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Kaistella Soli Sp. Nov., Isolated from Oil-Contaminated Soil

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A001 Kaistella soli sp. nov., Isolated from Oil-contaminated Soil Dhiraj Kumar Chaudhary1, Ram Hari Dahal2, Dong-Uk Kim3, and Yongseok Hong1* 1Department of Environmental Engineering, Korea University Sejong Campus, 2Department of Microbiology, School of Medicine, Kyungpook National University, 3Department of Biological Science, College of Science and Engineering, Sangji University A light yellow-colored, rod-shaped bacterial strain DKR-2T was isolated from oil-contaminated experimental soil. The strain was Gram-stain-negative, catalase and oxidase positive, and grew at temperature 10–35°C, at pH 6.0– 9.0, and at 0–1.5% (w/v) NaCl concentration. The phylogenetic analysis and 16S rRNA gene sequence analysis suggested that the strain DKR-2T was affiliated to the genus Kaistella, with the closest species being Kaistella haifensis H38T (97.6% sequence similarity). The chemotaxonomic profiles revealed the presence of phosphatidylethanolamine as the principal polar lipids;iso-C15:0, antiso-C15:0, and summed feature 9 (iso-C17:1 9c and/or C16:0 10-methyl) as the main fatty acids; and menaquinone-6 as a major menaquinone. The DNA G + C content was 39.5%. In addition, the average nucleotide identity (ANIu) and in silico DNA–DNA hybridization (dDDH) relatedness values between strain DKR-2T and phylogenically closest members were below the threshold values for species delineation. The polyphasic taxonomic features illustrated in this study clearly implied that strain DKR-2T represents a novel species in the genus Kaistella, for which the name Kaistella soli sp. nov. is proposed with the type strain DKR-2T (= KACC 22070T = NBRC 114725T). [This study was supported by Creative Challenge Research Foundation Support Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF- 2020R1I1A1A01071920).] A002 Chitinibacter bivalviorum sp. nov., Isolated from the Gut of Freshwater Mussel Anodonta arcaeformis Jee-Won Choi, Jae-Yun Lee, and Jin-Woo Bae* Department of Biology and Department of Biomedical and Pharmaceutical Sciences and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University A novel Gram-negative, aerobic, rod-shaped bacterium with a single polar flagellum, designated strain 2T18T, was isolated from the gut of the freshwater mussel Anodonta arcaeformis. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain belonged to the genus Chitinibacter. Strain 2T18T formed a monophyletic clade with C. fontanus KCTC 42982T, C. tainanensis KACC 11706T, and C. alvei KCTC 23839T. Strain 2T18T exhibited optimal growth at 30°C, pH 8, with 0.5% (w/v) NaCl. The major isoprenoid quinone was ubiquinone-8. The predominant fatty acids were summed feature 3 (C16:1 ω6c and/or C16:1 ω7c) and C16:0. The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified lipid, three unidentified phospholipids, and two unidentified aminophospholipids. The G+C content of the genomic DNA was 50.6 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strains 2T18T and C. fontanus KCTC 42982T were below the thresholds used for the delineation of a novel species. Based on the phylogenetic, phenotypic, chemotaxonomic, and genotypic characteristics, strain 2T18T represents a novel species of the genus Chitinibacter, for which the name Chitinibacter bivalviorum sp. nov. is proposed. The type strain is 2T18T (= KCTC 72821T = CCUG 74764T). [This work was supported by a grant by Ministry of Food and Drug Safety (20172MFDS195), Republic of Korea.] A003 Agave Virus T, a Novel Tepovirus, Identified in the Blue Agave Transcriptome Data Chul Jun Goh, Dongbin Park, and Yoonsoo Hahn* Department of Life Science, Chung-Ang University The genome sequence of a novel RNA virus was identified by analyzing transcriptome data obtained from the stem sample of a blue agave (Agave tequilana) plant. Sequence comparison and phylogenetic analysis showed that the RNA virus, Agave virus T (AgVT), was a new member of the genus Tepovirus in the family Betaflexiviridae. AgVT genome had three open reading frames: a 1605-amino acid (aa) replicase (REP), 355-aa movement protein (MP), and 220-aa coat protein (CP). Phylogenetic analyses based on the REP, MP, and CP sequences of AgVT, previously reported tepoviruses, and other Betaflexiviridae viruses revealed that tepoviruses could be classified into two subclades: “potato virus T (PVT)-clade” and “Prunus virus T (PrVT)-clade.” PVT, the type species and founding member of the genus Tepovirus, belonged to “PVT-clade” along with AgVT, while the other five tepoviruses belonged to “PrVT-clade.” The genome sequence of AgVT may be useful for studying the phylogenetic relationships between tepoviruses and other closely related viruses. [This research was supported by grants from the National Research Foundation of Korea funded by the Government of Korea (grant Nos. NRF-2018R1A5A1025077 and 2020R1A2C1013403).] A004 Zostera Associated Varicosavirus 1, a Novel Negative-sense RNA Virus, Identified in the Common Eelgrass Transcriptome Data Chaerim Shin, Dongjin Choi, and Yoonsoo Hahn* Department of Life Science, Chung-Ang University Varicosaviruses (genus Varicosavirus) are bipartite, negative-sense, single-stranded RNA viruses that infect plants. We analyzed a transcriptome dataset isolated from the common eelgrass (Zostera marina) and identified a novel varicosavirus named Zostera associated varicosavirus 1 (ZaVV1). The ZaVV1 genome consists of two genomic segments: RNA1 (6,632-nt) has an open reading frame (ORF) encoding a large multi-functional polymerase protein (L), while RNA2 (4,304-nt) has four ORFs: one for a nucleocapsid protein and three for proteins with unknown functions (P2, P3, and P4). Sequence comparison and phylogenetic analysis using L proteins showed that ZaVV1 is a novel member of the genus Varicosavirus of the family Rhabdoviridae. The conserved regulatory elements involved in transcription termination/polyadenylation and transcription initiation were identified in the ZaVV1 gene-junction regions with the consensus sequence 3'-UAUUAUUCUUUUUGCUCU-5' (in the negative-sense genome). The ZaVV1 genome sequence may be useful for studying the phylogenetic relationships of varicosaviruses and genome evolution of rhabdoviruses. [This research was supported by grants from the National Research Foundation of Korea funded by the Government of Korea (grant Nos. NRF-2018R1A5A1025077 and 2020R1A2C1013403).] A005 A Novel Acetate-producing Bacteroides Species, Isolated from Human Faeces Han Sol Kim1,2, Ji-Sun Kim1, Min Kuk Suh1,2, Mi Kyung Eom1, Ju Huck Lee1, Seung-Hwan Park1, Se Won Kang1, and Jung-Sook Lee1,3* 1Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 2Department of Lifestyle Medicine, Jeonbuk National University, 3University of Science and Technology Two obligately anaerobic, Gram-stain-negative, non-motile, non-spore-forming, and short rod, and catalase-, oxidase-negative bacteria, designated KGMB07931T and KGMB10229, were isolated from the faeces of a healthy Korean. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains KGMB07931T and KGMB10229 were very similar to each other (99.9 %) and the two strains were grouped within the genus Bacteroides, displaying the highest similarity with B. uniformis ATCC 8492T (97.5%), B. rodentium JCM 16496T (96.6%), and B. fluxus YIT 12057T (94.5%). Both strains grew optimally at 37°C and pH 7.5 in the presence of 0.5% (w/v) NaCl. The draft genome of KGMB07931T comprises 3,435 putative genes with a total of 4,196,373 bp and an average G + C content of 46.3 mol%. The major fatty acids were C18:1 cis9 (26.4%) and anteiso-C15:0 (22.5%); the predominant respiratory quinone were MK-9 and MK-10; the major fermentation end products acetate, isobutyrate. On the basis of polyphasic taxonomic data, strain KGMB07931T and KGMB10229 represent a novel species of the genus Bacteroides. The type strain is KGMB07931T (= KCTC 25160T). [This work was supported by the Bio and Medical Technology Development program of the National Research Foundation of Korea (NRF) funded by the Ministry of Science and ICT (MSIT) of the Republic of Korea (NRF- 2016M3A9F3946674) and a grant from the Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research initiative program.] A006 Microbiome Analysis of Sponge in the Genus Discodermia Using Illumina Miseq Jae yeon Kim and Jin-Sook Park* College of Life Science & Nano Technology, Department of Biological Science and Biotechnology, Hannam University The symbiotic microbial community structures of D. calyx, D. japonica, D. emarginata, and Microscleoderma sp. sponges collected from Munseom Island (October 2019) and Gapa Island (May 2020) in Jeju Island were compared using Illumina Miseq. The gDNA of each of five specimens from four species of sponges were extracted, and the V3-V4 region was amplified using a pair of Bacterial 16S rRNA gene primers and used for analysis. In alpha-diversity analysis, D. calyx sponge was the most abundant in symbiotic microbial species than the other sponges. The result of beta-diversity analysis, revealed differences in the symbiotic microbial communities of different species of sponges and comparative analysis of the sponges showed the specificity according to the species of the sponge and the specificity according to the habitat environment. Microbiome analysis results of D. emarginata, D. calyx, D. japonica collected from
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  • Responses to Ecopollutants and Pathogenization Risks of Saprotrophic Rhodococcus Species

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    pathogens Review Responses to Ecopollutants and Pathogenization Risks of Saprotrophic Rhodococcus Species Irina B. Ivshina 1,2,*, Maria S. Kuyukina 1,2 , Anastasiia V. Krivoruchko 1,2 and Elena A. Tyumina 1,2 1 Perm Federal Research Center UB RAS, Institute of Ecology and Genetics of Microorganisms UB RAS, 13 Golev Str., 614081 Perm, Russia; [email protected] (M.S.K.); [email protected] (A.V.K.); [email protected] (E.A.T.) 2 Department of Microbiology and Immunology, Perm State University, 15 Bukirev Str., 614990 Perm, Russia * Correspondence: [email protected]; Tel.: +7-342-280-8114 Abstract: Under conditions of increasing environmental pollution, true saprophytes are capable of changing their survival strategies and demonstrating certain pathogenicity factors. Actinobacteria of the genus Rhodococcus, typical soil and aquatic biotope inhabitants, are characterized by high ecological plasticity and a wide range of oxidized organic substrates, including hydrocarbons and their derivatives. Their cell adaptations, such as the ability of adhering and colonizing surfaces, a complex life cycle, formation of resting cells and capsule-like structures, diauxotrophy, and a rigid cell wall, developed against the negative effects of anthropogenic pollutants are discussed and the risks of possible pathogenization of free-living saprotrophic Rhodococcus species are proposed. Due to universal adaptation features, Rhodococcus species are among the candidates, if further anthropogenic pressure increases, to move into the group of potentially pathogenic organisms with “unprofessional” parasitism, and to join an expanding list of infectious agents as facultative or occasional parasites. Citation: Ivshina, I.B.; Kuyukina, Keywords: actinobacteria; Rhodococcus; pathogenicity factors; adhesion; autoaggregation; colonization; M.S.; Krivoruchko, A.V.; Tyumina, defense against phagocytosis; adaptive strategies E.A.
  • Micrococcus Luteus (Schroeter 1872) Cohn 1872, and Desig- Nation of the Neotype Strain M

    Micrococcus Luteus (Schroeter 1872) Cohn 1872, and Desig- Nation of the Neotype Strain M

    INTERNATIONAL JOURNAL of SYSTEMATIC BACTERIOLOGY Vol. 22, No. 4 October 1972, p. 218-223 Printed in U.S.A. Copyright 0 1972 International Association of Microbiological Societies Taxonomic Status of Micrococcus luteus (Schroeter 1872) Cohn 1872, and Desig- nation of the Neotype Strain M. KOCUR, ZDENA PkCOVA, and T. MARTINEC Czechoslovak Collection of Microorganisms, J. E. PurkynE University, Brno, Czechoslovakia An amended description of Micrococcus luteus (Schroeter 1872) Cohn 1872, at present a broad-based species characterized primarily on negative charact er- istics, is proposed on the basis of a taxonomic analysis of 30 strains. CCM 169 (= ATCC 4698) is designated a's the neotype strain of M. luteus. A large number of species of aerobic, diameter and arranged in tetrads and in catalase-positive, yellow-pigmented micrococci irregular clumps of tetrads. Strains CCM 248, have been described, but their incomplete 337, 1674, and 2494 formed packets and characterization has hindered their classifica- irregular clusters of packets. These strains also tion. Some of them are known as Micrococcus produced the largest cells (1.5 to 1.8 pm) of all luteus, M. flaws, M. lysodeikticus, Sarcina of those studied. None of the strains was motile lutea, and S. flava. At present only two of these or produced spores. are generally accepted: M. luteus and M. varians Cultural characteristics. Colonies of all of the (13, 21). strains were circular, convex, and smooth, with Although M. luteus is the type species of the either a glistening or a dull surface. Tetrad- and genus Micrococcus, it is not sufficiently de- packet-forming strains produced matted colo- fined.