Factors affecting arbuscular mycorrhizal colonisation (AMF) in grapevines : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University

Abstract

In New Zealand, the wine industry constitutes 29% of its total horticultural exports and is the second largest horticultural export commodity. Increasing sustainability and reducing the environmental impacts are key drivers for the New Zealand wine industry. To achieve this, part of the focus should be on integrating sustainable strategies to optimise services from beneficial microbes, such as arbuscular mycorrhizal fungi (AMF), to improve grapevine health and production. Due to difficulties in culturing and identifying AMF little is known about the AMF communities associated with grapevines in New Zealand. Further, there is a significant gap in knowledge regarding the potential effect of vineyard management practices on these communities and hence the resilience of the ecosystem services they provide. For these reasons, the goal of this project was to i) identify the AMF communities associated with grapevines in New Zealand and the effect of abiotic and biotic factors on these communities, ii) determine the beneficial impact of these communities on grapevine growth and health, and iii) determine the effect of vineyard management practices on these communities. Denaturing gradient gel electrophoresis (DGGE) and trap cultures were used to characterise the AMF communities colonising different grapevine rootstocks. Root materials from three vineyards were analysed by DGGE and used in trap cultures for AMF recovery. This is the first study to identify the AMF community associated with grapevine in New Zealand and trap cultures allowed the recovery of six AMF spore morphotypes that belonged to Ambispora sp., Funneliformis sp., Glomus sp. and Claroideoglomus sp. Fifty-four of the eighty sequenced DGGE bands from root samples were AMF. The aligned sequences were assigned to Glomus spp., Rhizophagus spp. and Claroideoglomus spp. The two complementary techniques (DGGE and trap culture) also showed that the rootstock cultivar was the main driver of the arbuscular mycorrhizal community colonising the roots, therefore a rootstock can select a particular AMF community to form a mutualism with, from the diverse community present at a site. Site soil factors such as soil type, pH, soil moisture, soil organic matter, carbon and nitrogen content also had a significant (p < 0.05) effect on the AMF community, probably since these factors affect the community present in the soil at that particular vineyard which are then available for a rootstock to form a symbiosis with. This study is the first to investigate the effect of ‘home’ and ‘away’ AMF communities on grapevine rootstock growth parameters using whole communities as inoculum. The findings revealed that overall a grapevine rootstock cultivar grew better with the AMF community selected by that particular rootstock than when it is grown with the AMF community of another rootstock cultivar. This indicated that the rootstock selects an AMF community which is more beneficial to its growth and this is probably related to improved nutrient uptake. This study also showed that AMF spore diversity and the relative abundance of certain species is an important factor as when present in equal abundance competition between species could occur resulting in a reduction in the positive growth outcomes. Moreover, the AMF communities had a significant (p < 0.05) direct effect by increasing plant biomass and nutrient uptake and indirectly by influencing the production of hormones and the chlorophyll content in grapevine leaves through the increase of specific nutrients such as K, Mn and Zn. The findings also indicated that due to the presence of different species in the different communities, some AMF species may deliver particular benefits to grapevine plants. The effect of AMF on black foot disease was also investigated in a ‘home’ and ‘away experiment using commercial grapevine rootstocks. The study produced limited evidence that AMF treatments lowered disease incidence and severity in vines and that the presence of high disease incidence may have limited the effect of AMF community. However, despite the high disease incidence and severity AMF inoculation was seen to result in an increase in vine growth parameters by 60% to 80% compared to the vines inoculated with the pathogen only. This study was also the first to provide a comprehensive analysis of the community composition and structure of AMF associated with grapevine roots in both conventional and organic systems in New Zealand using high-throughput next generation sequencing (Illumina Miseq). The identified AMF species/genera belonged mainly to Glomeraceae and Claroideoglomeraceae followed by Diversisporaceae, Paraglomeraceae, Archaeosporaceae and Gigasporaceae. The outcomes also revealed a significant (p < 0.05) difference in AMF alpha diversity in management practices and in the interaction effect between the rootstock and the management practices. However, no significant (p > 0.05) difference on AMF beta diversity was observed in any of the studied factors. Overall, this study revealed that by using complementary techniques a comprehensive identification of AMF communities associated with grapevines in New Zealand was done. The major outcome was that rootstock plays a key role in the selection of taxa in their mutualism with AMF. More research on the ‘home’ communities may uncover additional benefits towards the grapevine from the selected AMF community. This study has increased knowledge of the ecosystem services they provide which will benefit the wine growers and the viticulture industry.