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Assessment of dieback pathogens of apple trees to be removed and the detection of diplodia seriata on chipped apple wood
Thesis (MScAgric)--Stellenbosch University, 2022.
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Stellenbosch : Stellenbosch University
2022
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| access_status_str | Open Access |
| author | Jacobs, Vernon Guy |
| author2 | Mostert, Lizel |
| author_browse | Jacobs, Vernon Guy Mostert, Lizel |
| author_facet | Mostert, Lizel Jacobs, Vernon Guy |
| author_sort | Jacobs, Vernon Guy |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (MScAgric)--Stellenbosch University, 2022. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/125138 |
| institution | Stellenbosch University (South Africa) |
| language | en_ZA |
| last_indexed | 2026-06-10T12:43:51.865Z |
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| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
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| spelling | oai:scholar.sun.ac.za:10019.1/125138 Assessment of dieback pathogens of apple trees to be removed and the detection of diplodia seriata on chipped apple wood Jacobs, Vernon Guy Mostert, Lizel Halleen, Francois Stellenbosch University. Faculty of AgriSciences. Dept. of Plant Pathology. Apples -- Breeding Canker (Plant disease) -- Pathogenesis Apples -- Diseases and pests Wood -- Deterioration Wood-decaying fungi -- Genetics Dieback Apples -- Mulching UCTD Thesis (MScAgric)--Stellenbosch University, 2022. ENGLISH ABSTRACT: The use of chipped fruit trees as mulch in apple orchards is a common practice in the deciduous fruit industry of South Africa. Apple trees destined to be removed are usually old, do not produce optimally or need to make way for new varieties. These apple trees often have visible dieback symptoms, caused by canker and wood rot pathogens. The use of mulch produced from infected trees holds a risk to young or newly established apple orchards that could get infected with the spread of diseased wood chips as mulch. However, the presence and ability of canker and wood rot pathogens to survive on mulch made from apple trees need to be determined. Therefore, the aim of this study was to assess the diversity of canker and wood rot pathogens present on apple trees destined to be removed and chipped, and to determine the presence and viability of the canker pathogen, Diplodia seriata, on chipped apple tree wood used for mulches. The diversity of canker and wood rot pathogens present in apple trees to be removed was determined. Branches or trunks showing dieback symptoms, cankers or wood rot were sampled from 14 orchards in the Grabouw, Vyeboom and Kouebokkeveld apple producing areas in the Western Cape of South Africa. Isolations were made from a diseased branch or trunk sample taken from ten trees of every orchard. Canker and wood rot pathogens were isolated from 118 of the 144 trees sampled. Known canker pathogens identified included Cytospora parasitica, Diaporthe eres, Diplodia seriata, Eutypa lata, Phaeoacremonium fraxinopennsylvanicum, Pm. minimum and Pm. viticola. Of the canker pathogens, E. lata was predominantly isolated, followed by D. seriata and species of Phaeoacremonium. Species not frequently reported were Cy. parasitica and Dia. eres. Lesser-known fungi reported included Coniochaeta ligniaria, C. velutina and Pleurostoma richardsiae. The most diverse taxonomic group identified was the wood rotting fungus Agaricomycetes. Trametes versicolor was predominantly isolated. Chondrostereum purpureum and Schizophyllum commune were reported less. Lesser-known wood rot species identified included Bjerkandera adusta, Coprinellus micaceus, Fomitiporia capensis, Fomitiporella americana, Fo. viticola, Inocutis spp. (Taxon 3), Oxyporus latemarginatus, Phanerochaeta chrysosporium, and Phlebia sp. Several fungal species were reported for the first time from apple trees: C. ligniaria, Pl. richardsiae, F. capensis and two species of Fomitiporella, Fo. americana and Fo. viticola. Diplodia seriata is an important canker pathogen of apple trees often associated with dieback symptoms of young and mature trees. The presence of D. seriata on chipped wood pieces was investigated. Chipped apple wood pieces were sampled from heaps and when spread onto the orchard floor of three orchards in the Grabouw and Vyeboom production regions. Wood chips were sampled four times from October 2020 (heaps) to April 2021 (orchard floor). Visual inspections were done on samples collected, whereas quantitative PCR (qPCR) analyses of DNA isolated from water washes of wood pieces were done on samples from the first and last sampling. Two apple wood chip heaps were generated in the winter of 2020 (F1-2020, F2-2020), and one heap from 2019 (F1-2019). The presence of D. seriata pycnidia and viable conidia was investigated on a selection of samples. Pycnidia and/ or conidia of D. seriata were present on all wood chips assessed for F1-2019, F1-2020 and F2- 2020 sampled in October 2020 and April 2021. Diplodia seriata cultures obtained from 52 of 60 wood chips were able to survive for 20-months (F1-2019). A qPCR assay was developed to detect D. seriata from mulch wood pieces. The species-specific primers developed was specific for D. seriata and the limit of detection and limit of quantification were 571 fg and 2859 fg, respectively. Diplodia seriata was detected from DNA extracted from water washes of wood chips sampled in October 2020 and April 2021 from all three orchards. From 120 samples, 84% tested positive for D. seriata. This study showed that apple trees, chipped and used for mulch, harbour important canker and wood rot pathogens. Many of these pathogens can form fruiting structures on the wood. Visual field observations during this study confirmed the presence of basidiocarps for wood rot pathogens such T. versicolor and S. commune and pycnidia of canker pathogen, D. seriata, from cankered areas on trees in orchards sampled from. Spores could easily be distributed from wood chips made from infected trees as inoculum could be present. The presence of viable D. seriata inoculum on apple tree wood chips used for mulch in younger orchards illustrates a risk of using wood chips made from old orchards. A similar risk could be expected for other canker and wood rot pathogens associated with dieback of apple trees. However, further investigation should be done to assess the risk of transmission of other known disease-causing pathogens. The level of dieback of older orchards further contributes to the risk of the mulch. Decision-making should, therefore, include assessing the health status of orchards to be removed and if it should be used as mulch. Alternatively cankered wood or dead wood can be removed before the removal of orchards and chipping. If apple tree wood chips are used as mulch other options can be explored such as composting and the application of heat treatments to ensure that mulch material does not contribute to inoculum of canker and wood rot pathogens. AFRIKAANSE OPSOMMING: Die gebruik van verwyderde vrugtebome as deklaag in appelboorde is 'n algemene praktyk in die sagtevrugtebedryf van Suid-Afrika. Appelbome wat verwyder word, is dikwels oud en, produseer nie optimaal nie of moet plek maak vir nuwe variëteite. Hierdie appelbome het dikwels sigbare terugsterwing simptome wat veroorsaak word deur kanker- en houtverrottings patogene. Die gebruik van ʼn deklaag van sulke bome hou 'n risiko in vir jong of nuutgevestigde appelboorde wat geïnfekteer kan word met die verspreiding van ou materiaal. Die teenwoordigheid en vermoë van kanker- en houtverrotting patogene om te oorleef op deklaag materiaal gemaak van appelbome moet nog bepaal word. Daarom was die doel van hierdie studie om die diversiteit van kanker- en houtverrotting patogene teenwoordig op terugsterf- appelbome te bepaal asook die teenwoordigheid en lewensvatbaarheid van die kanker patogeen, Diplodia seriata, op verwyderde appelboomhout wat gebruik word vir deklae. Die diversiteit van kanker- en houtverrotting patogene teenwoordig in ou appelbome wat verwyder moet word, is bepaal. Monsters is geneem van takke of stamme wat afsterfsimptome, kankers of houtvrotting toon, uit 14 boorde in die Grabouw-, Vyeboom- en Kouebokkeveld-appelproduserende gebiede in die Wes-Kaap van Suid-Afrika. Isolasies is gemaak vanuit 'n siek tak of stam wat van tien bome geneem was per boord. Kanker- en houtverrotting patogene is geïsoleer uit 118 van die 144 bome wat gemonster is. Bekende kankerpatogene wat geïdentifiseer is, sluit in Cytospora parasitica, Diaporthe eres, Diplodia seriata, Eutypa lata, Phaeoacremonium fraxinopennsylvanicum, Pm. minimum en Pm. viticola. Van die kankerpatogene was E. lata oorheersend geïsoleer, gevolg deur D. seriata en spesies van Phaeoacremonium. Spesies wat nie gereeld geïsoleer was nie sluit in Cy. parasitica en Dia. eres. Minder bekende swamme wat aangemeld is, sluit in Coniochaeta ligniaria, C. velutina en Pleurostoma richardsiae. Die mees diverse taksonomiese groep was houtverrotting swamme in die groep Agaricomycetes. Trametes versicolor was oorheersend geïsoleer. Chondrostereum purpureum en Schizophyllum commune was ook gevind, maar nie gereeld nie. Minder bekende houtverrotting spesies wat geïdentifiseer was, sluit in Bjerkandera adusta, Coprinellus micaceus, Fomitiporia capensis, Fomitiporella americana, Fo. viticola, Inocutis spp. (Taxon 3), Oxyporus latemarginatus, Phanerochaeta chrysosporium en Phlebia sp. Verskeie swamspesies is vir die eerste keer vanaf appelbome aangemeld. Hierdie sluit in C. ligniaria, Pl. richardsiae, F. capensis en twee spesies van Fomitiporella, naamlik Fo. americana en Fo. viticola. Diplodia seriata is 'n belangrike kanker patogeen van appelbome wat dikwels geassosieer word met terugsterwing van jong en volwasse appelbome. Die teenwoordigheid van D. seriata op hout deklaag materiaal was ondersoek. Monsters van deklaag materiaal was geneem vanaf deklaag hope asook vanaf die boordvloer van drie boorde in die Grabouw- en Vyeboom-produksiestreke waar dit versprei was. Hout deklaag materiaal was geneem vanaf Oktober 2020 (hope) tot April 2021 (boordvloer) vir ‘n totaal van vier steekproef geleenthede. Visuele inspeksies was gedoen op verteenwoordigende monsters wat ingesamel was vir alle monsternemings, terwyl kwantitatiewe PKR (kPKR) ontledings van DNS geïsoleer uit waterspoelings van houtstukke gedoen was op monsters van die eerste en laaste monsterneming. Twee boorde was verwyder in die winter van 2020 (F1-2020, F2-2020), en een hoop vanaf 2019 (F1-2019). Die teenwoordigheid van D. seriata piknidia en lewensvatbare konidia is op 'n seleksie van monsters ondersoek. Piknidia en/of konidia van D. seriata was teenwoordig op alle hout deklaag materiaal wat vir F1-2019, F1-2020 en F2- 2020 geassesseer is in Oktober 2020 en April 2021. Lewensvatbare Diplodia seriata-kulture was verkry vanuit 52 van 60 houtstukkies. Inokulum kon oorleef vir 20 maande (F1-2019). 'n kPKR-toets is ontwikkel om D. seriata van deklaaghoutstukke op te spoor. Die spesie- spesifieke inleiers wat ontwikkel is, was spesifiek vir D. seriata en die limiet van opsporing en kwantifiseringslimiet was onderskeidelik 571 fg en 2859 fg. Diplodia seriata is opgespoor van DNS wat onttrek is uit waterspoelings van houtstukkies wat in Oktober 2020 en April 2021 van al drie boorde gemonster is. Uit 120 monsters het 84% positief getoets vir D. seriata. Hierdie studie het getoon dat appel bome wat verwyder word en as deklaag gebruik word, belangrike kanker- en houtverrotting patogene huisves. Baie van hierdie patogene kan vrugstrukture op die hout vorm. Visuele veldwaarnemings tydens hierdie studie het die teenwoordigheid van vrugstrukture van bekende houtverrotting patogene soos T. versicolor en S. commune en piknidia van die kanker patogeen, D. seriata, getoon. Spore kon maklik versprei word vanaf houtstukkies wat van besmette bome gemaak is, aangesien inokulum teenwoordig kan wees. Die teenwoordigheid van lewensvatbare D. seriata inokulum op appelboomhoutstukkies wat vir deklaag in jonger boorde gebruik word, illustreer 'n risiko om houtstukkies wat van ou boorde gemaak is, te gebruik. 'n Soortgelyke risiko kan verwag word vir ander kanker- en houtverrotting patogene wat verband hou met terugsterwing van ou appelbome. Verdere ondersoek moet egter gedoen word om die risiko van oordrag van ander bekende siekteveroorsakende patogene te bepaal. Die vlak van terugsterwing van ouer boorde dra verder by tot die risiko van die deklaag. Die gesondheidstatus van ou appel bome wat verwyder word uit boorde moet dus in ag geneem word wanneer die bome geprosesseer en gebruik word as deklaag. Alternatiewelik kan terugsterf houtmateriaal of dooie hout verwyder word voor die verwydering van boorde en die gebruik daarvan as deklaag. As ou appel boom houtstukkies as deklaag gebruik word, kan ander opsies ondersoek word soos kompostering en die toepassing van hittebehandelings om te verseker dat deklaagmateriaal nie bydra tot inokulum verspreiding van kanker- en houtverrotting patogene nie. Masters 2022-03-11T09:21:21Z 2022-04-29T12:55:38Z 2022-03-11T09:21:21Z 2022-03 Thesis http://hdl.handle.net/10019.1/125138 en_ZA Stellenbosch University ix, 131 pages : illustrations (some color) application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Apples -- Breeding Canker (Plant disease) -- Pathogenesis Apples -- Diseases and pests Wood -- Deterioration Wood-decaying fungi -- Genetics Dieback Apples -- Mulching UCTD Jacobs, Vernon Guy Assessment of dieback pathogens of apple trees to be removed and the detection of diplodia seriata on chipped apple wood |
| title | Assessment of dieback pathogens of apple trees to be removed and the detection of diplodia seriata on chipped apple wood |
| title_full | Assessment of dieback pathogens of apple trees to be removed and the detection of diplodia seriata on chipped apple wood |
| title_fullStr | Assessment of dieback pathogens of apple trees to be removed and the detection of diplodia seriata on chipped apple wood |
| title_full_unstemmed | Assessment of dieback pathogens of apple trees to be removed and the detection of diplodia seriata on chipped apple wood |
| title_short | Assessment of dieback pathogens of apple trees to be removed and the detection of diplodia seriata on chipped apple wood |
| title_sort | assessment of dieback pathogens of apple trees to be removed and the detection of diplodia seriata on chipped apple wood |
| topic | Apples -- Breeding Canker (Plant disease) -- Pathogenesis Apples -- Diseases and pests Wood -- Deterioration Wood-decaying fungi -- Genetics Dieback Apples -- Mulching UCTD |
| url | http://hdl.handle.net/10019.1/125138 |
| work_keys_str_mv | AT jacobsvernonguy assessmentofdiebackpathogensofappletreestoberemovedandthedetectionofdiplodiaseriataonchippedapplewood |