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Bacillus Pycnus Spa Nov. and Bacillus Neidei Spa Nov., Round-Spored

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674 International Journal ofSystematic and Evolutionary Microbiology (2002),52,501-505 DOl: 10.1099/ijs.0.01836-0 Bacillus pycnus Spa nov. and Bacillus neidei Spa NOTE nov., round-spored bacteria from soil 1 Microbial Properties L. K. Nakamura,1 O. Shida/ H. Takagi2 and K. Komagata3 Research Unit, National Center for Agricultural Utilization Research, 1815 N. University Street, Peoria, Author for correspondence: L K. Nakamura. Tel: + 13096816395. Fax: + 13096816672. IL 61604, USA e-mail: nakamulki"mail.ncaur.usda.gov 2 Research Laboratory, Higeta Shoyu Co. Ltd, Bacillus sphaericus sensu lato currently consists of seven or more groups of Choshi, Chiba 288, Japan unrelated taxa, one of which is B. sphaericus sensu stricto and another of 3 Department of which is Bacillus fusiformis. Members of two groups (groups 6 and 7), in Agricultural Chemistry, Tokyo University of common with all other B. sphaericus-like organisms, are unable to grow Agriculture, Setagaya-ku, anaerobically or to use common hexoses, pentoses and hexitols as sources of Tokyo 156, Japan carbon, have G+C contents of 34-36 mol % and form round spores. Groups 6 and 7 can be differentiated from other B. sphaericus-like organisms by low DNA relatedness and by variations in whole-cell fatty acid composition. Unique characteristics of group 6 include the ability to oxidize fi-hydroxybutyrate, the non-requirement for biotin and thiamin and failure to grow in 5 % NaCI. Distinctive traits of group 7 include the inability to oxidize pyruvate and a requirement for biotin, thiamin and cystine for growth. These data show that groups 6 and 7 represent two novel species, for which the names Bacillus pycnus sp. nov. and Bacillus neidei sp. nov., respectively, are proposed; the corresponding type strains are NRRL NRS-1691 T (= JCM 11075T) and NRRL BD-87T (= JCM 11077T). Keywords: Bacillus PYC/lUS, Bacillus /leidei, novel species, 165 rDNA The round-spored, mesophilic species Bacillus sphaeri­ comprised B. fils(jonnis: group I appeared to be a cus was first described by Neide (1904). Because early subgroup of 2. Groups 4-7 were unknown taxa. differentiation tests \vere ineffective, all round-spored In the present study, DNA relatedness evaluation and mesophiles were classified as B. sphaericus: the lack of phenotypic characterization were used to differentiate adequate differentiating tools deterred taxonomic groups 6 and 7 from each other, from representative study of mesophilic, round-spored bacteria. However, strains of groups 4 and 5 and from type strains of the discovery ofmosquitocidal activity among some of recognized round-spare-forming relatives. these organisms (Kellen et al., 1965) and the de­ velopment of molecular-biological techniques have DNA was extracted from 24-h cultures from groups I rekindled taxonomic and phylogenetic examination of (NRRL B-23269), 4 (NRRL NRS-593), 5 (NRRL T the round-spored organisms. Taxonomic heterogen­ B-1876), 6 (NRRL NRS-1691 , NRRL NRS-1693, eity of B. sphaericus had been suggested by variability NRRL NRS-1694, NRRL NRS-1695) and 7 (NRRL T of insecticidal activity among strains and was con­ BD-87 , NRRL BD-IOL NRRL BD-I03) and the firmed by comparative studies using DNA similarity following type cultures: 'Bacillus aminovorans' DSM T assessment (Krych et al., 1980), numerical taxonomy 4337, B. fils(jormis DSM 2898 , Sporosarcina globis­ T (Alexander & Priest, 1990: Priest et al., 1988), ran­ pora NRRL NRS-1533 , Bacillus insolitus NRRL T domly amplified polymorphic DNA fingerprinting NRS-1531 T, Marinibacillusmarinus DSM 1297 ,Sporo­ (Woodburn et al., 1995) and rRNA gene restriction sarcina psychrophila IFO 15381 T, B. silvestris DSM T T (Aquino de Muro et al., 1992). These developments led 12223 , B. sphaericus JCM 2502 and Ureibacillus T to the discovery of two more mesophilic species, thermosphaericus DSM 10633 . DNA reassociation Bacillus fils(lormis (Priest et al., 1988) and Bacillus was carried out using the method ofEzaki et al. (1989). silvestris (Rheims et al., 1999). In a phylogenetic study Probes were prepared with DNA from B. sphaericus T T based on 16S rDNA sequences (Nakamura, 2000), B. JCM 2502 , B. tllsijormis DSM 2898 , NRRL NRS­ T T sphaericus-like species segregated into seven groups 1691 • NRRL NRS-1694. NRRL BD-87 and NRRL wherein group 3 represented B. sphaericus and group 2 BD-I03. 01836 Printed in Great Britain 501 L. K. Nakamura and others Group 1 !-=::::::::::==~-I Group 2 93 Bacillus fusiformis Group 3 99 B. sphaericus Group 4 65 95 L-----I Group 5 '--------- B. silvestris NRS·1695 (AF169535) ] NRS·1691 T (AF169531) Group 6 ,..-__--"""00'-1 NRS·1694 (AF169534) (B. pycnussp. nov.) NRS·1693 (AF169533) 77 '-----i100 80-101 (AF169508) ] 82 Group 7 '-----1110<00 80-103 (AF169509) (B. neidei sp. nov.) 80-87 (AF169520) 89 L...... _ B. thermosphaericus P·11 (X90640) ........----1'00 B. psychrophilus ATCC 23304 T (X60634) B. globisporus OSM 4 T (X68415) ,..----1'00 L..... B. pasteurii NCIMB 8841 (X60631) L..... B. insolitus OSM 5 T (X60642) ........------ 'B. aminovorans'NCIMB 8292 (X62178) '-------- B. marinus OSM 1297 T (AJ237708) B. atrophaeus NCIMB 12899 (X60607) ,...------j1GG 99 B. subtilis NCOO 1769 (X60646) B. licheniformis OSM 13 T (X68416) '-------- B. cereus NCTC 11143 (X55063) ,...------ B.lentus lAM 12466T (016272) UL------- B. circulans lAM 12462 T (078312) '------ B. megaterium lAM 13418T (016273) 76 ,...------------- B. stearothermophilus T10 (X57309) L- B. smithii OSM 4216T (X60643) L.- ''"'oo''-j B. laevo/acticus lAM 12322 (016269) 7' 'B. myxolacticus'IAM 12326 (016274) -----------r;;;;;--- Brevibacillus centrosporus NRRL NRS·664T (078458) ,... '00 T 72 B. brevis JCM 2503 (078457) T L------------j'oo Aneurinibacillus migulanus ATCC 9999 (078462) A. aneurinilyticus NCIMB 10056 (X60645) -------G~========'00 Paenibacillus larvae NCDO 1141 (X60036) ~ P. polymyxa NCOO 1774 (60632) L..... Alicyclobacillus cycloheptanicus 1457 (X51928) Fig_ 1. Neighbour-joining tree showing the phylogenetic position of groups 6 and 7 among the mesophilic and psychrophilic round-spored Bacillus species and selected oval-spored species. The tree is based on 1321-nt sequences. Confidence limits estimated from bootstrap analyses (500 replicates) appear at the nodes. This is a modification of the tree generated by Nakamura (2000). A maximum-parsimony tree generated from the sequence data showed a similar topology. Alicyclobacillus cycloheptanicus was designated the outgroup species for the analysis. B. thermosphaericus has been reclassified as Ureibacillus thermosphaericus (Fortina et al., 2001); B. globisporus, B. psychrophilus and B. pasteurii have been reclassified as Sporosarcina globispora, Sporosarcina psychrophila and Sporosarcina pasteurii, respectively (Yoon et al., 2001 a); B. marinus has been reclassified as Marinibacillus marinus (Yoon et al., 2001 b); and B. stearothermophilus has been reclassified as Geobacillus stearothermophilus (Nazina et al., 2001). Bar, 1 nt substitution per 10 nt. Substrate oxidation profiles were obtained using the mercially prepared antibiotic discs on TGY agar plates BIOLOG GP system under conditions prescribed by spread-inoculated with the test organisms. The test the manufacturer. Other physiological traits were plates were incubated at 28 DC and the extent of examined using the methods of Gordon et al. (1973). inhibition was determined at 48 h. Decomposition Antibiotic sensitivity was assessed by placing com- of Tweens 40 and 80 was determined by the method 502 International Journal ofSystematic and Evolutionary Microbiology 52 Bacillus PYCllllS sp. nov. and B. neidei sp. nov. of Breuil & Gounot (1972). Vitamin and amino acid Table 1. Traits useful for differentiating the requirements were determined using the method of B. sphaericus-like groups Proom el al. (1955). ~ The BIOLOG system was used to evaluate substrate The extent of similarity among strains based on fatty oxidation. Substrates listed are those givin a 0 or 100 % acid composition data (Nakamura, 2000) was esti­ reactions. L-Glutamate was used bv all stn~ins: 64 substrates mated using the simple matching coefficient and were not used at all and variable r~actions were obtained with 26 substrates. AII organisms tested were sensitive to clustering was based on the unweighted pair group er~thromvcin. method with arithmetic averages (Sneath & SokaL chloramphenicol, tetracvcline and tobramvcin. Groups: 1 and 2 (n ~ 20), B..fils(fbrll1i~·: 3 (n = 7), . 1973). All cultures were grown on trypticase soy agar B..ljJ!IaericlIs: 4 (n = 10), unknown: 5 (n = 7). unknown: for 24 hat 30°C. Cell-wall peptidoglycan composition 6 (n = 3). B. pycnlls sp. nov.: and 7 (n = 4), B. neidei sp. nov. was analysed using the method described by Suzuki el al. (1993). Character Group In a phylogenetic tree based on 16S rDNA sequences, strains of groups 4-7 were positioned within a clade I and 2 3 4 5 6 7 that consisted generally of mesophilic, round-spored species, namely B. sphaericlls, B. jils(jorillis and Substrate oxidized: B. silveslris; the thermophile, U. lherillosphaericlls, is Pyruvate T + + + + situated outside the clade [Fig. 1; this tree is a fJ-Hydroxybutyrate + modification of one generated by Nakamura (2000)]. L-Alanine + + + + High bootstrap values validate the uniqueness of Glycyl L-glutamate + + + + + groups 4-7 within the clade of round-spored organ­ 2'-Deoxyadenosine + + + + + isms. Groups 6 and 7 were more closely related to Inosine + + + + each other than to the other mesophilic groups. AlvIP + + + UMP + + + High levels of
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    Adaptation au froid de la bactérie pathogène Bacillus cereus : étude de mécanismes impliqués et exploitation de la diversité génétique Sara Esther Diomande To cite this version: Sara Esther Diomande. Adaptation au froid de la bactérie pathogène Bacillus cereus : étude de mécanismes impliqués et exploitation de la diversité génétique. Agronomie. Université d’Avignon, 2014. Français. NNT : 2014AVIG0666. tel-01408068 HAL Id: tel-01408068 https://tel.archives-ouvertes.fr/tel-01408068 Submitted on 3 Dec 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Ecole Doctorale Agrosciences et Sciences Thèse Pour obtenir le titre de Docteur de l’Université d’Avignon et des Pays de Vaucluse Discipline : Biotechnologie et Microbiologie Sara Esther DIOMANDE Adaptation au froid de la bactérie pathogène Bacillus cereus : étude de mécanismes impliqués et exploitation de la diversité génétique Soutenue publiquement le 02 Décembre 2014 devant le Jury composé de : Rapporteurs Dr. Emmanuelle BOUVERET Directrice de recherche, CNRS, Marseille Dr. Pascale SERROR Directrice de Recherche, INRA Jouy-en-Josas Examinateurs Pr. Catherine DUPORT Professeur de l’Université d’Avignon Pr. Marc FEUILLOLEY Professeur de l’Université de Rouen Dr. Vincent SANCHIS Directeur de recherche, INRA Jouy-en Josas Directeurs de thèse Dr.

  • Yoon Et Al (2001) Sporosarcina Aquimarina Sp.Nov.Pdf

    International Journal of Systematic and Evolutionary Microbiology (2001), 51, 1079–1086 Printed in Great Britain Sporosarcina aquimarina sp. nov., a bacterium isolated from seawater in Korea, and transfer of Bacillus globisporus (Larkin and Stokes 1967), Bacillus psychrophilus (Nakamura 1984) and Bacillus pasteurii (Chester 1898) to the genus Sporosarcina as Sporosarcina globispora comb. nov., Sporosarcina psychrophila comb. nov. and Sporosarcina pasteurii comb. nov., and emended description of the genus Sporosarcina 1 Korea Research Institute of Jung-Hoon Yoon,1 Keun-Chul Lee,1 Norbert Weiss,4 Yung Hee Kho,1 Bioscience and 3 1,2 Biotechnology (KRIBB), Kook Hee Kang and Yong-Ha Park PO Box 115, Yusong, Taejon, Korea Author for correspondence: Yong-Ha Park. Tel: 82 42 860 4620. Fax: 82 42 860 4598. 2 j j Probionic Corporation e-mail: yhpark!mail.kribb.re.kr Bio-venture Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), A light-orange-coloured, facultatively anaerobic, rod-shaped bacterium (strain PO Box 115, Yusong, SW28T), which was isolated from seawater in Korea, was taxonomically studied Taejon, Korea by a polyphasic approach. This organism formed round terminal endospores in 3 Department of Food and swollen sporangia. The peptidoglycan type is A4α, based on L-Lys-L-Ala-D-Asp. Life Science, The predominant menaquinone is MK-7 and the major fatty acid is ante-C15:0. Sungkyunkwan University, The GMC content of the DNA is 40 mol%. Phylogenetic analysis based on 16S Chunchun-dong 300, rDNA sequences showed that strain SW28T falls within the radiation of a Jangan-gu, Suwon, Korea cluster comprising the rRNA group 2 bacilli and non-Bacillus-type organisms.
  • Metagenomics and Metatranscriptomics of Lake Erie Ice

    Metagenomics and Metatranscriptomics of Lake Erie Ice

    METAGENOMICS AND METATRANSCRIPTOMICS OF LAKE ERIE ICE Opeoluwa F. Iwaloye A Thesis Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE August 2021 Committee: Scott Rogers, Advisor Paul Morris Vipaporn Phuntumart © 2021 Opeoluwa Iwaloye All Rights Reserved iii ABSTRACT Scott Rogers, Lake Erie is one of the five Laurentian Great Lakes, that includes three basins. The central basin is the largest, with a mean volume of 305 km2, covering an area of 16,138 km2. The ice used for this research was collected from the central basin in the winter of 2010. DNA and RNA were extracted from this ice. cDNA was synthesized from the extracted RNA, followed by the ligation of EcoRI (NotI) adapters onto the ends of the nucleic acids. These were subjected to fractionation, and the resulting nucleic acids were amplified by PCR with EcoRI (NotI) primers. The resulting amplified nucleic acids were subject to PCR amplification using 454 primers, and then were sequenced. The sequences were analyzed using BLAST, and taxonomic affiliations were determined. Information about the taxonomic affiliations, important metabolic capabilities, habitat, and special functions were compiled. With a watershed of 78,000 km2, Lake Erie is used for agricultural, forest, recreational, transportation, and industrial purposes. Among the five great lakes, it has the largest input from human activities, has a long history of eutrophication, and serves as a water source for millions of people. These anthropogenic activities have significant influences on the biological community. Multiple studies have found diverse microbial communities in Lake Erie water and sediments, including large numbers of species from the Verrucomicrobia, Proteobacteria, Bacteroidetes, and Cyanobacteria, as well as a diverse set of eukaryotic taxa.