Systematic and applied microbiology最新文献_第4页

Nitrogen fixation in Pampinifervens, a new species-rich genus of Aquificaceae that inhabits a wide pH range in terrestrial hot springs 水栖科丰富物种的新属Pampinifervens的固氮作用，它栖息在陆地温泉的广泛pH范围内

IF 4.2 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Systematic and applied microbiology

Pub Date : 2025-07-29 DOI: 10.1016/j.syapm.2025.126644

Marike Palmer , Nancy O. Nou , Lara A. Turello , Carolyn E. Power , John C. Ong , Jonathan K. Covington , Dengxun Lai , Xavier Mayali , Anna-Louise Reysenbach , Yan-Ling Qi , Jeremy A. Dodsworth , Jian-Yu Jiao , Lan Liu , Zheng-Han Lian , Meng-Meng Li , Yitai Liu , Ranjani Murali , Brandon R. Briggs , Hongyan Zuo , Stephen R. Quake , Brian P. Hedlund

Members of the Aquificota play important roles in hydrogen, sulfur, and carbon cycles in geothermal systems as ubiquitous and abundant chemolithoautotrophs; however, their roles in the nitrogen cycle are poorly defined. Here, we show that Aquificaceae isolate T-2^T from Tengchong, China, fixes nitrogen based on growth with dinitrogen as the sole nitrogen source and incorporation of ¹⁵N atoms when grown with ¹⁵N₂. We further show evidence that suggests its nitrogen fixation (nif) genes are transcribed in situ in a nearby spring. We propose the name Pampinifervens diazotrophicum gen. et sp. nov., with strain T-2^T (= JCM 35475^T = DSM 116324^T) as the nomenclatural type. Its close relative designated Pampinifervens florentissimum sp. nov. T-8^T (= CGMC 1.5214^T = JCM 33569^T) does not fix nitrogen but respires nitrate. Analysis of 104 metagenome-assembled genomes from 84 metagenomes allowed us to circumscribe the genus Pampinifervens and identify at least 16 sympatric Pampinifervens species that dominate the Aquificaceae populations in diverse hot springs in southwest China, with distinct species globally. Analysis of these Pampinifervens genomes revealed variable presence of nif and denitrification genes and frequent gene loss and horizontal transfer. Genes for pH homeostasis were also present in Pampinifervens genomes, with a proliferation in species from Tengchong, consistent with the wide pH growth range of both Pampinifervens isolates and the prevalence of Pampinifervens in both alkaline and acidic springs. The dynamic evolution of nif and denitrification genes, along with pH homeostasis genes, may facilitate the diversification of Pampinifervens into diverse springs with different nitrogen availability.

水螅门成员在地热系统的氢、硫和碳循环中发挥着重要作用，是普遍存在的丰富的化能岩石自养生物；然而，它们在氮循环中的作用尚不明确。本研究表明，来自腾冲的水仙花科分离菌T-2T在以二氮为唯一氮源的条件下生长，并在15N2条件下结合15N原子来固定氮。我们进一步证明，它的固氮（nif）基因在附近的泉水中就地转录。我们建议命名为Pampinifervens重氮营养菌gen. et sp. nov.，以菌株T-2T （= JCM 35475T = DSM 116324T）为命名型。其近亲Pampinifervens florentissimum sp. nov. T-8T （= CGMC 1.5214T = JCM 33569T）不固定氮，但呼吸硝酸盐。通过对来自84个宏基因组的104个宏基因组的分析，我们确定了Pampinifervens属，并确定了至少16种同域Pampinifervens种，这些种在中国西南不同温泉中占主导地位，在全球范围内具有独特的物种。对这些Pampinifervens基因组的分析显示，nif和反硝化基因的存在是可变的，并且频繁的基因丢失和水平转移。在Pampinifervens基因组中也存在pH稳态基因，并且在腾冲种中有增殖，这与Pampinifervens分离株的pH生长范围广以及Pampinifervens在碱性和酸性泉中的普遍存在一致。氮化和反硝化基因的动态演化以及pH稳态基因可能促进Pampinifervens向不同氮有效度的多样性多样性。

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引用次数: 0

Assessment of cluster analysis of elastic light scatter profiles for the identification of foodborne Bacteria 弹性光散射聚类分析在食源性细菌鉴定中的应用评价

IF 3.3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Systematic and applied microbiology

Pub Date : 2025-07-20 DOI: 10.1016/j.syapm.2025.126641

Sana Bari , Yuwei Zhang , Valery Patsekin , J. Paul Robinson , Bartek Rajwa , Andrew Gehring , James Lindsay , Don Kulasiri , Stephen L.W. On

Elastic Light Scatter (ELS) profiling is a novel approach for simultaneous detection and identification of bacteria cultured on solid agar media. The profiles comprise a range of different scatter features that can be used jointly or individually as a basis for comparison. We examined the utility of cluster analysis of ELS profiles for classification and identification of bacteria of relevance to foods. A total of 1562 colonies from 48 strains, representing 17 different species distributed among four genera, were examined. Each of three scatter-derived features (Zernike moments, pseudo-Zernike moments, proprietary Patsekin elements) were used individually and in combination for the cluster analysis. Of these, a combination of Patsekin elements and pseudo-Zernike moments yielded clusters that best reflected the known taxonomic relationships among the strains examined. Evidence of Genus-level markers of colony architecture was seen and there was a general agreement of clustering at the species level. Nonetheless, some individual colonies did not cluster with the majority of others from the same taxon, which could reflect an aberrant ELS phenotype, or known challenges in depicting strain relationships using cluster analytical methods. However, when compared with UMAP data processing, relationships between individual colonies were more easily discerned by inspecting the dendrogram. Cluster analysis of ELS profiles is a useful adjunctive tool for the classification and identification of bacteria and results may also be helpful in informing the development and improvement of other data analytical tools for ELS profile analysis.

弹性光散射（ELS）分析是一种同时检测和鉴定在固体琼脂培养基上培养的细菌的新方法。所述轮廓包括一系列不同的散点特征，可联合或单独用作比较的基础。我们检查了聚类分析的ELS概况分类和鉴定相关的食品细菌的效用。共检测了4属17种48株的1562个菌落。三个散点衍生特征（Zernike矩、伪Zernike矩、专有Patsekin元素）中的每一个都被单独或组合用于聚类分析。其中，Patsekin元素和伪zernike矩的组合产生了最能反映所检查菌株之间已知分类关系的簇。发现了属水平的群体结构标记的证据，并且在种水平上有普遍一致的聚类。尽管如此，一些单独的菌落没有与来自同一分类单元的大多数其他菌落聚集在一起，这可能反映了异常的ELS表型，或者在使用聚类分析方法描述菌株关系方面存在已知的挑战。然而，与UMAP数据处理相比，通过检查树突图更容易识别单个菌落之间的关系。聚类分析是一种有益的细菌分类和鉴定辅助工具，其结果也可为其他用于细菌分类和鉴定的数据分析工具的开发和改进提供参考。

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引用次数: 0

Astrobacterium formosum gen. nov., sp. nov., a novel psychrotolerant rosette-forming bacterium from a laboratory psychrophilic EGSB bioreactor 从实验室嗜冷的EGSB生物反应器中获得的一种新型耐冷玫瑰形细菌

IF 3.3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Systematic and applied microbiology

Pub Date : 2025-07-13 DOI: 10.1016/j.syapm.2025.126640

V.V. Potokina , S.N. Parshina , A.Y. Merkel , A.G. Elcheninov , A.V. Vishnyakova , A.N. Avtukh , N.A. Kostrikina , V.M. Tereshina , Y.V. Litti

A new psychrotolerant, facultative anaerobic bacterium, strain Astr-EGSB^T, was isolated from a syntrophic propionate-oxidizing consortium obtained from a low-temperature expanded granular sludge bed (EGSB) bioreactor fed with a mixture of volatile fatty acids. The cells of this strain were Gram-negative and non-spore-forming rods (0.5·0.8–1.5·9 μm), grew either as individual cells or formed rosettes of various sizes, resembling stars. Bacteria reproduced by budding, and each cell has a sticky, non-reproductive pole that allows them to attach to other cells, forming rosette-like clusters. This strain could grow between 5 and 40 °C, with pH ranging from 4.5 to 7.5 and NaCl concentration of 0 to 2 %. It could degrade a variety of carbon substrates, including sugars, alcohols, casamine acids and several organic acids, but could not grow under photoautotrophic conditions. During glucose fermentation, the products include lactate, acetate, isobutyrate, CO₂, and traces of succinate. Major cellular fatty acids were C_18:1ω9c and C_19:0 cyclo ω9c, menaquinone МХ-10(H10). Main polar lipids were phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. Sequence comparison of the 16S rRNA gene revealed that strain Astr-EGSB^T was related to Pseudorhodoplanes sinuspersici RIPI 110^T with a similarity of 95.0 %. Based on phylogenomic analysis using 120 marker genes, strain Astr-EGSB^T belongs to the distinct genus-level phylogenetic lineage that is most related to the genus Rhodoplanes. The G + C content of genomic DNA was 65.8 mol%. Based on genomic and physiological characteristics of strain Astr-EGSB^T, a new genus and a new species, Astrobacterium formosum gen. Nov., sp. nov., is proposed, with Astr-EGSB^T as the type strain.

从低温膨胀颗粒污泥床（EGSB）生物反应器中获得的合养丙酸氧化联合体中分离出一株新的耐冷兼性厌氧细菌astra - egsbt。该菌株的细胞为革兰氏阴性，不形成孢子的棒状细胞（0.5·0.8 ~ 1.5·9 μm），可作为单个细胞生长，也可形成大小不一的星形莲座。细菌通过出芽繁殖，每个细胞都有一个粘性的非生殖极，使它们能够附着在其他细胞上，形成玫瑰状的簇。该菌株可在5 ~ 40℃、pH为4.5 ~ 7.5、NaCl浓度为0 ~ 2%的条件下生长。它可以降解多种碳底物，包括糖、醇、酪胺酸和几种有机酸，但不能在光自养条件下生长。在葡萄糖发酵过程中，产物包括乳酸盐、醋酸盐、异丁酸盐、二氧化碳和微量琥珀酸盐。主要细胞脂肪酸为C18:1ω9c和C19:0 cyclo ω9c，甲基萘醌МХ-10（H10）。主要极性脂质为磷脂酰胆碱、磷脂酰乙醇胺和磷脂酰甘油。16S rRNA基因序列比较表明，astra - egsbt菌株与sinuspersicpseudorhodoplanes RIPI 110T亲缘关系为95.0%。基于120个标记基因的系统基因组分析，菌株astra - egsbt属于与Rhodoplanes属亲缘关系最密切的独特属级系统发育谱系。基因组DNA G + C含量为65.8 mol%。根据菌株astra - egsbt的基因组学和生理特性，以astra - egsbt为型菌株，提出了新属新种——星状菌formosum gen. Nov., sp. Nov.。

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引用次数: 0

Pyranulibacter aquaticus gen. nov., sp. nov., the first nitrate-reducing representative of the class Ignavibacteria from an Iturup well 水生Pyranulibacter aquaticus gen. nov., sp. nov.， Iturup井中发现的第一个硝酸盐还原伊格纳维细菌的代表

IF 3.3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Systematic and applied microbiology

Pub Date : 2025-07-11 DOI: 10.1016/j.syapm.2025.126639

Olga A. Podosokorskaya , Alexander Y. Merkel , Andrei A. Novikov , Alexandra A. Klyukina , Alexander G. Elcheninov

A novel facultatively anaerobic moderately thermophilic bacterium, strain 4301-Me^T was isolated from the well 13k on the Iturup Island (Kuril Islands, Russian Federation). Gram-stain-negative, motile rods were present singly, in pairs, rosettes, and aggregates, or formed biofilms. The strain grew optimally at 50–55 °C, pH 6.7–7.0 and 0.2–0.4 % NaCl. It did not require yeast extract for growth and utilized mono-, di- and polysaccharides (cellulose, starch, xanthan gum, locust bean gum, glucomannan, lichenan, amorphous chitin) as well as proteinaceous substrates (gelatin, peptone, beef and yeast extract). Growth under anaerobic conditions was observed in the presence and absence of external electron acceptors. Sulfur, thiosulfate, nitrate, arsenate, Fe-citrate, and ferrihydrite were reduced with acetate, or yeast extract as electron donors. The respiratory quinone was MK-7. Major cellular fatty acids were iso-C_15:0, iso-C_16:0, anteiso-C_15:0, 3OH-C_14:0, 3OH-C_13:0. The size of the genome and genomic DNA G + C content of strain 4301-Me^T were 3.34 Mb and 33 %, respectively. According to the 16S rRNA gene sequence and conserved protein sequences phylogenies, strain 4301-Me^T represented a distinct lineage of the family Melioribacteraceae within the class Ignavibacteria. Based on phylogenomic analysis and phenotypic features, the novel isolate was assigned to a novel genus, for which the name Pyranulibacter gen. nov. is proposed. Strain 4301-Me^T represents its type species Pyranulibacter aquaticus sp. nov. (=CGMCC 1.18061^T = B-3822^T = BIM B-2047^T = UQM 41592^T).

菌株4301-MeT是一种新型兼性厌氧适度嗜热细菌，分离自Iturup岛（Kuril群岛，俄罗斯联邦）的13k井。革兰氏染色阴性，可运动的杆呈单、双、莲座、聚集体或形成生物膜。菌株在50 ~ 55℃、pH 6.7 ~ 7.0和0.2 ~ 0.4% NaCl条件下生长最佳。它不需要酵母提取物来生长，利用单、双多糖和多糖（纤维素、淀粉、黄原胶、刺槐豆胶、葡甘露聚糖、地衣、无定形几丁质）以及蛋白质基质（明胶、蛋白胨、牛肉和酵母提取物）。在有无外部电子受体的情况下，观察了厌氧条件下的生长。硫、硫代硫酸盐、硝酸盐、砷酸盐、柠檬酸铁和水合铁用醋酸盐或酵母提取物作为电子供体进行还原。呼吸醌为MK-7。主要细胞脂肪酸为iso-C15:0、iso-C16:0、anteiso-C15:0、3OH-C14:0、3OH-C13:0。菌株4301-MeT的基因组大小为3.34 Mb，基因组DNA G + C含量为33%。根据16S rRNA基因序列和保守蛋白序列的系统发育，菌株4301-MeT代表了Ignavibacteria纲Melioribacteraceae的一个独特谱系。基于系统基因组分析和表型特征，该新分离物被归入一个新属，并被命名为Pyranulibacter gen. 11。菌株4301-MeT代表其类型种Pyranulibacter aquaticus sp. nov. （=CGMCC 1.18061T = B-3822T = BIM B-2047T = UQM 41592T）。

{"title":"Pyranulibacter aquaticus gen. nov., sp. nov., the first nitrate-reducing representative of the class Ignavibacteria from an Iturup well","authors":"Olga A. Podosokorskaya , Alexander Y. Merkel , Andrei A. Novikov , Alexandra A. Klyukina , Alexander G. Elcheninov","doi":"10.1016/j.syapm.2025.126639","DOIUrl":"10.1016/j.syapm.2025.126639","url":null,"abstract":"<div><div>A novel facultatively anaerobic moderately thermophilic bacterium, strain 4301-MeT was isolated from the well 13k on the Iturup Island (Kuril Islands, Russian Federation). Gram-stain-negative, motile rods were present singly, in pairs, rosettes, and aggregates, or formed biofilms. The strain grew optimally at 50–55 °C, pH 6.7–7.0 and 0.2–0.4 % NaCl. It did not require yeast extract for growth and utilized mono-, di- and polysaccharides (cellulose, starch, xanthan gum, locust bean gum, glucomannan, lichenan, amorphous chitin) as well as proteinaceous substrates (gelatin, peptone, beef and yeast extract). Growth under anaerobic conditions was observed in the presence and absence of external electron acceptors. Sulfur, thiosulfate, nitrate, arsenate, Fe-citrate, and ferrihydrite were reduced with acetate, or yeast extract as electron donors. The respiratory quinone was MK-7. Major cellular fatty acids were iso-C15:0, iso-C16:0, anteiso-C15:0, 3OH-C14:0, 3OH-C13:0. The size of the genome and genomic DNA G + C content of strain 4301-MeT were 3.34 Mb and 33 %, respectively. According to the 16S rRNA gene sequence and conserved protein sequences phylogenies, strain 4301-MeT represented a distinct lineage of the family Melioribacteraceae within the class Ignavibacteria. Based on phylogenomic analysis and phenotypic features, the novel isolate was assigned to a novel genus, for which the name Pyranulibacter gen. nov. is proposed. Strain 4301-MeT represents its type species Pyranulibacter aquaticus sp. nov. (=CGMCC 1.18061T = B-3822T = BIM B-2047T = UQM 41592T).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 5","pages":"Article 126639"},"PeriodicalIF":3.3,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144623499","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}

引用次数: 0

Genomic and phylogenetic re-assessment of the genus Stenotrophomonas: Description of Stenotrophomonas thermophila sp. nov., and the proposal of Parastenotrophomonas gen. Nov., Pseudostenotrophomonas gen. Nov., Pedostenotrophomonas gen. Nov., and Allostenotrophomonas gen. Nov. 窄养单胞菌属的基因组和系统发育再评价：嗜热窄养单胞菌的描述，以及11 .副窄养单胞菌、11 .假窄养单胞菌、11 .足窄养单胞菌和11 .异位窄养单胞菌的提出。

IF 3.3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Systematic and applied microbiology

Pub Date : 2025-06-18 DOI: 10.1016/j.syapm.2025.126630

Amandine Chauviat, Danis Abrouk, Elisabeth Brothier, Daniel Muller, Thibault Meyer , Sabine Favre-Bonté

The Stenotrophomonas maltophilia species complex (Smc) currently comprises 19 genomospecies, known for their ecological versatility and role as opportunistic human pathogens. However, significant genomic variability among strains has complicated their classification, and only a few species within the Smc have been validly described. Despite successive taxonomic revisions, there remains no consensus on the naming of many genomospecies, largely due to the phenotypic heterogeneity across the complex.

In this study, we performed a comprehensive genomic and phylogenetic re-assessment to clarify the boundaries of the Stenotrophomonas genus and its species complex. Using whole-genome phylogeny and Overall Genome-Related Indices (OGRIs) such as digital DNA-DNA hybridization (dDDH), Average Nucleotide Identity (ANIb and ANIm), and Average Amino Acid Identity (AAI), we established precise cutoffs for defining the genus and the Smc. Our analysis led to the formal revision of the Stenotrophomonas genus, resulting in the delineation of four novel bacterial genera: Allostenotrophomonas gen. Nov., Pedostenotrophomonas gen. Nov., Parastenotrophomonas gen. Nov., and Pseudostenotrophomonas gen. Nov. Additionally, we standardized the nomenclature within the Smc by identifying reference strains for each genomospecies. Among these, we describe a novel species, Stenotrophomonas thermophila sp. nov. (type strain BurA1^T = LMG 33562^T = EML 1882^T). This study provides a robust framework for future taxonomic and ecological studies within the Stenotrophomonas genus.

嗜麦芽寡养单胞菌物种复合体（Smc）目前包括19个基因组物种，以其生态多样性和作为机会性人类病原体的作用而闻名。然而，菌株之间显著的基因组变异性使它们的分类变得复杂，并且在Smc中只有少数物种被有效描述。尽管连续的分类修订，仍然没有在许多基因组物种的命名上达成共识，很大程度上是由于整个复合体的表型异质性。在这项研究中，我们进行了全面的基因组和系统发育重新评估，以澄清窄养单胞菌属及其物种复合体的界限。利用全基因组系统发育和总体基因组相关指数（OGRIs），如数字DNA-DNA杂交（dDDH）、平均核苷酸身份（ANIb和ANIm）和平均氨基酸身份（AAI），我们建立了精确的截断值来定义属和Smc。我们的分析导致了窄养单胞菌属的正式修订，导致了四个新的细菌属的描述：同种窄养单胞菌gen. Nov、养足单胞菌gen. Nov、副窄养单胞菌gen. Nov和伪窄养单胞菌gen. Nov。此外，我们通过确定每个基因组种的参考菌株，在Smc内标准化了命名法。其中，我们描述了一个新种，嗜热窄养单胞菌sp. nov（型菌株BurA1T = LMG 33562T = EML 1882T）。本研究为今后窄养单胞菌属的分类学和生态学研究提供了一个强有力的框架。

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引用次数: 0

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 波兰Tatra山Szczelina Chochołowska洞穴月乳中分离的放线菌Streptomyces tritrimontium sp. nov.的多相分类描述和对Streptomyces manipurensis Nimaichand等人2021和nojiriensis Ishida等人1967的修正描述

IF 3.3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Systematic and applied microbiology

Pub Date : 2025-06-14 DOI: 10.1016/j.syapm.2025.126627

Patrycja Bielańska , Patrycja Golińska , Elaine Romines , Łukasz Rąbalski , Grzegorz Węgrzyn

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 Streptomyces. They are Gram-stain-positive filamentous bacteria which formed an extensively branched substrate mycelium and straight long chains of smooth surfaced spores. They contain LL-diaminopimelic acid, glucose and ribose in whole-organism hydrolysates, produce major proportions of straight, iso- and anteiso- 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 Streptomyces 16S rRNA gene tree sharing 100 % sequence similarity with Streptomyces stoeckheimensis 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 Streptomyces as Streptomyces tritrimontium sp. nov. with strain 2.9^T (DSM 119353^T = PCM 3548^T) as the type strain.

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.

Data acquired in the present study have also been used to emend the descriptions of Streptomyces manipurensis and Streptomyces nojiriensis.

本文采用多相分类学方法确定了波兰Tatra山Szczelina Chochołowska洞穴月乳中分离的两株链霉菌的分类位置。菌株2.9T和4.24的形态特征和化学分类特征与它们在链霉菌属中的分类一致。它们是革兰氏染色阳性丝状细菌，形成广泛分支的底菌丝体和表面光滑的直长链孢子。它们在整个生物体水解物中含有l -二氨基苯甲酸、葡萄糖和核糖，产生主要比例的直、异和反异脂肪酸，六氢化和八氢化具有九个异戊二烯单位的甲基萘醌，并与磷脂酰乙醇胺（诊断脂质）具有极性脂质模式。菌株2.9T和4.24在Streptomyces 16S rRNA基因树中形成了一个独立的分支，与Streptomyces stoeckheimensis DSM 116496序列具有100%的相似性。菌株2.9T和4.24及其亲缘关系较近的邻居株全基因组序列的平均核苷酸同一性（ANI）和数字DNA-DNA杂交（dDDH）值分别为90.4%和36.3%，表明它们属于不同的基因组种。因此，基于基因组学、系统发育和相关表型数据，我们建议将菌株2.9T和4.24归入链霉菌属，以菌株2.9T （DSM 119353T = PCM 3548T）为型菌株。菌株2.9T和菌株4.24的基因组中含有较多的生物合成基因簇（分别为28和27个），其中一些基因簇呈不连续分布，表明它们可能表达新的特化代谢物。在本研究中获得的数据也被用于修正操纵链霉菌和野尻链霉菌的描述。

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引用次数: 0

Revisiting carbon monoxide metabolism in the Moorella genus and isolation of a novel Moorella species 重新审视摩尔氏菌属的一氧化碳代谢和一种新的摩尔氏菌的分离

IF 3.3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Systematic and applied microbiology

Pub Date : 2025-06-10 DOI: 10.1016/j.syapm.2025.126628

Anastasia Galani , Melissa Antony Venancius , Ben Tumulero , Detmer Sipkema , Diana Z. Sousa

Thermophilic acetogens hold great potential for syngas fermentation, as they efficiently convert CO and H₂/CO₂ into added-value chemical building blocks. Among these, Moorella 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 Moorella: strain AZ13.I, representing a novel species, and strain AZ24.1, which is closely related to M. humiferrea. We further investigated CO metabolism in this genus and found that all Moorella species isolated to date can utilise CO, contradicting earlier reports suggesting that the type strains of M. humiferrea (DSM 23265^T) and M. mulderi (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 Moorella species.

嗜热性醋酸具有合成气发酵的巨大潜力，因为它们有效地将CO和H2/CO2转化为附加值的化学成分。其中，摩尔氏菌是研究最多的物种，以其多功能性而闻名，可以在C1气体化合物上自养生长，也可以在糖和有机酸上异养生长。在这项研究中，我们分离了两种新的嗜热co利用的酵母菌属：菌株AZ13。1，代表一个新种，以及与M. humiferrea有密切关系的菌株AZ24.1。我们进一步研究了该属的CO代谢，发现迄今为止分离的所有摩尔氏菌都能利用CO，这与早期报道的M. humiferrea （DSM 23265T）和M. mulderi （DSM 14911T）型菌株不能代谢这种底物的说法相矛盾。最后，基于属水平的基因组分析，我们认为CO代谢是所有摩尔氏菌物种的普遍特征。

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引用次数: 0

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 多形Liberiplasma polymorphum gen. nov., sp. nov.，一种从陆相泥火山中分离出来的新型无细胞壁的自由生活厌氧菌。11月和自由等离子体

IF 3.3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Systematic and applied microbiology

Pub Date : 2025-06-10 DOI: 10.1016/j.syapm.2025.126629

M.A. Khomyakova , A.Y. Merkel , A.A. Novikov , A.I. Slobodkin

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 Acholeplasmatales within the class Mollicutes, hitherto referred to as “Izemoplasmatales”, which contains no representatives with validly published names. We propose to assign strain C05PYG^T to a novel species of a novel genus, Liberiplasma polymorphum 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, Liberiplasmataceae fam. nov. within the novel order Liberiplasmatales ord. nov., class Mollicutes.

从俄罗斯塔曼半岛陆相泥火山中分离到一株新的厌氧自由生活细菌（菌株C05PYGT）。细胞呈多形性，但主要由小的、无细胞壁的、不运动的球菌组成，直径为0.40 ~ 0.46 μm。生长温度范围为5 ~ 37℃（最适温度为30℃）。生长的pH范围为7.5 ~ 10.0，最适pH为8.0 ~ 9.0。它是一种化学有机异养菌，发酵单、双多糖和多糖（糊精、淀粉）、蛋白质底物和有机酸（乳酸和丙酮酸）。酵母提取物是生长所必需的。菌株C05PYGT具有降解外来DNA的能力。主要细胞脂肪酸为C16:0和i-C17:0；主要的二甲基缩醛为C14:0 DMA和i-C15:0 DMA。菌株C05PYGT的基因组大小为2.0 Mb， DNA G + C含量为33.0% （WGS）。基于120个标记基因的系统发育分析将菌株C05PYGT置于Mollicutes纲中与Acholeplasmatales相邻的一个单独的目，迄今为止被称为“Izemoplasmatales”，该目未包含具有有效发表名称的代表。我们建议将菌株C05PYGT归属于一个新属的新种，Liberiplasma polymorphum gen. nov., sp. nov.；型应变为C05PYGT （=VKM B-3767T = BIM B-2060T = UQM 41800T）。这个属被归入一个新的科，野浆科。11月在新目Liberiplasmatales目11月，Mollicutes纲。

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引用次数: 0

Identification and functional genomic analyses of Bartonella isolates from honey bees, and reassessment of the taxonomy of the genus Bartonella 蜜蜂巴尔通体分离株的鉴定和功能基因组分析，以及巴尔通体属分类的重新评估

IF 3.3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Systematic and applied microbiology

Pub Date : 2025-06-06 DOI: 10.1016/j.syapm.2025.126625

Juliana Botero , Nikolas Basler , Margo Cnockaert , Charlotte Peeters , Maria Schreiber , Manja Marz , Dirk C. de Graaf , Jelle Matthijnssens , Peter Vandamme

We used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and whole-genome sequence analyses to identify 90 Bartonella isolates from honey bee gut samples in Belgium. While the identification of 62 isolates as Bartonella apihabitans and three as Bartonella choladocola was straightforward, the identification of 25 Bartonella apis-like isolates was challenging. A taxonomic and functional analysis of four B. apis-like genomes and of publicly available B. apis genomes demonstrated that neither OrthoANIu and digital DNA-DNA hybridization analyses, nor functional annotation supported a clear separation of B. apis and B. apis-like genomes. Different phylogenomic analyses showed that B. apis and B. apis-like strains formed a monophyletic clade with an inconsistent internal structure. We therefore considered the remaining 25 isolates identified as B. apis. We subsequently re-addressed an earlier phylogenetic and functional divergence between three major clades of Bartonella 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 Bartonella tamiae clade into the novel genus Attibartonella gen. nov., with Attibartonella tamiae comb. nov. as the type species. Similarly, we propose to reclassify species of the honey bee-associated Bartonella clade into the novel genus Ditibartonella gen. nov., with Ditibartonella apis comb. nov. as the type species. The phylogenomic analyses of publicly available genome and metagenome sequences revealed additional Ditibartonella species in honey bee samples, highlighted an evolutionary adaptation of Ditibartonella bacteria to bee hosts and suggested shared transmission routes.

采用基质辅助激光解吸/电离飞行时间质谱法和全基因组序列分析对比利时蜜蜂肠道样本中的90株巴尔通体分离株进行了鉴定。62株蜜蜂巴尔通体和3株choladocola巴尔通体的鉴定比较简单，而25株类似蜜蜂巴尔通体的鉴定则比较困难。对4个类人猿基因组和已公开的类人猿基因组的分类和功能分析表明，OrthoANIu和数字DNA-DNA杂交分析以及功能注释都不支持类人猿和类人猿基因组的明确分离。不同的系统发育分析表明，apis apis和apis apis apis样菌株形成了一个内部结构不一致的单系分支。因此，我们认为剩余的25株分离株为白僵菌。随后，我们重新研究了巴尔通体三个主要分支之间的早期系统发育和功能差异，这些差异不仅在系统发育位置和生态上存在差异，而且在基因组大小和基因组百分比G + C含量以及许多代谢能力上也存在差异。我们建议将tamiae巴尔通体分支的单一种重新分类为新属Attibartonella gen. nov.，并使用Attibartonella tamiae梳子。11月为模式种。同样，我们建议将与蜜蜂相关的巴尔通体分支重新分类为新属Ditibartonella gen. nov.，并使用蜜蜂双巴尔通体梳子。11月为模式种。对公开获得的基因组和元基因组序列的系统基因组学分析显示，蜜蜂样本中存在其他双提巴尔通体物种，突出了双提巴尔通体细菌对蜜蜂宿主的进化适应，并提出了共享的传播途径。

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引用次数: 0

Characterization of Sphingomicrobium aquimarinum sp. nov. and Sphingomicrobium maritimum sp. nov. highlights astaxanthin-producing bacteria in the family Sphingomonadaceae Sphingomicrobium aquimarinum sp. 11 .和Sphingomicrobium maritimum sp. 11 .的特性强调了Sphingomonadaceae家族虾青素生产细菌

IF 3.3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Systematic and applied microbiology

Pub Date : 2025-06-04 DOI: 10.1016/j.syapm.2025.126624

Dao-Feng Zhang , Hong-Chuan Wang , Shi Shi , Tian-Pu Li , Dan-Yuan Guo , Zi-Wen Yang , Yang Yuan , Jianke Huang , Wen-Jun Li

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 Sphingomicrobium aestuariivivum AH-M8^T, S. arenosum CAU 1457^T, and S. astaxanthinifaciens CC-AMO-30B^T, and should be recognized as two novel species of the genus Sphingomicrobium, for which the names Sphingomicrobium aquimarinum sp. nov. and Sphingomicrobium maritimum sp. nov. are proposed, respectively. Comparative genomic analysis revealed the complete AXT pathway (genes crtB, crtI, crtY, crtZ, and crtW) 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 Sphingomonadaceae, 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 <0.14). This study significantly enlarged the diversity of AXT-producing bacteria with highlighting such species in the family Sphingomonadaceae.

由于细菌生长速度快，便于下游提取，因此被认为是虾青素（AXT）工业化生产的较好模型。然而，迄今为止，很少有细菌种类的原生AXT生产者被探索。本研究从中国沿海海水中分离得到菌株XHP0235T （=GDMCC 1.3093T = MCCC 1K07532T = JCM 35574T）和XHP0239T （=GDMCC 1.3086T = MCCC 1K07530T = JCM 35575T）。多相分类学结果表明，菌株XHP0235T和XHP0239T与Sphingomicrobium aestuariivivum AH-M8T、s.a arensum CAU 1457T和s.a astaxanthinifaciens CC-AMO-30BT亲缘关系较近，应认定为Sphingomicrobium aquimarinum sp. 11和Sphingomicrobium maritimum sp. 11为Sphingomicrobium属新种。对比基因组分析显示，菌株XHP0235T、XHP0239T和三个相对菌株存在完整的AXT通路（crtB、crtI、crtY、crtZ和crtW基因），类胡萝卜素靶向代谢组分析证实了AXT和其他类胡萝卜素的产生。在此基础上，对Sphingomonadaceae植物的AXT通路进行了进一步的研究，在240株型菌株中鉴定出45株（18.8%）具有全部5个AXT合成基因，其中基因排列可划分为7个类型。侧翼基因含量变化很大，与AXT基因的进化史一致。然而，如果分离物与已知的AXT途径阳性菌株密切相关（进化距离<；0.14），则AXT途径仍然是可预测的。这项研究显著扩大了产生axt的细菌的多样性，重点研究了Sphingomonadaceae家族中的这种细菌。

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引用次数: 0