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Plant, Microbiology and Genetic Science and Technology Duccio
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Florence Research DOCTORAL THESIS IN Plant, Microbiology and Genetic Science and Technology section of " Plant Protection" (Plant Pathology), Department of Agri-food Production and Environmental Sciences, University of Florence Phytophthora in natural and anthropic environments: new molecular diagnostic tools for early detection and ecological studies Duccio Migliorini Years 2012/2015 DOTTORATO DI RICERCA IN Scienze e Tecnologie Vegetali Microbiologiche e genetiche CICLO XXVIII COORDINATORE Prof. Paolo Capretti Phytophthora in natural and anthropic environments: new molecular diagnostic tools for early detection and ecological studies Settore Scientifico Disciplinare AGR/12 Dottorando Tutore Dott. Duccio Migliorini Dott. Alberto Santini Coordinatore Prof. Paolo Capretti Anni 2012/2015 1 Declaration I hereby declare that this submission is my own work and that, to the best of my knowledge and belief, it contains no material previously published or written by another person nor material which to a substantial extent has been accepted for the award of any other degree or diploma of the university or other institute of higher learning, except where due acknowledgment has been made in the text. Duccio Migliorini 29/11/2015 A copy of the thesis will be available at http://www.dispaa.unifi.it/ Dichiarazione Con la presente affermo che questa tesi è frutto del mio lavoro e che, per quanto io ne sia a conoscenza, non contiene materiale precedentemente pubblicato o scritto da un'altra persona né materiale che è stato utilizzato per l’ottenimento di qualunque altro titolo o diploma dell'Università o altro istituto di apprendimento, a eccezione del caso in cui ciò venga riconosciuto nel testo. -
Background: Threat Abatement Plan for Disease in Natural Ecosystems Caused by Phytophthora Cinnamomi
Background: Threat abatement plan for disease in natural ecosystems caused by Phytophthora cinnamomi January 2014 Background: Threat abatement plan for disease in natural ecosystems caused by Phytophthora cinnamomi © Copyright Commonwealth of Australia, 2014 ISBN: 978-1-921733-94-9 Background: Threat abatement plan for disease in natural ecosystems caused by Phytophthora cinnamomi is licensed by the Commonwealth of Australia for use under a Creative Commons By Attribution 3.0 Australia licence with the exception of the Coat of Arms of the Commonwealth of Australia, the logo of the agency responsible for publishing the report, content supplied by third parties, and any images depicting people. For licence conditions see: http://creativecommons.org/licenses/by/3.0/au/. This report should be attributed as ‘Background: Threat abatement plan for disease in natural ecosystems caused by Phytophthora cinnamomi, Commonwealth of Australia, 2014’. The views and opinions expressed in this publication are those of the authors and do not necessarily reflect those of the Australian Government or the Minister for the Environment. The contents of this document have been compiled using a range of source materials and are valid as at August 2013. While reasonable efforts have been made to ensure that the contents of this publication are factually correct, the Commonwealth does not accept responsibility for the accuracy or completeness of the contents, and shall not be liable for any loss or damage that may be occasioned directly or indirectly through the use of, or reliance on, the contents of this publication. Photo credits Front cover: Mondurup Peak, Stirling Range, 2010 (Department of Parks and Wildlife, Western Australia) Back cover: Wildflowers on Mondurup Peak, Stirling Range, 1993 (Rob Olver) ii / Background: Threat abatement plan for disease in natural ecosystems caused by Phytophthora cinnamomi Contents 1. -
Aquatic Assemblages from Edna Metabarcoding 1 Casting a Broader
1 Running Head: Aquatic assemblages from eDNA metabarcoding 2 Casting a broader net: Using microfluidic metagenomics to capture aquatic biodiversity data from 3 diverse taxonomic targets 4 Laura L. Hauck1†, Kevin A. Weitemier2†, Brooke E. Penaluna1, Tiffany Garcia2, and Richard Cronn1* 5 1U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station, 3200 SW Jefferson Way, 6 Corvallis, OR 97331, email: [email protected] 7 2Oregon State University, Department of Fisheries and Wildlife, 104 Nash Hall, Corvallis, OR 97331 8 Tel: 1 (541) 737-7291 Fax: 1 (541) 750-7329 *Author for correspondence 9 †L. Hauck and K. Weitemier should be considered joint first author. 10 11 Abstract 12 Environmental DNA (eDNA) assays for single- and multi-species detection show promise for providing 13 standardized assessment methods for diverse taxa, but techniques for evaluating multiple taxonomically- 14 divergent assemblages are in their infancy. We evaluated whether microfluidic multiplex metabarcoding and 15 high-throughput sequencing could identify diverse aquatic and riparian assemblages from 48 taxon-general and 16 taxon-specific metabarcode primers. eDNA screening was paired with electrofishing along a stream continuum 17 to evaluate congruence between methods. A fish hatchery located midway along the stream continuum 18 provided a dispersal barrier, and a point source for non-native White Sturgeon (Acipencer transmontanus). 19 Microfluidic metabarcoding detected all 13 species observed by electrofishing, with overall accuracy of 86%. 20 Taxon-specific barcoding primers were more successful than taxon-general universal metabarcoding primers at 21 classifying sequences to species. Both types of markers detected a transition from downstream sites dominated 22 by multiple fish species, to upstream sites dominated by a single species; however, we failed to detect a 23 transition in amphibian population structure. -
Isolation and Pathogenicity of Phytophthora Species from Declining Rubus Anglocandicans
Plant Pathology (2015) Doi: 10.1111/ppa.12436 Isolation and pathogenicity of Phytophthora species from declining Rubus anglocandicans S. Aghighia*, T. I. Burgessa, J. K. Scottbc, M. Calvera and G. E. St. J. Hardya aCentre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, WA 6150; bSchool of Animal Science, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009; and cCSIRO Land & Water Flagship and Biosecurity Flagship, Private Bag 5, PO, Wembley, WA 6913, Australia Rubus anglocandicans is the most widespread and abundant blackberry species within the European blackberry (Rubus fruticosus) aggregate in Western Australia (WA). European blackberry is also one of the 32 Weeds of National Significance in Australia. A disease recorded as ‘blackberry decline’ was first observed in some blackberry sites in WA in 2006. A disease survey was conducted in the Manjimup-Pemberton region along the Warren and Donnelly River catchments in WA between 2010 and 2012. Phytophthora amnicola, P. bilorbang, P. cryptogea, P. inundata, P. litoralis, P. multivora, P. taxon personii, P. thermophila and a P. thermophila 9 amnicola hybrid were recovered from declining and adjacent decline-free sites, as well as from streams and rivers. Phytophthora cin- namomi was isolated from dying Banksia and Eucalyptus species from two non-decline sites. Of these species, P. bilorbang and P. cryptogea were more pathogenic than the others in under-bark inoculations using excised stems (primocanes), in planta primocane inoculations in blackberry growing wild in native forest stands, and in glasshouse pot trials. It was concluded that blackberry decline is a complex syndrome and Phytophthora species, in particular P. -
Agnes Virginia Simamora
The description, pathogenicity and epidemiology of Phytophthora boodjera, a new nursery pathogen of Eucalyptus from Western Australia by Agnes Virginia Simamora B.Sc. Agriculture (Universitas Nusa Cendana) MCP (Adelaide University) The thesis is submitted for the degree of Doctor of Philosophy School of Veterinary and Life Sciences Murdoch University Perth, Western Australia October 2016 Declaration I hereby declare that the work in this thesis is my own account of my research and contains as its main content work, which has not previously been submitted for a degree at any tertiary education institution. To the best of my knowledge, all work performed by others, published or unpublished, has been acknowledged. Agnes V. Simamora October 2016 ii Acknowledgments First and foremost I praise the Almighty God, my creator, the one who gives me strength and knows the plans intended for me; thank you for your graciousness and love. You are the one who gives me power to be successful. Many people have vitally assisted in making this PhD possible and pleasurable and I will be eternally grateful to you all. It is my great pleasure to express my gratitude to all those who have supported me and helped me during the past four years. Personally, I would like to especially thank my three supervisors (Prof. Giles Hardy, Assoc. Prof. Treena Burges, and Mike Stukely), whom I think had the hardest job. Thank you for giving me this opportunity, providing me with countless valuable guidance, and supporting me on my experiments and writing skills especially in times of adversity. Thank you so much for being patient with me when I still had much to learn. -
Canker and Decline Diseases Caused by Soil- and Airborne Phytophthora Species in Forests and Woodlands
Persoonia 40, 2018: 182–220 ISSN (Online) 1878-9080 www.ingentaconnect.com/content/nhn/pimj REVIEW ARTICLE https://doi.org/10.3767/persoonia.2018.40.08 Canker and decline diseases caused by soil- and airborne Phytophthora species in forests and woodlands T. Jung1,2, A. Pérez-Sierra 3, A. Durán4, M. Horta Jung1,2, Y. Balci 5, B. Scanu 6 Key words Abstract Most members of the oomycete genus Phytophthora are primary plant pathogens. Both soil- and airborne Phytophthora species are able to survive adverse environmental conditions with enduring resting structures, mainly disease management sexual oospores, vegetative chlamydospores and hyphal aggregations. Soilborne Phytophthora species infect fine epidemic roots and the bark of suberized roots and the collar region with motile biflagellate zoospores released from sporangia forest dieback during wet soil conditions. Airborne Phytophthora species infect leaves, shoots, fruits and bark of branches and stems invasive pathogens with caducous sporangia produced during humid conditions on infected plant tissues and dispersed by rain and wind nursery infestation splash. During the past six decades, the number of previously unknown Phytophthora declines and diebacks of root rot natural and semi-natural forests and woodlands has increased exponentially, and the vast majority of them are driven by introduced invasive Phytophthora species. Nurseries in Europe, North America and Australia show high infestation rates with a wide range of mostly exotic Phytophthora species. Planting of infested nursery stock has proven to be the main pathway of Phytophthora species between and within continents. This review provides in- sights into the history, distribution, aetiology, symptomatology, dynamics and impact of the most important canker, decline and dieback diseases caused by soil- and airborne Phytophthora species in forests and natural ecosystems of Europe, Australia and the Americas. -
GENETICS, EVOLUTION and BIOLOGICAL CONTROL Ch00-Prelims.Qxd 10/30/03 2:50 PM Page Ii Ch00-Prelims.Qxd 10/30/03 2:50 PM Page Iii
ch00-prelims.qxd 10/30/03 2:50 PM Page i GENETICS, EVOLUTION AND BIOLOGICAL CONTROL ch00-prelims.qxd 10/30/03 2:50 PM Page ii ch00-prelims.qxd 10/30/03 2:50 PM Page iii Genetics, Evolution and Biological Control Edited by L.E. Ehler University of California, Davis, USA R. Sforza USDA, Montpellier, France and T. Mateille IRD, Montpellier, France CABI Publishing ch00-prelims.qxd 10/30/03 2:50 PM Page iv CABI Publishing is a division of CAB International CABI Publishing CABI Publishing CAB International 875 Massachusetts Avenue Wallingford 7th Floor Oxon OX10 8DE Cambridge, MA 02139 UK USA Tel: +44 (0)1491 832111 Tel: +1 617 395 4056 Fax: +44 (0)1491 833508 Fax: +1 617 354 6875 E-mail: [email protected] E-mail: [email protected] Web site: www.cabi-publishing.org ©CAB International 2004. All rights reserved. No part of this publication may be reproduced in any form or by any means, electronically, mechanically, by photocopying, recording or otherwise, without the prior permission of the copyright owners. A catalogue record for this book is available from the British Library, London, UK. Library of Congress Cataloging-in-Publication Data Genetics, evolution, and biological control/edited by L. E. Ehler, R. Sforza, and T. Mateille. p. cm Papers from an International Organization for Biological Control symposium held in Montpellier, France, 2002. Includes bibliographical references and index. ISBN 0-85199-735-X (alk. paper) 1. Pests--Biological control--Congresses. 2. Biological pest control agents--Congresses. I. Ehler, Lester E. II. Sforza, R. -
Can Oldfield Regrowth Dominated by Non-Native Privet Trees Contribute to Biodiversity and Rainforest Regeneration?
Can oldfield regrowth dominated by non-native privet trees contribute to biodiversity and rainforest regeneration? Debbie Lynae Rudd B.Sc. Honours Dissertation A dissertation submitted in partial fulfilment of the requirements for the degree of Bachelor of Science with Honours. This thesis has been subject to examination and was deemed to meet a standard suited to the award of the BSc (Hons) degree. The work was conducted under the supervision of Carla Catterall and Jacinta Zalucki. Effort has been made to avoid errors in preparation and presentation of information. However it cannot be guaranteed that the thesis is entirely free from errors. It can be cited as: Rudd, D.L. (2017). Can oldfield regrowth dominated by non-native privet trees contribute to biodiversity and rainforest regeneration? BSc Hons Thesis, Griffith University. Griffith University School of Environment June 2017 1 ABSTRACT Widespread clearing of tropical and subtropical rainforests is a major threatening process for biodiversity and ecosystem functions worldwide. Deforestation has primarily occurred to create areas of livestock pasture and other agricultural uses, causing diverse and complex forest ecosystems to be replaced with much more simplistic ecosystems dominated by non-native species. To mitigate these impacts, reforestation is needed over large spatial scales. The process of unassisted regrowth on the oldfields that result from retirement of land from livestock grazing provides a potentially important pathway of rainforest restoration. However, oldfield regrowth in Australia is often dominated by non-native pioneer tree species, and the positive and negative roles of these species are strongly debated. This study investigated the role of a non-native species, small-leaved privet (Ligustrum sinense), in oldfield regrowth on the eastern Dorrigo Plateau of subtropical Australia. -
Frankston Vegetation Study 2006
Frankston Vegetation Study 2006 Project 05-5 Planning Review Prepared for: Frankston City Council Ecology Australia Pty Ltd Flora and Fauna Consultants 88B Station Street, Fairfield, Victoria, Australia 3078 Tel: (03) 9489 4191 Fax: (03) 9481 7679 www.ecologyaustralia.com.au [email protected] Copyright 2006 Ecology Australia Pty Ltd This publication is copyright. It may only be used in accordance with the agreed terms of the commission. Except as provided for by the Copyright Act 1968, no part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, without prior written permission of Ecology Australia Pty Ltd. Document information This is a controlled document. Details of the document ownership, location, distribution, status and revision history and are listed below. All comments or requests for changes to content should be addressed to the document owner. Owner Ecology Australia Pty Ltd Author Sarah Bedggood, Lisa Crowfoot, Nina Roberts, Cherie Campbell, Jamie McMahon and Ann McGregor Location Frankston Vegetation Study 2006.doc Document History Status Changes By Date Draft Draft 0.1 Sarah Bedggood 07/04/06 Final Draft Draft 0.2 Sarah Bedggood 12/05/2006 Final final Sarah Bedggood 02/08/2006 Final Frankston Vegetation Study 2006 with maps & App 4.doc i Frankston Vegetation Study 2006 Contents Summary 1 1 Introduction 2 2 Study Area 3 3 Methods 4 3.1 Literature review 4 3.2 GIS 4 3.3 Taxonomy 5 3.4 Field surveys 5 4 Vegetation 7 4.1 Ecological Vegetation Classes 7 4.2 EVC Descriptions 11 4.3 Significance of vegetation 34 5 Management Issues 36 6 Review of legislation and planning controls relating to native vegetation 39 6.1 Legislation and policies for native vegetation protection 39 6.2 Native vegetation protection in the Frankston Planning Scheme 48 7 Recommendations 51 8 Acknowlegements 53 9 References 54 Tables Table 1. -
Investigation of the Fungi Associated with Dieback of Prickly Acacia (Vachellia Nilotica Subsp
Investigation of the fungi associated with dieback of prickly acacia (Vachellia nilotica subsp. indica) in Northern Australia AHSANUL HAQUE B.Sc. Ag. (Hons) (Bangladesh Agricultural University, Bangladesh) MS in Plant Pathology (Bangabandhu Sheikh Mujibur Rahman Agricultural University, Bangladesh) A thesis submitted for the degree of Doctor of Philosophy at The University of Queensland in 2015 School of Agriculture and Food Sciences Abstract Prickly acacia (Vachellia nilotica subsp. indica), one of the most harmful weeds of the Australian rangelands, has been occasionally observed displaying natural dieback symptoms since 1970’s. More recently in 2010, a prominent widespread dieback event was observed among the plants growing around Richmond and Julia Creek in north-western Queensland. Affected plants were found with disease symptoms such as; ashy internal staining, defoliation, blackening of shoot tips through to widespread plant mortality. It was hypothesized that a pathogenic fungus/i could be implicated with this phenomenon and a potential for biological control of this invasive species might ensue. Fungi isolated from dieback-affected and healthy stands of prickly acacia were putatively identified by partial sequencing of the Internal Transcribed Spacer (ITS) region of genomic DNA. Botryosphaeriaceae was the best represented family of fungi associated with dieback. Among the Botryosphaeriaceae fungi, Cophinforma was found to be the most prevalent genus with 60% of the total isolates identified as Cophinforma spp. following BLAST searches. Cophinforma was also isolated from the healthy plants growing in the trial site at Richmond. Natural dieback on prickly acacia was previously observed in the surrounding areas. Phylogenetic analysis of the ITS sequences revealed the potential existence of new species of Cophinforma in Australia. -
Landscape Transformations Following Blackberry Decline in the South-West of Western Australia: Successful Restoration Or Back to Blackberry?
Twentieth Australasian Weeds Conference Landscape transformations following blackberry decline in the south-west of Western Australia: successful restoration or back to blackberry? Paul B. Yeoh1, Lee Fontanini3, Jenny A. Carley3, Andy T. Russell3, Kathy E. Dawson3, John K. Scott1,4, Caroline Y.M. Delaisse1,2 and Bruce L. Webber1,2 1 CSIRO Land & Water, Private Bag 5, PO Wembley, Western Australia 6913, Australia 2 School of Plant Biology, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia 3 Warren Catchments Council, 52 Bath Street, Manjimup, Western Australia 6258, Australia 4 School of Animal Biology, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia ([email protected]) Summary In recent years there has been a rapid de- Weber 2003). It is also the dominant weedy species of cline in blackberry (Rubus anglocandicans A.Newton) riparian areas in the Donnelly and Warren Catchments populations along waterways within the Warren Catch- of south-west Western Australia, an area targeted for ments region located in the south-west of Western ecosystem restoration. Australia. The soil pathogen, Phytophthora bilorbang Blackberry can normally be effectively suppressed S.Aghighi, G.E.S.J.Hardy, J.K.Scott & T.I.Burgess, is within accessible agriculture grazing systems espe- thought to be instrumental in the decline of these popula- cially if grazing can be integrated with herbicide and/or tions. For most waterways in the region, blackberry has physical control methods. However, control is usually dominated the forest understorey for decades. Conse- difficult and expensive within native ecosystems as the quently, the weed’s rapid decline typically results in ar- risk of off-target negative impacts on native flora or eas of bare soil or grassed landscapes lacking structure. -
Phytophthora Species and Riparian Alder Tree Damage in Western Oregon
AN ABSTRACT OF THE DISSERTATION OF Laura L. Sims for the degree of Doctor of Philosophy in Botany and Plant Pathology presented on February 13, 2014. Title: Phytophthora Species and Riparian Alder Tree Damage in Western Oregon Abstract approved: Everett M. Hansen The genus Phytophthora contains some of the most destructive pathogens of forest trees, including the most destructive pathogen of alder in recent times, Phytophthora alni. Alder trees were reported to be suffering from canopy dieback in riparian ecosystems in western Oregon, which prompted a survey of alder health and monitoring for P. alni. In 2010 surveys in western Oregon riparian ecosystems were initiated to gather baseline data on damage and on the Phytophthora species associated with alder. Damage was recorded and analyzed from transects containing alder trees with canopy dieback symptoms according to damage type: (1) pathogen, (2) insect, or (3) wound. Phytophthora species from western Oregon riparian ecosystems were systematically sampled, isolated, identified, stored and compared. Koch’s Postulates were evaluated for three key Phytophthora species recovered: P. alni, P. siskiyouensis and P. taxon Oaksoil, and alder disease in the western United States was described. Then, the ecological role of the most abundant Phytophthora species from streams was evaluated. The data indicated that many of the same agents reported causing damage to alder trees in the western United States were also damaging alder trees in western Oregon including the alder flea beetle, sawflies, flood debris, Septoria alnifolia, and Mycopappus alni. The most important damage correlated with canopy dieback was incidence of Phytophthora cankers, and isolation of Phytophthora siskiyouensis.