Systematic and applied microbiology最新文献

{"title":"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","authors":"Mohamed Hnini,&nbsp;Imane El Attar,&nbsp;Kaoutar Taha,&nbsp;Jamal Aurag","doi":"10.1016/j.syapm.2023.126434","DOIUrl":"10.1016/j.syapm.2023.126434","url":null,"abstract":"<div><p><span>In the present study, we analyzed the genetic diversity<span>, phylogenetic relationships<span>, stress tolerance, phytobeneficial traits, and symbiotic characteristics of rhizobial strains isolated from root nodules of </span></span></span><span><em>Vachellia</em><em> tortilis</em></span> subsp<em>. raddiana</em> grown in soils collected in the extreme Southwest of the Anti-Atlas Mountains in Morocco. Subsequent to Rep-PCR fingerprinting, <em>16S rDNA</em> gene sequencing of 15 representative strains showed that all of them belong to the genus <span><em>Ensifer</em></span><span>. Phylogenetic analysis and concatenation of the housekeeping genes </span><span><em>gyrB</em></span>, <em>rpoB</em>, <em>recA</em>, and <em>dnaK</em> revealed that the entire collection (except strain LMR678) shared 99.08 % to 99.92% similarity with <em>Ensifer</em> sp. USDA 257 and 96.92% to 98.79% with <span><em>Sinorhizobium</em></span> BJ1. Phylogenetic analysis of <em>nodC</em> and <em>nodA</em> sequences showed that all strains but one (LMR678) formed a phylogenetic group with the type strain “<em>E. aridi”</em> LMR001^T (similarity over 98%). Moreover, it was relevant that most strains belong to the symbiovar vachelliae. <em>In vitro</em><span> tests revealed that five strains produced IAA<span><span>, four solubilized inorganic phosphate, and one produced </span>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 </span></span><em>V. t.</em> subsp<em>. raddiana</em><span><span>, to be used as a pioneer plant for restoring arid soils threatened with </span>desertification.</span></p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 4","pages":"Article 126434"},"PeriodicalIF":3.4,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9784838","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":"Novel symbiovars ingae, lysilomae and lysilomaefficiens in bradyrhizobia from tree-legume nodules","authors":"Diana Hernández-Oaxaca,&nbsp;Karen Claro,&nbsp;Marco A. Rogel,&nbsp;Mónica Rosenblueth,&nbsp;Julio Martinez-Romero,&nbsp;Esperanza Martinez-Romero","doi":"10.1016/j.syapm.2023.126433","DOIUrl":"10.1016/j.syapm.2023.126433","url":null,"abstract":"<div><p><em>Inga vera</em> and <em>Lysiloma</em> tree legumes form nodules with <span><em>Bradyrhizobium</em></span><span><span><span> 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 </span>host specificity were found in ingae but not in lysilomae nor in lysilomaefficiens symbiovars and uptake </span>hydrogenase </span><em>hup</em> genes (that affect nitrogen fixation) were observed in bradyrhizobia from the symbiovars ingae and lysilomaefficiens. <span><em>nolA</em></span><span> 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 </span><em>nifH</em> gene sequences was proposed here.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 4","pages":"Article 126433"},"PeriodicalIF":3.4,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9796791","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":"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^T<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^T with the most related <em>P. graminis</em> type strain DSM 11363^T 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_16:0, Summed Feature 3 (C_16:1 <em>ω7c</em>/C_16:1 <em>ω6c</em>) and Summed Feature 8 (C_18:1 <em>ω7c</em>/C_18:1 <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^T (CCM 8850^T = DSM 112068^T = LMG 30619^T) 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}

{"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}

{"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^T, 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^T, 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}

{"title":"Magnetospirillum sulfuroxidans sp. nov., capable of sulfur-dependent lithoautotrophy and a taxonomic reevaluation of the order Rhodospirillales","authors":"Veronika V. Koziaeva ,&nbsp;Dimitry Y. Sorokin ,&nbsp;Tatiana V. Kolganova ,&nbsp;Denis S. Grouzdev","doi":"10.1016/j.syapm.2023.126406","DOIUrl":"10.1016/j.syapm.2023.126406","url":null,"abstract":"<div><p>A spiral-shaped, highly motile bacterium was isolated from freshwater sulfidic sediment. Strain J10^T<span> is a facultative autotroph<span> utilizing sulfide, thiosulfate, and sulfur as the electron donors in microoxic conditions. Despite high 16S rRNA gene sequence sequence identity to </span></span><span><em>Magnetospirillum</em><em> gryphiswaldense</em></span> MSR-1 ^T (99.6 %), digital DNA-DNA hybridisation homology and average nucleotide identity between the two strains was of the different species level (25 % and 83 %, respectively). Strain J10^T<span> is not magnetotactic. The DNA G + C content of strain J10</span>^T<span> is 61.9 %. The predominant phospholipid ester-linked fatty acids are C18:1ω7, C16:1ω7, and C16:0. Strain J10</span>^T (=DSM 23205 ^T = VKM B-3486 ^T) is the first strain of the genus <em>Magnetospirillum</em> showing lithoautotrophic growth and is proposed here as a novel species, <em>Magnetospirillum sulfuroxidans</em> sp. nov. In addition, we propose to establish a framework for distinguishing genera and families within the order <span><em>Rhodospirillales</em></span><span> based on phylogenomic<span> analysis using the threshold values for average amino acid identity at ̴ 72 % for genera and ̴ 60 % for families. According to this, we propose to divide the existing genus </span></span><em>Magnetospirillum</em> into three genera: <em>Magnetospirillum</em>, <em>Paramagnetospirillum</em>, and <em>Phaeospirillum</em>, constituting a separate family <em>Magnetospirillaceae</em> fam. nov. in the order <em>Rhodospirillales</em>. Furthermore, phylogenomic data suggest that this order should accomodate six more new family level groups including <em>Magnetospiraceae</em> fam. nov., <em>Magnetovibrionaceae</em> fam. nov., <em>Dongiaceae</em> fam. nov., <em>Niveispirillaceae</em> fam. nov., <em>Fodinicurvataceae</em> fam. nov., and <em>Oceanibaculaceae</em> fam. nov.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 3","pages":"Article 126406"},"PeriodicalIF":3.4,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9458481","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":"Ancylobacter mangrovi sp. nov., a novel endophytic bacterium isolated from mangrove plant","authors":"Fei-Na Li ,&nbsp;Zhou-Qing Zheng ,&nbsp;Ming-Sheng Chen ,&nbsp;Xiao-Hui Chen ,&nbsp;Li Tuo","doi":"10.1016/j.syapm.2023.126419","DOIUrl":"10.1016/j.syapm.2023.126419","url":null,"abstract":"<div><p>Two novel strains GSK1Z-4-2^T and MQZ15Z-1 were isolated from branches of mangrove plants collected from Guangxi Zhuang Autonomous Region, China. Both strains were Gram-negative, aerobic, non-flagellated and non-spore-forming bacteria. The comparison of 16S rRNA gene sequences initially indicated that the two strains were assigned to the genus <em>Ancylobacter</em> with sharing the highest similarity to <em>Ancylobacter pratisalsi</em> DSM 102029^T (97.3%). The 16S rRNA gene sequence similarity, average nucleotide identity (ANI) and <em>in silico</em> DNA-DNA hybridization (<em>is</em>DDH) values between strains GSK1Z-4-2^T<span><span> and MQZ15Z-1 were 99.9%, 97.4% and 77.4%, respectively, which revealed that the two strains belonged to the same species. Phylogenetic analyses based on 16S rRNA gene sequences and the core </span>proteome showed that the two strains formed a well-supported cluster with </span><em>A</em>. <em>pratisalsi</em> DSM 102029^T. Moreover, the ANI and <em>is</em>DDH values between strain GSK1Z-4-2^T and <em>A</em>. <em>pratisalsi</em> DSM 102029^T were 83.0% and 25.8%, respectively, demonstrating that strain GSK1Z-4-2^T was a previously undescribed species. Meanwhile, strains GSK1Z-4-2^T and MQZ15Z-1 exhibited most of chemotaxonomic and phenotypic features consistent with the description of the genus <em>Ancylobacter</em>. Based on the polyphasic data, strains GSK1Z-4-2^T and MQZ15Z-1 should represent a novel species of the genus <em>Ancylobacter</em>, for which the name <em>Ancylobacter mangrovi</em> sp. nov. is proposed. The type strain is GSK1Z-4-2^T (=MCCC 1K07181^T = JCM 34924^T).</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 3","pages":"Article 126419"},"PeriodicalIF":3.4,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9465949","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":"Govania unica gen. nov., sp. nov., a rare biosphere bacterium that represents a novel family in the class Alphaproteobacteria","authors":"Peter Vandamme ,&nbsp;Charlotte Peeters ,&nbsp;Amanda Hettiarachchi ,&nbsp;Margo Cnockaert ,&nbsp;Aurélien Carlier","doi":"10.1016/j.syapm.2023.126405","DOIUrl":"10.1016/j.syapm.2023.126405","url":null,"abstract":"<div><p>Strain LMG 31809 ^T<span><span><span> was isolated from a top soil sample of a temperate, mixed </span>deciduous forest in Belgium. Comparison of its 16S </span>rRNA gene sequence with that of type strains of bacteria with validly published names positioned it in the class </span><span><em>Alphaproteobacteria</em></span> and highlighted a major evolutionary divergence from its near neighbor species which represented species of the orders <em>Emcibacterales</em> and <span><em>Sphingomonadales</em></span><span>. 16S rRNA amplicon sequencing of the same soil sample revealed a highly diverse community in which </span><span><em>Acidobacteria</em></span> and <em>Alphaproteobacteria</em> predominated, but failed to yield amplicon sequence variants highly similar to that of strain LMG 31809 ^T<span>. There were no metagenome assembled genomes that corresponded to the same species and a comprehensive analysis of public 16S rRNA amplicon sequencing data sets demonstrated that strain LMG 31809 </span>^T<span> represents a rare biosphere bacterium that occurs at very low abundances in multiple soil and water-related ecosystems. The genome analysis suggested that this strain is a strictly aerobic heterotroph that is asaccharolytic and uses organic acids and possibly aromatic compounds as growth substrates. We propose to classify LMG 31809 </span>^T as a novel species within a novel genus, <em>Govania unica</em> gen. nov., sp. nov, within the novel family <em>Govaniaceae</em> of the class <em>Alphaproteobacteria.</em> Its type strain is LMG 31809 ^T (=CECT 30155 ^T). The whole-genome sequence of strain LMG 31809 ^T has a size of 3.21 Mbp. The G + C content is 58.99 mol%. The 16S rRNA gene and whole-genome sequences of strain LMG 31809 ^T are publicly available under accession numbers OQ161091 and JANWOI000000000, respectively.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 3","pages":"Article 126405"},"PeriodicalIF":3.4,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9465423","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":"Burkholderia semiarida sp. nov. and Burkholderia sola sp. nov., two novel B. cepacia complex species causing onion sour skin","authors":"Leandro S. Velez ,&nbsp;Flávia F. Aburjaile ,&nbsp;Antonio R.G. Farias ,&nbsp;Ana D.B. Baia ,&nbsp;Willams J. Oliveira ,&nbsp;Adriano M.F. Silva ,&nbsp;Ana M. Benko-Iseppon ,&nbsp;Vasco Azevedo ,&nbsp;Bertram Brenig ,&nbsp;Jong H. Ham ,&nbsp;Elineide B. Souza ,&nbsp;Marco A.S. Gama","doi":"10.1016/j.syapm.2023.126415","DOIUrl":"10.1016/j.syapm.2023.126415","url":null,"abstract":"<div><p>Two putative novel <span><em>Burkholderia</em><em> cenocepacia</em></span><span><span> lineages<span> found in the semi-arid region of north-east Brazil causing onion sour skin were studied using genomic approaches to determine their taxonomic position. Four strains belonging to one novel lineage (CCRMBC16, CCRMBC33, CCRMBC74, and CCRMBC171) and one strain (CCRMBC51) belonging to another novel lineage had their whole genome sequenced to carry out taxogenomic analyses. The </span></span>phylogenomic tree built using the type (strain) genome server (TYGS) clustered the strains CCRMBC16, CCRMBC33, CCRMBC74, and CCRMBC171 into the same clade, while grouped the strain CCRMBC51 separately. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) analysis showed values above 99.21 % and 93.2 %, respectively, among the strains CCRMBC16, CCRMBC33, CCRMBC74, and CCRMBC171, while ANI and dDDH values between these strains and the strain CCRMBC51 were below 94.49 % and 56.6 %, respectively. All these strains showed ANI and dDDH values below 94.78 % and 58.8 % concerning type strains of the </span><em>B. cepacia</em><span><span> complex (Bcc) species. The phylogenetic maximum likelihood tree constructed based on the </span>multilocus sequence analysis<span> of core genes (cMLSA) clustered the strains CCRMBC16, CCRMBC33, CCRMBC74, and CCRMBC171 and the strain CCRMBC51 in two exclusive clades, which did not cluster with any known species of the Bcc. Therefore, combined data from TYGS, ANI, dDDH, and cMLSA demonstrated that the strains represent two novel species of the Bcc, which we classified as </span></span><em>Burkholderia semiarida</em> sp. nov. and <em>Burkholderia sola</em> sp. nov., and proposed the strains CCRMBC74^T (=IBSBF 3371 ^T = CBAS 905 ^T) and CCRMBC51^T (=IBSBF3370^T = CBAS 904 ^T) as type strains, respectively.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 3","pages":"Article 126415"},"PeriodicalIF":3.4,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9458496","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":"Halonatronomonas betaini gen. nov., sp. nov., a haloalkaliphilic isolate from soda lake capable of betaine degradation and proposal of Halarsenatibacteraceae fam. nov. and Halothermotrichaceae fam. nov. within the order Halanaerobiales","authors":"Yulia V. Boltyanskaya ,&nbsp;Vadim V. Kevbrin ,&nbsp;Denis S. Grouzdev ,&nbsp;Ekaterina N. Detkova ,&nbsp;Veronika V. Koziaeva ,&nbsp;Andrey A. Novikov ,&nbsp;Tatjana N. Zhilina","doi":"10.1016/j.syapm.2023.126407","DOIUrl":"10.1016/j.syapm.2023.126407","url":null,"abstract":"<div><p><span><span>A search for the organisms responsible for anaerobic betaine degradation in soda lakes resulted in isolation of a novel </span>bacterial strain, designated Z-7014</span>^T. The cells were Gram-stain-negative, non-endospore-forming rods. Growth occurred at 8–52 °C (optimum 40–45 °C), pH 7.1–10.1 (optimum pH 8.1–8.8) and 1.0–3.5 M Na⁺<span> (optimum 1.8 M), i.e. it can be regarded as a haloalkaliphile. The strain utilized a limited range of substrates, mostly peptonaceous but not amino acids<span>, and was able to degrade betaine. Growth on betaine occurred only in the presence of peptonaceous substances which could not be replaced by vitamins. The G + C content of the genomic DNA of strain Z-7014</span></span>^T was 36.1 mol%. The major cellular fatty acids (&gt;5% of the total) were C_16:0 DMA, C_18: 0 DMA, C_16:1ω8, C_16:0, C_18:1 DMA, C_16:1 DMA, C_18:1ω9, and C_18:0<span>. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain Z-7014</span>^T<span> formed a distinct evolutionary lineage in the order </span><em>Halanaerobiales</em> with the highest similarity to <em>Halarsenitibacter silvermanii</em> SLAS-1^T (83.6%), <em>Halothermothrix orenii</em> H168^T (85.6%), and <em>Halocella cellulosilytica</em> DSM 7362^T (85.6%). AAI and POCP values between strain Z-7014^T and type strains of the order <em>Halanaerobiales</em><span> were 51.7–57.8%, and 33.8–58.3%, respectively. Based on polyphasic results including phylogenomic data, the novel strain could be distinguished from other genera, which suggests that strain Z-7014</span>^T<span> represents a novel species of a new genus, for which the name </span><em>Halonatronomonas betaini</em> gen. nov., sp. nov. is proposed. The type strain is Z-7014^T (=KCTC 25237^T = VKM B-3506^T). On the basis of phylogenomic data, it is also proposed to evolve two novel families <em>Halarsenitibacteraceae</em> fam. nov. and <em>Halothermotrichaceae</em> fam. nov. within the current order <em>Halanaerobiales</em>.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 3","pages":"Article 126407"},"PeriodicalIF":3.4,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9465430","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}