David R Arahal, Carolee T Bull, Henrik Christensen, Christopher Dunlap, Maria Del Carmen Montero-Calasanz, Charles T Parker, Peter Vandamme, Antonio Ventosa, Stefano Ventura, Peter Young, Markus Göker
Opinion 131 addresses a Request for an Opinion asking the Judicial Commission to conserve the genus name Proteus Hauser 1885 (Approved Lists 1980) over its earlier homonym, the protozoan genus name Proteus Müller 1786. The Judicial Commission agrees that the later homonym is illegitimate and that the replacement of the prokaryotic name Proteus would be undesirable. It is also concluded that Proteus Müller 1786 is an objectively invalid name under the International Code of Zoological Nomenclature. Judicial Opinions 9, 12 and 130 serve as precedents for the conservation of Proteus Hauser 1885 (Approved Lists 1980) over Proteus Müller 1786. This action is taken here and makes the prokaryotic name Proteus legitimate.
{"title":"Judicial Opinion 131.","authors":"David R Arahal, Carolee T Bull, Henrik Christensen, Christopher Dunlap, Maria Del Carmen Montero-Calasanz, Charles T Parker, Peter Vandamme, Antonio Ventosa, Stefano Ventura, Peter Young, Markus Göker","doi":"10.1099/ijsem.0.006692","DOIUrl":"https://doi.org/10.1099/ijsem.0.006692","url":null,"abstract":"<p><p>Opinion 131 addresses a Request for an Opinion asking the Judicial Commission to conserve the genus name <i>Proteus</i> Hauser 1885 (Approved Lists 1980) over its earlier homonym, the protozoan genus name <i>Proteus</i> Müller 1786. The Judicial Commission agrees that the later homonym is illegitimate and that the replacement of the prokaryotic name <i>Proteus</i> would be undesirable. It is also concluded that <i>Proteus</i> Müller 1786 is an objectively invalid name under the <i>International Code of Zoological Nomenclature</i>. Judicial Opinions 9, 12 and 130 serve as precedents for the conservation of <i>Proteus</i> Hauser 1885 (Approved Lists 1980) over <i>Proteus</i> Müller 1786. This action is taken here and makes the prokaryotic name <i>Proteus</i> legitimate.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 2","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143523282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Marion Yvin, Estelle Mühle, Olivier Chesneau, Hélène Laguerre, Benjamin Brillet, Yannick Fleury, Camille Jégou, Peter Kämpfer, André Lipski, Alexis Criscuolo, Dominique Clermont, Patrick Le Chevalier
Two motile bacterial strains, designated as cfHf56-1T and SW 252, were isolated from the coelomic fluid of Holothuria forskali and from the surrounding seawater at the animal sampling site, respectively. The sea cucumber was collected in the Glénan archipelago (Brittany, France). Strains cfHf56-1T and SW 252 were Gram-stain-negative, non-spore-forming and rod-shaped bacteria. Colonies made on marine agar plates were brown in color. The pH and temperature ranges for growth were 7-8 and 18-30 °C, respectively, in marine broth. The major fatty acids were 16 : 1 cis9 and 16 : 0. Phylogenetic analyses evidenced that both strains belong to a novel species in the genus Pseudoalteromonas. The strains were closely related to the type strains of Pseudoalteromonas caenipelagi, Pseudoalteromonas byunsanensis and Pseudoalteromonas amylolytica, with 75-78 % ANI and 19-21 % dDDH values. In this context, cfHf56-1T (= CIP 111854T = CECT 30642T) is considered as the type strain of the novel species for which the name Pseudoalteromonas holothuriae sp. nov. is proposed. The genome of the type strain is characterized by a size of 5.1 Mbp and a G+C content of 40.5%.
{"title":"<i>Pseudoalteromonas holothuriae</i> sp. nov.<i>,</i> isolated from the sea cucumber <i>Holothuria forskali</i>.","authors":"Marion Yvin, Estelle Mühle, Olivier Chesneau, Hélène Laguerre, Benjamin Brillet, Yannick Fleury, Camille Jégou, Peter Kämpfer, André Lipski, Alexis Criscuolo, Dominique Clermont, Patrick Le Chevalier","doi":"10.1099/ijsem.0.006601","DOIUrl":"https://doi.org/10.1099/ijsem.0.006601","url":null,"abstract":"<p><p>Two motile bacterial strains, designated as cfHf56-1<sup>T</sup> and SW 252, were isolated from the coelomic fluid of <i>Holothuria forskali</i> and from the surrounding seawater at the animal sampling site, respectively. The sea cucumber was collected in the Glénan archipelago (Brittany, France). Strains cfHf56-1<sup>T</sup> and SW 252 were Gram-stain-negative, non-spore-forming and rod-shaped bacteria. Colonies made on marine agar plates were brown in color. The pH and temperature ranges for growth were 7-8 and 18-30 °C, respectively, in marine broth. The major fatty acids were 16 : 1 cis9 and 16 : 0. Phylogenetic analyses evidenced that both strains belong to a novel species in the genus <i>Pseudoalteromonas</i>. The strains were closely related to the type strains of <i>Pseudoalteromonas caenipelagi</i>, <i>Pseudoalteromonas byunsanensis</i> and <i>Pseudoalteromonas amylolytica,</i> with 75-78 % ANI and 19-21 % dDDH values. In this context, cfHf56-1<sup>T</sup> (= CIP 111854<sup>T</sup> = CECT 30642<sup>T</sup>) is considered as the type strain of the novel species for which the name <i>Pseudoalteromonas holothuriae</i> sp. nov. is proposed. The genome of the type strain is characterized by a size of 5.1 Mbp and a G+C content of 40.5%.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 2","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143501314","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ju-Young Hong, Jung-Hun Jo, Se-Yoon Chun, Wan-Taek Im
Two novel Gram-stain-negative, aerobic, heterotrophic, non-motile bacterial strains, designated as AS3R-12T and PS1R-30T, were isolated from freshwater in South Korea. To determine their taxonomic positions, the strains were thoroughly characterized. Genomic analyses, based on 16S rRNA gene and draft genome sequence data, revealed that the two novel isolates, AS3R-12T and PS1R-30T, belonged to the genus Novosphingobium. AS3R-12T showed the highest 16S rRNA gene similarity (97.7%) with Novosphingobium flavum UCT-28T. In addition, PS1R-30T showed 97.9% 16S rRNA gene similarity with Novosphingobium lentum NBRC 107847T. The draft genome of strains AS3R-12T and PS1R-30T consisted of 4 149 275 and 4 969 838 bps, with DNA G+C content of 63.1 and 66.1 mol%, respectively. The average nucleotide identity between two strains and other related species was below 76.2%, and the digital DNA-DNA hybridization values with closely related species were below 20.8%, both lower than the species delineation threshold. Strains AS3R-12T and PS1R-30T contained the ubiquinone Q-10 as the major quinone and displayed a polyamine pattern with spermidine as the predominant polyamine. Additionally, their major fatty acids were characterized by C16:1 ω7c/C16:1 ω6c (summed feature 3) and C18:1 ω7c/C18:1 ω6c (summed feature 8). The major polar lipids of AS3R-12T and PS1R-30T were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), sphingoglycolipid (SGL) and phosphatidylcholine (PC). Moreover, physiological and biochemical results allowed the phenotypic and genotypic differentiation of strains AS3R-12T and PS1R-30T from their closest and other species of the genus Novosphingobium with validly published names. Therefore, AS3R-12T and PS1R-30T represented novel species of the genus Novosphingobium, for which the names Novosphingobium aquae sp. nov. (type strain AS3R-12T=KACC 23096T=LMG 32950T) and Novosphingobium anseongense sp. nov. (type strain PS1R-30T=KACC 23097T=LMG 32951T) are proposed.
{"title":"Isolation and characterization of <i>Novosphingobium aquae</i> sp. nov. and <i>Novosphingobium anseongense</i> sp. nov.<i>,</i> isolated from freshwater.","authors":"Ju-Young Hong, Jung-Hun Jo, Se-Yoon Chun, Wan-Taek Im","doi":"10.1099/ijsem.0.006688","DOIUrl":"10.1099/ijsem.0.006688","url":null,"abstract":"<p><p>Two novel Gram-stain-negative, aerobic, heterotrophic, non-motile bacterial strains, designated as AS3R-12<sup>T</sup> and PS1R-30<sup>T</sup>, were isolated from freshwater in South Korea. To determine their taxonomic positions, the strains were thoroughly characterized. Genomic analyses, based on 16S rRNA gene and draft genome sequence data, revealed that the two novel isolates, AS3R-12<sup>T</sup> and PS1R-30<sup>T</sup>, belonged to the genus <i>Novosphingobium</i>. AS3R-12<sup>T</sup> showed the highest 16S rRNA gene similarity (97.7%) with <i>Novosphingobium flavum</i> UCT-28<sup>T</sup>. In addition, PS1R-30<sup>T</sup> showed 97.9% 16S rRNA gene similarity with <i>Novosphingobium lentum</i> NBRC 107847<sup>T</sup>. The draft genome of strains AS3R-12<sup>T</sup> and PS1R-30<sup>T</sup> consisted of 4 149 275 and 4 969 838 bps, with DNA G+C content of 63.1 and 66.1 mol%, respectively. The average nucleotide identity between two strains and other related species was below 76.2%, and the digital DNA-DNA hybridization values with closely related species were below 20.8%, both lower than the species delineation threshold. Strains AS3R-12<sup>T</sup> and PS1R-30<sup>T</sup> contained the ubiquinone Q-10 as the major quinone and displayed a polyamine pattern with spermidine as the predominant polyamine. Additionally, their major fatty acids were characterized by C<sub>16:1</sub> <i> ω7c</i>/C<sub>16:1</sub> <i> ω6c</i> (summed feature 3) and C<sub>18:1</sub> <i> ω7c</i>/C<sub>18:1</sub> <i> ω6c</i> (summed feature 8). The major polar lipids of AS3R-12<sup>T</sup> and PS1R-30<sup>T</sup> were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), sphingoglycolipid (SGL) and phosphatidylcholine (PC). Moreover, physiological and biochemical results allowed the phenotypic and genotypic differentiation of strains AS3R-12<sup>T</sup> and PS1R-30<sup>T</sup> from their closest and other species of the genus <i>Novosphingobium</i> with validly published names. Therefore, AS3R-12<sup>T</sup> and PS1R-30<sup>T</sup> represented novel species of the genus <i>Novosphingobium</i>, for which the names <i>Novosphingobium aquae</i> sp. nov. (type strain AS3R-12<sup>T</sup>=KACC 23096<sup>T</sup>=LMG 32950<sup>T</sup>) and <i>Novosphingobium anseongense</i> sp. nov. (type strain PS1R-30<sup>T</sup>=KACC 23097<sup>T</sup>=LMG 32951<sup>T</sup>) are proposed.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 2","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143501064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Qianhui Sun, Limin Jiang, Lijian Liao, Alan Warren, Xiaozhong Hu
Ciliates of the class Nassophorea Small & Lynn, 1981, inhabit a wide range of aquatic environments and serve as a trophic link in microbial food webs. However, their diversity remains underestimated. In the present study, the morphology and molecular phylogeny of Rhinakis faurei Deroux, 1994, an insufficiently known nassulid ciliate, were investigated using an integrative taxonomic approach. The studied population was collected from a freshwater pond in Qingdao, China. Details of the live morphology and ciliature of R. faurei are documented for the first time, and an improved species diagnosis is provided. Phylogenetic analyses of the small subunit ribosomal RNA gene sequence revealed that R. faurei clusters within the family Nassulidae de Fromentel, 1874. However, evolutionary interrelationships within the Nassulidae remain obscure owing to under-sampling, the lack of sequence data for most nominal species, and low nodal support or unstable gene tree topologies.
{"title":"Redescription and phylogeny of the little-known type species <i>Rhinakis faurei</i> Deroux, 1994 (Alveolata, Ciliophora, Nassophorea).","authors":"Qianhui Sun, Limin Jiang, Lijian Liao, Alan Warren, Xiaozhong Hu","doi":"10.1099/ijsem.0.006651","DOIUrl":"https://doi.org/10.1099/ijsem.0.006651","url":null,"abstract":"<p><p>Ciliates of the class Nassophorea Small & Lynn, 1981, inhabit a wide range of aquatic environments and serve as a trophic link in microbial food webs. However, their diversity remains underestimated. In the present study, the morphology and molecular phylogeny of <i>Rhinakis faurei</i> Deroux, 1994, an insufficiently known nassulid ciliate, were investigated using an integrative taxonomic approach. The studied population was collected from a freshwater pond in Qingdao, China. Details of the live morphology and ciliature of <i>R. faurei</i> are documented for the first time, and an improved species diagnosis is provided. Phylogenetic analyses of the small subunit ribosomal RNA gene sequence revealed that <i>R. faurei</i> clusters within the family Nassulidae de Fromentel, 1874. However, evolutionary interrelationships within the Nassulidae remain obscure owing to under-sampling, the lack of sequence data for most nominal species, and low nodal support or unstable gene tree topologies.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 2","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143188763","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Definition of the rhizobial symbiovars caraganae, robiniae and sophorae within <i>Mesorhizobium</i> and albiziae within <i>Neomesorhizobium</i>.","authors":"Mitchell Andrews, Junjie Zhang","doi":"10.1099/ijsem.0.006678","DOIUrl":"https://doi.org/10.1099/ijsem.0.006678","url":null,"abstract":"","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 2","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143407953","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Bacterial strains, designated DD3T and DDX28, were isolated from field soil in Japan. The strains had the ability to use 2,4-dichlorophenoxyacetic acid as the sole carbon source. They were Gram-reaction-negative, oxidase-positive, weakly catalase-positive, aerobic and non-spore-forming. Their cells were rod-shaped and often lacked flagella, but some exhibited motility due to the presence of one or two polar flagella. The genomic DNA G+C content was 58.8 mol%, and the major cellular fatty acids (>10% of the total fatty acids) were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C18 : 0 and C17 : 0 cyclo. Phylogenetic analyses based on gyrB gene sequences and phylogenomic analysis using whole-genome sequences confirmed that the strains belong to the genus Afipia; however, their phylogenetic position did not match that of any known species of this genus. Comparative studies of the average nucleotide identity and digital DNA-DNA hybridization with closely related species revealed values lower than the thresholds used for prokaryotic species delineation (95-96 and 70%, respectively), with the highest values observed for Afipia broomeae ATCC 49717T (79.92 and 21.5%, respectively). Phenotypic characteristics, cellular fatty acid composition and specific metabolic processes and biosynthetic gene clusters could differentiate the strains from their closest relatives. Our phenotypic, chemotaxonomic and genotypic data indicate that DD3T/DDX28 constitute a novel Afipia species, for which we propose the name Afipia dichlorophenoxyacetatis sp. nov., with DD3T (MAFF 311804T=ICMP 25015T) as the type strain.
{"title":"<i>Afipia dichlorophenoxyacetatis</i> sp. nov., isolated from field soil in Japan, degrades 2,4-dichlorophenoxyacetic acid.","authors":"Hiroyuki Sawada, Yoriko Sakai, Yusuke Takashima, Ken Naito, Mitsuo Horita, Mamoru Satou","doi":"10.1099/ijsem.0.006672","DOIUrl":"10.1099/ijsem.0.006672","url":null,"abstract":"<p><p>Bacterial strains, designated DD3<sup>T</sup> and DDX28, were isolated from field soil in Japan. The strains had the ability to use 2,4-dichlorophenoxyacetic acid as the sole carbon source. They were Gram-reaction-negative, oxidase-positive, weakly catalase-positive, aerobic and non-spore-forming. Their cells were rod-shaped and often lacked flagella, but some exhibited motility due to the presence of one or two polar flagella. The genomic DNA G+C content was 58.8 mol%, and the major cellular fatty acids (>10% of the total fatty acids) were summed feature 8 (C<sub>18 : 1</sub> <i> ω7c</i> and/or C<sub>18 : 1</sub> <i> ω6c</i>), C<sub>18 : 0</sub> and C<sub>17 : 0</sub> cyclo. Phylogenetic analyses based on <i>gyrB</i> gene sequences and phylogenomic analysis using whole-genome sequences confirmed that the strains belong to the genus <i>Afipia</i>; however, their phylogenetic position did not match that of any known species of this genus. Comparative studies of the average nucleotide identity and digital DNA-DNA hybridization with closely related species revealed values lower than the thresholds used for prokaryotic species delineation (95-96 and 70%, respectively), with the highest values observed for <i>Afipia broomeae</i> ATCC 49717<sup>T</sup> (79.92 and 21.5%, respectively). Phenotypic characteristics, cellular fatty acid composition and specific metabolic processes and biosynthetic gene clusters could differentiate the strains from their closest relatives. Our phenotypic, chemotaxonomic and genotypic data indicate that DD3<sup>T</sup>/DDX28 constitute a novel <i>Afipia</i> species, for which we propose the name <i>Afipia dichlorophenoxyacetatis</i> sp. nov., with DD3<sup>T</sup> (MAFF 311804<sup>T</sup>=ICMP 25015<sup>T</sup>) as the type strain.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 2","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143382452","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of <i>Leptospiraceae</i>: minutes of the closed meeting, 3 September 2024, Brussels, Belgium.","authors":"Nathan E Stone, Mathieu Picardeau","doi":"10.1099/ijsem.0.006691","DOIUrl":"https://doi.org/10.1099/ijsem.0.006691","url":null,"abstract":"","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 2","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143500856","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of Rhizobia and Agrobacteria: minutes of the 2024 closed annual meeting.","authors":"Seyed Abdollah Mousavi, J Peter W Young","doi":"10.1099/ijsem.0.006680","DOIUrl":"10.1099/ijsem.0.006680","url":null,"abstract":"","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 2","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143390785","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hiroyuki Sawada, Hirosuke Shinohara, Yusuke Takashima, Ken Naito, Mamoru Satou
Phytopathogenic bacteria (MAFF 311311T and MAFF 311313) were isolated from sugarcane plants exhibiting leaf stripe symptoms associated with red stripe disease in Okinawa Prefecture, Japan. The strains were Gram-reaction-negative, aerobic, motile with one polar flagellum, rod-shaped and non-spore-forming. The genomic DNA G+C content was 69.0 mol%, and the major cellular fatty acids (>10 % of the total fatty acids) included summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). Phylogenomic analyses using whole-genome sequences consistently placed these strains within the genus Acidovorax. However, their phylogenetic positions did not correspond to any known species within this genus. Comparative analyses, including average nucleotide identity and digital DNA-DNA hybridization with closely related species, yielded values below the thresholds for prokaryotic species delineation (95-96 and 70 %, respectively), with the highest values observed for Acidovorax oryzae ATCC 19882T (93.98 and 54.3 %, respectively). Phenotypic characteristics, cellular fatty acid composition and a repertoire of secretion systems and their effectors can differentiate these strains from their closest relatives. The phenotypic, chemotaxonomic and genotypic data obtained in this study indicate that MAFF 311311T and MAFF 311313 constitute a novel species within the genus Acidovorax, for which we propose the name Acidovorax sacchari sp. nov., with MAFF 311311T (=ICMP 25276T) designated as the type strain.
{"title":"<i>Acidovorax sacchari</i> sp. nov., a pathogen causing red stripe of sugarcane in Japan.","authors":"Hiroyuki Sawada, Hirosuke Shinohara, Yusuke Takashima, Ken Naito, Mamoru Satou","doi":"10.1099/ijsem.0.006575","DOIUrl":"10.1099/ijsem.0.006575","url":null,"abstract":"<p><p>Phytopathogenic bacteria (MAFF 311311<sup>T</sup> and MAFF 311313) were isolated from sugarcane plants exhibiting leaf stripe symptoms associated with red stripe disease in Okinawa Prefecture, Japan. The strains were Gram-reaction-negative, aerobic, motile with one polar flagellum, rod-shaped and non-spore-forming. The genomic DNA G+C content was 69.0 mol%, and the major cellular fatty acids (>10 % of the total fatty acids) included summed feature 3 (C<sub>16 : 1</sub> <i> ω7c</i> and/or C<sub>16 : 1</sub> <i> ω6c</i>), C<sub>16 : 0</sub> and summed feature 8 (C<sub>18 : 1</sub> <i> ω7c</i> and/or C<sub>18 : 1</sub> <i> ω6c</i>). Phylogenomic analyses using whole-genome sequences consistently placed these strains within the genus <i>Acidovorax</i>. However, their phylogenetic positions did not correspond to any known species within this genus. Comparative analyses, including average nucleotide identity and digital DNA-DNA hybridization with closely related species, yielded values below the thresholds for prokaryotic species delineation (95-96 and 70 %, respectively), with the highest values observed for <i>Acidovorax oryzae</i> ATCC 19882<sup>T</sup> (93.98 and 54.3 %, respectively). Phenotypic characteristics, cellular fatty acid composition and a repertoire of secretion systems and their effectors can differentiate these strains from their closest relatives. The phenotypic, chemotaxonomic and genotypic data obtained in this study indicate that MAFF 311311<sup>T</sup> and MAFF 311313 constitute a novel species within the genus <i>Acidovorax</i>, for which we propose the name <i>Acidovorax sacchari</i> sp. nov., with MAFF 311311<sup>T</sup> (=ICMP 25276<sup>T</sup>) designated as the type strain.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 2","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11797039/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143189291","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Meri Nakajima, Ryosuke Nakai, Yuga Hirakata, Kengo Kubota, Hisashi Satoh, Masaru K Nobu, Takashi Narihiro, Kyohei Kuroda
In the domain Bacteria, one of the largest, most diverse and environmentally ubiquitous phylogenetic groups, Candidatus Patescibacteria (also known as candidate phyla radiation/CPR), remains poorly characterized, leaving a major knowledge gap in microbial ecology. We recently discovered a novel cross-domain symbiosis between Ca. Patescibacteria and Archaea in highly purified enrichment cultures and proposed Candidatus taxa for the characterized species, including Ca. Minisyncoccus archaeophilus and the corresponding family Ca. Minisyncoccaceae. In this study, we report the isolation of this bacterium, designated strain PMX.108T, in a two-strain co-culture with a host archaeon, Methanospirillum hungatei strain DSM 864T (JF-1T), and hereby describe it as the first representative species of Ca. Patescibacteria. Strain PMX.108T was isolated from mesophilic methanogenic sludge in an anaerobic laboratory-scale bioreactor treating synthetic purified terephthalate- and dimethyl terephthalate-manufacturing wastewater. The strain could not grow axenically and is obligately anaerobic and parasitic, strictly depending on M. hungatei as a host. The genome was comparatively large (1.54 Mbp) compared to other members of the clade, lacked some genes involved in the biosynthesis pathway and encoded type IV pili-related genes associated with the parasitic lifestyle of ultrasmall microbes. The G+C content of the genomic DNA was 36.6 mol%. Here, we report the phenotypic and genomic properties of strain PMX.108T; we propose Minisyncoccus archaeiphilus gen. nov., sp. nov. to accommodate this strain. The type strain of the species is PMX.108T (=JCM 39522T). We also propose the associated family, order, class and phylum as Minisyncoccaceae fam. nov. Minisyncoccales nov., Minisyncoccia class. nov. and Minisyncoccota phyl. nov. within the bacterial kingdom Bacillati.
{"title":"<i>Minisyncoccus archaeiphilus</i> gen. nov., sp. nov., a mesophilic, obligate parasitic bacterium and proposal of <i>Minisyncoccaceae</i> fam. nov., <i>Minisyncoccales</i> ord. nov., <i>Minisyncoccia</i> class. nov. and <i>Minisyncoccota</i> phyl. nov. formerly referred to as <i>Candidatus</i> Patescibacteria or candidate phyla radiation.","authors":"Meri Nakajima, Ryosuke Nakai, Yuga Hirakata, Kengo Kubota, Hisashi Satoh, Masaru K Nobu, Takashi Narihiro, Kyohei Kuroda","doi":"10.1099/ijsem.0.006668","DOIUrl":"10.1099/ijsem.0.006668","url":null,"abstract":"<p><p>In the domain <i>Bacteria</i>, one of the largest, most diverse and environmentally ubiquitous phylogenetic groups, <i>Candidatus</i> Patescibacteria (also known as candidate phyla radiation/CPR), remains poorly characterized, leaving a major knowledge gap in microbial ecology. We recently discovered a novel cross-domain symbiosis between <i>Ca</i>. Patescibacteria and <i>Archaea</i> in highly purified enrichment cultures and proposed <i>Candidatus</i> taxa for the characterized species, including <i>Ca</i>. Minisyncoccus archaeophilus and the corresponding family <i>Ca</i>. Minisyncoccaceae. In this study, we report the isolation of this bacterium, designated strain PMX.108<sup>T</sup>, in a two-strain co-culture with a host archaeon, <i>Methanospirillum hungatei</i> strain DSM 864<sup>T</sup> (JF-1<sup>T</sup>), and hereby describe it as the first representative species of <i>Ca</i>. Patescibacteria. Strain PMX.108<sup>T</sup> was isolated from mesophilic methanogenic sludge in an anaerobic laboratory-scale bioreactor treating synthetic purified terephthalate- and dimethyl terephthalate-manufacturing wastewater. The strain could not grow axenically and is obligately anaerobic and parasitic, strictly depending on <i>M. hungatei</i> as a host. The genome was comparatively large (1.54 Mbp) compared to other members of the clade, lacked some genes involved in the biosynthesis pathway and encoded type IV pili-related genes associated with the parasitic lifestyle of ultrasmall microbes. The G+C content of the genomic DNA was 36.6 mol%. Here, we report the phenotypic and genomic properties of strain PMX.108<sup>T</sup>; we propose <i>Minisyncoccus archaeiphilus</i> gen. nov., sp. nov. to accommodate this strain. The type strain of the species is PMX.108<sup>T</sup> (=JCM 39522<sup>T</sup>). We also propose the associated family, order, class and phylum as <i>Minisyncoccaceae</i> fam. nov. <i>Minisyncoccales</i> nov., <i>Minisyncoccia</i> class. nov. and <i>Minisyncoccota</i> phyl. nov. within the bacterial kingdom <i>Bacillati</i>.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 2","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143382475","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}