Book of Abstracts

Total Page:16

File Type:pdf, Size:1020Kb

Book of Abstracts 11th Conference of the European Foundation for Plant Pathology Healthy plants – healthy people Book of abstracts 8–13 September 2014, Kraków, Poland Organizing Committee Presidium Małgorzata Mańka – chair Stanisław Mazur – v-ce chair Hanna Stępniewska – v-ce chair Conference Secretariat Marta Bełka Joanna Kaczmarek [email protected] Members Czesław Bartnik Zbigniew Burgieł Joanna Dłużniewska Ewa Hanus-Fajerska Robert Jankowiak Zbigniew Karolewski Maria Kowalik Tadeusz Kowalski Halina Kurzawińska Jacek Nawrocki Scientific Committee Piotr Sobiczewski, Skierniewice, Poland – chairman Małgorzata Mańka, Poznań, Poland – deputy chairman Małgorzata Jędryczka, Poznań, Poland – secretary Piet Boonekamp, Wageningen, The Netherlands Maria I. Clara, Évora, Portugal Zenonas Dabkevičius, Kėdainių, Lithuania Tatjana Gagkaeva, St. Petersburg-Pushkin, Russia Paolo Gonthier, Turin, Italy Nenad Keca, Belgrade, Serbia Maria M. Lopez, Valencia, Spain László Palkovics, Budapest, Hungary Henryk Pospieszny, Poznań, Poland Andreas von Tiedemann, Göttingen, Germany Steve Woodward, Aberdeen, Scotland, UK Disclaimer The book of abstracts contains abstracts as provided by their authors. Technical support Publishing House of the University of Agriculture in Krakow 31-425 Kraków, al. 29 Listopada 46 e-mail: [email protected] www.wydawnictwo.ur.krakow.pl Content Oral presentations Session 1. New pathogens and shifts in pathogenicity Molecular tools allow the description of new taxons at species and infra-specific levels among plant pathogenic bacteria María M. López, Pablo López-Soriano, Silvia Barbé, Javier Peñalver, Pablo Llop, Ester Marco-Noales, Jerson Garita-Cambronero, Aitana Ares-Yebra, Adela Abelleira, Olga Aguín, Jaime Cubero, Ana Palacio-Bielsa . 23 The genus Torradovirus, an overview Martin Verbeek. 24 Umbel browning and stem necrosis on some cultivated apiaceous hosts in European domain Rossitza Rodeva, Audrius Kacergius, Jutta Gabler (emeritus senior researcher), Zornitsa Stoyanova. 25 New data for the taxonomy and variability of the Enterobacteriaceae family Anita Végh, László Palkovics . 26 Biodiversity and phylogenetic position of bacteria causing bacterial canker of stone fruits trees in Poland Monika Kałużna, Joanna Puławska, Piotr Sobiczewski . 27 Genetic diversity of Colletotrichum acutatum causing bitter rot on sour and sweet cherries in Poland Monika Michalecka, Joanna Puławska. 28 Session 2. Toxic metabolites of pathogens Mycotoxins in pathogen – patogen interactions: adaptation and response within Fusarium genus Adam Dawidziuk, Grzegorz Koczyk, Delfina Popiel . 30 Current distribution of Fusarium fungi on small grain cereals in Russia: species complex and related mycotoxins Tatiana Gagkaeva, Olga Gavrilova . 31 Molecular quantification and genetic diversity of toxigenic usariumF species in northern Europe and Asia Tapani Yli-Mattila, Sari Rämö, Veli Hietaniemi, Taha Hussien, Olga Gavrilova, Tatiana Gagkaeva . 32 Gene expression of ABC-transporters in Clonostachys rosea IK726 in response to anti-fungal metabolites from Pseudomonas chlororaphis ToZa7 and Serratia rubidaea S55 Nathalie Kamou, Mukesh Dubey, Georgios Tzelepis, Magnus Karlsson, Anastasia Lagopodi, Dan Funck Jensen . 33 Segregation of Alternaria strains isolated from cereals in Germany and Russia according to their morphological, molecular and toxigenic features Sandra Kahl, Andreas Ulrich, Marina Müller. 34 The ABC transporter AbreAtr1 affects phytotoxin secretion and the pathogenicity of Alternaria brassicae isolates Bahram Sharifnabi,Masoumeh Mostafa, Abolghasem Esmaeili, Mohammad Reza Mofid, Mahdi Abbasian . 35 Fusarium Head Blight of spring wheat: mycotoxins, causal agents and their quantitative analysis with Real Time PCR Aleksander Łukanowski, Leszek Lenc, Czesław Sadowski, Krzysztof Jończyk, Jan Kuś . 36 3 A survey of genetic diversity of Rhizoctonia solani anastomosis groups associated with potatoes in South Africa Norman Muzhinji, J.E. van der Waals, J.W. Woodhall, M. Truter . 37 Session 3. Pathogen identification, detection and monitoring Modification of vegetative compatibility test Maria Rataj-Guranowska . 39 Genetic diversity among Rhizoctonia solani AG-4 isolates recovered from different hosts based on ITS-rDNA markers in Isfahan, IRAN Farzanaeh Badpa, G. Reza Balali, Bahram Sharifnabi, Parvin Yavari . 40 How precisely diagnose whether the Trifolium ambiguum is infested by Sclerotinia trifoliorum or Sclerotinia sclerotiorum? Anna Baturo-Ciesniewska, Jadwiga Andrzejewska, Aleksander Lukanowski . 41 Identification of fungi associated with apple fruit rot before harvest and during storage in integrated agricultural system Julija Volkova, Lelde Grantina-Ievina . 42 High Resolution Melting Analysis for identification ofColletotrichum species causing pepper anthracnose Rossitza Rodeva, Zornitsa Stoyanova, Vasilissa Manova, Ralitsa Georgieva, Lubomir Stoilov . 43 The main causal agents of winter wheat crown rot in Latvia Biruta Bankina, Antons Ruža, Gunita Bimšteine, Ingrīda Neusa-Luca, Ance Roga, Dāvids Fridmanis . 44 Virulence variation in cucurbit powdery mildew populations in the Czech Republic Božena Sedláková, Aleš Lebeda, Eva Křístková, Kateřina Gryczová . 45 Crown gall and the diversity and detection of its causal agent – screening of Polish stone fruits nurseries Joanna Puławska . 46 Nectrotrophic behaviour of Erwinia amylovora in apple and tobacco leaf tissues Piotr Sobiczewski, Artur Mikiciński, Barbara Dyki, Elżbieta Węgrzynowicz-Lesiak. 47 Detection, identification and monitoring ofDickeya spp. in potato, water and weed samples with molecular methods Marta Potrykus, Małgorzata Golanowska, Wojciech Śledź, Aleksandra Binek, Agata Motyka, Sabina Żołędowska, Monika Sławiak, Ewa Łojkowska . 48 Viruses infecting horseradish (Armoracia rusticana P.Gaertn., B.Mey. et Scherb) plants in Poland Tadeusz Malinowski, Maria Burian, Lidia Fornal, Grażyna Szczechowicz, Krystyna Górecka . 49 Monitoring and characterisation of Pectobacterium wasabiae isolated from potato fields in Poland Agata Motyka, Sabina Żołędowska, Wojciech Śledź, Robert Czajkowski, Ewa Łojkowska. 50 Potato virus Y – important pathogen of tobacco Grażyna Korbecka, Marcin Przybyś, Anna Czubacka. 51 Special session. Special session in Wieliczka Salt Mine EFPP Conferences Małgorzata Mańka . 53 Biological monitoring in the treatment salt chambers of the ‘Wieliczka’ Salt Mine Health Resort Dorota Myszkowska, Magdalena Kostrzon, Wojciech Dyga, Maciej Mikołajczyk, Krystyna Obtułowicz, Monika Zagórska, Jolanta Kędzierska, Ewa Czarnobilska . 54 Session 4. Genomics, proteomics and bioinformatics Role of different molecular mechanisms in resistance to synthetic fungicide substances Delfina Popiel, Adam Dawidziuk, Grzegorz Koczyk . 56 Towards probing the toxigenic potential of fungal communities in environmental samples Grzegorz Koczyk, Delfina Popiel, Adam Dawidziuk . 57 Cell wall-degrading effectors are crucial for the fungal plant pathogen V. longisporum to infect Arabidopsis Jonas Roos, Sarosh Bejai, Johan Fogelqvist, Tim Kamber, Arne Schwelm, Christina Dixelius . 58 4 Role of a pleiotropic drug transporter protein abcG5 in xenobiotic tolerance and antagonism in fungal biocontrol agent Clonostachys rosea Mukesh Dubey, Dan Funck Jensen, and Magnus Karlsson . 59 The effect of reversible point mutations in the Pepino mosaic virus coat protein gene on viral aggressiveness Beata Hasiów-Jaroszewska, Anneleen Paeleman, Nelia Ortega Parra, Natasza Borodynko, Julia Minicka, Anna Czerwoniec, Bart PHJ Thomma, Inge M. Hanssen . 60 Fungal cellulases on both sides of the fence: cellulolytic enzymes as an infectious agent of Fusarium pathogens and as an inducer of plant resistance by the Trichoderma fungi Judyta Strakowska, Łukasz Stępień, Lidia Błaszczyk . 61 Molecular detection and identification of begomoviruses and its associated satellite molecules affecting some important plants in India Sunil Kumar Snehi, Shri Krishna Raj . 62 Leaf symptoms image analysis by using biology inspired algorithms Michal Obořil, Tomáš Kašparovský, Jan Lochman . 63 Quantifying the resistance risks associated with systemic seed treatments: a modelling analysis James L. Kitchen . 64 Session 5. Diseases of trees in forests and recreation sites Healthy forest – healthy society Andrzej Grzywacz, Małgorzata Mańka . 66 Alien invasive threats to UK forests: a reassessment in the wake of ash dieback Steve Woodward, Eric Boa . 67 An integrated approach to monitor and control the invasive fungal pathogen Heterobasidion irregulare in European forest stands Paolo Gonthier, Naldo Anselmi, Paolo Capretti, Filippo Bussotti, Matteo Feducci, Luana Giordano, Tommaso Honorati, Guglielmo Lione, Nicola Luchi, Marco Michelozzi, Bruno Paparatti, Martina Pollastrini, Fabiano Sillo, Anna Maria Vettraino, Matteo Garbelotto . 68 Role of Armillaria species in tree dying in Turkey oak (Quercus cerris L.) and Hungarian oak (Quercus frainetto Ten.) forest Nenad Keča, Ljiljana Keča . 69 Modelling the effects of climate on the incidence of the nut rot of chestnuts caused by Gnomoniopsis castanea Guglielmo Lione, Luana Giordano, Fabiano Sillo, Paolo Gonthier . 70 Genetic differentiation within and between Swiss and Lithuanian populations of Hymenoscyphus pseudoalbidus using microsatellite analysis Daiva Burokiene, Esther Jung, Vaidotas Lygis, Karin Moosbrugger, Simone Prospero, Daniel Rigling, Corine N. Schoebel . 71 Virulence of Hymenoscyphus pseudoalbidus isolates originating from Lithuanian (post-epidemic) and Swiss (epidemic) populations Vaidotas Lygis,
Recommended publications
  • Studies on Authentication of True Source of Honey Using Pollen DNA
    Journal of Entomology and Zoology Studies 2018; 6(3): 255-261 E-ISSN: 2320-7078 P-ISSN: 2349-6800 Studies on authentication of true source of honey JEZS 2018; 6(3): 255-261 © 2018 JEZS using pollen DNA barcoding Received: 09-03-2018 Accepted: 10-04-2018 Praghadeesh Manivanan Praghadeesh Manivanan, Srinivasan Madapuji Rajagopalan and Department of Plant Mohankumar Subbarayalu Biotechnology, Centre for Plant Molecular Biology& Biotechnology, Tamil Nadu Abstract Agricultural University, Plant pollen DNA comprising unique barcode signatures– serve as a highly resilient biomarker to Coimbatore, Tamil Nadu, India establish its true biological origin. Over a decade, DNA barcoding of plants has evolved as an effective tool to identify its origin down to species level that promptedits practical applications in various fields of Srinivasan Madapuji Rajagopalan applied biology. Premium unifloral honey, due to its economic value as a medicinal product is vulnerable Department of Agricultural to intentional mislabelling and adulteration to fetch higher price. Melissopalynological and Entomology, Tamil Nadu physiochemical based approaches to ascertain the true source of honey is not yet available on commercial Agricultural University, scale. DNA barcoding of pollen trapped in honey can be effectively used to identify the true source of Coimbatore, Tamil Nadu, India honey with high feasibility across labs at cheaper price. The current study was carried out to standardise Mohankumar Subbarayalu an efficient pollen DNA isolation protocol and to assess the efficiency of two barcode (rbcL and matK Professor and Head, Department gene) combinations in identifying the botanical origin of pollen and to ascertain its true source. Six honey of Plant Biotechnology, Centre samples with diverse characteristics were used in the study.
    [Show full text]
  • 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.
    [Show full text]
  • Using RNA-Seq to Characterize Pollen–Stigma Interactions for Pollination
    www.nature.com/scientificreports OPEN Using RNA‑seq to characterize pollen–stigma interactions for pollination studies Juan Lobaton1,3*, Rose Andrew1, Jorge Duitama2, Lindsey Kirkland1, Sarina Macfadyen3 & Romina Rader1 Insects are essential for the reproduction of pollinator‑dependent crops and contribute to the pollination of 87% of wild plants and 75% of the world’s food crops. Understanding pollen fow dynamics between plants and pollinators is thus essential to manage and conserve wild plants and ensure yields are maximized in food crops. However, the determination of pollen transfer in the feld is complex and laborious. We developed a feld experiment in a pollinator‑dependent crop and used high throughput RNA sequencing (RNA‑seq) to quantify pollen fow by measuring changes in gene expression between pollination treatments across diferent apple (Malus domestica Borkh.) cultivars. We tested three potential molecular indicators of successful pollination and validated these results with feld data by observing single and multiple visits by honey bees (Apis mellifera) to apple fowers and measured fruit set in a commercial apple orchard. The frst indicator of successful outcrossing was revealed via diferential gene expression in the cross‑pollination treatments after 6 h. The second indicator of successful outcrossing was revealed by the expression of specifc genes related to pollen tube formation and defense response at three diferent time intervals in the stigma and the style following cross‑pollination (i.e. after 6, 24, and 48 h). Finally, genotyping variants specifc to donor pollen could be detected in cross‑pollination treatments, providing a third indicator of successful outcrossing. Field data indicated that one or fve fower visits by honey bees were insufcient and at least 10 honey bee fower visits were required to achieve a 25% probability of fruit set under orchard conditions.
    [Show full text]
  • 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.
    [Show full text]
  • Fungal Genomes Tell a Story of Ecological Adaptations
    Folia Biologica et Oecologica 10: 9–17 (2014) Acta Universitatis Lodziensis Fungal genomes tell a story of ecological adaptations ANNA MUSZEWSKA Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland E-mail: [email protected] ABSTRACT One genome enables a fungus to have various lifestyles and strategies depending on environmental conditions and in the presence of specific counterparts. The nature of their interactions with other living and abiotic elements is a consequence of their osmotrophism. The ability to degrade complex compounds and especially plant biomass makes them a key component of the global carbon circulation cycle. Since the first fungal genomic sequence was published in 1996 mycology has benefited from the technolgical progress. The available data create an unprecedented opportunity to perform massive comparative studies with complex study design variants targeted at all cellular processes. KEY WORDS: fungal genomics, osmotroph, pathogenic fungi, mycorrhiza, symbiotic fungi, HGT Fungal ecology is a consequence of osmotrophy Fungi play a pivotal role both in encountered as leaf endosymbionts industry and human health (Fisher et al. (Spatafora et al. 2007). Since fungi are 2012). They are involved in biomass involved in complex relationships with degradation, plant and animal infections, other organisms, their ecological fermentation and chemical industry etc. repertoire is reflected in their genomes. They can be present in the form of The nature of their interactions with other resting spores, motile spores, amebae (in organisms and environment is defined by Cryptomycota, Blastocladiomycota, their osmotrophic lifestyle. Nutrient Chytrydiomycota), hyphae or fruiting acquisition and communication with bodies. The same fungal species symbionts and hosts are mediated by depending on environmental conditions secreted molecules.
    [Show full text]
  • 1 Molecular Analysis of Honey Bee Foraging Ecology Dissertation
    Molecular analysis of honey bee foraging ecology Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Rodney Trey Richardson Graduate Program in Entomology The Ohio State University 2018 Dissertation Committee Professor Reed Johnson, Advisor Professor Mary Gardiner Professor John Christman Professor Roman Lanno 1 Copyrighted by Rodney Trey Richardson 2018 2 Abstract While numerous factors currently impact the health of honey bees and other pollinating Hymenoptera, poor floral resource availability due to habitat loss and land conversion is thought to be important. This issue is particularly salient in the upper Midwest, a location which harbors approximately 60 percent of the US honey bee colonies each summer for honey production. This region has experienced a dramatic expansion in the area devoted to crop production over the past decade. Consequently, understanding how changes to landscape composition affect the diversity, quality and quantity of available floral resources has become an important research goal. Here, I developed molecular methods for the identification of bee-collected pollen by adapting and improving upon the existing amplicon sequencing infrastructure used for microbial community ecology. In thoroughly benchmarking our procedures, I show that a simple and cost-effective three-step PCR-based library preparation protocol in combination with Metaxa2-based hierarchical classification yields an accurate and highly quantitative pollen metabarcoding approach when applied across multiple plant markers. In Chapter 1, I conducted one of the first ever proof-of-concept studies applying amplicon sequencing, or metabarcoding, to the identification of bee-collected pollen.
    [Show full text]
  • 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.
    [Show full text]
  • Experimental Quantification of Pollen with DNA Metabarcoding Using
    www.nature.com/scientificreports OPEN Experimental quantifcation of pollen with DNA metabarcoding using ITS1 and trnL Sandra Baksay 1*, André Pornon1, Monique Burrus1, Jérôme Mariette2, Christophe Andalo1 & Nathalie Escaravage1 Although the use of metabarcoding to identify taxa in DNA mixtures is widely approved, its reliability in quantifying taxon abundance is still the subject of debate. In this study we investigated the relationships between the amount of pollen grains in mock solutions and the abundance of high- throughput sequence reads and how the relationship was afected by the pollen counting methodology, the number of PCR cycles, the type of markers and plant species whose pollen grains have diferent characteristics. We found a signifcant positive relationship between the number of DNA sequences and the number of pollen grains in the mock solutions. However, better relationships were obtained with light microscopy as a pollen grain counting method compared with fow cytometry, with the chloroplastic trnL marker compared with ribosomal ITS1 and with 30 when compared with 25 or 35 PCR cycles. We provide a list of recommendations to improve pollen quantifcation. Environmental DNA metabarcoding is a molecular method that consists of investigating environmental DNA samples made of complex mixtures of genomes from numerous organisms1. Due to new sequencing technologies and bioinformatics tools, metabarcoding has been increasingly used to identify taxa in environmental samples1 to monitor biodiversity2–4, to investigate ecosystem functioning5 and interaction networks6–8, in both aquatic and terrestrial ecosystems. Nevertheless, its reliability in quantitative approaches, which depend on the match between counts of high-throughput sequence reads and the amount of sampled biological material2, is still the subject of debate9,10.
    [Show full text]
  • Access the .Pdf File
    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.
    [Show full text]
  • Pollen DNA Barcoding: Current Applications and Future Prospects
    Page 1 of 43 Pollen DNA barcoding: current applications and future prospects Authors: Karen L. Bell 1, Natasha de Vere 2, Alexander Keller 3, Rodney T. Richardson 4, Annemarie Gous 5,6 , Kevin S. Burgess 7, Berry J. Brosi 1 1Emory University, School of Environmental Sciences, Atlanta, GA, USA 2National Botanic Garden of Wales, Llanarthne, United Kingdom 3Department of Animal Ecology and Tropical Biology, University of Würzburg, Würzburg, Germany 4Department of Entomology, The Ohio State University, Columbus, OH, USA 5Biotechnology Platform , Agricultural Research Council , Pretoria, South Africa 6School of Life Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa 7Columbus State University, Columbus, GA, USA Keywords (3-6): DNA metabarcoding; metagenomics; pollen; palynology; high-throughput sequencing; next-generation sequencing Genome Downloaded from www.nrcresearchpress.com by MICHIGAN STATE UNIV on 04/18/16 1 For personal use only. This Just-IN manuscript is the accepted prior to copy editing and page composition. It may differ from final official version of record. Page 2 of 43 ABSTRACT (<200 words) Identification of the species origin of pollen has many applications, including assessment of plant-pollinator networks, reconstruction of ancient plant communities, product authentication, allergen monitoring, and forensics. Such applications, however, have previously been limited by microscopy-based identification of pollen, which is slow, has low taxonomic resolution, and few expert practitioners. One alternative is pollen DNA barcoding, which could overcome these issues. Recent studies demonstrate that both chloroplast and nuclear barcoding markers can be amplified from pollen. These recent validations of pollen metabarcoding indicate that now is the time for researchers in various fields to consider applying these methods to their research programs.
    [Show full text]
  • 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”.
    [Show full text]
  • Working Party on Poplar and Willow Diseases
    WORKING PARTY ON POPLAR AND WILLOW DISEASES 159 160 HOST-RANGE STUDIES OF MELAMPSORA ON SALIX IN THE PACIFIC NORTHWEST REGION OF THE UNITED STATES Chandalin Bennett1, George Newcombe, Catherine Aime Melampsora is known as an important cause of disease on willows throughout the world. Even so, little is known about the occurrence, distribution, and specific hosts of these leaf rusts in North America. Current classification places all willow rusts occurring in North America into the species complex Melampsora epitea Thuem. This is a result of supposed morphological continuity throughout the complex. Several lines of study have been initiated in an effort to understand what is represented by this complex on a regional scale. Host-range inoculation experiments of Melampsora on Salix are the main components of this baseline study. Although wild collections are still in progress, a preliminary inoculation has been performed with rust from Salix sitchensis. Ten different Salix species that occur throughout the Pacific Northwest (PNW) region of the United States were used as test plants. It was found that this Melampsora isolate was able to infect across the range of its host plant, which represents six geographically distinct S. sitchensis populations throughout Washington and Idaho states. Three others: Salix spp., S. wolfii, S. bebbiana, and S. scouleriana were also susceptible to this inoculum, although both S. bebbiana and S. scouleriana displayed an hypersensitive response and prolonged latent period (> 15 days). Five other Salix species - S. geyeriana, S. exigua, S. melanopsis, S. alba, and S. eriocephala - from locations throughout this region were resistant to the inoculum. These preliminary results clearly demonstrate that Melampsora is host specific and that certain populations of Salix are resistant to this particular isolate.
    [Show full text]