Combining inferential and deductive approaches to estimate the potential geographical range of the invasive plant pathogen, Phytophthora ramorum

Climate Change Effects on Pathogen Emergence: Artificial Intelligence to Translate Big Data for Mitigation

Plant pathology has developed a wide range of concepts and tools for improving plant disease management, including models for understanding and responding to new risks from climate change. Most of these tools can be improved using new advances in artificial intelligence (AI), such as machine learning to integrate massive data sets in predictive models. There is the potential to develop automated analyses of risk that alert decision-makers, from farm managers to national plant protection organizations, to the likely need for action and provide decision support for targeting responses. We review machine-learning applications in plant pathology and synthesize ideas for the next steps to make the most of these tools in digital agriculture. Global projects, such as the proposed global surveillance system for plant disease, will be strengthened by the integration of the wide range of new data, including data from tools like remote sensors, that are used to evaluate the risk ofplant disease. There is exciting potential for the use of AI to strengthen global capacity building as well, from image analysis for disease diagnostics and associated management recommendations on farmers' phones to future training methodologies for plant pathologists that are customized in real-time for management needs in response to the current risks. International cooperation in integrating data and models will help develop the most effective responses to new challenges from climate change.

Improving climate suitability for Bemisia tabaci in East Africa is correlated with increased prevalence of whiteflies and cassava diseases

Projected climate changes are thought to promote emerging infectious diseases, though to date, evidence linking climate changes and such diseases in plants has not been available. Cassava is perhaps the most important crop in Africa for smallholder farmers. Since the late 1990’s there have been reports from East and Central Africa of pandemics of begomoviruses in cassava linked to high abundances of whitefly species within the Bemisia tabaci complex. We used CLIMEX, a process-oriented climatic niche model, to explore if this pandemic was linked to recent historical climatic changes. The climatic niche model was corroborated with independent observed field abundance of B. tabaci in Uganda over a 13-year time-series, and with the probability of occurrence of B. tabaci over 2 years across the African study area. Throughout a 39-year climate time-series spanning the period during which the pandemics emerged, the modelled climatic conditions for B. tabaci improved significantly in the areas where the pandemics had been reported and were constant or decreased elsewhere. This is the first reported case where observed historical climate changes have been attributed to the increase in abundance of an insect pest, contributing to a crop disease pandemic.

An Overview of Canadian Research Activities on Diseases Caused by Phytophthora ramorum: Results, Progress, and Challenges

International trade and travel are the driving forces behind the spread of invasive plant pathogens around the world, and human-mediated movement of plants and plant products is now generally accepted as the primary mode of their introduction, resulting in huge disturbance to ecosystems and severe socio-economic impact. These problems are exacerbated under the present conditions of rapid climatic change. We report an overview of the Canadian research activities on Phytophthora ramorum. Since the first discovery and subsequent eradication of P. ramorum on infected ornamentals in nurseries in Vancouver, British Columbia, in 2003, a research team of Canadian government scientists representing the Canadian Forest Service, Canadian Food Inspection Agency, and Agriculture and Agri-Food Canada worked together over a 10-year period and have significantly contributed to many aspects of research and risk assessment on this pathogen. The overall objectives of the Canadian research efforts were to gain a better understanding of the molecular diagnostics of P. ramorum, its biology, host-pathogen interactions, and management options. With this information, it was possible to develop pest risk assessments and evaluate the environmental and economic impact and future research needs and challenges relevant to P. ramorum and other emerging forest Phytophthora spp.

Regeneration Dynamics of Coast Redwood, a Sprouting Conifer Species: A Review with Implications for Management and Restoration

Coast redwood (Sequoia sempervirens (Lamb. ex. D. Don) Endl.) is unique among conifer species because of its longevity, the great sizes of individual trees, and its propensity to reproduce through sprouts. Timber harvesting in the native redwood range along the coast of the western United States has necessitated restoration aimed to promote old forest structures to increase the total amount of old forest, the connectivity between old forests, and to enhance the resiliency of these ecosystems. After disturbance or harvest, healthy redwood stumps sprout vigorously, often producing dozens of sprouts within two years of disturbance. These sprouts form highly aggregated spatial patterns because they are clustered around stumps that may number less than 50 ha−1. Thinning of sprouts can accelerate individual tree growth, providing an effective restoration strategy to accelerate formation of large trees and old forest structures or increase stand growth for timber production. However, management, including restoration activities, is a contentious issue throughout the native range of redwood because of the history of overexploitation of this resource and perceptions that overexploitation is continuing. This paper reviews the science of early stand dynamics in coast redwood and their implications for restoration and other silvicultural strategies.

Distribution and diversity of Phytophthora across Australia

The introduction and subsequent impact of Phytophthora cinnamomi within native vegetation is one of the major conservation issues for biodiversity in Australia. Recently, many new Phytophthora species have been described from Australia’s native ecosystems; however, their distribution, origin, and potential impact remain unknown. Historical bias in Phytophthora detection has been towards sites showing symptoms of disease, and traditional isolation methods show variable effectiveness of detecting different Phytophthora species. However, we now have at our disposal new techniques based on the sampling of environmental DNA and metabarcoding through the use of high-throughput sequencing. Here, we report on the diversity and distribution of Phytophthora in Australia using metabarcoding of 640 soil samples and we compare the diversity detected using this technique with that available in curated databases. Phytophthora was detected in 65% of sites, and phylogenetic analysis revealed 68 distinct Phytophthora phylotypes. Of these, 21 were identified as potentially unique taxa and 25 were new detections in natural areas and/or new introductions to Australia. There are 66 Phytophthora taxa listed in Australian databases, 43 of which were also detected in this metabarcoding study. This study revealed high Phytophthora richness within native vegetation and the additional records provide a valuable baseline resource for future studies. Many of the Phytophthora species now uncovered in Australia’s native ecosystems are newly described and until more is known we need to be cautious with regard to the spread and conservation management of these new species in Australia’s unique ecosystems.

Emerging oomycete threats to plants and animals

Oomycetes, or water moulds, are fungal-like organisms phylogenetically related to algae. They cause devastating diseases in both plants and animals. Here, we describe seven oomycete species that are emerging or re-emerging threats to agriculture, horticulture, aquaculture and natural ecosystems. They include the plant pathogens Phytophthora infestans, Phytophthora palmivora, Phytophthora ramorum, Plasmopara obducens, and the animal pathogens Aphanomyces invadans, Saprolegnia parasitica and Halioticida noduliformans For each species, we describe its pathology, importance and impact, discuss why it is an emerging threat and briefly review current research activities.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.

Foliar phosphite application has minor phytotoxic impacts across a diverse range of conifers and woody angiosperms

Phytophthora plant pathogens cause tremendous damage in planted and natural systems worldwide. Phosphite is one of the only effective chemicals to control broad-scale Phytophthora disease. Little work has been done on the phytotoxic effects of phosphite application on plant communities especially in combination with plant physiological impacts. Here, we tested the phytotoxic impact of phosphite applied as foliar spray at 0, 12, 24 and 48 kg a.i. ha(-1) . Eighteen-month-old saplings of 13 conifer and angiosperm species native to New Zealand, and two exotic coniferous species were treated and the development of necrotic tissue and chlorophyll-a-fluorescence parameters (optimal quantum yield, Fv /Fm ; effective quantum yield of photosystem II, ΦPSII ) were assessed. In addition, stomatal conductance (gs ) was measured on a subset of six species. Significant necrosis assessed by digital image analysis occurred in only three species: in the lauraceous canopy tree Beilschmiedia tawa (8-14%) and the understory shrub Dodonaea viscosa (5-7%) across phosphite concentrations and solely at the highest concentration in the myrtaceous pioneer shrub Leptospermum scoparium (66%). In non-necrotic tissue, Fv /Fm , ΦPSII and gs remained unaffected by the phosphite treatment. Overall, our findings suggest minor phytotoxic effects resulting from foliar phosphite application across diverse taxa and regardless of concentration. This study supports the large-scale use of phosphite as a management tool to control plant diseases caused by Phytophthora pathogens in plantations and natural ecosystems. Long-term studies are required to ascertain potential ecological impacts of repeated phosphite applications.

Mapping Global Potential Risk of Establishment of Rhagoletis pomonella (Diptera: Tephritidae) Using MaxEnt and CLIMEX Niche Models

The apple maggot, Rhagoletis pomonella (Walsh) (Diptera: Tephritidae), is a major quarantine pest of apples (Malus domestica Borkhausen) in the United States. Apple maggot is found only in North America and negatively impacts the apple industry in the western United States by reducing grower access to export markets. To reduce the threat of apple maggot to export countries and to facilitate the movement of commercial apples, an assessment of potential risk of establishment of apple maggot is needed to predict which regions are suitable or unsuitable for the fly. We used a correlative niche model MaxEnt and a mechanistic model CLIMEX to model global potential risk of establishment of apple maggot. The MaxEnt model was developed by integrating apple maggot occurrences with global climatic variables. Apple (a major host of apple maggot) climatic suitability was used as an additional variable to include species interactions in the MaxEnt model. The CLIMEX model was developed using published apple maggot physiological tolerance thresholds. Both the MaxEnt and CLIMEX models correctly predicted the known distribution of apple maggot in North America, met biological expectations when projected to the world, and mostly agreed on climatic suitability worldwide for the fly. Degree-days at 6.7 °C, elevation, precipitation seasonality, and apple climatic suitability were the most important predictors associated with apple maggot distribution in North America. Our results can be used to make science-based international trade decisions by policy makers, and for monitoring apple maggot potential introductions in countries where it currently does not occur.

Winter Conditions Correlate with Phytophthora alni Subspecies Distribution in Southern Sweden

During the last century, the number of forest pathogen invasions has increased substantially. Environmental variables can play a crucial role in determining the establishment of invasive species. The objective of the present work was to determine the correlation between winter climatic conditions and distribution of two subspecies of the invasive forest pathogen Phytophthora alni: P. alni subspp. alni and uniformis killing black alder (Alnus glutinosa) in southern Sweden. It is known from laboratory experiments that P. alni subsp. alni is more pathogenic than P. alni subsp. uniformis, and that P. alni subsp. alni is sensitive to low temperatures and long frost periods. By studying the distribution of these two subspecies at the northern limit of the host species, we could investigate whether winter conditions can affect the geographical distribution of P. alni subsp. alni spreading northward. Sixteen major river systems of southern Sweden were systematically surveyed and isolations were performed from active cankers. The distribution of the two studied subspecies was highly correlated with winter temperature and duration of periods with heavy frost. While P. alni subsp. uniformis covered the whole range of temperatures of the host, P. alni subsp. alni was recovered in areas subjected to milder winter temperatures and shorter frost periods. Our observations suggest that winter conditions can play an important role in limiting P. alni subsp. alni establishment in cold locations, thus affecting the distribution of the different subspecies of P. alni in boreal regions.

Assessing the Global Risk of Establishment of Cydia pomonella (Lepidoptera: Tortricidae) using CLIMEX and MaxEnt Niche Models

Accurate assessment of insect pest establishment risk is needed by national plant protection organizations to negotiate international trade of horticultural commodities that can potentially carry the pests and result in inadvertent introductions in the importing countries. We used mechanistic and correlative niche models to quantify and map the global patterns of the potential for establishment of codling moth (Cydia pomonella L.), a major pest of apples, peaches, pears, and other pome and stone fruits, and a quarantine pest in countries where it currently does not occur. The mechanistic model CLIMEX was calibrated using species-specific physiological tolerance thresholds, whereas the correlative model MaxEnt used species occurrences and climatic spatial data. Projected potential distribution from both models conformed well to the current known distribution of codling moth. None of the models predicted suitable environmental conditions in countries located between 20°N and 20°S potentially because of shorter photoperiod, and lack of chilling requirement (<60 d at ≤10°C) in these areas for codling moth to break diapause. Models predicted suitable conditions in South Korea and Japan where codling moth currently does not occur but where its preferred host species (i.e., apple) is present. Average annual temperature and latitude were the main environmental variables associated with codling moth distribution at global level. The predictive models developed in this study present the global risk of establishment of codling moth, and can be used for monitoring potential introductions of codling moth in different countries and by policy makers and trade negotiators in making science-based decisions.