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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. -
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http://wjst.wu.ac.th Natural Sciences Diversity Analysis of an Extremely Acidic Soil in a Layer of Coal Mine Detected the Occurrence of Rare Actinobacteria Megga Ratnasari PIKOLI1,*, Irawan SUGORO2 and Suharti3 1Department of Biology, Faculty of Science and Technology, Universitas Islam Negeri Syarif Hidayatullah Jakarta, Ciputat, Tangerang Selatan, Indonesia 2Center for Application of Technology of Isotope and Radiation, Badan Tenaga Nuklir Nasional, Jakarta Selatan, Indonesia 3Department of Chemistry, Faculty of Science and Computation, Universitas Pertamina, Simprug, Jakarta Selatan, Indonesia (*Corresponding author’s e-mail: [email protected], [email protected]) Received: 7 September 2017, Revised: 11 September 2018, Accepted: 29 October 2018 Abstract Studies that explore the diversity of microorganisms in unusual (extreme) environments have become more common. Our research aims to predict the diversity of bacteria that inhabit an extreme environment, a coal mine’s soil with pH of 2.93. Soil samples were collected from the soil at a depth of 12 meters from the surface, which is a clay layer adjacent to a coal seam in Tanjung Enim, South Sumatera, Indonesia. A culture-independent method, the polymerase chain reaction based denaturing gradient gel electrophoresis, was used to amplify the 16S rRNA gene to detect the viable-but-unculturable bacteria. Results showed that some OTUs that have never been found in the coal environment and which have phylogenetic relationships to the rare actinobacteria Actinomadura, Actinoallomurus, Actinospica, Streptacidiphilus, Aciditerrimonas, and Ferrimicrobium. Accordingly, the highly acidic soil in the coal mine is a source of rare actinobacteria that can be explored further to obtain bioactive compounds for the benefit of biotechnology. -
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. -
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. -
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 -
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; -
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. -
Actinomadura Keratinilytica Sp. Nov., a Keratin- Degrading Actinobacterium Isolated from Bovine Manure Compost
International Journal of Systematic and Evolutionary Microbiology (2009), 59, 828–834 DOI 10.1099/ijs.0.003640-0 Actinomadura keratinilytica sp. nov., a keratin- degrading actinobacterium isolated from bovine manure compost Aaron A. Puhl,1 L. Brent Selinger,2 Tim A. McAllister1 and G. Douglas Inglis1 Correspondence 1Agriculture and Agri-Food Canada Research Centre, 5403 1st Avenue S, Lethbridge, AB T1J G. Douglas Inglis 4B1, Canada [email protected] 2Department of Biological Sciences, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada A novel keratinolytic actinobacterium, strain WCC-2265T, was isolated from bovine hoof keratin ‘baited’ into composting bovine manure from southern Alberta, Canada, and subjected to phenotypic and genotypic characterization. Strain WCC-2265T produced well-developed, non- fragmenting and extensively branched hyphae within substrates and aerial hyphae, from which spherical spores possessing spiny cell sheaths were produced in primarily flexuous or straight chains. The cell wall contained meso-diaminopimelic acid, whole-cell sugars were galactose, glucose, madurose and ribose, and the major menaquinones were MK-9(H6), MK-9(H8), MK- 9(H4) and MK-9(H2). These characteristics suggested that the organism belonged to the genus Actinomadura and a comparative analysis of 16S rRNA gene sequences indicated that it formed a distinct clade within the genus. Strain WCC-2265T could be differentiated from other species of the genus Actinomadura by DNA–DNA hybridization, morphological and physiological characteristics and the predominance of iso-C16 : 0, iso-C17 : 0 and 10-methyl C17 : 0 fatty acids. The broad range of phenotypic and genetic characters supported the suggestion that this organism represents a novel species of the genus Actinomadura, for which the name Actinomadura keratinilytica sp. -
DAIANI CRISTINA SAVI.Pdf
1 UNIVERSIDADE FEDERAL DO PARANÁ DAIANI CRISTINA SAVI GÊNERO Microbispora: RECLASSIFICAÇÃO FILOGENÉTICA, BIOPROSPECÇÃO E IDENTIFICAÇÃO DE METABÓLITOS SECUNDÁRIOS CURITIBA 2015 2 UNIVERSIDADE FEDERAL DO PARANÁ DAIANI CRISTINA SAVI GÊNERO Microbispora: RECLASSIFICAÇÃO FILOGENÉTICA, BIOPROSPECÇÃO E IDENTIFICAÇÃO DE METABÓLITOS SECUNDÁRIOS Tese apresentada ao Programa de Pós- Graduação em Microbiologia, Parasitologia e Patologia, Setor de Ciências Biológicas, Universidade Federal do Paraná como requisito parcial à obtenção de título de Doutora em Microbiologia. Orientadora: Profª Drª Chirlei Glienke Co-Orientadores: Drª Josiane Gomes Figueiredo e Dr Jurgen Rohr CURITIBA 2015 3 4 AGRADECIMENTOS A Deus pela oportunidade e ensinamentos; Aos meus pais e irmã pelo apoio, compreensão e incentivo; Ao Programa de Pós-graduação em Microbiologia, Parasitologia e Patologia pela oportunidade; À Profª Drª Chirlei Glienke pela confiança, respeito, paciência e ensinamentos que ajudaram a me moldar tanto quando pesquisadora como pessoa, gratidão eterna; À Profa Dra Lygia Vitória Galli Terasawa e à Profa Dra Vanessa Kava-Cordeiro por todo o ensinamento, paciência e disponibilidade dentro e fora do laboratório; Ao Prof Dr Jurgen Rohr, pela oportunidade, por me receber tão bem, paciência e orientação na parte química; À Drª Josiane Gomes Figueiredo, pela co-orientação, auxílio, ensinamentos e pela amizade; Ao Dr Khaled Shaaban por todo auxílio e ensinamentos no desenvolvimento da parte de identificação de compostos; Ao Rodrigo Aluízio pela amizade e auxílio -
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 .................................................................................................... -
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. -
Draft Genome of Thermomonospora Sp. CIT 1 (Thermomonosporaceae) and in Silico Evidence of Its Functional Role in Filter Cake Biomass Deconstruction
Genetics and Molecular Biology, 42, 1, 145-150 (2019) Copyright © 2019, Sociedade Brasileira de Genética. Printed in Brazil DOI: http://dx.doi.org/10.1590/1678-4685-GMB-2017-0376 Genome Insight Draft genome of Thermomonospora sp. CIT 1 (Thermomonosporaceae) and in silico evidence of its functional role in filter cake biomass deconstruction Wellington P. Omori1, Daniel G. Pinheiro2, Luciano T. Kishi3, Camila C. Fernandes3, Gabriela C. Fernandes1, Elisângela S. Gomes-Pepe3, Claudio D. Pavani1, Eliana G. de M. Lemos3 and Jackson A. M. de Souza4 1Programa de Pós-Graduação em Microbiologia Agropecuária, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil. 2Departamento de Tecnologia, Laboratório de Bioinformática, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil. 3Laboratório Multiusuário Centralizado para Sequenciamento de DNA em Larga Escala e Análise de Expressão Gênica (LMSeq), Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil. 4Departamento de Biologia Aplicada à Agropecuária, Laboratório de Genética Aplicada, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil. Abstract The filter cake from sugar cane processing is rich in organic matter and nutrients, which favors the proliferation of mi- croorganisms with potential to deconstruct plant biomass. From the metagenomic data of this material, we assem- bled a draft genome that was phylogenetically related to Thermomonospora curvata DSM 43183, which shows the functional and ecological importance of this bacterium in the filter cake. Thermomonospora is a gram-positive bacte- rium that produces cellulases in compost, and it can survive temperatures of 60 ºC.