The mitogenome of Phytophthora agathidicida: Evidence for a not so recent arrival of the "kauri killing" Phytophthora in New Zealand.

Phytophthora agathidicida is associated with a root rot that threatens the long-term survival of the iconic New Zealand kauri. Although it is widely assumed that this pathogen arrived in New Zealand post-1945, this hypothesis has yet to be formally tested. Here we describe evolutionary analyses aimed at evaluating this and two alternative hypotheses. As a basis for our analyses, we assembled complete mitochondrial genome sequences from 16 accessions representing the geographic range of P. agathidicida as well as those of five other members of Phytophthora clade 5. All 21 mitogenome sequences were very similar, differing little in size with all sharing the same gene content and arrangement. We first examined the temporal origins of genetic diversity using a pair of calibration schemes. Both resulted in similar age estimates; specifically, a mean age of 303.0-304.4 years and 95% HPDs of 206.9-414.6 years for the most recent common ancestor of the included isolates. We then used phylogenetic tree building and network analyses to investigate the geographic distribution of the genetic diversity. Four geographically distinct genetic groups were recognised within P. agathidicida. Taken together the inferred age and geographic distribution of the sampled mitogenome diversity suggests that this pathogen diversified following arrival in New Zealand several hundred to several thousand years ago. This conclusion is consistent with the emergence of kauri dieback disease being a consequence of recent changes in the relationship between the pathogen, host, and environment rather than a post-1945 introduction of the causal pathogen into New Zealand

A LAMP at the end of the tunnel: A rapid, field deployable assay for the kauri dieback pathogen, Phytophthora agathidicida.

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

Cross-Cultural Leadership Enables Collaborative Approaches to Management of Kauri Dieback in Aotearoa New Zealand

In Aotearoa/New Zealand, the soilborne pathogen Phytophthora agathidicida threatens the survival of the iconic kauri, and the ecosystem it supports. In 2011, a surveillance project to identify areas of kauri dieback caused by Phytophthora agathidicida within the Waitākere Ranges Regional Park (WRRP) highlighted the potential impact of the pathogen. A repeat of the surveillance in 2015/16 identified that approximately a quarter of the kauri area within the Regional Park was infected or possibly infected, an increase from previous surveys. The surveillance program mapped 344 distinct kauri areas and showed that 33.4% of the total kauri areas were affected or potentially affected by kauri dieback and over half (58.3%) of the substantial kauri areas (above 5 ha in size) were showing symptoms of kauri dieback. Proximity analysis showed 71% of kauri dieback zones to be within 50 m of the track network. Spatial analysis showed significantly higher proportions of disease presence along the track network compared to randomly generated theoretical track networks. Results suggest that human interaction is assisting the transfer of Phytophthora agathidicida within the area. The surveillance helped trigger the declaration of a cultural ban (rāhui) on recreational access. Te Kawerau ā Maki, the iwi of the area, placed a rāhui over the kauri forest eco-system of the Waitākere Forest (Te Wao Nui o Tiriwa) in December 2017. The purpose of the rāhui was to help prevent the anthropogenic spread of kauri dieback, to provide time for investment to be made into a degraded forest infrastructure and for research to be undertaken, and to help protect and support forest health (a concept encapsulated by the term mauri). Managing the spread and impact of the pathogen remains an urgent priority for this foundation species in the face of increasing pressures for recreational access. Complimentary quantitative and qualitative research programs into track utilization and ecologically sensitive design, collection of whakapapa seed from healthy and dying trees, and remedial phosphite treatments are part of the cross-cultural and community-enabled biosecurity initiatives to Kia Toitu He Kauri “Keep Kauri Standing”

Cross-Cultural Leadership Enables Collaborative Approaches to Management of Kauri Dieback in Aotearoa New Zealand

In Aotearoa/New Zealand, the soilborne pathogen Phytophthora agathidicida threatens the survival of the iconic kauri, and the ecosystem it supports. In 2011, a surveillance project to identify areas of kauri dieback caused by Phytophthora agathidicida within the Waitākere Ranges Regional Park (WRRP) highlighted the potential impact of the pathogen. A repeat of the surveillance in 2015/16 identified that approximately a quarter of the kauri area within the Regional Park was infected or possibly infected, an increase from previous surveys. The surveillance program mapped 344 distinct kauri areas and showed that 33.4% of the total kauri areas were affected or potentially affected by kauri dieback and over half (58.3%) of the substantial kauri areas (above 5 ha in size) were showing symptoms of kauri dieback. Proximity analysis showed 71% of kauri dieback zones to be within 50 m of the track network. Spatial analysis showed significantly higher proportions of disease presence along the track network compared to randomly generated theoretical track networks. Results suggest that human interaction is assisting the transfer of Phytophthora agathidicida within the area. The surveillance helped trigger the declaration of a cultural ban (rāhui) on recreational access. Te Kawerau ā Maki, the iwi of the area, placed a rāhui over the kauri forest eco-system of the Waitākere Forest (Te Wao Nui o Tiriwa) in December 2017. The purpose of the rāhui was to help prevent the anthropogenic spread of kauri dieback, to provide time for investment to be made into a degraded forest infrastructure and for research to be undertaken, and to help protect and support forest health (a concept encapsulated by the term mauri). Managing the spread and impact of the pathogen remains an urgent priority for this foundation species in the face of increasing pressures for recreational access. Complimentary quantitative and qualitative research programs into track utilization and ecologically sensitive design, collection of whakapapa seed from healthy and dying trees, and remedial phosphite treatments are part of the cross-cultural and community-enabled biosecurity initiatives to Kia Toitu He Kauri “Keep Kauri Standing”

Two new Nothophytophthora species from streams in Ireland and Northern Ireland: Nothophytophthora irlandica and N. lirii sp. nov

Slow growing oomycete isolates with morphological resemblance to Phytophthora were obtained from forest streams during routine monitoring for the EU quarantine forest pathogen Phytophthora ramorum in Ireland and Northern Ireland. Internal Transcribed Spacer (ITS) sequence analysis indicated that they belonged to two previously unknown species of Nothophytophthora, a recently erected sister genus of Phytophthora. Morphological and temperature-growth studies were carried out to characterise both new species. In addition, Bayesian and Maximum-Likelihood analyses of nuclear 5-loci and mitochondrial 3-loci datasets were performed to resolve the phylogenetic positions of the two new species. Both species were sterile, formed chlamydospores and partially caducous nonpapillate sporangia, and showed slower growth than any of the six known Nothophytophthora species. In all phylogenetic analyses both species formed distinct, strongly supported clades, closely related to N. chlamydospora and N. valdiviana from Chile. Based on their unique combination of morphological and physiological characters and their distinct phylogenetic positions the two new species are described as Nothophytophthora irlandica sp. nov. and N. lirii sp. nov. Their potential lifestyle and geographic origin are discussed