup> was able to grow in the absence of yeast extract on glucose, fructose, arabinose, cellobiose, galactose, maltose, raffinose, sucrose, lactose, and pyruvate. In the presence of 0.2 % yeast extract, strain m5<sup>T</sup> grew on wide range of carbohydrates and amino acids, and was able to use complex substrates such cellulose and xylan. Major end products from cellulose and xylan degradation were valerate and propionate. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the new isolate was most closely related to <em>Seramator thermalis</em> SYSU GA16112<sup>T</sup> (94.42 % 16S rRNA gene sequence identity). Genome-based relatedness as well as both Average Nucleotide Identity (ANI), and Average Amino Acid Identity (AAI) strongly supported that strain m5<sup>T</sup> belongs to the <em>Dysgonomonadaceae</em> family. Metagenomic analysis of the landfill bioreactor community revealed that the <em>Dysgonomonadaceae</em> family was the most abundant in the constructed bioreactors. Based on its unique genomic features, strain m5<sup>T</sup> is considered to represent a novel genus, for which the name <em>Anaerorudis</em> is proposed. Moreover, several phenotypic, biochemical, and physiological properties differentiated the novel bacterial strain from related species, indicating that the strain represents a new species for which the name <em>Anaerorudis cellulosivorans</em> sp. nov. is proposed, with strain m5<sup>T</sup> (= DSM 112743<sup>T</sup> = ATCC TSD-267<sup>T</sup>) being the type of strain. This study highlights the biotechnological potential of strain m5<sup>T</sup>, specifically in the bioconversion of cellulose and xylan, a recalcitrant substrate within lignocellulosic plant biomass, to enhance biogas production.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 2","pages":"Article 126590"},"PeriodicalIF":3.3,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143402976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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