DOCSLIB.ORG

Microbial Community and Biogeochemical Characteristics in Reclaimed Soils at Pt Bukit Asam Coal Mine, South Sumatra, Indonesia

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Microbial Community and Biogeochemical Characteristics in Reclaimed Soils at Pt Bukit Asam Coal Mine, South Sumatra, Indonesia MICROBIAL COMMUNITY AND BIOGEOCHEMICAL CHARACTERISTICS IN RECLAIMED SOILS AT PT BUKIT ASAM COAL MINE, SOUTH SUMATRA, INDONESIA A thesis presented to the faculty of the Graduate School of Western Carolina University in partial fulfillment of the requirements for the degree of Master of Science in Biology By Kyle Bryce Corcoran Co-Directors: Dr. Jerry R. Miller, Dr. John P. Gannon Department of Geosciences and Natural Resources Committee Members: Dr. Sean P. O’Connell, Department of Biology Dr. Thomas H. Martin, Department of Biology March 2018 ACKNOWLEDGEMENTS I would like to express my sincere gratitude to my thesis co-advisors, Dr. Jerry Miller and Dr. JP Gannon for their dedication, and encouragement throughout my graduate school experience. If it weren’t for the many hours spent helping me build the framework of this project, and critiquing my work, I would have never built the confidence that I have now. I would also like to thank all of my committee members: Dr. Sean P. O’Connell, Dr. Thomas H. Martin for the time you took to teach me new techniques regarding microbial and statistical analyses. In addition, thank you so much Micky Aja, Amar Amay, and Adi Arti Elettaria for accompanying me during my stay in Indonesia. I truly appreciate the friendships I have built with you all throughout this time and will never forget how much you all helped me throughout this experience. Trip Krenz, you have watched over me and seen me grow over the last several years. Thank you for always telling me to hold my head high and to look at the positive things that were meant to come my way. I truly appreciate your support and watching over me as an older brother. To Joe Brazelton who has helped and supported me from the start of my master’s project in the humid tropics of South Sumatra, Indonesia up until the very end. You have no idea how much your support and guidance has meant to me over the years, thank you for everything bud. To all my friends and family who always believed in me, and watched me grow as an individual. I can not express how much your support has meant to me over the last several years. The amount of time each and everyone one of you took to give me advice and pick me up in a time of need makes me forever grateful. Lastly, to my father who passed away. I promise to hold on to my dreams for you. Thank you all very much! ii TABLE OF CONTENTS List of Tables ................................................................................................................................. iv List of Figures ..................................................................................................................................v List of Abbreviations ..................................................................................................................... vi Abstract ........................................................................................................................................ vii Chapter One: Introduction ...............................................................................................................1 Chapter Two: Methods and Materials..............................................................................................6 2.1: Study Area ...........................................................................................................................6 2.2: Sample Collection and Well Installation .............................................................................8 2.3: Soil Microbial Analysis .....................................................................................................12 2.3.1: DNA Extraction ...........................................................................................................12 2.3.2: Polymerase Chain Reaction (PCR) ..............................................................................13 2.3.3: DGGE and 16S rDNA Sequencing ..............................................................................14 2.4: Water Analysis ...................................................................................................................14 2.5: Soil Analysis ......................................................................................................................15 2.5.1: CNS Analysis ...............................................................................................................15 2.5.2: Acid Digestion and ICP Analysis ................................................................................15 2.5.3: Grain Size Analysis ......................................................................................................16 2.6: Statistical Analysis .............................................................................................................16 Chapter Three: Results ...................................................................................................................17 3.1: Soil Microbial Analysis .....................................................................................................17 3.1.1: Polymerase Chain Reaction (PCR) ..............................................................................17 3.1.2: DGGE and 16S rDNA Sequencing ..............................................................................17 3.1.3: Principal Components Analysis (PCA)........................................................................19 3.2: Water Analysis ...................................................................................................................27 3.3: Soil Analysis ......................................................................................................................31 3.3.1: Total Carbon ................................................................................................................31 3.3.2: Total Metal Concentrations in Soil ..............................................................................33 3.3.3: Grain Size Distribution ................................................................................................42 Chapter Four: Discussion ...............................................................................................................45 4.1: 16S rDNA Sequence Descriptions .....................................................................................45 4.2: Total Major and Trace Metal Concentrations in Soils .......................................................48 4.3: Potential Age Effect(s) on Soil Characteristics and Microbiology ....................................50 4.4: Major and Trace Metal Mobility in Soils and Subsurface Waters ....................................53 Chapter Five: Conclusions .............................................................................................................56 References ......................................................................................................................................58 Appendix ........................................................................................................................................72 iii LIST OF TABLES Table 1. Naming scheme and locations of monitoring wells and samples collected at PTBA ......12 Table 2. DNA sequence matches to genus for 16S rRNA gene fragments for isolates .................19 Table 3. DNA sequence matches to species for 16S rRNA gene fragments for isolates ..............19 Table 4. Principal components analysis (PCA) results of sediment samples and median .............21 Table 5. Principal components analysis (PCA) correlation results of total metal .........................24 Table 6. Principal components analysis (PCA) correlation results of total metal .........................25 Table 7. Principal components analysis (PCA) correlation results of total metal .........................27 Table 8. Correlation matrix for metal concentrations in subsurface water samples ......................28 Table 9. Metal concentrations (medians, means [standard deviations]) in subsurface water ........31 Table 10. Percent carbon (medians, means [standard deviations]) in topsoil and subsoil.............33 Table 11. Metal concentrations (medians, means [standard deviations]) for (A) topsoil and .......34 Table 12. Percent silt plus clay (medians, means [standard deviations]) in topsoil and subsoil ...42 Table 13. Correlation matrix for metal concentrations in soil samples. Bold values ....................44 Table A1. DNA sequence matches for partial 16S rRNA gene fragments for isolates .................72 iv LIST OF FIGURES Figure 1. PT Bukit Asam coal mine is located in South Sumatra, Indonesia ..................................7 Figure 2. Photograph depicting monitoring wells that were installed in the Agrotourism ............10 Figure 3. Conceptual model based on soil profiles observed in the field in reforested .................11 Figure 4. Denaturing gradient gel electrophoresis (DGGE) gel of bacterial communities ...........18 Figure 5. Principal components analysis (PCA) of sediment samples and median metal .............20 Figure 6. (A) Principal components analysis (PCA) of all surface samples and denaturing .........23 Figure 7. Principal components analysis (PCA) of surface samples and denaturing gradient ......26 Figure 8. Concentrations of (A) aluminum (ng/mL), (B) iron (ng/mL), (C) manganese ..............30 Figure 9. Percent carbon in sediment collected from (A) topsoil and (B) subsoil .........................32 Figure 10. Concentrations of Al (mg/Kg) in sediment collected from the
Load more

Recommended publications
  • Diverse Bacterial Communities Are Recruited on Spores of Different
    1 Diverse bacterial communities are recruited on spores of different 2 arbuscular mycorrhizal fungal isolates 3 Monica Agnolucci*, Fabio Battini, Caterina Cristani, Manuela Giovannetti 4 Department of Agriculture, Food and Environment, University of Pisa, Via del 5 Borghetto 80, 56124 Pisa, Italy 6 7 RUNNING HEAD: Diverse bacterial communities recruited on AMF spores 8 *Corresponding author: M. Agnolucci, Department of Agriculture, Food and 9 Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy 10 Phone: +39.0502216647, Fax: +39.0502220606, e-mail address: 11 [email protected] 12 13 Abstract 14 Arbuscular mycorrhizal fungi (AMF) establish mutualistic symbioses with the roots of 15 most food crops, playing a key role in soil fertility and plant nutrition and health. The 16 beneficial activity of AMF may be positively affected by bacterial communities living 17 associated with mycorrhizal roots, spores and extraradical hyphae. Here we investigated 18 the diversity of bacterial communities associated with the spores of six AMF isolates, 19 belonging to different genera and species and maintained for several generations in pot- 20 cultures with the same host plant, under the same environmental conditions and with the 21 same soil. The occurrence of large bacterial communities intimately associated with 22 spores of the AMF isolates was revealed by PCR-DGGE analysis and sequencing of 1 23 DGGE bands. Cluster and canonical correspondence analysis showed that the six AMF 24 isolates displayed diverse bacterial community profiles unrelated with their taxonomic 25 position, suggesting that each AMF isolate recruits on its spores a different microbiota. 26 The 48 sequenced fragments were affiliated with Actinomycetales, Bacillales, 27 Pseudomonadales, Burkholderiales, Rhizobiales and with Mollicutes related 28 endobacteria (Mre).
    [Show full text]
  • Communautés Microbiennes De La Baie De Raisin : Incidence Des Facteurs Biotiques Et Abiotiques Guilherme Marques Martins
    Communautés microbiennes de la baie de raisin : Incidence des facteurs biotiques et abiotiques Guilherme Marques Martins To cite this version: Guilherme Marques Martins. Communautés microbiennes de la baie de raisin : Incidence des facteurs biotiques et abiotiques : Incidence des facteurs biotiques et abiotiques. Sciences du Vivant [q-bio]. Université de Bordeaux Ségalen (Bordeaux 2), 2012. Français. tel-02802218 HAL Id: tel-02802218 https://hal.inrae.fr/tel-02802218 Submitted on 5 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. Année 2012 Thèse n°1924 THÈSE pour le DOCTORAT DE L’UNIVERSITÉ BORDEAUX 2 Ecole doctorale Mention : Sciences, Technologie, Santé Option : Œnologie Présentée et soutenue publiquement Le 3 juillet 2012 Par Guilherme MARTINS Né le 7/10/81 à Coimbra, Portugal Communautés microbiennes de la baie de raisin Incidence des facteurs biotiques et abiotiques Membres du Jury Mr. P. REY, Professeur à Bordeaux Sciences Agro Président Mr. R. DURAN, Professeur à l’Université de Pau et des Pays de l'Adour Rapporteur Mme M.C. MONTEL, Directrice de recherche à l’INRA de Clermont-Ferrand Rapporteur Mr. S. COMPANT, Maître de conférences à l’Université de Toulouse Examinateur Mme A.
    [Show full text]
  • Optimized Analysis of the Lung Allograft Microbiota from Bronchoalveolar Lavage Fluid
    Optimized Analysis of the Lung Allograft Microbiota from Bronchoalveolar Lavage Fluid by Janice Evana Prescod A thesis submitted in conformity with the requirements for the degree of Master of Science Department of Laboratory of Medicine and Pathobiology University of Toronto © Copyright by Janice Evana Prescod 2018 Optimized Analysis of the Lung Allograft Microbiota from Bronchoalveolar Lavage Fluid Janice Prescod Master of Science Department of Laboratory of Medicine and Pathobiology University of Toronto 2018 Abstract Introduction: Use of bronchoalveolar lavage fluid (BALF) for analysis of the allograft microbiota in lung transplant recipients (LTR) by culture-independent analysis poses specific challenges due to its highly variable bacterial density. Approach: We developed a methodology to analyze low- density BALF using a serially diluted mock community and BALF from uninfected LTR. Methods/Results: A mock microbial community was used to establish the properties of true- positive taxa and contaminants in BALF. Contaminants had an inverse relationship with input bacterial density. Concentrating samples increased the bacterial density and the ratio of community taxa (signal) to contaminants (noise), whereas DNase treatment decreased density and signal:noise. Systematic removal of contaminants had an important impact on microbiota-inflammation correlations in BALF. Conclusions: There is an inverse relationship between microbial density and the proportion of contaminants within microbial communities across the density range of BALF. This study has implications for the analysis and interpretation of BALF microbiota. ii Acknowledgments To my supervisor, Dr. Bryan Coburn, I am eternally grateful for the opportunity you have given me by accepting me as your graduate student. Over the past two years working with you has been both rewarding and at times very challenging.
    [Show full text]
  • Metagenomic Characterization of Bacterial Communities on Ready-To-Eat Vegetables and Effects of Household Washing on Their Diversity and Composition
    pathogens Article Metagenomic Characterization of Bacterial Communities on Ready-to-Eat Vegetables and Effects of Household Washing on their Diversity and Composition Soultana Tatsika 1,2, Katerina Karamanoli 3, Hera Karayanni 4 and Savvas Genitsaris 1,* 1 School of Economics, Business Administration and Legal Studies, International Hellenic University, 57001 Thermi, Greece; [email protected] 2 Hellenic Food Safety Authority (EFET), 57001 Pylaia, Greece 3 School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; [email protected] 4 Department of Biological Applications and Technology, University of Ioannina, 45100 Ioannina, Greece; [email protected] * Correspondence: [email protected] Received: 8 February 2019; Accepted: 15 March 2019; Published: 19 March 2019 Abstract: Ready-to-eat (RTE) leafy salad vegetables are considered foods that can be consumed immediately at the point of sale without further treatment. The aim of the study was to investigate the bacterial community composition of RTE salads at the point of consumption and the changes in bacterial diversity and composition associated with different household washing treatments. The bacterial microbiomes of rocket and spinach leaves were examined by means of 16S rRNA gene high-throughput sequencing. Overall, 886 Operational Taxonomic Units (OTUs) were detected in the salads’ leaves. Proteobacteria was the most diverse high-level taxonomic group followed by Bacteroidetes and Firmicutes. Although they were processed at the same production facilities, rocket showed different bacterial community composition than spinach salads, mainly attributed to the different contributions of Proteobacteria and Bacteroidetes to the total OTU number. The tested household decontamination treatments proved inefficient in changing the bacterial community composition in both RTE salads.
    [Show full text]
  • Massilia Umbonata Sp. Nov., Able to Accumulate Poly-B-Hydroxybutyrate, Isolated from a Sewage Sludge Compost–Soil Microcosm
    International Journal of Systematic and Evolutionary Microbiology (2014), 64, 131–137 DOI 10.1099/ijs.0.049874-0 Massilia umbonata sp. nov., able to accumulate poly-b-hydroxybutyrate, isolated from a sewage sludge compost–soil microcosm Marina Rodrı´guez-Dı´az,1,23 Federico Cerrone,33 Mar Sa´nchez-Peinado,3 Lucı´a SantaCruz-Calvo,3 Clementina Pozo1,3 and Jesu´s Gonza´lez Lo´pez1,3 Correspondence 1Department of Microbiology, University of Granada, Granada, Spain Clementina Pozo 2Max-Planck-Institut fu¨r Marine Mikrobiologie, Celsiusstrasse 1, 28359 Bremen, Germany [email protected] 3Water Research Institute, University of Granada, Granada, Spain A bacterial strain, designated strain LP01T, was isolated from a laboratory-scale microcosm packed with a mixture of soil and sewage sludge compost designed to study the evolution of microbial biodiversity over time. The bacterial strain was selected for its potential ability to store polyhydroxyalkanoates (PHAs) as intracellular granules. The cells were aerobic, Gram-stain- negative, non-endospore-forming motile rods. Phylogenetically, the strain was classified within the genus Massilia, as its 16S rRNA gene sequence had similarity of 99.2 % with respect to those of Massilia albidiflava DSM 17472T and M. lutea DSM 17473T. DNA–DNA hybridization showed low relatedness of strain LP01T to the type strains of other, phylogenetically related species of the genus Massilia. It contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1v7c and/or iso-C15 : 0 2-OH) as the major fatty acid(s). It was found to contain small amounts of the fatty acids C18 : 0 and C14 : 0 2-OH, a feature that served to distinguish it from its closest phylogenetic relatives within the genus Massilia.
    [Show full text]
  • Massilia Tieshanensis Sp. Nov., Isolated from Mining Soil
    %paper no. ije034306 charlesworth ref: ije034306& New Taxa - Proteobacteria International Journal of Systematic and Evolutionary Microbiology (2012), 62, 000–000 DOI 10.1099/ijs.0.034306-0 Massilia tieshanensis sp. nov., isolated from mining soil Yan Du, Xiang Yu and Gejiao Wang Correspondence State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Gejiao Wang Huazhong Agricultural University, Wuhan, Hubei 430070, PR China [email protected] or [email protected] A bacterial isolate, designated strain TS3T, was isolated from soil collected from a metal mine in Tieshan District, Daye City, Hubei Province, in central China. Cells of this strain were Gram- negative, motile and rod-shaped. The strain had ubiquinone Q-8 as the predominant respiratory quinone, phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as the major polar lipids and summed feature 3 (C16 : 1v7c and/or iso-C15 : 0 2-OH), C16 : 0 and C18 : 1v7c as the major fatty acids. The G+C content was 65.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain TS3T was most closely related to Massilia niastensis 5516S-1T (98.5 %), Massilia consociata CCUG 58010T (97.6 %), Massilia aerilata 5516S-11T (97.4 %) and Massilia varians CCUG 35299T (97.2 %). DNA–DNA hybridization revealed low relatedness between strain TS3T and M. niastensis KACC 12599T (36.5 %), M. consociata CCUG 58010T (27.1 %), M. aerilata KACC 12505T (22.7 %) and M. varians CCUG 35299T (46.5 %). On the basis of phenotypic and phylogenetic characteristics, strain TS3T belongs to the genus Massilia, but is clearly differentiated from other members of the genus.
    [Show full text]
  • Molecular and Biochemical Characterization of a Novel Xylanase from Massilia Sp. RBM26 Isolated from the Feces of Rhinopithecus
    J. Microbiol. Biotechnol. (2016), 26(1), 9–19 http://dx.doi.org/10.4014/jmb.1504.04021 Research Article Review jmb Molecular and Biochemical Characterization of a Novel Xylanase from Massilia sp. RBM26 Isolated from the Feces of Rhinopithecus bieti S Bo Xu1,2,3†, Liming Dai1†, Junjun Li1,2,3, Meng Deng1, Huabiao Miao1, Junpei Zhou1,2,3, Yuelin Mu1,2,3, Qian Wu1,2,3, Xianghua Tang1,2,3, Yunjuan Yang1,2,3, Junmei Ding1,2,3, Nanyu Han1,2,3, and Zunxi Huang1,2,3* 1School of Life Science, Yunnan Normal University, Kunming 650500, P.R. China 2Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming 650500, P.R. China 3Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming 650500, P.R. China Received: April 8, 2015 Revised: July 17, 2015 Xylanases sourced from different bacteria have significantly different enzymatic properties. Accepted: September 17, 2015 Therefore, studying xylanases from different bacteria is important to their applications in different fields. A potential xylanase degradation gene in Massilia was recently discovered through genomic sequencing. However, its xylanase activity remains unexplored. This paper First published online is the first to report a xylanase (XynRBM26) belonging to the glycosyl hydrolase family (GH10) September 18, 2015 from the genus Massilia. The gene encodes a 383-residue polypeptide (XynRBM26) with the *Corresponding author highest identity of 62% with the endoxylanase from uncultured bacterium BLR13. The Phone: +86-871-5920830; XynRBM26 expressed in Escherichia coli BL21 is a monomer with a molecular mass of 45.0 kDa.
    [Show full text]
  • Massilia Norwichensis Sp. Nov., Isolated from an Air Sample
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by ZENODO International Journal of Systematic and Evolutionary Microbiology (2015), 65, 56–64 DOI 10.1099/ijs.0.068296-0 Massilia norwichensis sp. nov., isolated from an air sample Ivana Orthova´,1 Peter Ka¨mpfer,2 Stefanie P. Glaeser,2 Rene´ Kaden3 and Hans-Ju¨rgen Busse1 Correspondence 1Institut fu¨r Bakteriologie, Mykologie und Hygiene, Veterina¨rmedizinische Universita¨t, A-1210 Wien, Hans-Ju¨rgen Busse Austria hans-juergen.busse@vetmeduni. 2Institut fu¨r Angewandte Mikrobiologie, Justus-Liebig-Universita¨t Giessen, D-35392 Giessen, ac.at Germany 3Department of Medical Sciences, Clinical Bacteriology, University of Uppsala, SE-75185 Uppsala, Sweden A Gram-negative, rod-shaped and motile bacterial isolate, designated strain NS9T, isolated from air of the Sainsbury Centre for Visual Arts in Norwich, UK, was subjected to a polyphasic taxonomic study including phylogenetic analyses based on partial 16S rRNA, gyrB and lepA gene sequences and phenotypic characterization. The 16S rRNA gene sequence of NS9T identified Massilia haematophila CCUG 38318T, M. niastensis 5516S-1T (both 97.7 % similarity), M. aerilata 5516S-11T (97.4 %) and M. tieshanensis TS3T (97.4 %) as the next closest relatives. In partial gyrB and lepA sequences, NS9T shared the highest similarities with M. haematophila CCUG 38318T (94.5 %) and M. aerilata 5516-11T (94.3 %), respectively. These sequence data demonstrate the affiliation of NS9T to the genus Massilia. The detection of the predominant ubiquinone Q-8, a polar lipid profile consisting of the major compounds diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol and a polyamine pattern containing 2- hydroxyputrescine and putrescine were in agreement with the assignment of strain NS9T to the genus Massilia.
    [Show full text]
  • Molecular Analysis of Root-Associated Diazotrophs in Important Plants from Southern Africa and South America
    Molecular analysis of root-associated diazotrophs in important plants from Southern Africa and South America Claudia Sofía Burbano Roa Dissertation submitted in partial fulfillment of the requirements for the degree Dr. rer. nat. Bremen, April 2011 The experiments of the presented work have been carried out from May 2007 until October 2010 at the Department of Biology/Chemistry of Bremen University, Germany, under the guidance of Prof. Dr. Barbara Reinhold-Hurek and Dr. Thomas Hurek. Die Untersuchungen zur folgenden Arbeit wurden von Mai 2007 bis Oktober 2010 am Fachbereich Biologie/Chemie der Universität Bremen unter der Leitung von Prof. Dr. Barbara Reinhold-Hurek und Dr. Thomas Hurek durchgeführt. Vom Fachbereich Biologie/Chemie der Universität Bremen als Dissertation angenommen am: Datum der Disputation: First reviewer: Prof. Dr. Barbara Reinhold-Hurek Second reviewer: Prof. Dr. Michael Friedrich Dedicated to the memory of my grandfather Ignacio Parts of the presented results have been written as manuscript, submitted to a journal, or are already published: Burbano CS, Reinhold-Hurek B, Hurek T. LNA-substituted degenerate primers improve detection of nitrogenase gene transcription in environmental samples. Environ. Microbiol. Rep. 2010 (2): 251-257. Burbano CS, Liu Y, Rösner K, Reis V, Caballero-Mellado J, Reinhold-Hurek B, Hurek T. Predominant nifH transcript phylotypes related to Rhizobium rosettiformans in field grown sugarcane plants and in Norway spruce. Environ. Microbiol. Rep. doi:10.1111/j.1758-2229.2010.00238.x Burbano CS, Grönemeyer JL, Hurek T, Reinhold-Hurek B. Study of the microbial community structure and functional diazotrophic diversity in Collophospermum mopane. In preparation. Grönemeyer JL, Burbano CS, Hurek T, Reinhold-Hurek B.
    [Show full text]
  • A Report on 15 Unrecorded Bacterial Species of Korea Isolated in 2016, Belonging to the Class Betaproteobacteria
    Journal of Species Research 7(2):97-103, 2018 A report on 15 unrecorded bacterial species of Korea isolated in 2016, belonging to the class Betaproteobacteria Dong-Uk Kim1, Chi-Nam Seong2, Kwangyeop Jahng3, Soon Dong Lee4, Chang-Jun Cha5, Kiseong Joh6, Che Ok Jeon7, Seung-Bum Kim8 and Myung Kyum Kim1,* 1Department of Bio & Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul 01797, Republic of Korea 2Department of Biology, Sunchon National University, Suncheon 57922, Republic of Korea 3Department of Life Sciences, Chonbuk National University, Jeonju 54899, Republic of Korea 4Department of Science Education, Jeju National University, Jeju 63243, Republic of Korea 5Department of Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea 6Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea 7Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea 8Department of Microbiology, Chungnam National University, Daejeon 34134, Republic of Korea *Correspondent: [email protected] In 2016, as a subset study to discover indigenous prokaryotic species in Korea, a total of 15 bacterial strains were isolated and assigned to the class Betaproteobacteria. From the high 16S rRNA gene sequence similarity (>98.8%) and formation of a robust phylogenetic clade with the closest species, it was determined that each strain belonged to each independent and predefined bacterial species. There is no official report that these 15 species have been described in Korea; therefore, 1 strain of the Aquitalea, 5 strains of the Paraburkholderia, 2 strains of the Comamonas, 1 strain of the Cupriavidus, 1 strain of the Diaphorobacter, 2 strains of the Hydrogenophaga, 1 strain of the Iodobacter, 1 strain of the Massilia and 1 strain of the Rhodoferax within the Betaproteobacteria are described for unreported bacterial species in Korea.
    [Show full text]
  • The Microbial Ecology and Horticultural Sustainability of Organically and Conventionally Managed Apples
    ABSTRACT Title of Document: THE MICROBIAL ECOLOGY AND HORTICULTURAL SUSTAINABILITY OF ORGANICALLY AND CONVENTIONALLY MANAGED APPLES. Andrea R. Ottesen, PhD, 2008 Directed By: Professor, Dr. Christopher S. Walsh, Plant Sciences and Landscape Architecture Objectives Organically and conventionally managed apple trees (Malus domestica Borkh) were evaluated for three growing seasons (2005-2007) to examine the impact of organic and conventional pesticide applications on the microbial ecology of phyllosphere and soil microflora. An important objective was to establish if organic or conventional selection pressures contribute to an increased presence of enteric pathogens in phyllosphere microflora. The horticultural and economic sustainability of the organic crop was also compared to the conventional crop with regard to fruit yield and input costs. Methods Microbial populations from phyllosphere and soil environments of apple trees were evaluated using clone libraries of 16S rRNA gene fragments. Clones were sequenced and software was used to assess diversity indices, identify shared similarities and compute statistical differences between communities. These measurements were subsequently used to examine treatment effects on the microbial libraries. Phyllosphere Results Eight bacterial phyla and 14 classes were found in this environment. A statistically significant difference between organically and conventionally managed phyllosphere bacterial microbial communities was observed at four of six sampling time points. Unique phylotypes were found associated with each management treatment but no increased human health risk could be associated with either treatment with regard to enteric pathogens. Soil Results Seventeen bacterial phyla spanning twenty-two classes, and two archaeal phyla spanning eight classes, were seen in the 16S rRNA gene libraries of organic and conventional soil samples.
    [Show full text]
  • Plant Growth Promotion Potential Is Equally Represented in Diverse Grapevine Root-Associated Bacterial Communities from Different Biopedoclimatic Environments
    Hindawi Publishing Corporation BioMed Research International Volume 2013, Article ID 491091, 17 pages http://dx.doi.org/10.1155/2013/491091 Research Article Plant Growth Promotion Potential Is Equally Represented in Diverse Grapevine Root-Associated Bacterial Communities from Different Biopedoclimatic Environments Ramona Marasco,1 Eleonora Rolli,1 Marco Fusi,1 Ameur Cherif,2 Ayman Abou-Hadid,3 Usama El-Bahairy,3 Sara Borin,1 Claudia Sorlini,1 and Daniele Daffonchio1 1 Department of Food, Environment, and Nutritional Sciences, University of Milan, Via Celoria 2, 20133 Milan, Italy 2 Laboratory of Microorganisms and Active Biomolecules, University of Tunis El Manar, Campus Universitaire, Rommana 1068, Tunis BP 94, Tunisia and Laboratory BVBGR, ISBST, University of Manouba, La Manouba 2010, Tunisia 3 Department of Horticulture, Faculty of Agriculture, Ain Shams University, Shubra Elkheima, Cairo, Egypt Correspondence should be addressed to Daniele Daffonchio; [email protected] Received 13 March 2013; Revised 14 May 2013; Accepted 21 May 2013 Academic Editor: George Tsiamis Copyright © 2013 Ramona Marasco et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Plant-associated bacteria provide important services to host plants. Environmental factors such as cultivar type and pedoclimatic conditions contribute to shape their diversity. However, whether these environmental factors may influence the plant growth promoting (PGP) potential of the root-associated bacteria is not widely understood. To address this issue, the diversity and PGP potential of the bacterial assemblage associated with the grapevine root system of different cultivars in three Mediterranean environments along a macrotransect identifying an aridity gradient were assessed by culture-dependent and independent approaches.
    [Show full text]