Dissertations / Theses on the topic 'Roots (Botany) Diseases and pests'

Boschniakia hookeri Walpers has been found to parasitize the roots of Gaultheria shallon Pursh, Arctostaphylos uva-ursi (l.) Spreng, and Vaccinium ovatum Pursh, all members of the Ericaceae. This is the first documented report of the parasitism of Vaccinium ovatum. The subterranean shoot of B. hookeri originates endogenously from the perennial tubercle of the parasite. The shoot has an eustele, composed of collateral vascular bundles, arranged in four composite fronts and separated by four wide 'leaf gaps.' Pits on metaHylem vessels range from nearly circular to laterally elongated. Rll vessel members have simple perforations. Ouerall, the Hylem of subterranean shoots contained relatively few tracheary elements. Phloem is abundant, with radial series of sieve tube members that have simple sieve plates. Brachysclereids forming large clusters are positioned to both the inside and outside of the vascular bundles. Abundant stomata are present and frequently raised above the shoot surface. RHillary buds along subterranean shoots are capable of producing flowers or branch shoots. Considerable secondary growth occurs in maintained shoots below developing branch shoots. This manifested by the additional production of secondary Hylem and phloem, and the formation of a protective cuticular epithelium. This study of B. hookeri supports the view that the short and fleshy character of the subterranean shoot, increased presence of phloem, reduction of leaves to scales, and a perennial nature are specializations associated with the holoparasitic mode of life.

South Africa has the highest species diversity of ericaceous plants belonging to the Erica genus. There are over 850 identified species in the Cape Floral Region. The Albany Centre of Endemism (ACOE) is located within this region and is a hotspot of diversity consisting of various plant genera. The success of Erica plants is ubiquitously attributed to mycorrhizal relationships they engage in with a diverse group of fungi. This symbiosis is known as the ericoid mycorrhizal (ERM) association. The overall aim of this study was to establish the diversity of root fungi associated with Erica plants using morphological, molecular and 454 pyrosequencing techniques. Six Erica species were identified using leaf and flower morphology according to taxonomic keys. The identified plants were Erica cerinthoides, Erica demissa, Erica chamissonis, Erica glumiflora, Erica caffra and Erica nemorosa. Roots from sampled plants were stained and examined microscopically to determine their mycorrhizal status. Ericoid mycorrhizal associations together with dark septate endophyte (DSE) structures and hyphae that did not form any specific structure were observed in all the roots. In addition arbuscular mycorrhizal (AM) structures in the form of vesicles were detected in E. glumiflora and E. cerinthoides. In order to identify the culturable fungi associated with the respective hosts, sterilised roots were placed on various culture media for cultivation. Thereafter isolated fungi were morphologically classified into 67 morphotypes. These were mostly sterile and darkly pigmented. Non-sporulating mycelia of variable colouration such as white, cream-yellowish, beige, green and brown were also observed. Further identification was carried out using molecular techniques. DNA was extracted separately from pure cultures and amplified using ITS1 and ITS4 primers in a polymerase chain reaction (PCR). Thereafter sequencing and Basic Local Alignment Search Tool (BLAST) were used to identify the isolates to generic level. The fungi were taxonomically classified into 54 operational taxonomic units and 94 percent were Ascomycetes and Helotiales was the dominant order. Unclassified Helotiales with affinities to fungi currently identified as Epacrid root fungus was common in all hosts. Other isolates that were identified included Oidiodendron, Meliniomyces, Phialocephala, Cadophora, Lachnum, Leohumicola Cryptosporiopsis, Chaetomium, Acremonium and Epicoccum species. Basidiomycetes were represented by two OTUs belonging to the genus Mycena. Four OTUs comprised fungi that had no significant alignments in the reference databases. Direct root DNA extraction together with 454 pyrosequencing was used to detect the diversity of culturable and unculturable fungi associated with the identified hosts. The ITS2 region was targeted for sequencing. Although Ascomycetes remained the dominant phyla, Basidiomycetes were also detected in all host plants. Glomeromycota was present in E. caffra and E. cerinthoides. Helotiales was dominant in all Erica plants with the exception of E. cerinthoides and E. chamissonis which were dominated by the order Chaetothyriales. The OTUs identified to genus level included Epacris pulchella root fungus, Oidiodendron cf. maius, Acremonium implicatum, Leohumicola, Lachnum, Capronia and Mycena species. Culture-based techniques and pyrosequencing detected similar fungal composition comprising Ascomycetes, while, pyrosequencing was able to detect Glomeromycetes and Basidiomycetes.

Thesis (MScAgric)--University of Stellenbosch, 2003.
ENGLISH ABSTRACT: Characterizing the genetic structure of a pest population can provide an understanding of the factors influencing its evolution and assist in its ultimate control. The aim of the present study was to characterize the genetic structure of woolly apple aphid Eriosoma lanigerum (Hausmann) populations in the Western Cape Province in South Africa. Since this economically important apple pest has not previously been characterized at molecular level, it was necessary to evaluate methods for determining the genetic structure of E. lanigerum populations. Two different molecular techniques were evaluated viz. random amplification of polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP). This study represents the first application of the latter technique to members of the Aphididae. Aphids were sampled from four regions in the Western Cape in South Africa viz. Elgin, Ceres, Vyeboom and Villiersdorp. A spatially nested sampling design was used to establish the distribution of the genetic variance of aphids. A total of 192 individuals from 13 farms were analysed. Ten RAPD primers were chosen for analysis from an initial assay of 25 after fragment reproducibility had been confirmed. For AFLP analysis three different rare-cutting restriction enzymes were evaluated for AFLP analysis, viz. EcoRI, SseI and MluI. The latter yielded the best results in combination with the frequent-cutting enzyme MseI. Twenty-five AFLP selective primer pairs were evaluated, out of which five were chosen for analysis of the total population. Two hundred and fifty AFLP fragments and 47 RAPD fragments were scored for analysis. Both analyses indicated that a low level of genetic variation was apparent in E. lanigerum populations and that no differentiation resulted from geographic isolation. From RAPD analyses it was deduced that all variation could be attributed to differences between individuals. AFLP analysis indicated that, whereas genetic differences in E. lanigerum populations between orchards were negligible, a significant portion of genetic variation could be attributed to differences between farms and individuals within farms. Therefore, AFLP analysis allowed for finer discrimination of the genetic structure of E. lanigerum populations than RAPD analysis and is recommended for studies of other aphid species. The fact that most of the genetic variation present in E. lanigerum populations could be found on small spatial scales indicated that sampling individuals over a wide geographic area was an ineffective way of detecting the genetic diversity present in E. lanigerum populations. The low level of variation in populations is most likely due to the exclusive occurrence of parthenogenetic reproduction, founder effects (including distribution of infested plant material from a limited source) and selective factors such as the use of resistant rootstocks or pesticides. Furthermore, the low level of variation found indicated that the possibility of controlling E. lanigerum in the Western Cape using host plant resistance is favourable. Thus, plant breeders developing resistance to E. lanigerum can expect plant entries to be exposed to most of the genetic diversity present in Western Cape populations, regardless of location.
AFRIKAANSE OPSOMMING: Die bepaling van die genetiese struktuur van 'n landboukundige plaagpopulasie kan lei tot begrip van die faktore wat die populasie beïnvloed en kan uiteindelike beheer vergemaklik. Die doel van die huidige studie was om die genetiese struktuur van die appelbloedluis Eriosoma lanigerum (Hausmann) in die Wes-Kaap Provinsie van Suid-Afrika te bepaal. Aangesien hierdie belangrike appelplaag nie van tevore op molekulêre vlak bestudeer is nie, was dit nodig om metodes vir die bepaling van die genetiese struktuur van E. lanigerum populasies te evalueer. Twee molekulêre tegnieke is geëvalueer, nl. lukraak geamplifiseerde polimorfiese ONS (RAPD) en geamplifiseerde fragment-lengte polimorfismes (AFLP). Hierdie studie is die eerste om laasgenoemde tegniek te gebruik om lede van die Aphididae te bestudeer. Plantluise is verkry van vier verskillende gebiede in die Wes-Kaap Provinsie van Suid-Afrika nl. Elgin, Ceres, Vyeboom en Villiersdorp. 'n Hierargiese sisteem is gebruik om die verspreiding van die genetiese variasie van plantluise te bepaal. In totaal is 192 individue van 13 plase geanaliseer. Tien RAPD inleiers is gekies uit 'n analise van 25 verskillende inleiers nadat fragment reproduseerbaarheid bevestig is. Drie verskillende restriksie ensieme is geëvalueer vir AFLP analise nl. EcoRI, SseI en Mlul. Die beste resultate is verkry toe MluI saam met MseI gebruik is. Vyf-en-twintig AFLP selektiewe inleier pare is geëvalueer waarvan vyf gekies is vir analise van die totale populasie. Twee-honderd-en-vyftig AFLP fragmente en 47 RAPD fragmente is gedokumenteer vir analise. Beide RAPD en AFLP analises het getoon dat daar 'n lae vlak van genetiese variasie in E. lanigerum populasies is en dat geen differensiasie as gevolg van geografiese isolasie ontstaan het nie. Uit RAPD analise is daar afgelei dat al die variasie toegeskryf kon word aan verskille tussen individue. AFLP het aangetoon dat alhoewel verskille in E. lanigerum populasies tussen boorde laag was, kon 'n hoë persentasie van die variasie toegeskryf word aan verskille tussen plase en individue binne plase. AFLP analise het meer insig in die genetiese struktuur van E. lanigerum populasies verskaf, en word dus aanbeveel vir studies van ander plantluise. Omdat meeste van die genetiese variasie oor klein geografiese afstande verkry word, is steekproefueming oor groot gebiede 'n ondoeltreffende manier om die genetiese variasie binne 'n monster te meet. Die lae vlak van genetiese variasie is waarskynlik te wyte aan partenogenetiese vermeerdering, stigter gevolge (insluitend verspreiding van geïnfesteerde plantmateriaal vanaf 'n beperkte bron), sowel as selektiewe faktore soos die gebruik van bestande onderstokke en insekdoders. Verder dui die lae vlak van variasie aan dat die moontlikheid vir beheer deur gasheerplantbestandheid goed is in die Wes-Kaap. Planttelers kan verseker wees dat hulle plante blootgestel sal wees aan meeste van die genetiese variasie in die Wes-Kaap appelbloedluis populasies ongeag hulle ligging.

Studies were conducted on three field trials of wheat cv. Kopara to investigate the lack of compensation by later determined components of yield because of early disease constraints. The investigation was based on the hypothesis that early disease reduces root development and thus causes the plants to be water constrained at later growth stages when soil water deficits usually occur. The reduced root development and soil water deficits may reduce the ability of the plant to compensate for reductions in early determined components. The hypothesis was tested by the application of irrigation to alleviate water stress. In a disease free crop, the possible phytotonic effects of the fungicides benomyl and triadimefon on wheat were investigated. These fungicides had no phytotonic effects on shoot, root growth, or yield under the prevailing conditions. The effect of disease on root development was analysed by root length measurements. Disease present in the crop at any stage of growth affected root development. Root development in the upper zones of the soil profile was reduced more by disease compared to those zones below 35 cm. A full disease epidemic reduced root development more than an early or late disease epidemic. The early and late disease epidemics had similar effects on root length. Alleviation of early disease constraints enabled greater development of roots to offset any earlier reductions. Soil water deficits increased root development in the lower zones of the nil disease plants. The presence of adequate soil water from irrigation reduced the requirement for further root growth in all treatments. In the 1981-1982 field trial a full disease epidemic reduced yield by 14% whereas an early disease epidemic reduced yield by 7%. The reduction in yield was attributed to a lower grain number. With irrigation the yield reduction in the full disease plants was 12% whereas in the early disease plants the reduction was only 2.4%. This indicated that plants affected by the early disease epidemic were water constrained. In this study, the results suggested that, for conditions prevailing in Canterbury, the supply of water at later growth stages increased grain weight in plants which were subject to early disease epidemics. This suggests that reduced root development caused by early disease and soil water deficits may prevent compensation by grain weight. Water use was similar in all disease treatments. After irrigation the irrigated plants of all treatments used more water. Disease affected water use in relation to yield production however, and was better expressed by water use efficiency. Water use efficiency was reduced in the full disease plants. A stepwise regression analysis suggested that water use efficiency was affected directly by disease at later growth stages, and indirectly via an effect on total green leaf area at early growth stages. This study partially proves the hypothesis that reductions in root development caused by an early disease epidemic may constrain the plants at later growth stages when water deficits usually occur. It was shown that the reduction in root development caused by disease could be counteracted by irrigation. In this respect, water served as a tool to study the effect of disease constraints on the yield of wheat. A knowledge of cereal crop physiology, root growth and function is used to explain and discuss the observations made in this research programme. The results are discussed in relation to the way in which disease affects yield through its effect on root development. The possible reasons for the continued effects of disease even after the control of disease at later growth stages are discussed. The economic use of fungicides and water in diseased crops are also outlined. Suggestions for future studies on disease-yield loss relationships are provided. The repetition of these experiments in different sites and climatic regions could provide information which may be incorporated in disease-yield loss simulation models. This could then be used to predict root development and water requirements of diseased plants, and provide a basis for economic use of fungicides and water, and for better disease management programmes.

Cylindrocladium black rot (CBR) is a destructive root disease of peanut caused by Cylindrocladium crotalariae. New and quantitative approaches were developed to estimate the inoculum potential for this soil-borne pathogen under soil-temperature tank conditions favorable for CBR development. Using cultural plating methods, numerous Q. crotalariae infections (1 to > 1,000 per plant) were observed on asymptomatic root systems of peanut plants, susceptible and resistant to CBR, grown in naturally infested soils at 25 C. Regression-line slope values of log10-log10 plots for microsclerotial inoculum density versus the number of observed root infections per plant and per unit root length [0.98 (R2 =0.94) and 0.99 (R2 = 0.94), respectively] indicated direct proportionality between the respective variables. Efficiency of inoculum for observed infection (percent of germinating microsclerotia that infect roots) estimates were high (near 100%), while efficiency of observed infection for necrosis (percent of infections that develop into necroses) estimates were low (0.27 to 0.28%). Observed infection observed infections per m root per day per rates, I 0 r (the number of microsclerotium per g of soil) were significantly lower (P = 0.001) for CBR-resistant 'Spancross• than for CBR-susceptible 'Florigiant•. The majority of observed infections did not appear to be restricted to outer cortical root tissues. A portion of observea infections near root surfaces resulted in subsequent colonization of the inner cortex and stele of plants for each cultivar. A significantly greater (P = 0.05) number of segments from steles of CBR-susceptible Florigiant taproots were colon~zed by Q. crotalariae than those from CBR-resistant Spancross. Using naturally infested peanut field soils, a dose of 7.4 )-lg NaN3 (sodium azide)/g soil was effective in reducing initial microsclerotial populations by 50%, based upon a highly significant dosage-response curve (R2 = 0.96, P = 0.0001). CBR development was reduced significantly (P = 0.05) for Florigiant plants grown in Q. crotalariae-infested soils treated with 7.5 fl' NaN3/g soil or higher, compared to plants grown in untreated soils. Sublethal doses of NaN3 combined with biological control agents may be useful in the development of integrated CBR control measures.
Ph. D.

Thesis (MScAgric)--University of Stellenbosch, 2004.
ENGLISH ABSTRACT: Soilborne diseases of grapevines represent a complex problem with limited information available, both locally and internationally. Previous research in South Africa indicated that Phytophthora and Pythium spp. were the most widespread and devastating pathogens in grapevine nurseries and vineyards in the Western Cape province. The local grapevine industry is currently expanding; new cultivars, methods and agricultural chemicals are being used which can affect soilborne pathogens. It has therefore become necessary to reassess the status of soilborne pathogens in nurseries, since information in this regard is crucial for the development of disease management practices for the expanding local grapevine industry. Soilborne fungal genera associated with roots and crowns of declining nursery grapevines were assessed in surveys conducted at three different grapevine nurseries in the Western Cape province. Cylindrocarpon, Fusarium, Pythium, and Rhizoctonia spp. were consistently isolated from roots and crowns of declining nursery grapevines. Cylindrocladiella spp. and Phytophthora cinnamomi were infrequently isolated from diseased roots, crowns and soil whereas Pythium spp. were abundant in most of the soils. Results suggest that the status of soilborne fungal pathogens in grapevine nurseries in the Western Cape province has changed over the last 30 years. The DNA phylogeny and pathogenicity of the isolates of Cylindrocladiella were determined. Four species of Cylindrocladiella occur on grapevines in South Africa, namely C. lageniformis, C. parva, C. peruviana, as well as a new species, described in this study as C. viticola, which forms part of the C. infestans species complex. Pathogenicity trials were inconclusive. Ten Fusarium spp. were isolated from roots and crowns of declining nursery grapevines, namely F. acuminatum, F. anthophilum, F. chlamydosporum, F. equiseti, F. nygamai, F. oxysporum, F. proliferatum, F. scirpi, F. semitectum and F. solani. The dominant species was F. oxysporum, followed by F. proliferatum and F. solani. In pathogenicity trials F. oxysporum and F. solani significantly reduced root volume, root dry mass, length of new shoots, stem diameter and number of leaves, but increased the percentage of chlorotic leaves and root rot severity. Fusarium proliferatum also caused a significant reduction in new shoot growth, number of leaves and increased root rot severity compared to the controls. Fusarium so/ani seems to be more virulent than F. oxysporum, followed by F. pro/iferatum. This is the first report of F. oxysporum, F. pro/iferatum and F. so/ani as pathogens of grapevines in South Africa, and the first report of F. proliferatum as a pathogen of grapevines in the world. Phytophthora cinnamomi was isolated at low frequencies from declined grapevines, although present in the rhizosphere soil. It is possible that the extensive use of downy mildew chemicals in grapevine nurseries may protect grapevines from infection by P. cinnamomi. The effect of chemicals used to combat downy mildew on Phytophthora root rot of nursery grapevines was evaluated in a glasshouse. There was very little discernable effect of the chemicals tested relative to the control plants for the parameters measured and it was concluded that the inoculation technique needed refinement. However, plants treated with phosphorous acid tended to be taller and have more leaves, greater stem diameter and root volume than controls or plants treated with the other chemicals. The data obtained in this study are not conclusive, but indicated certain trends that more glasshouse trials and field trials would resolve. Results presented in this thesis indicate that a major shift has occurred in the status of soilborne fungi associated with roots and crowns of grapevines in nurseries in the Western Cape since the 1970s when Phytophthora and Pythium were predominant. The prevalence and role of soilborne fungi need to be determined so that new appropriate disease management strategies can be developed to limit losses in grapevine nurseries and ensure the sustainable production of healthy plants for the grapevine industry.
AFRIKAANSE OPSOMMING: 'N ONDERSOEK NA GRONDGEDRAAGDE SWAMME GEASSOSIEER MET WORTELS EN KRONE VAN WINGERD IN KWEKERYE Grondgedraagde siektes van wingerd is 'n komplekse probleem waaroor min inligting, beide plaaslik en internasionaal, beskikbaar is. Vorige navorsing in Suid-Afrika het aangedui dat swamme van die genera Phytophthora en Pythium die mees algemene en vernietigende grondgedraagde patogene in kwekerye en wingerde in die Wes-Kaap provinsie is. Die plaaslike wingerdbedryf brei huidiglik uit; nuwe kultivars, metodes en landbouchemikalieë word gebruik wat 'n invloed kan hê op grondgedraagde patogene. Gevolglik het dit noodsaaklik geword om die status van grondgedraagde patogene in wingerdkwekerye weer te bepaal, aangesien inligting in hierdie verband noodsaaklik is vir die ontwikkeling van siekte bestuurspraktyke vir die ontwikkelende plaaslike wingerdbedryf. Grondgedraagde swamgenera geassosieer met wortels en krone van terugsterwende wingerd in kwekerye is bepaal in opnames wat by drie verskillende wingerdkwekerye in die Wes-Kaap provinsie uitgevoer is. Cylindrocarpon, Fusarium, Pythium, en Rhizoctonia spp. is konstant vanuit wortels en krone van terugsterwende wingerdplante in kwekery geïsoleer, Cylindrocladiella spp. en Phytophthora cinnamomi is ongereeld vanuit siek wortels, krone en grond geïsoleer, terwyl Pythium spp. algemeen in meeste gronde voorgekom het. Resultate dui daarop dat die status van grondgedraagde swampatogene in wingerdkwekerye in die Wes- Kaap provinsie oor die laaste 30 jaar verander het. Die DNA filogenie en patogenisiteit van die isolate van Cylindrocladiella is bepaal. Vier spesies van Cylindrocladiella kom voor op wingerd in Suid-Afrika, naamlik C. lageniformis, C. parva, C. peruviana, sowel as 'n nuwe spesie, wat in hierdie studie as C. viticola aangedui is en wat deel is van die C. infestans spesie kompleks. Patogenisiteits proewe was onvoldoende om die patogeniese status van die swam me te bepaal. Tien Fusarium spp. is vanuit wortels en krone van terugsterwende wingerdplante in kwekery geïsoleer, naamlik F. acuminatum, F. anthophilum, F. chlamydosporum, F. equiseti, F. nygamai, F. oxysporum, F. proliferatum, F. scirpi, F. semitectum en F. solani. Die dominante spesies was F. oxysporum, gevolg deur F. proliferatum en F. solani. In pathogenisteitsproewe het F. oxysporum en F. solani gelei tot 'n betekenisvolle laer wortelvolume, droë massa van wortels, lengte en droë massa van nuwe groei en aantal blare, maar het die persentasie chlorotiese blare en graad van wortelvrot verhoog. Fusarium proliferatum het ook gelei tot 'n betekenisvolle afname in lengte en massa van nuwe groei, aantal blare en 'n verhoogde graad van wortelvrot in vergelyking met die kontrole behandelings. Dit wil voorkom asof Fusarium solani meer virulent is as F. oxysporum, gevolg deur F. proliferatum. Hierdie is die eerste aanmelding van F. oxysporum, F. proliferatum en F. solani as patogene van wingerd in Suid-Afrika, en die eerste aanmelding van F. proliferatum as 'n patogeen van wingerd in die wêreld. Phytophthora cinnamomi is konstant teen lae frekwensies vanuit terugsterwende wingerd in kwekerye geïsoleer, alhoewel dit in risosfeer gronde teenwoordig was. Dit is moontlik dat die ekstensiewe gebruik van chemikalieë teen donsskimmel in wingerdkwekerye die wingerdplante kan beskerm teen infeksie deur P. cinnamomi. Die effek van chemikalieë wat gebruik word teen donsskimmel op Phytophthora wortelverrotting van wingerd in kwekerye, is 'n glashuis geëvalueer. Die chemikalieë wat gestoets is, het vir die gemete parameters, tot baie min onderskeibare effek gelei relatief tot die kontrole plante, en daar is afgelei dat die inokulasie tegniek verbetering benodig. Plante wat met fosforiensuur behandel is, het egter geneig om langer te wees met meer blare, 'n groter stamdeursnee en wortelvolume as kontrole plante of plante behandel met ander chemikalieë. Data verkry vanuit die hierdie studie was onvoldoende, maar sekere neigings is aangedui wat deur verdere glashuis- en veldproewe verklaar sal word. Resultate wat in hierdie tesis weergegee is, het aangedui dat 'n algehele verskuiwing in die status van grondgedraagde swamme geassosieer met wortels en krone van wingerd in kwekerye vanaf die 1970s, toe Phytophthora en Pythium die dominante genera was, plaasgevind het. Die voorkoms en rol van grondgedraagde swamme moet bepaal word, sodat nuwe voldoende siektebestuurspraktyke ontwikkel kan word om verliese in wingerdkwekerye te beperk en sodoende die volhoubare produksie van gesonde plante vir die wingerdbedryf te verseker.

Thesis (MSc)--Stellenbosch University, 2014.
ENGLISH ABSTRACT: Two genera of ophiostomatoid fungi occur in the seed-bearing structures of serotinous Protea species in the Cape Floristic Region. These fungi are dispersed by arthropods, including mites and beetles that visit the Protea host plants. Although the vectors of Proteaassociated ophiostomatoid fungi are known, their dispersal patterns remain unknown – especially the manner in which recently burnt fynbos vegetation is recolonized. Additionally, their reproduction strategy has not previously been investigated. The focus of this study was, therefore, to determine the extent of within- and between-plant dispersal of Proteaassociated ophiostomatoid fungi at the population level and to investigate their reproductive strategy. One Protea-associated ophiostomatoid fungus, Knoxdaviesia proteae, is found exclusively in the fruiting structures of P. repens and was the focus of this study. In order to interrogate natural populations of this fungus, 12 polymorphic microsatellite markers specific to K. proteae were developed with an ISSR-PCR enrichment strategy and pyrosequencing. These markers were amplified in two distantly separated populations of K. proteae. The genetic and genotypic diversities of both populations were exceptionally high and neither showed significant population differentiation. The lack of population structure in both populations implies that K. proteae individuals within a P. repens stand are in panmixia. As one of the sampling sites had burnt recently, the process whereby young fynbos is recolonized could be investigated. Compared to the adjacent, unburnt area, K. proteae individuals in the burnt area of this population had significantly less private alleles, suggestive of a young population that had experienced a genetic bottleneck. Knoxdaviesia proteae individuals that did not originate from the adjacent unburnt area were encountered within the burnt site and, additionally, isolation-by-distance could not be detected. The parsimony-based haplotype networks and the tests for linkage disequilibrium indicated that recombination is taking place within as well as between the two distantly separated populations. The observed panmixia in P. repens stands, widespread recolonization and the high genetic similarity and number of migrants between the two populations emphasizes long-distance dispersal and therefore the role of beetles in the movement of K. proteae. This cohesive genetic structure and connection across large distances is likely a result of multiple migration events facilitated by beetles carrying numerous phoretic mites.
AFRIKAANSE OPSOMMING: Twee genera ophiostomatoid swamme kom in die saad-draende strukture van bloeiende Protea spesies in the Kaapse Floristiese Streek voor. Hierdie Protea-verwante ophiostomatoid swamme word gekenmerk deur hul assosiasie met geleedpotige vektore – spesifiek die myt en kewer besoekers van die Protea gasheer plante. Alhoewel die geleedpotige vektore van Protea-verwante ophiostomatoid swamme bekend is, is die wyse waarop hierdie swamme versprei onbekend; veral die manier waarop onlangse gebrande fynbos geherkoloniseer word. Verder is die voortplantings-strategie van hierdie swamme nog nie voorheen ondersoek nie. Die fokus van hierdie studie was dus om die omvang van binne- en tussen-plant verspreiding van Protea-verwante ophiostomatoid swamme te bepaal op die populasie vlak en om hul voorplantings-strategie te ondersoek. Een Protea-verwante ophiostomatoid swam, Knoxdaviesia proteae, word uitsluitlik in die vrugdraende strukture van P. repens aangetref en was die fokus van hierdie studie. Om natuurlike populasies van hierdie swam te ondersoek is 12 mikrosatelliet-merkers spesifiek vir K. proteae ontwerp deur ‘n ISSR-PCR strategie en “pyro”-basisvolgorde bepaling te gebruik. Hierdie merkers is geamplifiseer in twee K. proteae populasies wat ver van mekaar geskei is. Die genetiese en genotipiese diversiteit van beide populasies was uitsonderlik hoog en nie een het beduidende populasie-differensiasie getoon nie. Die gebrek aan populasie struktuur in beide populasies veronderstel dat K. proteae individue binne ‘n P. repens stand in panmiksia is. Aangesien een van die steekproef terreine onlangs gebrand het, kon die herkolonisasie proses van jong fynbos ondersoek word. In vergelyking met die aangrensende, ongebrande area, het K. proteae individue in die gebrande area beduidend minder private allele gehad. Dit dui op ‘n jong populasie wat ‘n genetiese bottelnek beleef het. Knoxdaviesia proteae individue wat nie van die aangrensende, ongebrande area afkomstig is nie is ook binne die gebrande terrein aangetref. Verder is afsondering-deur-afstand nie aangetref nie. Die parsimonie-gebaseerde haplotiepe-netwerke en die toetse vir koppeling-onewewigtigheid het aangedui dat rekombinasie binne sowel as tussen die twee populasies plaasvind. Die panmiksia wat waargeneem is in P. repens populasies, wydverspreide herkolonisasie en die hoë genetiese ooreenkoms en hoeveelheid immigrante tussen die twee populasies beklemtoon lang afstand verspreiding en dus die rol van kewers in die beweging van K. proteae. Hierdie samehangende genetiese struktuur en die verband oor groot afstande is waarskynlik ‘n gevolg van verskeie migrasies gefasiliteer deur kewers wat talle foretiese myte dra.

Bacterial galls on Douglas-fir (Pseudotsuga menzeisii [Mirb.] Franco), collected from the southern tip of Vancouver Island, the Greater Vancouver area and the Hope region of British Columbia, were generally globose in shape with rough, irregular surfaces and measured between 0.5 and 2.0 cm in diameter. The galls were generally located on the tips of branches or twigs of 10- to 20-year old Douglas-fir trees. The bacterial gall disease appeared to affect few Douglas-fir trees in the collection areas and bacterial galls were not found on any other coniferous species. Furthermore, there have been no reports of serious damage to natural forests in British Columbia due to bacterial gall disease. Young, greenhouse-grown Douglas-fir seedlings occasionally died if the tip of the main stem was artificially inoculated. Often new growing tips would be produced affecting the growth form of the seedlings. Two types of gall-forming Erwinia spp. were isolated from Douglas-fir galls. Typical isolates, tentatively identified by fatty acid analysis as Erwinia salicis, produced galls which were rough and irregular in shape composed of multiple outgrowths marked by a single or cross-shaped fissure. The atypical isolate, tentatively identified by fatty acid analysis as Erwinia herbicola subsp. herbicola, produced galls which were smooth and generally round in shape with the surface cracking as the gall expanded. Colonies of the typical isolates grown on casein-peptone-glucose media were characteristically round, slightly domed with somewhat concentric ridging observed near the margins of the colonies. Three to 4 day old colonies of the atypical isolates grown on casein-peptone-glucose media were characteristically round and concave while older colonies produced an extracellular slime and were more irregular in shape. In Luria Broth, the typical isolates grew at temperatures of up to 32°C while the atypical isolate grew at temperatures of up 34°C. The typical isolate was resistant to a wider range of antibiotics than the atypical isolate. Polyclonal antisera were produced against glutaraldehyde-fixed whole cells of both the typical T-2789 and atypical A-0181 gall-forming Erwinia isolates. The purified antisera were isolate specific as tested by immunodiffusion and an indirect ELISA against several different phytopathogenic bacteria including Pseudomonas syringae pv. syringae, Erwinia herbicola subsp. herbicola, Agrobacterium tumefaciens, Rhizobium leguminosarum and Erwinia carotovora subsp. carotovora. Plasmid profiles of the typical Erwinia isolates contained one band while the atypical isolate characteristically contained 4 to 5 bands which appeared to be different forms of at least one plasmid. Restriction digests of the typical isolates suggested a size of approximately 50 kb while complex digestion profiles were obtained for the atypical isolates because of the difficulty in isolating individual plasmid types. From visual estimates against Hindlll-digested lambda DNA, a size of between 10 and 20 kb was suggested for the fastest moving plasmid band of the atypical isolate. No homology was observed between the different plasmid types characteristic of the two isolates. The role of the plasmid DNA of the atypical isolate in pathogenesis was not determined because curing of the plasmid(s) was not successful using high temperature treatments plus chemical curing agents. Heat treatment experiments, in which the pathogen was selectively killed at various times after inoculation, demonstrated that the bacteria are required to be present for gall induction and continued development of the gall for both of the gall-forming Erwinia isolate types. Pathogenicity of the isolated bacteria was tested on 14 conifer species, other than Douglas-fir, including Abies, Chamaecyparis, Pinus and Thuja spp. The typical isolates were weakly pathogenic on Abies, Larix and Picea spp. The atypical isolate was weakly pathogenic on Abies, Chamaecyparis, Larix, Picea and Pinus spp. Due to the limited damage caused on the conifers tested and to their infrequent occurrence, these gall-forming pathogens do not appear to be of economic importance to the forestry industry.
Land and Food Systems, Faculty of
Graduate

The root system is a vital and dynamic part of a plant throughout its lifetime. Its spatial distribution is the consequence of multiple interactions with the surrounding soil medium. In particular, the presence of pathogens in soil may influence the development of the plant, especially the below-ground part, in both its physiology and its structure. Studies of diseased plant roots may take different approaches and investigate disease effects at different levels. In this study, two groups of four potato (Solanum tuberosum L.) plants were grown in middle-sized plastic pots in a greenhouse, and their root systems, together with the soil medium (i.e., sieved and autoclaved homogeneous sand), were submitted to computed tomography (CT) scanning every two weeks until 10 weeks after planting. For the "diseased" group, sand was inoculated with Streptomyces scabies EF-35, the causal agent of potato common scab, at the time of planting. Disease effects on tissue density of roots and below-ground organs, space occupancy and complexity were assessed by analyzing the CT scanning data in the spatio-temporal approach. Fluctuations of tissue density over time were different, on average, between the two groups. They were characterized by an increase of density in Week 2 for the diseased group, reflecting a hardening of tissue, and a delayed decrease relative to the "healthy" group, suggesting a slower transfer of energy from the seed potato to growing roots. Space occupancy, which was studied via volumetric growth rates evaluated from CT scan data, and complexity, which was quantified by the fractal dimension estimated from skeletonized 3-D images constructed from CT scan data, also showed differences in the first part of the experiment. Original analytical procedures based on data transformation and curve fitting in histogram analysis of CT numbers were developed to obtain those results. In conclusion, the new approach presented here, which is based on the advanced processing of CT scanning data collected over time on developing plant root systems and below-ground organs, can be recommended for future phytopathological applications.

The tropical rainforest has interested ecologists for hundreds of years because of its vast species diversity. The distribution and establishment of trees is related to soil properties and rootassociated microorganisms. The coexistence of hyper-diverse plant communities in tropical rainforests has resulted in associations being formed with belowground communities, mycorrhizas (particularly arbuscular mycorrhizal (AM), ectomycorrhizas (ECM)) and root associated bacterial communities. The rapid deforestation in Southeast Asia is causing the loss of the dominant and important tree species belonging to the family Dipterocarpaceae. It is important to understand whether different host species in the same environment maintain mycorrhizal and bacterial diversity, especially mycorrhizas with a restricted host range. In this study, I examine the ecology of mycorrhizas and bacteria associated with Dipterocarpaceae and also the plant community as a whole. The aim of this project is to understand the effect of host properties (e.g. species, size), soil factors (e.g. nutrient concentrations) and spatial factors on mycorrhizal fungi and bacterial diversity and community structure. The research took place in two Centre for Tropical Forest Science (CTFS) plots in Malaysia: Pasoh Forest Reserve (in Negeri Sembilan) and Danum Valley Conservation Area (in Sabah). Molecular protocols and a modern technique, Next Generation Sequencing (NGS), were adopted to quantify mycorrhizal and bacterial loads in tropical plants. ITS1 and ITS2 regions were used for ECM, 18S rRNA were used for AM, and 16S rRNA were used for bacteria. Mycorrhizas and bacteria present in the roots of Dipterocarpaceae from 60 individual plants belonged to 25 species within 6 genera were traced and sampled in 2015. To my knowledge, this study is the first attempt to study root-associated bacteria across multiple species within a single family, Dipterocarpaceae. Dipterocarpaceae's species was found to significantly influence root bacteria. Analyses showed that mycorrhizal communities are similar on the host, unlike the null model. Dipterocarpaceae was previously believed to solely host ECM, but this study disproves this. This study shows that Dipterocarpaceae can have dual colonization, as it iv can also associate with AM fungi. One soil core of 10 cm × 10 cm × 7.5 cm were collect randomly in three subplot and further divided at 2.5 cm each slice into 75 individual 'microcubes' of 2 cm × 2 cm × 2.5 cm depths enumerates a total of 192 fine root samples. Multivariate analysis revealed that AM fungi tend to associate with non-dipterocarp (as well as unidentified families) while ECM fungi tend to associate with dipterocarps. Data was also collected on host attributes, plant size, and root density. Dipterocarpaceae size does not influence the distribution of mycorrhizal or bacterial communities. The root density reduces as depth increases. Therefore, root density does have a significant influence on mycorrhizal community structure. The diversity of ECM and AM fungal communities within cubes decreased significantly with depth (p < 0.001), whereas the mycorrhizal communities did not change across horizontal distances within cubes. To investigate whether there is a relationship between belowground communities and soil properties, soil macro and micro nutrients were examined and a multivariate analysis was performed. The results showed that communities of belowground (mycorrhizal and bacterial) species correlate with soil parameters. Spatial scale also had an effect on community assembly, independent of environmental variation. These results demonstrate that mycorrhizal fungal communities can vary substantially over very fine spatial scales, and that the distribution of roots from different species do not reflect their proximity aboveground. This study clearly demonstrates the widespread presence of mycorrhizal fungi and root associated bacteria in tropical rainforest plants.

Thesis (PhD)--Stellenbosch University, 2014.
ENGLISH ABSTRACT: Very little is known about the diversity of fungi associated with Afromontane forests of the Cape Floristic Region (CFR) of South Africa. The ophiostomatoid fungi include many species, some known as pathogens in the CFR, while others are well-known saprophytes important in wood degradation. This study focused on the biodiversity and ecology of tree-associated ophiostomatoid fungi (Ophiostomatales) in the CFR. In addition to this, mites and subcortical beetles associated with the CFR trees were collected, regardless of whether they were associated with ophiostomatoid fungi or not. A relatively high diversity of ophiostomatoid fungi were collected from native trees, ten of which were newly described here. Three further fungal species, two of which are probably new to science, were also collected from exotic Pinus species growing in these forests. Four Ophiostomatales species (including three newly described species) were associated with subcortical beetles on Rapanea melanophloeos and Olea capensis ssp. macrocarpa. These were Sporothrix pallida, Sporothrix aemuluphilus, Raffaelea scabbardiae and Raffaelea rapaneae, associated with the beetles Lanurgus sp. 1, Ctonoxylon sp. 1, Xyleborinus aemuluphilus and a Platypodinae species. This represents a first study to explore the associations between subcortical beetles and ophiostomatoid fungi on native trees in the CFR. In addition to fungi associated with subcortical beetles, several members of the Ophiostomatales associated with wounds on Rapanea melanophloes trees were also collected. These included Ophiostoma stenoceras, Sporothrix reniformis, S. rapaneae, S. lunateae and S. noisomeae. All but O. stenoceras were new to science, and were formally described here. All of these wound-associated species from R. melanophloeos belong to the Sporothrix schenckii – O. stenoceras complex, except for S. noisomeae that was provisionally placed in the S. lignivora complex. Besides fungal taxa collected from wounds on Rapanea melanophloeos, other fungi were also collected from wounds on other host trees species. Three more previously undescribed ophiostomatoid fungal species were collected from this niche. They included Sporothix capensis collected from O. capensis ssp. macrocarpa, Graphilbum roseus collected from many different, unrelated host trees and Graphium ilexiense (Microascales), isolated from wounds on Ilex mitis. The latter represented the first isolation of an ophiostomatoid fungus from this host tree species. Two possibly new fungal species (Sporothrix sp. 1, Ceratocystiopsis sp. 1) and Ophiostoma ips, associated with three bark beetles (Orthotomicus erosus, Hylurgus ligniperda and Hylastes angustatus), were collected from Pinus. Several fungal species were collected from both native trees and non-native trees. These included Sporothrix fusiforme from Brabejum stellatifolium and Acacia mearnsii, O. quercus and O. pluriannulatum-like fungus from several native trees and from A. mearnsii. This suggests a possibility for host shifting of some of these fungi between native and non-native hosts or even between different native hosts. Eight non-ophiostomatoid fungi associated subcortical beetles taxa were found also to infest native trees in the Afromontane forests and in total more than 4500 beetle individuals were collected. Some species of ophiostomatoid fungi collected in this study were found to be associated with other arthropods such as mites. Four phoretic mites species associated with ophiostomatoid fungi (Dendrolaelaps quadrisetus, Histiogaster sp. 3, Elattoma sp. 1 & 2) were collected. In addition, sixteen species of tree wound-associated mites were collected from 12 native trees. Of these, nine were associated with several ophiostomatoid fungi (Graphilbum roseus, O. pluriannulatum-like, O. quercus) that were isolated from several different host trees. This suggests that they may aid in the transport of these fungi from one host species to another. The possible consequences of transfers of Ophiostomatales species between hosts were tested using pathogenicity tests, which highlighted that some fungi are pathogenic on several different trees. Transfers seemed most likely in fungal species isolated from wounds, especially those associated with mites, because the mites may aid in the vectoring of these. When phoretic mites were tested for their specificity to their vector beetles, they proved to be highly specific. Although some of the fungi associated with these mites and their sub-cortical beetles were also pathogenic, it is less likely for these fungi to be transferred to other host tree species due to the high specificity of their arthropod associates. This study represents one of a few studies that focused on ophiostomatoid fungi, subcortical beetles and mites associated with trees in the Afromontane forests of South Africa. Although we collected a high diversity of Ophiostomatales members, many more still await discovery. It is recommended that future studies focus on the complex inter-organismal interactions in many of the systems uncovered in this study.
AFRIKAANSE OPSOMMING: Baie min is bekend oor die diversiteit van fungi wat met die Afromontane woude van die Kaapse Floristiese Streek (KFS) van Suid Afrika geassosieer is. Die ophiostomatoïde fungi sluit baie spesies in, sommiges bekend as patogene in die KFS, terwyl ander bekende en belangrike saprofiete in houtdegradasie is. Hierdie studie het op die biodiversiteit en ekologie van die boom-geassosieerde ophiostomatoïde fungi (Ophiostomatales) in die KFS gefokus. Daarbenewens is myte en subkortikale kewers wat met die KFS bome geassosieer word ook versamel, ongeag of hulle geassosieerd was met ophiostomatoïde fungi of nie. „n Relatief hoë diversiteit van ophiostomatoïde fungi is van inheemse bome versamel, tien waarvan hier nuut beskryf is. Drie verdere fungi spesies, twee waarvan ook waarskynlik nuut is tot die wetenskap, is ook vanaf Pinus spesies versamel wat in hierdie woude gegroei het. Vier Ophiostomatales spesies (insluitend drie nuut beskryfde spesies) wat met subkortikale kewers op Rapanea melanophloeos en Olea capensis L. ssp. macrocarpa geassosieer is, is ook versamel. Hulle was Sporothrix pallida, Sporothrix aemuluphilus, Raffaelea scabbardiae en Raffaelea rapaneae, geassosieer met die kewers Lanurgus sp. 1, Ctonoxylon sp. 1, Xyleborinus aemuluphilus en „n Platypodinae spesie. Hierdie verteenwoordig die eerste studie wat die assosiasies tussen subkortikale kewers en ophiostomatoïde fungi op inheemse bome in die KFS ondersoek. Addisioneel tot fungi geassosieer met die subkortikale kewers, is verskeie lede van die Ophiostomatales vanaf wonde op Rapanea melanophloes bome versamel. Hulle sluit in Ophiostoma stenoceras, Sporothrix reniformis, S. rapaneae, S. lunateae en S. noisomeae. Almal behalwe O. stenoceras was nuut tot die wetenskap, en is hier formeel beskryf. Al hierdie wond-geassosieerde spesies vanaf R. melanophloeos behoort aan die Sporothrix schenckii – O. stenoceras kompleks, behalwe vir S. noisomeae wat voorlopig in die S. lignivora kompleks geplaas is. Benewens fungi taxa wat van die wonde op Rapanea melanophloes versamel is, is ander fungi ook vanaf die wonde op ander gasheer boom spesies versamel. Drie verdere ophiostomatoïde fungus spesies is in hierdie nis versamel. Hulle sluit in Sporothix capensis wat vanaf O. capensis ssp. macrocarpa versamel is, Graphilbum roseus wat vanaf baie verskillende, onverwante gasheer bome versamel is en Graphium ilexiense (Microascales), wat vanaf wonde op Ilex mitis versamel is. Laasgenoemde verteenwoordig die eerste isolasie van „n ophiostomatoïde fungus vanaf hierdie gasheer boom spesie. Twee moontlik nuwe fungus spesies (Sporothrix sp. 1, Ceratocystiopsis sp. 1) en Ophiostoma ips, geassosieer met drie baskewers (Orthotomicus erosus, Hylurgus ligniperda en Hylastes angustatus) is vanaf Pinus versamel. Verskeie fungi spesies is van beide inheemse en nie-inheemse bome versamel. Hulle het Sporothrix fusiforme vanaf Brabejum stellatifolium en Acacia mearnsii, O. quercus en O. pluriannulatum-like fungus vanaf verskeie inheemse bome en vanaf A. mearnsii ingesluit. Dit suggereer die moontlikheid van gasheer-skuiwing van sommige van hierdie fungi tussen inheemse en uitheemse gashere of selfs tussen verskillende inheemse gashere. Agt nie- ophiostomatoïde geassosieerde subkortikale kewers was ook versamel en in totaal is meer as 4500 kewer indiwidue versamel. Sommige ophiostomatoïde fungus spesies wat in hierdie studie versamel is, was met ander geleedpotiges soos myte geassosieer. Vier foretiese myt spesies wat met ophiostomatoïde fungi geassosieer is (Dendrolaelaps quadrisetus, Histiogaster sp. 3, Elattoma sp. 1 & 2), is versamel. Nege addisioneële myt spesies was met verskeie ophiostomatoïde spesies vanaf verskeie boomspesies geassosieer (Graphilbum roseus, O. pluriannulatum-like, O. quercus). Dit suggereer dat myte die vervoer van hierdie fungi van een gasheer spesie na die ander mag bewerkstellig. Die moontlike gevolge van die oordrag van Ophiostomatales spesies tussen gashere is getoets deur patogeniteitstoetse. Dit het beklemtoon dat sommige fungi patogenies is op verskeie onverwante boomspesies. Oordraag van spesies is mees waarskynlik in fungi spesies wat vanaf wonde geisoleer is, veral dié wat met myte geassosieer is, want die myte mag hierdie fungi help vervoer. Toe foretiese myte getoets is vir hulle spesifisiteit tot hulle vektore, is hulle hoogs spesifiek bevind. Alhoewel sommige fungi wat met hierdie myte en hulle geassosieerde kewers geassosieer word wel patogenies is, is dit minder waarskylik dat hulle na ander gasheer bome sal verskuif as gevolg van die hoë spesifisiteit van hulle geleedpotige assosiate. Hierdie studie verteenwoordig een van net enkele studies gefokus op ophiostomatoïde fungi, subkortikale kewers en myte wat met bome van die Afromontane woude van Suid-Afrika geassosieer is. Alhoewel ons „n hoë diversiteit van Ophiotomatale lede versamel het, wag baie meer fungi spesies waarskynlik nog op ontdekking. Daar word voorgestel dat toekomstige studies fokus op die komplekse inter-organismiese interaksies in baie van die sisteme wat in hierdie studie blootgelê is.

A compost consisting 95% of the sugar mill byproducts: bagasse, filter press mud, and fly ash, applied at 5 t ha$ sp{-1}$, increased vesicular-arbuscular mycorrhizal infection of sugarcane roots in one of three experimental fields in Barbados. In a plant cane field, compost stimulated formation of intracellular hyphal coils and arbuscules, but not vesicles or hyphae. Infection was greater in roots 35 cm and 65 cm than 5 cm distant from the plant stem, and compost effects were not significant at 5 cm. Two other sources of phosphorus, filter press mud and triple superphosphate, did not affect and suppressed mycorrhizal infection, respectively. Two ratoon crops showed no residual effect of compost on mycorrhizal infection. Compost also stimulated tillering, phosphorus content, and perhaps yield of cane, but did not differentially effect high versus low tillering or sloped versus flat areas. Root length, weight, and specific root length were unaffected by compost addition, but root branching was decreased.

Thesis (MSc)--Stellenbosch University, 2013.
ENGLISH ABSTRACT: The Cape Floristic Region (CFR) of South Africa is well-recognised for exceptionally high plant species diversity and endemism. However, little attention has been bestowed on the pests and pathogens in this region, even though these may greatly influence plant distribution and evolution. In this study we identify various arthropods and fungi as pests and diseasecausing organisms of the ecologically and economically important CFR-endemic tree taxa of Virgilia. We isolated, identified and determined the pathogenicity of key fungal taxa from diseased Virgilia trees throughout the CFR. In addition we evaluated the role of possible pest arthropod taxa, including bark beetles, phoretic mites, larvae of a cerambycid beetle and larvae of the endemic Leto venus (ghost moth), in the death of Virgilia trees. Key fungal taxa were identified by comparisons of the internal transcribed spacer rDNA regions of the isolated taxa with those available on GenBank. Pathogenicity of the most commonly encountered fungal taxa was determined both in the field and under greenhouse conditions. Five different disease symptoms were observed on Virgilia trees throughout the CFR. At Table Mountain, Virgilia oroboides subsp. oroboides showed symptoms of: (1) several small cankers on stems, seemingly caused by a Fusarium acuminatum-like fungus, (2) a root rot disease caused by Armillaria mellea and (3) small bracket fungi on stems associated with Schizophyllum commune. Virgilia oroboides from the Harold Porter National Botanical Garden was diagnosed with a root disease consistently associated with an un-described Phomopsis species. Virgilia oroboides subsp. ferruginea and V. divaricata from Knysna and the Tsitsikamma area often showed symptoms of rapid wilting and death. The Virgilia stems were damaged by the tunnelling larvae of the ghost moth and those of an unidentified cerambycid beetle. Galleries and the surrounding wood tissues often housed the ophiostomatoid fungi Ceratocystis tsitsikammensis and Ophiostoma plurianulatum. These seem to originate from nitidulid beetles found feeding on gum exudate. Pathogenicity trials confirmed the virulence of the undescribed Phomopsis species, the F. acuminatum-like fungus, S. commune and C. tsitsikammensis to Virgilia. All four morpho-species of bark beetles found in this study, together with phoretic mites on two of the beetle morphospecies, were only collected from dead and dying Virgilia hosts and were classified as secondary pests. Both beetle taxa and mites commonly carried spores of various Geosmithia spp. These are not pathogenic to Virgilia trees, but may be an important food source for the bark beetles, as it dominated the fungal community in galleries. The phoretic mites were unable to feed on their Geosmithia associates, but have been observed to feed on dead bark beetle larvae within galleries. This suggests that the relationship of bark beetles, mites and their associated Geosmithia species in this system is complex and in need of further study. Our results show that natural populations of Virgilia play host to numerous destructive pathogens, some of which are non-native (e.g. A. mellea) and a cause for special concern. Additionally, the isolation of the undescribed Phomopsis species and A. mellea from botanical gardens, with A. mellea now spreading to natural areas, calls for stricter control over the movement of organic material from these areas.
AFRIKAANSE OPSOMMING: Die Kaapse Floristiese Streek (KFS) van Suid-Afrika is bekend vir buitengewoon hoë plantspesie-diversiteit en endemisme. Min aandag is egter tot dusver geskenk aan die peste en patogene in hierdie streek, al mag hulle plantverspreiding en evolusie dramaties beinvloed. In hierdie studie identifiseer ons verskeie geleedpotige diere en fungi as peste en organismes wat siektes veroorsaak in die ekologies en ekonomies belangrike, KFS-endemiese boom genus Virgilia. Ons het die sleutel fungi vanaf Virgilia oor die hele KFS geisoleer, geidentifiseer en hulle patogeniteit bepaal. Addisioneel het ons ook die rol van moontlike pes geleedpotiges, insluitende baskewers, cerambycid kewerlarwes en die endemiese Leto venus (spookmot) in die dood van Virgilia bome geevalueer. Sleutel fungi taksa is geidentifiseer deur die interne getranskribeerde spasieerder rDNS streke van die geisoleerde taksa met die wat op GenBank beskikbaar was te vergelyk. Patogenisiteit van die mees algemeen geisoleerde fungi taxa is beide in die veld en onder glashuis-toestande bepaal. Vyf verskillende siekte simptome is by Virgilia bome regdeur die KFS waargeneem. By Tafelberg het Virgilia oroboides subsp. oroboides simptome getoon van: (1) verskeie klein kankers op stamme, blykbaar veroorsaak deur ‘n Fusarium acuminatum-agtige fungus, (2) ‘n wortelvrot siekte veroorsaak deur Armillaria mellea en (3) klein rakswamme op stamme geassosieer met Schizophyllum commune. Virgilia oroboides in die Harold Porter Nationale Botaniese Tuin is gediagnoseer met ‘n wortelvrot siekte wat altyd met ‘n onbeskryfde Phomopsis spesie geassosieer is. Virgilia oroboides subsp. ferruginea and V. divaricata van Knysna en die Tsitsikamma area het dikwels simptome getoon van vinnige verwelking en dood. Die Virgilia stamme is deur die tonnelende larwes van die spookmot en dié van ‘n ongeidentifiseerde cerambycid kewer beskadig. Galerye en die omringende houtweefsel het dikwels die ophiostomatoid fungi Ceratocystis tsitsikammensis en Ophiostoma plurianulatum gehuisves. Dit lyk asof hierdie fungi van nitidulid kewers afkomstig is wat op die gomuitskeidings gevoed het. Patogeniteitsproewe het die kwaadaardigheid van die onbeskryfde Phomopsis spesie, die F. acuminatum-agtige fungus, S. commune en C. tsitsikammensis teenoor Virgilia bevestig. Al vier morfo-spesies baskewer wat in hierdie studie gevind is, sowel as die foretiese myte op twee van die kewer morfo-spesies, is slegs van dooie of sterwende Virgilia gashere versamel, en is as sekondêre peste geklassifiseer. Beide kewerspesies en myt taksa het algemeen spore van verskeie Geosmithia spesies (Geosmithia pallida, G. flava, G. microcorthyli, G. sp. 1 en G. sp. 2) gedra. Die Geosmithia spesies is nie patogenies teenoor Virgilia bome nie, maar mag ‘n belangrike voedselbron vir die baskewers wees, aangesien dit die fungus-gemeenskap in die galarye gedomineer het. Die foretiese myte was nie instaat om op Geosmithia-assosiate te voed nie, maar is waargeneem om op dooie baskewer larwes te voed binne die galerye. Dit stel voor dat die verhouding van die baskewers, myte en hulle geassosieerde Geosmithia spesies in die sisteem kompleks is, en verdere studie benodig. Ons resultate dui aan dat natuurlike populasies van Virgilia gashere is vir verskeie destruktiewe patogene, sommige waarvan nieinheems (bv. A. mellea) wat ‘n bron van groot kommer is. Verder noodsaak die isolasie van die Phomopsis spesie en A. mellea, wat beide wortelvrot siektes in botaniese tuine veroorsaak, strenger kontrole oor die verskuiwing van organiese materiaal uit hierdie areas, veral gegewe dat A. mellea reeds na natuurlike areas versprei het.
The Centre of Excellence In Tree Health Biotechnology for a bursary and funding the research conducted in this study

Thesis (MScAgric)--University of Stellenbosch, 2003.
ENGLISH ABSTRACT: Various aspects of the biology and ecology of woolly apple aphid, Eriosoma lanigerum, were investigated, including initial galling damage caused by E. lanigerum to the roots of apple trees, the possible relationship between E. lanigerum and Xiphinema and Pratylenchus nematodes and the effectiveness of Biostart 2000® and Furfural® as possible control agents of E. lanigerum in the orchard. Preliminary root damage by first instar E. lanigerum feeding was characterized by the mechanical injury of endodermis and parenchyma tissues. Damage by second, third and fourth instar E. lanigerum was similar, but the symptoms were more pronounced. Damage caused by adults included a pronounced swelling at infected areas of the root. Cell walls hardened until the root was radially strengthened with sclerenchyma tissue and nonconducting xylem vessels while the cuticle expanded greatly through the growth of corklike cambium tissue. There was no direct relationship between the population dynamics of E. lanigerum and those of Xiphinema and Pratylenchus nematodes. The occurrence of E. lanigerum appeared to be seasonal while P. penetrans and Xiphinema numbers fluctuated erratically. Undamaged root nitrogen levels seemed to correspond with the normal root growth cycle. Nitrogen levels from galled roots were significantly lower than those of undamaged roots, probably due to E. lanigerum feeding. Soils rich in fine sand and clay sustained higher populations of E. lanigerum and Xiphinema than sandy soils. The number of E. lanigerum found in soil samples correlated well with the damage index allocated to the samples. The numbers of Xiphinema found in soil samples also correlated well with the damage index allocated to the samples according to suspected Xiphinema damage symptoms. Both Biostart 2000® and Furfural® were effective as control agents of woolly apple aphid. Furfural'Ï, a chemical waste product of the sugarcane industry, was however not as effective as Biostart 2000®, a product that includes an activator and three bacterial species, Bacillus laterosporus, B. chitinosporus and B. licheniformis. The bacteria in the Biostart 2000® treated pots could replicate themselves under suitable conditions while Furfural® dilutes with each watering. Biostart 2000® is also easier to prepare than Furfural® since the components of Biostart 2000® readily mix to form a paste easily thinned by water, whereas Furfural® is an oily substance that does not easily disperse in water. Root damage was initiated soon after E. lanigerum started feeding, however there was no apparent relationship between E. lanigerum and the nematode species. The most promising, environmentally friendly control measure was Biostart 2000®.
AFRIKAANSE OPSOMMING: Verskeie aspekte van biologie en die ekologie van die appel bloedluis, Eriosoma lanigerum, was ondersoek insluitende aanvanklike galvorming veroorsaak deur E. lanigerum op wortels van appelbome, die moontlike verwantskap tussen E. lanigerum en Xiphinema en Pratylenchus nematodes en die effektiwiteit van Biostart 2000® en Furfural® as moontlike beheeragente van E. lanigerum in die boord. Aanvanklike wortelskade deur eerste ins tar E. lanigerum voeding was gekenmerk deur die meganiese beskadiging van endodermale en parenchiem weefsel. Skade veroorsaak deur tweede, derde en vierde instar E. lanigerum was soortgelyk alhoewel die simptome meer beklemtoond was. Skade deur volwassenes het 'n meer duidelike swelsel by geïnfekteerde wortelareas ingesluit. Selwande het verhard totdat die wortel radiaalsgewys versterk was met skierenchiem weefsel en nie-geleidende xileemvate terwyl die kutikula grootliks toegeneem het deur die groei van kurkagtige kambiumweefsel. Daar was geen direkte verwantskap tussen die bevolkingsdinamika van E. lanigerum en dié van Xiphinema en Pratylenchus nematodes nie. Die voorkoms van E. lanigerum was seisoenaal terwyl P. penetrans en Xiphinema se getalle onvoorspelbaar gefluktueer het. Onbeskadigde wortel stikstofvlakke het ooreengestem met die normale wortel groeisiklus. Stikstof vlakke van galwortels was noemenswaardig laer as dié van onbeskadigde wortels, heel waarskynlik as gevolg van voeding deur E. lanigerum. Grond ryk aan fyn sand en klei het groter bevolkings van E. lanigerum en Xiphinema onderhou as sanderige gronde. Die aantal E. lanigerum in grondmonsters het goed ooreengestem met die skade indeks wat aan die monsters toegeken was. Die aantal Xiphinema in grondmonsters het ook goed ooreengestem met die beskadigingsindeks wat aan die monsters toegeken is weens vermoedelike Xiphinema skade simptome. Beide Biostart 2000® en Furfural® was effektief as beheeragente van die appelbloedluis. Furfural'", 'n afvalproduk van die suikerriet industrie, was egter minder effektief as Biostart 2000®, 'n produk bestaande uit 'n aktiveerder en drie bakterie spesies, Bacillus laterosporus, B. chitinosporus en B. licheniformis. Die bakterië in die Biostart 2000® behandelde potte kon vermeerder onder gunstige toestande terwyl Furfural® na elke besproeiing verdun het. Biostart 2000® is ook makliker om aan te maak as Furfural® aangesien die bestanddele van Biostart 2000® geredelik meng tot 'n wateroplosbare pasta, terwyl Furfural® 'n olierige vloeistofis wat moeilik 'n waterige suspensie vorm. Wortelskade het plaasgevind kort nadat E. lanigerum begin voed het, alhoewel daar geen duidelike verwantskap tussen E. lanigerum en nematode spesies voorgekom het nie. Die mees belowende omgewingsvriendelike beheermaatreël was Biostart 2000®.

Thesis (MSc)--Stellenbosch University, 2012.
ENGLISH ABSTRACT: Only a limited number of systems involving anther-smut fungi have been studied, usually due to the economic significance of their crop plant hosts. A smut fungus of the genus Thecaphora has been discovered infecting Oxalis hosts in South Africa. This pathogenic fungus, Thecaphora capensis, produces dark-coloured spores in the anthers of host flowers, rendering it an anther-smut fungus. The host genus is the seventh largest plant genus in the Cape Floristic Region (CFR) and the largest geophytic genus of this region. Nine Oxalis species that host T. capensis have been identified across a wide distribution in the CFR of South Africa. A preliminary assessment of T. capensis infections of Oxalis was conducted in 2009, which provided a foundation for further research into the ecological and evolutionary consequences of hosting this fungus. In this study, a comprehensive host diversity assessment was conducted to determine the extent of infected Oxalis individuals within the CFR. Three new Oxalis host species for Thecaphora capensis were discovered. This brings the total number of known hosts to twelve. The morphological and reproductive effects of the fungus were assessed on two host species (O. incarnata and O. lanata) by comparing healthy and infected individuals of these species. Infection by Thecaphora capensis had a significantly negative effect on both of these factors. Host resources appear to be co-opted for fungal spore production, since floral morphological characters of infected individuals were reduced in size. Furthermore, infection by T. capensis ensured near-universal sterility in both hosts. Differences in floral characters and pollinator preferences for healthy Oxalis incarnata and O. lanata individuals from disease-free and diseased populations were compared to determine the evolutionary influence of Thecaphora capensis infections. It was shown that this pathogen can have a significant evolutionary influence on its hosts, showing its ability to shape flower size and pollinator activity in O. lanata, but not in O. incarnata. A need has therefore been identified to assess these evolutionary forces independently for each host and its pathogen before making erroneous assumptions for conservation practices. Plant pollinators play an integral role in plant fitness. Pollinator movements within a population are important when between-flower spore transfer by pollinators increases the likelihood of new infections. Pollinator movements may be influenced by host density and the frequency of diseased individuals, amongst other factors. Pollinators were found to mediate Thecaphora capensis spore transfers within diseased Oxalis populations. Host density and disease frequency affected the number of spores transferred under field and standardized conditions. More research is required to investigate confounding factors in these complex systems. This study highlighted the complexities of a fungal-plant-insect relationship, the evolutionary consequences of such fungal infections and the various factors influencing the likelihood of new infections. This research adds to the limited body of knowledge on multi-organismal interactions in the CFR and provides a base for more detailed future studies on this intriguing system.
AFRIKAANSE OPSOMMING: 'n Brandswam, wat deel is van die Thecaphora genus,is ontdek in 'n Oxalis blom waar dit die gasheer plant se blom gebruik om spore in te produseer. Die swam, Thecaphora capensis, produseer donker gekleurde spore in die helmknoppe van die blomme van gasheer plante, daarom word dit geklasifiseer as 'n brandswam van die helmknop. Die gasheer plante van die swam is deel van die genus Oxalis, die sewende grootste plant genus in die Kaapse Floristiese Streek (KFS) en die grootste geofitiese genus in die streek. Nege Oxalis species is al klaar identifiseer as gasheer plante van T. capensis. Hulle is versprei oor 'n groot area van die KFS van Suid Afrika. 'n Primêre ondersoek van T. capensis infeksies op Oxalis is in 2009 onderneem. Hierdie ondersoek het gelei tot meer vrae oor die sisteem en het 'n goeie fondasie geskep vir verdere navorsing rakende die ekologiese koste verbonde daaraan om as gasheer plant vir 'n swam op te tree. 'n Deeglike ondersoek is in die KFS aangepak om die Oxalis gasheer plante van die brand swam te identifiseer en om voort te bou op die basiskennis wat in die primêre ondersoek daargestel is. Drie nuwe Oxalis gasheer plante van Thecaphora capensis is ontdek. Die totale aantal gasheer plante staan nou op twaalf. Gesonde en geinfekteerde individuele gasheer plante is gebruik om die morfologiese en reproduktiewe effekte van die swam te toets in twee Oxalis spesies (O. incarnata en O. lanata). Die negatiewe gevolge om 'n gasheer plant van die brand swam te wees was duidelik toe gesonde en geinfekteerde individuele met mekaar vergelyk is. Dit kom voor asof gasheer plante se hulpbronne vir spoor produksie gebruik word, want hulle is morfologies kleiner en meestal steriel. Die evolusionêre effek van Thecaphora capensis op 'n populasie is getoets met gesonde individuele in populasies van twee Oxalis spesies. Blomkenmerke en insek bestuiwers van gesonde individue in gesonde en geinfekteerde populasies is ondersoek om die effekte van T. capensis op populasies te toets. Daar is suksesvol gedemonstreer dat swamme sterk evolusionêre kragte uitoefen, en die vermoë het om plantpopulasies te vorm en te verander, ofskoon nie in alle gevalle ewe sterk nie. Daarom is dit belangrik om die evolusionêre kragte vir elke gasheer plant en sy patogeen onafhanklik te assesseer, sonder om algemene aannames te maak in bewaringspraktyke. Plantbestuiwers speel 'n belangrike rol in die fiksheid van plante. Hulle kan hul fiksheid verbeter deur bestuiwers te lok met blomme en deur aspekte geassosieer met blomme. Die bewegingspatrone van plantbestuiwers is baie belangrik indien hulle helmknop-geproduseerde spore van brandswamme vervoer instede van stuifmeel, want dit vergroot die kanse vir nuwe infeksies. Die bewegingspatrone van plantbestuiwers word, onder andere, beinvloed deur die digtheid en frekwensie van geinfekteerde individue. Plantbestuiwers speel 'n belangrike rol in die vervoer van Thecaphora capensis spore in geinfekteerde Oxalis populasies. Die digtheid en frekwensie van geinfekteerde blomme het die vervoer van spore geaffekteer onder veld en gestandardiseerde kondisies, alhoewel baie veranderlikes so 'n komplekse natuurlike sisteem beinvloed. Hierdie studie beklemtoon die kompleksiteit van 'n fungus-plant-insek verhouding, die gevolge van so 'n interaksie en die verskeie faktore wat die waarskynlikheid van nuwe infeksies beinvloed. Tot dusver is daar 'n beperkte aantal sisteme soos hierdie bestudeer waarin 'n brandswam van die helmknop betrokke is, en die enkele beskikbare studies is onderneem meestal as gevolg van hulle ekonomiese effekte op landboukundig belangrike gasheer plante. Hierdie studie verteenwoordig 'n belangrike byvoeging tot die inter-organismiese studies in die KFS. 'n Holistiese ekologiese oorsig soos hierdie verskaf 'n belangrike basis vir toekomstige studies en bewarings- en bestuurspraktyke.

The overall goal of this research was to determine what, if any, role grapevine rhizosphere bacteria play in the differing susceptibilities of New Zealand grown rootstocks to Cylindrocarpon black foot disease. The size and diversity of bacterial populations associated with the rhizospheres of grapevine rootstocks: 101-14, 5C, Schwarzmann and Riparia Gloire were evaluated. Dilution plating showed that total bacterial (P=0.012, P=0.005 for NA and KB, respectively) and fluorescent Pseudomonad (P=0.035) rhizosphere counts differed between rhizosphere and bulk soils but did not correlate with the differing susceptibilities of the rootstock varieties to black foot. No varietal differences were found for spore forming bacteria (P=0.201). SSCP banding patterns showed that species diversity was similar for most rootstocks, but that there were some differences in the composition of bacterial populations, probably attributable to vigour. Some functional characteristics of the bacteria isolated from the rhizospheres of the most and least susceptible rootstock varieties were assessed to investigate their potential to suppress the pathogen. In dual culture, bacteria from Riparia Gloire, 101-14 and the control soil all had little ability to antagonise Cylindrocarpon destructans. However, they differed in their degrees of activity for glucanase (P=0.000), protease (P=0.001) and siderophores (P=0.000). In all tests, bacterial isolates from the rhizosphere of 101-14 had the largest number of active isolates (P≤0.002); however, those from Riparia Gloire had the greatest degree of positive responses for the glucanase and siderophore assays. Bacterial isolates from the control soil produced few glucanases and no siderophores, but had the highest degree of protease activity. Bands excised and sequenced from SSCP gels frequently matched to other ‘uncultured bacteria’ in GenBank, as well as to other bacterial phyla, classes and genera commonly isolated from soil and sediment samples. These included members of the Firmicutes, Proteobacteria (α, δ, γ), Verrucomicrobia, Acidobacteria and Chromatiales. The pathogenicity of C. destructans and Fusarium oxysporum was investigated by inoculating soil containing wounded ungrafted rootstocks of 101-14, 5C, Schwarzmann and Riparia Gloire. Results indicated that F. oxysporum might be a more aggressive pathogen than C. destructans. Inoculation with F. oxysporum or C. destructans increased disease severity, P=0.018 and P=0.056, respectively at 0 cm. Rootstock variety influenced disease severity caused by C. destructans (P<0.001) and F. oxysporum (P=0.090), with rootstocks 101-14 and 5C being most susceptible to C. destructans, and Riparia Gloire and Schwarzmann most susceptible to F. oxysporum. There was also an indication that inoculation with one pathogen increased plant susceptibility to the other, with increased F. oxysporum infection in the C. destructans inoculated treatments of Riparia Gloire and Schwarzmann (P<0.05). The effect of carbohydrate stress (leaf trimming) and inoculation on C. destructans disease severity, incidence, and rootstock rhizosphere bacterial populations was evaluated by inoculating the soil containing one year old plants of Sauvignon Blanc scion wood grafted to rootstocks 101-14 and Schwarzmann. Disease severity and incidence was similar for both Schwarzmann (8.4% and 29.3%, respectively) and 101-14 (14.9% and 31.0%, respectively). When data for the moderate and no stress treatments were combined, because their effects were similar, the disease severity was significantly higher for the highly stressed plants(P=0.043). Stress did not influence disease incidence (P=0.551). Infection occurred in the non-inoculated plants, but disease severity was higher in the plants inoculated with C. destructans than those that were not. Root dry weight of highly stressed plants was lower than in both the moderately stressed (P=0.000) and unstressed plants (P=0.003). An interaction between inoculation and stress (P=0.031) showed that inoculated and highly stressed plants had the lowest root dry weight but there was no effect of rootstocks (P=0.062). There was no significant effect of carbohydrate stress (P=0.259) or inoculation (P=0.885) on shoot dry weight. SSCP banding patterns showed that bacterial diversity was generally similar between rootstocks, but stress and inoculation altered rhizosphere bacterial communities. This study has demonstrated that functionality of grapevine rhizosphere bacteria do differ between grapevine rootstock varieties that have different susceptibilities to black foot disease, but that this role needs to be further investigated if more accurate and practically relevant conclusions are to be drawn.

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Fundação de Amparo a Pesquisa do Estado de Minas Gerais
The culture of strawberry , Fragaria x ananassa Duch, has faced several problems, among which we highlight those caused by pathogens. In addition to widely known diseases such as gray mold, new diseases have caused serious damage to the crop. In order to study the various problems of strawberry culture, this study aimed to: i) identify the causal agent of a postharvest fruit rot in strawberry , ii) to study the temporal and spatial dynamics of the redness in strawberry, whose etiology is still unknown; iii) determine the species of Botrytis that cause gray mold in strawberry in Brazil iv) conduct a survey of the current situation of fungicides for control of gray mold on strawberry v) to study the sensitivity of isolates of B. cinerea to dicarboxamide and benzimidazole fungicides. In order to identify the causal agent of post harvest fruit rot of strawberry, isolates from symptomatic fruits were analyzed by morphologic and phylogenetic analyzes. After confirming the pathogenicity of the isolates, species identification as Neofusicoccum kwambonambiense and N. parvum was taken. This is the first report of the occurrence of Neofusicoccum kwambonambiense in Brazil and the first report of Neofusicoccum spp. causing rot in strawberry. By studying the pattern of temporal and spatial distribution of the redness of strawberry was conducted in four areas of commercial cultivation. With the data on incidence of disease progress curves and dispersion maps were constructed, and analysis of aggregation of plants by ordinary runs test. The results showed that the disease has a similar disease biotic distribution pattern similar to diseases which are dispersed in the row. To achieve other goals, isolates were obtained from plants with symptoms of gray mold on various properties of different cities in the states of Espírito Santo, Minas Gerais and São Paulo, totaling 200 isolates. Initially, a study was conducted to verify the occurrence of other species of Botrytis in the fields of strawberry cultivation in Brazil. For this, the extraction of DNA from all strains was performed, followed by PCR with the specific species and B. cinerea and B. caroliniana primers. Despite the morphological variation observed among isolates , all were identified as B. cinerea . The survey on the practices used to control gray mold on strawberry was performed directly with the producers, who were asked about the products used for the control of disease, efficiency of these products and use of the practice of removing diseased material . It was possible to observe many problems, especially reduced use of cultural control measures, the use of products not recommended for culture and the low level of knowledge of the farmers. Finally, the sensitivity analysis of the isolated main culture fungicides (iprodione , procymidone and thiophanate- methyl) was carried. Thus, a total of 100 isolates were grown in culture medium containing different doses of the fungicide was used. The results showed that 89% of isolates were insensitive to thiophanate-methyl fungicide, 36% to and 54% to procymidone. Considering the limited number of fungicides registered for the control of gray mold and the low sensitivity of isolates of B. cinerea to these products , it becomes difficult to manage this important disease of strawberry.
A cultura do morangueiro, Fragaria x ananassa Duch, tem enfrentado diversos problemas, dentre os quais destacam-se os causados por patógenos. Além de doenças amplamente conhecidas, como o mofo cinzento, novas doenças vêm causando sérios danos à cultura. Visando estudar os diversos problemas da cultura do morangueiro, este trabalho teve por objetivos: i) identificar o agente causal de uma podridão pós-colheita em frutos de morango; ii) estudar a dinâmica temporal e espacial do vermelhão do morangueiro, cuja etiologia é ainda desconhecida; iii) determinar as espécies de Botrytis que causam mofo cinzento em morangueiro no Brasil; iv) realizar um levantamento da situação atual do uso de fungicidas para controle do mofo cinzento do morangueiro; v) estudar a sensibilidade de isolados de B. cinerea aos fungicidas dicarboxamidas e benzimidazóis. A fim de identificar o agente causal da podridão pós-colheita de frutos de morango, isolados obtidos a partir de frutos sintomáticos foram analisados por meio de análises morfológicas e filogenéticas. Após a confirmação da patogenicidade dos isolados, foi feita a identificação das espécies como Neofusicoccum kwambonambiense e N. parvum. Este é o primeiro relato da ocorrência de Neofusicoccum kwambonambiense no Brasil e o primeiro relato de Neofusicoccum spp. causando podridão em morango. O estudo do padrão de distribuição temporal e espacial do vermelhão do morangueiro foi realizado em quatro áreas de cultivo comercial. Com os dados de incidência da doença foram construídas curvas de progresso e mapas de dispersão, além da análise de agregação de plantas pelo teste de ordinário runs. Os resultados mostraram que a doença apresenta comportamento semelhante a uma doença biótica com padrão de distribuição semelhante ao de doenças que se dispersam na linha de plantio. Para atingir os demais objetivos, foram obtidos isolados a partir de plantas com sintomas do mofo cinzento, em diversas propriedades de diferentes cidades nos estados do Espírito Santo, Minas Gerais e São Paulo, totalizando 200 isolados. Inicialmente, foi realizado um estudo para verificar a ocorrência de outra espécie de Botrytis nos campos de cultivo de morango no Brasil. Para isso, foi feita a extração de DNA de todos os isolados, seguindo-se à reação de PCR com primers específicos para as espécies B. cinerea e B. caroliniana. Apesar da variação morfológica observada entre os isolados, todos foram identificados como B. cinerea. O levantamento sobre as práticas utilizadas para controle do mofo cinzento do morangueiro foi realizado diretamente com os produtores, que foram questionados quanto aos produtos utilizados para o controle da doença, eficiência de controle dos produtos e uso da prática de retirada de material doente. Foi possível observar diversos problemas, destacando-se o reduzido uso de medidas de controle cultural, o uso de produtos não recomendados para a cultura e o baixo nível de conhecimento dos produtores. Por fim, foi realizada a análise de sensibilidade dos isolados aos principais fungicidas utilizados na cultura (iprodiona, procimidona e tiofanato-metílico). Para isso, foi utilizado um total de 100 isolados, os quais foram crescidos em meio de cultura contendo diferentes doses dos fungicidas. Os resultados mostraram que 89% dos isolados foram insensíveis ao fungicida tiofanato-metílico, 36% ao iprodiona e 54% ao procimidona. Considerando o número restrito de fungicidas registrados para o controle do mofo cinzento e a baixa sensibilidade dos isolados de B. cinerea a estes produtos, torna-se difícil o manejo dessa importante doença do morangueiro.

Characteristics of quantitative resistance in pea (Pisum sativum L.) to Erysiphe pisi DC, the pathogen causing powdery mildew, were investigated. Cultivars and seedlines of pea expressing quantitative resistance to E. pisi were identified and evaluated, by measuring the amounts of pathogen present on plant surfaces in field and glasshouse experiments. Disease severity on cv. Quantum was intermediate when compared with that on cv. Bolero (susceptible) and cv. Resal (resistant) in a field experiment. In glasshouse experiments, two groups of cultivars, one with a high degree of resistance and the other with nil to low degrees of resistance to E. pisi, were identified. This indicated either that a different mechanism of resistance applied in the two groups, or that there has been no previous selection for intermediate resistance. Several other cultivars expressing quantitative resistance were identified in a field experiment. Quantitative resistance in Quantum did not affect germination of E. pisi conidia, but reduced infection efficiency of conidia on this cultivar compared with cv. Pania (susceptible). Other epidemiological characteristics of quantitative resistance expression in Quantum relative to Pania were a 33% reduction in total conidium production and a 16% increase in time to maximum daily conidium production, both expressed on a colony area basis. In Bolero, the total conidium production was reduced relative to Pania, but the time to maximum spore production on a colony area basis was shorter. There were no differences between the cultivars in pathogen colony size or numbers of haustoria produced by the pathogen. Electron microscope studies suggested that haustoria in Quantum plants were smaller and less lobed than those in Pania plants and the surface area to volume ratios of the lobes and haustorial bodies were larger in Pania than in Quantum. The progress in time and spread in space of E. pisi was measured in field plots of cultivars Quantum, Pania and Bolero as disease severity (proportion of leaf area infected). Division of leaves (nodes) into three different age groups (young, medium, old) was necessary because of large variability in disease severity within plants. Disease severity on leaves at young nodes was less than 4% until the final assessment at 35 days after inoculation (dai). Exponential disease progress curves were fitted for leaves at medium nodes. Mean disease severity on medium nodes 12 dai was greatest (P<0.001) on Bolero and Pania (9.3 and 6.8% of leaf area infected respectively), and least on Quantum (1.6%). The mean disease relative growth rate was greatest (P<0.001) for Quantum, but was delayed compared to Pania and Bolero. Gompertz growth curves were fitted to disease progress data for leaves at old nodes. The asymptote was 78.2% of leaf area infected on Quantum, significantly lower (P<0.001) than on Bolero or Pania, which reached 100%. The point of inflection on Quantum occurred 22.8 dai, later (P<0.001) than on Pania (18.8 dai) and Bolero (18.3 dai), and the mean disease severity at the point of inflection was 28.8% for Quantum, less (P<0.00l) than on Pania (38.9%) or Bolero (38.5%). The average daily rates of increase in disease severity did not differ between the cultivars. Disease progress on Quantum was delayed compared with Pania and Bolero. Disease gradients from inoculum foci to 12 m were detected at early stages of the epidemic but the effects of background inoculum and the rate of disease progress were greater than the focus effect. Gradients flattened with time as the disease epidemic intensified, which was evident from the large isopathic rates (between 2.2 and 4.0 m d⁻¹) Some epidemiological variables expressed in controlled environments (low infection efficiency, low maximum daily spore production and long time to maximum spore production) that characterised quantitative resistance in Quantum were correlated with disease progress and spread in the field. These findings could be utilised in pea breeding programmes to identify parent lines from which quantitatively resistant progeny could be selected.

Commercial AM fungi isolates, Rhizophagus clarus, Gigaspora gigantea, Funneliformis mosseae, Claroideoglomus etunicatum and Paraglomus occulum were tested on four seasonal ornamentals, Dianthus chinensis x barbatus, Impatiens wallerana, Petunia x hybrid and Viola x wittrockiana planted in peat-base medium. The experiment was conducted in a glasshouse with three replicates in a completely randomised design. Various vegetative (height, width, length, number of leaves, leaf area and dry biomass) and reproductive (number of flowers and buds) plant parts were measured in the course of three months. AM fungi was found to increase seedling growth and reduced seedling mortality rate of all the plants studied. Inoculated plants produced more leaves (16-33%) and grew taller (12-28%). Dry biomass of inoculated Dianthus, Impatiens and Viola plants were significantly increased by 25-53%. All plants under low colonisation rates displayed mycotrophic qualities and net growth output thereof were found to be similar to plants with equal or higher colonisation rate. Mortality were less frequent in inoculated plants and they were also less susceptible to transplant shock.
Agriculture, Animal Health and Human Ecology
M. Sc. (Ornamental Horticulture)

Plants regulate responses to their environment through complex hormone signaling; these hormones can be categorized broadly into two categories: growth and defense, though many have roles in both. Much remains to be understood about the complexity of hormone signaling in relation to environmental responses, especially species- and genotype-specific differences. Unraveling this complexity of hormone signaling will lead to the development of resilient crops that are able to respond appropriately to their environment. In this dissertation, I hypothesize novel roles for growth and defense hormones in Solanum spp. responses to 1) biochar, a black carbon soil amendment (Chapter 2), 2) infection with Ralstonia solanacearum, an economically important soilborne pathogen causing bacterial wilt (Chapter 3), and 3) endophytic colonization by the soil bacterial community (Chapter 4). In Chapter 2, I showed that biochar upregulates GA signaling and affects GA-related traits in a species- and cultivar-specific manner. Biochar amendment also downregulates defense signaling. In Chapter 3, I demonstrated a novel role for auxin in resistance against R. solanacearum, including differential expression of auxin signaling genes in resistant genotype H7996 compared to susceptible WV in response to R. solanacearum infection. In addition, I observed stronger and faster upregulation of defense hormone marker genes for SA and ET in H7996 compared to WV. In Chapter 4, I showed that SA and ET are required for normal tomato root microbial community assembly, affecting the colonization of a few key taxa in order to promote alpha diversity. H7996 and WV root communities differ in alpha diversity, and a panel of H7996 x WV RILs showed quantitative variation in alpha diversity that correlated negatively with the abundance of these key taxa. In conclusion, I elucidated novel roles for hormones in responses to the soil environment, pathogen infection, and root community colonization. These findings are important for developing resilient, sustainable crops.

Root disease is a serious concern for the softwood timber industry. This thesis reports on the development of a root disease detection procedure that applies lidar data integrated with imaging spectrometer data. Photosynthetic pigments are frequently cited as one of the most responsive indicators of vegetation stress. This study estimated pigment content from needle and canopy reflectance and characterized the sensitivity of these pigments to a fungal-mediated stress. Samples were collected from the Greater Victoria Watershed District on Vancouver Island, BC, Canada. Lab reflectance measurements were made and pigments were extracted. Reflectance spectra were transformed into derivative spectra and a continuum removal band depth analysis was conducted. Reflectance metrics were generated and used in modeling pigment content. Chlorophyll-a was found to be significantly affected by the disease in the needle level portion of this study. The predictive power of reflectance attributes were assessed and yielded strong coefficients of determination (R2>0.80). Samples exhibiting stress responses affected by root disease were discriminated. It was determined that younger trees were more severely affected by the root pathogen than mature colonized trees. In the canopy level component of the study, chlorophyll-a was estimated through the application of partial least squares regression and achieved an R2 value of 0.82. Continuum removal metrics, which proved to be good estimators at the needle level, were found to be insufficient at the canopy level. Through the use of hyperspectral forest chemistry products, potential root disease sites can be identified.
Graduate

Potato leafroll virus (PLRV) is one of the most destructive potato viruses in South Africa. In order to establish resistance against PLRV in commercial potato cultivars, the coat protein (CP) gene of the virus was previously isolated, cloned and subcloned into the plant expression vector pBI121 in both the sense and antisense orientations (BURGER, unpublished results). The pBI121 constructs containing the PLRV-CP gene were subsequently transferred to Agrobacterium tumefaciens LBA 4404 in a triparental mating process with the helper plasmid pRK2013. Two A. tumefaciens- mediated transformation methods for potatoes were investigated, viz. vacuum infiltration and leaf disk transformation. In addition, optimal transformation and regeneration conditions were identified for potato cultivars Late Harvest and BP[1] In total, 27 transgenic potato lines containing the PLRV-CP, β-glucoronidase (GUS) and nptII (neomycin phosphotransferase II) trans genes were generated under kanamycin selection. Transgenic plants grown in the glasshouse appeared to be phenotypically normal, and no differences in ploidy level in comparison to non-transformed plants could be established. Stable transgene insertion into the genome of the transgenic plants was verified using PCR and Southern blot analysis. Expression of the GUS transgene was investigated using a fluorometric assay (JEFFERSON et al. 1987), and it was found that orientation of the inserted PLRV-CP gene upstream from the GUS gene had a direct influence on the levels of GUS expression. The expression of the PLRV-CP gene was analysed using DAS-ELISA and immunoblot detection. Coat protein could not be detected in either assay. RNA dot blots were used successfully to show PLRV-CP expression in transgenic potato plants at the mRNA level.
Thesis (M.Sc.)-University of Natal, Pietermaritzburg, 1995.

Kelpak®, a seaweed concentrate (SWC) prepared from the brown seaweed Ecklonia maxima (Osbeck) Papenfuss, improves overall plant mass and fruit yield in a variety of crops. The main active principals isolated from Kelpak® are cytokinins and auxins. Although these compounds are partly responsible for the growth promoting effect observed with Kelpak® application, they do not fully account for the complete effect of Kelpak® treatment. For this reason the focus has turned to polyamines (PAs) which are found in all cells of plants, animals and microorganisms, including eukaryotic algae. Polyamines also have growth promoting effects in plants. A study was carried out to investigate the PA levels in E. maxima and Kelpak® through a biennial cycle and to investigate if the PAs present in Kelpak® may have an effect on root growth, alleviating nutrient deficiency and the transport and accumulation of PAs in plants. To determine the amount of PA in the stipes, fronds and SWC prepared from E. maxima, samples were collected monthly over a two-year period (June 2009-June 2011). Extracts were benzoylated and quantified using a Varian HPLC. Putrescine concentrations ranged from 15.98-54.46 μg.g⁻¹, 6.01-40.46 μg.g⁻¹ and 50.66-220.49 μg.g⁻¹ DW in the stipe, fronds and SWC, respectively. Spermine concentrations ranged from 1.02-35.44 μg.g⁻¹, 1.05-26.92 μg.g⁻¹ and 7.28-118.52 μg.g⁻¹ DW in the stipe, fronds and SWC, respectively. Spermidine concentrations fell below the detection threshold. This is the first report of PAs being detected in a SWC. The seasonal pattern established for the stipe, frond and SWC followed the same trend over a biennial cycle. Polyamines accumulated in the seaweed tissue during periods of active growth and as a stress response elicited by rough wave action. This PA trend was similar to the cytokinin trend reported by MOONEY and VAN STADEN (1984b) for Sargassum heterophyllum which suggests that PAs play an important role in the hormone cascade during active growth. Routine monthly screening of Kelpak® carried out in the Research Centre for Plant Growth and Development indicated that Kelpak® consistently resulted in more rooting in the mung bean bioassay than the IBA control. The potential root promoting effect of PAs were investigated. Individually applied PAs did not increase rooting in the mung bean bioassay, but a synergistic relationship was observed between Put (10⁻³ M) and IBA (10⁻⁴ M). When applied together, rooting increased significantly above Put (10⁻³ M) and IBA (10⁻⁴ M) applied separately. The Put-auxin combination produced a similar number of roots to those treated with Kelpak®. It is possible that the PAs present in Kelpak® have a synergistic effect with auxins present in Kelpak® to promote root development and growth. Several physiological effects of Kelpak® and PAs on plant growth were investigated in a series of pot trials. Kelpak® significantly improved the growth of P- and K-deficient okra seedlings and masked the detrimental effects exerted by P- and K-deficiency. The application of PAs (10⁻⁴ M) significantly improved the seedling vigour index (SVI) of okra seedlings subjected to N-deficiency. The statistical difference was attributed to the N-containing growth regulators and polyamines being degraded and metabolized by the okra seedlings. Polyamine application did not alleviate P- and K-deficiency but increased root growth significantly in seedlings receiving an adequate supply of nutrients. It is likely that the additional PAs supported auxin-mediated root growth. A pot trial with okra plants was conducted to establish if the PAs in Kelpak®, applied as a soil drench or foliar application, are absorbed and translocated in a plant. Plants were also treated with Put, Spm, Spd to establish if PAs can be absorbed and translocated. Once the fruit had matured, plants were harvested and the endogenous PA content quantified by HPLC in the roots, stems and fruits. Applying PAs as a soil drench was not as effective as a foliar spray at increasing the PA content in the different plant parts. Kelpak® treatment (0.4%) did not contribute more PAs in any plant part. Spermidine concentrations were higher, in the various plant parts, than Put or Spm, irrespective of the mode of application. The application of Put, Spd and Spm increased Spd concentrations in the roots. Considering that Spd is the main PA produced in the roots and that exogenously applied PAs are readily converted to Spd, it seems evident that Spd is the preferred PA for long-distance transport in plants. The cytokinins and auxins in Kelpak® play an important role in stimulating growth in plants. It is, however, the totality of different compounds in Kelpak® that gives it its unique growth stimulating ability. Polyamines, occurring within the seaweed contribute to this activity, having an active role in root production and thus increased plant growth.
Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2011.

Meloidogyne javanica is the most widely spread nematode pest on soybean in South Africa. Only a few registered cultivars have some resistance to this nematode and there is an urgent need for an efficient breeding programme for resistant cultivars of all maturity groups. However, breeding is hampered by laborious screening procedures for selection of resistant lines. The objective of this study was to develop an economically viable molecular marker system for application in selection procedures. Three techniques of marker identification were investigated, i.e. RAPD, RFLP and AFLP analysis. The RAPD technique proved to be applicable in fingerprinting soybean varieties, but was too sensitive for interplant variation to be used as an efficient system for identification of molecular markers linked to nematode resistance. Both RFLP and AFLP screening identified markers linked to gall index variation in a segregating population of 60 F₂ progeny from across between a resistant cultivar, Gazelle, and a highly susceptible variety, Prima. A codominant RFLP marker( B212) was linked significantly to resistance and explained 62% of the variation in gall index. Seven AFLP markers were linked significantly to the resistance trait, of which four were linked in repulsion phase and three in coupling phase. All seven AFLP markers mapped to LG-F on the public soybean molecular map. The QTL for resistance mapped between markers E-ACC/M-CTC2 linked in coupling phase, 8212 and E-AAC/M-CAT1, linked in repulsion phase. These two AFLP markers bracketing the major resistance QTL were successfully converted to SCARs. Marker E-ACC/M-CTC2 was converted to a codominant SCAR marker SOJA6, which acounted for 41% of variation in gall index in the mapping population. Marker E-AAC/M-CAT1 was converted to a dominant SCAR marker (SOJA7) and explained 42% of gall index variation in the mapping population. These two markers mapped approximately 3.8 cM and 2.4 cM respectively from the resistance QTL. This study represents the first report of the development of PCR-based sequence specific markers linked to resistance to M. javanica in soybean.
Thesis (Ph.D.)-University of Natal, Pietermaritzburg, 2000.

Five cultivars, all belonging to the family Cucurbitaceae, have been tested for the ability to regenerate shoots or somatic embryos from cotyledonary explants. The influence of several combinations of growth regulators on regeneration from cotyledonary and other explants was tested. No regeneration was obtained from the two cultivars Cucurbita maxima Duch. cv A-Line and Cucurbitapepo L. cv Rolet. Somatic embryos developed on Cucurbita maxima Duch. cv Chicago Waited, a Hubbard squash. A shoot regeneration response was observed for the cultivar Cucumis sativus L. cv Ashley, but the frequency was low and results could not be repeated in subsequent experiments. A reliable shoot regeneration protocol was developed for Cucumis melo L. cv Hales Best 36. The influence of the antibiotics kanamycin sulphate and cefotaxime on shoot regeneration from cotyledonary explants of Cucumis melo L. cv Hales Best 36 was tested. The plasmid pBI121 was transferred from Escherichia coli strain HB101 into Agrobacterium tumefaciens strain LBA4404 via a triparental mating. The plasmid pBI121, contains the screenable marker gene β-glucuronidase (GUS) and the selectable neomycin phosphotransferase-II gene (NPT-II) that confers kanamycin resistance. Cotyledonary tissue was transformed using this Agrobacterium tumefaciens transformation system. The influence of co-cultivation time, inoculation time and the wound factor acetosyringone on transformation was established. Rooted plantlets were regenerated from transformed cotyledonary tissue placed on kanamycin supplemented regeneration media. Plantlets tested positive for the presence of the GUS gene, using fluorometric and histochemical assays. The developed protocol was used to transform Cucumis melo cv Hales best 36 with the pat gene that provides resistance to the herbicide Ignite®. A selection medium was developed containing phosphinothricin, the active ingredient of the herbicide Transformants were selected on this medium and five lines were recovered. These plants were acclimatized and the herbicide resistance was confirmed in greenhouse spray tests. The ploidy level of these plants was deduced from indirect evidence of micro- and macroscopic characteristics that have been shown to have a correlation with the chromosome number of melon plants. The five lines were subjected to molecular analysis. The polymerase chain reaction was used to give an indication of the transformed nature of the selected plants. Agarose gel electrophoresis confirmed that the correct size band could be obtained from the putative transformants and the presence of pat in the product was verified using a non-radioactive system for nucleic acid analysis. Stable gene insertion into the genome of the plant was verified with a Southern blot of the total genomic DNA. This was achieved by hybridising a radioactively labelled ³²P probe specific for the pat gene to a blot of restriction digested plant DNA.
Thesis (Ph.D.)-University of Natal, Pietermaritzburg, 1998.

Attempts were made to grow Fergusobia nematodes in a dual aseptic culture with Eucalyptus camaldulensis. Callus tissue was grown from E. camaldulensis stem pieces in aseptic conditions. Calli were prone to deterioration after 14 days unless transferred to fresh growth medium. Lower levels of solutes (25% Murashige and Skoog salts, 25% plant vitamins and 0.5% sucrose) were more successful than published concentrations. Fergusobia J2 nematodes were surface sterilised with either Hibitane or washed with water to prepare them for inoculation of callus (Hay, 1994). Fergusobia subsequently recovered from plates of callus were all dead, which raised questions of how the nematodes are suited to Murashige and Skoog salt solutions. The survival of Fergusobia in aqueous solutions was then observed. It has been assumed that Fergusobia live about 2 days after dissection. Amphimictic nematodes from E. camaldulensis axial bud galls were used for a survival study. Nematodes lived for as long as 12 days in fresh tap water and 11 days in 1% M.S. solution. They were more active in tap water than in 1% M.S. solution. Nematodes in a dish together with dissected gall material died within 2 days. Nematodes in a separate dish with fresh tap water and clean gall fibres were observed to gather around the fibres. Observations of Fergusobia could be made within fresh solutions providing deteriorating gall tissues were removed from the dish. Gall production was attempted on E. camaldulensis grown in the glasshouse. These tree saplings were pruned to encourage new growth and periodically treated for infestations of scale insects leading to growth of sooty mould. Two forms of cage construction were used: (1) 1 m ³ screened cages and (2) acetate sleeves as used by Goolsby et al., 2000. Within the 1 m ³ cages containing flies, the growing points on saplings were blackened, possibly due to over-exploitation by ovipositing flies. One growing point caged in an acetate sleeve showed oviposition scars but did not produce a mature gall. Production of galls in the glasshouse was hindered by a lack in coincidence of flies emerging from mature galls and the flush of new growth following pruning. The production of galls within the glasshouse was not achieved. The phenology of E. camaldulensis, a host for the Fergusonina/Fergusobia mutualism, and gall ecology were observed in a two-year, non-destructive, field study in the Urrbrae Wetlands, Adelaide, South Australia. Tree growth and gall development was observed in the lower regions (0 – 2 m) of young trees. Three bud forms, terminal leaf bud, axial leaf bud and flower bud galls were monitored on the trees. The densities of galls were highly seasonal. Greatest density of growing points, axial leaf bud and flower bud galls occurred mostly during mid-winter to spring, whereas that of terminal leaf bud galls occurred during mid-spring to summer. Galling of flower buds did not appear to influence flowering and more flower buds and flowers occurred in the second year of the study as the trees matured. Trees mostly had medium (30-70%) levels of leaf damage, but there were seasonal trends in damage levels. Low scores for leaf damage were associated with increases in flower bud and flower production. Leaf damage, including sooty mould, appeared to increase during the cooler winter months. There were no significant seasonal relationships between levels of leaf damage and either growing point density or the occurrence of galls. When trees were compared with each other, those with lower leaf damage were more likely to have more growing points. The appearance of the canopy and the likelihood of a tree to have galls varied greatly between the trees. One tree was particularly susceptible to leaf attack, rarely had new leaves and produced no mature galls during the study. The colouring of leaves varied between trees, which indicates possible genetic variations causing some trees to be more likely hosts for Fergusonina/Fergusobia. Both new vegetative growth and terminal leaf bud galls were concentrated on the northern and eastern quadrants. Axial leaf bud and flower bud galls occurred more on the western or southern quadrants where they were possibly more protected from sun exposure on the northern or eastern quadrants. Axial galls on the northern side of one tree became reddened while those in the southern and western quadrants remained green. Reddening of axial galls may increase their likelihood of parasitism and predation by birds. Each of the three gall forms occurred within certain positions in the canopy. The tree host resource is partitioned effectively, with the three gall forms occurring on three different host structures. Additionally, the two vegetative forms terminal leaf bud and axial leaf bud galls occur on different shoot regions and in different seasons. The numbers of the galls is probably also affected by biotic and climatic influences. Parasitism, plant canopy shading, nutrient levels and host genetics are possible influences. Assuming an interval of 4 weeks between oviposition and first observation within the current study, terminal leaf bud galls had an average longevity of 11 weeks and axial leaf bud galls an average longevity of 14 weeks. Flower bud galls had longevities of 14 to 27 weeks from oviposition to senescence, assuming an interval of 6 weeks between oviposition and first observation within the current study. Flowers and flower buds occur irregularly within the eucalypts so it would be advantageous for flies and nematodes developing within flower bud galls to have extended or variable longevities to allow fly emergences to coincide with new flower buds. Not all of the galls recorded matured to produce adult flies. Nearly half of the terminal leaf bud galls initiated were aborted, recorded as absent, parasitised or eaten (45% of initiated galls). Of the three gall forms, they were the most prone to obvious parasitism and as many as 12 hymenopteran species have been reared from terminal leaf bud galls on E. camaldulensis (Taylor et al., 1996). These galls obviously provide a resource for many species within multiple trophic levels. Fourteen percent of axial leaf bud galls were absent or eaten and birds were seen breaking off and feeding on the galls. More than half (55%) of the initiated flower bud galls disappeared during the period of observation, possibly due to the foraging of birds. Destructive sampling and rearing out of parasitoids from both axial leaf bud and flower bud gall forms is needed to establish what species exist within them. Terminal leaf bud galls ranged from 7.5 to 30.1 mm in diameter and 10.0 to 43.6 mm in length. Flower bud gall size varied, with the largest being 15.0 mm by 22.3 mm. Axial leaf bud galls, ranged from 2.6 to 13.0 mm in diameter and length ranged from 2.3 to 10.5 mm. The larger axial leaf bud galls were nodular and appeared to have multiple locules. Destructive sampling and rearing out of flies is needed to establish the relationship between size and numbers of flies emerging. Terminal leaf bud galls increased in size, including many locules and exit holes per gall. Axial leaf bud galls were much smaller than the terminal leaf bud galls and 99% had only one to three exit holes. The rounded shape and presence of few locules within the axial leaf bud galls indicate that this form is limited to a shape and size producing few flies. The observation of greater size of terminal leaf bud galls suggests that these galls may have multiple foundresses. Twelve of the 13 flower bud galls with exit holes had either one or two holes. In flower bud galls on E. camaldulensis. the operculum remains sealed and the characteristic Fergusonina “window” appears at the side of the flower bud before fly emergence through a single hole. Destructive sampling is also necessary to determine parasitism of each of the gall forms.
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Thesis (M.Sc.) -- University of Adelaide, School of Agriculture, Food and Wine, 2008

Aphids are a widespread family of plant pests, whose abilities to suppress shoot and root growth are well documented for many terrestrial plants. Only a few studies have been conducted on conifer aphids of the genus Cinara. Cinara pseudotsugae are known to attack Douglas-fir seedlings, an important crop in the Pacific Northwest. Douglas-fir are most susceptible to aphid damage as seedlings, especially in nurseries where conditions favor aphid outbreaks. A parasitoid wasp (Pauesia sp.) attacks C. pseudotsugae, and may be useful as a biological control agent. Studies of its natural history and host interactions are needed to assess its potential as a bio-control agent. This study examined the effects of an experimental range of aphid densities on the growth of total shoot and root volume and biomass and shoot morphology of Douglas-fir seedlings. Eighteen-week tests explored short term effects of different aphid feeding intensities in both the greenhouse and field. Long term effects were tested by exposing greenhouse seedlings to 16 months of aphid feeding. The ability of the plants to recover was tested by allowing one set of seedlings to grow aphid free for one year, after being exposed to aphid feeding for 18 weeks. The success rate of parasitoids over an 18 week period was compared to aphid density in both greenhouse and field tests. Increasing aphid destiny was significantly related to decreasing root and shoot dry weights in greenhouse tests. Growth suppression increased slightly during the second year of testing, regardless of whether or not aphid feeding continued. The results for root and shoot volumes were highly variable. However, root tissue density was significantly reduced after the second year of testing. Few shoot characteristics showed consistently significant aphid effects among the trials. Stem diameter and height decreased and needle density of new buds increased significantly with aphid feeding in most tests. Root and shoot growth of field plants did not show any significant aphid effects. Percentage of parasitoid success was independent of aphid density except at the lowest aphid densities. There was a block effect on parasitoid success in the field test, that may have been a result of varying environmental conditions. These results indicate that even short term aphid feeding can have long lasting effects on plant growth and structure. The effect on shoot and root growth was small, but there were no signs of recovery. The long term effects of the reduced root tissue density on Douglas-fir is unknown.
Graduation date: 1998

Content removed due to copyright restrictions: Taylor, C. H., & Long, P. G. (2000). Review of literature on camellia flower blight caused by ciborinia camelliae. New Zealand Journal of Crop and Horticultural Science, 28(2), 123-138.
Camellias are popular ornamental plants and the most serious pathogen of this plant is camellia flower blight, caused by the fungal pathogen Ciborinia camelliae Kohn. Ascospores of this fungus attack the flowers, turning them brown, rendering infected flowers unattractive. Little is known about the pathogen and control measures are not particularly effective. In this thesis, various aspects of the pathogen's basic and molecular biology and interaction with host species were studied. Surveys of the distribution and spread of C. camelliae within New Zealand determined that the pathogen was present in most regions of the North Island, and north and east coasts of the South Island. Over the distances and time involved, it appeared that the disease was spreading mainly by windborne ascospores rather than human transfer. Sclerotia were germinated out of season to increase the period during which ascospores were available for infection work. Greatest germination was achieved at low temperatures (5°C-10°C) in 24 h darkness. Isolate-specific primers were designed to the ribosomal DNA Internal Transcribed Spacer region to detect the pathogen in planta and distinguish between New Zealand isolates of C. camelliae and other fungal pathogens. Phylogenetic analysis of the ITS region with other Ciborinia, Sclerotinia and Botrytis species showed that C. camelliae was more closely related to S. sclerotiorum than other Ciborinia species. Two inoculation techniques for infecting Camellia petals with ascospores of C. camelliae were developed and tested. Inoculation using airborne ascospores in a settling chamber was a simple and quick method for testing large numbers of species for resistance. Inoculation of ascospores in suspension produced qualitative data, but was more time consuming. Of the four mechanisms of resistance tested, levels of aluminium hyperaccumulation and the presence of phenolic compounds did not correlate with resistance in Camellia species. The large uptake of aluminium, however, did indicate that Camellia species would be good plants for phytoremediation of acid soils. Some resistant species were found to have cell wall modifications and/or lignification of cell walls in response to C. camelliae infection and chitinase activity was found in most resistant Camellia species tested. Further research into these latter two mechanisms is recommended and indicates that the development of resistant Camellia cultivars is possible.

Control of weeds that have survived a postemergence (POST) herbicide often need to be controlled in order to prevent seed production and interference with crops. The most efficacious herbicides and timings used for respray applications has not been determined in many problematic weed species. Previous research has demonstrated that weeds clipped to simulate a failed herbicide application responded differently to herbicide applications to regrowth based on herbicide used and weed species. Other research is conflicting as to the optimum timing of an herbicide respray application with various herbicides. Gaining a better understanding of how to maximize respray herbicide performance will help growers and land managers to preserve crop yield and prevent weed seed production in the event of POST contact herbicide failure. The objectives of this research were to determine the optimum respray herbicide and timing combinations for control of four problematic weed species in the midwestern United States that have survived an application of either glufosinate or fomesafen: waterhemp [Amaranthus tuberculatus (Moq.) J. D. Sauer], Palmer amaranth (Amaranthus palmeri S. Watts), giant ragweed (Ambrosia trifida L.), and horseweed (Erigeron canadensis L). Through a series of field and greenhouse experiments we determined that respray herbicide, respray application timing, initial herbicide, and level of injury from the initial application influence efficacy of the respray herbicide in a species-specific manner. Waterhemp regrowth following a failed glufosinate application was controlled most effectively by applying glufosinate or fomesafen 7 to 11 days after initial treatment. When following fomesafen, applications of 2,4-D 3-7 days after initial treatment or glufosinate 7 to11 days after initial treatment were most effective. Control of Palmer amaranth regrowth following either initial herbicide is best achieved with respray applications of glufosinate, fomesafen, or 2,4-D applied no later than 7 days after initial treatment. The best strategy to control giant ragweed regrowth following a failed fomesafen applications is to apply 2,4-D, dicamba, fomesafen, or glufosinate at any timing between 3 and 11 days after initial treatment. Efficacy of the respray glufosinate application was maximized when applied 11 days after the initial application rather than 3 days after initial application. Horseweed regrowth was best controlled by 2,4-D, dicamba, or glufosinate applied at any timing between 3 and 11 days after the initial application. Where injury from the initial herbicide application is high, there were fewer differences among herbicide treatments and treatment timings. A greenhouse bioassay revealed that as waterhemp injury from an initial glufosinate application increases, control with a respray herbicide also increases. Therefore, complete control of weed regrowth is achieved more easily with increasing injury from the initial application. This research suggests that timing of herbicide respray applications is more urgent than previously thought, so scouting must be done within days of a contact herbicide application to ensure adequate control.

Root rot diseases of bean (Phaseolus vulgaris L.) are a problem wherever they are grown, and are a major constraint to dry edible and snap bean production. Root rot is a primary yield limitation of snap bean production in the US, especially within the top three snap bean producing states of Wisconsin, Oregon and New York. Bean root rot pathogens will be present by the end of the first season even when starting with clean ground. The decline in yield can be relatively slow, so growers might not notice or appreciate the hidden yield cost associated with root rot disease. Traditional methods for disease control such as fungicides, crop rotations, cover crops, seedbed preparations have been proven ineffective (either physically ineffective or economically unviable) against root rot. Therefore, genetic resistance is needed. In order to address the need for genetic resistance to root rot in snap beans, the highly root rot resistant line RR6950, a small seeded black indeterminate type IIIA accession of unknown origin, was crossed with OSU5446, a highly root rot susceptible determinate type I blue lake four-sieve breeding line to produce the RR138 recombinant inbred mapping population. In this study we evaluated the RR138 RI population in the F₆ generation for resistance to Fusarium solani root rot in Oregon and Aphanomyces euteiches root rot in Wisconsin. We also evaluated this population for morphological traits and root structural traits including pod height, pod width, pod length, pod wall thickness, strings, seed color, flower color, tap and basal root diameter, and root angle measurements. The RR138 population was also genotyped on the 10K BeanCAP Illumina Beadchip. The Single Nucleotide Polymorphism (SNP) data was used to assemble a high-density linkage map and Quantitative Trait Loci (QTL) for phenotypic data were evaluated. The linkage map produced from this study contained 1,689 SNPs across 1,196cM. The map was populated with 1 SNP for every 1.4cM, spanning across 11 linkage groups. Three QTL associated with A. euteiches root rot resistance were consistently expressed in 2011 and 2012 trials. A. euteiches QTL were found on Pv02, Pv04, and Pv06 and accounted for 7-17% of total genetic variation. Two QTL associated with F. solani were found in 2011 trial on Pv03 and Pv07, account for 9 and 22% of total genetic variation, respectively. We also found several QTL for morphological traits and root structural traits including QTL for pod fiber and pod height on Pv04, pod length on Pv01, strings on Pv01, taproot diameter on Pv05, and shallow basal root angle on Pv05, accounting for 21, 26, 12, 20, 11, and 19% of total genetic variation, respectively. QTL discovered from Oregon data for F. solani resistance did not cluster with QTL for A. euteiches root rot resistance. "SNP0928_7", was highly associated with F. solani resistance on Pv07 and "SNP0508_2", was highly associated with A. euteiches on Pv02. QTL and markers associated with QTL from this study will be of value to snap bean breeders developing root rot resistant lines with processing traits, and provide more information about targeting the mechanism of resistance.
Graduation date: 2013