Kauri (Agathis australis), which is one of the world's largest and longest‐living conifer species, is under threat from a root and collar dieback disease caused by the oomycete pathogen Phytophthora agathidicida. The noted incidence of kauri dieback has increased in the past decade, and even trees >1000 years old are not immune. This disease has profound effects on both forest ecosystems and human society, particularly indigenous Māori, for whom kauri is a taonga or treasure of immense significance. This review brings together existing scientific knowledge about the pathogen and the devastating disease it causes, as well as highlighting important knowledge gaps and potential approaches for disease management. The life cycle of P. agathidicida is similar to those of other soilborne Phytophthora pathogens, with roles for vegetative hyphae, zoospores and oospores in the disease. However, there is comparatively little known about many aspects of the biology of P. agathidicida, such as its host range and disease latency, or about the impact on the disease of abiotic and biotic factors such as soil health and co‐occurring Phytophthora species. This review discusses current and emerging tools and strategies for surveillance, diagnostics and management, including a consideration of genomic resources, and the role these play in understanding the pathogen and how it causes this deadly disease. Key aspects of indigenous Māori knowledge, which include rich ecological and historical knowledge of kauri forests and a holistic approach to forest health, are highlighted.

Phytophthora Clade 5 is a very poorly studied group of species of oomycete chromists, consisting of only two known species P. castaneae (≡ P. katsurae, nom. illegit.) and P. heveae with most isolates from East Asia and the Pacific Islands. However, isolates of two important disease-causing chromists in Clade 5, one of kauri (Agathis australis) in New Zealand, the other of coconut (Cocos nucifera) in Hawaii, poorly match the current species descriptions. To verify whether these isolates belong to separate species a detailed morphological study and phylogenetic analysis consisting of eight genetic loci was conducted. On the basis of genetic and morphological differences and host specificity, we present the formal description of two new species in Clade 5, Phytophthora agathidicida sp. nov. and Phytophthora cocois sp. nov. To clarify the typification of the other Clade 5 species, an authentic ex-holotype culture of Phytophthora castaneae is designated and P. heveae is lectotypified and epitypified.

Kauri Agathis australis, an iconic tree of New Zealand, is under threat from an introduced disease-causing pathogen provisionally named Phytophthora 'taxon Agathis' (referred to as PTA). This soilborne, Pythiaceous species belongs to the Chromista and causes a collar rot resulting in yellowing of the foliage and thinning of the canopy, which eventually causes death of the infected tree. The management and containment of this pathogen requires rapid and reliable detection in the soil. The current method for soil detection utilizes a soil bioassay involving lupin baits and soil flooding in a process that takes between ten and twenty days. We describe a real-time PCR assay based on TaqMan chemistry for the specific detection of PTA, which targets the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA. This TaqMan real-time PCR assay could be used with DNA extracted directly from bulk soil samples to enable rapid quantification of PTA within soil. The detection limit was 2 fg of PTA DNA from pure culture, or 20 fg in the presence of DNA extracted from soil. The assay was validated using soil samples taken from a PTA-infested site and soil spiked with a known concentration of oospores. We conclude that the TaqMan real-time PCR assay offers a more time-efficient method for detection of PTA in soil than existing methods.

The root rot causing oomycete, Phytophthora agathidicida, threatens the long-term survival of the iconic New Zealand kauri. Currently, testing for this pathogen involves an extended soil bioassay that takes 14-20 days and requires specialised staff, consumables, and infrastructure. Here we describe a loop-mediated isothermal amplification (LAMP) assay for the detection of P. agathidicida that targets a portion of the mitochondrial apocytochrome b coding sequence. This assay has high specificity and sensitivity; it did not cross react with a range of other Phytophthora isolates and detected as little as 1 fg of total P. agathidicida DNA or 116 copies of the target locus. Assay performance was further investigated by testing plant tissue baits from flooded soil samples using both the extended soil bioassay and LAMP testing of DNA extracted from baits. In these comparisons, P. agathidicida was detected more frequently using the LAMP test. In addition to greater sensitivity, by removing the need for culturing, the hybrid baiting plus LAMP approach is more cost effective than the extended soil bioassay and, importantly, does not require a centralised laboratory facility with specialised staff, consumables, and equipment. Such testing will allow us to address outstanding questions about P. agathidicida. For example, the hybrid approach could enable monitoring of the pathogen beyond areas with visible disease symptoms, allow direct evaluation of rates and patterns of spread, and allow the effectiveness of disease control to be evaluated. The hybrid LAMP bioassay also has the potential to empower local communities to evaluate the pathogen status of local kauri stands, providing information for disease management and conservation initiatives.

As the only endemic member in New Zealand of the ancient conifer family, Araucariaceae, Agathis australis is an ideal species to study putatively long-evolved mycorrhizal symbioses. However, little is known about A. australis root and nodular arbuscular mycorrhizal fungi (AMF), and how mycorrhizal colonisation occurs. We used light, scanning and transmission electron microscopy to characterise colonisation, and 454-sequencing to identify the AMF associated with A. australis roots and nodules. We interpreted the results in terms of the edaphic characteristics of the A. australis-influenced ecosystem. Representatives of five families of Glomeromycota were identified via high-throughput pyrosequencing. Imaging studies showed that there is abundant, but not ubiquitous, colonisation of nodules, which suggests that nodules are mostly colonised by horizontal transmission. Roots were also found to harbour AMF. This study is the first to demonstrate the multiple Glomeromycota lineages associated with A. australis including some that may not have been previously detected.