Systematic and applied microbiology最新文献

{"title":"Identification and functional genomic analyses of Bartonella isolates from honey bees, and reassessment of the taxonomy of the genus Bartonella","authors":"Juliana Botero ,&nbsp;Nikolas Basler ,&nbsp;Margo Cnockaert ,&nbsp;Charlotte Peeters ,&nbsp;Maria Schreiber ,&nbsp;Manja Marz ,&nbsp;Dirk C. de Graaf ,&nbsp;Jelle Matthijnssens ,&nbsp;Peter Vandamme","doi":"10.1016/j.syapm.2025.126625","DOIUrl":"10.1016/j.syapm.2025.126625","url":null,"abstract":"<div><div>We used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and whole-genome sequence analyses to identify 90 <em>Bartonella</em> isolates from honey bee gut samples in Belgium. While the identification of 62 isolates as <em>Bartonella apihabitans</em> and three as <em>Bartonella choladocola</em> was straightforward, the identification of 25 <em>Bartonella apis</em>-like isolates was challenging. A taxonomic and functional analysis of four <em>B. apis</em>-like genomes and of publicly available <em>B. apis</em> genomes demonstrated that neither OrthoANIu and digital DNA-DNA hybridization analyses, nor functional annotation supported a clear separation of <em>B. apis</em> and <em>B. apis</em>-like genomes. Different phylogenomic analyses showed that <em>B. apis</em> and <em>B. apis</em>-like strains formed a monophyletic clade with an inconsistent internal structure. We therefore considered the remaining 25 isolates identified as <em>B. apis</em>. We subsequently re-addressed an earlier phylogenetic and functional divergence between three major clades of <em>Bartonella</em> species which differed not only in phylogenomic position and ecology, but also in genome size and genomic percentage G + C content, and in many metabolic capabilities. We propose to reclassify the single species of the <em>Bartonella tamiae</em> clade into the novel genus <em>Attibartonella</em> gen. nov., with <em>Attibartonella tamiae</em> comb. nov. as the type species. Similarly, we propose to reclassify species of the honey bee-associated <em>Bartonella</em> clade into the novel genus <em>Ditibartonella</em> gen. nov., with <em>Ditibartonella apis</em> comb. nov. as the type species. The phylogenomic analyses of publicly available genome and metagenome sequences revealed additional <em>Ditibartonella</em> species in honey bee samples, highlighted an evolutionary adaptation of <em>Ditibartonella</em> bacteria to bee hosts and suggested shared transmission routes.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 4","pages":"Article 126625"},"PeriodicalIF":3.3,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144271231","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":"2025-06-04","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":"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":"2025-06-02","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":"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":"2025-06-01","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":"Classification of MAGs associated with trace gas metabolism in volcanic soils named following SeqCode rules","authors":"Shamik Roy ,&nbsp;Gary M. King ,&nbsp;Marcela Hernández","doi":"10.1016/j.syapm.2025.126622","DOIUrl":"10.1016/j.syapm.2025.126622","url":null,"abstract":"<div><div>Trace gas metabolism is important for nutrient flow in all ecosystems, particularly volcanic ecosystems. Microbes in volcanic ecosystems are among the early colonisers and can play key roles in ecological succession. Here, we describe the taxonomic and functional characteristics of two new metagenome-assembled genomes (MAGs), one belonging to <em>Bacteria</em> (MAG_1957-2.1) and one to <em>Archaea</em> (MAG_C2-3), retrieved from soils in volcanoes located in Chile (Llaima) and the USA (Kilauea), respectively. MAG_1957-2.1 has a genome size of 6.36<!--> <!-->Mb with 96.21 % completeness. MAG_C2-3 has a genome size of 3.02<!--> <!-->Mb with 97.57 % completeness. Phylogenetic analyses of the bacterial MAGs placed MAG_1957-2.1 in the class <em>Ktedonobacteria</em>, while the archaeal MAG_C2-3 was placed in the class <em>Nitrososphaeria</em>. Functional characterisation for potential trace gas metabolism showed that MAG_1957-2.1 contains a <em>coxL</em> gene encoding the large subunit of form I carbon monoxide dehydrogenase (CoxL), which is associated with the oxidation of carbon monoxide (CO). It also contains the form I <em>cox</em> gene cluster with a <em>coxMSL</em> arrangement. On the other hand, MAG_C2-3 contains gene subunit A (<em>amoA</em>) as well as subunit B (<em>amoB</em>), which encode for ammonia monooxygenase, the enzyme that catalyses the oxidation of ammonia. Based on the sequence characteristics and phylogenomic analyses we propose the names <em>Paraktedonobacter carboxidivorans sp.</em> nov for MAG_1957-2.1 and <em>Nitrososphaera maunauluensis sp.</em> nov for MAG_C2-3. The names are proposed following the rules of the published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 4","pages":"Article 126622"},"PeriodicalIF":3.3,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144230868","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":"2025-05-24","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":"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":"2025-05-23","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":"Unveiling the hidden microbiome: a microbiological exploration of untouched burial crypts in Krakow, Poland","authors":"Patrycja Tarnawska ,&nbsp;Aleksandra Burkowska-But ,&nbsp;Maria Swiontek Brzezińska ,&nbsp;Anna Drążkowska ,&nbsp;Adriana Osińska ,&nbsp;Maciej Walczak","doi":"10.1016/j.syapm.2025.126618","DOIUrl":"10.1016/j.syapm.2025.126618","url":null,"abstract":"<div><div>Cultural heritage objects provide valuable historical information, but can also harbour biological threats. Still, little is said about the potential risks that may await unaware researchers, conservators, and archaeologists. Our work discusses the study results from the crypts in Krakow, which were opened for the first time. The human and coffin remains were examined. The number of actinomycetes, other mesophilic bacteria, bacterial spores, and xerophilic and non-xerophilic fungi was determined. In general, a low number of microbes was observed. However, scanning electron microscope (SEM) images showed many bacterial conglomerates and confirmed that microbial activity affected the fibres covering cadavers in the crypts. The most abundant were mesophilic bacteria, followed by bacterial spores and actinomycetes. They reached up to 10⁷ CFU/g in fabric remains, 5.2 × 10⁶ CFU/g in burial remains, and 1.6 × 10⁶ CFU/g found under the coffin, and above 7.5 × 10⁵ CFU/g for xerophilic and non-xerophilic fungi. NGS (Next-Generation Sequencing) results suggested that the low presence of microorganisms may be due to the dominance of unculturable or long-growing bacteria belonging to <em>Mycobacterium</em>, such as <em>M. coloregonium</em>, <em>M. arupense</em>, and <em>M. pinnipedii.</em> Moreover, other obligatory/non-obligatory pathogens, <em>Bacteroides fragilis, Clostridium botulinum, Coxiella burnetii</em>, <em>Clostridium tetani</em>, <em>Corynebacterium diphtheriae</em>, <em>Enterobacter cloacae</em>, <em>Escherichia coli</em>, <em>Legionella pneumophila</em>, <em>Mycobacterium leprae</em>, <em>Rhodococcus equi</em>, and <em>Staphylococcus aureus</em> have been recorded in examined samples, with the dominance in bone samples. Results indicate the risk of dangerous pathogens present in historical objects, the impact on health may be severe, and the need to use personal protective equipment and proper measures to control the physical conditions of crypts.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 4","pages":"Article 126618"},"PeriodicalIF":3.3,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144168667","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":"2025-05-20","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}

{"title":"N-glyceroyl alkylamine phosphoglycolipids dominate the lipidome of several Bacillota bacteria","authors":"Nicole J. Bale ,&nbsp;Michel Koenen ,&nbsp;Su Ding ,&nbsp;Jaap S. Sinninghe Damsté","doi":"10.1016/j.syapm.2025.126609","DOIUrl":"10.1016/j.syapm.2025.126609","url":null,"abstract":"<div><div>Elucidation of the membrane lipid composition of bacteria can help to better understand how bacterial cells interact with their surroundings, adapt to environmental stress, and resist antimicrobial agents. Here we describe for the first time the detection of a wide array of N-glyceroyl alkylamine phosphoglycolipids (NGAPs) in a range of <em>Bacillota</em> bacteria (formerly <em>Firmicutes</em>). <em>Bacillota</em> includes a diverse range of bacteria that are typically highly resistant to harsh conditions such as heat, radiation, and pH, allowing the bacteria to survive in unfavorable environments. In 9 out 18 investigated strains of <em>Bacillota</em>, spread across 5 orders (<em>Thermoanaerobacterales, Thermosediminibacterales, Eubacteriales, Halanaerobiales</em>, and <em>Sulfobacillia</em>) mild acid hydrolysis released N-glyceroyl alkylamines (NGAs), which were detectable by gas chromatography–mass spectrometry (GC–MS) during routine fatty acid analysis. One strain, <em>Moorella thermoacetica</em> was found to produce long-chain NGAs (C₃₀-C₃₂), which are postulated to have <em>iso</em>diabolic acid-like structures. A wide variety of intact polar NGAPs were identified using ultra-high pressure liquid chromatography high resolution multi-stage mass spectrometry (UHPLC-HRMSⁿ). These include many previously undescribed lipids with a variety of sugar moieties and glycerol-bound core lipid moieties, including ether-bound components and alkyl 1,2-diols. The NGAPs constituted the majority of the intact polar lipid composition of these strains and presumably contribute to their tough cell membranes. The presence of NGAs in <em>Bacillota</em> appears to be associated with thermophilia. Both the hydrolysis-derived NGAs and intact polar NGAPs have potential to be biomarkers for extremophilic and, in particular, thermophilic bacteria.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 4","pages":"Article 126609"},"PeriodicalIF":3.3,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143918523","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}