Phylogenomics Insights Into Order and Families of Lysobacterales
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The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service. -
Mineral Types and Tree Species Determine the Functional And
Mineral types and tree species determine the functional and taxonomic structures of forest soil bacterial communities Yannick Colin, Océane Nicolitch-Café, Marie-Pierre Turpault, Stéphane Uroz To cite this version: Yannick Colin, Océane Nicolitch-Café, Marie-Pierre Turpault, Stéphane Uroz. Mineral types and tree species determine the functional and taxonomic structures of forest soil bacterial communities. Applied and Environmental Microbiology, American Society for Microbiology, 2017, 83 (5), pp.e02684- 16. 10.1128/AEM.02684-16. hal-01548673 HAL Id: hal-01548673 https://hal.archives-ouvertes.fr/hal-01548673 Submitted on 27 Jun 2017 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. GEOMICROBIOLOGY crossm Mineral Types and Tree Species Determine the Functional and Taxonomic Structures of Forest Soil Bacterial Communities Downloaded from Y. Colin,a,b O. Nicolitch,a,b M.-P. Turpault,b S. Uroza,b INRA, Université de Lorraine, UMR 1136 Interactions Arbres Micro-organismes, Centre INRA de Nancy, Champenoux, Francea; INRA UR 1138 Biogéochimie des Ecosystèmes Forestiers, Centre INRA de Nancy, Champenoux, Franceb ABSTRACT Although minerals represent important soil constituents, their impact on Received 22 September 2016 Accepted 15 the diversity and structure of soil microbial communities remains poorly docu- http://aem.asm.org/ mented. -
Seed Interior Microbiome of Rice Genotypes Indigenous to Three
Raj et al. BMC Genomics (2019) 20:924 https://doi.org/10.1186/s12864-019-6334-5 RESEARCH ARTICLE Open Access Seed interior microbiome of rice genotypes indigenous to three agroecosystems of Indo-Burma biodiversity hotspot Garima Raj1*, Mohammad Shadab1, Sujata Deka1, Manashi Das1, Jilmil Baruah1, Rupjyoti Bharali2 and Narayan C. Talukdar1* Abstract Background: Seeds of plants are a confirmation of their next generation and come associated with a unique microbia community. Vertical transmission of this microbiota signifies the importance of these organisms for a healthy seedling and thus a healthier next generation for both symbionts. Seed endophytic bacterial community composition is guided by plant genotype and many environmental factors. In north-east India, within a narrow geographical region, several indigenous rice genotypes are cultivated across broad agroecosystems having standing water in fields ranging from 0-2 m during their peak growth stage. Here we tried to trap the effect of rice genotypes and agroecosystems where they are cultivated on the rice seed microbiota. We used culturable and metagenomics approaches to explore the seed endophytic bacterial diversity of seven rice genotypes (8 replicate hills) grown across three agroecosystems. Results: From seven growth media, 16 different species of culturable EB were isolated. A predictive metabolic pathway analysis of the EB showed the presence of many plant growth promoting traits such as siroheme synthesis, nitrate reduction, phosphate acquisition, etc. Vitamin B12 biosynthesis restricted to bacteria and archaea; pathways were also detected in the EB of two landraces. Analysis of 522,134 filtered metagenomic sequencing reads obtained from seed samples (n=56) gave 4061 OTUs. -
Scope of the Thesis
Unraveling predatory-prey interactions between bacteria Dissertation To Fulfill the Requirements for the Degree of „Doctor rerum naturalium“ (Dr. rer. nat.) Submitted to the Council of the Faculty of Biology and Pharmacy of the Friedrich Schiller University Jena By Ivana Seccareccia (M.Sc. in Biology) born on 8th April 1986 in Rijeka, Croatia Die Forschungsarbeit im Rahmen dieser Dissertation wurde am Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e.V. – Hans-Knöll–Institut in der Nachwuchsgruppe Sekundärmetabolismus räuberischer Bakterien unter der Betreuung von Dr. habil. Markus Nett von Oktober 2011 bis Oktober 2015 in Jena durchgeführt. Gutachter: ……………………………………………. ………………………………………….… ……………………………………………. Tag der öffentlichen Verteidigung: We make our world significant by the courage of our questions and by the depth of our answers. Carl Sagan Table of Contents 1 Introduction ......................................................................................................................... 6 1.1 Predation in the microbial community ........................................................................... 6 1.2 Bacterial predators .......................................................................................................... 7 1.3 Phases of predation ......................................................................................................... 8 1.3.1 Seeking prey ......................................................................................................... 9 1.3.2 Prey recognition -
Genome-Scale Data Suggest Reclassifications in the Leisingera
ORIGINAL RESEARCH ARTICLE published: 11 August 2014 doi: 10.3389/fmicb.2014.00416 Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov. Sven Breider 1†, Carmen Scheuner 2†, Peter Schumann 2, Anne Fiebig 2, Jörn Petersen 2, Silke Pradella 2, Hans-Peter Klenk 2, Thorsten Brinkhoff 1 and Markus Göker 2* 1 Department of Biology of Geological Processes - Aquatic Microbial Ecology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany 2 Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany Edited by: Earlier phylogenetic analyses of the marine Rhodobacteraceae (class Alphaproteobacteria) Martin G. Klotz, University of North genera Leisingera and Phaeobacter indicated that neither genus might be monophyletic. Carolina at Charlotte, USA We here used phylogenetic reconstruction from genome-scale data, MALDI-TOF Reviewed by: mass-spectrometry analysis and a re-assessment of the phenotypic data from the Martin G. Klotz, University of North Carolina at Charlotte, USA literature to settle this matter, aiming at a reclassification of the two genera. Neither Aharon Oren, The Hebrew Phaeobacter nor Leisingera formed a clade in any of the phylogenetic analyses conducted. University of Jerusalem, Israel Rather, smaller monophyletic assemblages emerged, which were phenotypically more *Correspondence: homogeneous, too. We thus propose the reclassification of Leisingera nanhaiensis as the Markus Göker, Department of type species of a new genus as Sedimentitalea nanhaiensis gen. nov., comb. nov., the Microorganisms, Leibniz Institute DSMZ - German Collection of reclassification of Phaeobacter arcticus and Phaeobacter leonis as Pseudophaeobacter Microorganisms and Cell Cultures, arcticus gen. -
Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater
Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg -
Lysobacter Enzymogenes
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Dissertations and Theses in Biological Sciences Biological Sciences, School of 8-2010 Detection Methods for the Genus Lysobacter and the Species Lysobacter enzymogenes Hu Yin University of Nebraska at Lincoln, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/bioscidiss Part of the Life Sciences Commons Yin, Hu, "Detection Methods for the Genus Lysobacter and the Species Lysobacter enzymogenes" (2010). Dissertations and Theses in Biological Sciences. 15. https://digitalcommons.unl.edu/bioscidiss/15 This Article is brought to you for free and open access by the Biological Sciences, School of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Dissertations and Theses in Biological Sciences by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Detection Methods for the Genus Lysobacter and the Species Lysobacter enzymogenes By Hu Yin A THESIS Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Master of Science Major: Biological Sciences Under the Supervision of Professor Gary Y. Yuen Lincoln, Nebraska August, 2010 Detection Methods for the Genus Lysobacter and the Species Lysobacter enzymogenes Hu Yin, M.S. University of Nebraska, 2010 Advisor: Gary Y. Yuen Strains of Lysobacter enzymogenes, a bacterial species with biocontrol activity, have been detected via 16S rDNA sequences in soil in different parts of the world. In most instances, however, their occurrence could not be confirmed by isolation, presumably because the species occurred in low numbers relative to faster-growing species of Bacillus or Pseudomonas. -
Within-Arctic Horizontal Gene Transfer As a Driver of Convergent Evolution in Distantly Related 1 Microalgae 2 Richard G. Do
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.31.454568; this version posted August 2, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Within-Arctic horizontal gene transfer as a driver of convergent evolution in distantly related 2 microalgae 3 Richard G. Dorrell*+1,2, Alan Kuo3*, Zoltan Füssy4, Elisabeth Richardson5,6, Asaf Salamov3, Nikola 4 Zarevski,1,2,7 Nastasia J. Freyria8, Federico M. Ibarbalz1,2,9, Jerry Jenkins3,10, Juan Jose Pierella 5 Karlusich1,2, Andrei Stecca Steindorff3, Robyn E. Edgar8, Lori Handley10, Kathleen Lail3, Anna Lipzen3, 6 Vincent Lombard11, John McFarlane5, Charlotte Nef1,2, Anna M.G. Novák Vanclová1,2, Yi Peng3, Chris 7 Plott10, Marianne Potvin8, Fabio Rocha Jimenez Vieira1,2, Kerrie Barry3, Joel B. Dacks5, Colomban de 8 Vargas2,12, Bernard Henrissat11,13, Eric Pelletier2,14, Jeremy Schmutz3,10, Patrick Wincker2,14, Chris 9 Bowler1,2, Igor V. Grigoriev3,15, and Connie Lovejoy+8 10 11 1 Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, 12 INSERM, Université PSL, 75005 Paris, France 13 2CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, 14 FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France 15 3 US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 16 Cyclotron Road, Berkeley, -
Dual Oxidase Gene Duox and Toll-Like Receptor 3 Gene TLR3 in the Toll
bioRxiv preprint doi: https://doi.org/10.1101/844696; this version posted November 15, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Dual oxidase gene Duox and Toll-like receptor 3 gene TLR3 2 in the Toll pathway suppress zoonotic pathogens through 3 regulating the intestinal bacterial community homeostasis in 4 Hermetia illucens L. 5 Yaqing Huang1, Yongqiang Yu1, Shuai Zhan2, Jeffery K. Tomberlin3, Dian Huang1, 6 Minmin Cai1, Longyu Zheng1, Ziniu Yu1, Jibin Zhang1* 7 1State Key Laboratory of Agricultural Microbiology, National Engineering Research 8 Center of Microbial Pesticides, College of Life Science and Technology, Huazhong 9 Agricultural University, Wuhan, P.R. China 430070. 10 2 Institute of Plant Physiology & Ecology, SIBS, CAS, China 200032. 11 3Department of Entomology, Texas A&M University, USA; 12 * Correspondence: 13 Professor Jibin Zhang 14 [email protected] 15 1 bioRxiv preprint doi: https://doi.org/10.1101/844696; this version posted November 15, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 16 Abstract: 17 Black soldier fly (BSF; Hermetia illucens L.) larvae can convert fresh pig manure 18 into protein and fat-rich biomass, which can then be used as livestock feed. Currently, 19 it is the only insect approved for such purposes in Europe, Canada, and the USA. -
Mycophagous Soil Bacteria
MYCOPHAGOUS SOIL BACTERIA MAX-BERNHARD RUDNICK Thesis committee Promotor Prof. Dr Wietse de Boer Professor of Microbial Soil Ecology Wageningen University Co-promotor Prof. Dr Hans van Veen Professor of Microbial Ecology Leiden University Other members Prof. Dr Kornelia Smalla, Technical University Braunschweig, Germany Prof. Dr Michael Bonkowski, Cologne University, Germany Prof. Dr Joana Falcão Salles, Groningen University Prof. Dr Hauke Smidt, Wageningen University This research was conducted under the auspices of the C.T. de Wit Graduate School for Production Ecology & Resource Conservation (PE&RC) MYCOPHAGOUS SOIL BACTERIA MAX-BERNHARD RUDNICK Thesis submitted in fulfilment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. Dr M.J. Kropff, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Friday 13th of February 2015 at 1.30 p.m. in the Aula. Max-Bernhard Rudnick Mycophagous soil bacteria 161 pages. PhD thesis, Wageningen University, Wageningen, NL (2015) With references, with summaries in Dutch and English. ISBN: 978-94-6257-253-9 “Imagination is more important than knowledge” - Albert Einstein - - A l b e r t E i n s t e i n - TABLE OF CONTENTS ABSTRACT 9 INTRODUCTION COLLIMONADS AND OTHER MYCOPHAGOUS SOIL BACTERIA 11 CHAPTER TWO OXALIC ACID: A SIGNAL MOLECULE FOR FUNGUS-FEEDING BACTERIA OF THE GENUS COLLIMONAS? 21 CHAPTER THREE EARLY COLONIZERS OF NEW HABITATS REPRESENT A MINORITY OF THE SOIL BACTERIAL COMMUNITY -
Disease of Aquatic Organisms 103:77
The following supplement accompanies the article Screening bacterial metabolites for inhibitory effects against Batrachochytrium dendrobatidis using a spectrophotometric assay Sara C. Bell1,*, Ross A. Alford1, Stephen Garland2, Gabriel Padilla3, Annette D. Thomas4 1School of Marine and Tropical Biology, James Cook University, Townsville, Queensland 4811, Australia 2School of Public Health, Tropical Medicine and Rehabilitation Sciences, James Cook University, Townsville, Queensland 4811, Australia 3Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil 4Tropical and Aquatic Animal Health Laboratory, Department of Employment, Economic Development and Innovation, Oonoonba, Queensland 4811, Australia *Email: [email protected] Diseases of Aquatic Organisms 103: 77–85 (2013) Supplement. The taxonomic affiliation of bacterial isolates that were totally inhibitory to Batrachochytrium dendrobatidis and details of the molecular methods that were used to generate these data MATERIALS AND METHODS DNA extraction Axenic isolates in 400 μl molecular grade water were subjected to 3 freeze–thaw cycles (+70/–80°C; 10 min each) and then centrifuged at 7500 × g (5 min) to pellet the cells. The supernatant was used directly as a template in the DNA amplification reaction. If this was unsuccessful, isolates were extracted using a Qiagen DNeasy Blood and Tissue Kit as per the manufacturer’s protocol, with pretreatment for Gram-negative bacteria. Amplification of 16s rRNA gene DNA from pure bacterial isolates was amplified by polymerase chain reaction (PCR) on Bio-Rad C1000/S1000 thermal cyclers with the bacteria-specific primer 8F (5’-AGA GTT TGA TCC TGG CTC AG-3’) and the universal primer 1492R (5’-GGT TAC CTT GTT ACG ACT T-3’) (Lane 1991). -
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.