Systematic and applied microbiology最新文献

{"title":"Desulfurivibrio nitratireducens sp. nov. and Desulfurivibrio modestus sp. nov., two novel alkaliphilic anaerobes isolated from terrestrial mud volcanoes.","authors":"M A Khomyakova, A Y Merkel, D S Kopitsyn, A I Slobodkin","doi":"10.1016/j.syapm.2026.126693","DOIUrl":"https://doi.org/10.1016/j.syapm.2026.126693","url":null,"abstract":"<p><p>Anaerobic enrichments with 4-aminobenzoic acid and nitrate yielded two novel representatives of genus Desulfurivibrio. Strain C05AmB^T was isolated from terrestrial mud volcano Gnilaya Gora (Taman Peninsula, Russia), and strain D14AmB^T from terrestrial mud volcano Bakhar satellite (Azerbaijan). Both strains were mesophilic and alkaliphilic (pH optimum 9.0-9.5). The isolates were strict anaerobes with respiratory metabolism, utilizing organic substrates or molecular hydrogen as electron donors with sulfur compounds as electron acceptors. Strain C05AmB^T utilized additionally elemental sulfur and sulfide as electron donors with nitrate as electron acceptor, while strain D14AmB^T was incapable of nitrate reduction. Both strains can also disproportionate sulfur compounds including elemental sulfur, sulfite and thiosulfate. Major cellular fatty acids were C_16:0, C_16:1ω6c (the dominant fatty acid in strain C05AmB^T), C_18:0 and C_18:1 ω9c (the dominant fatty acid in strain D14AmB^T). The genomes had a size of 2.7-3.0 Mb for strains C05AmB^T and D14AmB^T respectively. Genome analysis allowed to identify the main pathways encoding carbon and energy metabolism. According to both phylogenetic analyses, based on 16S rRNA gene sequences and conserved protein sequences, as well as genome-based comparisons, each strain forms separate species-level lineage within Desulfurivibrio genus of Desulfurivibrionaceae family (phylum Desulfobacterota). Here we propose two novel species Desulfurivibrio nitratireducens sp. nov. with type strain C05AmB^T (=CGMCC 1.18106^T = VKM B-3838^T = KCTC 25857^T = UQM 41817^T) and Desulfurivibrio modestus sp. nov. with type strain D14AmB^T (=CGMCC 1.18059^T = VKM B-3769^T = UQM 41803^T). These are the first sulfur-disproportionating microorganisms isolated from terrestrial mud volcanoes.</p>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"49 2","pages":"126693"},"PeriodicalIF":4.2,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146126534","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":"Caldiplasma sukawensis gen. nov., sp. nov., and Cuniculiplasma thermophilum sp. nov., mesophilic, acidophilic, cell–wall–less, archaea of the order Thermoplasmatales, isolated from extremely acidic hot spring","authors":"Yuya Tsukamoto ,&nbsp;Hiroyuki D. Sakai ,&nbsp;Yoshinori Takano ,&nbsp;Toshiki Koga ,&nbsp;Arisa Nishihara ,&nbsp;Shigeru Kawai ,&nbsp;Susumu Yoshizawa ,&nbsp;Moriya Ohkuma","doi":"10.1016/j.syapm.2025.126686","DOIUrl":"10.1016/j.syapm.2025.126686","url":null,"abstract":"<div><div>Four mesophilic, acidophilic, cell wall–less archaea, strains—SKW1, SKW2^T, SKW3, and SKW4^T—were isolated from a green microbial mat in an acidic hot spring. SKW1 and SKW2^T cells were predominantly coccoid and rarely pleomorphic, whereas SKW3 and SKW4^T cells were mostly pleomorphic. The cell sizes ranged from 0.3 to 2.0 μm. SKW1 and SKW2^T grew at temperatures between 15 and 55 °C (optimally at 37–40 °C) and pH 1.5–5.0 (optimally 3.0–4.0). SKW3 and SKW4^T also grew at temperatures between 15 and 55 °C (optimally at 30 °C) and pH 1.5–5.0 (optimally 1.8–2.0). All the strains were facultatively anaerobic and heterotrophic, requiring tryptone for growth. The dominant membrane lipid in both SKW2^T and SKW3 was glycerol dibiphytanyl glycerol tetraether (GDGT). The genomic G+C mol% of SKW1 to SKW4^T ranged from 35.8 to 38.1 mol%. In the 16S rRNA gene–based phylogenetic tree, all the strains were placed within the family <em>Cuniculiplasmataceae</em> and the order Thermoplasmatales<em>.</em> Sequence identities to the closest strain, <em>Cuniculiplasma divulgatum</em> strain S5^T, were 94.28 % (SKW1), 94.35 % (SKW2^T), 95.81 % (SKW3), and 95.88 % (SKW4^T). Phylogenetic analyses showed that SKW 1 and SKW2^T were distantly related to <em>C. divulgatum</em> strain S5^T, whereas SKW3 and SKW4^T were more closely related. Based on phylogenetic analyses and physiological properties of the four isolates, a novel genus, <em>Caldiplasma</em> gen. nov.<em>,</em> and two novel species <em>Caldiplasma sukawensis</em> sp. nov. and <em>Cuniculiplasma thermophilum</em> sp. nov. are proposed: <em>Caldiplasma sukawensis</em> SKW1 (=JCM 39523) and SKW2^T (=JCM 39524^T), and <em>Cuniculiplasma thermophilum</em> SKW3 (=JCM 39525) and SKW4^T (=JCM 39526^T).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"49 2","pages":"Article 126686"},"PeriodicalIF":4.2,"publicationDate":"2025-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145908846","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":"Ningiella algicola sp. nov. and Marinicella algicola sp. nov., proposal of Paralteromonas gen. Nov. and Neoalteromonas gen. Nov. with reclassification of Alteromonas species, and reclassification of Methylophaga aminisulfidivorans as a later heterotypic synonym of Methylophaga thalassica","authors":"Hülya Bayburt ,&nbsp;Jeong Min Kim ,&nbsp;Byeong Jun Choi,&nbsp;Jae Kyeong Lee,&nbsp;Che Ok Jeon","doi":"10.1016/j.syapm.2025.126685","DOIUrl":"10.1016/j.syapm.2025.126685","url":null,"abstract":"<div><div>Two Gram-stain-negative, obligately aerobic, non-motile rod-shaped bacteria, designated strains W23^T and W31^T, exhibiting catalase- and oxidase-positive activities, were isolated from the phycosphere of a marine red alga. Strain W23ᵀ grew optimally at 25 °C, pH 8.0–9.0, and 3.0–4.0 % (<em>w</em>/<em>v</em>) NaCl, whereas strain W31^T grew optimally at 25–30 °C, pH 8.0, and 3.0–4.0 % NaCl. Ubiquinone-8 was the major respiratory quinone in both strains. Strain W23^T predominantly contained C_16:0, summed features 3 (C_16:1 <em>ω</em>7<em>c</em> and/or C_16:1 <em>ω</em>6<em>c</em>) and 8 (C_18:1 <em>ω</em>7<em>c</em> and/or C_18:1 <em>ω</em>6<em>c</em>), and C_12:0 as major fatty acids, with phosphatidylglycerol and phosphatidylethanolamine as main polar lipids. In contrast, strain W31^T exhibited isoC_15:0, summed feature 1 (isoC_15:1H and/or C_13:0 3-OH), C_12:0, and isoC_11:0, with diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylmonomethylethanolamine as dominant polar lipids. The genomic DNA G + C contents were 44.5 % for strain W23^T and 42.3 % for strain W31^T. Phylogenetic, genomic, and phenotypic analyses support the classification of strains W23ᵀ and W31ᵀ as novel species within the genera <em>Ningiella</em> and <em>Marinicella</em>, for which the names <em>Ningiella algicola</em> sp. nov. (W23^T = KACC 23126^T = JCM 35964^T) and <em>Marinicella algicola</em> sp. nov. (W31^T = KACC 23129^T = JCM 35965^T) are proposed. Genome-based phylogenomic analyses also supported the reclassification of <em>Alteromonas lipolytica</em>, <em>Alteromonas alba</em>, and <em>Alteromonas oceani</em> into the genus <em>Marisediminitalea</em>; <em>Alteromonas sediminis</em> into a new genus, <em>Paralteromonas</em>; and <em>Alteromonas flava</em>, <em>Alteromonas facilis</em>, and <em>Alteromonas arenosi</em> into another new genus, <em>Neoalteromonas</em>. Furthermore, <em>Methylophaga aminisulfidivorans</em> is reclassified as a later heterotypic synonym of <em>Methylophaga thalassica</em>.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"49 1","pages":"Article 126685"},"PeriodicalIF":4.2,"publicationDate":"2025-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145790422","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":"Heterotrophic lifestyle in the phylum Thermodesulfobiota revealed by physiological and genomic characterization of the acidophilic sulfate-reducing bacterium Thermodesulfobium fumaratoxidans sp. nov.","authors":"Anastasia I. Maltseva ,&nbsp;Alexander G. Elcheninov ,&nbsp;Alexandra A. Klyukina ,&nbsp;Alexandra A. Kuchierskaya ,&nbsp;Alexander V. Lebedinsky ,&nbsp;Evgenii N. Frolov","doi":"10.1016/j.syapm.2025.126684","DOIUrl":"10.1016/j.syapm.2025.126684","url":null,"abstract":"<div><div>The phylum <em>Thermodesulfobiota</em> is a deeply branching phylogenetic lineage of bacteria comprising two described species within a single genus. A novel <em>Thermodesulfobium</em> representative, strain 4217-1^T, was isolated from a thermal spring of Kamchatka Peninsula. Unlike previously known thermophilic <em>Thermodesulfobium</em> species, strain 4217-1^T was a thermotolerant bacterium that grew optimally at 42 °C. Moreover, the new isolate had a wider pH range (from 3.0 to 6.7) and lower pH optimum (4.3–4.5) for growth, which makes it one of the few acidophilic sulfate-reducing bacteria known to date. Like other <em>Thermodesulfobium</em> species, the new isolate grew autotrophically by reduction of sulfate or thiosulfate with hydrogen, but not with formate. Up to now, only autotrophic lifestyle has been known for representatives of the genus <em>Thermodesulfobium</em>. Surprisingly, strain 4217-1^T was also capable of chemolithoheterotrophic growth with H₂ as electron donor, sulfate as electron acceptor and acetate as the carbon source, as well as of chemoorganoheterotrophic growth with fumarate as the carbon source and electron donor and sulfate as electron acceptor. Genomic analysis of strain 4217-1^T revealed genetic determinants of the main metabolic processes, including genes encoding enzymes for fumarate and acetate assimilation during heterotrophic growth. On the basis of phylogenomic analysis, as well as distinct phenotypic and genomic properties, strain 4217-1^T is proposed as the novel species <em>Thermodesulfobium fumaratoxidans</em> sp. nov. (JCM 39391^T = KCTC 25626^T = VKM B-3675^T).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"49 1","pages":"Article 126684"},"PeriodicalIF":4.2,"publicationDate":"2025-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145790421","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":"Wenzhouxiangella psychrophila sp. nov., Wenzhouxiangella indolica sp. nov., and Halotectona sediminis gen. nov., sp.nov., three novel taxa with ability of IAA production from saline lake sediment","authors":"Qing-Yu Xu ,&nbsp;Tayyiba Habib ,&nbsp;Lei Gao ,&nbsp;Dildar Wu ,&nbsp;Xin-Yao Li ,&nbsp;Thi-Nhan Khieu ,&nbsp;Yue-Heng Chen ,&nbsp;Yao Zhang ,&nbsp;Yong-Hong Liu ,&nbsp;Ting-Ting She ,&nbsp;Bao-Zhu Fang ,&nbsp;Wen-Jun Li","doi":"10.1016/j.syapm.2025.126683","DOIUrl":"10.1016/j.syapm.2025.126683","url":null,"abstract":"<div><div>Indoleacetic acid synthesis (IAA), a crucial plant hormone, can be produced by many microorganisms through different metabolic pathways. While much research has focused on rhizosphere microorganisms, studies on IAA production functional strains in extreme environments are limited. In this study, two IAA-producing strains of the genus <em>Wenzhouxiangella</em> are isolated from saline lake sediment of Xinjiang, designated strains EGI_FJ10305^T and EGI_FJ10409^T, which show low 16S rRNA gene sequence identities to other validly published <em>Wenzhouxiangella</em> species (&lt; 98.65 %). A series of phylogenetic analysis concludes that two isolated strains represent two novel species within the genus <em>Wenzhouxiangella</em>. Two halotolerant strains are grown at 0–10.0 % (<em>w</em>/<em>v</em>) NaCl (optimum, 4.0 %, EGI_FJ10305^T) and 0–8.0 % (w/v) NaCl (optimum, 4.0 %, EGI_FJ10409^T), respectively. Result of functional test confirms that both isolated strains possess the capability to synthesize indole-3-acetic acid (IAA) with substrate tryptophan. Genomic analysis suggests that this capability likely operates through the tryptamine pathway (TAM) and has been inherited from their ancestors rather than acquired through horizontal gene transfer. The proposed names of strains EGI_FJ10305^T and EGI_FJ10409^T are <em>Wenzhouxiangella psychrophile</em> sp. nov. and <em>Wenzhouxiangella indolica</em> sp. nov., respectively. Concurrently, metagenomic analysis of the same samples yielded three high-quality MAGs. Phylogenetic analysis subsequently indicated that these three MAGs potentially represent a new genus within the family <em>Wenzhouxiangellaceae</em>, for which we propose the name <em>Halotectona sediminis</em> gen. Nov. sp. nov., in accordance with the published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"49 1","pages":"Article 126683"},"PeriodicalIF":4.2,"publicationDate":"2025-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145737514","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":"Phenotypic and functional genome characterization of Herbivorax alkaliphila sp. nov. and Natronospora cellulosivora gen. nov., sp. nov., obligately anaerobic, cellulotrophic, endospore-forming bacteria from soda lakes in southwestern Siberia","authors":"Dimitry Y. Sorokin,&nbsp;Alexander Y. Merkel,&nbsp;Tatjana V. Khizhniak","doi":"10.1016/j.syapm.2025.126682","DOIUrl":"10.1016/j.syapm.2025.126682","url":null,"abstract":"<div><div>Our recent study targeting anaerobic cellulose mineralization at moderate salinity in soda lakes of southwestern Siberia resulted in enrichment of three bacterial consortia of which two contained endospore-forming cellulotrophic members of <em>Bacillota</em>. One of the latter two yielded a pure culture, strain ANBcel31^T, while the other consisted of a cellulotrophic <em>Halanaerobiales</em> (strain ANBcel28^Ts) and its saccharolytic satellite from the genus <em>Natronincola</em>. Phylogenomic analysis placed strain ANBcel31^T into the genus <em>Herbivorax</em> (order <em>Acetivibrionales</em>) as a new species, while strain ANBcel28^Ts represents a new genus within the order <em>Halanaerobiales</em> most related to two halophilic cellulotrophic genera <em>Halocella</em> and “<em>Iocasia”</em>. The cells of both organisms are Gram-positive, endospore-forming rods. They utilize few polysacchartides, including insoluble cellulose, xylan and either laminarin and xyloglucan (ANBcel31^T) or barley glucan and lichenan (ANBcel28^Ts). The fermentation products during growth on cellulose were acetate, lactate, H₂ and formate. Both bacteria are moderately salt-tolerant obligate alkaliphiles, growing optimally at 0.6–1.5 M total Na⁺ as carbonates and pH 9.0–9.5. Their genomes contain large repertoire of genes coding for extracellular cellulases from the GH5 and GH9 families most of which are apparently assembled in cellulosomes. As common among the soda lake anaerobes, the isolates rely on sodium-based bioenergetics, including sodium-translocating Rnf complex, ATPase/synthase and membrane decarboxylases. Based on distinct phenotypic properties and results of phylogenomic analysis, strain ANBcel31^T is proposed to be classified as <em>Herbivorax alkaliphila</em> sp. nov. (DSM 113934^T = UQM 41585^T) (according to the ICNP nomenclature code), and strain ANBcel28^Ts – as <em>Natronospora cellulosivora</em> gen. nov., sp. nov. (according to the rules of SeqCode).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"49 1","pages":"Article 126682"},"PeriodicalIF":4.2,"publicationDate":"2025-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145716042","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":"LPSN-API Assistant: A Windows standalone tool for automating the bulk collection and organization of type strain 16S rRNA gene sequences and taxa information from the LPSN","authors":"Rashidin Abdugheni ,&nbsp;Yasen Maimaitiyiming ,&nbsp;Lu Lu ,&nbsp;Jian-Yu Jiao ,&nbsp;Wen-Jun Li","doi":"10.1016/j.syapm.2025.126681","DOIUrl":"10.1016/j.syapm.2025.126681","url":null,"abstract":"<div><div>The List of Prokaryotic Names with Standing in Nomenclature (LPSN) is a robust platform for prokaryotic taxonomists, providing the latest taxonomic information and 16S rRNA gene sequences. The type strain 16S rRNA gene sequence is a cornerstone in microbial taxonomy and an essential resource for researchers in the field of microbiology. However, manually collecting taxonomic information, downloading, and managing 16S rRNA gene sequences from LPSN can be time-consuming and laborious. The LPSN-API is a reliable tool for systematic microbiologists, yet for users with no experience in R or Python programming, readily applying the LPSN-API for taxonomic data collection and organization remains a challenge. To address this general challenge, we developed LPSN-API Assistant (version 1.0), a non-commercial Windows standalone tool with a user interface developed using Python to automate the collection of taxonomic information and bulk download of type strain 16S rRNA gene sequences of a given genus from the LPSN. LPSN-API Assistant streamlines the information collection and sequence downloading process, and provides functionalities for fast organizing and formatting sequence data of specified prokaryotic genera for phylogenetic analysis. Here, we present the design, implementation, and application of LPSN-API Assistant (<span><span>https://gitee.com/rashidin-abdugheni/lpsn-api_-assistant_1.0</span><svg><path></path></svg></span>), highlighting its applicability and potential to assist prokaryotic taxonomists.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"49 1","pages":"Article 126681"},"PeriodicalIF":4.2,"publicationDate":"2025-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145715968","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic insights into Izemobacterium crustae gen. nov., sp. nov., reveal metabolic adaptations for persistence in the oceanic crust","authors":"Tomeu Viver ,&nbsp;Alberto Robador","doi":"10.1016/j.syapm.2025.126679","DOIUrl":"10.1016/j.syapm.2025.126679","url":null,"abstract":"<div><div>Subsurface environments are often conceptualized as static ecosystems governed by slow processes and persistent energy scarcity, reinforcing the notion that microbial life is largely inactive or maintained in a state of metabolic dormancy. Yet mounting evidence suggests that the subseafloor crustal biosphere is more dynamic, shaped by hydrothermal circulation, fluid–rock interactions, and steep, fluctuating redox gradients. These processes create transient phases of increased energy supply that can sustain ecologically significant microbial activity. To better understand the metabolic strategies enabling survival under these conditions, we investigated the genomic and physiological potential of a spore-forming bacterium, strain JdFR-1ᵀ, enriched from crustal fluids of the Juan de Fuca Ridge. Its genome encodes traits associated with survival and metabolic maintenance under extreme resource limitation, including pathways for sporulation and germination, fermentative and hydrolytic metabolism, and scavenging of organic substrates. These features suggest a capacity to alternate between dormancy and metabolic activity in response to environmental fluctuations. Strain JdFR-1ᵀ represents a new lineage within the <em>Izemoplasmataceae</em> family, for which we propose the name <em>Izemobacterium crustae</em> gen. nov., sp. nov., in accordance with the SeqCode rules. Together, these findings provide genomic evidence for potential adaptive strategies that enable persistence and energy-efficient metabolism in the deep oceanic crustal biosphere.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"49 1","pages":"Article 126679"},"PeriodicalIF":4.2,"publicationDate":"2025-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145595007","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":"Natronorubrum marinum sp. nov., Natronorubrum amylolyticum sp. nov., Natronorubrum halobium sp. nov., and Natronorubrum salinum sp. nov., halophilic archaea from a coastal saline-alkali land and two saline lakes","authors":"Ya-Ling Mao,&nbsp;Yao Hu,&nbsp;Zhang-Ping Wu,&nbsp;Ya-Ping Sun,&nbsp;Jing Hou,&nbsp;Heng-Lin Cui","doi":"10.1016/j.syapm.2025.126680","DOIUrl":"10.1016/j.syapm.2025.126680","url":null,"abstract":"<div><div>Four novel halophilic archaeal strains, DTA7^T, DTA28^T, FCH18a^T, and WLHS9^T, were isolated from a coastal saline-alkali land and two saline lakes in China. The metagenomic analyses revealed that the coastal saline-alkali land from Dongtai tidal flat the highest relative abundance of archaea compared to the saline sediment samples of Feicui Salt Lake and Wulanhushao Salt Lake. These four strains showed high sequence similarities to current species within the genus <em>Natronorubrum</em> judged by 16S rRNA gene and <em>rpoB'</em> gene sequence similarities, and formed tight clusters with current <em>Natronorubrum</em> species based on the phylogenies of these two house-keeping genes. Phylogenomic analysis confirmed the phylogenies based on 16S rRNA gene and <em>rpoB'</em> genes. Comparative genomic analysis revealed that the average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values among these four strains and existing species of the genus <em>Natronorubrum</em> were 76.8–92.7 %, 22.8–52.7 %, and 73.4–94.7 %, respectively. These overall genome-related indexes were significantly below the thresholds for species delineation. These four strains showed optimal growth at 1.7–3.1 M NaCl, 37 °C, and pH 7.0–9.5. Strain WLHS9^T was found to be a neutrophilic halophile, while the others exhibited alkaliphilic halophilic characteristics. The major phospholipids detected in these four strains included phosphatidic acid (PA), phosphatidylglycerol (PG), and phosphatidylglycerol phosphate methyl ester (PGP-Me). The glycolipid of strain WLHS9^T was identical to that of the current neutrophilic species of <em>Natronorubrum</em>. Based on phylogenetic analysis, phenotypic characteristics, polar lipid profiles, and phylogenomic data, strains DTA7^T, DTA28^T, FCH18a^T, and WLHS9^T represent four novel species within the genus, namely, <em>Natronorubrum marinum</em> sp. nov., <em>Natronorubrum amylolyticum</em> sp. nov., <em>Natronorubrum halobium</em> sp. nov., and <em>Natronorubrum salinum</em> sp. nov., respectively.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"49 1","pages":"Article 126680"},"PeriodicalIF":4.2,"publicationDate":"2025-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145617272","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 and description of plant-growth-promoting methanotrophic bacteria belonging to the genus of Methylocaldum","authors":"Courtney C. Cameron ,&nbsp;William Gebbie ,&nbsp;Chynna Bowman ,&nbsp;Elizabeth R. Waters ,&nbsp;Marina G. Kalyuzhnaya","doi":"10.1016/j.syapm.2025.126670","DOIUrl":"10.1016/j.syapm.2025.126670","url":null,"abstract":"<div><div>Arid soil microbiomes present untapped resources of microbial diversity. Here, we describe twelve isolates, all belonging to the <em>Methylocaldum</em> genus. Based on metagenomic studies, the isolates represent the major clades of methanotrophic bacteria inhabiting the arid biomes of Southern California, comprising up to 0.03 % of the total soil microbiota. Phenotyping of isolates indicates that they are obligate methanotrophic bacteria, some capable of methanol utilization. All strains can fix nitrogen, use nitrate and ammonia as a N-source, and have key genetic signatures of autotrophy, methylotrophy, and N₂O assimilation. Based on the 16S rRNA phylogeny and whole -genome analyses, all strains are assigned to the species <em>M. gracile</em>. Three isolates from the rhizosphere of native Californian plants (Strains 0917, YM2 and S3V3) and GT1B-W are set apart from the other <em>M. gracile strains,</em> despite sharing &lt;98 % of average nucleotide identity. Microbes isolated from plant rhizosphere display 150 unique genetic features and a series of tandem gene duplications predicted to contribute to their interactions with plants, including the 20-gene polyketide biosynthesis cluster and the TRAP C4-dicarboxylate transport system. Consistent with the genetic properties that may indicate an enhancement of plant-cooperation functions, the rhizosphere isolates support the survival of plants, <em>Boechera depauperata</em> and <em>Arabidopsis thaliana,</em> under drought conditions. Based on genetic and phenotypic characteristics, we propose to designate strains 0917, YM2, S3V3, and GT1B-W as a new subspecies of <em>Methylocaldum gracile</em> – <em>Methylocaldum gracile</em> subspecies dēsertum, L.n. <em>dēsertum –</em> a desert, to represent the native habitat of the species. The amended description of the <em>M.gracile</em> species is provided.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"49 1","pages":"Article 126670"},"PeriodicalIF":4.2,"publicationDate":"2025-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145595011","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}