Systematic and applied microbiology最新文献

{"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}

{"title":"Phylogenomics reveals insights into the functional evolution of the genus Agrobacterium and enables the description of Agrobacterium divergens sp. nov","authors":"Henry D. Naranjo ,&nbsp;Liesbeth Lebbe ,&nbsp;Margo Cnockaert ,&nbsp;Florent Lassalle ,&nbsp;Chin Chin Too ,&nbsp;Anne Willems","doi":"10.1016/j.syapm.2023.126420","DOIUrl":"10.1016/j.syapm.2023.126420","url":null,"abstract":"<div><p>The genus <span><em>Agrobacterium</em></span> was initially described as mainly phytopathogenic strains. Nowadays, the genus includes phytopathogenic and non-phytopathogenic bacteria that are distinctive among the <span><em>Rhizobiaceae</em></span> family. Recently we have isolated two closely related strains, LMG 31531^T and LMG 31532, from soil and plant roots, respectively. Both strains differ from previously reported species based on the genomic and phenotypic data. <em>A. arsenijevicii</em> KFB 330^T and <em>A. fabacearum</em> LMG 31642^T showed the highest 16S rRNA similarity (98.9 %), followed by <em>A. nepotum</em> LMG 26435^T (98.7 %). A clear genomic feature that distinguishes LMG 31531^T and LMG 31532 from other <em>Agrobacterium</em><span> species is the absence of a linear chromid. Nevertheless, typical values of the core-proteome Average Amino Acid Identity (cpAAI &gt; 85 %) and 16S rRNA gene sequence similarity (&gt;96 %) when compared to other members of the genus confirm the position of these two strains as part of the </span><em>Agrobacterium</em> genus. They are therefore described as <em>Agrobacterium divergens</em> sp. nov. Besides, our comparative genomic study and survey for clade-specific markers resulted in the discovery of conserved proteins that provide insights into the functional evolution of this genus.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 3","pages":"Article 126420"},"PeriodicalIF":3.4,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9819693","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":"Stutzerimonas decontaminans sp. nov. isolated from marine polluted sediments","authors":"Magdalena Mulet ,&nbsp;Margarita Gomila ,&nbsp;Jorge Lalucat ,&nbsp;Rafael Bosch ,&nbsp;Ramon Rossello-Mora ,&nbsp;Elena García-Valdés","doi":"10.1016/j.syapm.2023.126400","DOIUrl":"10.1016/j.syapm.2023.126400","url":null,"abstract":"<div><p>Strains 19SMN4^T and ST27MN3 were isolated from marine sediments after enrichment with 2-methylnaphthalene and were classified as <em>Pseudomonas stutzeri</em> genomovar 4. Four other strains, BG 2, HT20, HT24, and A7, were isolated from sulphide-oxidizing bioreactors or activated sludge affiliated with the same clade in the 16S rRNA phylogenetic tree. <em>P. stutzeri</em> has been recently reclassified as a new genus, <em>Stutzerimonas,</em> and a preliminary analysis indicated that the strains in this study were distinct from any classified <em>Stutzerimonas</em> and are considered representatives of phylogenomic species 4 (pgs4). Strains 19SMN4^T and ST27MN3 were extensively characterized with phenotypic, chemotaxonomic, genomic and phylogenomic data. Strain 19SMN4^T had a well-characterized naphthalene degradative plasmid that has been compared with other plasmids, while in strain ST27MN3, the naphthalene degradative genes were detected in the chromosome sequence. Phylogenomic analysis of the core gene sequences showed that strains 19SMN4^T and ST27MN3 shared 3,995 genes and were closely related to members of the species “<em>Stutzerimonas songnenensis”</em> and <em>Stutzerimonas perfectomarina</em>, as well as to the <em>Stutzerimonas</em> phylogenomic species, pgs9, pgs16 and pgs24. The aggregate average nucleotide identity (ANI) indicated that strains 19SMN4^T and ST27MN3 belonged to the same genomic species, whereas the genomic indices with their closest-related type strains were below the accepted species threshold (95 %)<em>.</em> We therefore conclude that strains 19SMN4^T and ST27MN3 represent a novel species of <em>Stutzerimonas</em>, for which the name <em>Stutzerimonas decontaminans</em> is proposed; the type strain is 19SMN4^T (=CCUG44593^T = DSM6084^T = LMG18521^T).</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 2","pages":"Article 126400"},"PeriodicalIF":3.4,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9464363","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 and genomic characterization of Nocardioides bruguierae sp. nov., isolated from Bruguiera gymnorhiza","authors":"Xiaohui Chen ,&nbsp;Zhouqing Zheng ,&nbsp;Feina Li ,&nbsp;Xiao Ma ,&nbsp;Feng Chen ,&nbsp;Mingsheng Chen ,&nbsp;Li Tuo","doi":"10.1016/j.syapm.2022.126391","DOIUrl":"10.1016/j.syapm.2022.126391","url":null,"abstract":"<div><p>Strains BSK12Z-3^T<span><span> and BSK12Z-4, two Gram-stain-positive, aerobic, non-spore-forming strains, were isolated from Shankou Mangrove Nature Reserve, Guangxi Zhuang Autonomous Region, China. The diagnostic diamino acid in the cell-wall </span>peptidoglycan of strain BSK12Z-3</span>^T was LL-diaminopimelic acid and MK-8(H₄<span><span><span>) was the predominant menaquinone. The polar </span>lipids comprised diphosphatidylglycerol (DPG), </span>phosphatidylglycerol<span> (PG) and phospholipid (PL). The major fatty acids was </span></span><em>iso</em>-C_16:0<span>. Phylogenetic analysis based on 16S rRNA gene sequences suggested that the two strains fell within the genus </span><span><em>Nocardioides</em></span>, appearing most closely related to <em>Nocardioides ginkgobilobae</em> KCTC 39594^T (97.5–97.6 % sequence similarity) and <em>Nocardioides marinus</em> DSM 18248^T (97.4–97.6 %). Genome-based phylogenetic analysis confirmed that strains BSK12Z-3^T and BSK12Z-4 formed a distinct phylogenetic cluster within the genus <em>Nocardioides</em>. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of strains BSK12Z-3^T, BSK12Z-4 with their most related species <em>N</em>. <em>marinus</em> DSM18248^T were within the ranges of 77.2–77.3 % and 21.3–21.4 %, respectively, clearly indicated that strains BSK12Z-3^T, BSK12Z-4 represented novel species. Strains BSK12Z-3^T<span><span> and BSK12Z-4 exhibited 99.9 % 16S rRNA gene sequence similarity. The ANI and dDDH values between the two strains were 97.8 % and 81.1 %, respectively, suggesting that they belong to the same species. However, DNA fingerprinting discriminated that they were not from one clonal origin. Based on </span>phylogenomic and phylogenetic analyses coupled with phenotypic and chemotaxonomic characterizatons, strains BSK12Z-3</span>^T and BSK12Z-4 could be classified as a novel species of the genus <em>Nocardioides</em>, for which the name <em>Nocardioides bruguierae</em> sp. nov., is proposed. The type strain is BSK12Z-3^T (=CGMCC 4.7709^T = JCM 34554^T).</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 2","pages":"Article 126391"},"PeriodicalIF":3.4,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9447962","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":"Methylomonas rapida sp. nov., a novel species of fast-growing, carotenoid-producing obligate methanotrophs with high biotechnological potential","authors":"Ekaterina N. Tikhonova ,&nbsp;Ruslan Z. Suleimanov ,&nbsp;Kirill K. Miroshnikov ,&nbsp;Igor Y. Oshkin ,&nbsp;Svetlana E. Belova ,&nbsp;Olga V. Danilova ,&nbsp;Aleksandr A. Ashikhmin ,&nbsp;Aleksey A. Konopkin ,&nbsp;Sergey Y. But ,&nbsp;Valentina N. Khmelenina ,&nbsp;Nikolai V. Pimenov ,&nbsp;Svetlana N. Dedysh","doi":"10.1016/j.syapm.2023.126398","DOIUrl":"10.1016/j.syapm.2023.126398","url":null,"abstract":"<div><p>The genus <span><em>Methylomonas</em></span><span> accommodates strictly aerobic, obligate methanotrophs, with their sole carbon and energy sources restricted to methane and methanol. These bacteria inhabit oxic-anoxic interfaces of various freshwater habitats and have attracted considerable attention as potential producers of a single-cell protein. Here, we characterize two fast-growing representatives of this genus, strains 12 and MP1</span>^T, which are phylogenetically distinct from the currently described <em>Methylomonas</em> species (94.0–97.3 % 16S rRNA gene sequence similarity). Strains 12 and MP1^T<span> were isolated from freshwater sediments<span><span><span> collected in Moscow and Krasnodar regions, respectively. Cells of these strains are Gram-negative, red-pigmented, highly motile thick rods that contain a type I intracytoplasmic membrane system and possess a particulate methane monooxygenase (pMMO) </span>enzyme. These bacteria grow between 8 and 45 °C (optimum 35 °C) in a relatively narrow pH range of 5.5–7.3 (optimum pH 6.6–7.2). Major </span>carotenoids synthesized by these methanotrophs are 4,4′-diaplycopene-4,4′-dioic acid, 1,1′-dihydroxy-3,4-didehydrolycopene and 4,4′-diaplycopenoic acid. High biomass yield, of up to 3.26 g CDW/l, is obtained during continuous cultivation of MP1</span></span>^T<span> on natural gas in a bioreactor at a dilution rate of 0.22 h</span>⁻¹. The complete genome sequence of strain MP1^T<span> is 4.59 Mb in size; the DNA G + C content is 52.8 mol%. The genome encodes four rRNA operons, one pMMO operon and 4,216 proteins. The genome sequence displays 82–85 % average nucleotide identity to those of earlier described </span><em>Methylomonas</em> species. We propose to classify these bacteria as representing a novel species of the genus <em>Methylomonas</em>, <em>M. rapida</em> sp. nov., with the type strain MP1^T (=KCTC 92586^T = VKM B-3663^T).</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 2","pages":"Article 126398"},"PeriodicalIF":3.4,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9094968","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":"Dominance of mixed ether/ester, intact polar membrane lipids in five species of the order Rubrobacterales: Another group of bacteria not obeying the “lipid divide”","authors":"Jaap S. Sinninghe Damsté ,&nbsp;W. Irene C. Rijpstra ,&nbsp;Katharina J. Huber ,&nbsp;Luciana Albuquerque ,&nbsp;Conceição Egas ,&nbsp;Nicole J. Bale","doi":"10.1016/j.syapm.2023.126404","DOIUrl":"10.1016/j.syapm.2023.126404","url":null,"abstract":"<div><p>The composition of the core lipids and intact polar lipids (IPLs) of five <em>Rubrobacter</em> species was examined. Methylated (ω-4) fatty acids (FAs) characterized the core lipids of <em>Rubrobacter radiotolerans</em>, <em>R. xylanophilus</em> and <em>R. bracarensis</em>. In contrast, <em>R. calidifluminis</em> and <em>R. naiadicus</em> lacked ω-4 methyl FAs but instead contained abundant (i.e., 34–41 % of the core lipids) ω-cyclohexyl FAs not reported before in the order <em>Rubrobacterales</em>. Their genomes contained an almost complete operon encoding proteins enabling production of cyclohexane carboxylic acid CoA thioester, which acts as a building block for ω-cyclohexyl FAs in other bacteria. Hence, the most plausible explanation for the biosynthesis of these cyclic FAs in <em>R. calidifluminis</em> and <em>R. naiadicus</em> is a recent acquisition of this operon. All strains contained 1-O-alkyl glycerol ether lipids in abundance (up to 46 % of the core lipids), in line with the dominance (&gt;90 %) of mixed ether/ester IPLs with a variety of polar headgroups. The IPL head group distribution of <em>R. calidifluminis</em> and <em>R. naiadicus</em> differed, e.g. they lacked a novel IPL tentatively assigned as phosphothreoninol. The genomes of all five <em>Rubrobacter</em> species contained a putative operon encoding the synthesis of the 1-O-alkyl glycerol phosphate, the presumed building block of mixed ether/ester IPLs, which shows some resemblance with an operon enabling ether lipid production in various other aerobic bacteria but requires more study. The uncommon dominance of mixed ether/ester IPLs in <em>Rubrobacter</em> species exemplifies our recent growing awareness that the lipid divide between archaea and bacteria/eukaryotes is not as clear cut as previously thought.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 2","pages":"Article 126404"},"PeriodicalIF":3.4,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9096451","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}