Systematic and applied microbiology最新文献

{"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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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}

{"title":"Weizmannia acidilactici sp. nov., a lactic acid producing bacterium isolated from soils","authors":"Vasana Tolieng ,&nbsp;Naoto Tanaka ,&nbsp;Yuh Shiwa ,&nbsp;Sitanan Thitiprasert ,&nbsp;Pawina Kanchanasin ,&nbsp;Wongsakorn Phongsopitanun ,&nbsp;Auttaporn Booncharoen ,&nbsp;Nuttha Thongchul ,&nbsp;Somboon Tanasupawat","doi":"10.1016/j.syapm.2022.126389","DOIUrl":"10.1016/j.syapm.2022.126389","url":null,"abstract":"<div><p>The strains designed PP-18^T, JC-4 and JC-7 isolated from soils, were Gram-stain-positive rods, facultative anaerobe, endospore-forming bacteria. The strains produced <span>l</span>-lactic acid from glucose. They showed positive for catalase but negative for oxidase, nitrate reduction and arginine hydrolysis. Strains P-18^T, JC-4 and JC-7 were closely related to <em>Weizmannia coagulans</em> LMG 6326^T (97.27–97.64%) and <em>W. acidiproducens</em> KCTC 13078^T (96.46–96.74%) based on 16S rRNA gene sequence similarity, respectively. They contained <em>meso</em>-diaminopimelic acid in cell wall peptidoglycan and had seven isoprene units (MK-7) as the predominant menaquinone. The major cellular fatty acids of strain PP-18^T were <em>iso</em>-C_15:0, anteiso-C_17:0, iso-C_16:0 and anteiso-C_15:0. The ANIb and ANIm values among the genomes of strains PP-18^T, JC-4 and JC-7 are above 99.4% while their ANIb and ANIm values among them and <em>W. coagulans</em> LMG 6326^T and <em>W. acidiproducens</em> KCTC 13078^T were ranged from 76.61 to 79.59%. These 3 strains showed the digital DNA-DNA hybridization (dDDH) values of 20.7–23.6% when compared with <em>W. coagulans</em> LMG 6326^T and W. <em>acidiproducens</em> DSM 23148^T. The DNA G + C contents of strains PP-18^T, JC-4 and JC-7 were 45.82%, 45.86% and 45.86%, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphoglycolipids. The results of phenotypic and chemotaxonomic characteristics and whole-genome analysis indicated that the strains PP-18^T, JC-4 and JC-7 should be represented as a novel species within the genus <em>Weizmannia</em> for which the name <em>Weizmannia acidilactici</em> sp. nov. is proposed. The type strain is PP-18^T (=KCTC 33974^T = NBRC 113028^T = TISTR 2515^T).</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10534111","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 a moderately acidotolerant and aerotolerant anaerobic bacterium Acidilutibacter cellobiosedens gen. nov., sp. nov. within the family Acidilutibacteraceae fam. nov., and proposal of Sporanaerobacteraceae fam. nov. and Tepidimicrobiaceae fam. nov.","authors":"Hui Fan ,&nbsp;Jiang Li ,&nbsp;Weidong Wu ,&nbsp;Rui Chen ,&nbsp;Min Yang ,&nbsp;Yinggang Zhang ,&nbsp;Lulu Cong ,&nbsp;Lirong Dai ,&nbsp;Yu Deng ,&nbsp;Lei Cheng ,&nbsp;Shichun Ma","doi":"10.1016/j.syapm.2022.126376","DOIUrl":"10.1016/j.syapm.2022.126376","url":null,"abstract":"<div><p><span>A Gram-stain positive, moderately thermophilic, acidotolerant and aerotolerant anaerobic bacterium, designated JN-28 </span>^T, was isolated from the pit mud of Chinese strong-flavor liquor. Growth was observed at 25–50 °C and pH 5.5–8.0 in the presence of 0–25 g l⁻¹ NaCl (optimally at 45 °C, pH 6.0, without NaCl). Strain JN-28 ^T was heterotrophic, requiring yeast extract for growth. The major cellular fatty acids were <em>iso</em>-C_15:0 and C_14:0<span><span>. The DNA G + C content of genomic DNA was 33.54 mol%. The strain was resistant to </span>vancomycin (10 mg l</span>⁻¹<span><span>). Genome analysis revealed the presence of genes involved in the response to mild acid stress and oxidative stress, and resistance to vancomycin. 16S rRNA gene-based </span>phylogenetic analysis showed that strain JN-28 </span>^T shares ≤ 89.3 % sequence similarity with its closest relatives <em>Sporanaerobacter acetigenes</em> DSM 13106 ^T and other members in the order <em>Tissierellales</em>. Based on phenotypic and phylogenetic characteristics, <em>Acidilutibacter cellobiosedens</em><span> gen. nov., sp. nov. is proposed for the new genus and novel species with the type strain JN-28 </span>^T (=CCAM 418 ^T = JCM 39087 ^T<span>). Further phylogenetic and phylogenomic analyses suggested strain JN-28 </span>^T represents a novel family within the order <em>Tissierellales</em>, for which <em>Acidilutibacteraceae</em> fam. nov. is proposed. In addition, the family <em>Tissierellaceae</em> was reclassified, <em>Sporanaerobacteraceae</em> fam. nov. and <em>Tepidimicrobiaceae</em> fam. nov. were formally proposed. Emended description of the family <em>Tissierellaceae</em> is also provided.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10533130","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":"How Systematic and Applied Microbiology will deal with two nomenclature codes (ICNP and SeqCode) for prokaryotes, and which classification standards are recommended for new taxa descriptions","authors":"Ramon Rosselló-Móra ,&nbsp;Konstantinos T. Konstantinidis ,&nbsp;Rudolf Amann","doi":"10.1016/j.syapm.2022.126371","DOIUrl":"10.1016/j.syapm.2022.126371","url":null,"abstract":"","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10666076","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":"Genomic insight into Chryseobacterium turcicum sp. nov. and Chryseobacterium muglaense sp. nov. isolated from farmed rainbow trout in Turkey","authors":"Izzet Burcin Saticioglu ,&nbsp;Hilal Ay ,&nbsp;Soner Altun ,&nbsp;Muhammed Duman","doi":"10.1016/j.syapm.2022.126385","DOIUrl":"10.1016/j.syapm.2022.126385","url":null,"abstract":"<div><p>Four strains, designated as C-2, C-17^T, C-39^T<span> and Ch-15, were isolated from farmed rainbow trout<span> samples showing clinical signs during an investigation for a fish-health screening study. The pairwise 16S rRNA gene sequence analysis showed that strain C-17</span></span>^T shared the highest identity level of 98.1 % with the type strain of <span><em>Chryseobacterium</em><em> piscium</em></span> LMG 23089^T while strains C-2, C-39^T and Ch-15 were closely related to <em>Chryseobacterium balustinum</em> DSM 16775^T with an identity level of 99.3 %. A polyphasic approach involving phenotypic, chemotaxonomic and genome-based analyses was employed to determine the taxonomic provenance of the strains. The overall genome relatedness indices including dDDH and ANI analyses confirmed that strains C-2, C-17^T, C-39^T and Ch-15 formed two novel species within the genus <em>Chryseobacterium</em>. Chemotaxonomic analyses showed that strains C-17^T and C-39^T have typical characteristics of the genus <em>Chryseobacterium</em><span><span><span> by having phosphatidylethanolamine in their polar </span>lipid profile<span>, MK-6 as only isoprenoid </span></span>quinone and the presence of </span><em>iso</em>-C_15:0<span><span><span> as major fatty acid. The genome size and G + C content of the strains ranged between 4.4 and 5.0 Mb and 33.5 – 33.6 %, respectively. Comprehensive genome analyses revealed that the strains have </span>antimicrobial resistance genes, </span>prophages and horizontally acquired genes in addition to secondary metabolite-coding gene clusters. In conclusion, based on the polyphasic analyses conducted on the present study, strains C-17</span>^T and C-39^T are representatives of two novel species within the genus <em>Chryseobacterium</em>, for which the names <em>Chryseobacterium turcicum</em> sp. nov. and <em>Chryseobacterium muglaense</em> sp. nov. with the type strains C-17^T (=JCM 34190^T = KCTC 82250^T) and C-39^T (=JCM 34191^T = KCTC 822251^T), respectively, are proposed.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10538003","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":"Novel species of Frankia, Frankia gtarii sp. nov. and Frankia tisai sp. nov., isolated from a root nodule of Alnus glutinosa","authors":"Imen Nouioui ,&nbsp;Faten Ghodhbane-Gtari ,&nbsp;Gabriele Pötter ,&nbsp;Hans-Peter Klenk ,&nbsp;Michael Goodfellow","doi":"10.1016/j.syapm.2022.126377","DOIUrl":"10.1016/j.syapm.2022.126377","url":null,"abstract":"<div><p>The status of four <em>Frankia</em> strains isolated from a root nodule of <em>Alnus glutinosa</em> was established in a polyphasic study. Taxogenomics and phenotypic features show that the isolates belong to the genus <em>Frankia.</em> All four strains form extensively branched substrate mycelia, multilocular sporangia, vesicles, lack aerial hyphae, but contain <em>meso</em>-diaminopimelic acid as the diamino acid of the peptidoglycan, galactose, glucose, mannose, ribose, xylose and traces of rhamnose as cell wall sugars, <em>iso</em>-C_16:0 as the predominant fatty acid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol as the major polar lipids, have comparable genome sizes to other cluster 1, <em>Alnus</em>-infective strains with structural and accessory genes associated with nitrogen fixation. The genome sizes of the isolates range from 7.0 to 7.7 Mbp and the digital DNA G + C contents from 71.3 to 71.5 %. The four sequenced genomes are rich in biosynthetic gene clusters predicted to express for novel specialized metabolites, notably antibiotics. 16S rRNA gene and whole genome sequence analyses show that the isolates fall into two lineages that are closely related to the type strains of <em>Frankia alni</em> and <em>Frankia torreyi.</em> All of these taxa are separated by combinations of phenotypic properties and by digital DNA:DNA hybridization scores which indicate that they belong to different genomic species. Based on these results, it is proposed that isolates Agncl-4^T and Agncl-10, and Agncl-8^T and Agncl-18, be recognised as <em>Frankia gtarii</em> sp. nov. and <em>Frankia tisai</em> sp. nov. respectively, with isolates Agncl-4^T (=DSM 107976^T = CECT 9711^T) and Agncl-8^T (=DSM 107980^T = CECT 9715^T) as the respective type strains.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10537992","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}