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  • 1
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    Streptomyces bathyalis sp. nov., an actinobacterium isolated from the sponge in a deep sea
    Springer Science and Business Media LLC ; 2021
    In:  Antonie van Leeuwenhoek Vol. 114, No. 4 ( 2021-04), p. 425-435
    Details
    In: Antonie van Leeuwenhoek, Springer Science and Business Media LLC, Vol. 114, No. 4 ( 2021-04), p. 425-435
    Abstract: A novel actinobacterium, designated ASO4wet T , was isolated from the unidentified sponge (SO4) in the deep sea collected of the North Atlantic Ocean. Study of 16S rRNA gene sequences indicated that strain ASO4wet T is a member of the genus Streptomyces and showed the closest similarities to Streptomyces karpasiensis K413 T (98.87 %), Streptomyces glycovorans YIM M 10366 T (98.38 %), and Streptomyces abyssalis YIM M 10400 T (97.53 %). Strain ASO4wet T contained MK-9(H8) as the predominant menaquinone and the major fatty acids are iso-C 16:0 , anteiso-C 15:0 , and iso-C 15:0 . Polyphasic taxonomy was carried out between strain ASO4wet T and its phylogenetically closely related Streptomyces strains, which further elucidated their relatedness and revealed that strain ASO4wet T could be distinguished from currently known Streptomyces species. Strain ASO4wet T clearly represents a novel species in genus Streptomyces . We propose the name Streptomyces bathyalis sp. nov., with the type strain ASO4wet T (= DSM 106605 T  = NCCB 100657 T ). Analysis of the whole-genome sequence of S. bathyalis revealed that genome size is 7,377,472 bp with 6332 coding sequences.
    Type of Medium: Online Resource
    ISSN: 0003-6072 , 1572-9699
    URL: Article
    DOI: 10.1007/s10482-021-01528-4
    RVK:
    WA 15000
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 1478112-8
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  • 2
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    Streptomonospora litoralis sp. nov., a halophilic thiopeptides producer isolated from sand collected at Cuxhaven beach
    Springer Science and Business Media LLC ; 2021
    In:  Antonie van Leeuwenhoek Vol. 114, No. 10 ( 2021-10), p. 1483-1496
    Details
    In: Antonie van Leeuwenhoek, Springer Science and Business Media LLC, Vol. 114, No. 10 ( 2021-10), p. 1483-1496
    Abstract: Strain M2 T was isolated from the beach of Cuxhaven, Wadden Sea, Germany, in course of a program to attain new producers of bioactive natural products. Strain M2 T produces litoralimycin and sulfomycin-type thiopeptides. Bioinformatic analysis revealed a potential biosynthetic gene cluster encoding for the M2 T thiopeptides. The strain is Gram-stain-positive, rod shaped, non-motile, spore forming, showing a yellow colony color and forms extensively branched substrate mycelium and aerial hyphae. Inferred from the 16S rRNA gene phylogeny strain M2 T affiliates with the genus Streptomonospora. It shows 96.6% 16S rRNA gene sequence similarity to the type species Streptomonospora salina DSM 44593  T and forms a distinct branch with Streptomonospora sediminis DSM 45723  T with 97.0% 16S rRNA gene sequence similarity. Genome-based phylogenetic analysis revealed that M2 T is closely related to Streptomonospora alba YIM 90003  T with a digital DNA-DNA hybridisation (dDDH) value of 26.6%. The predominant menaquinones of M2 T are MK-10(H 6 ), MK-10(H 8 ), and MK-11(H 6 ) ( 〉  10%). Major cellular fatty acids are iso-C 16:0, anteiso C 17:0 and C 18:0 10-methyl. The polar lipid profile consisted of diphosphatidylglycerol phosphatidyl glycerol, phosphatidylinositol, phosphatidylcholine, phosphatidylethanolamine, three glycolipids, two unknown phospholipids, and two unknown lipids. The genome size of type strain M2 T is 5,878,427 bp with 72.1 mol % G + C content. Based on the results obtained from phylogenetic and chemotaxonomic studies, strain M2 T (= DSM 106425  T  = NCCB 100650  T ) is considered to represent a novel species within the genus Streptomonospora for which the name Streptomonospora litoralis sp. nov. is proposed.
    Type of Medium: Online Resource
    ISSN: 0003-6072 , 1572-9699
    URL: Article
    DOI: 10.1007/s10482-021-01609-4
    RVK:
    WA 15000
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 1478112-8
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  • 3
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    Methylicorpusculum oleiharenae gen. nov., sp. nov., an aerobic methanotroph isolated from an oil sands tailings pond
    Microbiology Society ; 2020
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 70, No. 4 ( 2020-04-01), p. 2499-2508
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 70, No. 4 ( 2020-04-01), p. 2499-2508
    Abstract: An aerobic methane oxidizing bacterium, designated XLMV4 T , was isolated from the oxic surface layer of an oil sands tailings pond in Alberta, Canada. Strain XLMV4 T is capable of growth on methane and methanol as energy sources. NH 4 Cl and sodium nitrate are nitrogen sources. Cells are Gram-negative, beige to yellow-pigmented, motile (via a single polar flagellum), short rods 2.0–3.3 µm in length and 1.0–1.6 µm in width. A thick capsule is produced. Surface glycoprotein or cup shape proteins typical of the genera Methylococcus, Methylothermus and Methylomicrobium were not observed. Major isoprenoid quinones are Q-8 and Q-7 at an approximate molar ratio of 71 : 22. Major polar lipids are phosphoglycerol and ornithine lipids. Major fatty acids are C 16 : 1  ω8+C 16 : 1  ω7 (34 %), C 16 : 1  ω5 (16 %), and C 18 : 1  ω7 (11 %). Optimum growth is observed at pH 8.0 and 25 °C. The DNA G+C content based on a draft genome sequence is 46.7 mol%. Phylogenetic analysis of 16S rRNA genes and a larger set of conserved genes place strain XLMV4 T within the class Gammaproteobacteria and family Methylococcaceae , most closely related to members of the genera Methylomicrobium and Methylobacter (95.0–97.1 % 16S rRNA gene sequence identity). In silico genomic predictions of DNA–DNA hybridization values of strain XLMV4 T to the nearest phylogenetic neighbours were all below 26 %. On the basis of the data presented, strain XLMV4 T is considered to represent a new genus and species for which the name Methylicorpusculum oleiharenae is proposed. Strain XLMV4 T (=DSMZ DSM 27269=ATCC TSD-186) is the type strain.
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijsem.0.004064
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2020
    detail.hit.zdb_id: 215062-1
    detail.hit.zdb_id: 2056611-6
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  • 4
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    Corrigendum: Genotype–phenotype correlations within the Geodermatophilaceae
    Frontiers Media SA ; 2023
    In:  Frontiers in Microbiology Vol. 13 ( 2023-1-20)
    Details
    In: Frontiers in Microbiology, Frontiers Media SA, Vol. 13 ( 2023-1-20)
    Type of Medium: Online Resource
    ISSN: 1664-302X
    URL: Article
    DOI: 10.3389/fmicb.2022.1100319
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2023
    detail.hit.zdb_id: 2587354-4
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  • 5
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    Arthrobacter ulcerisalmonis sp. nov., isolated from an ulcer of a farmed Atlantic salmon (Salmo salar), and emended description of the genus Arthrobacter sensu lato
    Microbiology Society ; 2020
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 70, No. 3 ( 2020-03-01), p. 1963-1968
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 70, No. 3 ( 2020-03-01), p. 1963-1968
    Abstract: A Gram-stain positive, pleomorphic, oxidase-negative, non-motile isolate from the ulcer of a farmed Atlantic salmon ( Salmo salar ), designated strain T11b T , was subjected to a comprehensive taxonomic investigation. A comparative analysis of the 16S rRNA gene sequence showed highest similarities to the type strains of Pseudarthrobacter siccitolerans (98.1 %) and Arthrobacter methylotrophus and Pseudarthrobacter phenanthrenivorans (both 98.0 %). The highest ANI value observed between the assembled genome of T11b T and the publicly available Pseudarthrobacter and Arthrobacter type strain genomes were 81.15 and 80.99 %, respectively. The major respiratory quinone was menaquinone MK-9(H 2 ). The polyamine pattern contained predominantly spermidine. The polar lipid profile consisted of the major lipids diphosphatidylglycerol, phosphatidylglycerol, monogalactosyl-diacylglycerol and dimannosylglyceride. Minor amouts of trimannosyldiacylglycerol and phosphatidylinositol were also detected. The peptidoglycan was of the type A3α l -Lys– l -Ser –l -Thr– l -Ala (A11.23). In the fatty acid profile, anteiso and iso branched fatty acids predominated (anteiso C 15 : 0 , iso C 16 : 0 , anteiso C 17 : 0 ). Moderate to low DNA–DNA similarities, physiological traits as well as unique traits in the fatty acid pattern distinguished strain T11b T from the next related species. All these data point to the fact that strain T11b T represents a novel species of the genus Arthrobacter for which we propose the name Arthrobacter ulcerisalmonis sp. nov. The type strain is T11b T (=CIP 111621 T =CCM 8854 T =LMG 30632 T =DSM 107127 T ).
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijsem.0.004002
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2020
    detail.hit.zdb_id: 215062-1
    detail.hit.zdb_id: 2056611-6
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  • 6
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    Pseudomonas khazarica sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from Khazar Sea sediments
    Springer Science and Business Media LLC ; 2020
    In:  Antonie van Leeuwenhoek Vol. 113, No. 4 ( 2020-04), p. 521-532
    Details
    In: Antonie van Leeuwenhoek, Springer Science and Business Media LLC, Vol. 113, No. 4 ( 2020-04), p. 521-532
    Type of Medium: Online Resource
    ISSN: 0003-6072 , 1572-9699
    URL: Article
    DOI: 10.1007/s10482-019-01361-w
    RVK:
    WA 15000
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
    detail.hit.zdb_id: 1478112-8
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  • 7
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    Presentation_1.pptx
    Frontiers Media SA ; 2022
    In:  Frontiers in Microbiology Vol. 13 ( 2022-11-10)
    Details
    In: Frontiers in Microbiology, Frontiers Media SA, Vol. 13 ( 2022-11-10)
    Abstract: The integration of genomic information into microbial systematics along with physiological and chemotaxonomic parameters provides for a reliable classification of prokaryotes. In silico analysis of chemotaxonomic traits is now being introduced to replace characteristics traditionally determined in the laboratory with the dual goal of both increasing the speed of the description of taxa and the accuracy and consistency of taxonomic reports. Genomics has already successfully been applied in the taxonomic rearrangement of Geodermatophilaceae (Actinomycetota) but in the light of new genomic data the taxonomy of the family needs to be revisited. In conjunction with the taxonomic characterisation of four strains phylogenetically located within the family, we conducted a phylogenetic analysis of the whole proteomes of the sequenced type strains and established genotype–phenotype correlations for traits related to chemotaxonomy, cell morphology and metabolism. Results indicated that the four isolates under study represent four novel species within the genus Blastococcus . Additionally, the genera Blastococcus , Geodermatophilus and Modestobacter were shown to be paraphyletic. Consequently, the new genera Trujillonella , Pleomorpha and Goekera were proposed within the Geodermatophilaceae and Blastococcus endophyticus was reclassified as Trujillonella endophytica comb. nov., Geodermatophilus daqingensis as Pleomorpha daqingensis comb. nov. and Modestobacter deserti as Goekera deserti comb. nov. Accordingly, we also proposed emended descriptions of Blastococcus aggregatus, Blastococcus jejuensis, Blastococcus saxobsidens and Blastococcus xanthilyniticus . In silico chemotaxonomic results were overall consistent with wet-lab results. Even though in silico discriminatory levels varied depending on the respective chemotaxonomic trait, this approach is promising for effectively replacing and/or complementing chemotaxonomic analyses at taxonomic ranks above the species level. Finally, interesting but previously overlooked insights regarding morphology and ecology were revealed by the presence of a repertoire of genes related to flagellum synthesis, chemotaxis, spore production and pilus assembly in all representatives of the family. A rich carbon metabolism including four different CO 2 fixation pathways and a battery of enzymes able to degrade complex carbohydrates were also identified in Blastococcus genomes.
    Type of Medium: Online Resource
    ISSN: 1664-302X
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.3389/fmicb.2022.975365
    DOI: 10.3389/fmicb.2022.975365.s001
    DOI: 10.3389/fmicb.2022.975365.s002
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
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  • 8
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    Genomic Analysis of a Novel Heavy Metal Resistant Isolate from a Black Sea Contaminated Sediment with the Potential to Degrade Alkanes: Plantactinospora alkalitolerans sp. nov.
    MDPI AG ; 2022
    In:  Diversity Vol. 14, No. 11 ( 2022-11-04), p. 947-
    Details
    In: Diversity, MDPI AG, Vol. 14, No. 11 ( 2022-11-04), p. 947-
    Abstract: Microorganisms that grow in poorly studied environments are of special interest when new biotechnological applications are searched. The Melet river offshore sediments at the Black Sea have been described to contain an important number of contaminants from upstream industries which have been accumulating for years. Bacteria of such habitats must be adapted to the presence of those compounds and in some cases, are able to use them as carbon sources. In the analysis of some samples recovered from this environment, an actinobacterial strain was isolated, named as S1510T, and its taxonomic position was determined using a combination of phenotypic and genotypic properties. Strain S1510T presented phenotypic properties typical of members of the family Micromonosporaceae and was assigned to the Plantactinospora genus, based on the phylogenetic analyses of the 16S rRNA gene and whole-genome sequences. Low dDDH (digital DNA-DNA hybridization) values with other members of the genus confirmed that Plantactinospora sp. S1510T represents a novel species, and is proposed with the new name Plantactinospora alkalitolerans. The strain presented characteristics not previously described for other species in the genus, such as its high tolerance to alkaline pHs, the presence of genes related to the production and degradation of alkanes (oleABCD, ssuAD, almA), the degradation of several aromatic compounds, and the tolerance to high heavy metal concentrations. In addition, Plantactinospora sp. S1510T presents several bioclusters to produce nonribosomal peptide-synthetases, terpenes, polyketide synthases, and bacteriocins, that possess low similarities with known compounds.
    Type of Medium: Online Resource
    ISSN: 1424-2818
    URL: Article
    DOI: 10.3390/d14110947
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2518137-3
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  • 9
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    Halomonas lysinitropha sp. nov., a novel halophilic bacterium isolated from a hypersaline wetland
    Microbiology Society ; 2020
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 70, No. 12 ( 2020-12-01), p. 6098-6105
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 70, No. 12 ( 2020-12-01), p. 6098-6105
    Abstract: We carried out a polyphasic taxonomic study on a new halophilic strain designated 3(2) T , isolated from Meighan wetland, Iran. Cells of the novel strain were Gram-stain-negative, non-hemolytic, catalase- and oxidase-positive, rod-shaped, non-endospore-forming and motile. Cell growth occurred at 3–15 % NaCl (w/v; optimum, 5 %), pH 7.0–9.0 (optimum, pH 7.5–8.0) and 15–35 °C (optimum, 30 °C). 16S rRNA gene sequence comparisons confirmed the affiliation of strain 3(2) T to the class Gammaproteobacteria and the genus Halomonas with highest similarity to Halomonas daqiaonensis YCSA28 T (98.4 %) and Halomonas ventosae Al12 T (97.9 %). Experimental and in silico DNA–DNA hybridization values were 42.7 and 35.1% with H. daqiaonensis IBRC-M 10931 T and 48 and 35.2% with H. ventosae IBRC-M 10566 T , respectively, and indicated that they are different members of the same genus. The genome of the type strain was characterized by a size of 3.83 Mbp with 63 scaffolds and a G+C content of 64.8 mol%. Moreover, the average nucleotide identity values against H. ventosae Al12 T and H. daqiaonensis YCSA28 T were 88.8 and 88.5 %, respectively. The predominant respiratory quinone was Q-9 (92 %) with Q-8 (8 %) as a minor component. Major fatty acids were C 16 : 0 cyclo, C 19 : 0  ω8 c , C 16 : 1  ω7 c and/or iso-C 15:0 2-OH, C 12 : 0 3-OH and C 18 : 1  ω7 c . The polar lipid profile of the strain contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphoaminoglycolipid and four unidentified phospholipids. According to our results, strain 3(2) T could be classified as a novel species in the genus Halomonas for which the name Halomonas lysinitropha sp. nov. is proposed. The type strain is 3(2) T (=IBRC M 10929 T =LMG 29450 T =CIP 111708 T ).
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijsem.0.004504
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2020
    detail.hit.zdb_id: 215062-1
    detail.hit.zdb_id: 2056611-6
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  • 10
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    Nocardiopsis dassonvillei subsp. crassaminis subsp. nov., isolated from freshwater sediment, and reappraisal of Nocardiopsis alborubida Grund and Kroppenstedt 1990 emend. Nouioui et al. 2018
    Microbiology Society ; 2020
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 70, No. 12 ( 2020-12-01), p. 6172-6179
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 70, No. 12 ( 2020-12-01), p. 6172-6179
    Abstract: An actinomycete, strain D1 T , was isolated from a freshwater sediment sample collected from the San Pablo river in the La Risueña community, Santiago de Cuba province, Cuba. The strain was identified as a member of the genus Nocardiopsis by means of a polyphasic taxonomic study. It produced a light yellow non-fragmented substrate mycelium, a white well-developed aerial mycelium and straight to flexuous hyphae. No specific spore chains were observed. Strain D1 T contained meso- diaminopimelic acid, no diagnostic sugars, and MK-10(H 2 ), MK-10(H 4 ), MK-10 and MK-10(H 6 ) as predominant menaquinones, but not phosphatidylcholine as diagnostic polar lipid of the genus Nocardiopsis . The predominant fatty acids were iso-C 16 : 0 , 10-methyl-C 18 : 0 and anteiso-C 17 : 0 . Strain D1 T showed the highest degree of 16S rRNA gene sequence similarity to Nocardiopsis synnematoformans DSM 44143 T (99.8 %), Nocardiopsis dassonvillei subsp. albirubida NBRC 13392 T (99.8 %) and Nocardiopsis dassonvillei subsp. dassonvillei DSM 43111 T (99.6 %). A genomic OrthoANIu value between D1 T and N. dassonvillei subsp. dassonvillei DSM 43111 T of 97.63 % and a dDDH value of 78.9 % indicated that strain D1 T should be classified in N. dassonvillei . However, phenotypic characteristics distinguished strain D1 T from its nearest neighbour taxon. On basis of these results we propose to classify strain D1 T (=LMG 30468 T =CECT 30033 T ) as a representative of a novel subspecies of the genus Nocardiopsis , for which the name Nocardiopsis dassonvillei subsp. crassaminis subsp. nov. is proposed. In addition, the genomic distance between N. dassonvillei subsp. albirubida NBRC 13392 T and N. dassonvillei subsp. dassonvillei DSM 43111 T as determined through OrthoANIu (93.64 %) and dDDH (53.40 %), along with considerable phenotypic and chemotaxonomic differences reported in earlier studies, indicated that the classification of this taxon as Nocardiopsis alborubida Grund and Kroppenstedt 1990 is to be preferred over its classification as N. dassonvillei subsp. albirubida Evtushenko et al. 2000.
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijsem.0.004514
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2020
    detail.hit.zdb_id: 215062-1
    detail.hit.zdb_id: 2056611-6
    SSG: 12
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