Monitoring of Endophytic Brenneria Salicis in Willow and Its Relation to Watermark Disease
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Approaches for Integrating Heterogeneous RNA-Seq Data Reveals Cross-Talk Between Microbes and Genes in Asthmatic Patients
bioRxiv preprint doi: https://doi.org/10.1101/765297; this version posted September 11, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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-ND 4.0 International license. 1 Approaches for integrating heterogeneous RNA-seq data reveals cross-talk 2 between microbes and genes in asthmatic patients 3 4 Daniel Spakowicz*1,2,3,4, Shaoke Lou*1, Brian Barron1, Tianxiao Li1, Jose L Gomez5, Qing Liu5, Nicole Grant5, 5 Xiting Yan5, George Weinstock2, Geoffrey L Chupp5, Mark Gerstein1,6,7,8 6 7 1 Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 8 2 The Jackson Laboratory for Genomic Medicine, Farmington, CT 9 3 Division of Medical Oncology, Ohio State University College of Medicine, Columbus, OH 10 4 Department of Biomedical Informatics, Ohio State University College of Medicine, Columbus, OH 11 5 Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University 12 School of Medicine, New Haven, CT 13 6 Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 14 7 Department of Computer Science, Yale University, New Haven, CT 15 8 Department of Statistics and Data Science, Yale University, New Haven, CT 16 * These authors contributed equally 17 18 ABSTRACT (337 words) 19 Sputum induction is a non-invasive method to evaluate the airway environment, particularly for asthma. RNA 20 sequencing (RNAseq) can be used on sputum, but it can be challenging to interpret because sputum contains 21 a complex and heterogeneous mixture of human cells and exogenous (microbial) material. -
University of California Santa Cruz Responding to An
UNIVERSITY OF CALIFORNIA SANTA CRUZ RESPONDING TO AN EMERGENT PLANT PEST-PATHOGEN COMPLEX ACROSS SOCIAL-ECOLOGICAL SCALES A dissertation submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in ENVIRONMENTAL STUDIES with an emphasis in ECOLOGY AND EVOLUTIONARY BIOLOGY by Shannon Colleen Lynch December 2020 The Dissertation of Shannon Colleen Lynch is approved: Professor Gregory S. Gilbert, chair Professor Stacy M. Philpott Professor Andrew Szasz Professor Ingrid M. Parker Quentin Williams Acting Vice Provost and Dean of Graduate Studies Copyright © by Shannon Colleen Lynch 2020 TABLE OF CONTENTS List of Tables iv List of Figures vii Abstract x Dedication xiii Acknowledgements xiv Chapter 1 – Introduction 1 References 10 Chapter 2 – Host Evolutionary Relationships Explain 12 Tree Mortality Caused by a Generalist Pest– Pathogen Complex References 38 Chapter 3 – Microbiome Variation Across a 66 Phylogeographic Range of Tree Hosts Affected by an Emergent Pest–Pathogen Complex References 110 Chapter 4 – On Collaborative Governance: Building Consensus on 180 Priorities to Manage Invasive Species Through Collective Action References 243 iii LIST OF TABLES Chapter 2 Table I Insect vectors and corresponding fungal pathogens causing 47 Fusarium dieback on tree hosts in California, Israel, and South Africa. Table II Phylogenetic signal for each host type measured by D statistic. 48 Table SI Native range and infested distribution of tree and shrub FD- 49 ISHB host species. Chapter 3 Table I Study site attributes. 124 Table II Mean and median richness of microbiota in wood samples 128 collected from FD-ISHB host trees. Table III Fungal endophyte-Fusarium in vitro interaction outcomes. -
Synthesis of Country Progress Reports
INTERNATIONAL POPLAR COMMISSION 22nd Session Santiago, Chile, 29 November – 9 December 2004 THE CONTRIBUTION OF POPLARS AND WILLOWS TO SUSTAINABLE FORESTRY AND RURAL DEVELOPMENT Synthesis of Country Progress Reports Activities Related to Poplar and Willow Cultivation and Utilization, 2000 through 2003 November 2004 Forest Resources Development Service Working Paper IPC/3 Forest Resources Division FAO, Rome, Italy Forestry Department Disclaimer Twenty one member countries of the IPC, and the Russian Federation, a non-member country, have provided national progress reports to the 22nd Session of the International Poplar Commission. A synthesis has been made by the Food and Agriculture Organization of the United Nations and summarizes issues, highlights status and identifies trends affecting cultivation, management and utilization of Poplars and Willows in temperate and boreal regions of the world. Comments and feedback are welcome. For further information please contact: Mr. Jim Carle Secretary International Poplar Commission Technical Statutory Body Forestry Department Food and Agriculture Organization of the United Nations (FAO) Viale delle Terme di Caracalla I-00100 Rome ITALY E-mail: [email protected] For quotation: FAO, November 2004. Synthesis of Country Progress Reports received prepared for the 22nd Session of the International Poplar Commission, jointly hosted by FAO and the National Poplar Commissions of Chile and Argentina; Santiago, Chile, 29 November – 2 December, 2004. International Poplar Commission Working Paper IPC/3. Forest Resources Division, FAO, Rome (unpublished). Web references: For details relating to the International Poplar Commission as a Technical Statutory Body of FAO including National Poplar Commissions, working parties and initiatives can be viewed on http://www.fao.org/forestry/ipc and highlights of the 22nd Session of the International Poplar Commission, 2004 can be viewed on http://www.fao.org/forestry/ipc2004. -
Reporting Service 2005, No
ORGANISATION EUROPEENNE EUROPEAN AND MEDITERRANEAN ET MEDITERRANEENNE PLANT PROTECTION POUR LA PROTECTION DES PLANTES ORGANIZATION EPPO Reporting Service Paris, 2005-05-01 Reporting Service 2005, No. 5 CONTENTS 2005/066 - First report of Tomato chlorosis crinivirus in Réunion 2005/067 - Viroids detected on tomato samples in the Netherlands 2005/068 - Recent studies on Thecaphora solani 2005/069 - Studies on Bursaphelenchus species associated with Pinus pinaster in Portugal 2005/070 - Survey on nematodes associated with Pinus trees in Spain: absence of Bursaphelenchus xylophilus 2005/071 - Studies on Bursaphelenchus species in Lithuania 2005/072 - Surveys on Bursaphelenchus xylophilus, Monilinia fructicola, Phytophthora ramorum and Pepino mosaic potexvirus in Emilia-Romagna, Italy 2005/073 - Aphelenchoides besseyi does not occur in Slovakia 2005/074 - Pests absent in Slovakia 2005/075 - Situation of several quarantine pests in Lithuania in 2004: first report of rhizomania 2005/076 - Further spread of Aulacaspis yasumatsui, a scale pest of Cycads 2005/077 - Ctenarytaina spatulata is a new psyllid pest of Eucalyptus: addition to the EPPO Alert List 2005/078 - First report of Brenneria quercina causing bark canker on oaks in Spain: addition to the EPPO Alert List 2005/079 - EPPO report on notifications of non-compliance (detection of regulated pests) 2005/080 - PQR version 4.4 has now been released 2005/081 - EPPO Conference on Phytophthora ramorum and other forest pests (Cornwall, GB, 2005-10- 05/07) 1, rue Le Nôtre Tel. : 33 1 45 20 77 94 E-mail : [email protected] 75016 Paris Fax : 33 1 42 24 89 43 Web : www.eppo.org EPPO Reporting Service 2005/066 First report of Tomato chlorosis crinivirus in Réunion In 2004/2005, pronounced leaf yellowing symptoms were observed on tomato plants growing under protected conditions on the island of Réunion. -
Brenneria Goodwinii Sp. Nov., a Novel Species Associated with Acute Oak Decline in Britain Sandra Denman1*, Carrie Brady2, Susan
1 Brenneria goodwinii sp. nov., a novel species associated with Acute Oak Decline in 2 Britain 3 4 Sandra Denman1*, Carrie Brady2, Susan Kirk1, Ilse Cleenwerck2, Stephanus Venter3, Teresa 5 Coutinho3 and Paul De Vos2 6 7 1Forest Research, Centre for Forestry and Climate Change, Alice Holt Lodge, Farnham, 8 Surrey, GU10 4LH, United Kingdom 9 10 2BCCM/LMG Bacteria Collection, Ghent University, K.L. Ledeganckstraat 35, B-9000 11 Ghent, Belgium. 12 13 3Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology 14 Institute (FABI), University of Pretoria, Pretoria 0002, South Africa 15 16 *Corresponding author: 17 email: [email protected] 18 Tel: +441420 22255 Fax: +441420 23653 19 20 Running title: Brenneria goodwinii, sp. nov. on Quercus spp. 21 22 Note: The GenBank/EMBL accession numbers for the sequences determined in this study 23 are: JN544202 – JN544204 (16S rRNA), JN544205 – JN544213 (atpD), JN544214 – 24 JN544222 (gyrB), JN544223 – JN544231 (infB) and JN544232 – JN544240 (rpoB). 25 26 ABSTRACT 27 A group of nine Gram-negative staining, facultatively anaerobic bacterial strains isolated 28 from native oak trees displaying symptoms of Acute Oak Decline (AOD) in Britain were 29 investigated using a polyphasic approach. 16S rRNA gene sequencing and phylogenetic 30 analysis revealed that these isolates form a distinct lineage within the genus Brenneria, 31 family Enterobacteriaceae, and are most closely related to Brenneria rubrifaciens (97.6 % 32 sequence similarity). MLSA based on four housekeeping genes (gyrB, rpoB, infB and atpD) 33 confirmed their position within the genus Brenneria, while DNA-DNA hybridization 34 indicated that the isolates belong to a single taxon. -
For Publication European and Mediterranean Plant Protection Organization PM 7/24(3)
For publication European and Mediterranean Plant Protection Organization PM 7/24(3) Organisation Européenne et Méditerranéenne pour la Protection des Plantes 18-23616 (17-23373,17- 23279, 17- 23240) Diagnostics Diagnostic PM 7/24 (3) Xylella fastidiosa Specific scope This Standard describes a diagnostic protocol for Xylella fastidiosa. 1 It should be used in conjunction with PM 7/76 Use of EPPO diagnostic protocols. Specific approval and amendment First approved in 2004-09. Revised in 2016-09 and 2018-XX.2 1 Introduction Xylella fastidiosa causes many important plant diseases such as Pierce's disease of grapevine, phony peach disease, plum leaf scald and citrus variegated chlorosis disease, olive scorch disease, as well as leaf scorch on almond and on shade trees in urban landscapes, e.g. Ulmus sp. (elm), Quercus sp. (oak), Platanus sycamore (American sycamore), Morus sp. (mulberry) and Acer sp. (maple). Based on current knowledge, X. fastidiosa occurs primarily on the American continent (Almeida & Nunney, 2015). A distant relative found in Taiwan on Nashi pears (Leu & Su, 1993) is another species named X. taiwanensis (Su et al., 2016). However, X. fastidiosa was also confirmed on grapevine in Taiwan (Su et al., 2014). The presence of X. fastidiosa on almond and grapevine in Iran (Amanifar et al., 2014) was reported (based on isolation and pathogenicity tests, but so far strain(s) are not available). The reports from Turkey (Guldur et al., 2005; EPPO, 2014), Lebanon (Temsah et al., 2015; Habib et al., 2016) and Kosovo (Berisha et al., 1998; EPPO, 1998) are unconfirmed and are considered invalid. Since 2012, different European countries have reported interception of infected coffee plants from Latin America (Mexico, Ecuador, Costa Rica and Honduras) (Legendre et al., 2014; Bergsma-Vlami et al., 2015; Jacques et al., 2016). -
Acute Oak Decline and Bacterial Phylogeny
Forest Research Acute Oak Decline and bacterial phylogeny Carrie L. Brady1, Sandra Denman2, Susan Kirk2, Ilse Cleenwerck1, Paul De Vos1, Stephanus N. Venter3, Pablo Rodríguez-Palenzuela4, Teresa A. Coutinho3 1 BCCM/LMG Bacteria Collection, Ghent University, K.L. Ledeganckstraat 35, B-9000, Ghent, Belgium. 2 Forest Research, Centre for Forestry and Climate Change, Alice Holt Lodge, Farnham, Surrey, GU10 4LH, United Kingdom. 3 Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa 4 Centro de Biotecnología y Genómica de Plantas UPM-INIA, Campus de Montegancedo, Autovía M-40 Km 38, 28223 Pozuelo de Alarcón, Madrid Background Oak decline is of complex cause, and is attributed to suites of factors that may vary spatially and temporally (Camy et al., 2003; Vansteenkiste et al., 2004). Often a succession of biotic and abiotic factors is involved. Two types of oak decline are recognised, an acute form and a chronic form (Vansteenkiste et al., 2004, Denman & Webber, 2009). Figure 2: Necrotic tissue under bleeding patches on Figure 3: Larva gallery () of Agrilus biguttatus and An episode of Acute Oak Decline (AOD) currently taking stems of AOD trees. necrotic tissues (). place in Britain (Denman & Webber, 2009) has a rapid effect on tree health. Tree mortality can occur within three to five years of the onset of symptom development (Denman et al., 2010). Affected trees are identified by patches on stems showing ‘bleeding’ (Fig.1). Tissues underlying the stem bleed are n e c r o t i c (F i g . 2) . L a r v a l g a l l e r i e s o f t h e b a r k b o r i n g b u p r e s t i d Agrilus biguttatus are usually associated with necrotic patches (Fig.3). -
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REAL-TIME PCR DETECTION AND DEVELOPMENT OF A BIOASSAY FOR THE DEEP BARK CANKER PATHOGEN, BRENNERIA RUBRIFACIENS Ali E. McClean, Padma Sudarshana, and Daniel A. Kluepfel ABSTRACT Deep Bark Canker (DBC), caused by the bacterium Brenneria rubrifaciens afflicts English walnut cultivars and is characterized by late onset of symptoms in trees greater than 15 years old. These symptoms include deep bleeding vertical cankers along the trunk and larger branches that exude a bacterial-laden reddish brown sap. B. rubrifaciens produces a unique water-soluble red pigment called rubrifacine when cultured in the laboratory. Here we describe the new primer pair, BR-1 and BR-3 that amplify a unique 409bp region of the 16S rDNA sequence that facilitates the sensitive and specific detection of B. rubrifaciens. Using these primers in a realtime-PCR system we were able to detect as few as 8 B. rubrifaciens colony forming units (CFU). A survey of 11 antibiotics revealed that B. rubrifaciens is resistant to erythromycin and novobiocin at 10 mg/L and 30 mg/L respectively. Amending the cultivation medium with these antibiotics has improved the semi-selective cultivation of B. rubrifaciens on solid media. Both walnut cultivars, Hartley and Chandler, grown in tissue culture are susceptible to infection by B. rubrifaciens. With in 21 days after inoculation Hartley shoots turned necrotic and died. Chandler shoots exhibited a similar phenotytpe 10wk after inoculation. This latter finding will be useful in our search for Brennaria genes involved in pathogenesis and the identification of walnut genotypes resistant to deep bark canker. OBJECTIVES 1. Develop sensitive and species-specific DNA primers for use in a PCR based-detection system for Brenneria rubrifaciens. -
DIVERSITY of Pectobacterium STRAINS by BIOCHEMICAL, PHYSIOLOGICAL, and MOLECULAR CHARACTERIZATION DIVERSIDADE DE ISOLADOS DE Pe
316 Bioscience Journal Original Article DIVERSITY OF Pectobacterium STRAINS BY BIOCHEMICAL, PHYSIOLOGICAL, AND MOLECULAR CHARACTERIZATION DIVERSIDADE DE ISOLADOS DE Pectobacterium spp. PELA CARACTERIZAÇÃO BIOQUÍMICA, FISIOLÓGICA E MOLECULAR Adelaide Siqueira SILVA 1; José Magno Queiroz LUZ 1; Nilvanira Donizete TEBALDI 1; Tâmara Prado de MORAIS 2 1. Universidade Federal de Uberlândia, Instituto de Ciências Agrárias, Uberlândia, MG, Brasil. [email protected]; 2. Instituto Federal de Educação, Ciência e Tecnologia do Sul de Minas Gerais, Campus de Machado, Machado, MG, Brasil. ABSTRACT: Pectobacterium is a complex taxon of strains with diverse characteristics. It comprises several genera, including Erwinia , Brenneria , Pectobacterium , Dickeya , and Pantoea . Pectobacterium and Dickeya cause diseases in a wide range of plants, including potatoes, where they are causative agents of soft rot in tubers and blackleg in field-grown plants. Characterizing Pectobacterium species allows for the analysis of the diversity of pectinolytic bacteria, which may support control strategies for plant bacterial diseases. The aim of this study was to perform biochemical, physiological, and molecular characterizations of Pectobacterium spp. from different sites and host plants. The isolated strains were characterized by the glucose fermentation test, Gram staining, catalase activity, oxidase activity, growth at 37 ºC, reducing substances from sucrose, phosphatase activity, indole production, acid production from different sources (sorbitol, melibiose, citrate, and lactose), pathogenicity in potato, and hypersensitivity reactions. Molecular characterization was performed with species-specific primers ECA1f/ECA2r and EXPCCF/EXPCCR, which identify P. atrosepticum and P. carotovorum subsp. carotovorum (Pcc), respectively, and with primers 1491f/L1RA/L1RG and Br1f/L1RA/L1RG that differentiate Pcc from Dickeya chrysanthemi and from P. -
International Journal of Systematic and Evolutionary Microbiology (2016), 66, 5575–5599 DOI 10.1099/Ijsem.0.001485
International Journal of Systematic and Evolutionary Microbiology (2016), 66, 5575–5599 DOI 10.1099/ijsem.0.001485 Genome-based phylogeny and taxonomy of the ‘Enterobacteriales’: proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. Mobolaji Adeolu,† Seema Alnajar,† Sohail Naushad and Radhey S. Gupta Correspondence Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Radhey S. Gupta L8N 3Z5, Canada [email protected] Understanding of the phylogeny and interrelationships of the genera within the order ‘Enterobacteriales’ has proven difficult using the 16S rRNA gene and other single-gene or limited multi-gene approaches. In this work, we have completed comprehensive comparative genomic analyses of the members of the order ‘Enterobacteriales’ which includes phylogenetic reconstructions based on 1548 core proteins, 53 ribosomal proteins and four multilocus sequence analysis proteins, as well as examining the overall genome similarity amongst the members of this order. The results of these analyses all support the existence of seven distinct monophyletic groups of genera within the order ‘Enterobacteriales’. In parallel, our analyses of protein sequences from the ‘Enterobacteriales’ genomes have identified numerous molecular characteristics in the forms of conserved signature insertions/deletions, which are specifically shared by the members of the identified clades and independently support their monophyly and distinctness. Many of these groupings, either in part or in whole, have been recognized in previous evolutionary studies, but have not been consistently resolved as monophyletic entities in 16S rRNA gene trees. The work presented here represents the first comprehensive, genome- scale taxonomic analysis of the entirety of the order ‘Enterobacteriales’. -
Brenneria (Erwinia) Quercina (Bark Canker and Drippy Nut of Quercus)
EPPO, 2007 Mini data sheet on Brenneria quercina Alert List: added in 2005 – deleted in 2007 Reasons for deletion: Brenneria quercina was removed from the EPPO Alert List in 2007 because was considered to be a common and secondary pest in Spain. Brenneria (Erwinia) quercina (bark canker and drippy nut of Quercus) Why In 1967, a new bacterial disease of oak caused by Erwinia quercina (later reclassified as Brenneria quercina) was reported in California (US) and called drippy nut, due to significant bacterial ooze observed on acorns. Apparently, this disease was no longer observed in USA nor reported from other countries until 1992, when the bacterium was found on forest oaks in Spain, causing slightly different types of damage (i.e. bark cankers and bacterial ooze on leaf buds). Where EPPO region: Spain (near Madrid and Segovia; first isolated in 1992 on Q. ilex; in 2001, also reported in Comunidad Valenciana). North America: USA (California, first description made in 1967 and apparently no further reports were made since then). On which plants Quercus spp. (Q. agrifolia and Q. wislizenii in California, Q. ilex and Q. pyrenaica in Spain). More data is needed on the susceptibility of other European Quercus species. Damage In California, the disease was described as ‘drippy nut’. The first visible symptoms were darkening and oozing at insect punctures in the acorns. Bacterial ooze was observed at the base of the nut. Rotting of the nuts was also observed. After the nut had fallen, in some cases the acorn cup produced bacterial ooze. The disease occurred in later summer when day temperatures were hot (average around 29°C). -
Bangor University DOCTOR of PHILOSOPHY Genomic Analysis of Bacterial Species Associated with Acute Oak Decline Doonan, James
Bangor University DOCTOR OF PHILOSOPHY Genomic analysis of bacterial species associated with Acute Oak Decline Doonan, James Award date: 2016 Awarding institution: Bangor University Link to publication General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Download date: 09. Oct. 2021 Genomic analysis of bacterial species associated with Acute Oak Decline James Doonan September 2016 A thesis submitted to Bangor University in candidature for the degree Philosophiae Doctor School of Biological Sciences Bangor University, Deiniol Road, Bangor, LL57 2UW Declaration and Consent Details of the Work I hereby agree to deposit the following item in the digital repository maintained by Bangor University and/or in any other repository authorized for use by Bangor University. Author Name: James Doonan Title: Genomic analysis of bacterial species associated with acute oak decline Supervisor/Department: Dr James McDonald (School of Biological Sciences) Funding body (if any): Woodland Heritage Qualification/Degree obtained: PhD This item is a product of my own research endeavours and is covered by the agreement below in which the item is referred to as “the Work”.