Systematic and applied microbiology最新文献_第3页

Taxonomic and metabolic diversity of microbial communities in a thermal water stream in Uzbekistan and proposal of two new classes of uncultivated bacteria, Desulfocorpusculia class. nov. and Tepidihabitantia class. nov., named following the rules of SeqCode 乌兹别克斯坦热水中微生物群落的分类和代谢多样性及两种未培养细菌——Desulfocorpusculia类的提出。十一月和暖地类。11、按照SeqCode规则命名

IF 4.2 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Systematic and applied microbiology

Pub Date : 2025-09-01 DOI: 10.1016/j.syapm.2025.126650

Galina B. Slobodkina , Alexander Y. Merkel , Kseniya V. Kondrasheva , Alexandra R. Stroeva , Elizaveta A. Bonch-Osmolovskaya , Kahramon D. Davranov , Alexander I. Slobodkin

Thermal ecosystems in Uzbekistan remain poorly characterized, particularly through culture-independent approaches. In this study, we performed 16S rRNA gene metabarcoding and metagenomic sequencing of microbial communities from a hot stream formed by the discharge of thermal artesian groundwater in the Navoiy region. The taxonomic composition of microbial communities varied with temperature and sample type, with the phylum Chloroflexota abundant in most samples. Members of Aquificota, Deinococcota, and Thermotogota dominated in sediments with temperatures around 60 °C, while Desulfobacterota and Cyanobacteriota were more abundant at lower temperatures. Metagenomic sequencing of the microbial community in sediment under orange-brown mat (54 °C) revealed a dominance of the phyla Chloroflexota, Armatimonadota, Aquificota, Ignavibacteriota, Desulfobacterota and Bacteroidota. Metagenomic data indicated that fermentation, aerobic degradation of organic matter, hydrogen oxidation, and sulfur cycling are the main metabolic processes. Two high-quality metagenome-assembled genomes (MAGs) were described as novel taxa named following the rules of SeqCode. Genome analysis suggests that both organisms are heterotrophic anaerobes capable of sulfate reduction or fermentation. We provide the description of Desulfocorpusculum asiaticum^Ts gen. nov., sp. nov. affiliated with the novel family Desulfocorpusculaceae fam. nov., order Desulfocorpusculales ord. nov. and class Desulfocorpusculia class. nov.; and the description of the new species and genus Tepidihabitans asiaticus^Ts gen. nov., sp. nov. affiliated with the novel family Tepidihabitantaceae fam. nov., order Tepidihabitantales ord. nov. and class Tepidihabitantia class. nov.

乌兹别克斯坦的热生态系统特征仍然很差，特别是通过与文化无关的方法。在这项研究中，我们对纳瓦伊地区热自流地下水排放形成的热流中的微生物群落进行了16S rRNA基因元条形码和宏基因组测序。微生物群落的分类组成随温度和样品类型的不同而变化，大多数样品中含有丰富的氯氟门。在60°C左右的温度下，Aquificota、Deinococcota和Thermotogota在沉积物中占主导地位，而Desulfobacterota和Cyanobacteriota在较低温度下更为丰富。橙棕垫（54°C）沉积物微生物群落元基因组测序结果显示，Chloroflexota、Armatimonadota、Aquificota、Ignavibacteriota、Desulfobacterota和Bacteroidota占主导地位。宏基因组数据表明，发酵、有机物好氧降解、氢氧化和硫循环是主要的代谢过程。两个高质量的宏基因组组装基因组（MAGs）被描述为按照SeqCode规则命名的新分类群。基因组分析表明，这两种生物都是异养厌氧菌，能够硫酸盐还原或发酵。我们提供了新家族Desulfocorpusculaceae fam的Desulfocorpusculum asiaticumTs gen. nov., sp. nov.的描述。11月，订购Desulfocorpusculales， 11月，分类Desulfocorpusculia类。11月;新科Tepidihabitans asiaticussts gen. nov., sp. nov.属的描述。11月，火蚁目和火蚁纲。11月。

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引用次数: 0

Corrigendum to “Govania unica gen. nov., sp. nov., a rare biosphere bacterium that represents a novel family in the class Alphaproteobacteria” [Syst. Appl. Microbiol. 46(3) (2023) 126405] “Govania unica gen. nov., sp. nov.，一种罕见的生物圈细菌，代表了α变形菌纲中的一个新家族”的勘误表。达成。微生物学通报，2016,32(3)(2023):1264 - 1264。

IF 4.2 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Systematic and applied microbiology

Pub Date : 2025-09-01 DOI: 10.1016/j.syapm.2025.126642

Peter Vandamme , Charlotte Peeters , Amanda Hettiarachchi , Margo Cnockaert , Aurélien Carlier

引用次数: 0

Erratum to “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” [Syst. Appl. Microbiol. 48 (2025) 126627] 《波兰Tatra山脉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》[系统]的勘误。达成。微生物学报，48(2025)126627。

IF 4.2 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Systematic and applied microbiology

Pub Date : 2025-09-01 DOI: 10.1016/j.syapm.2025.126647

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

引用次数: 0

Altererythrobacter guangdongensis sp. nov. and Tsuneonella sediminis sp. nov., two novel carotenoid-producing species isolated from tidal flat sediment 从潮滩沉积物中分离的两个新的类胡萝卜素生成种广东变红杆菌和沉积海啸杆菌

IF 4.2 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Systematic and applied microbiology

Pub Date : 2025-08-22 DOI: 10.1016/j.syapm.2025.126649

Huan-Huan He , Ying Wang , Bing-Yu Li , Chun-Yan Lu , Shuai Li , Zhuo-Huan Zheng , Liang Zhang , Wen-Hui Lian , Xin-Tao Luo , Hai-Wei Lin , Lei Dong , Wen-Jun Li

Four aerobic, Gram-stain-negative, rod-shaped, and non-motile bacterial strains, designated SYSU HZ0097ᵀ, SYSU HZ0136, SYSU LHT278ᵀ, and SYSU LHT272, were isolated from tidal flat sediment collected in Zhuhai, China. Phylogenetic analysis based on 16S rRNA gene sequences assigned all four strains to the family Erythrobacteraceae. Strains SYSU HZ0097ᵀ and SYSU HZ0136 showed the highest 16S rRNA gene sequence similarity (98.6 %) to Altererythrobacter epoxidivorans CGMCC 1.7731ᵀ, while SYSU LHT278ᵀ and SYSU LHT272 were most closely related (98.5 %) to Tsuneonella litorea KCTC 82812ᵀ. Whole-genome comparisons, including average nucleotide identity (ANI < 85.0 %) and digital DNA–DNA hybridization (dDDH <30.0 %), supported their assignment to two distinct species. All isolates contained ubiquinone-10 (Q-10) as the predominant respiratory quinone, and the major fatty acids (>10 %) were C_18:1 ω7c and C_18:1 ω6c. The polar lipid profiles included phosphatidylglycerol, phosphatidylethanolamine, and an unidentified glycolipid. The colonies exhibited yellow pigmentation, and genes associated with carotenoid biosynthesis (crtB, crtI) were identified in their genomes. Based on phylogenetic, genomic, phenotypic, and chemotaxonomic characteristics, strains SYSU HZ0097ᵀ and SYSU HZ0136 represent a new species of the genus Altererythrobacter, for which the name Altererythrobacter guangdongensis sp. nov. is proposed (type strain SYSU HZ0097ᵀ = MCCC 1K09423ᵀ = KCTC 8714ᵀ). Strains SYSU LHT278ᵀ and SYSU LHT272 represent a new species of the genus Tsuneonella, for which the name Tsuneonella sediminis sp. nov. is proposed (type strain SYSU LHT278ᵀ = MCCC 1K09543ᵀ = KCTC 8862ᵀ).

从珠海采集的潮滩沉积物中分离到4株需氧、革兰氏阴性、棒状和非运动细菌菌株，分别为SYSU HZ0097、SYSU HZ0136、SYSU LHT278和SYSU LHT272。基于16S rRNA基因序列的系统发育分析将4株菌株归属于红杆菌科。菌株SYSU HZ0097和SYSU HZ0136与环氧改红杆菌CGMCC 1.7731等位基因的16S rRNA基因序列相似性最高（98.6%），而菌株SYSU LHT278和SYSU LHT272与litoreella KCTC 82812等位基因的亲缘性最高（98.5%）。全基因组比较，包括平均核苷酸一致性（ANI < 85.0%）和数字DNA-DNA杂交（dDDH < 30.0%），支持它们被分配到两个不同的物种。所有菌株的主要呼吸醌为泛醌-10 (Q-10)，主要脂肪酸为C18:1 ω7c和C18:1 ω6c （> 10%）。极性脂质谱包括磷脂酰甘油、磷脂酰乙醇胺和一种未识别的糖脂。菌落呈现黄色色素沉着，并在其基因组中鉴定出类胡萝卜素生物合成相关基因（crtB, crtI）。基于系统发育、基因组学、表型和化学分类特征，提出菌株SYSU HZ0097和SYSU HZ0136为Altererythrobacter属的一个新种，命名为Altererythrobacter guangdongensis sp. 11（型菌株SYSU HZ0097 = MCCC 1K09423 = KCTC 8714 =）。菌株SYSU LHT278和SYSU LHT272代表了海啸单胞菌属的一个新种，建议将其命名为沉积海啸单胞菌sp. 11 .（型菌株SYSU LHT278 = MCCC 1K09543 = KCTC 8862 =）。

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引用次数: 0

Carnimonas bestiolae sp. nov. and Cernens ardua gen. nov., sp. nov.: new halotolerant bacteria from the invasive solitary bee Megachile sculpturalis 牛膝单胞菌（Carnimonas bestiolae sp. 11 .）和牛膝单胞菌（Cernens ardua gen. nov., sp. 11 .）：来自入侵独居蜜蜂巨蜂的耐盐新细菌

IF 4.2 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Systematic and applied microbiology

Pub Date : 2025-08-18 DOI: 10.1016/j.syapm.2025.126648

Juliana Botero, Margo Cnockaert, Yakun Zhang, Charlotte Peeters, Peter Vandamme

Fifteen isolates from gut samples of the invasive solitary bee Megachile sculpturalis remained unidentified after matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis. Phylogenomic and overall genome relatedness indices analyses of five representative isolates demonstrated that 14 isolates represented a novel Carnimonas species for which we propose the name Carnimonas bestiolae sp. nov., with LMG 33810^T as the type strain. A single isolate represented a distinct lineage within the Halomonadaceae family with the genera Carnimonas and Halotalea as nearest neighbor taxa and is classified as Cernens ardua gen. nov., sp. nov., with LMG 33818^T as the type strain. Comparative genomic analysis and physiological characterization revealed functional differences between C. bestiolae, Ce. ardua and established Carnimonas and Halotalea species in central metabolism, fatty acid metabolism, and osmoregulatory pathways, the latter being consistent with adaptation to a saline environment. A reanalysis of previously published insect microbiome studies in which Carnimonas was reported, revealed 16S rRNA amplicon sequence variants with >99 % identity to C. bestiolae LMG 33810^T 16S rRNA in gut samples of Megachile sculpturalis, Anthidium florentinum, and the psyllid Leptynoptera sulfurea. In contrast, 16S rRNA amplicon sequence variants corresponding to Ce. ardua were rarely detected and only at low relative abundances, suggesting a transient association with the insect gut.

基质辅助激光解吸/电离飞行时间质谱分析显示，15株入侵独居蜂（Megachile sculpturalis）的肠道样本尚未被鉴定。对5个代表性分离株的系统基因组学和全基因组相关性分析表明，其中14个分离株为一种新的卡尼单胞菌，我们将其命名为卡尼单胞菌bestiolae sp. nov.，并以LMG 33810T为型菌株。单株分离菌株与Carnimonas属和Halotalea属有明显的亲缘关系，属Cernens ardua gen. nov., sp. nov.， LMG 33818T为类型菌株。比较基因组分析和生理特性分析表明，双歧杆菌、大肠杆菌和大肠杆菌在功能上存在差异。并在中枢代谢、脂肪酸代谢和渗透调节途径中建立了Carnimonas和Halotalea两个物种，后者与适应盐碱环境一致。对先前发表的关于Carnimonas的昆虫微生物组研究的重新分析显示，在巨型雕塑菌、花栗蚁和细翅虫的肠道样本中，16S rRNA扩增子序列变异与C. bestiolae LMG 33810t16s rRNA具有99%的一致性。相比之下，16S rRNA扩增子序列变异对应于Ce。Ardua很少被检测到，而且相对丰度很低，这表明它与昆虫肠道有短暂的联系。

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引用次数: 0

BISMiS Live: a digital platform for global communication among microbial systematists BISMiS Live：微生物系统学家全球交流的数字平台

IF 4.2 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Systematic and applied microbiology

Pub Date : 2025-08-13 DOI: 10.1016/j.syapm.2025.126646

Kamlesh Jangid , Wen-Jun Li , Stephanus Venter , Wee Fei Aaron Teo , William Whitman

BISMiS Live, launched on March 20, 2021, emerged as a timely response to the disruption caused by the CoViD-19 pandemic, offering a global virtual platform for discourse in microbial systematics. Spearheaded by the Bergey's International Society for Microbial Systematics (BISMiS), this monthly webinar series hosted renowned experts and engaged thousands of participants across 84 countries. The initiative emphasized inclusivity, scientific depth, and digital accessibility, with sessions archived on YouTube (@BISMiS_) for broader impact. Behind each event lies a dedicated team managing speaker coordination, technical execution, and global outreach. BISMiS Live has grown into an educational resource, integrated into university curricula and inspiring the next generation of microbial taxonomists. With suggestions for future innovation, such as student lightning talks, thematic series, and podcast formats, the platform is poised to evolve further. BISMiS Live stands as a digital bridge connecting systematists worldwide, sustaining knowledge exchange and community through innovation and collaboration.

BISMiS Live于2021年3月20日推出，是对CoViD-19大流行造成的中断的及时回应，为微生物系统学的讨论提供了一个全球虚拟平台。由Bergey国际微生物系统学会（BISMiS）牵头，这个每月一次的网络研讨会系列邀请了来自84个国家的知名专家和数千名参与者。该倡议强调包容性、科学深度和数字可访问性，会议被存档在YouTube （@BISMiS_）上，以产生更广泛的影响。每个活动背后都有一个专门的团队负责协调演讲者，技术执行和全球推广。BISMiS Live已经成长为一个教育资源，整合到大学课程和激励下一代微生物分类学家。随着对未来创新的建议，如学生闪电讲座，专题系列和播客格式，该平台准备进一步发展。BISMiS Live是连接全球系统学家的数字桥梁，通过创新和协作保持知识交流和社区。

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引用次数: 0

Genomic characterization of Gillisia xinjiangensis sp. nov.: insights into nitrogen metabolism, stress adaptation, and application potential 新疆Gillisia ensis sp. nov.的基因组特征：氮代谢、胁迫适应和应用潜力的见解

IF 4.2 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Systematic and applied microbiology

Pub Date : 2025-08-13 DOI: 10.1016/j.syapm.2025.126645

Hao-hao Wang , Chi Zhang , Ya-qin Chen , Yi-fan Guo , Li-jian Ding , Sheng-fa Zhang , Gai-jun Du , Wei-yan Zhang , Shan He

High-altitude saline lakes host distinctive microbial communities characterized by specialized adaptations to extreme environmental conditions. However, the underlying mechanisms enabling bacterial survival and physiological function in these habitats remain largely unexplored. In this study, a novel Gram-stain-negative, non-motile, rod-shaped bacterium, designated strain Q332^T, was isolated from sediment samples collected from Achikkul Lake, a high-altitude saline lake in Xinjiang, northwestern China. The strain was facultatively aerobic, and grew optimally at 28 °C, pH 7.0, and 3.0 % (w/v) NaCl. Catalase and oxidase activities were positive. Major fatty acids identified in strain Q332^T included anteiso‐C_15:0, anteiso-C_17:1, iso‐C_15:0 and C_16:0. The primary respiratory quinone detected was menaquinone-6 (MK-6). Polar lipid analyses identified phosphatidylethanolamine (PE), one unidentified acyloxyacyl phosphatidylglycerol (APGL), three unidentified lipids (L), three glycolipids (GL), one phospholipid (PL), and four amidolipids (AL). The genomic DNA G + C content is 38.9 %. Genomic characterization revealed a versatile metabolic repertoire, including unique C1-unit metabolic pathways and comprehensive nitrogen cycling capabilities, notably denitrification and assimilatory nitrate reduction. Furthermore, strain Q332^T displayed robust mechanisms for stress adaptation, encompassing tolerance to cold and osmotic stress, defenses against oxidative stress, and resistance to heavy metals. Based on phenotypic, chemotaxonomic, phylogenetic, and genomic features, strain Q332^T is considered to represent a novel species of the genus Gillisia, for which the name Gillisia xinjiangensis sp. nov. is proposed. The type strain is Q332^T (=KCTC 102200^T = MCCC 1K09490^T).

高海拔盐湖拥有独特的微生物群落，其特征是对极端环境条件的特殊适应。然而，使细菌在这些栖息地生存和生理功能的潜在机制仍未被探索。本研究从新疆高海拔盐湖阿奇库尔湖沉积物样品中分离到一种新型革兰氏阴性、非运动杆状细菌Q332T。该菌株为兼性好氧菌株，在28°C、pH 7.0和3.0 % (w/v) NaCl条件下生长最佳。过氧化氢酶和氧化酶活性呈阳性。在菌株Q332T中鉴定出的主要脂肪酸包括anteiso- C15:0、anteiso- c17:1、iso- C15:0和C16:0。主要检测呼吸醌为甲基萘醌-6 （MK-6）。极性脂质分析鉴定出磷脂酰乙醇胺（PE）、一种未鉴定的酰基酰磷脂酰甘油（APGL）、三种未鉴定的脂质(L)、三种糖脂质（GL）、一种磷脂质（PL）和四种酰胺脂质（AL）。基因组DNA G + C含量为38.9%。基因组特征揭示了一个多功能的代谢库，包括独特的c1单位代谢途径和全面的氮循环能力，特别是反硝化和同化硝酸盐还原。此外，菌株Q332T显示出强大的逆境适应机制，包括对寒冷和渗透胁迫的耐受性，对氧化应激的防御，以及对重金属的抗性。基于表型、化学分类、系统发育和基因组特征，认为菌株Q332T代表了Gillisia属的一个新种，并建议将其命名为Gillisia xinjiangensis sp. 11。型应变为Q332T （=KCTC 102200T = MCCC 1K09490T）。

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引用次数: 0

A practical guide on environmental genomics for prokaryotic systematics 原核生物系统学环境基因组学实用指南

IF 4.2 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Systematic and applied microbiology

Pub Date : 2025-08-05 DOI: 10.1016/j.syapm.2025.126643

Nathan M. Ernster , Luis M. Rodriguez-R

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 Code of Nomenclature of Prokaryotes Described from Sequence Data (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.

环境霰弹枪测序可以深入了解微生物群落概况，功能能力，以及代表微生物组个体成员的宏基因组组装基因组（MAGs）的恢复。同样，通过微流体和测序技术的进步，单细胞扩增基因组（sag）的组装也成为可能。这些领域已经经历了数据量的巨大增长，分析工具的不断发展，最终，恢复的基因组数量缺乏有效的名称。由于大多数微生物是不可培养的，因此与传统的命名要求不兼容，序列数据库中充满了质量不一的基因组，没有标准化的命名法，阻碍了交流和数据的可用性。为了克服这些限制，最近推出的序列数据描述原核生物命名代码（SeqCode）包括基因组质量标准和基于DNA序列有效命名未培养原核生物的命名标准。宏基因组学和系统学对新用户来说可能是一个压倒性的领域，所以我们在这里提供一个指南来帮助澄清主题并指出特殊的注意事项。这些主题包括宏基因组管道，基因组质量评估标准，其次是分类和性状预测工具。接下来，我们将介绍源元数据、丰度和占用测量方法，最后介绍命名法和名称注册。社区努力生成具有完整描述和有效名称的高质量原核基因组对环境基因组数据的未来可用性和交流至关重要。

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引用次数: 0

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