Interactions between nematodes, potato and soil-borne micro-organisms and their effect on the management of potato cyst nematodes

Potato cyst nematodes (PCN) cause significant damage to the potato crop worldwide and growers experience economic losses related to yield loss and the cost of control measures. Experiments were set up to further elucidate the complex tritrophic PCNpotato-soil bacteria relationship. Bacterial strains isolated from the sugar beet rhizosphere were shown to be hatch active towards Globodera pallida and to be capable of successfully colonising the sugar beet rhizosphere when applied exogenously. A trap-crop system, based on these isolates, was proposed. Ridge and bulk soil taken from a commercial potato field were incubated with sterile potato root leachate (sPRL) and subsequent in vitro hatching assays showed that PCN hatch was influenced by microorganisms present in the ridge, but not in the bulk soil. Community level physiological profiling (CLPP) of ridge and bulk soil, using BIOLOG EcoplatesTM, demonstrated differences in bacterial functional diversity between the two soil types. An investigation of the inter-species competition between G. pallida and G. rostochiensis showed that G. pallida performed significantly better, in terms of multiplication rate, in competition with G. rostochiensis compared to its multiplication rate in single-species populations. Effectively removing the early hatch of G. rostochiensis in pot trials led to the removal of this competitive advantage of G. pallida suggesting that this advantage was due, at least in part, to morphological changes to the root caused by the early hatching of G. rostochiensis.

Electron beam lithography assisted high-resolution pattern generation

This thesis details the top-down fabrication of nanostructures on Si and Ge substrates by electron beam lithography (EBL). Various polymeric resist materials were used to create nanopatterns by EBL and Chapter 1 discusses the development characteristics of these resists. Chapter 3 describes the processing parameters, resolution and topographical and structural changes of a new EBL resist known as ‘SML’. A comparison between SML and the standard resists PMMA and ZEP520A was undertaken to determine the suitability of SML as an EBL resist. It was established that SML is capable of high-resolution patterning and showed good pattern transfer capabilities. Germanium is a desirable material for use in microelectronic applications due to a number of superior qualities over silicon. EBL patterning of Ge with high-resolution hydrogen silsesquioxane (HSQ) resist is however difficult due to the presence of native surface oxides. Thus, to combat this problem a new technique for passivating Ge surfaces prior to EBL processes is detailed in Chapter 4. The surface passivation was carried out using simple acids like citric acid and acetic acid. The acids were gentle on the surface and enabled the formation of high-resolution arrays of Ge nanowires using HSQ resist. Chapter 5 details the directed self-assembly (DSA) of block copolymers (BCPs) on EBL patterned Si and, for the very first time, Ge surfaces. DSA of BCPs on template substrates is a promising technology for high volume and cost effective nanofabrication. The BCP employed for this study was poly (styrene-b-ethylene oxide) and the substrates were pre-defined by HSQ templates produced by EBL. The DSA technique resulted into pattern rectification (ordering in BCP) and in pattern multiplication within smaller areas.

Interspecific competition between the potato cyst nematode species Globodera pallida and G. rostochiensis

The two potato cyst nematode species, Globodera pallida and G. rostochiensis, are among the most important pests of potato. PCN are difficult to manage, while the two species respond differently to the main control methods. An increase in the incidence of G. pallida had been reported and is generally attributed to greater effectiveness of control measures against G. rostochiensis. The status of PCN in Ireland was studied using PCR. The results demonstrated qPCR to be an efficient means of high-throughput PCN sampling, being able to accurately identify both species in mixed-species populations. Species discrimination using qPCR revealed an increase in the incidence of G. pallida in Ireland in the absence of G. pallida-selective control measures. The population dynamics of G. pallida and G. rostochiensis in Ireland were studied in mixed- and single-species competition assays in vivo. G. pallida proved to be the more successful species, with greater multiplication in mixed- than single-species populations, with G. rostochiensis showing the opposite. This effect was similarly observed in staggered inoculation trials and population proportion trials. It was hypothesised that the greater G. pallida competitiveness could be attributed to its later hatch. G. pallida exhibited a later peak in hatching activity and more prolonged hatch, relative to G. rostochiensis. G. rostochiensis hatch was significantly reduced in mixedspecies hatching assays. G. pallida hatch was significantly higher when hatch was induced in potato root leachates containing G. rostochiensis-specific compounds, indicating that G. pallida hatch is stimulated upon perception of G. rostochiensis–derived compounds. Rhizotron studies revealed that root damage, caused by feeding of the early-hatching G. rostochiensis, resulted in increased lateral root proliferation and significantly increased G. pallida multiplication. Split-root trials indicated a significant G. pallida-induced ISR effect. G. rostochiensis multiplication was significantly reduced in split-root rhizotrons when G. pallida colonised roots before or after G. rostochiensis infection.