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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
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  • 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

    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