Diversity of Phytophthora species in Canterbury waterways: A thesis submitted in partial fulfilment of the requirements for the Degree of Master of Agriculture at Lincoln University

Abstract

Spread worldwide, the genus Phytophthora includes a diverse group of pathogens that affect a wide range of agricultural crops and plants in native ecosystems. Water surveys have become popular in regions where early detection of infected areas is important for containment and eradication of Phytophthora spp., with more than 20 new Phytophthora spp. isolated from waterways around the world. This study identified the best method and leaf bait for Phytophthora recovery which was used for a more extensive Phytophthora diversity study in Canterbury, New Zealand, waterways. Additionally, four methods for screening pathogenicity of Phytophthora spp. recovered from the waterways was also done to identify a rapid assay that could identify pathogenic isolates. Three methods (laboratory baiting, river baiting (in situ) and filtration method) were evaluated for Phytophthora recovery from two sites in the Halswell River in summer (February 2018). Phytophthora baiting was done by floating leaf baits in water samples (laboratory baiting) or waterways (river baiting) for 7 days after which the lesions on the leaf baits were cut and cultured on Phytophthora selective media for Phytophthora isolation. For filtration method membrane filters (3-μm pore size) was used to filter water samples and the membrane filters cultured on Phytophthora selective media for isolation of Phytophthora isolates. The study identified water baiting, either laboratory baiting or river baiting as being suitable to study of Phytophthora spp. diversity in waterways. Filtration method was not effective due to high Pythium recovery which contaminated the Phytophthora colonies. Additionally, seven leaf baits (Banksia attenuata, Camelia japonica, Cedrus deodara, Pinus radiata, Pittosporum undulatum, Pittosporum eugenioides and Rhododendron arboreum) were evaluated for Phytophthora recovery. Rhododendron arboreum recovered the highest number of Phytophthora isolates and species. As identified in this study, future Phytophthora diversity studies should focus on using laboratory baiting and river baiting methods with R. arboreum leaf bait. The laboratory baiting method was used for the Phytophthora diversity study (autumn baiting; May 2018) using Ce. deodara, Pi radiata and R. arboreum leaf baits in six waterways (Selwyn River (Waikirikiri), Ashburton River (Hakatere), Prices Valley River, Kaituna Valley River, Halswell River and Lake Hood) with a total of 25 sites. Phytophthora lacustris was the most commonly isolated species, followed by Ph. gonapodyides, Ph. chlamydospora x Ph. amnicola hybrid and Ph. thermophila x amnicola hybrid. Rhododendron arboreum was found to be more effective at isolating Phytophthora spp. over a range of water pH, and again recovered the highest number of Phytophthora isolates and species. This study reports the first recovery of some species in the Canterbury region and includes; Ph. thermophila x amnicola hybrids, Ph. chlamydospora x Ph. thermophila hybrids, Ph. amnicola x Ph. chlamydospora hybrids, Ph. chlamydospora, Ph. bilorbang, Ph. lacustris, and Phytophthora sp. LS-2018c strain CL181. Phytophthora gonapodyides and Ph. cryptogea were also recovered however, these species have been previously reported to be widely spread throughout New Zealand. Phytophthora cactorum has mostly been found in association with orchards in New Zealand, however this study reports the first isolation from waterways. Phytophthora sp. LS-2018c strain CL181 and Ph. thermophila are new species in New Zealand identified through this study. The study also identified seasonal difference in Phytophthora spp. diversity in the two sites in the Halswell River stressing the need to carry out Phytophthora spp. diversity studies over all seasons. Pathogenicity of three commonly recovered Phytophthora spp. from Canterbury waterways, Phytophthora sp. LS-2018c strain CL 181, Ph. chlamydospora and Ph. gonapodyides, was evaluated using four methods. Testing Phytophthora isolates using agar plugs on lupin seedlings grown on sterile paper towels was identified as a good rapid assay for determining the pathogenicity of Phytophthora isolates recovered from waterways, with results observed 4 days post inoculation. All three Phytophthora species isolates were found to be pathogenic on lupin seedlings. Phytophthora isolates that are shown to be pathogenic in the screening assay should be included in further pathogenicity test using crops, fruit trees, native and exotic tree species to evaluate the risks these species pose to New Zealand’s agricultural and native ecosystems. Overall, recovery of new Phytophthora spp. in Canterbury waterways has provided new insights on the importance of carrying out Phytophthora surveillance in waterways. Additionally, this study provides recommendations on improvements for future Phytophthora diversity studies.