Systematic and applied microbiology最新文献

{"title":"Microbial community on industrial salty bovine hides: From the slaughterhouse to the salting","authors":"Francisco Nadal-Molero ,&nbsp;Alicia Campos-Lopez ,&nbsp;Juan Tur-Moya ,&nbsp;Ana-Belen Martin-Cuadrado","doi":"10.1016/j.syapm.2023.126421","DOIUrl":"10.1016/j.syapm.2023.126421","url":null,"abstract":"<div><p>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.</p><p>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 <em>Psychrobacter</em> and <em>Acinetobacter</em> 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 <em>Halomonas</em> OTU represented 57.66 % of the reads. Halobacteria, mainly <em>Halovenus, Halorubrum</em> and <em>Halovivax,</em> 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 <em>Halomonas utahensis</em> COIN160 damaged the collagen fibers similarly to <em>Halorubrum</em>, and together they were considered to be one of the major causes. Putative degrading inhibitors were also identified from among the <em>Alkalibacillus</em> isolates.</p><p>It was concluded that hide contaminations were driven by clonal outbreaks of a few specific microbes, which may have been non-pigmented collagen degraders. <em>Acinetobacter</em> and <em>Alkalibacillus</em>, members of the core microbiome of raw and well-cured salted hides, are suggested as hide contaminant inhibitors that need further analysis.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9850658","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":"Identification, classification, and functional characterization of novel sponge-associated acidimicrobiial species","authors":"Viet Hung Nguyen ,&nbsp;Bernd Wemheuer ,&nbsp;Weizhi Song ,&nbsp;Holly Bennett ,&nbsp;Nicole Webster ,&nbsp;Torsten Thomas","doi":"10.1016/j.syapm.2023.126426","DOIUrl":"10.1016/j.syapm.2023.126426","url":null,"abstract":"<div><p><span>Sponges are known to harbour an exceptional diversity of uncultured microorganisms, including members of the phylum </span><em>Actinobacteriota</em>. While members of the actinobacteriotal class <em>Actinomycetia</em><span> have been studied intensively due to their potential for secondary metabolite production, the sister class of </span><em>Acidimicrobiia</em> is often more abundant in sponges. However, the taxonomy, functions, and ecological roles of sponge-associated <em>Acidimicrobiia</em> are largely unknown. Here, we reconstructed and characterized 22 metagenome-assembled genomes (MAGs) of <em>Acidimicrobiia</em> 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 <em>Acidimicrobiales</em><span>) 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 </span><em>Acidimicrobiia</em><span><span> with respect to amino acid </span>biosynthesis<span> and utilization of sulfur compounds. However, sponge-associated </span></span><em>Acidimicrobiia</em><span><span> 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 </span>genetic capacity to degrade aromatic compounds that are frequently found in sponges. The novel </span><em>Acidimicrobiia</em><span> 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.</span></p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9782668","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":"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)","authors":"Olga A. Podosokorskaya ,&nbsp;Alexander G. Elcheninov ,&nbsp;Andrei A. Novikov ,&nbsp;Alexander Y. Merkel ,&nbsp;Ilya V. Kublanov","doi":"10.1016/j.syapm.2023.126438","DOIUrl":"10.1016/j.syapm.2023.126438","url":null,"abstract":"<div><p><span>A novel facultatively anaerobic moderately thermophilic bacterium, strain B-154 </span>^T<span>, 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 </span>^T<span><span><span><span> was a chemoorganoheterotroph, growing on mono-, di- and polysaccharides (xylan, starch, </span>galactan, </span>galactomannan<span><span>, glucomannan<span>, xyloglucan, </span></span>pullulan<span>, arabinan, lichenan, beta-glucan, pachyman, </span></span></span>locust bean gum, xanthan gum). It did not require sodium chloride or yeast extract for growth. Major cellular fatty acids were anteiso-C</span>_15:0, <em>iso</em>-C_16:0 and <em>iso</em>-C_14:0<span>. The respiratory quinone was MK-7. The complete genome of strain B-154 </span>^T<span> was 4.73 Mbp in size; its G + C content was 61%. According to the phylogenomic analysis strain B-154 </span>^T<span> forms a separate family-level phylogenetic<span> lineage. Moreover, together with </span></span><em>Limisphaera ngatamarikiensis</em> and <em>“Pedosphaera parvula”</em> this strain forms a separate order-level phylogenetic lineage within <em>Verrucomicrobiae</em> class. Hence, we propose a novel order, <em>Limisphaerales</em> ord. nov., with two families <em>Limisphaeraceae</em> fam. nov. and <em>Fontisphaeraceae</em> fam. nov., and a novel genus and species <em>Fontisphaera persica</em> gen. nov., sp. nov. with type strain B-154 ^T. Ecogenomic analysis showed that representatives of the <em>Limisphaerales</em> are widespread in various environments. Although some of them were detected in hot springs the majority of <em>Limisphaerales</em><span> (54% of the studied metagenome-assembled genomes) were found in marine habitats. This study allowed a better understanding of physiology and ecology of </span><em>Verrucomicrobiota</em><span> – a rather understudied bacterial phylum.</span></p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9851738","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":"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^T and IT-P374^T 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^T and IT-194P and clustering (whole genome analysis) next to <em>P. umsongensis</em> DSM16611^T, and another species containing strains IT-P374^T and IT-215P and clustering next to <em>P. koreensis</em> LMG21318^T. Genome analysis confirmed the proposition of novel species, as ANI was below the threshold of 95% and dDDH below 70% for strains IT-P366^T (compared with <em>P. umsongensis</em> DSM16611^T) and IT-P374^T (compared with <em>P. koreensis</em> LMG21318^T). Unlike <em>P. umsongensis</em> DSM16611^T, 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^T, 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^T (=CFBP 9060 ^T = LMG 32732 ^T = EML 1791 ^T) and <em>Pseudomonas serboccidentalis</em> sp. nov., with the type strain IT-P374^T (=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).</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"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}

{"title":"Description of Dellaglioa carnosa sp. nov., a novel species isolated from high-oxygen modified-atmosphere packaged meat","authors":"Victoria Werum,&nbsp;Matthias Ehrmann","doi":"10.1016/j.syapm.2023.126423","DOIUrl":"10.1016/j.syapm.2023.126423","url":null,"abstract":"<div><p><span>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 </span><em>Dellaglioa algida</em>. However, the <em>in-silico</em> DNA-DNA hybridization (DDH) values indicate that they belong to a different genomic species. The <em>in silico</em> DDH estimate value between TMW 2.2523^T and the type strain of <em>Dellaglioa algida</em> DSM 15638^T was only 63.2 %. The whole genome average nucleotide identity blast (ANIb) value of 95.1 % between TMW 2.2523^T and the closely related type strain of <em>D. algida</em><span><span> was within the recommended threshold value of 95–96 % for bacterial species delineation. Additionally, the phylogenomic analyses based on multi locus </span>sequence alignment (MLSA) showed that strain TMW 2.2523</span>^T<span> and additional strains TMW 2.2444 and TMW 2.2533 formed a monophyletic group separate from </span><em>D. algida</em><span> 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 </span><em>Dellaglioa</em> for which we propose the name <em>Dellaglioa carnosa</em> sp. nov. The designated respective type strain is TMW 2.2523^T (DSM 114968^T = LMG 32819^T).</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9792893","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":"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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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}