DOCSLIB.ORG

A Taxonomic Study of the Genus Streptomyces by Analysis Of

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
A Taxonomic Study of the Genus Streptomyces by Analysis Of INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, July 1995, p. 507-514 Vol. 45, No. 3 0020-7713/95/$04.00+ 0 Copyright 0 1995, International Union of Microbiological Societies A Taxonomic Study of the Genus Streptomyces by Analysis of Ribosomal Protein AT-L30 KOZO OCHI” National Food Research Institute, 2-1-2 Kannondai, Tsukuba, Ibaraki 305, Japan The ribosomal AT-I30 proteins from 81 species of the genus Streptomyces as listed by Williams et al. in Bergey’s Manual of Systematic Bacteriology were analyzed. My results provided further evidence that the genus Streptomyces is well circumscribed. On the basis of levels of AT-L30 N-terminal amino acid sequence homology, the strains were classified into four groups (groups I to IV) and a nongrouped category, whose members contained amino acid sequences characteristic of each species. A phylogenetic tree constructed on the basis of the levels of similarity of the amino acid sequences revealed the existence of six clusters within the genus. The first cluster contains the members of groups I and I1 together with several other species; the second cluster contains the members of groups I11 and IV and several other species; the third cluster contains Streptomyces ramulosus and Streptomyces ochraceiscleroticus; the fourth cluster contains only Streptomyces rimosus; the fifth cluster contains Streptomyces aurantiacus and Streptomyces tubercidicus; and the sixth cluster contains Strepto- myces albus and Streptomyces sulphureus. Considerable agreement between the results of the AT-L30 analyses and the results of numerical phenetic classification was found, although there were numerous disagreements in details. For example, four groups (groups I to IV) defined by the AT-L30 analysis data did not correlate with the aggregate groups defined by numerical classification. In general, but not always, the species classified in a particular cluster in the numerical classification system had the same or similar AT-L30 terminal amino acid sequences. The AT-UO analysis data were more consistent with the 16s rRNA analysis data than with the numerical classification data, indicating that there was a good correlation between the four groups defined by AT-L30 analysis data and the aggregate groups defined by 16s rRNA analysis data. I stress that discrepancies between results of phenetic analyses and results of phylogenetic analyses should be taxonomically significant and can be resolved by other taxonomic approaches, such as DNA relatedness analysis. The genus Streptomyces of the family Streptomycetaceae con- ered species complexes. These results of this study are sum- tains the largest number of species among the genera of the marized in Beeq’s Manual of Systematic Bacteriology (33). Actinornycetales and can be separated from other actinomycete A numerical phenetic survey of Streptomyces species was also genera with wall chemotype I by using a combination of chem- performed by Kampfer et al. (8). The phenetic data of these ical and morphological properties (reviewed in references 2, authors in most cases confirmed the existence of the major 10, and 33). Traditionally, streptomycete systematics has been phena found in the study of Williams et al. (34), although only based mainly on morphology, pigmentation, and physiological some of the cluster groups defined in the study of Williams et properties, but increasing weight is now given to chemical and al. were detected by Kampfer et al. Data which describe DNA genetic features (2, 3, 9, 11, 15, 28), especially for generic relatedness among strains are also valuable for taxonomy, es- circumspection. As mentioned by O’Donnell (27), analysis of pecially at the species level, and such data have been applied to quantitative data by appropriate cluster analysis techniques streptomycetes by Labeda and Lyons (12-14). The phenetic may be essential for the characterization of streptomycetes at clustering of these organisms actually reflects their genomic the subgeneric level. Because of importance of the genus Strep- relationships as determined by DNA relatedness analyses and tomyces as a source of novel antibiotics, the number of pro- rRNA-based analyses (1, 35). posed streptomycete species, including those only cited in the On the basis of the heterogeneity of the ribosomal proteins patent literature, is more than 3,000. The names of 378 validly of Streptomyces species, I (17) developed a novel method for described streptomycete species are listed on the Approved identifying and classifying actinomycetes. Ribosomal protein Lists of Bacterial Names (29). patterns determined by two-dimensional polyacrylamide gel Many attempts to delimit Streptomyces species have been electrophoresis (PAGE) could be used for Streptomyces taxon- made. In particular, a large-scale numerical phenetic survey of omy at the species level, while analysis of ribosomal AT-L30 the genus Streptomyces and related taxa was performed by proteins (homologous to Escherichia coli L30 protein) could be Williams et al. (34) to clarify the infrastructure of the genus; used to classify actinomycetes at the genus level (18, 19,21,23, 394 Streptomyces type cultures were examined for 139 unit 25, 26). The latter method is based on the electrophoretic characters, and the data were analyzed statistically. The result- mobilities of the AT-L30 proteins and N-terminal amino acid ing classification indicated that the type strains of Streptomyces sequences. L30 protein analysis has been proven to be effective species were distributed in 23 major clusters (containing four in the taxonomy of not only actinomycetes but also other eu- or more strains), 20 minor clusters (containg two or three bacteria (20, 22). Witt and Stackebrandt (35) have proposed strains), and 25 clusters containing a single member. The mi- that the genera Streptoverticillium and Streptomyces should be nor clusters and the single-member clusters were considered united on the basis of their high levels of phylogenetic and species by Williams et al., and the major clusters were consid- phenetic similarity. Wellington et al. (32) have proposed that the genus Kitasatosporia, whose members’ cell walls contain similar amounts of the LL and mesu isomers of diaminopimelic acid, as well as glycine and galactose, is a synonym of the genus * Phone: 0298-38-8125. Fax: 0298-38-7996. Streptomyces. Recent AT-L30 sequence analysis data have con- 507 508 OCHI INT.J. SYST. BACTERIOL. TABLE 1. Strains used in this study TABLE l-Continued Cluster of Cluster of Species or subspecies Strain Williams Species or subspecies Strain Williams et al." et al." Streptomyces aburaviensis JCM 4613' (= ATCC 23869T)b A-2 Streptomyces ochraceisclero- JCM 4801' (= ATCC 15814') A-41 Streptomyces albidoflavus JCM 4446T (= ATCC 25422') A- 1A ticus Streptomyces albofluvus JCM 4615T (= ATCC 12626') E-54 Streptomyces olivaceoviridis JCM 4499' (= ATCC 25478') A-20 Streptomyces albus subsp. JCM 4450T (= ATCC 25426T) A-16 Streptomyces pactum JCM 4809T (= ATCC 27456') c-44 albus Streptomyces parvulus ATCC 12434' A-12" Streptomyces amakusaensis JCM 4617T (= ATCC 23876') B" Streptomyces phaeochromo- JCM 4659' (= ATCC 23945T) A-40 Streptomyces aminophilus JCM 4619T (= ATCC 13558') A-16* genes Streptomyces antibioticus JCM 4620T (= ATCC 23879T) A-3 1 Streptomyces poonensis JCM 4815' (= ATCC 15723') A-22 Streptomyces anulatus JCM 4721' (= ATCC 27416T) A-1B Streptomyces prasinopilosus JCM 4404' (= ATCC 19799') A-37* Streptomyces atroolivaceus JCM 4345T (= ATCC 19725') A-3 Streptomyces prasinosporus JCM 4816T (= ATCC 1791gT) A-38 Streptomyces aurantiacus JCM 4453T (= ATCC 19822') c-45 Streptomyces prunicolor JCM 4508T (= ATCC 25487T) A-11 Streptomyces aurantiogriseus JCM 4346T (= ATCC 19887') A" Streptomyces psammoticus JCM 4434T ( = ATCC 2548gT) F-67 Streptomyces aureofaciens JCM 4624' (= ATCC 23884T) A-14 Streptomyces pupreus JCM 3172T (= ATCC 27787') F-65 Streptomyces badius JCM 4350' (= ATCC 19888T) c" Streptomyces ramulosus JCM 4604' (= ATCC 19802') c Streptomyces bambergiensis JCM 472gT (= ATCC 13879') A' Streptomyces rimosus subsp. JCM 4667' (= ATCC 239.559 B-42 Streptomyces bikiniensis JCM 4011T (= ATCC 11062') F-64 rimosus Streptomyces bluensis JCM 4729' (= ATCC 27420') A-39" Streptomyces rochei JCM 4074' (= ATCC 23956') A-12 Streptomyces cacaoi JCM 4352' (= ATCC 19732T) A-16d Streptomyces sulphureus JCM 4835' (= ATCC 27468') c Streptomyces califomicus JCM 4567' (= ATCC 19734T) A-9 Streptomyces tendae JCM 4610' (= ATCC 19812') A-12d Streptomyces canus JCM 456gT (= ATCC 1973T) A-25 Streptomyces thermonitrifi- JCM 4841' (= ATCC 23385') A-36d Streptomyces cellulosae JCM 4462T (= ATCC 25439T) A-13 cans Streptomyces chattanoogensis JCM 4571T (= ATCC 19739') A-35 Streptomyces thermoviolaceus JCM 4843' ( = ATCC 19283') c-45* Streptomyces chromofiscus JCM 4354' (= ATCC 23896') A-15 subsp. thermoviolaceus Streptomyces cyanoalbus JCM 4363T (= ATCC 23902T) A-37* Streptomyces thermovulgaris JCM 4520' (= ATCC 25501T) A-36 Streptomyces diastaticus JCM 4745T (= ATCC 3315') A-19 Streptomyces tubercidicus JCM 4558' (= ATCC 25502T) c-47 subsp. diastaticus Streptomyces varsoviensis JCM 4523T (= ATCC 25505T) C-46 Streptomyces exfoliatus JCM 4366T (= ATCC 19750T) A-5 Streptomyces venezuelae IF0 13096T (= ATCC 25508') A-6' Streptomyces jilipinensis JCM 4369T (= ATCC 23905') A-30 Streptomyces violaceus JCM 4533' (= ATCC 25515') A-6 Streptomyces jinlayi JCM 4637T (= ATCC 23906') I' Streptomyces violaceusniger JCM 4850T (= ATCC 27477') A-32 Streptomyces flaveolus JCM 4577T (= ATCC 19754') A-24 Streptomyces viridochromoge-
Load more

Recommended publications
  • Kaistella Soli Sp. Nov., Isolated from Oil-Contaminated Soil
    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.
    [Show full text]
  • Estimation of Antimicrobial Activities and Fatty Acid Composition Of
    Estimation of antimicrobial activities and fatty acid composition of actinobacteria isolated from water surface of underground lakes from Badzheyskaya and Okhotnichya caves in Siberia Irina V. Voytsekhovskaya1,*, Denis V. Axenov-Gribanov1,2,*, Svetlana A. Murzina3, Svetlana N. Pekkoeva3, Eugeniy S. Protasov1, Stanislav V. Gamaiunov2 and Maxim A. Timofeyev1 1 Irkutsk State University, Irkutsk, Russia 2 Baikal Research Centre, Irkutsk, Russia 3 Institute of Biology of the Karelian Research Centre of the Russian Academy of Sciences, Petrozavodsk, Karelia, Russia * These authors contributed equally to this work. ABSTRACT Extreme and unusual ecosystems such as isolated ancient caves are considered as potential tools for the discovery of novel natural products with biological activities. Acti- nobacteria that inhabit these unusual ecosystems are examined as a promising source for the development of new drugs. In this study we focused on the preliminary estimation of fatty acid composition and antibacterial properties of culturable actinobacteria isolated from water surface of underground lakes located in Badzheyskaya and Okhotnichya caves in Siberia. Here we present isolation of 17 strains of actinobacteria that belong to the Streptomyces, Nocardia and Nocardiopsis genera. Using assays for antibacterial and antifungal activities, we found that a number of strains belonging to the genus Streptomyces isolated from Badzheyskaya cave demonstrated inhibition activity against Submitted 23 May 2018 bacteria and fungi. It was shown that representatives of the genera Nocardia and Accepted 24 September 2018 Nocardiopsis isolated from Okhotnichya cave did not demonstrate any tested antibiotic Published 25 October 2018 properties. However, despite the lack of antimicrobial and fungicidal activity of Corresponding author Nocardia extracts, those strains are specific in terms of their fatty acid spectrum.
    [Show full text]
  • Streptomyces Sannurensis Sp. Nov., a New Alkaliphilic Member of the Genus Streptomyces Isolated from Wadi Sannur in Egypt
    African Journal of Microbiology Research Vol. 5(11), pp. 1329-1334, 4 June, 2011 Available online http://www.academicjournals.org/ajmr DOI: 10.5897/AJMR11.200 ISSN 1996-0808 ©2011 Academic Journals Full Length Research Paper Streptomyces sannurensis sp. nov., a new alkaliphilic member of the genus Streptomyces isolated from Wadi Sannur in Egypt Wael N. Hozzein1,2*, Mohammed I. A. Ali3, Ola Hammouda2, Ahmed S. Mousa2 and Michael Goodfellow4 1Chair of Advanced Proteomics and Cytomics Research, Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia. 2Botany Department, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt. 3Botany Department, Faculty of Science, Cairo University, Giza, Egypt. 4School of Biology, University of Newcastle, Newcastle upon Tyne, NE1 7RU, UK. Accepted 19 April, 2011 The taxonomic position of an actinomycete isolated from a soil sample collected from Wadi Sannur in Egypt was established using a polyphasic approach. The isolate, which was designated WS 51T, was shown to have chemical and morphological properties typical of streptomycetes. An almost complete 16S rDNAgene sequence of the strain was generated and compared with corresponding sequences of representative streptomycetes. The resultant data confirmed the classification of the strain in the genus Streptomyces but also showed that it formed a distinct phyletic line within the 16S rDNAStreptomyces gene tree. The organism was most closely associated to the type strains of Streptomyces hygroscopicus, Streptomyces malaysiensis and Streptomyces yatensis but was readily separated from them using a range of phenotypic properties. It is proposed that strain WS 51T (= CCTCC 001032T = DSM 41834T) be classified in the genus Streptomyces as Streptomyces sannurensis sp.
    [Show full text]
  • View Details
    INDEX CHAPTER NUMBER CHAPTER NAME PAGE Extraction of Fungal Chitosan and its Chapter-1 1-17 Advanced Application Isolation and Separation of Phenolics Chapter-2 using HPLC Tool: A Consolidate Survey 18-48 from the Plant System Advances in Microbial Genomics in Chapter-3 49-80 the Post-Genomics Era Advances in Biotechnology in the Chapter-4 81-94 Post Genomics era Plant Growth Promotion by Endophytic Chapter-5 Actinobacteria Associated with 95-107 Medicinal Plants Viability of Probiotics in Dairy Products: A Chapter-6 Review Focusing on Yogurt, Ice 108-132 Cream, and Cheese Published in: Dec 2018 Online Edition available at: http://openaccessebooks.com/ Reprints request: [email protected] Copyright: @ Corresponding Author Advances in Biotechnology Chapter 1 Extraction of Fungal Chitosan and its Advanced Application Sahira Nsayef Muslim1; Israa MS AL-Kadmy1*; Alaa Naseer Mohammed Ali1; Ahmed Sahi Dwaish2; Saba Saadoon Khazaal1; Sraa Nsayef Muslim3; Sarah Naji Aziz1 1Branch of Biotechnology, Department of Biology, College of Science, AL-Mustansiryiah University, Baghdad-Iraq 2Branch of Fungi and Plant Science, Department of Biology, College of Science, AL-Mustansiryiah University, Baghdad-Iraq 3Department of Geophysics, College of remote sensing and geophysics, AL-Karkh University for sci- ence, Baghdad-Iraq *Correspondense to: Israa MS AL-Kadmy, Department of Biology, College of Science, AL-Mustansiryiah University, Baghdad-Iraq. Email: [email protected] 1. Definition and Chemical Structure Biopolymer is a term commonly used for polymers which are synthesized by living organisms [1]. Biopolymers originate from natural sources and are biologically renewable, biodegradable and biocompatible. Chitin and chitosan are the biopolymers that have received much research interests due to their numerous potential applications in agriculture, food in- dustry, biomedicine, paper making and textile industry.
    [Show full text]
  • Improved Taxonomy of the Genus Streptomyces
    UNIVERSITEIT GENT Faculteit Wetenschappen Vakgroep Biochemie, Fysiologie & Microbiologie Laboratorium voor Microbiologie Improved taxonomy of the genus Streptomyces Benjamin LANOOT Scriptie voorgelegd tot het behalen van de graad van Doctor in de Wetenschappen (Biochemie) Promotor: Prof. Dr. ir. J. Swings Co-promotor: Dr. M. Vancanneyt Academiejaar 2004-2005 FACULTY OF SCIENCES ____________________________________________________________ DEPARTMENT OF BIOCHEMISTRY, PHYSIOLOGY AND MICROBIOLOGY UNIVERSITEIT LABORATORY OF MICROBIOLOGY GENT IMPROVED TAXONOMY OF THE GENUS STREPTOMYCES DISSERTATION Submitted in fulfilment of the requirements for the degree of Doctor (Ph D) in Sciences, Biochemistry December 2004 Benjamin LANOOT Promotor: Prof. Dr. ir. J. SWINGS Co-promotor: Dr. M. VANCANNEYT 1: Aerial mycelium of a Streptomyces sp. © Michel Cavatta, Academy de Lyon, France 1 2 2: Streptomyces coelicolor colonies © John Innes Centre 3: Blue haloes surrounding Streptomyces coelicolor colonies are secreted 3 4 actinorhodin (an antibiotic) © John Innes Centre 4: Antibiotic droplet secreted by Streptomyces coelicolor © John Innes Centre PhD thesis, Faculty of Sciences, Ghent University, Ghent, Belgium. Publicly defended in Ghent, December 9th, 2004. Examination Commission PROF. DR. J. VAN BEEUMEN (ACTING CHAIRMAN) Faculty of Sciences, University of Ghent PROF. DR. IR. J. SWINGS (PROMOTOR) Faculty of Sciences, University of Ghent DR. M. VANCANNEYT (CO-PROMOTOR) Faculty of Sciences, University of Ghent PROF. DR. M. GOODFELLOW Department of Agricultural & Environmental Science University of Newcastle, UK PROF. Z. LIU Institute of Microbiology Chinese Academy of Sciences, Beijing, P.R. China DR. D. LABEDA United States Department of Agriculture National Center for Agricultural Utilization Research Peoria, IL, USA PROF. DR. R.M. KROPPENSTEDT Deutsche Sammlung von Mikroorganismen & Zellkulturen (DSMZ) Braunschweig, Germany DR.
    [Show full text]
  • Potential of Bioremediation and PGP Traits in Streptomyces As Strategies for Bio-Reclamation of Salt-Affected Soils for Agriculture
    pathogens Review Potential of Bioremediation and PGP Traits in Streptomyces as Strategies for Bio-Reclamation of Salt-Affected Soils for Agriculture Neli Romano-Armada 1,2 , María Florencia Yañez-Yazlle 1,3, Verónica P. Irazusta 1,3, Verónica B. Rajal 1,2,4,* and Norma B. Moraga 1,2 1 Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Av. Bolivia 5150, Salta 4400, Argentina; [email protected] (N.R.-A.); fl[email protected] (M.F.Y.-Y.); [email protected] (V.P.I.); [email protected] (N.B.M.) 2 Facultad de Ingeniería, UNSa, Salta 4400, Argentina 3 Facultad de Ciencias Naturales, UNSa, Salta 4400, Argentina 4 Singapore Centre for Environmental Life Sciences Engineering (SCELSE), School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore * Correspondence: [email protected] Received: 15 December 2019; Accepted: 8 February 2020; Published: 13 February 2020 Abstract: Environmental limitations influence food production and distribution, adding up to global problems like world hunger. Conditions caused by climate change require global efforts to be improved, but others like soil degradation demand local management. For many years, saline soils were not a problem; indeed, natural salinity shaped different biomes around the world. However, overall saline soils present adverse conditions for plant growth, which then translate into limitations for agriculture. Shortage on the surface of productive land, either due to depletion of arable land or to soil degradation, represents a threat to the growing worldwide population. Hence, the need to use degraded land leads scientists to think of recovery alternatives.
    [Show full text]
  • Study of Actinobacteria and Their Secondary Metabolites from Various Habitats in Indonesia and Deep-Sea of the North Atlantic Ocean
    Study of Actinobacteria and their Secondary Metabolites from Various Habitats in Indonesia and Deep-Sea of the North Atlantic Ocean Von der Fakultät für Lebenswissenschaften der Technischen Universität Carolo-Wilhelmina zu Braunschweig zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigte D i s s e r t a t i o n von Chandra Risdian aus Jakarta / Indonesien 1. Referent: Professor Dr. Michael Steinert 2. Referent: Privatdozent Dr. Joachim M. Wink eingereicht am: 18.12.2019 mündliche Prüfung (Disputation) am: 04.03.2020 Druckjahr 2020 ii Vorveröffentlichungen der Dissertation Teilergebnisse aus dieser Arbeit wurden mit Genehmigung der Fakultät für Lebenswissenschaften, vertreten durch den Mentor der Arbeit, in folgenden Beiträgen vorab veröffentlicht: Publikationen Risdian C, Primahana G, Mozef T, Dewi RT, Ratnakomala S, Lisdiyanti P, and Wink J. Screening of antimicrobial producing Actinobacteria from Enggano Island, Indonesia. AIP Conf Proc 2024(1):020039 (2018). Risdian C, Mozef T, and Wink J. Biosynthesis of polyketides in Streptomyces. Microorganisms 7(5):124 (2019) Posterbeiträge Risdian C, Mozef T, Dewi RT, Primahana G, Lisdiyanti P, Ratnakomala S, Sudarman E, Steinert M, and Wink J. Isolation, characterization, and screening of antibiotic producing Streptomyces spp. collected from soil of Enggano Island, Indonesia. The 7th HIPS Symposium, Saarbrücken, Germany (2017). Risdian C, Ratnakomala S, Lisdiyanti P, Mozef T, and Wink J. Multilocus sequence analysis of Streptomyces sp. SHP 1-2 and related species for phylogenetic and taxonomic studies. The HIPS Symposium, Saarbrücken, Germany (2019). iii Acknowledgements Acknowledgements First and foremost I would like to express my deep gratitude to my mentor PD Dr.
    [Show full text]
  • Diversity of Free-Living Nitrogen Fixing Bacteria in the Badlands of South Dakota Bibha Dahal South Dakota State University
    South Dakota State University Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange Theses and Dissertations 2016 Diversity of Free-living Nitrogen Fixing Bacteria in the Badlands of South Dakota Bibha Dahal South Dakota State University Follow this and additional works at: http://openprairie.sdstate.edu/etd Part of the Bacteriology Commons, and the Environmental Microbiology and Microbial Ecology Commons Recommended Citation Dahal, Bibha, "Diversity of Free-living Nitrogen Fixing Bacteria in the Badlands of South Dakota" (2016). Theses and Dissertations. 688. http://openprairie.sdstate.edu/etd/688 This Thesis - Open Access is brought to you for free and open access by Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange. For more information, please contact [email protected]. DIVERSITY OF FREE-LIVING NITROGEN FIXING BACTERIA IN THE BADLANDS OF SOUTH DAKOTA BY BIBHA DAHAL A thesis submitted in partial fulfillment of the requirements for the Master of Science Major in Biological Sciences Specialization in Microbiology South Dakota State University 2016 iii ACKNOWLEDGEMENTS “Always aim for the moon, even if you miss, you’ll land among the stars”.- W. Clement Stone I would like to express my profuse gratitude and heartfelt appreciation to my advisor Dr. Volker Brӧzel for providing me a rewarding place to foster my career as a scientist. I am thankful for his implicit encouragement, guidance, and support throughout my research. This research would not be successful without his guidance and inspiration.
    [Show full text]
  • Book of Abstracts
    Book of Abstracts VI International Conference on Environmental, Industrial and Applied Microbiology – BioMicroWorld2015 Barcelona (Spain), 28-30 October 2015 VI International Conference on Environmental, Industrial and Applied Microbiology - BioMicroWorld2015 VI International Conference on Environmental, Industrial and Applied Microbiology - BioMicroWorld2015 Barcelona (Spain), 28-30 October 2015 Barcelona (Spain), 28-30 October 2015 Effect on Metaresistome and metabolic profile (CLPP) soil bacterial communities of different 30 Introduction XXIII agricultural management in Vitis vinifera plots Plenary Lectures XXIX Effects of Inorganic Fertilizers and Organic Manure on Cyanobacteria of Paddy Fields 31 Endophytic bacteria isolated from two varieties of Oryza sativa cultivated in southern Brazil. 32 Session 1: Agriculture, soil, forest microbiology 1 Evaluation of the biological activity of extracts obtained from bacteria associated with nematodes 33 1-Aminocyclopropane-1-carboxylate deaminase producing bacteria promote wheat growth under 2 against Leaf Cutting Ants Atta cephalotes Linnaeus (Hymenoptera Formicidae) water stress Exploration of microorganisms associated with insects, searching for active substances produced 34 454-Pyrosequencing reveals high and differential level of fungal diversity in the Oasis farming 3 from bacteria system in Oman Functional traits of endophytic and rhizosphere fungi and bacteria of Butia archeri Glassman roots 35 A new Cryphonectria hypovirus 1 subtype found in Portugal 4 Genetic tools for site-specific
    [Show full text]
  • Ep 2434019 A1
    (19) & (11) EP 2 434 019 A1 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 28.03.2012 Bulletin 2012/13 C12N 15/82 (2006.01) C07K 14/395 (2006.01) C12N 5/10 (2006.01) G01N 33/50 (2006.01) (2006.01) (2006.01) (21) Application number: 11160902.0 C07K 16/14 A01H 5/00 C07K 14/39 (2006.01) (22) Date of filing: 21.07.2004 (84) Designated Contracting States: • Kamlage, Beate AT BE BG CH CY CZ DE DK EE ES FI FR GB GR 12161, Berlin (DE) HU IE IT LI LU MC NL PL PT RO SE SI SK TR • Taman-Chardonnens, Agnes A. 1611, DS Bovenkarspel (NL) (30) Priority: 01.08.2003 EP 03016672 • Shirley, Amber 15.04.2004 PCT/US2004/011887 Durham, NC 27703 (US) • Wang, Xi-Qing (62) Document number(s) of the earlier application(s) in Chapel Hill, NC 27516 (US) accordance with Art. 76 EPC: • Sarria-Millan, Rodrigo 04741185.5 / 1 654 368 West Lafayette, IN 47906 (US) • McKersie, Bryan D (27) Previously filed application: Cary, NC 27519 (US) 21.07.2004 PCT/EP2004/008136 • Chen, Ruoying Duluth, GA 30096 (US) (71) Applicant: BASF Plant Science GmbH 67056 Ludwigshafen (DE) (74) Representative: Heistracher, Elisabeth BASF SE (72) Inventors: Global Intellectual Property • Plesch, Gunnar GVX - C 6 14482, Potsdam (DE) Carl-Bosch-Strasse 38 • Puzio, Piotr 67056 Ludwigshafen (DE) 9030, Mariakerke (Gent) (BE) • Blau, Astrid Remarks: 14532, Stahnsdorf (DE) This application was filed on 01-04-2011 as a • Looser, Ralf divisional application to the application mentioned 13158, Berlin (DE) under INID code 62.
    [Show full text]
  • Genomic and Phylogenomic Insights Into the Family Streptomycetaceae Lead to Proposal of Charcoactinosporaceae Fam. Nov. and 8 No
    bioRxiv preprint doi: https://doi.org/10.1101/2020.07.08.193797; this version posted July 8, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Genomic and phylogenomic insights into the family Streptomycetaceae 2 lead to proposal of Charcoactinosporaceae fam. nov. and 8 novel genera 3 with emended descriptions of Streptomyces calvus 4 Munusamy Madhaiyan1, †, * Venkatakrishnan Sivaraj Saravanan2, † Wah-Seng See-Too3, † 5 1Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 6 Singapore 117604; 2Department of Microbiology, Indira Gandhi College of Arts and Science, 7 Kathirkamam 605009, Pondicherry, India; 3Division of Genetics and Molecular Biology, 8 Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 9 Malaysia 10 *Corresponding author: Temasek Life Sciences Laboratory, 1 Research Link, National 11 University of Singapore, Singapore 117604; E-mail: [email protected] 12 †All these authors have contributed equally to this work 13 Abstract 14 Streptomycetaceae is one of the oldest families within phylum Actinobacteria and it is large and 15 diverse in terms of number of described taxa. The members of the family are known for their 16 ability to produce medically important secondary metabolites and antibiotics. In this study, 17 strains showing low 16S rRNA gene similarity (<97.3 %) with other members of 18 Streptomycetaceae were identified and subjected to phylogenomic analysis using 33 orthologous 19 gene clusters (OGC) for accurate taxonomic reassignment resulted in identification of eight 20 distinct and deeply branching clades, further average amino acid identity (AAI) analysis showed 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.08.193797; this version posted July 8, 2020.
    [Show full text]
  • Taxonomy, Identification and Biological Activities of a Novel Isolate of Streptomyces Albus
    Kadiri Sunanda Kumari et al. / Journal of Pharmacy Research 2011,4(12),4678-4680 Research Article Available online through ISSN: 0974-6943 www.jpronline.info Taxonomy, Identification and Biological Activities of a Novel Isolate of Streptomyces albus Kadiri Sunanda Kumari* and Vidavalur Siddaiah Department of Organic Chemistry & FDW, Andhra University, Visakhapatnam 530 003, India Received on:20-08-2011; Revised on: 15-09-2011; Accepted on:10-11-2011 ABSTRACT Various isolates of streptomycetes species were isolated from different soil sediments of Visakhapatnam Coast. Preliminary screening by cross-streak method showed that 19 isolates exhibited good antimicrobial activity. Among these 19 isolates tested, isolate MB201 was the most active one and thus was selected for identification. Morphological, cultural, physiological, biochemical characteristics and biological properties as well as enzymatic activities and cell wall composition suggested that the isolate belonged to the genus streptomyces. The 16S ribosomal DNA amplification for phylogenetic study revealed that the isolate was highly related to Streptomyces albus (~99%), so it was designated as Streptomyces albus gangavarams. This new strain produced antimicrobial agents active against Gram +ve and Gram –ve bacteria and fungi. KEY WORDS: Streptomyces, S.albus INTRODUCTION: Numerous classifications were devised to accommodate the increasing number Morphological characterization: of streptomyces species, most of them based on a few subjectively chosen The spore chain morphology of the
    [Show full text]