Systematic and applied microbiology最新文献

{"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 ,&nbsp;Nihed Ajmi ,&nbsp;Orkid Coskuner-Weber ,&nbsp;Semih Alpsoy ,&nbsp;Hilal Ay ,&nbsp;Fuat Aydin ,&nbsp;Seçil Abay ,&nbsp;Emre Karakaya ,&nbsp;Tuba Kayman ,&nbsp;Cem Dalyan ,&nbsp;Fatih Doğan Koca ,&nbsp;Gorkem Tasci ,&nbsp;Doğancan Yarim ,&nbsp;Danny Morick ,&nbsp;Artun Yibar ,&nbsp;Serdar Erdogan ,&nbsp;Soner Altun ,&nbsp;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^T, Mu-80^T, and Mu-86^T, 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^T showed 99.0 % 16S rRNA similarity to <em>M. bandirmense</em> Mu-80^T, 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^T exhibited 99.2 % similarity to <em>M. esteraromaticum</em> DSM 8609^T, with dDDH and ANIb values of 23.6 % and 80 %. <em>M. marmarense</em> Mu-86^T showed 97.4 % similarity to <em>M. arthrosphaerae</em> JCM 30492^T, 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^T (LMG 33297^T = DSM 117065^T), <em>M. bandirmense</em> sp. nov. Mu-80^T (LMG 33295^T = DSM 117210^T), and <em>M. marmarense</em> sp. nov. Mu-86^T (LMG 33293^T = DSM 117066^T).</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}

{"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,&nbsp;Ya-Ling Mao,&nbsp;Yao Hu,&nbsp;Ya-Ping Sun,&nbsp;Jing Hou,&nbsp;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^T, YCN56^T, SYNS191^T, and SYNS196^T 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^T, YCN56^T, SYNS191^T, and SYNS196^T 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^T (= CGMCC 1.19060^T = JCM 35607^T), YCN56^T (= CGMCC 1.62603^T = JCM 36493^T), SYNS191^T (= CGMCC 1.62607^T = JCM 36494^T), and SYNS196^T (= CGMCC 1.62608^T = JCM 36495^T) 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}

{"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 ,&nbsp;Maria I. Prokofeva ,&nbsp;Alexandra A. Kuchierskaya ,&nbsp;Alexandra A. Klyukina ,&nbsp;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^T, 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_15:0 and anteiso-C_15:0. The quinone was MK-7. The size of the whole genome of strain 4138-str^T 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^T 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^T 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^T(=KCTC 25386^T = VKM B-3628^T = UQM 41477^T).</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}

{"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 ,&nbsp;Morgan Carpenter ,&nbsp;Daniel Chaplin ,&nbsp;Peter Golyshin ,&nbsp;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^T, 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 C_14:0, C_16:0, C_18:0, C_18:1 <em>ω</em>9<em>c</em>, and anteisoC_15:0. Strain m5^T 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^T 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^T (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^T 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^T 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^T (= DSM 112743^T = ATCC TSD-267^T) being the type of strain. This study highlights the biotechnological potential of strain m5^T, 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}

{"title":"Description and genomic characterization of Mesorhizobium marinum sp. nov., a bacterium isolated from sea sediment","authors":"Chengshao Zan ,&nbsp;Xiao Ma ,&nbsp;Zhouqing Zheng ,&nbsp;Feina Li ,&nbsp;Xian Yang ,&nbsp;Yifen Luo ,&nbsp;Li Tuo","doi":"10.1016/j.syapm.2025.126589","DOIUrl":"10.1016/j.syapm.2025.126589","url":null,"abstract":"<div><div>Two Gram-stain-negative, aerobic strains, designed ZMM04-4^T and ZMM04–5, were isolated from sea sediment collected from Qinzhou Bay, Guangxi Zhuang Automous Region, China. The predominant respiratory quinone was ubiquinone-10. The polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, aminophospholipid and phospholipid. The predominant fatty acids were C_18:1<em>ω</em>7c, C_19:0 cyclo <em>ω</em>8c and C_16:0. Strain ZMM04-4^T shared 99.7 % similarity of 16S rRNA gene sequence with ZMM04–5. The digital DNA-DNA hybridization and average nucleotide identity values between strain ZMM04-4^T and ZMM04–5 were 92.9 % and 98.6 %, respectively, indicating that strains ZMM04-4^T, ZMM04–5 belong to the same species. Phylogenetic and phylogenomic analysis indicated that strains ZMM04-4^T and ZMM04–5 belong to the genus <em>Mesorhizobium</em> and showed the highest sequence similarity to <em>Mesorhizobium qingshengii</em> CGMCC 1.12097^T (97.7 %–97.8 % sequence similarity) and <em>Mesorhizobium shangrilense</em> DSM 21850^T (97.7 %–97.8 %). The average nucleotide identity and digital DNA-DNA hybridization values between strains ZMM04-4^T, ZMM04–5 and their closely related species were within the ranges of 76.5 %–77.2 % and 20.9 %–21.8 %, respectively, indicating that strains ZMM04-4^T, ZMM04–5 were novel species. In accordance with phylogenetic and genomic as well as phenotypic and chemotaxonomic characterizations, strains ZMM04-4^T and ZMM04–5 should be assigned to the genus <em>Mesorhizobium</em> and indentified as a novel species, for which the name <em>Mesorhizobium marinum</em> sp. nov., is proposed. The type strain is ZMM04-4^T (=MCCC 1K08883^T = KCTC 8273^T).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 2","pages":"Article 126589"},"PeriodicalIF":3.3,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143080997","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":"Flavobacterium plantiphilum sp. nov., Flavobacterium rhizophilum sp. nov., Flavobacterium rhizosphaerae sp. nov., Chryseobacterium terrae sp. nov., and Sphingomonas plantiphila sp. nov. isolated from salty soil showing 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.2025.126588","DOIUrl":"10.1016/j.syapm.2025.126588","url":null,"abstract":"<div><div>Members of the genera <em>Flavobacterium</em>, <em>Chryseobacterium</em> and <em>Sphingomonas</em> constitute a group of microorganisms in the rhizosphere associated with plant growth promoting (PGP) features. A polyphasic approach was employed to ascertain the taxonomic status of five selected strains. Overall genome relatedness indices of digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) between the strains and the other members of the genera <em>Flavobacterium</em>, <em>Chryseobacterium</em> and <em>Sphingomonas</em> were found to be below the established thresholds, respectively. Morphological, physiological, and biochemical characteristics of the strains confirmed their status as five novel species. A large variety of genes involved in plant growth promotion and carbohydrate utilization were found in all strains suggesting a contribution of all strains to PGP.</div><div>Based on the result of the polyphasic characterization, the following names are proposed: <em>Chryseobacterium terrae</em> sp. nov., with the strain ST-37^T as the type strain (= CCM 9260^T = LMG 32728^T); <em>Flavobacterium plantiphilum</em> sp. nov., with the strain ST-87^T as the type strain CIP 112180^T = DSM 114790^T = LMG 32757^T); <em>Flavobacterium rhizophilum</em> sp. nov., with the strain ST-75^T as the type strain (= CIP 112185^T = DSM 114831^T = LMG 32758^T); <em>Flavobacterium rhizosphaerae</em> sp. nov., with the strain ST-119^T as the type strain (CIP 112181^T = DSM 114832^T = LMG 32756^T); and <em>Sphingomonas plantiphila</em> sp. nov. with the strain ST-64 ^T as the type strain (= CCM 9261^T = CIP 112178^T = DSM 114515^T = LMG 32729^T).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 2","pages":"Article 126588"},"PeriodicalIF":3.3,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143067773","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}

{"title":"MIRRI-ERIC's position on the recent evolution of the international code of nomenclature of prokaryotes","authors":"Rosa Aznar ,&nbsp;Michel-Yves Mistou ,&nbsp;Praveen Rahi ,&nbsp;Jean-Luc Legras ,&nbsp;Anete Boroduske ,&nbsp;Amalia Stefaniu ,&nbsp;Nelson Lima ,&nbsp;Amalia D. Karagouni ,&nbsp;Vincent Van de Perre ,&nbsp;Ana M.P. Melo","doi":"10.1016/j.syapm.2025.126587","DOIUrl":"10.1016/j.syapm.2025.126587","url":null,"abstract":"","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 2","pages":"Article 126587"},"PeriodicalIF":3.3,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143029840","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":"Description of Hyphococcus formosus sp. nov. and Hyphococcus lacteus sp. nov., isolated from coastal sediment, and reclassification of Marinicaulis flavus as Hyphococcus luteus nom. nov. and Marinicaulis aureus as Hyphococcus aureus comb. nov","authors":"Yu-Qi Ye ,&nbsp;Xin-Yue Zhang ,&nbsp;Hong-Nan Gong ,&nbsp;Meng-Qi Ye ,&nbsp;Zong-Jun Du","doi":"10.1016/j.syapm.2024.126575","DOIUrl":"10.1016/j.syapm.2024.126575","url":null,"abstract":"<div><div>During a study on sediment bacterial diversity in coastal China, three bacterial strains, DH-69^T, EH-24, and ECK-19^T, were isolated from coastal sediments off Xiaoshi Island, Weihai. These strains were Gram-staining-negative, aerobic, and coccoid to rod-shaped with prosthecae and flagella. Comparison of the 16S rRNA gene showed that they shared the highest identity values with <em>Hyphococcus flavus</em> MCCC 1K03223^T (96.2–97.6 %), followed by <em>Marinicaulis flavus</em> SY-3-19^T (95.2–96.8 %) and <em>Marinicaulis aureus</em> HHTR114^T (95.2–96.2 %). Genome comparisons using average nucleotide identity (ANI) and average amino acid identity (AAI) suggested that the three novel strains and the three related strains belonged to the same genus, with strains DH-69^T, EH-24, and ECK-19^T identified as two distinct novel species. Pan-genome analysis revealed that 995 core genes were shared among 23 <em>Hyphococcus</em> genomes/MAGs. Secondary metabolites analysis identified a biosynthesis gene cluster for microsclerodermin, a potent antifungal peptide, in the novel strains. Moreover, these newly isolated strains were detected in various ecosystems, with a particular prevalence in marine environments, based on analysis of 500,048 amplicon datasets, underscoring their ecological preference. Based on polyphasic characterizations, strains DH-69^T and EH-24 represent a novel species of the genus <em>Hyphococcus</em>, for which the name <em>Hyphococcus formosus</em> sp. nov. is proposed with the type strain DH-69^T (= MCCC 1H00436^T = KCTC 8010^T). Strain ECK-19^T represents another novel <em>Hyphococcus</em> species, for which the name <em>Hyphococcus lacteus</em> sp. nov. is proposed with the type strain ECK-19^T (= MCCC 1H00435^T = KCTC 8009^T). Furthermore, <em>Marinicaulis flavus</em> and <em>Marinicaulis aureus</em> are proposed to be reclassified as <em>Hyphococcus luteus</em> nom. nov. and <em>Hyphococcus aureus</em> comb. nov., respectively, accompanied by an emended description of the genus <em>Hyphococcus</em>.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"Article 126575"},"PeriodicalIF":3.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142814030","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":"Phenylobacterium ferrooxidans sp. nov., isolated from a sub-surface geothermal aquifer in Iceland","authors":"Eva Pouder,&nbsp;Erwann Vince,&nbsp;Karen Jacquot,&nbsp;Maimouna batoma Traoré,&nbsp;Ashley Grosche,&nbsp;Maria Ludwig,&nbsp;Mohamed Jebbar,&nbsp;Loïs Maignien,&nbsp;Karine Alain,&nbsp;Sophie Mieszkin","doi":"10.1016/j.syapm.2024.126578","DOIUrl":"10.1016/j.syapm.2024.126578","url":null,"abstract":"<div><div>A novel bacterial strain, HK31-G^T, was isolated from a subsurface geothermal aquifer (Hellisheidi, SW-Iceland) and was characterized using a polyphasic taxonomic approach. Phylogenetic analysis of 16S rRNA gene along with phylogenomic position indicated that the novel strain belongs to the genus <em>Phenylobacterium</em>. Cells are motile Gram-negative thin rods. Physiological characterization showed that strain HK31-G^T is a mesophilic bacterium able to grow from 10 to 30 °C, at pH values between 6 and 8 and at NaCl concentrations between 0 and 0.5 %. Optimal growth was observed without sodium chloride at 25 °C and pH 6. Strain HK31-G^T is chemoorganoheterotroph and its major saturated fatty acids are C_18:1<em>ω7c</em>, C₁₆_:1<em>ω6c</em> and C_16:0, the predominant quinone is Q-10 and the major polar lipid is phosphatidylglycerol. The new strain also possesses the capacity to use ferrous iron (Fe(II)) as the sole energy source and can also be considered as a chemolithoautotrophic microorganism. The overall genome of strain HK31-G^T was estimated to be 4.46 Mbp in size with a DNA G + C content of 67.95 %. Genes involved in iron metabolism were identified, but no genes typically involved in Fe(II)-oxidation were found. According to the overall genome relatedness indices (OGRI) values, six MAGs from groundwater have been assigned to the same species as the new strain HK31-G^T. Furthermore, OGRI values between the genome of strain HK31-G^T and the genomes of its closest relatives are below the species delineation threshold. Therefore, given the polyphasic approach used, strain HK31-G^T represents a novel species of the genus <em>Phenylobacterium</em>, for which the name <em>Phenylobacterium ferrooxidans</em> sp. nov. is proposed. The type strain is HK31-G^T (DSM 116432^T = UBOCC-M-3429^T = LMG 33376^T).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"Article 126578"},"PeriodicalIF":3.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142883026","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}

{"title":"Diversity and physiology of abundant Rhodoferax species in global wastewater treatment systems","authors":"Jette F. Petersen ,&nbsp;Laura C. Valk ,&nbsp;Maarten D. Verhoeven,&nbsp;Marta A. Nierychlo,&nbsp;Caitlin M. Singleton,&nbsp;Morten K.D. Dueholm,&nbsp;Per H. Nielsen","doi":"10.1016/j.syapm.2024.126574","DOIUrl":"10.1016/j.syapm.2024.126574","url":null,"abstract":"<div><div>Wastewater treatment plants rely on complex microbial communities for bioconversion and removal of pollutants, but many process-critical species are still poorly investigated. One of these genera is <em>Rhodoferax,</em> an abundant core genus in wastewater treatment plants across the world. The genus has been associated with many metabolic traits such as iron reduction and oxidation and denitrification. We used 16S rRNA gene amplicon data to uncover the diversity and abundance of <em>Rhodoferax</em> species in Danish and global treatment plants. Publicly available metagenome-assembled genomes were analyzed based on phylogenomics to delineate species and assign taxonomies based on the SeqCode. The phylogenetic analysis of “<em>Rhodoferax</em>” revealed that species previously assigned to <em>Rhodoferax</em> in wastewater treatment plants should be considered as at least eight different genera, with five representing previously undescribed genera. Genome annotation showed potential for several key-bioconversions in wastewater treatment, such as nitrate reduction, carbohydrate degradation, and accumulations of various storage compounds. Iron oxidation and reduction capabilities were not predicted for abundant species. Species-resolved FISH-Raman was performed to gain an overview of the morphology and ecophysiology of selected taxa to clarify their potential role in global wastewater treatment systems. Our study provides a first insight into the functional and ecological characteristics of several novel genera abundant in global wastewater treatment plants, previously assigned to the <em>Rhodoferax</em> genus.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"Article 126574"},"PeriodicalIF":3.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142865414","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}