Systematic and applied microbiology最新文献

{"title":"A practical guide on environmental genomics for prokaryotic systematics","authors":"Nathan M. Ernster ,&nbsp;Luis M. Rodriguez-R","doi":"10.1016/j.syapm.2025.126643","DOIUrl":"10.1016/j.syapm.2025.126643","url":null,"abstract":"<div><div>Environmental shotgun sequencing can provide great insight into microbial community profiles, functional capabilities, and the recovery of metagenome-assembled genomes (MAGs) which represent individual microbiome members. Similarly, assembly of single-cell amplified genomes (SAGs) is possible through advances in microfluidics and sequencing techniques. These fields have experienced tremendous growth in the amount of data produced, the ongoing development of analytical tools, and ultimately, the number of genomes recovered lacking valid names. As most microbes are uncultivable and therefore incompatible with traditional naming requirements, sequence databases are filled with genomes of varying quality and without standardized nomenclature, hindering communication and data usability. Overcoming these limitations, the recently introduced C<em>ode of Nomenclature of Prokaryotes Described from Sequence Data</em> (SeqCode) includes genome quality criteria and nomenclature standards to validly name uncultivated prokaryotes based on DNA sequence. Metagenomics and systematics can be overwhelming fields for new users, so here we provide a guide to help clarify topics and point out special considerations. These topics include metagenomic pipelines, genome quality assessment criteria, followed by taxonomy and trait prediction tools. Next, we cover source metadata, methods for abundance and occupancy measurement, and lastly, nomenclature and name registration. Community efforts to generate high-quality prokaryotic genomes with thorough descriptions and valid names are crucial for the future usability and communication of environmental genomic data.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 5","pages":"Article 126643"},"PeriodicalIF":4.2,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144773221","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":"Cellulosispirillum alkaliphilum, gen. nov., sp. nov., an obligately anaerobic cellulotrophic member of the phylum Fibrobacterota from soda lakes","authors":"Dimitry Y. Sorokin ,&nbsp;Alexander Y. Merkel ,&nbsp;Tatjana V. Khizhniak","doi":"10.1016/j.syapm.2025.126623","DOIUrl":"10.1016/j.syapm.2025.126623","url":null,"abstract":"<div><div>Intensive microbiology studies of the past several decades of soda lakes, uncovered a rich functional diversity of haloalkaliphilic microbes driving carbon, nitrogen and sulfur cycles in these unique double-extreme habitats. One of the unexpected finding was a discovery there of aerobic extremely halophilic cellulotrophic natronoarchaea. Yet, little is still known about the identity of the soda lake bacteria able to use native cellulose as growth substrate, except for a single case of an anaerobic clostridium. In this work we present results of phenotypic and functional genomic analysis of an anaerobic bacterium, strain ANBcel5^T, enriched from hypersaline Siberian soda lakes with amorphous cellulose as growth substrate. Phylogenetic analysis placed the isolate into the family <em>Chitinispirillaceae</em> in the phylum <em>Fibrobacterota</em> as a new genus and species lineage with the 16S rRNA gene identity and Relative Evolutionary Divergence (RED) to its only known species <em>Chitinispirillum alkaliphilum</em> ACht6–1^T of 95.2 % and 0.847, respectively. In contrast, despite obvious morphological resemblance to ACht6–1^T, strain ANBcel5^T is a narrow cellulose-utilizing fermentative anaerobe fermenting cellulose and cellobiose to acetate, H₂ and succinate. It is a moderately salt-tolerant obligate alkaliphile growing optimally at 0.6 M total Na⁺ as carbonates and pH 9.5. Functional genome analysis of the isolate revealed the presence of multiple genes encoding extracellular endocellulases from the GH families 5 and 9, three sodium-translocating membrane complexes and osmolytes <em>Nε</em>-acetyl-β-lysine and glycine betaine biosynthesis. The bacterium is proposed to be classified as <em>Cellulosispirillum alkaliphilum</em> gen. nov., sp. nov. (DSM 113825 = UQM 41584).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 4","pages":"Article 126623"},"PeriodicalIF":3.3,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144222371","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":"Revisiting carbon monoxide metabolism in the Moorella genus and isolation of a novel Moorella species","authors":"Anastasia Galani ,&nbsp;Melissa Antony Venancius ,&nbsp;Ben Tumulero ,&nbsp;Detmer Sipkema ,&nbsp;Diana Z. Sousa","doi":"10.1016/j.syapm.2025.126628","DOIUrl":"10.1016/j.syapm.2025.126628","url":null,"abstract":"<div><div>Thermophilic acetogens hold great potential for syngas fermentation, as they efficiently convert CO and H₂/CO₂ into added-value chemical building blocks. Among these, <em>Moorella</em> species are the most studied, known for their versatility by growing autotrophically on C1 gaseous compounds and heterotrophically on sugars and organic acids. In this study, we isolated two novel thermophilic CO-utilising acetogens belonging to the genus <em>Moorella</em>: strain AZ13.I, representing a novel species, and strain AZ24.1, which is closely related to <em>M. humiferrea</em>. We further investigated CO metabolism in this genus and found that all <em>Moorella</em> species isolated to date can utilise CO, contradicting earlier reports suggesting that the type strains of <em>M. humiferrea</em> (DSM 23265^T) and <em>M. mulderi</em> (DSM 14911^T) were incapable of metabolising this substrate. Finally, based on genomic analyses at the genus level, we suggest that CO metabolism is a universal trait across all <em>Moorella</em> species.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 4","pages":"Article 126628"},"PeriodicalIF":3.3,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144297924","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":"Magnetovirga frankeli gen. Nov., sp. nov., a magnetotactic bacterium isolated from the Salton Sea, California, that represents a novel lineage in the Gammaprotoeobacteria","authors":"Mila Sirinelli-Kojadinovic ,&nbsp;Elsa C.A. Turrini ,&nbsp;Emma Ropion ,&nbsp;Béatrice Alonso ,&nbsp;Marine Bergot ,&nbsp;Emilie Gachon ,&nbsp;Philippe Ortet ,&nbsp;Paul E.D. Soto-Rodriguez ,&nbsp;Caroline L. Monteil ,&nbsp;Christopher T. Lefevre","doi":"10.1016/j.syapm.2025.126621","DOIUrl":"10.1016/j.syapm.2025.126621","url":null,"abstract":"<div><div>A magnetotactic bacterium, designated strain SS-5^T, was isolated from the Salton Sea, a highly saline lake in California, USA, and cultivated in axenic culture. The Gram-negative cells of strain SS-5^T are relatively small and rod-shaped and possess a single polar flagellum (monotrichous). This strain is a magnetotactic bacterium producing magnetite nanocrystals aligned in one chain per cell. Strain SS-5^T is a microaerophile that grows chemolithoautotrophically while reducing oxygen as a terminal electron acceptor. Optimal growth occurred at pH 7.0–7.3 and 28–36 °C with thiosulfate used as an electron donor and sodium bicarbonate as a carbon source. Based on its genome sequence, the G + C content is 61.6 %. Phylogenomic and phylogenetic analyses indicate that strain SS-5^T belongs to the <em>Sedimenticolaceae</em> family within the <em>Gammaproteobacteria</em> class. Based on average amino acid identity, strain SS-5^T can be considered as a novel species of a new genus, for which the name <em>Magnetovirga frankeli</em> is proposed. The type strain of <em>M. frankeli</em> is SS-5^T (=DSM 116211^T = JCM 39467^T).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 4","pages":"Article 126621"},"PeriodicalIF":3.3,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144154697","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":"Liberiplasma polymorphum gen. nov., sp. nov., a novel cell-wall-less free-living anaerobe, isolated from a terrestrial mud volcano, and proposal of Liberiplasmataceae fam. nov. and Liberiplasmatales ord. nov","authors":"M.A. Khomyakova ,&nbsp;A.Y. Merkel ,&nbsp;A.A. Novikov ,&nbsp;A.I. Slobodkin","doi":"10.1016/j.syapm.2025.126629","DOIUrl":"10.1016/j.syapm.2025.126629","url":null,"abstract":"<div><div>A novel anaerobic free-living bacterium (strain C05PYG^T) was isolated from a terrestrial mud volcano (Taman Peninsula, Russia). Cells were pleomorphic but mainly consisted of small, cell wall-less, non-motile cocci, 0.40–0.46 μm in diameter. The temperature range for growth was 5–37 °C (optimum at 30 °C). The pH range for growth was 7.5–10.0, with an optimum at pH 8.0–9.0. It was a chemoorganoheterotroph, fermenting mono-, di- and polysaccharides (dextrin, starch), proteinaceous substrates and organic acids (lactate and pyruvate). Yeast extract was essential for growth. Strain C05PYG^T possessed an ability to degrade extraneous DNA. Major cellular fatty acids were C_16:0 and i-C_17:0; major dimethyl acetals were C_14:0 DMA and i-C_15:0 DMA. The genome of strain C05PYG^T had a size of 2.0 Mb with a DNA G + C content of 33.0 % (WGS). Phylogenetic analysis based on 120 marker genes placed strain C05PYG^T in a separate order adjacent to the order <em>Acholeplasmatales</em> within the class <em>Mollicutes</em>, hitherto referred to as “<em>Izemoplasmatales</em>”, which contains no representatives with validly published names. We propose to assign strain C05PYG^T to a novel species of a novel genus, <em>Liberiplasma polymorphum</em> gen. nov., sp. nov.; the type strain is C05PYG^T (=VKM B-3767^T = BIM B-2060^T = UQM 41800^T). This genus is placed in a novel family, <em>Liberiplasmataceae</em> fam. nov. within the novel order <em>Liberiplasmatales</em> ord. nov<em>.,</em> class <em>Mollicutes</em>.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 4","pages":"Article 126629"},"PeriodicalIF":3.3,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144261618","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":"Macrococcus capreoli sp. nov., a new fosfomycin resistant species isolated from feces and nasal swabs of deer","authors":"Carolin J. Schiffer ,&nbsp;Matthias A. Ehrmann","doi":"10.1016/j.syapm.2025.126620","DOIUrl":"10.1016/j.syapm.2025.126620","url":null,"abstract":"<div><div>Five strains of Gram-stain-positive, non-motile, and coccoid-shaped bacteria, designated as TMW 2.2395^T, TMW 2.2628, TMW 2.2670, TMW 2.2756 and TMW 2.2757 were isolated from feces and nasal mucosa of wild living roe deer (<em>Capreolus capreolus</em>) and red deer (<em>Cervus elaphus</em>), respectively. The isolates share identical 16S rRNA gene sequences and are classified within the genus <em>Macrococcus</em> based on 16S and MALDI-TOF MS analyses. Phylogenetic analysis revealed that average nucleotide identity (ANI) values were below the accepted thresholds for prokaryotic species delineation, with the type strains of <em>M. goetzii</em>, <em>M. bohemicu</em><em>s</em> and <em>M. epidermidis</em> showing the highest relatedness values (79.59 %, 79.30 % and 79.52 %, respectively). Digital DNA–DNA hybridization (dDDH) values were below 23 % confirming that all five strains belong to a new species within the genus <em>Macrococcus</em>. All strains were catalase and oxidase positive, grew optimally at 37 °C and pH 7.0, but demonstrated considerably lower salt tolerance (&lt; 7.5 % <em>w</em><em>/</em><em>v</em> nit iterativ) compared to other species in the genus. Moreover, the data of this study suggests that members of this new species possess an intrinsic resistance to fosfomycin, putatively mediated by a <em>fosB</em> homologue. The genomes range from 2.4 and 2.5 Mb in size, with a G+C content of 34.8 to 35.1 %. The primary respiratory quinone of the type strain TMW 2.2395^T is Menaquinone 6 (MK-6, 98.6 %), the cell wall peptidoglycan type is A3α L-Lys-Gly₃-L-Ser and the major fatty acids are C_14:0, C_16:0 and C_18:0. Phylogenetic, phenotypic and chemotaxonomic data collectively suggest that these strains represent a novel species of the genus <em>Macrococcus</em>, for which the name <em>Macrococcus capreoli</em> sp. nov. is proposed. The type strain is TMW 2.2395^T = DSM 113939^T = LMG 32618^T.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 4","pages":"Article 126620"},"PeriodicalIF":3.3,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144168666","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":"Polyphasic taxonomic description of Streptomyces tritrimontium sp. nov., actinomycetes isolated from moonmilk in Szczelina Chochołowska cave of Tatra Mountains in Poland and emended descriptions of Streptomyces manipurensis Nimaichand et al. 2021 and Streptomyces nojiriensis Ishida et al. 1967","authors":"Patrycja Bielańska ,&nbsp;Patrycja Golińska ,&nbsp;Elaine Romines ,&nbsp;Łukasz Rąbalski ,&nbsp;Grzegorz Węgrzyn","doi":"10.1016/j.syapm.2025.126627","DOIUrl":"10.1016/j.syapm.2025.126627","url":null,"abstract":"<div><div>In the present study the taxonomic position of two streptomycete strains, isolated from moonmilk in Szczelina Chochołowska cave located in Tatra Mountains in Poland, was established using a polyphasic taxonomic approach. Strains 2.9^T and 4.24 have morphological characteristics and chemotaxonomic properties consistent with their classification in the genus <em>Streptomyces</em>. They are Gram-stain-positive filamentous bacteria which formed an extensively branched substrate mycelium and straight long chains of smooth surfaced spores. They contain <em>LL</em>-diaminopimelic acid, glucose and ribose in whole-organism hydrolysates, produce major proportions of straight, iso- and <em>anteiso</em>- fatty acids, hexa- and octa‑hydrogenated menaquinones with nine isoprene units and have a polar lipid pattern with phosphatidylethanolamine (diagnostic lipid). Strains 2.9^T and 4.24 formed a distinct clade within the <em>Streptomyces</em> 16S rRNA gene tree sharing 100 % sequence similarity with <em>Streptomyces stoeckheimensis</em> DSM 116496ᵀ. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values calculated from the whole genome sequences of strains 2.9^T and 4.24 and their closely related phylogenomic neighbour were found to be 90.4 and 36.3 %, respectively, indicating that they belong to different genomic species. Consequently, based on the genomic, phylogenetic and associated phenotypic data it is proposed that strains 2.9^T and 4.24 be assigned to the genus <em>Streptomyces</em> as <em>Streptomyces tritrimontium</em> sp. nov. with strain 2.9^T (DSM 119353^T = PCM 3548^T) as the type strain.</div><div>The genomes of strains 2.9^T and 4.24 contain relatively high number of biosynthetic gene clusters (28 and 27, respectively), some of which were discontinuously distributed, indicating ones predicted to express for novel specialized metabolites.</div><div>Data acquired in the present study have also been used to emend the descriptions of <em>Streptomyces manipurensis</em> and <em>Streptomyces nojiriensis</em>.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 4","pages":"Article 126627"},"PeriodicalIF":3.3,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144280462","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":"Halosimplex amylolyticum sp. nov., Halosimplex halobium sp. nov., Halosimplex marinum sp. nov., Halosimplex rarum sp. nov., Halovenus amylolytica sp. nov., Halovenus halobia sp. nov., and Halovenus marina sp. nov., halophilic archaea isolated from a marine tidal flat, a marine solar saltern, three coarse sea salts, and two saline lakes","authors":"Ya-Ling Mao,&nbsp;Shun Tan,&nbsp;Bei-Bei Wang,&nbsp;Xiao-Yan Yang,&nbsp;Jing Hou,&nbsp;Heng-Lin Cui","doi":"10.1016/j.syapm.2025.126626","DOIUrl":"10.1016/j.syapm.2025.126626","url":null,"abstract":"<div><div>Seven novel halophilic archaeal strains DYHT-AS-1^T, GDY60^T, TS25^T, XH63^T, SHR40^T, SYNS179^T, and ZY30^T were isolated from tidal flat, saline lakes, marine solar saltern and coarse sea salts from different regions of China. Metagenomic and amplicon analyses indicated that the abundance of these seven strains in respective habitats was low. Phylogenetic and comparative genomic analyses indicated that strains DYHT-AS-1^T, GDY60^T, TS25^T, and XH63^T formed a tight cluster with <em>Halosimplex</em> species, exhibiting high 16S rRNA gene sequence similarity (90.4–99.4 %). The ANI, dDDH, and AAI values among these four strains and current <em>Halosimplex</em> species were 80.8–92.3 %, 24.5–53.3 %, and 77.8–91.5 %, respectively. Strains SHR40^T, SYNS179^T, and ZY30^T were related to <em>Halovenus</em> species, with 16S rRNA gene sequence similarities ranging from 88.8 % to 98.4 %. The ANI, dDDH, and AAI values among these three strains and current <em>Halovenus</em> species were 69.9–77.8 %, 19.4–21.5 %, and 62.1–78.1 %, respectively. These values are significantly lower than the thresholds for species demarcation. The optimal growth conditions for these seven strains in terms of NaCl, MgCl₂, temperature, and pH were 3.1–3.4 M, 0.05–0.5 M, 35–40 °C, and 6.5–7.5, respectively. According to phenotypic differences in nutrition, biochemical activity, and antibiotic sensitivity, these seven strains can be distinguished from their related species. Based on the above results, strains DYHT-AS-1^T, GDY60^T, TS25^T, and XH63^T represent four new species of the genus <em>Halosimplex</em>, and strains SHR40^T, SYNS179^T, and ZY30^T represent three novel species of the genus <em>Halovenus</em>.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 4","pages":"Article 126626"},"PeriodicalIF":3.3,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144222370","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":"Characterization of Sphingomicrobium aquimarinum sp. nov. and Sphingomicrobium maritimum sp. nov. highlights astaxanthin-producing bacteria in the family Sphingomonadaceae","authors":"Dao-Feng Zhang ,&nbsp;Hong-Chuan Wang ,&nbsp;Shi Shi ,&nbsp;Tian-Pu Li ,&nbsp;Dan-Yuan Guo ,&nbsp;Zi-Wen Yang ,&nbsp;Yang Yuan ,&nbsp;Jianke Huang ,&nbsp;Wen-Jun Li","doi":"10.1016/j.syapm.2025.126624","DOIUrl":"10.1016/j.syapm.2025.126624","url":null,"abstract":"<div><div>Bacteria are considered as better models for industrial production of astaxanthin (AXT) because of their fast growth and convenience for the downstream extraction. Nevertheless, few bacterial species of native AXT producers are explored to date. In this study, bacterial strains XHP0235^T (=GDMCC 1.3093^T = MCCC 1K07532^T = JCM 35574^T) and XHP0239^T (=GDMCC 1.3086^T = MCCC 1K07530^T = JCM 35575^T) were isolated from coastal seawater of China. Polyphasic taxonomy suggested that strains XHP0235^T and XHP0239^T were closely related to <em>Sphingomicrobium aestuariivivum</em> AH-M8^T, <em>S. arenosum</em> CAU 1457^T, and <em>S. astaxanthinifaciens</em> CC-AMO-30B^T, and should be recognized as two novel species of the genus <em>Sphingomicrobium</em>, for which the names <em>Sphingomicrobium aquimarinum</em> sp. nov. and <em>Sphingomicrobium maritimum</em> sp. nov. are proposed, respectively. Comparative genomic analysis revealed the complete AXT pathway (genes <em>crtB</em>, <em>crtI</em>, <em>crtY</em>, <em>crtZ</em>, and <em>crtW</em>) present in strains XHP0235^T, XHP0239^T and the three relative strains, and the carotenoid-targeted metabolome analysis confirmed the productions of AXT and other carotenoids. Inspired by these findings, the AXT pathway was further explored in the family <em>Sphingomonadaceae</em>, and 45 (18.8 %) out of the 240 type strains was identified to harbor all the five genes for AXT synthesis, of which the gene arrangement can be classified as seven types. The flanking gene contents were extremely variable with a concerted evolutionary history of the AXT genes. However, the AXT pathway is still predictable if an isolate is closely related to a known AXT-pathway-positive strain (evolutionary distance &lt;0.14). This study significantly enlarged the diversity of AXT-producing bacteria with highlighting such species in the family <em>Sphingomonadaceae</em>.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 4","pages":"Article 126624"},"PeriodicalIF":3.3,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144230869","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":"Rhizobium binxianense sp. nov. and Rhizobium mulingense sp. nov., isolated from nodules of Phaseolus vulgaris in Heilongjiang Province of China","authors":"Yuxi Liu ,&nbsp;Lili Liu ,&nbsp;Ziqi Wang ,&nbsp;Xiaoqian Huang ,&nbsp;Yuxin Dong ,&nbsp;Dong Hu ,&nbsp;Chuntao Gu ,&nbsp;En Tao Wang ,&nbsp;Hao Wang","doi":"10.1016/j.syapm.2025.126619","DOIUrl":"10.1016/j.syapm.2025.126619","url":null,"abstract":"<div><div>Rhizobial isolates from <em>Phaseolus vulgaris</em> (common bean) grown in Heilongjiang Province were grouped into two clusters based upon the phylogenies of 16S rRNA and <em>recA-atpD</em> genes representing by BJ04^T, MJ22, MJ37, BC56, MC62 and MC63^T, MJ21, MJ31, respectively. The phylogenetic analysis of whole genomes further revealed that BJ04^T, MJ22, MJ37, BC56 and MC62 formed a cluster neighbored <em>Rhizobium chutanense</em> C5^T, while MC63^T, MJ21 and MJ31 formed a cluster most related with <em>Rhizobium croatiense</em> 13T^T. The whole genome average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the strains BJ04^T and <em>R. chutanense</em> C5^T and between MC63^T and <em>R. croatiense</em> 13T^T were lower than the species thresholds 95 % and 70 %, respectively. While the G + C content of the whole genome of the novel strains were 61.16–61.56 %, within the allowable GC content range of the <em>Rhizobium</em> genus (57–66 %). These results, combined with chemical classification and phenotype analysis, supported that BJ04^T and MC63^T represented two novel species and the names <em>Rhizobium binxianense</em> sp. nov. and <em>Rhizobium mulingense</em> sp. nov. were described for them. BJ04^T (=CCTCC AB 2022367^T, = JCM 35885^T) and MC63^T (=CCTCC AB 2024025^T, = JCM 36652^T) were designed as the type strains, respectively for these two novel species.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 4","pages":"Article 126619"},"PeriodicalIF":3.3,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144137847","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}