DOCSLIB.ORG

Characterization of Bacterial Species in Steinkopf a Communal Farming Area in South Africa: a Closer Look at Pathogenesis

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Characterization of Bacterial Species in Steinkopf a Communal Farming Area in South Africa: a Closer Look at Pathogenesis Characterization of bacterial species in Steinkopf a communal farming area in South Africa: A closer look at pathogenesis By Jodene Foster Thesis presented in fulfilment of the requirements of the degree Masters of Science at the University of the Western Cape Supervisors: Dr Adriaan Engelbrecht, Dr Morné Du Plessis, Dr Oriel Moeti Taioe Faculty of Natural Science Department of Biodiversity and Conservation Biology April 2019 1 | P a g e http://etd.uwc.ac.za/ Declaration By submitting this thesis/dissertation electronically I declare that the entirety of the work contained therein is my own, original work, and that I have not previously in its entirety or in part submitted it for obtaining any qualification April 2019 Signature: Date: 02/05/2019 2 | P a g e http://etd.uwc.ac.za/ Abstract The human population in sub-Saharan Africa has been increasing due to decreases in mortality rates and increases in average human age; in turn increasing poverty and pressure placed on agriculture and agricultural production. However, livestock production in South Africa, and globally, is declining due to disease and parasite prevalence, lack of feed, poor breeding, marketing management, change in nutrition in both livestock and humans, rapid urbanization, encroachment on wildlife and unfavourable climatic conditions brought about by global change. One unintended consequence has been the emergence and spread of transboundary animal diseases and, more specifically, the resurgence and emergence of zoonotic disease. Zoonotic diseases are sicknesses transmissible from animals to humans, resulting from direct contact or environmental reservoirs. Previous studies have identified small-scale farmers as the group most prevalent to contracting zoonotic diseases, especially those working in a communal dispensation. Therefore, this study focused on the communal farming area of Steinkopf in the semi-arid Namaqualand region of South Africa. Steinkopf is one of the largest Act 9 areas, with communal land tenure and a mixed farming system, sheep and goats, on about 759 ha. Steinkopf is divided into two rainfall regions, the Succulent Karoo (winter rainfall region) and the Nama Karoo (summer rainfall region). This study aims to identify and characterise the bacterial microbial communities found in the topsoil layer and faecal matter (dung) within the winter and summer rainfall regions of Steinkopf communal rangeland using Next-generation sequencing. Further, the aim is to assess whether pathogenic bacteria are present within the rangeland and what their potential impact on the local farming community might be if present. A high-throughput sequencing technique (Next-generation sequencing) was used to amplify 16S rRNA targeting the V3-V4 hypervariable regions. The phylotypes produced were 37 phyla, 353 families and 634 genera of which the most abundant bacterial phyla were Planctomycetes, Firmicutes and Bacteroidetes and the most 3 | P a g e http://etd.uwc.ac.za/ abundant genera were Gemmata, Akkermansia and Arthrobacter. Alpha diversity indices showed a variation in species diversity, evenness and richness between soil and dung samples, it shows a higher species richness, evenness and unique OTUs detected in summer soil samples and at natural water holes. Through these analysis soil samples were regarded as superior to dung samples within this particular environment and for this particular study. Natural water holes were identified as a safer option when compared to man-made water holes as there are natural systems in place that combat the spread and growth of harmful bacterial microbes. It was found that seasonality has a great impact on the development and growth of environmental bacterial microbiota and that the current randomness of grazing routes and migrations within the Steinkopf communal rangeland is not a detriment but instead acts as a benefits to environmental and livestock health. Furthermore, a total of three pathogenic bacteria were identified however, they occurred at relatively low abundances. It can thus be concluded that this study thoroughly describes the usefulness of using a high-throughput sequencing technique such as Next-generation sequencing when amplifying a small sample size in order to achieve a large volume of information; and that currently the Steinkopf communal rangeland is not subjected to or at risk of a potential zoonotic threat. 4 | P a g e http://etd.uwc.ac.za/ Acknowledgments This study would not have been possible without the constant support, encouragement, motivation and advice from my supervisors, Dr Adriaan Engelbrecht, Dr Morne Du Plessis and Dr Oriel Moeti Taioe. Their constant support during this project was greatly appreciated. I would also like to send my heartfelt appreciation to the ARC (Agricultural Research Council) at UWC for the guidance in the field and assistance with fieldwork, as well as the community of Steinkopf for accepting the study openheartedly and working with us during the research period, sharing rare knowledge and allowing access into the culture. Funding for this project, in the form of a study bursary was provided by the NRF (RTF grant) awarded to the Agricultural Research Council. The running cost for this study was provided by the Early Career Research Grant awarded to Dr. Engelbrecht. Finally, I would like to thank my colleagues, especially Taryn Joy Jacbos and Yameen Badrodien at UWC in the department of Biodiversity and Conservation Biology, as well as all family and friends who have been supportive during this time. Lastly, a special thank you, to my mother Denise Foster as well as my grandmother Joan Foster, and dear friends Jody Mathew Taft and Kay-Lynn Esau for their constant motivation, sacrifices, assistance where possible, and guidance. Their constant support and presence was motivating and inspiring. 5 | P a g e http://etd.uwc.ac.za/ Table of Content Declaration………………………………………………………………………………..................................2 Abstract……………………………………………………………………………………………...………….3 Acknowledgements……………………………………………………………………………………...…...5 Table of Contents……….……………………..……………………………………………………………...6 List of Tables…………………………………………………………………………………………………..8 List of Figures…………………………………………………………………………………………………9 Chapter 1: Introduction……………………………………………………………………………….….11 1 Preamble………………………………………………………………………………………………...….11 1.1 Modernisation of agriculture……………………………………………………………………...…..12 1.2 The livestock sector in South Africa…………………………………………………………………13 1.3 Communal farming and its associated risks and benefits…………………………………..…….16 1.4 Disease and its impact on agriculture………………………………………………………..……….19 1.5 Pathogens in livestock waste…………………………………………………………………………..22 1.6 Pathogens in livestock soil……………………………………………………………………….…….24 1.7 The role of bioinformatics……………………………………………………………………….……..24 1.8 Study sites………………………………………………………………………………………………....26 1.9 Study aim………………………………………………………………………………………….………28 1.9.1 Study questions…………………………………………………………………………………..……29 Chapter 2: Identification of environmental bacterial microbes in the winter rainfall region of Steinkopf communal rangeland, South Africa…………………………………...…….30 2.1 Introduction……………………………………………………………………………………………..30 2.2 Methods and Materials……………………………………………………………………………….31 2.2.1 Study site and collection……………………………………………………………………………..31 2.2.2 DNA extraction…………………………………………………………………………………..……34 2.2.3 Amplification of the V3 and V4 region of 16S rDNA…………………………………………35 2.2.4 Metagenomic data preparation and analysis………………………………………………….….36 2.2.5 Diversity comparison and statistical analysis……………………………………………......…..36 2.3 Results……………………………………………………………………………………………………….….……37 2.3.1 Classification of bacterial OTUs…………………………………………………………………...37 2.3.2 Alpha diversity…………………………………………………………………………………………39 6 | P a g e http://etd.uwc.ac.za/ 2.3.3 Beta diversity………………………………………………………………………………………......40 2.4 Discussion…………………………………………………………………………………….…………..48 2.4.1 Sample type………………………………………………………………………………….…………48 2.4.2 Location……………..…………………………………………………………………………………..51 2.4.3 Description……………………………………………………………………………………………..53 2.5 Conclusion……………………………………………………………………………………………….54 Chapter 3: Identification and characterization of bacterial microbes within the Steinkopf communal rangeland: Is bacterial pathogenesis a threat? ………………………………………56 3.1 Introduction……………………………………………………………………………………………..56 3.2 Methods and Materials……………………………………………………………………………….60 3.2.1 Study site and collection……………………………………………………………………………..60 3.2.2 DNA processing……………………………………………………………………………………….60 3.3 Results………………………………………………………………………………………………….…62 3.3.1 Classification of bacterial OTUs…………………………………………………………………...62 3.4 Discussion………………………………………………………………………………………………...68 3.4.1 Identification of bacterial taxa…………………………………………………………………...….68 3.4.2 Pathogenic and unclassified taxa…………………………………………………………………...72 3.5 Conclusion……………………………………………………………………………………………….74 Chapter 4: General conclusion……………………………………………………………………...…..75 References………………………………………………………………………………………………….....78 Appendix 1…………………………………………………………………………………………………....92 Appendix 2…………………………………………………………………………………………………....94 Appendix 3…………………………………………………………………………………………………....95 Appendix 4.…………………………………………………………………………………………………...97 Appendix 5...……………………………………………………………………………………………….…98 Appendix 6...……………………………………………………………………………………….…………99 Appendix 7..……………………………………………………………………………….………………...100 Appendix 8...………………………………………………………………………………….……………..101 Appendix 9......................................................................................................................................................102
Load more

Recommended publications
  • Patterns, Processes and Models of Microbial Recovery in a Chronosequence Following Reforestation of Reclaimed Mine Soils
    PATTERNS, PROCESSES AND MODELS OF MICROBIAL RECOVERY IN A CHRONOSEQUENCE FOLLOWING REFORESTATION OF RECLAIMED MINE SOILS Shan Sun Dissertation submitted to the faculty of the Virginia Polytechnic Institute and State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Crop and Soil Environmental Sciences Brian Badgley, Chair Song Li Brian Strahm Michael Strickland Carl Zipper Virginia Polytechnic Institute and State University Blacksburg, Virginia July 2017 Keywords: soil microorganism, recovery, chronosequence, reclaimed mine soils, amplicon sequencing, shotgun metagenomics, bacterial co-occurrence groups, artificial neural network PATTERNS, PROCESSES AND MODELS OF MICROBIAL RECOVERY IN A CHRONOSEQUENCE FOLLOWING REFORESTATION OF RECLAIMED MINE SOILS Shan Sun Abstract Soil microbial communities mediate important ecological processes and play essential roles in biogeochemical cycling. Ecosystem disturbances such as surface mining significantly alter soil microbial communities, which could lead to changes or impairment of ecosystem functions. Reforestation procedures were designed to accelerate the reestablishment of plant community and the recovery of the forest ecosystem after reclamation. However, the microbial recovery during reforestation has not been well studied even though this information is essential for evaluating ecosystem restoration success. In addition, the similar starting conditions of mining sites of different ages facilitate a chronosequence approach for studying decades-long microbial community change, which could help generalize theories about ecosystem succession. In this study, the recovery of microbial communities in a chronosequence of reclaimed mine sites spanning 30 years post reforestation along with unmined reference sites was analyzed using next-generation sequencing to characterize soil-microbial abundance, richness, taxonomic composition, interaction patterns and functional genes.
    [Show full text]
  • Successful Drug Discovery Informed by Actinobacterial Systematics
    Successful Drug Discovery Informed by Actinobacterial Systematics Verrucosispora HPLC-DAD analysis of culture filtrate Structures of Abyssomicins Biological activity T DAD1, 7.382 (196 mAU,Up2) of 002-0101.D V. maris AB-18-032 mAU CH3 CH3 T extract H3C H3C Antibacterial activity (MIC): S. leeuwenhoekii C34 maris AB-18-032 175 mAU DAD1 A, Sig=210,10 150 C DAD1 B, Sig=230,10 O O DAD1 C, Sig=260,20 125 7 7 500 Rt 7.4 min DAD1 D, Sig=280,20 O O O O Growth inhibition of Gram-positive bacteria DAD1 , Sig=310,20 100 Abyssomicins DAD1 F, Sig=360,40 C 75 DAD1 G, Sig=435,40 Staphylococcus aureus (MRSA) 4 µg/ml DAD1 H, Sig=500,40 50 400 O O 25 O O Staphylococcus aureus (iVRSA) 13 µg/ml 0 CH CH3 300 400 500 nm 3 DAD1, 7.446 (300 mAU,Dn1) of 002-0101.D 300 mAU Mode of action: C HO atrop-C HO 250 atrop-C CH3 CH3 CH3 CH3 200 H C H C H C inhibitior of pABA biosynthesis 200 Rt 7.5 min H3C 3 3 3 Proximicin A Proximicin 150 HO O HO O O O O O O O O O A 100 O covalent binding to Cys263 of PabB 100 N 50 O O HO O O Sea of Japan B O O N O O (4-amino-4-deoxychorismate synthase) by 0 CH CH3 CH3 CH3 3 300 400 500 nm HO HO HO HO Michael addition -289 m 0 B D G H 2 4 6 8 10 12 14 16 min Newcastle Michael Goodfellow, School of Biology, University Newcastle University, Newcastle upon Tyne Atacama Desert In This Talk I will Consider: • Actinobacteria as a key group in the search for new therapeutic drugs.
    [Show full text]
  • Coffee Microbiota and Its Potential Use in Sustainable Crop Management. a Review Duong Benoit, Marraccini Pierre, Jean Luc Maeght, Philippe Vaast, Robin Duponnois
    Coffee Microbiota and Its Potential Use in Sustainable Crop Management. A Review Duong Benoit, Marraccini Pierre, Jean Luc Maeght, Philippe Vaast, Robin Duponnois To cite this version: Duong Benoit, Marraccini Pierre, Jean Luc Maeght, Philippe Vaast, Robin Duponnois. Coffee Mi- crobiota and Its Potential Use in Sustainable Crop Management. A Review. Frontiers in Sustainable Food Systems, Frontiers Media, 2020, 4, 10.3389/fsufs.2020.607935. hal-03045648 HAL Id: hal-03045648 https://hal.inrae.fr/hal-03045648 Submitted on 8 Dec 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. Distributed under a Creative Commons Attribution| 4.0 International License REVIEW published: 03 December 2020 doi: 10.3389/fsufs.2020.607935 Coffee Microbiota and Its Potential Use in Sustainable Crop Management. A Review Benoit Duong 1,2, Pierre Marraccini 2,3, Jean-Luc Maeght 4,5, Philippe Vaast 6, Michel Lebrun 1,2 and Robin Duponnois 1* 1 LSTM, Univ. Montpellier, IRD, CIRAD, INRAE, SupAgro, Montpellier, France, 2 LMI RICE-2, Univ. Montpellier, IRD, CIRAD, AGI, USTH, Hanoi, Vietnam, 3 IPME, Univ. Montpellier, CIRAD, IRD, Montpellier, France, 4 AMAP, Univ. Montpellier, IRD, CIRAD, INRAE, CNRS, Montpellier, France, 5 Sorbonne Université, UPEC, CNRS, IRD, INRA, Institut d’Écologie et des Sciences de l’Environnement, IESS, Bondy, France, 6 Eco&Sols, Univ.
    [Show full text]
  • Escherichia Coli, Fusarium Proliferatum, F
    ใบรับรองวิทยานิพนธ์ บัณฑิตวิทยาลัย มหาวิทยาลัยเกษตรศาสตร์ วิทยาศาสตรมหาบัณฑิต (พันธุศาสตร์) ปริญญา พันธุศาสตร์ พันธุศาสตร์ สาขา ภาควิชา เรื่อง การวิเคราะห์ลักษณะและติดตามแอคติโนมัยสีทเอนโดไฟต์ที่คัดแยกจากกระถินณรงค์ (Acacia auriculiformis A. Cunn. ex Benth.) โดยเทคนิคทางโมเลกุล Characterization and Monitoring of Endophytic Actinomycetes Isolated from Wattle tree (Acacia auriculiformis A. Cunn. ex Benth.) Using Molecular Techniques นามผู้วิจัย นายชาคริต บุญอยู่ ได้พิจารณาเห็นชอบโดย อาจารย์ที่ปรึกษาวิทยานิพนธ์หลัก วิทยา ( รองศาสตราจารย์อรินทิพย์ ธรรมชัยพิเนต, Ph.D. ) อาจารย์ที่ปรึกษาวิทยานิพนธ์ร่วม ( ผู้ช่วยศาสตราจารย์วิภา หงษ์ตระกูล, Ph.D. ) หัวหน้าภาควิชา ( รองศาสตราจารย์เลิศลักษณ์ เงินศิริ, Ph.D. ) บัณฑิตวิทยาลัย มหาวิทยาลัยเกษตรศาสตร์รับรองแล้ว ( รองศาสตราจารย์กัญจนา ธีระกุล, D.Agr. ) คณบดีบัณฑิตวิทยาลัย วันที่ เดือน พ.ศ . กกกกก (Acacia auriculiformis A. Cunn. ex Benth.) ก Characterization and Monitoring of Endophytic Actinomycetes Isolated from Wattle tree (Acacia auriculiformis A. Cunn. ex Benth.) Using Molecular Techniques ก () .. 2553 2553: กกกก ก ( Acacia auriculiformis A. Cunn. ex Benth.) ก () กก: , Ph.D. 90 ก 11 กกกกกก ก 16S rRNA ก Streptomyces, Actinoallomurus, Amycolatopsis, Kribbella and Microbispora กก 5 GMKU 932 Bacillus cereus GMKU 937 GMKU 938 Aspergillus niger GMKU 940 B. cereus, Staphylococcus aureus, Escherichia coli, Fusarium proliferatum, F. moniliforme A. niger GMKU 944 B. cereus, S. aureus, Ralstonia solanacearum A. niger egfp Streptomyces sp. GMKU 937 GMKU 944 กก MS MgCl2 10
    [Show full text]
  • Compile.Xlsx
    Silva OTU GS1A % PS1B % Taxonomy_Silva_132 otu0001 0 0 2 0.05 Bacteria;Acidobacteria;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un; otu0002 0 0 1 0.02 Bacteria;Acidobacteria;Acidobacteriia;Solibacterales;Solibacteraceae_(Subgroup_3);PAUC26f; otu0003 49 0.82 5 0.12 Bacteria;Acidobacteria;Aminicenantia;Aminicenantales;Aminicenantales_fa;Aminicenantales_ge; otu0004 1 0.02 7 0.17 Bacteria;Acidobacteria;AT-s3-28;AT-s3-28_or;AT-s3-28_fa;AT-s3-28_ge; otu0005 1 0.02 0 0 Bacteria;Acidobacteria;Blastocatellia_(Subgroup_4);Blastocatellales;Blastocatellaceae;Blastocatella; otu0006 0 0 2 0.05 Bacteria;Acidobacteria;Holophagae;Subgroup_7;Subgroup_7_fa;Subgroup_7_ge; otu0007 1 0.02 0 0 Bacteria;Acidobacteria;ODP1230B23.02;ODP1230B23.02_or;ODP1230B23.02_fa;ODP1230B23.02_ge; otu0008 1 0.02 15 0.36 Bacteria;Acidobacteria;Subgroup_17;Subgroup_17_or;Subgroup_17_fa;Subgroup_17_ge; otu0009 9 0.15 41 0.99 Bacteria;Acidobacteria;Subgroup_21;Subgroup_21_or;Subgroup_21_fa;Subgroup_21_ge; otu0010 5 0.08 50 1.21 Bacteria;Acidobacteria;Subgroup_22;Subgroup_22_or;Subgroup_22_fa;Subgroup_22_ge; otu0011 2 0.03 11 0.27 Bacteria;Acidobacteria;Subgroup_26;Subgroup_26_or;Subgroup_26_fa;Subgroup_26_ge; otu0012 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_5;Subgroup_5_or;Subgroup_5_fa;Subgroup_5_ge; otu0013 1 0.02 13 0.32 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_or;Subgroup_6_fa;Subgroup_6_ge; otu0014 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_un;Subgroup_6_un;Subgroup_6_un; otu0015 8 0.13 30 0.73 Bacteria;Acidobacteria;Subgroup_9;Subgroup_9_or;Subgroup_9_fa;Subgroup_9_ge;
    [Show full text]
  • Inter-Domain Horizontal Gene Transfer of Nickel-Binding Superoxide Dismutase 2 Kevin M
    bioRxiv preprint doi: https://doi.org/10.1101/2021.01.12.426412; this version posted January 13, 2021. 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 Inter-domain Horizontal Gene Transfer of Nickel-binding Superoxide Dismutase 2 Kevin M. Sutherland1,*, Lewis M. Ward1, Chloé-Rose Colombero1, David T. Johnston1 3 4 1Department of Earth and Planetary Science, Harvard University, Cambridge, MA 02138 5 *Correspondence to KMS: [email protected] 6 7 Abstract 8 The ability of aerobic microorganisms to regulate internal and external concentrations of the 9 reactive oxygen species (ROS) superoxide directly influences the health and viability of cells. 10 Superoxide dismutases (SODs) are the primary regulatory enzymes that are used by 11 microorganisms to degrade superoxide. SOD is not one, but three separate, non-homologous 12 enzymes that perform the same function. Thus, the evolutionary history of genes encoding for 13 different SOD enzymes is one of convergent evolution, which reflects environmental selection 14 brought about by an oxygenated atmosphere, changes in metal availability, and opportunistic 15 horizontal gene transfer (HGT). In this study we examine the phylogenetic history of the protein 16 sequence encoding for the nickel-binding metalloform of the SOD enzyme (SodN). A comparison 17 of organismal and SodN protein phylogenetic trees reveals several instances of HGT, including 18 multiple inter-domain transfers of the sodN gene from the bacterial domain to the archaeal domain.
    [Show full text]
  • Hungarian University of Agriculture and Life Sciences Doctoral School of Biological Sciences Doctoral (Ph.D) Dissertation Respon
    HUNGARIAN UNIVERSITY OF AGRICULTURE AND LIFE SCIENCES DOCTORAL SCHOOL OF BIOLOGICAL SCIENCES DOCTORAL (PH.D) DISSERTATION RESPONSES OF SOIL CO2 EFFLUX TO BIOTIC AND ABIOTIC DRIVERS IN AGRICULTURAL SOILS BY MALEK INSAF GÖDÖLLŐ 2021 Title: Responses of soil CO2 efflux to biotic and abiotic drivers in agricultural soils Discipline: Biological Sciences Name of Doctoral School: Doctoral School of Biological Sciences Head: Prof. Dr. Zoltán Nagy Department of Plant Physiology and Plant Ecology Institute of Agronomy Hungarian University of Agriculture and Life Sciences, Supervisor 1: Dr: János Balogh, Department of Plant Physiology and Plant Ecology Institute of Agronomy Hungarian University of Agriculture and Life Sciences, Supervisor 2: Prof. Dr. Katalin Andrea Posta Department of Microbiology and Microbial Biotechnology Institute of Genetics and Biotechnology Hungarian University of Agriculture and Life Sciences, ..................................................... ................................................. Approval of Head of Doctoral School Approval of Supervisors TABLE OF CONTENT 1. Introduction: .......................................................................................................................... 1 1.1. Foreword ......................................................................................................................... 1 1.2. Objectives ........................................................................................................................ 3 2. LITERATURE REVIEW ....................................................................................................
    [Show full text]
  • Novel Polyethers from Screening Actinoallomurus Spp
    Article Novel Polyethers from Screening Actinoallomurus spp. Marianna Iorio 1, Arianna Tocchetti 1, Joao Carlos Santos Cruz 2, Giancarlo Del Gatto 1, Cristina Brunati 2, Sonia Ilaria Maffioli 1, Margherita Sosio 1,2 and Stefano Donadio 1,2,* 1 NAICONS Srl, Viale Ortles 22/4, 20139 Milano, Italy; [email protected] (M.I.); [email protected] (A.T.); [email protected] (G.D.G.); [email protected] (S.I.M.); [email protected] (M.S.) 2 KtedoGen Srl, Viale Ortles 22/4, 20139 Milano, Italy; [email protected] (J.C.S.C.); [email protected] (C.B.) * Correspondence: [email protected] Received: 1 May 2018; Accepted: 13 June 2018; Published: 14 June 2018 Abstract: In screening for novel antibiotics, an attractive element of novelty can be represented by screening previously underexplored groups of microorganisms. We report the results of screening 200 strains belonging to the actinobacterial genus Actinoallomurus for their production of antibacterial compounds. When grown under just one condition, about half of the strains produced an extract that was able to inhibit growth of Staphylococcus aureus. We report here on the metabolites produced by 37 strains. In addition to previously reported aminocoumarins, lantibiotics and aromatic polyketides, we described two novel and structurally unrelated polyethers, designated α- 770 and α-823. While we identified only one producer strain of the former polyether, 10 independent Actinoallomurus isolates were found to produce α-823, with the same molecule as main congener. Remarkably, production of α-823 was associated with a common lineage within Actinoallomurus, which includes A. fulvus and A. amamiensis. All polyether producers were isolated from soil samples collected in tropical parts of the world.
    [Show full text]
  • Download (6Mb)
    A Thesis Submitted for the Degree of PhD at the University of Warwick Permanent WRAP URL: http://wrap.warwick.ac.uk/81849 Copyright and reuse: This thesis is made available online and is protected by original copyright. Please scroll down to view the document itself. Please refer to the repository record for this item for information to help you to cite it. Our policy information is available from the repository home page. For more information, please contact the WRAP Team at: [email protected] warwick.ac.uk/lib-publications Unlocking the potential of novel taxa – a study on Actinoallomurus João Carlos Santos Cruz Submitted for the degree of Doctor of Philosophy School of Life Sciences, University of Warwick March, 2016 1 TABLE OF CONTENTS Table of Contents .......................................................................................................... i Acknowledgments...................................................................................................... iv List of Figures ................................................................................................................. v List of Tables ................................................................................................................. ix Declaration .................................................................................................................. xi Summary ....................................................................................................................... xii Abbreviations .............................................................................................................
    [Show full text]
  • Tropical Legume Trees and Their Soil-Mineral Microbiome: Biogeochemistry and Routes to Enhanced Mineral Access
    Tropical legume trees and their soil-mineral microbiome: biogeochemistry and routes to enhanced mineral access A thesis submitted by Dimitar Zdravkov Epihov in partial fulfilment of the requirements for the Degree of Doctor of Philosophy in the Department of Animal and Plant Sciences, University of Sheffield October 29th, 2018 1 © Copyright by Dimitar Zdravkov Epihov, 2018. All rights reserved. 2 Acknowledgements First and foremost, I would like to thank my academic superivising team including Professor David J. Beerling and Professor Jonathan R. Leake for their guidance and support throughout my PhD studies as well as the European Research Council (ERC) for funding my project. Secondly, I would like to thank my girlfriend, Gabriela, my parents, Zdravko and Mariyana, and my grandmother Gina, for always believing in me. My biggest gratitude goes for my girlfriend for always putting up with working ridiculous hours and for helping me during field work even if it meant getting stuck in the Australian jungle at night and stumbling across a well-grown python. I would also want to express my thanks to my first ever Biology teacher Mrs Moskova for inspiring and nurturing the interest that grew to be a life-lasting passion, curiousity and love towards all things living. Lastly, I would like to thank Irene Johnson, our laboratory manager and senior technician for always been there for advice, help and general cheering up as well as all other great scientists and collaborators I have had the chance to talk to and work with during my PhD project. I devote this work to a future with more green in it.
    [Show full text]
  • Coffee Microbiota and Its Potential Use in Sustainable Crop Management
    REVIEW published: 03 December 2020 doi: 10.3389/fsufs.2020.607935 Coffee Microbiota and Its Potential Use in Sustainable Crop Management. A Review Benoit Duong 1,2, Pierre Marraccini 2,3, Jean-Luc Maeght 4,5, Philippe Vaast 6, Michel Lebrun 1,2 and Robin Duponnois 1* 1 LSTM, Univ. Montpellier, IRD, CIRAD, INRAE, SupAgro, Montpellier, France, 2 LMI RICE-2, Univ. Montpellier, IRD, CIRAD, AGI, USTH, Hanoi, Vietnam, 3 IPME, Univ. Montpellier, CIRAD, IRD, Montpellier, France, 4 AMAP, Univ. Montpellier, IRD, CIRAD, INRAE, CNRS, Montpellier, France, 5 Sorbonne Université, UPEC, CNRS, IRD, INRA, Institut d’Écologie et des Sciences de l’Environnement, IESS, Bondy, France, 6 Eco&Sols, Univ. Montpellier, CIRAD, INRAE, IRD, SupAgro, Montpellier, France Intensive coffee production is accompanied by several environmental issues, including soil degradation, biodiversity loss, and pollution due to the wide use of agrochemical inputs and wastes generated by processing. In addition, climate change is expected to Edited by: decrease the suitability of cultivated areas while potentially increasing the distribution Everlon Cid Rigobelo, São Paulo State University, Brazil and impact of pests and diseases. In this context, the coffee microbiota has been Reviewed by: increasingly studied over the past decades in order to improve the sustainability of the Ugo De Corato, coffee production. Therefore, coffee associated microorganisms have been isolated and Energy and Sustainable Economic characterized in order to highlight their useful characteristics and study their potential Development (ENEA), Italy Erica Lumini, use as sustainable alternatives to agrochemical inputs. Indeed, several microorganisms Italian National Research Council, Italy (including bacteria and fungi) are able to display plant growth-promoting capacities *Correspondence: and/or biocontrol abilities toward coffee pests and diseases.
    [Show full text]
  • Contents Topic 1. Introduction to Microbiology. the Subject and Tasks
    Contents Topic 1. Introduction to microbiology. The subject and tasks of microbiology. A short historical essay………………………………………………………………5 Topic 2. Systematics and nomenclature of microorganisms……………………. 10 Topic 3. General characteristics of prokaryotic cells. Gram’s method ………...45 Topic 4. Principles of health protection and safety rules in the microbiological laboratory. Design, equipment, and working regimen of a microbiological laboratory………………………………………………………………………….162 Topic 5. Physiology of bacteria, fungi, viruses, mycoplasmas, rickettsia……...185 TOPIC 1. INTRODUCTION TO MICROBIOLOGY. THE SUBJECT AND TASKS OF MICROBIOLOGY. A SHORT HISTORICAL ESSAY. Contents 1. Subject, tasks and achievements of modern microbiology. 2. The role of microorganisms in human life. 3. Differentiation of microbiology in the industry. 4. Communication of microbiology with other sciences. 5. Periods in the development of microbiology. 6. The contribution of domestic scientists in the development of microbiology. 7. The value of microbiology in the system of training veterinarians. 8. Methods of studying microorganisms. Microbiology is a science, which study most shallow living creatures - microorganisms. Before inventing of microscope humanity was in dark about their existence. But during the centuries people could make use of processes vital activity of microbes for its needs. They could prepare a koumiss, alcohol, wine, vinegar, bread, and other products. During many centuries the nature of fermentations remained incomprehensible. Microbiology learns morphology, physiology, genetics and microorganisms systematization, their ecology and the other life forms. Specific Classes of Microorganisms Algae Protozoa Fungi (yeasts and molds) Bacteria Rickettsiae Viruses Prions The Microorganisms are extraordinarily widely spread in nature. They literally ubiquitous forward us from birth to our death. Daily, hourly we eat up thousands and thousands of microbes together with air, water, food.
    [Show full text]