DOCSLIB.ORG

Évolution Génomique Au Sein D'une Population Naturelle De Streptomyces

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Évolution Génomique Au Sein D'une Population Naturelle De Streptomyces Évolution génomique au sein d’une population naturelle de Streptomyces Abdoul-Razak Tidjani To cite this version: Abdoul-Razak Tidjani. Évolution génomique au sein d’une population naturelle de Streptomyces. Ecosystèmes. Université de Lorraine, 2019. Français. NNT : 2019LORR0159. tel-02461512 HAL Id: tel-02461512 https://hal.univ-lorraine.fr/tel-02461512 Submitted on 22 Jun 2020 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. AVERTISSEMENT Ce document est le fruit d'un long travail approuvé par le jury de soutenance et mis à disposition de l'ensemble de la communauté universitaire élargie. Il est soumis à la propriété intellectuelle de l'auteur. Ceci implique une obligation de citation et de référencement lors de l’utilisation de ce document. D'autre part, toute contrefaçon, plagiat, reproduction illicite encourt une poursuite pénale. Contact : [email protected] LIENS Code de la Propriété Intellectuelle. articles L 122. 4 Code de la Propriété Intellectuelle. articles L 335.2- L 335.10 http://www.cfcopies.com/V2/leg/leg_droi.php http://www.culture.gouv.fr/culture/infos-pratiques/droits/protection.htm Ecole Doctorale SIReNa - Sciences et Ingénierie des Ressources Naturelles Thèse Présentée et soutenue publiquement pour l’obtention du titre de DOCTEUR DE l’UNIVERSITE DE LORRAINE Mention : « Ecotoxicologie, Biodiversité, Ecosystèmes » Par Abdoul-Razak TIDJANI Evolution génomique au sein d'une population naturelle de Streptomyces Soutenance publique prévue le Mardi 03 décembre 2019 Membres du jury : Rapporteurs : Dr. Philippe NORMAND Directeur de recherche CNRS, Lyon Pr. Dr. Gregory VELICER Professeur, Eidgenössische Technische Hochschule (ETH), Zürich Examinateurs : Pr. Stéphanie BURY-MONE Professeure, Université Paris-Sud Dr. Catherine MASSON-BOIVIN Directrice de recherche INRA, Toulouse Dr. Cyril BONTEMPS Maître de conférences, Université de lorraine, Co-directeur de thèse Pr. Pierre LEBLOND Professeur, Université de Lorraine, Directeur de thèse ----------------------------------------------------------------------------------------------------------------------------------- UMR 1128 DynAMic INRA-Université de Lorraine, Faculté des Sciences et Technologies, Boulevard des Aiguillettes, BP 70239, 54506 Vandœuvre-lès-Nancy 2 « Le commencement de toutes les sciences, c'est l'étonnement de ce que les choses sont ce qu'elles sont » Aristote 3 4 Dédicaces A ma Mère Assia et à mon Père Mashoud, Pour avoir toujours cru en moi, pour votre soutien indéfectible et pour tous les sacrifices consentis jusqu’à présent à mon égard. A mes sœurs, Kadira, Medina et à mes frères, Wassihou, Nazif, Rachid, Loin des yeux près du cœur dit-on souvent. Mais vous, vous ne m’aviez jamais perdu de vue. Et je comprends maintenant l’importance de tous ces messages quotidiens que nous échangeons. A Maud, Trois années de thèse c’est long, tout comme les 1018 km parcourus les week-ends pour nous voir. Merci pour ta patience, ta persévérance et ton indulgence au cours de ces presque 5 dernières années. 5 6 REMERCIEMENTS I would like to thank Prof. Gregory Velicer, Dr. Philippe Normand, Dr. Catherine Masson and Prof. Stéphanie Bury-Moné for accepting to review this manuscript. J’aimerais remercier Mr le Professeur Pierre Leblond et Mr le Docteur Cyril Bontemps. Le plus gratifiant est d’avoir eu l’honneur de vous avoir avant tout comme mentors, et puis comme directeur et co- directeur de thèse. Ces années passées à me guider sur ce chemin sinueux mais plein de promesses que représente le doctorat feront parties des plus riches et des plus intenses de ma vie. J’aimerais à travers ces modestes lignes vous dire merci(s) ; un pour chacun des 1126 jours passés à apprendre à vos côtés (week-ends compris). Je voudrais remercier le Pr Bertrand Aigle, pour son accueil (chez lui alors que je venais juste de poser mes valises à Nancy) et au labo ainsi que pour les multiples échanges scientifiques ou non que nous avions eus. Un grand merci à ma Lolo. Pour m’avoir initié à la grande messe que nous vouons à Streptomyces et pour ta disponibilité lorsque le besoin se faisait sentir. Merci à Emilie Pio pour tous ces moments intra et extra labo. Tu as été comme une bouffée d’air frais pendant cette thèse. Merci à mon frère Stéphane, pour ta présence, ta sollicitude et le fait d’être toi. Un grand merci également à Louise (pour les « on mange ? » de chaque midi), à Emilie Robert, à Johan et à Anthony. Ces 3 années n’auraient pas été pareilles sans vous tous. Merci à toi Layla (guide omniscient dans les méandres administratifs) pour ta sollicitude. Je voudrais remercier mes amis thésards doctorants : Milena, Matthieu, Julie, Li, Haïfa, et Caroline (je viens de remarquer que vous êtes arrivés au labo inversement chronologiquement à l’ordre alphabétique de vos prénoms. Oui je sais ! on ne change pas un scientifique). Merci pour ces moments passés ensemble dans la quête de ce « précieux ». Bon courage à vous. Sans oublier mes amis Docteurs, Maxime pour les moments de partage au cours de ta dernière année, Charles, Narimane, Clàudia, Greg, Xavier (pour les moments d’évasion scientifique PS4, d’exploration de débit de boissons jus d’ananas à Nancy), Yaouba, Estefania, Yordenka et Sonia. Je n’oublie pas dans cette équation complexe de remerciements les doctorantes du « labo d’à côté », Katleen et Rania. Et je terminerai par les « djeuns » (par ordre alphabétique) : Abbas, Anissa, Anthony, Camille, Louise, Maha et Redouane. J’aimerais remercier tous les membres du laboratoire, permanents et non, avec qui j’ai eu à partager une partie ou toutes ces 3 dernières années. Et puis … allez la farandole pour tout le monde…. Merci à Claire pour ton écoute et ta disponibilité ; merci à toi virginie pour ces moments de partage tant au labo qu’en extra labo ; Merci à Gérard pour nos discussions scientifiques et non, ces moments qui font « qu’on ne sent pas la thèse passer » ; merci à Annabelle (eh oui Artémis ça se transmet), Nicolas, Sophie, Nathalie, Yvonne, Florence, Badreddine pour ces discussions enrichissantes lors des repas de midi et pendant mes déambulations quotidiennes (que j’ose appeler pauses) dans les bureaux. 7 8 LISTE DES ABBREVIATIONS °C : Degrés Celsius µl : microlitre µM : micromolaire A : Adenylation ACP : Acyl Carrier Protein ACV : L-aminoadipyl-L-cysteinyl-D-valine ADN : Acide désoxyribonucléique ADNg : Acide désoxyribonucléique génomique AFLP : Amplified Fragment Length Polymorphism AICE : Actinomycete Integrative and Conjugative Element ANI : Average nucleotide identity antiSMASH : antibiotics and Secondary Metabolite Analysis Shell ARN : Acide ribonucléique ARNr : Acide ribonucléique ribosomique AT : Acyltransferase attB : site d’attachement bactérien attP : site d’attachement plasmidique BET : Bromure d’Ethidium BIR : Break Induced Replication C : Condensation CGSMS : Clusters de Gènes de Synthèse de Métabolites Spécialisés cm : Centimètre CRISPR : Clustered Regularly Interspaced Short Palindromic Repeats dNTP : Désoxyribose nucléoside triphosphate DO : Densité optique Hfr : Haute fréquence de recombinaison ICE : Integrative and Conjugative Element kb : Kilobases l : Litres Mb : Mégabases 9 MEB : Microscope Electronique à Balayage mg : Milligramme ml : millilitre MLST : MultiLocus Sequence Typing mM : Millimolaire NCBI : National Center of Biotechnology NGS : Next Generation Sequencing technologies NRP : Non-Ribosomal Peptide NRPS : Non ribosomal Protein Synthase nt : Nucléotide ORF : Open Reading Frame oriT : origine de Transfert PCR : Polymerase Reaction Chain pH : Potentiel d’hydrogène PKS : Polyketide Synthase PSAM2 : Streptomyces ambofaciens plamid 2 RAST : Rapid Annotation using Subsystem Technology REP-PCR : Repetitive Element Polymerase Reaction Chain RFLP : Restriction Fragment Length Polymorphism RIPP : RIbosomally synthetized and Post-translationally modified Peptide RPM : Rotations Par Minutes SDS : Sodium Dodecyl Sulfate SFM: Soya Floor Manitol SNP : SIngle Nucleotide Polymorphism ST : Sequence Type T4SS : Type IV Secretion System TAP : Telomere Associated Protein Te : Thioesterase TIR : Terminal Inverted Repeats TP : Terminal Protein UTO : Operational Taxonomic Unit 10 SOMMAIRE SOMMAIRE ............................................................................................................................................ 11 Préambule ............................................................................................................................................. 15 INTRODUCTION ..................................................................................................................................... 17 I. Un modèle d’étude : Le micro-habitat sol forestier ...................................................................... 19 I.1 Importance de l’échelle dans l’étude des bactéries du sol. .................................................. 21 I.2 Etude de la diversité et de la répartition des bactéries à la micro-échelle ........................... 22 I.2.1 L’étude des habitats à la micro-échelle et de leurs bactéries ..........................................
Load more

Recommended publications
  • 341388717-Oa
    ORIGINAL RESEARCH published: 16 May 2017 doi: 10.3389/fmicb.2017.00877 Streptomyces colonosanans sp. nov., A Novel Actinobacterium Isolated from Malaysia Mangrove Soil Exhibiting Antioxidative Activity and Cytotoxic Potential against Human Colon Cancer Cell Lines Jodi Woan-Fei Law 1, Hooi-Leng Ser 1, Acharaporn Duangjai 2, 3, Surasak Saokaew 1, 3, 4, Sarah I. Bukhari 5, Tahir M. Khan 1, 6, Nurul-Syakima Ab Mutalib 7, Kok-Gan Chan 8, Edited by: Bey-Hing Goh 1, 3* and Learn-Han Lee 1, 3* Dongsheng Zhou, Beijing Institute of Microbiology and 1 Novel Bacteria and Drug Discovery Research Group, School of Pharmacy, Monash University Malaysia, Bandar Sunway, Epidemiology, China Malaysia, 2 Division of Physiology, School of Medical Sciences, University of Phayao, Phayao, Thailand, 3 Center of Health Reviewed by: Outcomes Research and Therapeutic Safety, School of Pharmaceutical Sciences, University of Phayao, Phayao, Thailand, 4 Andrei A. Zimin, Faculty of Pharmaceutical Sciences, Pharmaceutical Outcomes Research Center, Naresuan University, Phitsanulok, 5 6 Institute of Biochemistry and Thailand, Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia, Department of 7 Physiology of Microorganisms (RAS), Pharmacy, Absyn University Peshawar, Peshawar, Pakistan, UKM Medical Molecular Biology Institute, UKM Medical Centre, 8 Russia University Kebangsaan Malaysia, Kuala Lumpur, Malaysia, Division of Genetics and Molecular Biology, Faculty of Science, Antoine Danchin, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia Institut de Cardiométabolisme et Nutrition (ICAN), France Streptomyces colonosanans MUSC 93JT, a novel strain isolated from mangrove forest *Correspondence: Bey-Hing Goh soil located at Sarawak, Malaysia. The bacterium was noted to be Gram-positive and [email protected] to form light yellow aerial and vivid yellow substrate mycelium on ISP 2 agar.
    [Show full text]
  • Anticancer Drug Discovery from Microbial Sources: the Unique Mangrove Streptomycetes
    molecules Review Anticancer Drug Discovery from Microbial Sources: The Unique Mangrove Streptomycetes Jodi Woan-Fei Law 1, Lydia Ngiik-Shiew Law 2, Vengadesh Letchumanan 1 , Loh Teng-Hern Tan 1, Sunny Hei Wong 3, Kok-Gan Chan 4,5,* , Nurul-Syakima Ab Mutalib 6,* and Learn-Han Lee 1,* 1 Novel Bacteria and Drug Discovery (NBDD) Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Selangor Darul Ehsan, Malaysia; [email protected] (J.W.-F.L.); [email protected] (V.L.); [email protected] (L.T.-H.T.) 2 Monash Credentialed Pharmacy Clinical Educator, Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville 3052, VIC, Australia; [email protected] 3 Li Ka Shing Institute of Health Sciences, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong, China; [email protected] 4 Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia 5 International Genome Centre, Jiangsu University, Zhenjiang 212013, China 6 UKM Medical Molecular Biology Institute (UMBI), UKM Medical Centre, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia * Correspondence: [email protected] (K.-G.C.); [email protected] (N.-S.A.M.); [email protected] (L.-H.L.) Academic Editor: Owen M. McDougal Received: 8 October 2020; Accepted: 13 November 2020; Published: 17 November 2020 Abstract: Worldwide cancer incidence and mortality have always been a concern to the community. The cancer mortality rate has generally declined over the years; however, there is still an increased mortality rate in poorer countries that receives considerable attention from healthcare professionals.
    [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]
  • Streptomyces Monashensis Sp. Nov., a Novel Mangrove Soil
    www.nature.com/scientificreports Corrected: Author Correction OPEN Streptomyces monashensis sp. nov., a novel mangrove soil actinobacterium from East Received: 13 September 2018 Accepted: 21 January 2019 Malaysia with antioxidative Published online: 28 February 2019 potential Jodi Woan-Fei Law1, Hooi-Leng Ser1,2,3, Nurul-Syakima Ab Mutalib 4, Surasak Saokaew 1,5,6, Acharaporn Duangjai1,5,7, Tahir Mehmood Khan2,8, Kok-Gan Chan 9,10, Bey-Hing Goh2,3,5 & Learn-Han Lee1,3,5 A new Streptomyces species discovered from Sarawak mangrove soil is described, with the proposed name – Streptomyces monashensis sp. nov. (strain MUSC 1JT). Taxonomy status of MUSC 1JT was determined via polyphasic approach. Phylogenetic and chemotaxonomic properties of strain MUSC 1JT were in accordance with those known for genus Streptomyces. Based on phylogenetic analyses, the strains closely related to MUSC 1JT were Streptomyces corchorusii DSM 40340T (98.7%), Streptomyces olivaceoviridis NBRC 13066T (98.7%), Streptomyces canarius NBRC 13431T (98.6%) and Streptomyces coacervatus AS-0823T (98.4%). Outcomes of DNA–DNA relatedness between strain MUSC 1JT and its closely related type strains covered from 19.7 ± 2.8% to 49.1 ± 4.3%. Strain MUSC 1JT has genome size of 10,254,857 bp with DNA G + C content of 71 mol%. MUSC 1JT extract exhibited strong antioxidative activity up to 83.80 ± 4.80% in the SOD assay, with signifcant cytotoxic efect against colon cancer cell lines HCT-116 and SW480. Streptomyces monashensis MUSC 1JT (=DSM 103626T = MCCC 1K03219T) could potentially be a producer of novel bioactive metabolites; hence discovery of this new species may be highly signifcant to the biopharmaceutical industry as it could lead to development of new and useful chemo-preventive drugs.
    [Show full text]
  • Diversity, Novelty, and Antimicrobial Activity of Endophytic Actinobacteria from Mangrove Plants in Beilun Estuary National Nature Reserve of Guangxi, China
    fmicb-09-00868 May 3, 2018 Time: 16:37 # 1 ORIGINAL RESEARCH published: 04 May 2018 doi: 10.3389/fmicb.2018.00868 Diversity, Novelty, and Antimicrobial Activity of Endophytic Actinobacteria From Mangrove Plants in Beilun Estuary National Nature Reserve of Guangxi, China Zhong-ke Jiang1, Li Tuo2, Da-lin Huang3, Ilya A. Osterman4,5, Anton P. Tyurin6,7, Shao-wei Liu1, Dmitry A. Lukyanov4, Petr V. Sergiev4,5, Olga A. Dontsova4,5, Vladimir A. Korshun6,7, Fei-na Li1 and Cheng-hang Sun1* 1 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China, 2 Research Center for Medicine and Biology, Zunyi Medical University, Zunyi, China, 3 College of Basic Medical Edited by: Sciences, Guilin Medical University, Guilin, China, 4 Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Wen-Jun Li, Biology, Lomonosov Moscow State University, Moscow, Russia, 5 Skolkovo Institute of Science and Technology, Moscow, Sun Yat-sen University, China Russia, 6 Gause Institute of New Antibiotics, Moscow, Russia, 7 Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia Reviewed by: Isao Yumoto, National Institute of Advanced Endophytic actinobacteria are one of the important pharmaceutical resources and Industrial Science and Technology (AIST), Japan well known for producing different types of bioactive substances. Nevertheless, Learn-Han Lee, detection of the novelty, diversity, and bioactivity on endophytic actinobacteria Monash University Malaysia, Malaysia isolated from mangrove plants are scarce. In this study, five different mangrove Virginia Helena Albarracín, Center for Electron Microscopy plants, Avicennia marina, Aegiceras corniculatum, Kandelia obovota, Bruguiera (CIME), Argentina gymnorrhiza, and Thespesia populnea, were collected from Beilun Estuary Zhiyong Li, Shanghai Jiao Tong University, China National Nature Reserve in Guangxi Zhuang Autonomous Region, China.
    [Show full text]
  • The Genome Analysis of the Human Lung-Associated Streptomyces Sp
    microorganisms Article The Genome Analysis of the Human Lung-Associated Streptomyces sp. TR1341 Revealed the Presence of Beneficial Genes for Opportunistic Colonization of Human Tissues Ana Catalina Lara 1,† , Erika Corretto 1,†,‡ , Lucie Kotrbová 1, František Lorenc 1 , KateˇrinaPetˇríˇcková 2,3 , Roman Grabic 4 and Alica Chro ˇnáková 1,* 1 Institute of Soil Biology, Biology Centre Academy of Sciences of The Czech Republic, Na Sádkách 702/7, 37005 Ceskˇ é Budˇejovice,Czech Republic; [email protected] (A.C.L.); [email protected] (E.C.); [email protected] (L.K.); [email protected] (F.L.) 2 Institute of Immunology and Microbiology, 1st Faculty of Medicine, Charles University, Studniˇckova7, 12800 Prague 2, Czech Republic; [email protected] 3 Faculty of Science, University of South Bohemia, Branišovská 1645/31a, 37005 Ceskˇ é Budˇejovice, Czech Republic 4 Faculty of Fisheries and Protection of Waters, University of South Bohemia, Zátiší 728/II, 38925 Vodˇnany, Czech Republic; [email protected] * Correspondence: [email protected] † Both authors contributed equally. ‡ Current address: Faculty of Science and Technology, Free University of Bozen-Bolzano, Universitätsplatz 5—piazza Università 5, 39100 Bozen-Bolzano, Italy. Citation: Lara, A.C.; Corretto, E.; Abstract: Streptomyces sp. TR1341 was isolated from the sputum of a man with a history of lung and Kotrbová, L.; Lorenc, F.; Petˇríˇcková, kidney tuberculosis, recurrent respiratory infections, and COPD. It produces secondary metabolites K.; Grabic, R.; Chroˇnáková,A. associated with cytotoxicity and immune response modulation. In this study, we complement The Genome Analysis of the Human our previous results by identifying the genetic features associated with the production of these Lung-Associated Streptomyces sp.
    [Show full text]
  • Phylogenetic Study of the Species Within the Family Streptomycetaceae
    Antonie van Leeuwenhoek DOI 10.1007/s10482-011-9656-0 ORIGINAL PAPER Phylogenetic study of the species within the family Streptomycetaceae D. P. Labeda • M. Goodfellow • R. Brown • A. C. Ward • B. Lanoot • M. Vanncanneyt • J. Swings • S.-B. Kim • Z. Liu • J. Chun • T. Tamura • A. Oguchi • T. Kikuchi • H. Kikuchi • T. Nishii • K. Tsuji • Y. Yamaguchi • A. Tase • M. Takahashi • T. Sakane • K. I. Suzuki • K. Hatano Received: 7 September 2011 / Accepted: 7 October 2011 Ó Springer Science+Business Media B.V. (outside the USA) 2011 Abstract Species of the genus Streptomyces, which any other microbial genus, resulting from academic constitute the vast majority of taxa within the family and industrial activities. The methods used for char- Streptomycetaceae, are a predominant component of acterization have evolved through several phases over the microbial population in soils throughout the world the years from those based largely on morphological and have been the subject of extensive isolation and observations, to subsequent classifications based on screening efforts over the years because they are a numerical taxonomic analyses of standardized sets of major source of commercially and medically impor- phenotypic characters and, most recently, to the use of tant secondary metabolites. Taxonomic characteriza- molecular phylogenetic analyses of gene sequences. tion of Streptomyces strains has been a challenge due The present phylogenetic study examines almost all to the large number of described species, greater than described species (615 taxa) within the family Strep- tomycetaceae based on 16S rRNA gene sequences Electronic supplementary material The online version and illustrates the species diversity within this family, of this article (doi:10.1007/s10482-011-9656-0) contains which is observed to contain 130 statistically supplementary material, which is available to authorized users.
    [Show full text]
  • 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.
    [Show full text]
  • Isolation, Characterization, and Antibacterial Activity of Hard-To-Culture Actinobacteria from Cave Moonmilk Deposits
    antibiotics Article Isolation, Characterization, and Antibacterial Activity of Hard-to-Culture Actinobacteria from Cave Moonmilk Deposits Delphine Adam 1,†, Marta Maciejewska 1,†, Aymeric Naômé 1, Loïc Martinet 1, Wouter Coppieters 2, Latifa Karim 2, Denis Baurain 3 and Sébastien Rigali 1,* ID 1 Integrative Biological Sciences (InBioS), Center for Protein Engineering, Liège University, B-4000 Liège, Belgium; [email protected] (D.A.); [email protected] (M.M.); [email protected] (A.N.); [email protected] (L.M.) 2 Genomics Platform, GIGA (Grappe Interdisciplinaire de Génoprotéomique Appliquée), University of Liège (B34), B-4000 Liège, Belgium; [email protected] (W.C.); [email protected] (L.K.) 3 Integrative Biological Sciences (InBioS), PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, B-4000 Liège, Belgium; [email protected] * Correspondence: [email protected]; Tel.: +32-4-366-9830 † These authors contributed equally to this work. Received: 26 February 2018; Accepted: 19 March 2018; Published: 22 March 2018 Abstract: Cave moonmilk deposits host an abundant and diverse actinobacterial population that has a great potential for producing novel natural bioactive compounds. In our previous attempt to isolate culturable moonmilk-dwelling Actinobacteria, only Streptomyces species were recovered, whereas a metagenetic study of the same deposits revealed a complex actinobacterial community including 46 actinobacterial genera in addition to streptomycetes. In this work, we applied the rehydration-centrifugation method to lessen the occurrence of filamentous species and tested a series of strategies to achieve the isolation of hard-to-culture and rare Actinobacteria from the moonmilk deposits of the cave “Grotte des Collemboles”.
    [Show full text]
  • Streptomyces Antioxidans Sp. Nov., a Novel Mangrove Soil Actinobacterium with Antioxidative and Neuroprotective Potentials
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Frontiers - Publisher Connector ORIGINAL RESEARCH published: 16 June 2016 doi: 10.3389/fmicb.2016.00899 Streptomyces antioxidans sp. nov., a Novel Mangrove Soil Actinobacterium with Antioxidative and Neuroprotective Potentials Hooi-Leng Ser 1, 2, Loh Teng-Hern Tan 1, 2, Uma D. Palanisamy 2, Sri N. Abd Malek 3, Wai-Fong Yin 4, Kok-Gan Chan 4, Bey-Hing Goh 1, 5* and Learn-Han Lee 1, 5* 1 Novel Bacteria and Drug Discovery Research Group, School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia, 2 Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, Malaysia, 3 Biochemistry Program, Faculty of Science, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia, 4 Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia, 5 Center of Health Outcomes Research and Therapeutic Safety (Cohorts), School of Pharmaceutical Sciences, University of Phayao, Phayao, Thailand Edited by: Yuji Morita, A novel strain, Streptomyces antioxidans MUSC 164T was recovered from mangrove Aichi Gakuin University, Japan forest soil located at Tanjung Lumpur, Malaysia. The Gram-positive bacterium forms Reviewed by: Jem Stach, yellowish-white aerial and brilliant greenish yellow substrate mycelium on ISP 2 University of Newcastle, UK agar. A polyphasic approach was used to determine the taxonomy status of strain Huda Mahmoud Mahmoud, T Kuwait University, Kuwait MUSC 164 . The strain showed a spectrum of phylogenetic and chemotaxonomic Janice Lorraine Strap, properties consistent with those of the members of the genus Streptomyces.
    [Show full text]
  • Streptomyces Antioxidans Sp. Nov., a Novel Mangrove Soil Actinobacterium with Antioxidative and Neuroprotective Potentials
    ORIGINAL RESEARCH published: 16 June 2016 doi: 10.3389/fmicb.2016.00899 Streptomyces antioxidans sp. nov., a Novel Mangrove Soil Actinobacterium with Antioxidative and Neuroprotective Potentials Hooi-Leng Ser 1, 2, Loh Teng-Hern Tan 1, 2, Uma D. Palanisamy 2, Sri N. Abd Malek 3, Wai-Fong Yin 4, Kok-Gan Chan 4, Bey-Hing Goh 1, 5* and Learn-Han Lee 1, 5* 1 Novel Bacteria and Drug Discovery Research Group, School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia, 2 Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, Malaysia, 3 Biochemistry Program, Faculty of Science, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia, 4 Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia, 5 Center of Health Outcomes Research and Therapeutic Safety (Cohorts), School of Pharmaceutical Sciences, University of Phayao, Phayao, Thailand Edited by: Yuji Morita, A novel strain, Streptomyces antioxidans MUSC 164T was recovered from mangrove Aichi Gakuin University, Japan forest soil located at Tanjung Lumpur, Malaysia. The Gram-positive bacterium forms Reviewed by: Jem Stach, yellowish-white aerial and brilliant greenish yellow substrate mycelium on ISP 2 University of Newcastle, UK agar. A polyphasic approach was used to determine the taxonomy status of strain Huda Mahmoud Mahmoud, T Kuwait University, Kuwait MUSC 164 . The strain showed a spectrum of phylogenetic and chemotaxonomic Janice Lorraine Strap, properties consistent with those of the members of the genus Streptomyces. University of Ontario Institute of The cell wall peptidoglycan was determined to contain LL-diaminopimelic acid.
    [Show full text]
  • Comparative Genomic Insights Into Secondary Metabolism Biosynthetic Gene Cluster Distributions of Marine Streptomyces
    marine drugs Article Comparative Genomic Insights into Secondary Metabolism Biosynthetic Gene Cluster Distributions of Marine Streptomyces Lin Xu 1,2,3,*, Kai-Xiong Ye 1,2, Wen-Hua Dai 1,2, Cong Sun 1,2,3 , Lian-Hua Xu 1,2 and Bing-Nan Han 1,2,* 1 Lab of Marine Functional Molecules, Zhejiang Sci-Tech University, Hangzhou 310018, China 2 College of Life Sciences and Medicine, Zhejiang Sci-Tech Univeristy, Hangzhou 310018, China 3 Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China * Correspondence: [email protected] (L.X.); [email protected] (B.-N.H.); Tel.: +86-13758243072 (L.X.); +86-15257165115 (B.-N.H.) Received: 31 July 2019; Accepted: 21 August 2019; Published: 26 August 2019 Abstract: Bacterial secondary metabolites have huge application potential in multiple industries. Biosynthesis of bacterial secondary metabolites are commonly encoded in a set of genes that are organized in the secondary metabolism biosynthetic gene clusters (SMBGCs). The development of genome sequencing technology facilitates mining bacterial SMBGCs. Marine Streptomyces is a valuable resource of bacterial secondary metabolites. In this study, 87 marine Streptomyces genomes were obtained and carried out into comparative genomic analysis, which revealed their high genetic diversity due to pan-genomes owning 123,302 orthologous clusters. Phylogenomic analysis indicated that the majority of Marine Streptomyces were classified into three clades named Clade I, II, and III, containing 23, 38, and 22 strains, respectively. Genomic annotations revealed that SMBGCs in the genomes of marine Streptomyces ranged from 16 to 84.
    [Show full text]