DOCSLIB.ORG

Denitrification by Zero-Valent Iron-Supported Mixed

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

DENITRIFICATION BY ZERO-VALENT IRON-SUPPORTED MIXED CULTURES by Inyoung Kim A dissertation submitted to the Faculty of the University of Delaware in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Civil Engineering Fall 2018 © 2018 Inyoung Kim All Rights Reserved DENITRIFICATION BY ZERO-VALENT IRON-SUPPORTED MIXED CULTURES by Inyoung Kim Approved: __________________________________________________________ Sue McNeil, Ph.D. Chair of the Department of Civil and Environmental Engineering Approved: __________________________________________________________ Levi T. Thompson, Ph.D. Dean of the College of Engineering Approved: __________________________________________________________ Douglas J. Doren, Ph.D. Interim Vice Provost for Graduate and Professional Education I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ Daniel K. Cha, Ph.D. Professor in charge of dissertation I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ Julia Anne Maresca, Ph.D. Member of dissertation committee I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ Pei C. Chiu, Ph.D. Member of dissertation committee I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ Jeffry Fuhrmann, Ph.D. Member of dissertation committee ACKNOWLEDGMENTS I would like to express my sincere gratitude to my advisor, Dr. Daniel K. Cha for his continuous guidance, assistant, and expertise that I needed during my degree. I gratefully acknowledge my Ph.D. committee members, Dr. Julia A. Maresca, Dr. Pei C. Chiu, and Dr. Jeffry Fuhrmann for their time and insightful feedback for my research and thesis. My sincere thanks also goes to Mr. Michael Davidson for his tremendous technical and substantial support for research and safety in the laboratory. I am thankful to Mrs. Christine Reoli, a graduate academic advisor of the department, for her guidance and support for better graduate school life. I also thank lab manager, Dr. Yu-han Yu, and staffs of the Department of Civil and Environmental Engineering, Mrs. Karen Greco, Sarah Palmer, and Christine Murray, for their tremendous help and support. The members of the Cha group have contributed immensely to my personal and professional time at UD. The members have been good friends as well as collaborators. All past and present group members that I have had the pleasure to work with are undergraduate and graduate students Beom-seok Kim, Taylor Smith, Philip McGuire, Yaseen Al-Qaraghuli, Xiangmin Liang, Larissa Gaul, Mingjun Shao, Aidan Meese, and Rachel Aukamp; and the numerous visiting scholars who have come through the lab. In regard to the technical support, I thank the staffs Deborah Powell at UD Bioimaging Center and Drs. Choaying Ni and Yong Zhao at Keck Center for iv Advanced Microscopy and Microanalysis for advising to acquire confocal and scanning electron microscopic images. Also, I thank Brewster F. Kingham at UD Sequencing & Genotyping Center and Dr. John Hanson, Rocio Navarro, and Lars Koenig at RTL genomics to help me to better understand microbial sequencing area. I am deeply thankful to my family: my parents and to my brother for supporting me spiritually throughout my life in general. Most of all for my loving, supportive, and encouraging husband Minho whose faithful support during the Ph.D. is appreciated. v TABLE OF CONTENTS LIST OF TABLES .................................................................................................... ix LIST OF FIGURES .................................................................................................... x ABSTRACT............................................................................................................. xii Chapter 1 INTRODUCTION .......................................................................................... 1 1.1 Nitrate .................................................................................................... 1 1.2 Nitrate Treatment Techniques ................................................................ 2 1.3 Objectives .............................................................................................. 3 2 LITERATURE REVIEW ............................................................................... 6 2.1 Hydrogenophillic Denitrifiers................................................................. 9 2.2 Ferrous-oxidizing Denitrifiers .............................................................. 10 2.3 Anaerobic Ammonium Oxidation (Anammox) ..................................... 11 2.4 Microbial-meditated Corrosion and Surface Colonization .................... 12 3 MICROBIAL COMMUNITY ANALYSIS OF DENITRIFYING CULTURES GROWN ON ZERO-VALENT IRON ..................................... 14 3.1 Introduction ......................................................................................... 15 3.2 Materials and Methods ......................................................................... 19 3.2.1 Microorganisms and Chemicals ................................................ 19 3.2.2 Denitrification Test with Various Electron Donors ................... 19 3.2.3 Chemical Analysis .................................................................... 20 3.2.4 DNA Extraction and Sequencing for Microbial Identification ... 21 3.2.5 Bacterial 16S rRNA Gene Sequence Analysis .......................... 21 3.2.6 Statistical Analysis with Sequence Results ............................... 22 3.3 Results and Discussion ......................................................................... 22 3.3.1 Nitrate Reduction in Batch Reactors ......................................... 22 3.3.2 Microbial Diversity under Different Conditions ........................ 24 3.3.3 Principal Component Analysis .................................................. 27 vi 4 EFFECT OF LOW TEMPERATURE ON ABIOTIC AND BIOTIC NITRATE REDUCTION BY ZERO-VALENT IRON ................................. 38 4.1 Introduction ......................................................................................... 39 4.2 Materials and Methods ......................................................................... 42 4.2.1 Chemicals and Microorganisms ................................................ 42 4.2.2 Batch Reduction Experiments ................................................... 43 4.2.3 Analytical Procedures ............................................................... 43 4.3 Results and Discussion ......................................................................... 44 4.3.1 Effects of Temperature on Nitrate Reduction by ZVI ................ 44 4.3.2 Effects of Temperature on Nitrate Reduction by ZVI and Microorganisms ........................................................................ 45 4.3.3 Enhanced Denitrification by Microbial Induced Corrosion ....... 46 4.4 Conclusion ........................................................................................... 48 5 NITROGEN REMOVAL BY MICROBIALLY-COLONIZED IRON GRANULES: ANAMMOX-LIKE PROCESS .............................................. 57 5.1 Introduction ......................................................................................... 58 5.2 Materials and Methods ......................................................................... 61 5.2.1 Batch Reduction Tests with Anammox Mixed Cultures ............ 61 5.2.2 Denitrification in Anaerobic Fluidized Bioreactor ..................... 63 5.2.3 Surface Study of Zero-valent Iron ............................................. 64 5.2.3.1 Confocal Microscopy ................................................. 64 5.2.3.2 Scanning Electron Microscopy ................................... 65 5.2.4 Identification of Bacterial Community Colonizing Zero-valent Iron .......................................................................................... 65 5.3 Results and Discussion ......................................................................... 66 5.3.1 Anammox Activities in the Presence of Zero-valent Iron: Preliminary Tests ...................................................................... 66 5.3.2 Enhanced Nitrate Reduction in Anaerobic Fluidized Bioreactor 67 5.3.2.1 Characterization of Biofilms on Zero-valent Iron ....... 68 5.3.2.2 Diversity of Microbial Communities in the Biofilm .... 69 6 CONCLUSIONS .......................................................................................... 85 vii 6.1 Summary of Results ............................................................................. 85 6.1.1 Denitrification Performances in the Mixed-culture System with Various Electron Donors and Zero-valent Iron .......................... 85 6.1.2 Enhanced Nitrate Removal by Microorganisms and Zero- valent Iron under Low Temperature .........................................
Recommended publications
  • Rajiv Kumar M.Phil

    Rajiv Kumar M.Phil

    PHYLOGENETIC ANALYSIS OF BACTERIAL DIVERSITY OF HEAVY METAL AFFECTED SOIL OF BATHINDA REGION (SOUTH WEST PUNJAB) A Dissertation submitted to the Central University of Punjab For the award of Master of Philosophy In Biosciences BY Rajiv Kumar Supervisor Dr. Sanjeev K. Thakur Centre for Biosciences School of Basic and Applied Sciences Central University of Punjab, Bathinda August, 2012 1 CERTIFICATE I declare that the dissertation entitled “PHYLOGENETIC ANALYSIS OF BACTERIAL DIVERSITY OF HEAVY METAL AFFECTED SOIL OF BATHINDA REGION (SOUTH WEST PUNJAB)” has been prepared by me under the guidance of Dr. Sanjeev K. Thakur, Assistant Professor, Centre for Biosciences, School of Basic and Applied Sciences, Central University of Punjab. No part of this dissertation has formed the basis for the award of any degree or fellowship previously. Rajiv Kumar Reg. No.:- CUP/M.Phil.-Ph.D/SBAS/BIO/2010-11/05 Centre for Biosciences, School of Basic and Applied Sciences, Central University of Punjab, Bathinda - 151001 DATE: i CERTIFICATE I certify that Rajiv Kumar has prepared his dissertation entitled “PHYLOGENETIC ANALYSIS OF BACTERIAL DIVERSITY OF HEAVY METAL AFFECTED SOIL OF BATHINDA REGION (SOUTH WEST PUNJAB)”, for the award of M.Phil. degree of the Central University of Punjab, under my guidance. He has carried out this work at the Centre for Biosciences, School of Basic and Applied Sciences, Central University of Punjab. Dr. Sanjeev K. Thakur Assistant Professor Centre for Biosciences, School of Basic and Applied Sciences, Central University of Punjab, Bathinda - 151001 DATE: ii ABSTRACT Phylogenetic Analysis of Bacterial Diversity of Heavy Metal Affected Soil of Bathinda Region (South West Punjab) Name of student: Rajiv Kumar Registration Number: CUP/M.Phil.-Ph.D./SBAS/BIO/2010-11/05 Degree for which submitted: Master of Philosophy Name of supervisor: Dr.
  • Changes in the Structure and Function of Microbial Communities in Drinking Water Treatment Bioreactors Upon Addition of Phosphorus

    Changes in the Structure and Function of Microbial Communities in Drinking Water Treatment Bioreactors Upon Addition of Phosphorus

    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by UNL | Libraries University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Civil Engineering Faculty Publications Civil Engineering 11-2010 Changes in the Structure and Function of Microbial Communities in Drinking Water Treatment Bioreactors upon Addition of Phosphorus Xu Li University of Nebraska-Lincoln, [email protected] Giridhar Upadhyaya University of Michigan, Ann Arbor Wangki Yuen Jess Brown Carollo Engineers, Sarasota, Florida Eberhard Morgenroth Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/civilengfacpub Part of the Civil Engineering Commons Li, Xu; Upadhyaya, Giridhar; Yuen, Wangki; Brown, Jess; Morgenroth, Eberhard; and Raskin, Lutgarde, "Changes in the Structure and Function of Microbial Communities in Drinking Water Treatment Bioreactors upon Addition of Phosphorus" (2010). Civil Engineering Faculty Publications. 35. https://digitalcommons.unl.edu/civilengfacpub/35 This Article is brought to you for free and open access by the Civil Engineering at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Civil Engineering Faculty Publications by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Xu Li, Giridhar Upadhyaya, Wangki Yuen, Jess Brown, Eberhard Morgenroth, and Lutgarde Raskin This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/ civilengfacpub/35 APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Nov. 2010, p. 7473–7481 Vol. 76, No. 22 0099-2240/10/$12.00 doi:10.1128/AEM.01232-10 Copyright © 2010, American Society for Microbiology. All Rights Reserved.
  • Metagenomics Analysis Reveals the Microbial Communities

    Metagenomics Analysis Reveals the Microbial Communities

    diversity Article Metagenomics Analysis Reveals the Microbial Communities, Antimicrobial Resistance Gene Diversity and Potential Pathogen Transmission Risk of Two Different Landfills in China Shan Wan 1,†, Min Xia 2,†, Jie Tao 1, Yanjun Pang 1, Fugen Yu 1,* , Jun Wu 3,* and Shanping Chen 2,* 1 State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China; [email protected] (S.W.); [email protected] (J.T.); [email protected] (Y.P.) 2 Shanghai Environmental Sanitation Engineering Design Institute Co., Ltd., Shanghai 200232, China; [email protected] 3 State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China * Correspondence: [email protected] (F.Y.); [email protected] (J.W.); [email protected] (S.C.) † There authors contribute equally to this work. Abstract: In this study, we used a metagenomic approach to analyze microbial communities, antibiotic resistance gene diversity, and human pathogenic bacterium composition in two typical Citation: Wan, S.; Xia, M.; Tao, J.; landfills in China. Results showed that the phyla Proteobacteria, Bacteroidetes, and Actinobacte- Pang, Y.; Yu, F.; Wu, J.; Chen, S. ria were predominant in the two landfills, and archaea and fungi were also detected. The genera Metagenomics Analysis Reveals the Methanoculleus, Lysobacter, and Pseudomonas were predominantly present in all samples. sul2, sul1, Microbial Communities, tetX, and adeF were the four most abundant antibiotic resistance genes. Sixty-nine bacterial pathogens Antimicrobial Resistance Gene were identified from the two landfills, with Klebsiella pneumoniae, Bordetella pertussis, Pseudomonas Diversity and Potential Pathogen aeruginosa, and Bacillus cereus as the major pathogenic microorganisms, indicating the existence of Transmission Risk of Two Different potential environmental risk in landfills.
  • Bacteria Responsible for Nitrate-Dependent Antimonite Oxidation in Antimony-Contaminated Paddy Soil Revealed by the Combination of DNA-SIP and Metagenomics

    Bacteria Responsible for Nitrate-Dependent Antimonite Oxidation in Antimony-Contaminated Paddy Soil Revealed by the Combination of DNA-SIP and Metagenomics

    Bacteria Responsible for Nitrate-dependent Antimonite Oxidation in Antimony-contaminated Paddy Soil Revealed by the Combination of DNA-SIP and Metagenomics Miaomiao Zhang Guangdong Institute of Eco-Environmental and Soil Sciences Zhe Li Wuhan Institute of Technology Max M. Häggblom Rutgers The State University of New Jersey Lily Young Rutgers The State University of New Jersey Fangbai Li Guangdong Institute of Eco-Environmental and Soil Sciences Zijun He Guangdong Institute of Eco-Environmental and Soil Sciences Guimei Lu Guangdong Institute of Eco-Environmental and Soil Sciences Rui Xu Guangdong Institute of Eco-Environmental and Soil Sciences Xiaoxu Sun Guangdong Institute of Eco-Environmental and Soil Sciences Lang Qiu Guangdong Institute of Eco-Environmental and Soil Sciences Weimin Sun ( [email protected] ) Guangdong Institute of Eco-Environmental and Soil Sciences https://orcid.org/0000-0002-3456-8177 Research Keywords: Nitrate-dependent antimonite oxidation, Nitrate-dependent Sb(III)-oxidizing bacteria, DNA-SIP, amplicon and shotgun metagenomics Posted Date: September 17th, 2020 Page 1/24 DOI: https://doi.org/10.21203/rs.3.rs-78069/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Version of Record: A version of this preprint was published at Soil Biology and Biochemistry on May 1st, 2021. See the published version at https://doi.org/10.1016/j.soilbio.2021.108194. Page 2/24 Abstract Background: Antimonite (Sb(III)) oxidation (SbO) can decrease the toxicity of antimony (Sb) and its uptake into plants (e.g., rice), thus serving an ecological role in bioremediation of Sb contamination. In some anoxic environments, Sb(III) can be oxidized coupled with nitrate as the electron acceptor.
  • Physiology and Biochemistry of Aromatic Hydrocarbon-Degrading Bacteria That Use Chlorate And/Or Nitrate As Electron Acceptor

    Physiology and Biochemistry of Aromatic Hydrocarbon-Degrading Bacteria That Use Chlorate And/Or Nitrate As Electron Acceptor

    Invitation for the public defense of my thesis Physiology and biochemistry of aromatic hydrocarbon-degrading of aromatic and biochemistry Physiology bacteria that use chlorate and/or nitrate as electron acceptor as electron nitrate and/or use chlorate that bacteria Physiology and biochemistry Physiology and biochemistry of aromatic hydrocarbon-degrading of aromatic hydrocarbon- degrading bacteria that bacteria that use chlorate and/or nitrate as electron acceptor use chlorate and/or nitrate as electron acceptor The public defense of my thesis will take place in the Aula of Wageningen University (Generall Faulkesweg 1, Wageningen) on December 18 2013 at 4:00 pm. This defense is followed by a reception in Café Carré (Vijzelstraat 2, Wageningen). Margreet J. Oosterkamp J. Margreet Paranimphs Ton van Gelder ([email protected]) Aura Widjaja Margreet J. Oosterkamp ([email protected]) Marjet Oosterkamp (911 W Springfield Ave Apt 19, Urbana, IL 61801, USA; [email protected]) Omslag met flap_MJOosterkamp.indd 1 25-11-2013 5:58:31 Physiology and biochemistry of aromatic hydrocarbon-degrading bacteria that use chlorate and/or nitrate as electron acceptor Margreet J. Oosterkamp Thesis-MJOosterkamp.indd 1 25-11-2013 6:42:09 Thesis committee Thesis supervisor Prof. dr. ir. A. J. M. Stams Personal Chair at the Laboratory of Microbiology Wageningen University Thesis co-supervisors Dr. C. M. Plugge Assistant Professor at the Laboratory of Microbiology Wageningen University Dr. P. J. Schaap Assistant Professor at the Laboratory of Systems and Synthetic Biology Wageningen University Other members Prof. dr. L. Dijkhuizen, University of Groningen Prof. dr. H. J. Laanbroek, University of Utrecht Prof.
  • Arenimonas Halophila Sp. Nov., Isolated from Soil

    Arenimonas Halophila Sp. Nov., Isolated from Soil

    TAXONOMIC DESCRIPTION Kanjanasuntree et al., Int J Syst Evol Microbiol 2018;68:2188–2193 DOI 10.1099/ijsem.0.002801 Arenimonas halophila sp. nov., isolated from soil Rungravee Kanjanasuntree,1 Jong-Hwa Kim,1 Jung-Hoon Yoon,2 Ampaitip Sukhoom,3 Duangporn Kantachote3 and Wonyong Kim1,* Abstract A Gram-staining-negative, aerobic, non-motile, rod-shaped bacterium, designated CAU 1453T, was isolated from soil and its taxonomic position was investigated using a polyphasic approach. Strain CAU 1453T grew optimally at 30 C and at pH 6.5 in the presence of 1 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that CAU 1453T represented a member of the genus Arenimonas and was most closely related to Arenimonas donghaensis KACC 11381T (97.2 % similarity). T CAU 1453 contained ubiquinone-8 (Q-8) as the predominant isoprenoid quinone and iso-C15 : 0 and iso-C16 : 0 as the major cellular fatty acids. The polar lipids consisted of diphosphatidylglycerol, a phosphoglycolipid, an aminophospholipid, two unidentified phospholipids and two unidentified glycolipids. CAU 1453T showed low DNA–DNA relatedness with the most closely related strain, A. donghaensis KACC 11381T (26.5 %). The DNA G+C content was 67.3 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, CAU 1453T represents a novel species of the genus Arenimonas, for which the name Arenimonas halophila sp. nov. is proposed. The type strain is CAU 1453T (=KCTC 62235T=NBRC 113093T). The genus Arenimonas, a member of the family Xantho- CAU 1453T was isolated from soil by the dilution plating monadaceae in the class Gammaproteobacteria was pro- method using marine agar 2216 (MA; Difco) [14].
  • Metabolic Capacities of Anammox Bacterium: Kuenenia Stuttgartiensis

    Metabolic Capacities of Anammox Bacterium: Kuenenia Stuttgartiensis

    Metabolic capacities of anammox bacterium: Kuenenia stuttgartiensis Mariana Itzel Velasco Alvarez December 2014 Master’s dissertation submitted in partial fulfilment of the requirements for the joint degree of International Master of Science in Environmental Technology and Engineering an Erasmus Mundus Master Course jointly organized by UGent (Belgium), ICTP (Prague) and UNESCO‐IHE (the Netherlands) Academic year 2014 – 2015 Metabolic capacities of anammox bacterium: Kuenenia stuttgartiensis Host University: Radboud University, Nijmegen UNESCO-IHE Institute for Water Education Mariana Itzel Velasco Alvarez Promotor: Prof. dr. ir. Mike Jetten Co-promoter: Prof. dr. ir. Piet Lens This thesis was elaborated at Radboud University and defended at UNESCO-IHE Delft within the framework of the European Erasmus Mundus Programme “Erasmus Mundus International Master of Science in Environmental Technology and Engineering " (Course N° 2011-0172) © 2014 Nijmegen, Mariana Velasco, Ghent University, all rights reserved. CONFIDENTIALITY NOTICE – IMPORTANT – PLEASE READ FIRST This document may contain confidential information proprietary to the Radboud University. It is strictly forbidden to publish, cite or make public in any way this document or any part thereof without the express written permission by the Radboud Universit. Under no circumstance this document may be communicated to or put at the disposal of third parties; photocopying or duplicating it in any other way is strictly prohibited. Disregarding the confidential nature of this document may cause irremediable damage to the Radboud University. CONFIDENTIAL DO NOT COPY, DISTRIBUTE OR MAKE PUBLIC IN ANY WAY PLEASE CONTACT RADBOUD UNIVERSITY IF YOU RECEIVED THIS DOCUMENT IN ERROR. Acknowledgments Every success is never achieved alone; is part of a whole, where directly or indirectly is the input of people and situations.
  • Environmental Microbiology, Second Edition Edited by Ralph Mitchell and Ji-Dong Gu Copyright © 2010 Wiley-Blackwell

    Environmental Microbiology, Second Edition Edited by Ralph Mitchell and Ji-Dong Gu Copyright © 2010 Wiley-Blackwell

    ENVIRONMENTAL MICROBIOLOGY SECOND EDITION Edited by Ralph Mitchell and Ji-Dong Gu A JOHN WILEY & SONS, INC., PUBLICATION ENVIRONMENTAL MICROBIOLOGY ENVIRONMENTAL MICROBIOLOGY SECOND EDITION Edited by Ralph Mitchell and Ji-Dong Gu A JOHN WILEY & SONS, INC., PUBLICATION Copyright © 2010 by Wiley-Blackwell. All rights reserved. Published by John Wiley & Sons, Inc., Hoboken, New Jersey Published simultaneously in Canada. Wiley-Blackwell is an imprint of John Wiley & Sons, formed by the merger of Wiley’s global Scientific, Technical, and Medical business with Blackwell Publishing. No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, scanning, or otherwise, except as permitted under Section 107 or 108 of the 1976 United States Copyright Act, without either the prior written permission of the Publisher, or authorization through payment of the appropriate per-copy fee to the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, 978-750-8400, fax 978-750-4470, or on the web at www.copyright.com. Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, 201-748-6011, fax 201-748-6008, or online at http://www.wiley.com/go/permission. Limit of Liability/Disclaimer of Warranty: While the publisher and author have used their best efforts in preparing this book, they make no representations or warranties with respect to the accuracy or completeness of the contents of this book and specifically disclaim any implied warranties of merchantability or fitness for a particular purpose.
  • Unveiling Bacterial Interactions Through Multidimensional Scaling and Dynamics Modeling Received: 06 May 2015 Pedro Dorado-Morales1, Cristina Vilanova1, Carlos P

    Unveiling Bacterial Interactions Through Multidimensional Scaling and Dynamics Modeling Received: 06 May 2015 Pedro Dorado-Morales1, Cristina Vilanova1, Carlos P

    www.nature.com/scientificreports OPEN Unveiling Bacterial Interactions through Multidimensional Scaling and Dynamics Modeling Received: 06 May 2015 Pedro Dorado-Morales1, Cristina Vilanova1, Carlos P. Garay3, Jose Manuel Martí3 Accepted: 17 November 2015 & Manuel Porcar1,2 Published: 16 December 2015 We propose a new strategy to identify and visualize bacterial consortia by conducting replicated culturing of environmental samples coupled with high-throughput sequencing and multidimensional scaling analysis, followed by identification of bacteria-bacteria correlations and interactions. We conducted a proof of concept assay with pine-tree resin-based media in ten replicates, which allowed detecting and visualizing dynamical bacterial associations in the form of statistically significant and yet biologically relevant bacterial consortia. There is a growing interest on disentangling the complexity of microbial interactions in order to both optimize reactions performed by natural consortia and to pave the way towards the development of synthetic consor- tia with improved biotechnological properties1,2. Despite the enormous amount of metagenomic data on both natural and artificial microbial ecosystems, bacterial consortia are not necessarily deduced from those data. In fact, the flexibility of the bacterial interactions, the lack of replicated assays and/or biases associated with differ- ent DNA isolation technologies and taxonomic bioinformatics tools hamper the clear identification of bacterial consortia. We propose here a holistic approach aiming at identifying bacterial interactions in laboratory-selected microbial complex cultures. The method requires multi-replicated taxonomic data on independent subcultures, and high-throughput sequencing-based taxonomic data. From this data matrix, randomness of replicates can be verified, linear correlations can be visualized and interactions can emerge from statistical correlations.
  • Phylogenomics Insights Into Order and Families of Lysobacterales

    Phylogenomics Insights Into Order and Families of Lysobacterales

    SHORT COMMUNICATION Kumar et al., Access Microbiology 2019;1 DOI 10.1099/acmi.0.000015 Phylogenomics insights into order and families of Lysobacterales Sanjeet Kumar†, Kanika Bansal, Prashant P. Patil‡ and Prabhu B. Patil* Abstract Order Lysobacterales (earlier known Xanthomonadales) is a taxonomically complex group of a large number of gamma-pro- teobacteria classified in two different families, namelyLysobacteraceae and Rhodanobacteraceae. Current taxonomy is largely based on classical approaches and is devoid of whole-genome information-based analysis. In the present study, we have taken all classified and poorly described species belonging to the order Lysobacterales to perform a phylogenetic analysis based on the 16 S rRNA sequence. Moreover, to obtain robust phylogeny, we have generated whole-genome sequencing data of six type species namely Metallibacterium scheffleri, Panacagrimonas perspica, Thermomonas haemolytica, Fulvimonas soli, Pseudoful- vimonas gallinarii and Rhodanobacter lindaniclasticus of the families Lysobacteraceae and Rhodanobacteraceae. Interestingly, whole-genome-based phylogenetic analysis revealed unusual positioning of the type species Pseudofulvimonas, Panacagri- monas, Metallibacterium and Aquimonas at family level. Whole-genome-based phylogeny involving 92 type strains resolved the taxonomic positioning by reshuffling the genus across families Lysobacteraceae and Rhodanobacteraceae. The present study reveals the need and scope for genome-based phylogenetic and comparative studies in order to address relationships of genera and species of order Lysobacterales. IMPact StatEMENT genus with unary species can serve as a reference and standard Species of order Lysobacterales have undergone several reclas- to compare later identified species of the respective genera. sifications, until today the taxonomy position of species within the order is largely devoid of whole-genome information.
  • Taxonomic Hierarchy of the Phylum Proteobacteria and Korean Indigenous Novel Proteobacteria Species

    Taxonomic Hierarchy of the Phylum Proteobacteria and Korean Indigenous Novel Proteobacteria Species

    Journal of Species Research 8(2):197-214, 2019 Taxonomic hierarchy of the phylum Proteobacteria and Korean indigenous novel Proteobacteria species Chi Nam Seong1,*, Mi Sun Kim1, Joo Won Kang1 and Hee-Moon Park2 1Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea 2Department of Microbiology & Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea *Correspondent: [email protected] The taxonomic hierarchy of the phylum Proteobacteria was assessed, after which the isolation and classification state of Proteobacteria species with valid names for Korean indigenous isolates were studied. The hierarchical taxonomic system of the phylum Proteobacteria began in 1809 when the genus Polyangium was first reported and has been generally adopted from 2001 based on the road map of Bergey’s Manual of Systematic Bacteriology. Until February 2018, the phylum Proteobacteria consisted of eight classes, 44 orders, 120 families, and more than 1,000 genera. Proteobacteria species isolated from various environments in Korea have been reported since 1999, and 644 species have been approved as of February 2018. In this study, all novel Proteobacteria species from Korean environments were affiliated with four classes, 25 orders, 65 families, and 261 genera. A total of 304 species belonged to the class Alphaproteobacteria, 257 species to the class Gammaproteobacteria, 82 species to the class Betaproteobacteria, and one species to the class Epsilonproteobacteria. The predominant orders were Rhodobacterales, Sphingomonadales, Burkholderiales, Lysobacterales and Alteromonadales. The most diverse and greatest number of novel Proteobacteria species were isolated from marine environments. Proteobacteria species were isolated from the whole territory of Korea, with especially large numbers from the regions of Chungnam/Daejeon, Gyeonggi/Seoul/Incheon, and Jeonnam/Gwangju.
  • Comparative Genomics Provides Insights Into the Taxonomy of Azoarcus and Reveals Separate Origins of Nif Genes in the Proposed Azoarcus and Aromatoleum Genera

    Comparative Genomics Provides Insights Into the Taxonomy of Azoarcus and Reveals Separate Origins of Nif Genes in the Proposed Azoarcus and Aromatoleum Genera

    G C A T T A C G G C A T genes Article Comparative Genomics Provides Insights into the Taxonomy of Azoarcus and Reveals Separate Origins of Nif Genes in the Proposed Azoarcus and Aromatoleum Genera Roberto Tadeu Raittz 1,*,† , Camilla Reginatto De Pierri 2,† , Marta Maluk 3 , Marcelo Bueno Batista 4, Manuel Carmona 5 , Madan Junghare 6, Helisson Faoro 7, Leonardo M. Cruz 2 , Federico Battistoni 8, Emanuel de Souza 2,Fábio de Oliveira Pedrosa 2, Wen-Ming Chen 9, Philip S. Poole 10, Ray A. Dixon 4,* and Euan K. James 3,* 1 Laboratory of Artificial Intelligence Applied to Bioinformatics, Professional and Technical Education Sector—SEPT, UFPR, Curitiba, PR 81520-260, Brazil 2 Department of Biochemistry and Molecular Biology, UFPR, Curitiba, PR 81531-980, Brazil; [email protected] (C.R.D.P.); [email protected] (L.M.C.); [email protected] (E.d.S.); [email protected] (F.d.O.P.) 3 The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK; [email protected] 4 John Innes Centre, Department of Molecular Microbiology, Norwich NR4 7UH, UK; [email protected] 5 Centro de Investigaciones Biológicas Margarita Salas-CSIC, Department of Biotechnology of Microbes and Plants, Ramiro de Maeztu 9, 28040 Madrid, Spain; [email protected] 6 Faculty of Chemistry, Biotechnology and Food Science, NMBU—Norwegian University of Life Sciences, 1430 Ås, Norway; [email protected] 7 Laboratory for Science and Technology Applied in Health, Carlos Chagas Institute, Fiocruz, Curitiba, PR 81310-020, Brazil; helisson.faoro@fiocruz.br 8 Department of Microbial Biochemistry and Genomics, IIBCE, Montevideo 11600, Uruguay; [email protected] Citation: Raittz, R.T.; Reginatto De 9 Laboratory of Microbiology, Department of Seafood Science, NKMU, Kaohsiung City 811, Taiwan; Pierri, C.; Maluk, M.; Bueno Batista, [email protected] M.; Carmona, M.; Junghare, M.; Faoro, 10 Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; H.; Cruz, L.M.; Battistoni, F.; Souza, [email protected] E.d.; et al.