Potential for biofumigation against soilborne diseases of potato caused by Rhizoctonia solani, and for effects on soil microbial communities : A thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy at Lincoln University

Abstract

The soilborne diseases of potato (Solanum tuberosum) caused by Rhizoctonia solani (stem canker and tuber black scurf) are important factors limiting yields and quality of intensively managed potato crops in New Zealand. International studies have shown that biofumigation using Brassica plants is a promising component of integrated disease management with potential to reduce agrichemical usage for disease control. To date, there is limited evidence on the efficacy of biofumigation for controlling soil-borne diseases of potato in New Zealand. The goal of this research was to investigate the biofumigation potential of selected plants for suppression of R. solani AG3-PT and AG2-1, which cause potato diseases. In vitro studies showed that of the 10 plant types tested, three, including ‘Caliente’ mustard, brown mustard and ‘Nemat’ arugula, gave the greatest inhibition of the mycelium growth of R. solani AG3-PT and AG2-1 isolates, at 5-10 g of macerated plant tissues per Petri dish, or 5-10% (w:w) when incorporated into soil. Shoot or shoot plus root tissues of selected biofumigants, harvested at the mid-flowering growth stage, were the most effective for reducing mycelium growth of R. solani isolates. Increased conversion of R. solani mycelium into sclerotia was observed at 1% or 5% (w:w) soil incorporation for ‘Caliente’ mustard and 1% (w:w) for brown mustard or ‘Nemat’ arugula. The subsequent germination of retrieved R. solani sclerotia was reduced at 10% (w:w) soil incorporation of ‘Nemat’ arugula. The subsequent mycelium growth from retrieved R. solani colonised barley grains was completely inhibited at 10% (w:w) soil incorporation of ‘Caliente’ mustard, brown mustard or ‘Nemat’ arugula. Biofumigation potential against R. solani AG3-PT was assessed in different soil edaphic conditions, using qPCR and measurements of soil microbial activity (dehydrogenase activity, DHA). Biofumigant treatments at soil pH of 6.6, 20°C and 40% water holding capacity (WHC), or at 15°C and 40% WHC, gave the greatest reductions of R. solani AG3-PT inoculum levels in soil. In addition, biofumigant treatments at pH 6.6, 15°C, and 40 or 70% WHC, or in the combination of 15°C and 40% WHC, resulted in the greatest DHA levels. The soils amended with macerated ‘Caliente’ mustard tissue (5% w:w) and after incubation at 15°C, reduced the stem canker severity on potato ‘Jersey Benne’ plants, and increased plant height and dry biomass compared with the pathogen inoculated controls. The effects of the selected biofumigant treatments for reducing R. solani AG3-PT inoculum, and suppressing infection of ‘Russet Burbank’ potato plants, were assessed in a shadehouse experiment, using qPCR and DHA assessments. The results showed that the biofumigant treatments reduced and maintained R. solani AG3-PT inoculum (and potentially other AGs) at low levels during the experiment, in soil, and stems, stolons and tubers of potato plants. However, there was no differential effect of biofumigant treatments on soil microbial activity (DHA). The biofumigant treatments also reduced severity of tuber powdery scab caused by Spongospora subterranea, and incidence of dead stems caused by Colletotrichum coccodes. Potato plant yield parameters were increased by the biofumigant treatments. Effects of cover crops, including ‘Caliente’ mustard, oat or ‘Graza’ radish, on soil microbial communities were assessed by DHA measurements, soil carbon utilisation profiles (CUP), and PCR-DGGE in soil samples taken from three potato field trials near Timaru (2015/16, 2016/17) and Ashburton (2015/16), Canterbury. DHA increased after cover crop treatments. The events of crop incorporation and plant growth over the sampling period and the oat treatment affected the CUPs of the soil microbial communities. Results from PCR-DGGE showed that different cover/potato crops or growth stages strongly affected the structure (species composition), richness, and diversity indices for communities of total fungi, arbuscular mycorrhizal fungi (AMF), Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. In addition, cover crop treatments affected the soil microbial communities. ‘Caliente’ mustard altered the community structures of total fungi in the three field trials, and reduced the richness and diversity indices for total fungi communities in the two Timaru field trials. ‘Caliente’ mustard also affected the Proteobacteria community structures in soil samples from the two Timaru field trials, but increased richness and reduced the diversity of Betaproteobacteria in soil from the Timaru trial (2015/16). This biofumigant treatment also reduced the diversity of Alphaproteobacteria in soil samples from the Ashburton field trial (2015/16). ‘Graza’ radish treatment only affected AMF community structure in samples from one field trial (Timaru, 2016/17), but had no effects on the community structures, richness or diversity of AMF or the other microbial groups in samples from the other fields. Oat treatment reduced the richness of the total fungi and Gammaproteobacteria communities in soil from the Timaru field trial (2016/17). This study has provided supportive information that biofumigant plants and crops could be incorporated as a management strategy to control economically important diseases of potato.