Systematic and applied microbiology最新文献

{"title":"Phylogenomics reveals insights into the functional evolution of the genus Agrobacterium and enables the description of Agrobacterium divergens sp. nov","authors":"Henry D. Naranjo ,&nbsp;Liesbeth Lebbe ,&nbsp;Margo Cnockaert ,&nbsp;Florent Lassalle ,&nbsp;Chin Chin Too ,&nbsp;Anne Willems","doi":"10.1016/j.syapm.2023.126420","DOIUrl":"10.1016/j.syapm.2023.126420","url":null,"abstract":"<div><p>The genus <span><em>Agrobacterium</em></span> was initially described as mainly phytopathogenic strains. Nowadays, the genus includes phytopathogenic and non-phytopathogenic bacteria that are distinctive among the <span><em>Rhizobiaceae</em></span> family. Recently we have isolated two closely related strains, LMG 31531^T and LMG 31532, from soil and plant roots, respectively. Both strains differ from previously reported species based on the genomic and phenotypic data. <em>A. arsenijevicii</em> KFB 330^T and <em>A. fabacearum</em> LMG 31642^T showed the highest 16S rRNA similarity (98.9 %), followed by <em>A. nepotum</em> LMG 26435^T (98.7 %). A clear genomic feature that distinguishes LMG 31531^T and LMG 31532 from other <em>Agrobacterium</em><span> species is the absence of a linear chromid. Nevertheless, typical values of the core-proteome Average Amino Acid Identity (cpAAI &gt; 85 %) and 16S rRNA gene sequence similarity (&gt;96 %) when compared to other members of the genus confirm the position of these two strains as part of the </span><em>Agrobacterium</em> genus. They are therefore described as <em>Agrobacterium divergens</em> sp. nov. Besides, our comparative genomic study and survey for clade-specific markers resulted in the discovery of conserved proteins that provide insights into the functional evolution of this genus.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 3","pages":"Article 126420"},"PeriodicalIF":3.4,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9819693","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":"Stutzerimonas decontaminans sp. nov. isolated from marine polluted sediments","authors":"Magdalena Mulet ,&nbsp;Margarita Gomila ,&nbsp;Jorge Lalucat ,&nbsp;Rafael Bosch ,&nbsp;Ramon Rossello-Mora ,&nbsp;Elena García-Valdés","doi":"10.1016/j.syapm.2023.126400","DOIUrl":"10.1016/j.syapm.2023.126400","url":null,"abstract":"<div><p>Strains 19SMN4^T and ST27MN3 were isolated from marine sediments after enrichment with 2-methylnaphthalene and were classified as <em>Pseudomonas stutzeri</em> genomovar 4. Four other strains, BG 2, HT20, HT24, and A7, were isolated from sulphide-oxidizing bioreactors or activated sludge affiliated with the same clade in the 16S rRNA phylogenetic tree. <em>P. stutzeri</em> has been recently reclassified as a new genus, <em>Stutzerimonas,</em> and a preliminary analysis indicated that the strains in this study were distinct from any classified <em>Stutzerimonas</em> and are considered representatives of phylogenomic species 4 (pgs4). Strains 19SMN4^T and ST27MN3 were extensively characterized with phenotypic, chemotaxonomic, genomic and phylogenomic data. Strain 19SMN4^T had a well-characterized naphthalene degradative plasmid that has been compared with other plasmids, while in strain ST27MN3, the naphthalene degradative genes were detected in the chromosome sequence. Phylogenomic analysis of the core gene sequences showed that strains 19SMN4^T and ST27MN3 shared 3,995 genes and were closely related to members of the species “<em>Stutzerimonas songnenensis”</em> and <em>Stutzerimonas perfectomarina</em>, as well as to the <em>Stutzerimonas</em> phylogenomic species, pgs9, pgs16 and pgs24. The aggregate average nucleotide identity (ANI) indicated that strains 19SMN4^T and ST27MN3 belonged to the same genomic species, whereas the genomic indices with their closest-related type strains were below the accepted species threshold (95 %)<em>.</em> We therefore conclude that strains 19SMN4^T and ST27MN3 represent a novel species of <em>Stutzerimonas</em>, for which the name <em>Stutzerimonas decontaminans</em> is proposed; the type strain is 19SMN4^T (=CCUG44593^T = DSM6084^T = LMG18521^T).</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 2","pages":"Article 126400"},"PeriodicalIF":3.4,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9464363","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 Nocardioides bruguierae sp. nov., isolated from Bruguiera gymnorhiza","authors":"Xiaohui Chen ,&nbsp;Zhouqing Zheng ,&nbsp;Feina Li ,&nbsp;Xiao Ma ,&nbsp;Feng Chen ,&nbsp;Mingsheng Chen ,&nbsp;Li Tuo","doi":"10.1016/j.syapm.2022.126391","DOIUrl":"10.1016/j.syapm.2022.126391","url":null,"abstract":"<div><p>Strains BSK12Z-3^T<span><span> and BSK12Z-4, two Gram-stain-positive, aerobic, non-spore-forming strains, were isolated from Shankou Mangrove Nature Reserve, Guangxi Zhuang Autonomous Region, China. The diagnostic diamino acid in the cell-wall </span>peptidoglycan of strain BSK12Z-3</span>^T was LL-diaminopimelic acid and MK-8(H₄<span><span><span>) was the predominant menaquinone. The polar </span>lipids comprised diphosphatidylglycerol (DPG), </span>phosphatidylglycerol<span> (PG) and phospholipid (PL). The major fatty acids was </span></span><em>iso</em>-C_16:0<span>. Phylogenetic analysis based on 16S rRNA gene sequences suggested that the two strains fell within the genus </span><span><em>Nocardioides</em></span>, appearing most closely related to <em>Nocardioides ginkgobilobae</em> KCTC 39594^T (97.5–97.6 % sequence similarity) and <em>Nocardioides marinus</em> DSM 18248^T (97.4–97.6 %). Genome-based phylogenetic analysis confirmed that strains BSK12Z-3^T and BSK12Z-4 formed a distinct phylogenetic cluster within the genus <em>Nocardioides</em>. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of strains BSK12Z-3^T, BSK12Z-4 with their most related species <em>N</em>. <em>marinus</em> DSM18248^T were within the ranges of 77.2–77.3 % and 21.3–21.4 %, respectively, clearly indicated that strains BSK12Z-3^T, BSK12Z-4 represented novel species. Strains BSK12Z-3^T<span><span> and BSK12Z-4 exhibited 99.9 % 16S rRNA gene sequence similarity. The ANI and dDDH values between the two strains were 97.8 % and 81.1 %, respectively, suggesting that they belong to the same species. However, DNA fingerprinting discriminated that they were not from one clonal origin. Based on </span>phylogenomic and phylogenetic analyses coupled with phenotypic and chemotaxonomic characterizatons, strains BSK12Z-3</span>^T and BSK12Z-4 could be classified as a novel species of the genus <em>Nocardioides</em>, for which the name <em>Nocardioides bruguierae</em> sp. nov., is proposed. The type strain is BSK12Z-3^T (=CGMCC 4.7709^T = JCM 34554^T).</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 2","pages":"Article 126391"},"PeriodicalIF":3.4,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9447962","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":"Methylomonas rapida sp. nov., a novel species of fast-growing, carotenoid-producing obligate methanotrophs with high biotechnological potential","authors":"Ekaterina N. Tikhonova ,&nbsp;Ruslan Z. Suleimanov ,&nbsp;Kirill K. Miroshnikov ,&nbsp;Igor Y. Oshkin ,&nbsp;Svetlana E. Belova ,&nbsp;Olga V. Danilova ,&nbsp;Aleksandr A. Ashikhmin ,&nbsp;Aleksey A. Konopkin ,&nbsp;Sergey Y. But ,&nbsp;Valentina N. Khmelenina ,&nbsp;Nikolai V. Pimenov ,&nbsp;Svetlana N. Dedysh","doi":"10.1016/j.syapm.2023.126398","DOIUrl":"10.1016/j.syapm.2023.126398","url":null,"abstract":"<div><p>The genus <span><em>Methylomonas</em></span><span> accommodates strictly aerobic, obligate methanotrophs, with their sole carbon and energy sources restricted to methane and methanol. These bacteria inhabit oxic-anoxic interfaces of various freshwater habitats and have attracted considerable attention as potential producers of a single-cell protein. Here, we characterize two fast-growing representatives of this genus, strains 12 and MP1</span>^T, which are phylogenetically distinct from the currently described <em>Methylomonas</em> species (94.0–97.3 % 16S rRNA gene sequence similarity). Strains 12 and MP1^T<span> were isolated from freshwater sediments<span><span><span> collected in Moscow and Krasnodar regions, respectively. Cells of these strains are Gram-negative, red-pigmented, highly motile thick rods that contain a type I intracytoplasmic membrane system and possess a particulate methane monooxygenase (pMMO) </span>enzyme. These bacteria grow between 8 and 45 °C (optimum 35 °C) in a relatively narrow pH range of 5.5–7.3 (optimum pH 6.6–7.2). Major </span>carotenoids synthesized by these methanotrophs are 4,4′-diaplycopene-4,4′-dioic acid, 1,1′-dihydroxy-3,4-didehydrolycopene and 4,4′-diaplycopenoic acid. High biomass yield, of up to 3.26 g CDW/l, is obtained during continuous cultivation of MP1</span></span>^T<span> on natural gas in a bioreactor at a dilution rate of 0.22 h</span>⁻¹. The complete genome sequence of strain MP1^T<span> is 4.59 Mb in size; the DNA G + C content is 52.8 mol%. The genome encodes four rRNA operons, one pMMO operon and 4,216 proteins. The genome sequence displays 82–85 % average nucleotide identity to those of earlier described </span><em>Methylomonas</em> species. We propose to classify these bacteria as representing a novel species of the genus <em>Methylomonas</em>, <em>M. rapida</em> sp. nov., with the type strain MP1^T (=KCTC 92586^T = VKM B-3663^T).</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 2","pages":"Article 126398"},"PeriodicalIF":3.4,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9094968","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":"Dominance of mixed ether/ester, intact polar membrane lipids in five species of the order Rubrobacterales: Another group of bacteria not obeying the “lipid divide”","authors":"Jaap S. Sinninghe Damsté ,&nbsp;W. Irene C. Rijpstra ,&nbsp;Katharina J. Huber ,&nbsp;Luciana Albuquerque ,&nbsp;Conceição Egas ,&nbsp;Nicole J. Bale","doi":"10.1016/j.syapm.2023.126404","DOIUrl":"10.1016/j.syapm.2023.126404","url":null,"abstract":"<div><p>The composition of the core lipids and intact polar lipids (IPLs) of five <em>Rubrobacter</em> species was examined. Methylated (ω-4) fatty acids (FAs) characterized the core lipids of <em>Rubrobacter radiotolerans</em>, <em>R. xylanophilus</em> and <em>R. bracarensis</em>. In contrast, <em>R. calidifluminis</em> and <em>R. naiadicus</em> lacked ω-4 methyl FAs but instead contained abundant (i.e., 34–41 % of the core lipids) ω-cyclohexyl FAs not reported before in the order <em>Rubrobacterales</em>. Their genomes contained an almost complete operon encoding proteins enabling production of cyclohexane carboxylic acid CoA thioester, which acts as a building block for ω-cyclohexyl FAs in other bacteria. Hence, the most plausible explanation for the biosynthesis of these cyclic FAs in <em>R. calidifluminis</em> and <em>R. naiadicus</em> is a recent acquisition of this operon. All strains contained 1-O-alkyl glycerol ether lipids in abundance (up to 46 % of the core lipids), in line with the dominance (&gt;90 %) of mixed ether/ester IPLs with a variety of polar headgroups. The IPL head group distribution of <em>R. calidifluminis</em> and <em>R. naiadicus</em> differed, e.g. they lacked a novel IPL tentatively assigned as phosphothreoninol. The genomes of all five <em>Rubrobacter</em> species contained a putative operon encoding the synthesis of the 1-O-alkyl glycerol phosphate, the presumed building block of mixed ether/ester IPLs, which shows some resemblance with an operon enabling ether lipid production in various other aerobic bacteria but requires more study. The uncommon dominance of mixed ether/ester IPLs in <em>Rubrobacter</em> species exemplifies our recent growing awareness that the lipid divide between archaea and bacteria/eukaryotes is not as clear cut as previously thought.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 2","pages":"Article 126404"},"PeriodicalIF":3.4,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9096451","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":"Functional characterization and taxonomic classification of novel gammaproteobacterial diversity in sponges","authors":"Viet Hung Nguyen ,&nbsp;Bernd Wemheuer ,&nbsp;Weizhi Song ,&nbsp;Holly Bennett ,&nbsp;Giorgia Palladino ,&nbsp;Ilia Burgsdorf ,&nbsp;Sofia Sizikov ,&nbsp;Laura Steindler ,&nbsp;Nicole S. Webster ,&nbsp;Torsten Thomas","doi":"10.1016/j.syapm.2023.126401","DOIUrl":"10.1016/j.syapm.2023.126401","url":null,"abstract":"<div><p><span><span><span><span>Sponges harbour exceptionally diverse microbial communities, whose members are largely uncultured. The class </span>Gammaproteobacteria often dominates the microbial communities of various sponge species, but most of its diversity remains functional and taxonomically uncharacterised. Here we reconstructed and characterised 32 metagenome-assembled genomes (MAGs) derived from three sponge species. These MAGs represent ten novel species and belong to seven orders, of which one is new. We propose nomenclature for all these taxa. These new species comprise sponge-specific bacteria with varying levels of </span>host specificity. Functional gene profiling highlights significant differences in metabolic capabilities across the ten species, though each also often exhibited a large degree of metabolic diversity involving various nitrogen- and sulfur-based compounds. The genomic features of the ten species suggest they have evolved to form </span>symbiotic interaction with their hosts or are well-adapted to survive within the sponge environment. These Gammaproteobacteria are proposed to scavenge substrates from the host environment, including metabolites or cellular components of the sponge. Their diverse metabolic capabilities may allow for efficient cycling of organic matter in the sponge environment, potentially to the benefit of the host and other </span>symbionts.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 2","pages":"Article 126401"},"PeriodicalIF":3.4,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9097059","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":"Pseudomonas petrae sp. nov. isolated from regolith samples in Antarctica.","authors":"D. Nováková, Vendula Koublová, K. Sedlář, E. Staňková, S. Králová, P. Švec, Meina Neumann-Schaal, Jacqueline Wolf, Sylva Koudelková, M. Barták, I. Sedláček","doi":"10.2139/ssrn.4334811","DOIUrl":"https://doi.org/10.2139/ssrn.4334811","url":null,"abstract":"A polyphasic taxonomic approach was used to characterize the four strains P2653T, P2652, P2498, and P2647, isolated from Antarctic regolith samples. Initial genotype screening performed by PCR fingerprinting based on repetitive sequences showed that the isolates studied formed a coherent cluster separated from the other Pseudomonas species. Identification results based on 16S rRNA gene sequences showed the highest sequence similarity with Pseudomonas graminis (99.7%), which was confirmed by multilocus sequence analysis using the rpoB, rpoD, and gyrB genes. Genome sequence comparison of P2653T with the most related P. graminis type strain DSM 11363T revealed an average nucleotide identity of 92.1% and a digital DNA-DNA hybridization value of 46.6%. The major fatty acids for all Antarctic strains were C16:0, Summed Feature 3 (C16:1ω7c/C16:1ω6c) and Summed Feature 8 (C18:1ω7c/C18:1ω6c). The predominant respiratory quinone was Q-9, and the major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, and phosphatidylglycerol. The regolith strains could be differentiated from related species by the absence of arginine dihydrolase, ornithine and lysine decarboxylase and by negative tyrosine hydrolysis. The results of this polyphasic study allowed the genotypic and phenotypic differentiation of four analysed strains from the closest related species, which confirmed that the strains represent a novel species within the genus Pseudomonas, for which the name Pseudomonas petrae sp. nov. is proposed with P2653T (CCM 8850T = DSM 112068T = LMG 30619T) as the type strain.","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 4 1","pages":"126424"},"PeriodicalIF":3.4,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49092969","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":"Agrobacterium cucumeris sp. nov. isolated from crazy roots on cucumber (Cucumis sativus)","authors":"Michał Warabieda ,&nbsp;Nemanja Kuzmanović ,&nbsp;Paweł Trzciński ,&nbsp;Joanna Puławska","doi":"10.1016/j.syapm.2023.126402","DOIUrl":"10.1016/j.syapm.2023.126402","url":null,"abstract":"<div><p>Three plant rhizogenic strains O132^T, O115 and O34 isolated from <span><em>Cucumis</em></span> sp. <em>L.</em><span> were assessed for taxonomic affiliation by using polyphasic taxonomic methods. Based on the results of the sequence analysis<span> of the 16S rRNA and multilocus sequence analysis<span> (MLSA) of the three housekeeping genes </span></span></span><em>atpD</em>, <em>recA</em> and <em>rpoB,</em> all the strains were clustered within the genus <span><em>Agrobacterium</em></span> where they form a novel branch. Their closest relative was <em>Agrobacterium tomkonis</em> (genomospecies G3)<em>.</em> Moreover, digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) comparisons between strains O132^T<span> and O34 and their closest relatives provided evidence that they constitute a new species, because the obtained values were significantly below the threshold considered as a borderline for the species delineation. Whole-genome phylogenomic<span> analysis also indicated that the cucumber strains are located within the separate, well-delineated biovar 1 sub-clade of the genus </span></span><em>Agrobacterium</em>. Furthermore, the physiological and biochemical properties of these strains allowed to distinguish them from their closest related species of the genus <em>Agrobacterium</em>. As a result of the performed overall characterization, we propose a new species as <em>Agrobacterium cucumeris</em> sp. nov., with O132^T (=CFBP 8997^T = LMG 32451^T) as the type strain.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 2","pages":"Article 126402"},"PeriodicalIF":3.4,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9464877","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":"Natronogracilivirga saccharolytica gen. nov., sp. nov. and Cyclonatronum proteinivorum gen. nov., sp. nov., haloalkaliphilic organotrophic bacteroidetes from hypersaline soda lakes forming a new family Cyclonatronaceae fam. nov. in the order Balneolales","authors":"Tatjana N. Zhilina ,&nbsp;Dimitry Y. Sorokin ,&nbsp;Stepan V. Toshchakov ,&nbsp;Ilya V. Kublanov ,&nbsp;Daria G. Zavarzina","doi":"10.1016/j.syapm.2023.126403","DOIUrl":"10.1016/j.syapm.2023.126403","url":null,"abstract":"<div><p><span><span>Two heterotrophic bacteroidetes strains were isolated as satellites from autotrophic enrichments inoculated with samples from hypersaline soda lakes in southwestern </span>Siberia. Strain Z-1702</span>^T<span> is an obligate anaerobic fermentative saccharolytic bacterium from an iron-reducing enrichment culture, while </span><em>Ca</em>. Cyclonatronum proteinivorum Omega^T<span> is an obligate aerobic proteolytic microorganism<span> from a cyanobacterial enrichment. Cells of isolated bacteria are characterized by highly variable morphology. Both strains are chloride-independent moderate salt-tolerant obligate alkaliphiles<span> and mesophiles. Strain Z-1702</span></span></span>^T<span><span><span> ferments glucose, maltose, fructose, </span>mannose, </span>sorbose<span>, galactose<span>, cellobiose, </span></span></span><em>N</em><span><span>-acetyl-glucosamine and alpha-glucans, including starch, glycogen, dextrin, and </span>pullulan. Strain Omega</span>^T<span> is strictly proteolytic utilizing a range of proteins and peptones<span>. The main polar lipid fatty acid in both strains is iso-C</span></span>_15:0, while other major components are various C₁₆ and C₁₇<span> isomers. According to pairwise sequence alignments using BLAST </span><em>Gracilimonas</em><span> was the nearest cultured relative to both strains (&lt;90% of 16S rRNA gene sequence identity). Phylogenetic analysis placed strain Z-1702</span>^T and strain Omega^T as two different genera in a deep-branching clade of the new family level within the order <em>Balneolales</em> with genus. Based on physiological characteristics and phylogenetic position of strain Z-1702^T it was proposed to represent a novel genus and species <em>Natronogracilivirga saccharolityca</em> gen. nov., sp. nov. (= DSMZ 109061^T =JCM 32930^T =VKM B 3262^T). Furthermore, phylogenetic and phenotypic parameters of <em>N. saccharolityca</em> and <em>C. proteinivorum</em> gen. nov., sp. nov., strain Omega^T (=JCM 31662^T, =UNIQEM U979^T), make it possible to include them into a new family with a proposed designation <em>Cyclonatronaceae</em> fam. nov..</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 2","pages":"Article 126403"},"PeriodicalIF":3.4,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9094982","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 Dryocola gen. nov. and two novel species, Dryocola boscaweniae sp. nov. and Dryocola clanedunensis sp. nov. isolated from the rhizosphere of native British oaks","authors":"Daniel Maddock ,&nbsp;Carrie Brady ,&nbsp;Sandra Denman ,&nbsp;Dawn Arnold","doi":"10.1016/j.syapm.2023.126399","DOIUrl":"10.1016/j.syapm.2023.126399","url":null,"abstract":"<div><p>While investigating the role of the rhizosphere in the development of Acute Oak Decline, bacterial strains belonging to the family <em>Enterobacteriaceae</em> were isolated from rhizosphere soil following enrichment for the Enterobacterales. Partial sequencing of several housekeeping genes showed that these strains could not be assigned to an existing genus. Overall, 16 strains were investigated using a polyphasic approach to determine their taxonomic status. This involved phenotypic testing and fatty acid analysis paired with phylogenetic analyses of 16S rRNA and housekeeping gene sequences, as well as phylogenomic analysis of whole genome sequences. Phylogenomic and phylogenetic analyses consistently demonstrated that the 16 isolates could be separated into two distinct clusters in a monophyletic clade situated between the genera <em>Cedecea</em> and <em>Buttiauxella.</em> The two clusters could be genotypically and phenotypically differentiated from each other and from their closest neighbours. As such we propose the description of <em>Dryocola boscaweniae</em> gen. nov. sp. nov. (type strain H6W4^T = CCUG 76177^T = LMG 32610^T) and <em>Dryocola clanedunesis</em> sp. nov. (type strain H11S18^T = CCUG 76181^T = LMG 32611^T)<em>.</em></p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 2","pages":"Article 126399"},"PeriodicalIF":3.4,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9103125","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}