Systematic and applied microbiology最新文献

{"title":"Peijinzhouia sedimentorum gen. Nov., sp. nov., isolated from polymetallic nodule fields of the Eastern Pacific, and proposal of the family Peijinzhouiaceae fam. Nov.","authors":"Yi-Ran Zhang ,&nbsp;Xu-Ya Lv ,&nbsp;Zhen Rong ,&nbsp;Xue-Wei Xu ,&nbsp;Yue-Hong Wu","doi":"10.1016/j.syapm.2025.126669","DOIUrl":"10.1016/j.syapm.2025.126669","url":null,"abstract":"<div><div>Deep-sea polymetallic nodules represent an important but unexploited resource of a wide range of critical metals, which indicates huge economic and scientific value. During an investigation in the bacterial diversity in the polymetallic nodule fields of the Eastern Pacific, strain EPR-FJ-38^T was isolated and characterized. Another strain SYC-11 was obtained from seawater sample of South China Sea. Strains EPR-FJ-38^T and SYC-11 showed the highest similarity to <em>Fulvivirga imtechensis</em> SW1-E11^T (89.6 %, family <em>Fulvivirgaceae</em>), followed by <em>Marinoscillum luteum</em> SJP7^T (89.3 %, family <em>Reichenbachiellaceae</em>), <em>Fulvivirga imtechensis</em> AK7^T (89.3 %), <em>Fulvivirga sediminis</em> 2943^T (89.0 %) and <em>Marivirga tractuosa</em> DSM 4126^T (89.0 %, family <em>Marivirgaceae</em>). Results of phylogenomic analysis showed that the strains EPR-FJ-38^T and SYC-11 form an independent branch separated from the family <em>Cyclobacteriaceae</em>. The AAI value between EPR-FJ-38^T and the reference strains was 46.0–53.3 %. Phenotypic, physiological, chemotaxonomic, genotypic properties and phylogenetic relationship indicate that strains EPR-FJ-38^T and SYC-11 possibly represents a novel family belonging to the <em>Cytophagales</em> order, for which the named <em>Peijinzhouiaceae</em> fam. Nov. is proposed. The genus and species of the <em>Peijinzhouiaceae</em> is <em>Peijinzhouia sedimentorum</em> sp. nov. (type strain EPR-FJ-38^T, MCCC M28192^T = KCTC 92505^T). In addition, two strains showed resistance and removal ability to Mn²⁺ and possessed biomineralization function, whereas microbes create an alkaline environment by carbonic anhydrase to form rhodochrosite. This study proposed a novel family belonging to the <em>Cytophagales</em> order and presents potential candidates for bioremediation in deep-sea environments.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"49 1","pages":"Article 126669"},"PeriodicalIF":4.2,"publicationDate":"2025-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145595012","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}

{"title":"Metagenome-assembled genomes reveal Pseudogracilibacillus amylolyticus sp. nov., a functional uncultured microorganism in high-temperature Daqu","authors":"Ai-Ping Lv ,&nbsp;Ying-Han ,&nbsp;Bao-Zhu Fang ,&nbsp;Guo-Zheng Wang ,&nbsp;Man-Chun Liu ,&nbsp;Bing-Ru Bian ,&nbsp;Zhuo-Huan Zheng ,&nbsp;Kai Li ,&nbsp;Bing-Yu Li ,&nbsp;Jian-Yu Jiao ,&nbsp;Lan Liu ,&nbsp;Lei Dong ,&nbsp;Liang-Qiang Chen ,&nbsp;Fan Yang ,&nbsp;Wen-Jun Li","doi":"10.1016/j.syapm.2025.126667","DOIUrl":"10.1016/j.syapm.2025.126667","url":null,"abstract":"<div><div>Daqu, a traditional fermentation starter for Chinese liquor production, harbors a complex microbial community that plays a pivotal role in shaping the flavor and quality of the final product of Baijiu. This study characterized three metagenome-assembled genomes (MAGs) from high-temperature Daqu of Jiang-flavor Baijiu, revealing a novel taxon within the genus <em>Pseudogracilibacillus</em>. Phylogenomic analysis demonstrated that three MAGs (A3–12A_bin_9^TS, M2–6-2A_bin_27 and M2–7-9A_bin_18) formed a distinct monophyletic clade, supported by the threshold value of ANI recommended for bacterial species, while showing significant divergence from other related type species within the genus <em>Pseudogracilibacillus</em>. Functional annotation revealed the metabolic versatility of this taxon, including starch and aromatic compound degradation (potentially contributing to flavor formation), biosynthetic capacity and adaptive traits such as oxidative phosphorylation flexibility and ABC transporter diversity, underscoring its ecological role in Daqu fermentation. Based on genomic and phylogenetic characteristics, these MAGs should be classified as representing a new taxon of this genus, for which the name <em>Pseudogracilibacillus amylolyticus</em> sp. nov. is proposed following the rules of the published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). This discovery expands the diversity of the family <em>Bacillaceae</em> in Baijiu fermentation and provides insights into the functional potential of uncultured microbes in traditional food ecosystems.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 6","pages":"Article 126667"},"PeriodicalIF":4.2,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145466175","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}

{"title":"Genome insights into Hydrogenophaga taeniospiralis and its R-body genetic determinants","authors":"Jorge Lalucat ,&nbsp;Antonio Busquets ,&nbsp;Magdalena Mulet ,&nbsp;Raúl Riesco ,&nbsp;Elena García-Valdés ,&nbsp;Margarita Gomila","doi":"10.1016/j.syapm.2025.126664","DOIUrl":"10.1016/j.syapm.2025.126664","url":null,"abstract":"<div><div>The genome of <em>Hydrogenophaga taeniospiralis</em> 2K1^T, the type and only strain of the species, was analysed. The genes encoding elements involved in autotrophic and chemolithotrophic growth that oxidize H₂ in addition to other metabolic traits, such as potential nitrogen fixation capability, are described. A phylogenomic analysis of the taxonomy of members of the genus reveals a high number of species not yet described in the genus, especially if the numerous metagenomes obtained from environmental samples are included. The differences from the closest related genera, <em>Malikia</em> and <em>Serpentinimonas</em>, are highlighted and the delineation of the genus <em>Hydrogenophaga</em> is discussed based on phylogenomic analysis. Furthermore, a survey of metagenomes available in public databases demonstrates the wide environmental and geographic distribution of <em>Hydrogenophaga</em> strains. <em>H. taeniospiralis</em> 2K1^T is the first free-living bacterium described for its ability to synthesize R- bodies, which are intracytoplasmic extendable protein ribbons associated mainly with toxic effects. The genetic determinants of R-body synthesis are analysed and compared with those found in other <em>Hydrogenophaga</em> genomes and strains from other genera.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 6","pages":"Article 126664"},"PeriodicalIF":4.2,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145417304","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}

{"title":"Denitraticella aggregata gen. nov., sp. nov. a denitrifying benzoate-utilizing bacterium isolated from a terrestrial mud volcano","authors":"Galina Slobodkina ,&nbsp;Alexander Merkel ,&nbsp;Andrei Novikov ,&nbsp;Alexander Slobodkin","doi":"10.1016/j.syapm.2025.126665","DOIUrl":"10.1016/j.syapm.2025.126665","url":null,"abstract":"<div><div>Microorganisms play a pivotal role in denitrification and in the degradation of aromatic compounds, processes essential for nitrogen and carbon recycling in diverse ecosystems. Mud volcanoes, with their fluctuating redox conditions and hydrocarbon emissions, represent potential natural sources of such microorganisms. A novel facultatively anaerobic, facultatively lithoautotrophic bacterium (strain SMB388^T) was isolated from terrestrial mud volcano (Krasnodar Krai, Russia). Cells of the strain were straight motile rods. Growth was observed at temperatures up to 42 °C (optimum at 30 °C), pH 6.0–10.0 (optimum at pH 8.0) and NaCl concentrations of 0–10% (<em>w</em>/<em>v</em>) (optimum at 2.0–2.5% (w/v)). The isolate grew chemolithoautotrophically with molecular hydrogen, elemental sulfur or thiosulfate as an electron donor, nitrate or oxygen as an electron acceptor and CO₂/HCO₃⁻ as a carbon source. It also grew with organic substrates such as carboxylic acids, benzoate, glycerol, propanol, yeast extract and peptone. The isolate did not utilize mono- or disaccharides. The total size of the genome of strain SMB388^T was 3.4 Mb, and the genomic DNA G + C content was 64.4 mol%. Phylogenomic analysis placed SMB388^T into the family <em>Zoogloeaceae</em>. Based on phenotypic and phylogenetic characteristics, strain SMB388^T represents a novel species of the novel genus for which we propose the name <em>Denitraticella aggregata</em> gen. nov., sp. nov. (the type strain is SMB388^T = KCTC 25769^T = VKM B-3859^T).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 6","pages":"Article 126665"},"PeriodicalIF":4.2,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145393279","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}

{"title":"Quyinboa mangrovi gen. nov., sp. nov., Quyinboa ferrireducens sp. nov., and Quyinboa sediminis sp. nov., three novel Fe(III)-reducing and nitrogen-fixing bacteria isolated from mangrove sediment, and the proposal of Quyinboaceae fam. nov. within the class Bacteroidia","authors":"Xiao-Xuan Song ,&nbsp;Le Liu ,&nbsp;Guan-Jun Chen ,&nbsp;Zhenxing Xu ,&nbsp;Zong-Jun Du","doi":"10.1016/j.syapm.2025.126668","DOIUrl":"10.1016/j.syapm.2025.126668","url":null,"abstract":"<div><div>Three marine bacteria in <em>Bacteroidales</em>, designated FJH62^T, FJH65^T and FJH54^T, were isolated from mangrove sediments at the Zhangjiang River estuary in Fujian, China. The cells were Gram-stain-negative, facultatively anaerobic, non-motile and straight to curved rod-shaped. Comparative analysis of the 16S rRNA gene showed that strains FJH62^T and FJH65^T shared 88.9–89.0 % identity with <em>Saccharicrinis carchari</em> SS12^T, while strain FJH54^T had the maximum similarity of 88.8 % to <em>Carboxylicivirga taeanensis</em> MEBiC 08093^T. Whole-genome relatedness indices further distinguished these isolates from other relatives, falling below the established thresholds, with strains FJH62^T, FJH65^T, and FJH54^T identified as three distinct novel species. Phylogenetic analysis based on both 16S rRNA gene and whole genome sequences indicated that these three novel strains form a monophyletic branch within the order <em>Bacteroidales</em>. These isolates were distinguished from their closest relatives by the presence of MK-10 as the major respiratory quinone and phosphatidylethanolamine, aminolipids, and phospholipids as the predominant polar lipids. The major cellular fatty acids and DNA G + C content were identified as iso-C_15:0 and anteiso-C_15:0 and 38.5–39.9 %, respectively. Genomic analysis and experimental validation confirmed nitrogen-fixing and Fe(III)-reducing abilities of these three strains. Based on polyphasic characterizations, these three strains represent three novel species of a novel genus, for which the names <em>Quyinboa mangrovi</em> gen. nov., sp. nov. (FJH62^T = KCTC 102258^T = MCCC 1H01534^T), <em>Quyinboa ferrireducens</em> sp. nov. (FJH65^T = KCTC 102259^T = MCCC 1H01536^T), and <em>Quyinboa sediminis</em> sp. nov. (FJH54^T = KCTC 102257^T = MCCC 1H01535^T) are proposed. Furthermore, a novel family, <em>Quyinboaceae</em> fam. nov., is proposed within the order <em>Bacteroidales</em>.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 6","pages":"Article 126668"},"PeriodicalIF":4.2,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145466176","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}

{"title":"Comparative genome analysis of the Sphaerotilus-Leptothrix group supports the unification of the genera Sphaerotilus and Leptothrix into a single emended genus Sphaerotilus","authors":"Dmitry D. Smolyakov ,&nbsp;Alexey V. Beletsky ,&nbsp;Tatyana S. Rudenko ,&nbsp;Maria V. Gureeva ,&nbsp;Nikolai V. Ravin ,&nbsp;Margarita Y. Grabovich","doi":"10.1016/j.syapm.2025.126666","DOIUrl":"10.1016/j.syapm.2025.126666","url":null,"abstract":"<div><div>The <em>Sphaerotilus-Leptothrix</em> group comprises two genera studied for 200 years. Attempts to unite these genera were made repeatedly, but have caused controversy due to differences in phenotypic characters identified in a small number of pure cultures. According to the latest release of Genome Taxonomy Database, <em>Sphaerotilus</em> and <em>Leptothrix</em> are combined into a single genus, <em>Sphaerotilus</em>. In this study, we analyzed 20 high-quality genomes forming 7 clusters on a phylogenetic tree constructed from concatenated sequences of 120 conserved genes, and investigated the distribution of metabolic genes. The <em>Sphaerotilus</em>-<em>Leptothrix</em> group formed a distinct monophyletic lineage within the family <em>Sphaerotilaceae</em>, where <em>Leptothrix</em> species were distributed among <em>Sphaerotilus</em> species. The average amino acid identities between the <em>Sphaerotilus</em>-<em>Leptothrix</em> genomes vary from 65 to 94.21%. All analyzed genomes contained genes of glycolysis, tricarboxylic acid cycle, and glyoxylate cycle. Genes for enzymes of dissimilatory sulfur metabolism were found, including oxidation of sulfide (<em>sqr</em>, <em>fccAB</em>), thiosulfate (<em>soxAXBYZCD</em>), elemental sulfur (<em>rDSR</em>) and sulfite (<em>soeABC</em>). Genes for manganese oxidation (<em>mnxG</em>, <em>mofABC</em>), previously considered unique to <em>Leptothrix</em>, were found in a number of other representatives of the combined genus. Also, some representatives contained genes for dissimilatory nitrate reduction and nitrogen fixation; autotrophic CO₂ fixation via the Calvin cycle; potential iron oxidation (<em>cyc2</em>, <em>mtoAB</em>). The identified metabolic pathways indicate a wide range of ecological strategies and occupied niches, determined by chemoorganoheterotrophic, chemolithoautotrophic and chemolithoheterotrophic nutritional types. Thus, the data obtained from phylogenetic analysis, large-scale genome analysis and assessment of metabolic potential support the unification of the genera <em>Sphaerotilus</em> and <em>Leptothrix</em> as a single genus <em>Sphaerotilus</em>.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 6","pages":"Article 126666"},"PeriodicalIF":4.2,"publicationDate":"2025-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145347362","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}

{"title":"Mycoplasma aquilae sp. nov., Mycoplasma paraquilae sp. nov., Mycoplasma haliaeeti sp. nov., Mycoplasma milvi sp. nov., and Mycoplasma razini sp. nov., isolated from predatory birds of the Accipitridae family","authors":"Joachim Spergser ,&nbsp;Sarah Kugler ,&nbsp;Anna Kübber-Heiss ,&nbsp;Ursula Höfle ,&nbsp;Nora Dinhopl ,&nbsp;Michael P. Szostak ,&nbsp;Igor Loncaric ,&nbsp;Tomeu Viver ,&nbsp;Ana S. Ramírez","doi":"10.1016/j.syapm.2025.126663","DOIUrl":"10.1016/j.syapm.2025.126663","url":null,"abstract":"<div><div>Mycoplasmas are regularly isolated from the upper respiratory tract of predatory birds; however, most of these <em>Mycoplasma</em> isolates remain unidentified. A cohort of such unidentified <em>Mycoplasma</em> strains (<em>n</em> = 42) recovered from birds of the <em>Accipitridae</em> family was subjected to a comprehensive taxonomic study. All strains grew well in modified Hayflick's medium, and colonies exhibited typical fried egg morphology. The strains neither produced acid from sugar carbon sources nor hydrolysed arginine or urea. Analyses of 16S rRNA gene, 16S<img>23S intergenic spacer, and partial <em>rpoB</em> gene sequences placed the strains within the <em>Mycoplasma</em> (<em>M.</em>) <em>synoviae</em> cluster (Hominis group) with <em>M. verecundum</em> and <em>M. seminis</em> being their closest relatives. Phylogenetic trees inferred from 16S rRNA and <em>rpoB</em> gene sequences subdivided the 42 strains into five strain clusters. MALDI-ToF mass spectrometry allowed the differentiation of one strain group from the others but failed to distinguish the remaining four strain groups. Genome and proteome similarity metrics (ANIb, ANIm, TETRA, dDDH, AAI) and phylogenomic analysis provided solid evidence that the strains examined are indeed representatives of five hitherto unclassified species of genus <em>Mycoplasma</em> for which the names <em>Mycoplasma aquilae</em> sp. nov., <em>Mycoplasma paraquilae</em> sp. nov., <em>Mycoplasma haliaeeti</em> sp. nov., <em>Mycoplasma milvi</em> sp. nov., constituting the newly defined <em>Mycoplasma aquilae</em> complex, and <em>Mycoplasma razini</em> sp. nov. are proposed, with their designated type strains 1449^T (ATCC BAA-1896^T = DSM 22458^T), 654^T (DSM 113738^T = NCTC 14855^T), VS42A^T (DSM 113741^T = NCTC 14856^T), Z331B^T (DSM 113740^T = NCTC 14858^T), and 005V^T (DSM 113739^T = NCTC 14838^T), respectively.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 6","pages":"Article 126663"},"PeriodicalIF":4.2,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145281042","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}

{"title":"Chryseobacterium hilariae sp. nov., Sphingomonas larreae sp. nov., Sphingomonas astragali sp. nov., Sphingomonas radicis sp. nov., Variovorax stachyos sp. nov., Parapedobacter brassicae sp. nov., Neorhizobium descurainiae sp. nov., and Erwinia artemisiae sp. nov. isolated from dry soils revealing a diverse plant growth promoting potential","authors":"Peter Kämpfer ,&nbsp;André Lipski ,&nbsp;Kathy S. Lawrence ,&nbsp;Walker R. Olive ,&nbsp;Molli M. Newman ,&nbsp;John A. McInroy ,&nbsp;Tomeu Viver","doi":"10.1016/j.syapm.2025.126662","DOIUrl":"10.1016/j.syapm.2025.126662","url":null,"abstract":"<div><div>Bacteria belonging to the genera <em>Chryseobacterium, Sphingomonas, Variovorax, Neorhizobium, Parapedobacter</em> and <em>Erwinia</em> have been isolated from different soils and have also been shown to exhibit plant growth promoting (PGP) features. A polyphasic approach was employed to ascertain the taxonomic status of eight selected strains all isolated from dry soils in association with plants showing high desiccation tolerances. Based on the result of the polyphasic characterization, the following names are proposed: <em>Chryseobacterium hilariae</em> sp. nov., with DT-3^T as the type strain (= CIP 112171^T = LMG 32722^T = CCM 9258^T); <em>Sphingomonas astragali</em> sp. nov., with DT-204^T as the type strain (= CCM 9255^T = LMG 33194^T = CIP 112175^T); <em>Sphingomonas radicis</em> sp. nov., with DT-207^T as the type strain (= CCM 9257^T = LMG 32727^T = DSM 114514^T); <em>Sphingomonas larreae</em> sp. nov., with DT-51^T as the type strain (= CCM 9259^T = CIP 112177^T = DSM 114511^T = LMG 32723^T); <em>Variovorax stachyos</em> sp. nov., with DT-64^T as the type strain (= LMG 32724^T = DSM 114531^T = CIP 112170^T); <em>Erwinia artemisiae</em> sp. nov., with DT-104^T as the type strain (CCM 9256^T = LMG 32725^T = DSM 114512^T); <em>Parapedobacter brassicae</em> sp. nov., with DT-150^T as the type strain (LMG 32759^T = DSM 115120^T); and <em>Neorhizobium descurainiae</em> sp. nov., with DT-125^T as the type strain (LMG 32760^T = CIP 112184^T).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 6","pages":"Article 126662"},"PeriodicalIF":4.2,"publicationDate":"2025-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145087440","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}

{"title":"Isolation of diverse Undibacterium-related strains from alpine lakes and re-examining the taxonomic status of this genus","authors":"Hui-Bin Lu ,&nbsp;Ling-Yang Kong ,&nbsp;Li Chen ,&nbsp;Guang-Jie Chen ,&nbsp;Jian-Jun Wang","doi":"10.1016/j.syapm.2025.126661","DOIUrl":"10.1016/j.syapm.2025.126661","url":null,"abstract":"<div><div>The genus <em>Undibacterium</em> is an important member of <em>Oxalobacteraceae</em> and most species of this genus were isolated from freshwater environments. The recent study based on the genomic analyses revised the taxonomic status of 23 <em>Undibacterium</em> species and proposed that these species should be assigned into four genera (<em>Undibacterium</em>, <em>Neoundibacterium</em>, <em>Affinundibacterium</em> and <em>Paraundibacterium</em>), respectively. During the investigation of microbial resources inhabited in alpine lakes from the southwestern China in 2023, 25 strains show the highest 16S rRNA gene sequence similarities with <em>Undibacterium</em> species were isolated. Utilizing the genomes of these 25 strains and 26 <em>Undibacterium</em> species, the phylogenies among these strains are reconstructed based on the core and pan-genome, respectively. The phylogenomic trees show that the 26 <em>Undibacterium</em> species should be divided into six clades and each clade should represent an independent genus. As the clades 2, 3, 4 and 5 proposed in this study have been revised in other study, the genera <em>Cognatundibacterium</em> and <em>Pseudundibacterium</em> are proposed in this study to accommodate the clades 1 and 6, respectively. The detailed genomic annotations reveal that all the 25 isolated <em>Undibacterium</em>-related strains harbor complete amino acids metabolisms and genes encoding DNA replication and repair, homologous recombination proteins, two-component and phosphate transport systems in response to the oligotrophic, high UV radiation and phosphorus-limited environments of alpine lakes. This study clarifies the role of <em>Undibacterium</em>-related strains in alpine lakes and demonstrates that isolating more strains is of great benefit to the bacterial taxonomy.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 6","pages":"Article 126661"},"PeriodicalIF":4.2,"publicationDate":"2025-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145097635","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}

{"title":"A chemotaxonomic and phylogenomic re-evaluation of the genus Alicyclobacillus: A proposal for reclassification of about half of the species into the new genus, Paenalicyclobacillus gen. nov., with an emended description of the genus Alicyclobacillus, and recognition that the names Alicyclobacillus tengchongensis and Alicyclobacillus montanus are later heterotypic synonyms of Alicyclobacillus tolerans","authors":"Jaap S. Sinninghe Damsté ,&nbsp;Laura Villanueva ,&nbsp;Rüdiger Pukall","doi":"10.1016/j.syapm.2025.126651","DOIUrl":"10.1016/j.syapm.2025.126651","url":null,"abstract":"<div><div>The genus <em>Alicyclobacillus</em> represents a group of mostly acidophilic, meso-thermophilic bacteria, which obtained their name through the biosynthesis of uncommon, alicyclic fatty acids (FAs), i.e., <em>ω</em>-cyclohexyl or <em>ω</em>-cycloheptyl FAs. However, there are also species belonging to this genus that do not possess this trait. In addition, the difference of up to 9 % of the 16S rRNA gene sequences of 33 type strains compared with the first isolated type species, <em>A. acidocaldarius</em> DSM 446^T, exceeds the 5.5 % threshold, which is typically used for the demarcation of a genus. This suggested that the taxonomy of the genus required a re-examination. We performed a phylogenomic and chemotaxonomic survey of the genus <em>Alicyclobacillus</em>. Phylogenetic trees based on the 16S rRNA gene and comparison of whole proteomes reconstructed from their genomes reveal that the genus <em>Alicyclobacillus</em> is reflected by two distinct clades; one represented by 14 type strains with a &gt;94.1 % 16S rRNA gene similarity to <em>A. acidocaldarius</em> DSM 446^T, and a second clade (composed of 14 type strains including <em>A. cycloheptanicus</em>) with a similarity of 91–94 %. This distinction fits well with their reported ability to produce alicyclic FAs, also revealed by the detection of two putative biosynthetic gene clusters (BGC) encoding their biosynthetic pathway in their genomes. The first BGC is responsible for the production of cyclohexane carboxylic acid-CoA and comprises five genes encoding proteins acting as an adjusted side branch of the shikimate pathway. The putative second BGC, responsible for production of cycloheptane carboxylic acid-CoA, comprises six genes encoding proteins acting as a side branch of the catabolic phenylacetic acid pathway. All <em>Alicyclobacillus</em> species of the first clade produce <em>ω</em>-cyclohexyl FAs and their genomes possess the corresponding BGC. In the second cluster, some species produce <em>ω</em>-cyclohexyl FAs, some produce <em>ω</em>-cycloheptyl FAs, whilst quite some members are not producing any alicyclic FAs. This corresponds to the presence or absence of the two BGCs in their genomes. We propose to reclassify all species of the second clade as members of a new genus, <em>Paenalicyclobacillus</em> gen. nov. and show that both <em>Alicyclobacillus tengchongensis</em> and <em>Alicyclobacillus montanus</em> are later heterotypic synonyms of <em>Alicyclobacillus tolerans</em>.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 6","pages":"Article 126651"},"PeriodicalIF":4.2,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145097139","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}