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Microbial community on industrial salty bovine hides: From the slaughterhouse to the salting 工业咸牛皮上的微生物群落:从屠宰场到盐渍
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2023-07-01 DOI: 10.1016/j.syapm.2023.126421
Francisco Nadal-Molero , Alicia Campos-Lopez , Juan Tur-Moya , Ana-Belen Martin-Cuadrado

The leather-making industry is an age-old industry and desiccation with salt has been one of the most used methodologies for obtaining valuable skins. However, halophiles may proliferate and affect the integrity of the hide-collagen structure, as well as leading to undesirable red colorations or less-frequent purple stains. To understand the basis of these industrial hide contaminations, the microbial community from raw hide samples, salt-cured samples and four different industrial salts, was analyzed by 16S rRNA gene metabarcoding together with standard cultivation methods.

Comparison of raw hides and correctly cured hides revealed a core microbiome that was absent from contaminated hides. In addition, archaea were missing from well-cured hides, whereas Psychrobacter and Acinetobacter were highly represented (23 % and 17.4 %, respectively). In damaged hides, only a few operational taxonomic units (OTUs), from among the hundreds detected, were able to proliferate and, remarkably, a single Halomonas OTU represented 57.66 % of the reads. Halobacteria, mainly Halovenus, Halorubrum and Halovivax, increased by up to 36.24–39.5 % in the red- and purple-affected hides. The major contaminants were isolated and hide infections, together with collagenase activity, were evaluated. The results showed that hides enriched with the non-pigmented isolate Halomonas utahensis COIN160 damaged the collagen fibers similarly to Halorubrum, and together they were considered to be one of the major causes. Putative degrading inhibitors were also identified from among the Alkalibacillus isolates.

It was concluded that hide contaminations were driven by clonal outbreaks of a few specific microbes, which may have been non-pigmented collagen degraders. Acinetobacter and Alkalibacillus, members of the core microbiome of raw and well-cured salted hides, are suggested as hide contaminant inhibitors that need further analysis.

皮革制造业是一个古老的行业,用盐干燥是获得有价值皮革的最常用方法之一。然而,嗜盐菌可能会增殖并影响皮胶原结构的完整性,并导致不希望的红色或不太常见的紫色污渍。为了了解这些工业皮革污染的基础,通过16S rRNA基因代谢编码和标准培养方法分析了生皮样品、盐腌样品和四种不同工业盐的微生物群落。生皮和正确腌制的生皮的比较揭示了受污染生皮中不存在的核心微生物组。此外,经过良好处理的兽皮中缺少古菌,而Psychrobacter和不动杆菌的比例很高(分别为23%和17.4%)。在受损的兽皮中,在检测到的数百个操作分类单元中,只有少数操作分类单元(OTU)能够增殖,值得注意的是,单个Halomonas OTU占读数的57.66%。在受红色和紫色影响的兽皮中,卤代细菌,主要是卤Venus、Halorbrum和Halovivax,增加了36.24-39.5%。对主要污染物进行了分离,并对皮肤感染和胶原酶活性进行了评估。结果表明,富含无色素分离物湖北Halomonas utahensis COIN160的生皮对胶原纤维的损伤与Halorrubrum相似,它们共同被认为是主要原因之一。在碱性芽孢杆菌分离株中也鉴定出推定降解抑制剂。得出的结论是,皮革污染是由一些特定微生物的克隆爆发引起的,这些微生物可能是非色素胶原降解物。不动杆菌和碱性芽孢杆菌是生腌生皮和腌制良好的腌生皮的核心微生物组成员,被认为是需要进一步分析的生皮污染物抑制剂。
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引用次数: 0
Identification, classification, and functional characterization of novel sponge-associated acidimicrobiial species 新型海绵相关酸性微生物的鉴定、分类和功能表征
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2023-07-01 DOI: 10.1016/j.syapm.2023.126426
Viet Hung Nguyen , Bernd Wemheuer , Weizhi Song , Holly Bennett , Nicole Webster , Torsten Thomas

Sponges are known to harbour an exceptional diversity of uncultured microorganisms, including members of the phylum Actinobacteriota. While members of the actinobacteriotal class Actinomycetia have been studied intensively due to their potential for secondary metabolite production, the sister class of Acidimicrobiia is often more abundant in sponges. However, the taxonomy, functions, and ecological roles of sponge-associated Acidimicrobiia are largely unknown. Here, we reconstructed and characterized 22 metagenome-assembled genomes (MAGs) of Acidimicrobiia from three sponge species. These MAGs represented six novel species, belonging to five genera, four families, and two orders, which are all uncharacterized (except the order Acidimicrobiales) and for which we propose nomenclature. These six uncultured species have either only been found in sponges and/or corals and have varying degrees of specificity to their host species. Functional gene profiling indicated that these six species shared a similar potential to non-symbiotic Acidimicrobiia with respect to amino acid biosynthesis and utilization of sulfur compounds. However, sponge-associated Acidimicrobiia differed from their non-symbiotic counterparts by relying predominantly on organic rather than inorganic sources of energy, and their predicted capacity to synthesise bioactive compounds or their precursors implicated in host defence. Additionally, the species possess the genetic capacity to degrade aromatic compounds that are frequently found in sponges. The novel Acidimicrobiia may also potentially mediate host development by modulating Hedgehog signalling and by the production of serotonin, which can affect host body contractions and digestion. These results highlight unique genomic and metabolic features of six new acidimicrobiial species that potentially support a sponge-associated lifestyle.

众所周知,海绵中含有异常多样的未培养微生物,包括放线菌门的成员。虽然放线菌类放线菌的成员由于其产生次级代谢产物的潜力而受到了深入研究,但酸性微生物菌的姐妹类通常在海绵中更为丰富。然而,与海绵相关的酸性微生物的分类、功能和生态作用在很大程度上是未知的。在这里,我们从三种海绵物种中重建并表征了酸性微生物的22个宏基因组组装基因组(MAG)。这些MAG代表了六个新物种,属于五个属、四个科和两个目,它们都没有特征(酸性微生物目除外),我们提出了命名法。这六种未培养的物种要么只在海绵和/或珊瑚中发现,对宿主物种具有不同程度的特异性。功能基因图谱表明,这六个物种在氨基酸生物合成和硫化合物利用方面与非共生酸性微生物具有相似的潜力。然而,海绵相关的酸性微生物与非共生微生物的不同之处在于,它们主要依赖有机而非无机能源,以及它们合成生物活性化合物或与宿主防御有关的前体的预测能力。此外,该物种具有降解海绵中常见的芳香化合物的遗传能力。新型酸性微生物也可能通过调节Hedgehog信号传导和血清素的产生来介导宿主的发育,血清素可以影响宿主的收缩和消化。这些结果突出了六种新的酸性微生物物种的独特基因组和代谢特征,这些物种可能支持海绵相关的生活方式。
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引用次数: 0
Fontisphaera persica gen. nov., sp. nov., a thermophilic hydrolytic bacterium from a hot spring of Baikal lake region, and proposal of Fontisphaeraceae fam. nov., and Limisphaeraceae fam. nov. within the Limisphaerales ord. nov. (Verrucomicrobiota) 来自贝加尔湖地区温泉的嗜热水解细菌Fontisphaera persica gen.nov.,sp.nov.和Fontisphaeraceae fam的提议。nov.和Limisphaeraceae家族。11月,在Limisphaerales ord.nov.(Verrucomicrobiota)内。
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2023-07-01 DOI: 10.1016/j.syapm.2023.126438
Olga A. Podosokorskaya , Alexander G. Elcheninov , Andrei A. Novikov , Alexander Y. Merkel , Ilya V. Kublanov

A novel facultatively anaerobic moderately thermophilic bacterium, strain B-154 T, was isolated from a terrestrial hot spring in the Baikal lake region (Russian Federation). Gram-negative, motile, spherical cells were present singly, in pairs, or aggregates, and reproduced by binary fission. The strain grew at 30–57 °C and within a pH range of 5.1–8.4 with the optimum at 50 °C and pH 6.8–7.1. Strain B-154 T was a chemoorganoheterotroph, growing on mono-, di- and polysaccharides (xylan, starch, galactan, galactomannan, glucomannan, xyloglucan, pullulan, arabinan, lichenan, beta-glucan, pachyman, locust bean gum, xanthan gum). It did not require sodium chloride or yeast extract for growth. Major cellular fatty acids were anteiso-C15:0, iso-C16:0 and iso-C14:0. The respiratory quinone was MK-7. The complete genome of strain B-154 T was 4.73 Mbp in size; its G + C content was 61%. According to the phylogenomic analysis strain B-154 T forms a separate family-level phylogenetic lineage. Moreover, together with Limisphaera ngatamarikiensis and “Pedosphaera parvula” this strain forms a separate order-level phylogenetic lineage within Verrucomicrobiae class. Hence, we propose a novel order, Limisphaerales ord. nov., with two families Limisphaeraceae fam. nov. and Fontisphaeraceae fam. nov., and a novel genus and species Fontisphaera persica gen. nov., sp. nov. with type strain B-154 T. Ecogenomic analysis showed that representatives of the Limisphaerales are widespread in various environments. Although some of them were detected in hot springs the majority of Limisphaerales (54% of the studied metagenome-assembled genomes) were found in marine habitats. This study allowed a better understanding of physiology and ecology of Verrucomicrobiota – a rather understudied bacterial phylum.

从贝加尔湖地区(俄罗斯联邦)的一个陆地温泉中分离到一种新的兼性厌氧中度嗜热细菌菌株B-154T。革兰氏阴性、可移动的球形细胞单独、成对或聚集存在,并通过二元分裂繁殖。菌株在30–57°C和5.1–8.4的pH范围内生长,最适温度为50°C,pH为6.8–7.1。菌株B-154T是一种化学有机异养菌,生长在单糖、二糖和多糖(木聚糖、淀粉、半乳聚糖、半乳甘露聚糖、葡甘聚糖、木葡聚糖、普鲁兰糖、阿拉伯糖、地衣、β-葡聚糖、厚皮豆、蝗灾豆胶、黄原胶)上。它的生长不需要氯化钠或酵母提取物。主要的细胞脂肪酸为antiso-C15:0、iso-C16:0和iso-C14:0。呼吸醌为MK-7。菌株B-154T的全基因组大小为4.73Mbp;其G+C含量为61%。根据系统发育分析,菌株B-154T形成了一个单独的家族级系统发育谱系。此外,该菌株与绿脓杆菌(Limisphaera ngatamarikinsis)和“Pedosphaera parvula”一起,在疣菌纲中形成了一个单独的目级系统发育谱系。因此,我们提出了一个新的目,Limisphaerales ord.nov.,包含两个科Limisphaaraceae fam。nov.和Fontisphaeraceae家族。nov.,和模式菌株B-154T。生态基因组分析表明,褐藻的代表性分布于各种环境中。尽管其中一些是在温泉中检测到的,但大多数Limisphaerales(所研究的宏基因组组装基因组的54%)是在海洋栖息地发现的。这项研究使我们能够更好地了解疣菌门的生理学和生态学,疣菌门是一个研究不足的细菌门。
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引用次数: 1
Two novel species isolated from wheat rhizospheres in Serbia: Pseudomonas serbica sp. nov. and Pseudomonas serboccidentalis sp. nov. 从塞尔维亚小麦根际分离的两个新种:塞尔维亚假单胞菌和偶然血清假单胞菌。
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2023-07-01 DOI: 10.1016/j.syapm.2023.126425
Irena Todorović , Danis Abrouk , Martina Kyselková , Céline Lavire , Marjolaine Rey , Vera Raičević , Jelena Jovičić-Petrović , Yvan Moënne-Loccoz , Daniel Muller

Pseudomonas strains IT-194P, IT-215P, IT-P366T and IT-P374T were isolated from the rhizospheres of wheat grown in soils sampled from different fields (some of them known to be disease-suppressive) located near Mionica, Serbia. Phylogenetic analysis of the 16S rRNA genes and of whole genome sequences showed that these strains belong to two potentially new species, one containing strains IT-P366T and IT-194P and clustering (whole genome analysis) next to P. umsongensis DSM16611T, and another species containing strains IT-P374T and IT-215P and clustering next to P. koreensis LMG21318T. Genome analysis confirmed the proposition of novel species, as ANI was below the threshold of 95% and dDDH below 70% for strains IT-P366T (compared with P. umsongensis DSM16611T) and IT-P374T (compared with P. koreensis LMG21318T). Unlike P. umsongensis DSM16611T, strains of P. serbica can grow on D-mannitol, but not on pectin, D-galacturonic acid, L-galactonic acid lactone and α-hydroxybutyric acid. In contrary to P. koreensis LMG21318T, strains of P. serboccidentalis can use sucrose, inosine and α-ketoglutaric acid (but not L-histidine) as carbon sources. Altogether, these results indicate the existence of two novel species for which we propose the names Pseudomonas serbica sp. nov., with the type strain IT-P366T (=CFBP 9060 T = LMG 32732 T = EML 1791 T) and Pseudomonas serboccidentalis sp. nov., with the type strain IT-P374T (=CFBP 9061 T = LMG 32734 T = EML 1792 T). Strains from this study presented a set of phytobeneficial functions modulating plant hormonal balance, plant nutrition and plant protection, suggesting a potential as Plant Growth-Promoting Rhizobacteria (PGPR).

假单胞菌菌株IT-194P、IT-215P、IT-P366T和IT-P374T是从塞尔维亚Mionica附近不同农田(其中一些已知是抗病的)土壤中生长的小麦根际分离出来的。16S rRNA基因和全基因组序列的系统发育分析表明,这些菌株属于两个潜在的新种,一个包含菌株IT-P366T和IT-194P,全基因组分析结果与umsongensis DSM16611T聚类,另一个包含菌株IT-P374T和IT-215P,聚类与韩国ensis LMG21318T聚类。基因组分析证实了新物种的主张,菌株IT-P366T(与P. umsongensis DSM16611T相比)和IT-P374T(与P. koreensis LMG21318T相比)的ANI低于95%阈值,dDDH低于70%。与非sonsongensis DSM16611T不同,serbica菌株可以在d -甘露醇上生长,但不能在果胶、d -半乳糖醛酸、l -半乳糖醛酸内酯和α-羟基丁酸上生长。与韩国假单胞菌LMG21318T相反,血清巧合假单胞菌可以利用蔗糖、肌苷和α-酮戊二酸(而不是l -组氨酸)作为碳源。综上所述,本文提出了两种新菌种的存在,分别为类型菌株IT-P366T (=CFBP 9060 T = LMG 32732 T = EML 1791 T)和类型菌株IT-P374T (=CFBP 9061 T = LMG 32734 T = EML 1792 T)。该菌株具有调节植物激素平衡、植物营养和植物保护的一系列有益植物功能。提示其为植物促生长根瘤菌(Plant Growth-Promoting Rhizobacteria, PGPR)
{"title":"Two novel species isolated from wheat rhizospheres in Serbia: Pseudomonas serbica sp. nov. and Pseudomonas serboccidentalis sp. nov.","authors":"Irena Todorović ,&nbsp;Danis Abrouk ,&nbsp;Martina Kyselková ,&nbsp;Céline Lavire ,&nbsp;Marjolaine Rey ,&nbsp;Vera Raičević ,&nbsp;Jelena Jovičić-Petrović ,&nbsp;Yvan Moënne-Loccoz ,&nbsp;Daniel Muller","doi":"10.1016/j.syapm.2023.126425","DOIUrl":"10.1016/j.syapm.2023.126425","url":null,"abstract":"<div><p><em>Pseudomonas</em> strains IT-194P, IT-215P, IT-P366<sup>T</sup> and IT-P374<sup>T</sup> were isolated from the rhizospheres of wheat grown in soils sampled from different fields (some of them known to be disease-suppressive) located near Mionica, Serbia. Phylogenetic analysis of the 16S rRNA genes and of whole genome sequences showed that these strains belong to two potentially new species, one containing strains IT-P366<sup>T</sup> and IT-194P and clustering (whole genome analysis) next to <em>P. umsongensis</em> DSM16611<sup>T</sup>, and another species containing strains IT-P374<sup>T</sup> and IT-215P and clustering next to <em>P. koreensis</em> LMG21318<sup>T</sup>. Genome analysis confirmed the proposition of novel species, as ANI was below the threshold of 95% and dDDH below 70% for strains IT-P366<sup>T</sup> (compared with <em>P. umsongensis</em> DSM16611<sup>T</sup>) and IT-P374<sup>T</sup> (compared with <em>P. koreensis</em> LMG21318<sup>T</sup>). Unlike <em>P. umsongensis</em> DSM16611<sup>T</sup>, strains of <em>P. serbica</em> can grow on D-mannitol, but not on pectin, D-galacturonic acid, L-galactonic acid lactone and α-hydroxybutyric acid. In contrary to <em>P. koreensis</em> LMG21318<sup>T</sup>, strains of <em>P. serboccidentalis</em> can use sucrose, inosine and α-ketoglutaric acid (but not L-histidine) as carbon sources. Altogether, these results indicate the existence of two novel species for which we propose the names <em>Pseudomonas serbica</em> sp. nov., with the type strain IT-P366<sup>T</sup> (=CFBP 9060 <sup>T</sup> = LMG 32732 <sup>T</sup> = EML 1791 <sup>T</sup>) and <em>Pseudomonas serboccidentalis</em> sp. nov., with the type strain IT-P374<sup>T</sup> (=CFBP 9061 <sup>T</sup> = LMG 32734 <sup>T</sup> = EML 1792 <sup>T</sup>). Strains from this study presented a set of phytobeneficial functions modulating plant hormonal balance, plant nutrition and plant protection, suggesting a potential as Plant Growth-Promoting Rhizobacteria (PGPR).</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 4","pages":"Article 126425"},"PeriodicalIF":3.4,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9848542","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: 1
Description of Dellaglioa carnosa sp. nov., a novel species isolated from high-oxygen modified-atmosphere packaged meat 从高氧修饰气氛包装肉类中分离的一种新种——肉糜Dellaglioa carnosa sp. nov.
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2023-07-01 DOI: 10.1016/j.syapm.2023.126423
Victoria Werum, Matthias Ehrmann

The study provides a taxonomic characterization of three bacterial strains isolated from high-oxygen modified-atmosphere packaged beef from Germany. The strains of the novel species shared identical 16S rRNA gene sequence to the closely related type strain of Dellaglioa algida. However, the in-silico DNA-DNA hybridization (DDH) values indicate that they belong to a different genomic species. The in silico DDH estimate value between TMW 2.2523T and the type strain of Dellaglioa algida DSM 15638T was only 63.2 %. The whole genome average nucleotide identity blast (ANIb) value of 95.1 % between TMW 2.2523T and the closely related type strain of D. algida was within the recommended threshold value of 95–96 % for bacterial species delineation. Additionally, the phylogenomic analyses based on multi locus sequence alignment (MLSA) showed that strain TMW 2.2523T and additional strains TMW 2.2444 and TMW 2.2533 formed a monophyletic group separate from D. algida strains. Furthermore, tyrosine decarboxylase activity could be attributed to strains of the new proposed species. The results of this polyphasic approach support the affiliation of these strains to a novel species within the genus Dellaglioa for which we propose the name Dellaglioa carnosa sp. nov. The designated respective type strain is TMW 2.2523T (DSM 114968T = LMG 32819T).

该研究提供了从德国高氧修饰气氛包装牛肉中分离的三株细菌的分类特征。该新种菌株的16S rRNA基因序列与近缘海藻藻型菌株相同。然而,计算机DNA-DNA杂交(DDH)值表明它们属于不同的基因组物种。TMW 2.2523T与褐藻型菌株DSM 15638T之间的计算机DDH估计值仅为63.2%。TMW 2.2523T与近缘型菌株之间的全基因组平均核苷酸鉴定blast (ANIb)值为95.1%,在95 - 96%的推荐阈值范围内。此外,基于多位点序列比对(MLSA)的系统发育分析表明,菌株TMW 2.2523T与附加菌株TMW 2.2444和TMW 2.2533组成了一个与藻芽胞杆菌菌株分离的单系群。此外,酪氨酸脱羧酶活性可能归因于新提出的物种菌株。这种多相方法的结果支持这些菌株属于Dellaglioa属中的一个新种,我们建议将其命名为Dellaglioa carnosa sp. 11 .指定的各自类型菌株为TMW 2.2523T (DSM 114968T = LMG 32819T)。
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引用次数: 2
Genetic diversity, symbiotic efficiency, stress tolerance, and plant growth promotion traits of rhizobia nodulating Vachellia tortilis subsp. raddiana growing in dryland soils in southern Morocco 玉米扁豆根瘤菌的遗传多样性、共生效率、抗逆性及促生性状。生长在摩洛哥南部旱地土壤中的一种植物
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2023-07-01 DOI: 10.1016/j.syapm.2023.126434
Mohamed Hnini, Imane El Attar, Kaoutar Taha, Jamal Aurag

In the present study, we analyzed the genetic diversity, phylogenetic relationships, stress tolerance, phytobeneficial traits, and symbiotic characteristics of rhizobial strains isolated from root nodules of Vachellia tortilis subsp. raddiana grown in soils collected in the extreme Southwest of the Anti-Atlas Mountains in Morocco. Subsequent to Rep-PCR fingerprinting, 16S rDNA gene sequencing of 15 representative strains showed that all of them belong to the genus Ensifer. Phylogenetic analysis and concatenation of the housekeeping genes gyrB, rpoB, recA, and dnaK revealed that the entire collection (except strain LMR678) shared 99.08 % to 99.92% similarity with Ensifer sp. USDA 257 and 96.92% to 98.79% with Sinorhizobium BJ1. Phylogenetic analysis of nodC and nodA sequences showed that all strains but one (LMR678) formed a phylogenetic group with the type strain “E. aridi” LMR001T (similarity over 98%). Moreover, it was relevant that most strains belong to the symbiovar vachelliae. In vitro tests revealed that five strains produced IAA, four solubilized inorganic phosphate, and one produced siderophores. All strains showed tolerance to NaCl concentrations ranging from 2 to 12% and grew at up to 10% of PEG6000. A greenhouse plant inoculation test conducted during five months demonstrated that most rhizobial strains were infective and efficient. Strains LMR688, LMR692, and LMR687 exhibited high relative symbiotic efficiency values (respectively 231.6 %, 171.96 %, and 140.84 %). These strains could be considered as the most suitable candidates for inoculation of V. t. subsp. raddiana, to be used as a pioneer plant for restoring arid soils threatened with desertification.

本研究分析了玉米Vachellia tortilis subsp根瘤菌的遗传多样性、系统发育关系、胁迫耐受性、植物有益性状和共生特性。raddiana生长在摩洛哥反阿特拉斯山脉最西南端收集的土壤中。经Rep-PCR指纹图谱分析,15株代表性菌株的16S rDNA基因测序结果均为Ensifer属。对gyrB、rpoB、recA和dnaK的系统发育分析和序列分析表明,除菌株LMR678外,所有菌株与Ensifer sp. USDA 257的相似性为99.08% ~ 99.92%,与Sinorhizobium BJ1的相似性为96.92% ~ 98.79%。对nodC和nodA序列的系统发育分析表明,除1株LMR678外,其余菌株均与E型菌株形成系统发育群。aridi“LMR001T”(相似度超过98%)。此外,大多数菌株属于共生菌vachelliae是相关的。体外实验表明,5株菌株产生IAA, 4株产生可溶性无机磷酸盐,1株产生铁载体。所有菌株对NaCl浓度在2 ~ 12%范围内均表现出耐受性,在PEG6000浓度高达10%的条件下生长。在5个月内进行的温室植物接种试验表明,大多数根瘤菌菌株具有传染性和有效性。菌株LMR688、LMR692和LMR687表现出较高的相对共生效率值(分别为231.6%、171.96%和140.84%)。这些菌株可以被认为是接种弧菌亚种的最合适的候选菌株。作为恢复受沙漠化威胁的干旱土壤的先锋植物。
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引用次数: 1
Novel symbiovars ingae, lysilomae and lysilomaefficiens in bradyrhizobia from tree-legume nodules 豆科植物根瘤慢根瘤菌中的新共生菌ingae、lysilomae和lysilomaefficiens。
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2023-07-01 DOI: 10.1016/j.syapm.2023.126433
Diana Hernández-Oaxaca, Karen Claro, Marco A. Rogel, Mónica Rosenblueth, Julio Martinez-Romero, Esperanza Martinez-Romero

Inga vera and Lysiloma tree legumes form nodules with Bradyrhizobium spp. from the japonicum group that represent novel genomospecies, for which we describe here using genome data, symbiovars lysilomae, lysilomaefficiens and ingae. Genes encoding Type three secretion system (TTSS) that could affect host specificity were found in ingae but not in lysilomae nor in lysilomaefficiens symbiovars and uptake hydrogenase hup genes (that affect nitrogen fixation) were observed in bradyrhizobia from the symbiovars ingae and lysilomaefficiens. nolA gene was found in the symbiovar lysilomaefficiens but not in strains from lysilomae. We discuss that multiple genes may dictate symbiosis specificity. Besides, toxin-antitoxin genes were found in the symbiosis islands in bradyrhizobia from symbiovars ingae and lysilomaefficiens. A limit (95%) to define symbiovars with nifH gene sequences was proposed here.

Inga vera和Lysiloma树豆类与Bradyrhizobium spp.形成结节。来自日本科,代表了新的基因组物种,我们在这里使用基因组数据描述了这些物种,共生菌lysilomae、lysilomaefficiens和ingae。在ingae中发现了编码三型分泌系统(TTSS)的基因,这些基因可以影响宿主的特异性,但在溶胞菌和溶胞菌共生体中都没有发现,在来自共生体ingae和溶胞杆菌的慢根瘤菌中观察到了摄取氢酶hup基因(影响固氮)。nolA基因在溶胞菌中发现,但在溶胞杆菌菌株中未发现。我们讨论了多个基因可能决定共生特异性。此外,在慢根瘤菌的共生岛中还发现了毒素-抗毒素基因。本文提出了用nifH基因序列定义共生体变体的限度(95%)。
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引用次数: 0
Pseudomonas petrae sp. nov. isolated from regolith samples in Antarctica 从南极洲风土样品中分离的假单胞菌
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2023-07-01 DOI: 10.1016/j.syapm.2023.126424
Dana Nováková , Vendula Koublová , Karel Sedlář , Eva Staňková , Stanislava Králová , Pavel Švec , Meina Neumann-Schaal , Jacqueline Wolf , Sylva Koudelková , Miloš Barták , Ivo Sedláček

A polyphasic taxonomic approach was used to characterize the four strains P2653T, P2652, P2498, and P2647, isolated from Antarctic regolith samples. Initial genotype screening performed by PCR fingerprinting based on repetitive sequences showed that the isolates studied formed a coherent cluster separated from the other Pseudomonas species. Identification results based on 16S rRNA gene sequences showed the highest sequence similarity with Pseudomonas graminis (99.7%), which was confirmed by multilocus sequence analysis using the rpoB, rpoD, and gyrB genes. Genome sequence comparison of P2653T with the most related P. graminis type strain DSM 11363T revealed an average nucleotide identity of 92.1% and a digital DNA-DNA hybridization value of 46.6%. The major fatty acids for all Antarctic strains were C16:0, Summed Feature 3 (C16:1 ω7c/C16:1 ω6c) and Summed Feature 8 (C18:1 ω7c/C18:1 ω6c). The predominant respiratory quinone was Q-9, and the major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, and phosphatidylglycerol. The regolith strains could be differentiated from related species by the absence of arginine dihydrolase, ornithine and lysine decarboxylase and by negative tyrosine hydrolysis. The results of this polyphasic study allowed the genotypic and phenotypic differentiation of four analysed strains from the closest related species, which confirmed that the strains represent a novel species within the genus Pseudomonas, for which the name Pseudomonas petrae sp. nov. is proposed with P2653T (CCM 8850T = DSM 112068T = LMG 30619T) as the type strain.

采用多相分类学方法对分离自南极风化层样品的4株菌株P2653T、P2652、P2498和P2647进行了鉴定。基于重复序列的PCR指纹图谱初步基因型筛选表明,所研究的分离株与其他假单胞菌属形成了一个连贯的簇。基于16S rRNA基因序列的鉴定结果显示,与graminis假单胞菌的序列相似性最高(99.7%),通过rpoB、rpoD和gyrB基因的多位点序列分析证实了这一点。P2653T与最相关的禾草单胞菌型菌株DSM 11363T的基因组序列比较显示,平均核苷酸同源性为92.1%,数字DNA-DNA杂交值为46.6%。南极菌株的主要脂肪酸为C16:0、总特征3 (C16:1 ω7c/C16:1 ω6c)和总特征8 (C18:1 ω7c/C18:1 ω6c)。主要的呼吸醌为Q-9,主要的极性脂质为磷脂酰乙醇胺、二磷脂酰甘油和磷脂酰甘油。由于缺乏精氨酸二水解酶、鸟氨酸脱羧酶和赖氨酸脱羧酶,以及酪氨酸负水解,可以将其与近缘种区分开来。本多相研究的结果表明,4株菌株的基因型和表型与最近的亲缘种不同,证实了这4株菌株是假单胞菌属中的一个新种,并以P2653T (CCM 8850T = DSM 112068T = LMG 30619T)为型菌株命名为Pseudomonas pee sp. 11。
{"title":"Pseudomonas petrae sp. nov. isolated from regolith samples in Antarctica","authors":"Dana Nováková ,&nbsp;Vendula Koublová ,&nbsp;Karel Sedlář ,&nbsp;Eva Staňková ,&nbsp;Stanislava Králová ,&nbsp;Pavel Švec ,&nbsp;Meina Neumann-Schaal ,&nbsp;Jacqueline Wolf ,&nbsp;Sylva Koudelková ,&nbsp;Miloš Barták ,&nbsp;Ivo Sedláček","doi":"10.1016/j.syapm.2023.126424","DOIUrl":"10.1016/j.syapm.2023.126424","url":null,"abstract":"<div><p>A polyphasic taxonomic approach was used to characterize the four strains P2653<sup>T</sup><span>, P2652, P2498, and P2647, isolated from Antarctic regolith<span> samples. Initial genotype screening performed by PCR fingerprinting based on repetitive sequences showed that the isolates studied formed a coherent cluster separated from the other </span></span><span><em>Pseudomonas</em></span> species. Identification results based on 16S rRNA gene sequences showed the highest sequence similarity with <em>Pseudomonas graminis</em><span> (99.7%), which was confirmed by multilocus sequence analysis using the </span><em>rpo</em>B, <em>rpo</em>D, and <em>gyr</em>B genes. Genome sequence comparison of P2653<sup>T</sup> with the most related <em>P. graminis</em> type strain DSM 11363<sup>T</sup> revealed an average nucleotide identity of 92.1% and a digital DNA-DNA hybridization value of 46.6%. The major fatty acids for all Antarctic strains were C<sub>16:0</sub>, Summed Feature 3 (C<sub>16:1</sub> <em>ω7c</em>/C<sub>16:1</sub> <em>ω6c</em>) and Summed Feature 8 (C<sub>18:1</sub> <em>ω7c</em>/C<sub>18:1</sub> <em>ω6c</em><span><span>). The predominant respiratory quinone<span><span> was Q-9, and the major polar lipids were </span>phosphatidylethanolamine, diphosphatidylglycerol, and </span></span>phosphatidylglycerol<span>. The regolith strains could be differentiated from related species by the absence of arginine dihydrolase, ornithine and lysine decarboxylase<span> and by negative tyrosine<span> hydrolysis. The results of this polyphasic study allowed the genotypic and phenotypic differentiation of four analysed strains from the closest related species, which confirmed that the strains represent a novel species within the genus </span></span></span></span><em>Pseudomonas</em>, for which the name <em>Pseudomonas petrae</em> sp. nov. is proposed with P2653<sup>T</sup> (CCM 8850<sup>T</sup> = DSM 112068<sup>T</sup> = LMG 30619<sup>T</sup>) as the type strain.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 4","pages":"Article 126424"},"PeriodicalIF":3.4,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9792160","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
How diverse a genus can be: An integrated multi-layered analysis into Desmonostoc (Nostocaceae, Cyanobacteriota) 一个属的多样性:对Desmonostoc (Nostocaceae, Cyanobacteriota)的综合多层分析
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2023-05-01 DOI: 10.1016/j.syapm.2023.126422
Allan Victor M. Almeida , Marcelo Gomes Marçal Vieira Vaz , Naira Valle de Castro , Diego Bonaldo Genuário , Jean Coutinho Oder , Pedro Augusto Marazzo de Souza , Sandy Bastos Martins , Mariana Machado , Adriano Nunes-Nesi , Wagner L. Araújo

Cyanobacteria (Phylum Cyanobacteriota) are Gram-negative bacteria capable of performing oxygenic photosynthesis. Although the taxonomic classification of cyanobacteria was for a long time based primarily on morphological characters, the application of other techniques (e.g. molecular phylogeny), especially in recent decades, has contributed to a better resolution of cyanobacteria systematics, leading to a revision of the phylum. Although Desmonostoc occurs as a new genus/cluster and some species have been described recently, relatively few studies have been carried out to elucidate its diversity, which encompasses strains from different ecological origins, or examine the application of new characterization tools. In this context, the present study investigated the diversity within Desmonostoc, based on morphological, molecular, metabolic, and physiological characteristics. Although the usage of physiological parameters is unusual for a polyphasic approach, they were efficient in the characterization performed here. The phylogenetic analysis based on 16S rRNA gene sequences put all studied strains (25) into the D1 cluster and indicated the emergence of novel sub-clusters. It was also possible to observe that nifD and nifH exhibited different evolutionary histories within the Desmonostoc strains. Collectively, metabolic and physiological data, coupled with the morphometric data, were in general, in good agreement with the separation based on the phylogeny of the 16S rRNA gene. Furthermore, the study provided important information on the diversity of Desmonostoc strains collected from different Brazilian biomes by revealing that they were cosmopolitan strains, acclimatized to low luminous intensities, with a large metabolic diversity and great biotechnological potential.

蓝藻(Phylum Cyanobacteriota)是一种能够进行含氧光合作用的革兰氏阴性细菌。尽管蓝藻的分类学分类在很长一段时间内主要基于形态学特征,但其他技术(如分子系统发育)的应用,尤其是近几十年来,有助于更好地解决蓝藻系统学问题,从而对门进行了修订。尽管Desmonostoc是一个新的属/簇,最近也描述了一些物种,但很少有研究来阐明其多样性,包括来自不同生态起源的菌株,或检查新的表征工具的应用。在这种情况下,本研究基于形态、分子、代谢和生理特征研究了Desmonostoc的多样性。尽管生理参数的使用对于多相方法来说是不寻常的,但它们在这里进行的表征中是有效的。基于16S rRNA基因序列的系统发育分析将所有研究菌株(25)归入D1聚类,并表明出现了新的亚聚类。还可以观察到,nifD和nifH在Desmonostoc菌株中表现出不同的进化史。总的来说,代谢和生理数据,加上形态计量学数据,总体上与基于16S rRNA基因系统发育的分离非常一致。此外,该研究提供了关于从巴西不同生物群落中收集的Desmonostoc菌株多样性的重要信息,揭示了它们是世界性菌株,适应低发光强度,具有巨大的代谢多样性和巨大的生物技术潜力。
{"title":"How diverse a genus can be: An integrated multi-layered analysis into Desmonostoc (Nostocaceae, Cyanobacteriota)","authors":"Allan Victor M. Almeida ,&nbsp;Marcelo Gomes Marçal Vieira Vaz ,&nbsp;Naira Valle de Castro ,&nbsp;Diego Bonaldo Genuário ,&nbsp;Jean Coutinho Oder ,&nbsp;Pedro Augusto Marazzo de Souza ,&nbsp;Sandy Bastos Martins ,&nbsp;Mariana Machado ,&nbsp;Adriano Nunes-Nesi ,&nbsp;Wagner L. Araújo","doi":"10.1016/j.syapm.2023.126422","DOIUrl":"10.1016/j.syapm.2023.126422","url":null,"abstract":"<div><p>Cyanobacteria (Phylum <em>Cyanobacteriota</em>) are Gram-negative bacteria capable of performing oxygenic photosynthesis. Although the taxonomic classification of cyanobacteria was for a long time based primarily on morphological characters, the application of other techniques (e.g. molecular phylogeny), especially in recent decades, has contributed to a better resolution of cyanobacteria systematics, leading to a revision of the phylum. Although <em>Desmonostoc</em> occurs as a new genus/cluster and some species have been described recently, relatively few studies have been carried out to elucidate its diversity, which encompasses strains from different ecological origins, or examine the application of new characterization tools. In this context, the present study investigated the diversity within <em>Desmonostoc</em>, based on morphological, molecular, metabolic, and physiological characteristics. Although the usage of physiological parameters is unusual for a polyphasic approach, they were efficient in the characterization performed here. The phylogenetic analysis based on 16S rRNA gene sequences put all studied strains (25) into the D1 cluster and indicated the emergence of novel sub-clusters. It was also possible to observe that <em>nif</em>D and <em>nif</em>H exhibited different evolutionary histories within the <em>Desmonostoc</em> strains. Collectively, metabolic and physiological data, coupled with the morphometric data, were in general, in good agreement with the separation based on the phylogeny of the 16S rRNA gene. Furthermore, the study provided important information on the diversity of <em>Desmonostoc</em> strains collected from different Brazilian biomes by revealing that they were cosmopolitan strains, acclimatized to low luminous intensities, with a large metabolic diversity and great biotechnological potential.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 3","pages":"Article 126422"},"PeriodicalIF":3.4,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9521604","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: 1
Description of two cultivated and two uncultivated new Salinibacter species, one named following the rules of the bacteriological code: Salinibacter grassmerensis sp. nov.; and three named following the rules of the SeqCode: Salinibacter pepae sp. nov., Salinibacter abyssi sp. nov., and Salinibacter pampae sp. nov. 两个已培育和两个未培育的新Salinibacter物种的描述,其中一个按照细菌编码规则命名:Salinibactergrassmerensis sp.nov。;三个按照SeqCode规则命名:Salinibacter pepae sp.nov.、Salinibacter-abssi sp.nov..和Salinibacer pampae sp.nov。
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2023-05-01 DOI: 10.1016/j.syapm.2023.126416
Tomeu Viver , Roth E. Conrad , Marianna Lucio , Mourad Harir , Mercedes Urdiain , Juan F. Gago , Ana Suárez-Suárez , Esteban Bustos-Caparros , Rodrigo Sanchez-Martinez , Eva Mayol , Federico Fassetta , Jinfeng Pang , Ionuț Mădălin Gridan , Stephanus Venter , Fernando Santos , Bonnie Baxter , María E. Llames , Adorján Cristea , Horia L. Banciu , Brian P. Hedlund , Ramon Rossello-Mora

Current -omics methods allow the collection of a large amount of information that helps in describing the microbial diversity in nature. Here, and as a result of a culturomic approach that rendered the collection of thousands of isolates from 5 different hypersaline sites (in Spain, USA and New Zealand), we obtained 21 strains that represent two new Salinibacter species. For these species we propose the names Salinibacter pepae sp. nov. and Salinibacter grassmerensis sp. nov. (showing average nucleotide identity (ANI) values < 95.09% and 87.08% with Sal. ruber M31T, respectively). Metabolomics revealed species-specific discriminative profiles. Sal. ruber strains were distinguished by a higher percentage of polyunsaturated fatty acids and specific N-functionalized fatty acids; and Sal. altiplanensis was distinguished by an increased number of glycosylated molecules. Based on sequence characteristics and inferred phenotype of metagenome-assembled genomes (MAGs), we describe two new members of the genus Salinibacter. These species dominated in different sites and always coexisted with Sal. ruber and Sal. pepae. Based on the MAGs from three Argentinian lakes in the Pampa region of Argentina and the MAG of the Romanian lake Fără Fund, we describe the species Salinibacter pampae sp. nov. and Salinibacter abyssi sp. nov. respectively (showing ANI values 90.94% and 91.48% with Sal. ruber M31T, respectively). Sal. grassmerensis sp. nov. name was formed according to the rules of the International Code for Nomenclature of Prokaryotes (ICNP), and Sal. pepae, Sal. pampae sp. nov. and Sal. abyssi sp. nov. are proposed following the rules of the newly published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). This work constitutes an example on how classification under ICNP and SeqCode can coexist, and how the official naming a cultivated organism for which the deposit in public repositories is difficult finds an intermediate solution.

目前的组学方法可以收集大量的信息,帮助描述自然界中的微生物多样性。在这里,由于培养组学方法收集了来自5个不同高盐地点(西班牙、美国和新西兰)的数千个分离株,我们获得了21个菌株,代表了两个新的盐杆菌物种。对于这些物种,我们提出了名称Salinibacter pepae sp.nov.和Salinibactergrassmerensis sp.nov..(显示平均核苷酸同一性(ANI)值<;Sal分别为95.09%和87.08%。ruber M31T)。代谢组学揭示了物种特异性的鉴别特征。Sal。鲁伯菌株的特征是多不饱和脂肪酸和特定的N-官能化脂肪酸的百分比较高;和Sal。天顶星的糖基化分子数量增加是其特征。基于宏基因组组装基因组(MAGs)的序列特征和推断表型,我们描述了盐杆菌属的两个新成员。这些物种在不同的地点占主导地位,并且总是与萨尔共存。ruber和Sal。佩佩。基于来自阿根廷潘帕地区三个阿根廷湖泊的MAG和罗马尼亚FărăFund湖的MAG,我们分别描述了Salinibacter pampae sp.nov.和Salinibacert abyssi sp.nov..物种(Sal.ruber M31T的ANI值分别为90.94%和91.48%)。Sal。grassmerensis sp.nov.名称是根据国际原核生物命名规则(ICNP)和Sal。萨勒佩佩。pampae sp.nov.和Sal。根据最新出版的《序列数据描述原核生物命名规范》(SeqCode)的规则,提出了深渊藻(Abysi sp.nov.)。这项工作构成了一个例子,说明ICNP和SeqCode下的分类如何共存,以及官方如何为难以存放在公共存储库中的栽培生物命名找到中间解决方案。
{"title":"Description of two cultivated and two uncultivated new Salinibacter species, one named following the rules of the bacteriological code: Salinibacter grassmerensis sp. nov.; and three named following the rules of the SeqCode: Salinibacter pepae sp. nov., Salinibacter abyssi sp. nov., and Salinibacter pampae sp. nov.","authors":"Tomeu Viver ,&nbsp;Roth E. Conrad ,&nbsp;Marianna Lucio ,&nbsp;Mourad Harir ,&nbsp;Mercedes Urdiain ,&nbsp;Juan F. Gago ,&nbsp;Ana Suárez-Suárez ,&nbsp;Esteban Bustos-Caparros ,&nbsp;Rodrigo Sanchez-Martinez ,&nbsp;Eva Mayol ,&nbsp;Federico Fassetta ,&nbsp;Jinfeng Pang ,&nbsp;Ionuț Mădălin Gridan ,&nbsp;Stephanus Venter ,&nbsp;Fernando Santos ,&nbsp;Bonnie Baxter ,&nbsp;María E. Llames ,&nbsp;Adorján Cristea ,&nbsp;Horia L. Banciu ,&nbsp;Brian P. Hedlund ,&nbsp;Ramon Rossello-Mora","doi":"10.1016/j.syapm.2023.126416","DOIUrl":"10.1016/j.syapm.2023.126416","url":null,"abstract":"<div><p>Current -omics methods allow the collection of a large amount of information that helps in describing the microbial diversity in nature. Here, and as a result of a culturomic approach that rendered the collection of thousands of isolates from 5 different hypersaline sites (in Spain, USA and New Zealand), we obtained 21 strains that represent two new <em>Salinibacter</em> species. For these species we propose the names <em>Salinibacter pepae</em> sp. nov. and <em>Salinibacter grassmerensis</em> sp. nov. (showing average nucleotide identity (ANI) values &lt; 95.09% and 87.08% with <em>Sal. ruber</em> M31<sup>T</sup>, respectively). Metabolomics revealed species-specific discriminative profiles. <em>Sal. ruber</em> strains were distinguished by a higher percentage of polyunsaturated fatty acids and specific N-functionalized fatty acids; and <em>Sal. altiplanensis</em> was distinguished by an increased number of glycosylated molecules. Based on sequence characteristics and inferred phenotype of metagenome-assembled genomes (MAGs), we describe two new members of the genus <em>Salinibacter</em>. These species dominated in different sites and always coexisted with <em>Sal. ruber</em> and <em>Sal. pepae.</em> Based on the MAGs from three Argentinian lakes in the Pampa region of Argentina and the MAG of the Romanian lake Fără Fund, we describe the species <em>Salinibacter pampae</em> sp. nov. and <em>Salinibacter abyssi</em> sp. nov. respectively (showing ANI values 90.94% and 91.48% with <em>Sal. ruber</em> M31<sup>T</sup>, respectively). <em>Sal. grassmerensis</em> sp. nov. name was formed according to the rules of the International Code for Nomenclature of Prokaryotes (ICNP), and <em>Sal. pepae</em>, <em>Sal. pampae</em> sp. nov. and <em>Sal. abyssi</em> sp. nov. are proposed following the rules of the newly published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). This work constitutes an example on how classification under ICNP and SeqCode can coexist, and how the official naming a cultivated organism for which the deposit in public repositories is difficult finds an intermediate solution.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 3","pages":"Article 126416"},"PeriodicalIF":3.4,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9819205","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
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Systematic and applied microbiology
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