DOCSLIB.ORG

Comparative Metagenomics of Disease Suppressive Soils Allison L.H

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Comparative Metagenomics of Disease Suppressive Soils Allison L.H Comparative metagenomics of disease suppressive soils Allison L.H. Jack, E. Chapelle, Katarzyna Siegel, Veronique Edel-Hermann, Christian Steinberg, Philippe Lemanceau, Jos M. Raaijmakers To cite this version: Allison L.H. Jack, E. Chapelle, Katarzyna Siegel, Veronique Edel-Hermann, Christian Steinberg, et al.. Comparative metagenomics of disease suppressive soils. 2. Thünen Symposium on Soil Metagenomics, Dec 2013, Braunschweig, Germany. pp.48-49. hal-01005058 HAL Id: hal-01005058 https://hal.archives-ouvertes.fr/hal-01005058 Submitted on 3 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. 2nd Thünen SympoSium on Soil meTagenomicS Mining and learning froM MetagenoMes plus Workshop on Bioinformatic tools december 11–13, 2013 Braunschweig, germany AMME R OG R www.soil-metagenomics.org p Scientific programme overview Wednesday, 11 December 2013 Thursday, 12 December 2013 Friday, 13 December 2013 08:00 08:30–10:00 Workshop on bioinformatic tools: 09:00 Part l – working with amplicon sequences l 09:00–10:45 09:00–10:45 Drivers of soil biodiversity The flexible metagenome 10:00 Industrial exhibition & coffee break 10:25–11:40 Industrial exhibition & coffee break Industrial exhibition & coffee break Workshop on bioinformatic tools: 11:00 Part l – working with amplicon sequences II 11:10–12:55 11:10–12:40 Impacts of agriculture and climate change From ecology to biotechnology Lunch break 12:00 only for workshop participants 12:40–13:30 Emerging issues & final discussion 13:00 13:00–13:15 Industrial exhibition & lunch break Opening of Symposium 13:15–15:00 Industrial exhibition & lunch break News from the bioinformatic toolbox 14:00 14:00–15:30 Linking structure to function I 14:30–15:30 Workshop on bioinformatic tools 15:00 Industrial exhibition & coffee break Part ll – assembly of Metagenomes I 15:25–17:10 Industrial exhibition & coffee break Coffee break Unraveling biodiversity 16:00 15:55–17:25 15:45–17:30 Linking structure to function II Workshop on bioinformatic tools Part ll – assembly of Metagenomes II 17:00 17:10–19:00 Posters & drinks 17:25–19:15 Posters 18:00 19:00 19:15–19:30 Bright surprise @ Thünen Forum 19:30-21:30 20:00 Conference buffet @ Thünen Forum 21:00 Table of contents Programme Overview ............................................................................................................................................................ 2 Organization and Imprint ....................................................................................................................................................... 4 Welcome Note of the Conference Chair ................................................................................................................................... 5 Scientific Programme Wednesday, 11 December 2013 ........................................................................................................................ 6 Thursday, 12 December 2013 ........................................................................................................................... 8 Friday, 13 December 2013 ................................................................................................................................ 10 Poster Sessions ...................................................................................................................................................................... 12 Poster Presentations • Wednesday, 11 December 2013 • (1710–1900) .............................................................. 13 Poster Presentations • Thursday, 12 December 2013 • (1725–1915) .................................................................. 18 Sponsors, Exhibitors and Media Cooperations ....................................................................................................................... 23 Plan of Exhibition Area ........................................................................................................................................................... 24 Social Programme .................................................................................................................................................................. 25 General Information ............................................................................................................................................................... 26 Index of speakers, poster presenters and chairs ..................................................................................................................... 30 General Terms and Conditions ................................................................................................................................................ 34 Abstracts ............................................................................................................................................................................... 35 3 organization and imprint Venue and Date Thünen Institute, Forum Bundesallee 50 38116 Braunschweig (Germany) December 11–13, 2013 conference Website www.soil-metagenomics.org conference chair Prof. Dr. Christoph C. Tebbe Thünen Institute of Biodiversity Bundesallee 50 38116 Braunschweig (Germany) local organizing committee Anja B. Dohrmann (Braunschweig) Astrid Näther (Braunschweig) Christoph C. Tebbe (Braunschweig) conference organization Conventus Congressmanagement & Marketing GmbH Claudia Tonn Carl-Pulfrich-Straße 1 07745 Jena (DE) Phone +49 3641 31 16-374 Fax +49 3641 31 16-243 [email protected] www.conventus.de Design/layout Layout www.krea.tif–design.de Print Druckhaus Hesseling GbR Circulation 310 Editorial Deadline 29 November 2013 4 Welcome note of the conference chair Dear colleagues, Johann Heinrich von Thünen, the name patron of the Thünen Institute, already recognized in the early 19th century the economic value of the “richness of soil”, a characteristic he defined by its agricultural productivity. In a world which needs to feed 10 billion people in the near future, while at the same time loosing large areas of fertile land and facing increasingly limited resources of fertilizers, soil richness for agricultural productivity becomes a very modern, if not the key issue for our future survival. A huge scientific and political effort is required to develop an agriculture which produces more and which is at the same time protective to its natural resources, including the richness of our soils. As microbiologists we know that a huge potential to address these challenges is hidden in the soil and its indigenous microbial inhabitants. Soil microorganisms sustain nutrient cycling, promote plant growth, inhibit plant diseases, and have the potential to produce bio-energy and products of outstanding values, including industrial enzymes, bio-pesticides and antibiotics. Much of our understanding of soil microorganisms, however, is still based on the relatively few members of the soil microbial community, which happen to be easily culturable on laboratory growth media. Facing these new challenges of increasing agricultural productivity in a sustainable way, a much deeper exploration and understanding of the total soil microbial communities and interactions as well as their responses to environmental changes is now required. Soil metagenomics and its sisters (metatranscriptomics, -proteomics, -metabolomics), which together directly look into the bio-molecular composition of soils, come at the right moment. First examples already demonstrate the importance of these new scientific fields for biotechnology, ecology and agriculture. The objective of this 2nd Thünen Symposium on Soil Metagenomics is to connect bioinformatics to microbial ecology research. The speed and cost efficiency of today’s DNA and RNA sequencing technologies now requires an effort for a corresponding response from soil microbial ecology. Vice versa, the requirements to characterize microbial communities and address ecologically relevant questions will instruct further bioinformatic efforts, e.g., for sound statistical evaluations and visualizations of results. This Thünen Symposium is meant as an instrument for communication and learning from each other. For the first time, the Thünen Symposium is flanked by a workshop on bioinformatic tools in which applications for nucleic aid analyses are demonstrated, shared and discussed. Welcome in Braunschweig, and thank you for your contribution to make this an exciting event. Prof. Dr. Christoph C. Tebbe 5 Workshop programme • Wednesday, 11 December 2013 0830–1140 Workshop on bioinformatic tools – part l Working with amplicon sequences Chair Folker Meyer (Argonne, IL/US) 0830 Welcome Anja Dohrmann (Braunschweig/DE) 0835 Introduction Folker Meyer (Argonne, IL/US) 0845 The basics of amplicon processing WS 01 Martin Hartmann (Zurich/CH) 1000–1025 Industrial exhibition and coffee break 1025 SILVA and SILVA NGS – practical guidance WS 02 Frank Oliver Glöckner (Bremen/DE) 1110 What’s the Cloud but for water? WS 03 Folker Meyer (Argonne, IL/US) 1140–1230 Lunch break (only
Load more

Recommended publications
  • Diversity of Rare and Abundant Prokaryotic
    Diversity of rare and abundant prokaryotic phylotypes in the Prony hydrothermal field and comparison with other serpentinite-hosted ecosystems Eléonore Frouin, Méline Bes, Bernard Ollivier, Marianne Quéméneur, Anne Postec, Didier Debroas, Fabrice Armougom, Gaël Erauso To cite this version: Eléonore Frouin, Méline Bes, Bernard Ollivier, Marianne Quéméneur, Anne Postec, et al.. Diver- sity of rare and abundant prokaryotic phylotypes in the Prony hydrothermal field and compari- son with other serpentinite-hosted ecosystems. Frontiers in Microbiology, Frontiers Media, 2018, 9, 10.3389/fmicb.2018.00102. hal-01734508 HAL Id: hal-01734508 https://hal.archives-ouvertes.fr/hal-01734508 Submitted on 12 Oct 2018 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 fmicb-09-00102 February 3, 2018 Time: 13:27 # 1 ORIGINAL RESEARCH published: 06 February 2018 doi: 10.3389/fmicb.2018.00102 Diversity of Rare and Abundant Prokaryotic Phylotypes in the Prony Hydrothermal Field and Comparison with Other Serpentinite-Hosted Ecosystems Eléonore Frouin1, Méline Bes1, Bernard Ollivier1, Marianne Quéméneur1, Anne Postec1, Didier Debroas2, Fabrice Armougom1 and Gaël Erauso1* 1 Aix-Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France, 2 CNRS UMR 6023, Laboratoire “Microorganismes – Génome et Environnement”, Université Clermont Auvergne, Clermont-Ferrand, France The Bay of Prony, South of New Caledonia, represents a unique serpentinite- hosted hydrothermal field due to its coastal situation.
    [Show full text]
  • Microbial Community Structure Dynamics in Ohio River Sediments During Reductive Dechlorination of Pcbs
    University of Kentucky UKnowledge University of Kentucky Doctoral Dissertations Graduate School 2008 MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS Andres Enrique Nunez University of Kentucky Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Nunez, Andres Enrique, "MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS" (2008). University of Kentucky Doctoral Dissertations. 679. https://uknowledge.uky.edu/gradschool_diss/679 This Dissertation is brought to you for free and open access by the Graduate School at UKnowledge. It has been accepted for inclusion in University of Kentucky Doctoral Dissertations by an authorized administrator of UKnowledge. For more information, please contact [email protected]. ABSTRACT OF DISSERTATION Andres Enrique Nunez The Graduate School University of Kentucky 2008 MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS ABSTRACT OF DISSERTATION A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the College of Agriculture at the University of Kentucky By Andres Enrique Nunez Director: Dr. Elisa M. D’Angelo Lexington, KY 2008 Copyright © Andres Enrique Nunez 2008 ABSTRACT OF DISSERTATION MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS The entire stretch of the Ohio River is under fish consumption advisories due to contamination with polychlorinated biphenyls (PCBs). In this study, natural attenuation and biostimulation of PCBs and microbial communities responsible for PCB transformations were investigated in Ohio River sediments. Natural attenuation of PCBs was negligible in sediments, which was likely attributed to low temperature conditions during most of the year, as well as low amounts of available nitrogen, phosphorus, and organic carbon.
    [Show full text]
  • Online Supplementary Figures of Chapter 3
    Online Supplementary Figures of Chapter 3 Fabio Gori Figures 1-30 contain pie charts showing the population characterization re- sulting from the taxonomic assignment computed by the methods. On the simulated datasets the true population distribution is also shown. 1 MTR Bacillales (47.11%) Thermoanaerobacterales (0.76%) Clostridiales (33.58%) Lactobacillales (7.99%) Others (10.55%) LCA Bacillales (48.38%) Thermoanaerobacterales (0.57%) Clostridiales (32.14%) Lactobacillales (10.07%) Others (8.84%) True Distribution 333 386 Prochlorales (5.84%) 535 Bacillales (34.61%) Halanaerobiales (4.37%) Thermoanaerobacterales (10.29%) Clostridiales (28.75%) Lactobacillales (9.38%) 1974 Herpetosiphonales (6.77%) 1640 249 587 Figure 1: Population distributions (rank Order) of M1, coverage 0.1x, by MTR and LCA, and the true population distribution. 2 MTR Bacillus (47.34%) Clostridium (14.61%) Lactobacillus (8.71%) Anaerocellum (11.41%) Alkaliphilus (5.14%) Others (12.79%) LCA Bacillus (51.41%) Clostridium (8.08%) Lactobacillus (9.23%) Anaerocellum (15.79%) Alkaliphilus (5.17%) Others (10.31%) True Distribution 386 552 Herpetosiphon (6.77%) 333 Prochlorococcus (5.84%) 587 Bacillus (34.61%) Clostridium (19.07%) Lactobacillus (9.38%) 249 Halothermothrix (4.37%) Caldicellulosiruptor (10.29%) Alkaliphilus (9.68%) 535 1974 1088 Figure 2: Population distributions (rank Genus) of M1, coverage 0.1x, by MTR and LCA, and the true population distribution. 3 MTR Prochlorales (0.07%) Bacillales (47.97%) Thermoanaerobacterales (0.66%) Clostridiales (32.18%) Lactobacillales (7.76%) Others (11.35%) LCA Prochlorales (0.10%) Bacillales (49.02%) Thermoanaerobacterales (0.59%) Clostridiales (30.62%) Lactobacillales (9.50%) Others (10.16%) True Distribution 3293 3950 Prochlorales (5.65%) 5263 Bacillales (36.68%) Halanaerobiales (3.98%) Thermoanaerobacterales (10.56%) Clostridiales (27.34%) Lactobacillales (9.03%) 21382 Herpetosiphonales (6.78%) 15936 2320 6154 Figure 3: Population distributions (rank Order) of M1, coverage 1x, by MTR and LCA, and the true population distribution.
    [Show full text]
  • Consistent Responses of Soil Microbial Communities to Elevated Nutrient Inputs in Grasslands Across the Globe
    Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe Jonathan W. Leffa,b, Stuart E. Jonesc, Suzanne M. Proberd, Albert Barberána, Elizabeth T. Borere, Jennifer L. Firnf, W. Stanley Harpoleg,h,i, Sarah E. Hobbiee, Kirsten S. Hofmockelj, Johannes M. H. Knopsk, Rebecca L. McCulleyl, Kimberly La Pierrem, Anita C. Rischn, Eric W. Seabloomo, Martin Schützn, Christopher Steenbockb, Carly J. Stevensp, and Noah Fierera,b,1 aCooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309; bDepartment of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309; cDepartment of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556; dCommonwealth Scientific and Industrial Research Organisation Land and Water Flagship, Wembley, WA 6913, Australia; eDepartment of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108; fSchool of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, QLD 4001, Australia; gDepartment of Physiological Diversity, Helmholtz Center for Environmental Research UFZ, 04318 Leipzig, Germany; hGerman Centre for Integrative Biodiversity Research Halle-Jena-Leipzig, D-04103 Leipzig, Germany; iInstitute of Biology, Martin Luther University Halle-Wittenberg, 06108 Halle (Saale), Germany; jEcology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA 50011; kSchool of Biological Sciences, University of Nebraska, Lincoln, NE 68588; lDepartment of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546; mDepartment of Integrative Biology, University of California, Berkeley, CA 94720; nCommunity Ecology, Swiss Federal Institute for Forest, Snow and Landscape Research, 8903 Birmensdorf, Switzerland; oDepartment of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108; and pLancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, United Kingdom Edited by Peter M.
    [Show full text]
  • Metagenomic and PCR-Based Diversity Surveys of [Fefe
    ORIGINAL RESEARCH published: 30 August 2016 doi: 10.3389/fmicb.2016.01301 Metagenomic and PCR-Based Diversity Surveys of [FeFe]-Hydrogenases Combined with Isolation of Alkaliphilic Hydrogen-Producing Bacteria from the Serpentinite-Hosted Prony Hydrothermal Field, New Caledonia Nan Mei 1, Anne Postec 1, Christophe Monnin 2, Bernard Pelletier 3, Claude E. Payri 3, Bénédicte Ménez 4, Eléonore Frouin 1, Bernard Ollivier 1, Gaël Erauso 1 and Marianne Quéméneur 1* 1 2 Edited by: Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France, GET UMR5563 (Centre National de la 3 Andreas Teske, Recherche Scientifique/UPS/IRD/CNES), Géosciences Environnement Toulouse, Toulouse, France, Institut pour la 4 University of North Carolina at Chapel Recherche et le Développement (IRD) Centre de Nouméa, MIO UM 110, Nouméa, Nouvelle-Calédonie, Institut de Physique Hill, USA du Globe de Paris, Sorbonne Paris Cité, Univ Paris Diderot, Centre National de la Recherche Scientifique, Paris, France Reviewed by: John R. Spear, High amounts of hydrogen are emitted in the serpentinite-hosted hydrothermal field Colorado School of Mines, USA of the Prony Bay (PHF, New Caledonia), where high-pH (∼11), low-temperature Igor Tiago, ◦ University of Coimbra, Portugal (<40 C), and low-salinity fluids are discharged in both intertidal and shallow submarine *Correspondence: environments. In this study, we investigated the diversity and distribution of potentially Marianne Quéméneur hydrogen-producing bacteria in Prony hyperalkaline springs by using metagenomic [email protected] analyses and different PCR-amplified DNA sequencing methods. The retrieved Specialty section: sequences of hydA genes, encoding the catalytic subunit of [FeFe]-hydrogenases and, This article was submitted to used as a molecular marker of hydrogen-producing bacteria, were mainly related to those Extreme Microbiology, a section of the journal of Firmicutes and clustered into two distinct groups depending on sampling locations.
    [Show full text]
  • Global Metagenomic Survey Reveals a New Bacterial Candidate Phylum in Geothermal Springs
    ARTICLE Received 13 Aug 2015 | Accepted 7 Dec 2015 | Published 27 Jan 2016 DOI: 10.1038/ncomms10476 OPEN Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs Emiley A. Eloe-Fadrosh1, David Paez-Espino1, Jessica Jarett1, Peter F. Dunfield2, Brian P. Hedlund3, Anne E. Dekas4, Stephen E. Grasby5, Allyson L. Brady6, Hailiang Dong7, Brandon R. Briggs8, Wen-Jun Li9, Danielle Goudeau1, Rex Malmstrom1, Amrita Pati1, Jennifer Pett-Ridge4, Edward M. Rubin1,10, Tanja Woyke1, Nikos C. Kyrpides1 & Natalia N. Ivanova1 Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum (‘Candidatus Kryptonia’) found exclusively in high-temperature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic ‘blind spot’ because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery. 1 Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA. 2 Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada.
    [Show full text]
  • EXPERIMENTAL STUDIES on FERMENTATIVE FIRMICUTES from ANOXIC ENVIRONMENTS: ISOLATION, EVOLUTION, and THEIR GEOCHEMICAL IMPACTS By
    EXPERIMENTAL STUDIES ON FERMENTATIVE FIRMICUTES FROM ANOXIC ENVIRONMENTS: ISOLATION, EVOLUTION, AND THEIR GEOCHEMICAL IMPACTS By JESSICA KEE EUN CHOI A dissertation submitted to the School of Graduate Studies Rutgers, The State University of New Jersey In partial fulfillment of the requirements For the degree of Doctor of Philosophy Graduate Program in Microbial Biology Written under the direction of Nathan Yee And approved by _______________________________________________________ _______________________________________________________ _______________________________________________________ _______________________________________________________ New Brunswick, New Jersey October 2017 ABSTRACT OF THE DISSERTATION Experimental studies on fermentative Firmicutes from anoxic environments: isolation, evolution and their geochemical impacts by JESSICA KEE EUN CHOI Dissertation director: Nathan Yee Fermentative microorganisms from the bacterial phylum Firmicutes are quite ubiquitous in subsurface environments and play an important biogeochemical role. For instance, fermenters have the ability to take complex molecules and break them into simpler compounds that serve as growth substrates for other organisms. The research presented here focuses on two groups of fermentative Firmicutes, one from the genus Clostridium and the other from the class Negativicutes. Clostridium species are well-known fermenters. Laboratory studies done so far have also displayed the capability to reduce Fe(III), yet the mechanism of this activity has not been investigated
    [Show full text]
  • Changes in Soil Microbial Communities After Long-Term Warming Exposure" (2019)
    University of Massachusetts Amherst ScholarWorks@UMass Amherst Doctoral Dissertations Dissertations and Theses October 2019 CHANGES IN SOIL MICROBIAL COMMUNITIES AFTER LONG- TERM WARMING EXPOSURE William G. Rodríguez-Reillo University of Massachusetts Amherst Follow this and additional works at: https://scholarworks.umass.edu/dissertations_2 Part of the Environmental Microbiology and Microbial Ecology Commons Recommended Citation Rodríguez-Reillo, William G., "CHANGES IN SOIL MICROBIAL COMMUNITIES AFTER LONG-TERM WARMING EXPOSURE" (2019). Doctoral Dissertations. 1757. https://doi.org/10.7275/15007293 https://scholarworks.umass.edu/dissertations_2/1757 This Open Access Dissertation is brought to you for free and open access by the Dissertations and Theses at ScholarWorks@UMass Amherst. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of ScholarWorks@UMass Amherst. For more information, please contact [email protected]. CHANGES IN SOIL MICROBIAL COMMUNITIES AFTER LONG-TERM WARMING EXPOSURE A Dissertation Presented by WILLIAM GABRIEL RODRÍGUEZ-REILLO Submitted to the Graduate School of the University of Massachusetts Amherst in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY SEPTEMBER 2019 Organismic and Evolutionary Biology © Copyright by William Gabriel Rodríguez-Reillo 2019 All Rights Reserved CHANGES IN SOIL MICROBIAL COMMUNITIES AFTER LONG-TERM WARMING EXPOSURE A Dissertation Presented by WILLIAM GABRIEL RODRÍGUEZ-REILLO Approved as to style and content by: _________________________________________ Jeffrey L. Blanchard, Chair _________________________________________ Courtney Babbitt, Member _________________________________________ David Sela, Member _________________________________________ Kristina Stinson, Member ______________________________________ Paige Warren, Graduate Program Director Organismic and Evolutionary Biology DEDICATION To my parents, William Rodriguez Arce and Carmen L. Reillo Batista. A quienes aún en la distancia me mantuvieron en sus oraciones.
    [Show full text]
  • Biochemical Characterization of Β-Xylan Acting Glycoside
    BIOCHEMICAL CHARACTERIZATION OF β-XYLAN ACTING GLYCOSIDE HYDROLASES FROM THE THERMOPHILIC BACTERIUM Caldicellulosiruptor saccharolyticus Thesis Submitted to The School of Engineering of the UNIVERSITY OF DAYTON In Partial Fulfillment of the Requirements for The Degree of Master of Science in Chemical Engineering By Jin Cao Dayton, Ohio December, 2012 BIOCHEMICAL CHARACTERIZATION OF β-XYLAN ACTING GLYCOSIDE HYDROLASES FROM THE THERMOPHILIC BACTERIUM Caldicellulosiruptor saccharolyticus Name: Cao, Jin APPROVED BY: ______________________ ________________________ Donald A. Comfort, Ph.D. Amy Ciric, Ph.D. Advisory Committee Chairman Committee Member Research Advisor & Assistant Professor Lecturer Department of Department of Chemical & Materials Engineering Chemical & Materials Engineering ________________________ Karolyn Hansen, Ph.D. Committee Member Assistant Professor Department of Biology _______________________ ________________________ John G. Weber, Ph.D. Tony E. Saliba, Ph.D. Associate Dean Dean, School of Engineering School of Engineering & Wilke Distinguished Professor ii ABSTRACT BIOCHEMICAL CHARACTERIZATION OF Β-XYLAN ACTING GLYCOSIDE HYDROLASES FROM THE THERMOPHILIC BACTERIUM Caldicellulosiruptor saccharolyticus Name: Cao, Jin University of Dayton Research Advisor: Donald A. Comfort Fossil fuels have been the dominant source for energy around the world since the industrial revolution, however, with the increasing demand for energy and decreasing fossil fuel reserves alternative energy sources must be exploited. Bio-ethanol is a promising prospect for an alternative energy source to petroleum, especially when plant biomass is used as the replacement carbon source. This gives greater benefit for implementation of bioethanol as a viable alternative transport fuel than food stocks such as starch from corn. The implementation of this next generation of bioethanol requires more robust and environmentally friendly methods for degrading cellulose and hemicellulose, the two major components of plant biomass.
    [Show full text]
  • Implications of Streamlining Theory for Microbial Ecology
    The ISME Journal (2014) 8, 1553–1565 & 2014 International Society for Microbial Ecology All rights reserved 1751-7362/14 www.nature.com/ismej WINOGRADSKY REVIEW Implications of streamlining theory for microbial ecology Stephen J Giovannoni1, J Cameron Thrash1,2 and Ben Temperton1,3 1Department of Microbiology, Oregon State University, Corvallis, OR, USA; 2Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA and 3Plymouth Marine Laboratory, Prospect Place, Plymouth, UK Whether a small cell, a small genome or a minimal set of chemical reactions with self-replicating properties, simplicity is beguiling. As Leonardo da Vinci reportedly said, ‘simplicity is the ultimate sophistication’. Two diverging views of simplicity have emerged in accounts of symbiotic and commensal bacteria and cosmopolitan free-living bacteria with small genomes. The small genomes of obligate insect endosymbionts have been attributed to genetic drift caused by small effective population sizes (Ne). In contrast, streamlining theory attributes small cells and genomes to selection for efficient use of nutrients in populations where Ne is large and nutrients limit growth. Regardless of the cause of genome reduction, lost coding potential eventually dictates loss of function. Consequences of reductive evolution in streamlined organisms include atypical patterns of prototrophy and the absence of common regulatory systems, which have been linked to difficulty in culturing these cells. Recent evidence from metagenomics suggests that streamlining is commonplace, may broadly explain the phenomenon of the uncultured microbial majority, and might also explain the highly interdependent (connected) behavior of many microbial ecosystems. Streamlining theory is belied by the observation that many successful bacteria are large cells with complex genomes.
    [Show full text]
  • Effects of Various Long-Term Tillage Systems on Some Chemical and Biological Properties of Soil
    Pol. J. Environ. Stud. Vol. 22, No. 6 (2013), 1835-1844 Original Research Effects of Various Long-Term Tillage Systems on Some Chemical and Biological Properties of Soil Dorota Swędrzyńska1*, Irena Małecka2, Andrzej Blecharczyk2, Arkadiusz Swędrzyński3, Justyna Starzyk1 1Department of General and Environmental Microbiology, Szydłowska 50, 60-656 Poznań 2Department of Agronomy, Dojazd 11, 60-632 Poznań 3Department of Grassland and Natural Landscape Sciences, Dojazd 11, 60-632 Poznań Poznań University of Life Sciences, Poland Received: 7 July 2013 Accepted: 30 October 2013 Abstract One of the directions of actions limiting the occurrence in soil environments of unfavorable phenome- na accompanying conventional tillage is the introduction of reduced tillage, even total abandonment of culti- vation operations. The objective of the performed investigation was to compare the impact of conventional tillage, reduced tillage, and no-tillage on some soil chemical (Corg., total N, pH) and microbiological (total bac- terial counts, numbers of oligotrophs, copiotrophs and fungi, activity of dehydrogenases and acid phosphatase) properties. Studies carried out in 2010-12 involved a static field experiment initiated in 1999 at Brody Research Station of Poznań University of Life Science, Poland, in temperate climate, on a soil classified as Albic Luvisols developed on loamy sands overlying loamy material. Analyses were performed on soil samples col- lected from under winter wheat from two horizons: 0-10 cm and 10-20 cm. In the 0-10 cm layer, the lowest values of almost all analyzed indices (Corg., total N, total bacterial counts, numbers of oligotrophs, copiotrophs and fungi, as well as the activity of dehydrogenases and acid phos- phatase) were determined in conditions of conventional tillage.
    [Show full text]
  • Phylogenomic Analysis Supports the Ancestral Presence of LPS-Outer Membranes in the Firmicutes
    Phylogenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes. Luisa Cs Antunes, Daniel Poppleton, Andreas Klingl, Alexis Criscuolo, Bruno Dupuy, Céline Brochier-Armanet, Christophe Beloin, Simonetta Gribaldo To cite this version: Luisa Cs Antunes, Daniel Poppleton, Andreas Klingl, Alexis Criscuolo, Bruno Dupuy, et al.. Phy- logenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes.. eLife, eLife Sciences Publication, 2016, 5, pp.e14589. 10.7554/eLife.14589.020. pasteur-01362343 HAL Id: pasteur-01362343 https://hal-pasteur.archives-ouvertes.fr/pasteur-01362343 Submitted on 8 Sep 2016 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 RESEARCH ARTICLE Phylogenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes Luisa CS Antunes1†, Daniel Poppleton1†, Andreas Klingl2, Alexis Criscuolo3, Bruno Dupuy4, Ce´ line Brochier-Armanet5, Christophe Beloin6, Simonetta Gribaldo1* 1Unite´ de
    [Show full text]