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International audience; Global changes play today an important role in altering patterns of human, animal, and plant host–pathogen interactions and invasive pest species. With rapid development in sequencing technology, there is also an increase in pathogen and pest studies adopting a macroscale, biogeographical perspective, and we present the most recent elements on existing ecological and biogeographical trends. We also compare the results on the one hand on emerging infectious diseases of animals and humans, and on the other hand on plant pathogens and pests. International exchanges of people, animals, and plant products currently contribute to their geographical extension but with notable differences across disease and pest systems, and regions. This review highlights that the subject of pathogens and plant pests, traditionally rooted in agronomic approaches, lacks work on macroecology and biogeography. We discuss the research orientations to better anticipate their ecological and economic impacts in order to better achieve environmental sustainability.

Spatial prediction of photosynthesis requires an understanding of how foliage nitrogen (N) and phosphorus (P) regulate this process and the relationship between these elements and scalable spectral proxies. Hyperspectral imagery has been used to predict important photosynthetic variables such as the maximum rate of carboxylation (Vcmax) and electron transport (Jmax). However, our understanding of how generally applicable these relationships are for plants that are limited by N and P, characterised by respective mass based ratios of N/P ≤ 10 and N/P > 10, is still incomplete as most studies assume N and P co-limit photosynthesis. Hyperspectral imagery and measurements of photosynthesis were obtained from one-year old Pinus radiata D. Don, grown under a factorial combination of N and P treatments. Using these data, the objectives of this study were to (i) identify whether trees were co-limited or independently limited by N and P, and then use hyperspectral imagery to (ii) partition N and P limited trees, (iii) build models of N and P from a range of hyperspectral indices and (iv) explore links between key plant traits and both Vcmax and Jmax. Compared to the use of all data, which assumes co-limitation, markedly stronger relationships between N and P and photosynthetic capacity were obtained through splitting data at N/P = 10 (independent limitation) for both Vcmax (R2 = 0.40 vs. 0.59) and Jmax (R2 = 0.38 vs. 0.64). A random forest model was used to accurately partition N from P limited trees and the two main variables used within this model were Photochemical Reflectance Index (PRI) and Solar-Induced Chlorophyll Fluorescence (SIF). Using data from the P limiting phase, the most precise models of P were created using PRI (R2 = 0.75) and SIF (R2 = 0.52). Indices that were proxies for chlorophyll were the most precise predictors of N within the N limiting phase but strong positive relationships were also evident between N and both PRI (R2 = 0.83) and SIF (R2 = 0.57). Through their correlations with N and P, there were strong positive relationships between both SIF, PRI and Vcmax (R2 = 0.78 and 0.83, respectively) and Jmax (R2 = 0.80 and 0.83, respectively) that were generalisable across both N and P limiting ranges. These results suggest that quantified SIF and PRI from hyperspectral images may have greater precision and generality for predicting both foliage nutrition and biochemical limitations to photosynthesis than other widely used hyperspectral indices., The project was partly funded through the Resilient Forests programme, which is funded through Scion SSIF as well as the Forest Grower’s Levy Trust. Funding was also received from the National Institute for Forest Products Innovation (Project Number NIF073-1819), which comprised contributions from the Australian Government, Australasian Forestry Companies and South Australian and Tasmanian State Governments.

Pathogenic diseases frequently occur in drought-stressed trees. However, their contribution to the process of drought-induced mortality is poorly understood. We combined drought and stem inoculation treatments to study the physiological processes leading to drought-induced mortality in Norway spruce (Picea abies) and Scots pine (Pinus sylvestris) saplings infected with Heterobasidion annosum s.s. We analysed the saplings' water status, gas exchange, nonstructural carbohydrates (NSCs) and defence responses, and how they related to mortality. Saplings were followed for two growing seasons, including an artificially induced 3-month dormancy period. The combined drought and pathogen treatment significantly increased spruce mortality; however, no interaction between these stressors was observed in pine, although individually each stressor caused mortality. Our results suggest that pathogen infection decreased carbon reserves in spruce, reducing the capacity of saplings to cope with drought, resulting in increased mortality rates. Defoliation, relative water content and the starch concentration of needles were predictors of mortality in both species under drought and pathogen infection. Infection and drought stress create conflicting needs for carbon to compartmentalize the pathogen and to avoid turgor loss, respectively. Heterobasidion annosum reduces the functional sapwood area and shifts NSC allocation patterns, reducing the capacity of trees to cope with drought. Ministry of Science and Education of Spain; Svenska Forskningsradet Formas

The selection of drought-tolerant genotypes is globally recognized as an effective strategy to maintain the growth and survival of commercial tree species exposed to future drought periods. New genomic selection tools that reduce the time of progeny trials are required to substitute traditional tree breeding programs. We investigated the genetic variation of water stress tolerance in New Zealand-grown Pinus radiata D. Don using 622 commercially-used genotypes from 63 families. We used quantitative pedigree-based (Genomic Best Linear Unbiased Prediction or ABLUP) and genomic-based (Genomic Best Linear Unbiased Prediction or GBLUP) approaches to examine the heritability estimates associated with water stress tolerance in P. radiata. Tree seedling growth traits, foliar carbon isotope composition (δ13C), and dark-adapted chlorophyll fluorescence (Y) were monitored before, during and after 10 months of water stress. Height growth showed a constant and moderate heritability level, while the heritability estimate for diameter growth and δ13C decreased with water stress. In contrast, chlorophyll fluorescence exhibited low heritability after 5 and 10 months of water stress. The GBLUP approach provided less breeding value accuracy than ABLUP, however, the relative selection efficiency of GBLUP was greater compared with ABLUP selection techniques. Although there was no significant relationship directly between δ13C and Y, the genetic correlations were significant and stronger for GBLUP. The positive genetic correlations between δ13C and tree biomass traits under water stress indicated that intraspecific variation in δ13C was likely driven by differences in the genotype’s photosynthetic capacity. The results show that foliar δ13C can predict P. radiata genotype tolerance to water stress using ABLUP and GBLUP approaches and that such approaches can provide a faster screening and selection of drought-tolerant genotypes for forestry breeding programs.

International audience; Species of Phytophthora pose one of the most serious biosecurity threats to forest ecosystems worldwide. Despite management efforts and increased awareness of forest pathogens, there is continued introduction and spread of Phytophthora species. Uncertainty about the center of origin for many of the invasive species hampers disease control efforts. Additionally, the management efforts are often made impossible either by the vast host range or the extreme susceptibility of naïve hosts. In this review, we discuss how genomics has shed light on the extent of spread and destruction caused by invasive Phytophthora species, and how approaches leveraged by genomics can be applied to enhance the management of these invasive forest pathogens. Four case studies, Phytophthora ramorum, Phytophthora lateralis, Phytophthora cinnamomi, and Phytophthora pluvialis are used to illustrate how genomics can be applied to forest management. We urge researchers, governmental research institutes, private companies, and citizens to collaborate in order to stop the spread of invasive Phytophthora species. To accomplish this, we see the following themes as critical parts of resolving this forest health crisis: i) integration of DNA-based pathogen detection into forest inventory programs; ii) development of practical and affordable DNA-based diagnostic methods; iii) sequence hosts as models for resistance gene identification; iv) prediction of pathogen impact based on genomic data; and v) increase collaborative projects and outreach to raise awareness of forest diseases.; Les espèces de Phytophthora représentent une des plus graves menaces en matière de risques pour la biosécurité des écosystèmes forestiers, et ce, partout dans le monde. Malgré les efforts de gestion et une plus grande prise de conscience à l’égard des agents pathogènes forestiers, des espèces de Phytophthora continuent d’être introduites et disséminées. L’incertitude quant au lieu d’origine de plusieurs des espèces envahissantes entrave les efforts de lutte contre les maladies. De plus, les efforts de gestion sont souvent anéantis soit par la vaste gamme d’hôtes ou l’extrême réceptivité des hôtes indigènes. Au cours de cet examen, il est question de génomique et de comment celle-ci a jeté un nouvel éclairage sur l’ampleur de la dissémination des espèces envahissantes de Phytophthora et de la destruction qui s’en suit, et comment les approches soutenues par la génomique peuvent être appliquées pour améliorer la gestion de ces agents pathogènes forestiers envahissants. Quatre études de cas, Phytophthora ramorum, Phytophthora lateralis, Phytophthora cinnamomi et Phytophthora pluvialis, sont utilisées pour illustrer comment la génomique peut être appliquée à la gestion des forêts. Nous conseillons vivement aux chercheurs, aux instituts de recherche gouvernementaux, aux compagnies privées et aux citoyens de collaborer afin d’enrayer la propagation des espèces envahissantes de Phytophthora. Pour y parvenir, nous considérons les thèmes suivants comme éléments essentiels en vue de la résolution de la crise sanitaire qui frappe les forêts: i) intégration de la détection des agents pathogènes basée sur l’ADN dans les programmes d’inventaire; ii) conception de méthodes diagnostiques pratiques et abordables basées sur l’ADN; iii) reséquençage des hôtes en tant que modèles pour répertorier les gènes de résistance; iv) prédiction des répercussions des agents pathogènes en se basant sur les données de génomique; et v) accroître le nombre de projets collaboratifs et les efforts de vulgarisation afin de sensibiliser davantage les parties prenantes aux maladies forestières.

Wilding conifers, the naturally regenerated scions of exotic conifer species, are a major ecological and economic issue in New Zealand. Hyperspectral imagery could provide a useful means of monitoring the efficacy of wilding control measures but little research has examined this possibility. Data were collected from an experiment, that included thirty-nine young Pinus contorta (Douglas) trees allocated to a control and two herbicide treatments (triclopyr butoxyethyl ester and diquat dibromide monohydrate). The objectives of this research were to examine the temporal impacts of herbicide on needle discolouration, spectral properties and tree physiology and to develop models to predict photosynthetic parameters from hyperspectral data. In accordance with obvious discolouration on the first day after treatment, values of net photosynthesis rate (A), electron transport rate (ETR), stomatal conductance (G) and optimal quantum yield of photosystem II (Fv/Fm) declined rapidly for plants treated with diquat. Discolouration following application of triclopyr was not evident before the second week, and values of A, ETR, G and Fv/Fm declined slower than those of diquat. Of the tested narrow-band spectral indices calculated from needle spectra photochemical reflectance index (PRI) exhibited the strongest correlation with the four photosynthetic parameters and R2 values between PRI and A, Fv/Fm, ETR and G were, respectively, 0.53, 0.46, 0.68 and 0.29. Models that used raw spectra as inputs showed that sparse partial least squares (SPLS) outperformed the three other approaches tested (PLS, Support Vector Machines, Elastic Net) and R2 values using this approach for A, Fv/Fm, ETR and G were, respectively, 0.64, 0.62, 0.65 and 0.42.

International audience; Phytophthora pluvialis is an oomycete that was first isolated from soil, water, and tree foliage in mixed Douglas-fir-tanoak forests of the US Pacific Northwest (PNW). It was then identified as the causal agent of red needle cast (RNC) of radiata pine (Pinus radiata) in New Zealand (NZ). Genotyping-by-sequencing (GBS) was used to obtain 1,543 single nucleotide polymorphisms (SNPs) across 145 P. pluvialis isolates to characterize the population structure in the PNW and NZ. We tested the hypothesis that P. pluvialis was introduced to NZ from the PNW using genetic distance measurements and population structure analyzes among locations between countries,. The low genetic distance, population heterozygosity, and lack of geographic structure in NZ, suggest a single colonization event from the US followed by clonal expansion in NZ. The PNW Coast Range was proposed as a presumptive center of origin of the currently known distribution of P. pluvialis based on its geographic range and position as the central cluster in a minimum spanning network. The Coastal cluster of isolates were located at the root of every US cluster, and emerged earlier than all NZ clusters. The Coastal cluster had the highest degree of heterozygosity (Hs = 0.254) and median pairwise genetic distance (0.093) relative to any other cluster. Finally, the rapid host diversification between closely related isolates of P. pluvialis in New Zealand, indicate that this pathogen has the potential to infect a broader range of hosts than is currently recognized.

The prediction of carbon uptake by forests across fertility gradients requires accurate characterisation of how biochemical limitations to photosynthesis respond to variation in key elements such as nitrogen (N) and phosphorus (P). Over the last decade, proxies for chlorophyll and photosynthetic activity have been extracted from hyperspectral imagery and used to predict important photosynthetic variables such as the maximal rate of carboxylation (Vcmax) and electron transport (Jmax). However, little research has investigated the generality of these relationships within the nitrogen (N) and phosphorus (P) limiting phases, which are characterised by mass based foliage ratios of N:P ≤ 10 for N limitations and N:P > 10 for P limitations. Using measurements obtained from one year old Pinus radiata D. Don grown under a factorial range of N and P treatments this research examined relationships between photosynthetic capacity (Vcmax, Jmax) and measured N, P and chlorophyll (Chla+b). Using functional traits quantified from hyperspectral imagery we then examined the strength and generality of relationships between photosynthetic variables and Photochemical Reflectance Index (PRI), Sun-Induced Chlorophyll Fluorescence (SIF) and chlorophyll a + b derived by radiative transfer model inversion. There were significant (P < .001) and strong relationships between photosynthetic variables and both N (R2 = 0.82 for Vcmax; R2 = 0.87 for Jmax) and Chla+b (R2 = 0.85 for Vcmax; R2 = 0.86 for Jmax) within the N limiting phase that were weak (R2 < 0.02) and insignificant within the P limiting phase. Similarly, there were significant (P < .05) positive relationships between P and photosynthetic variables (R2 = 0.50 for Vcmax; R2 = 0.58 for Jmax) within the P limiting phase that were insignificant and weak (R2 < 0.33) within the N limiting phase. Predictions of photosynthetic variables using Chla+b estimated by model inversion were significant (P < .001), positive and strong (R2 = 0.64 for Vcmax; R2 = 0.63 for Jmax) within the N limiting phase but insignificant and weak (R2 < 0.05) within the P limiting phase. In contrast, both SIF and PRI exhibited moderate to strong positive correlations with photosynthetic variables within both the N and P limiting phases. These results suggest that quantified SIF and PRI from hyperspectral images may have greater generality in predicting biochemical limitations to photosynthesis than proxies for N and chlorophyll a + b, particularly under high foliage N content, when P is limiting., The project was partly funded through the Resilient Forests programme, which is funded through Scion SSIF as well as the Forest Grower's Levy Trust. Funding was also received from the National Institute for Forest Products Innovation (Project Number NIF073-1819), which comprised contributions from the Australian Government, Australasian Forestry Companies and South Australian and Tasmanian State Governments.

Background and Aims Biotic and abiotic stressors can cause different defoliation patterns within trees. Foliar pathogens of conifers commonly prefer older needles and infection with defoliation that progresses from the bottom crown to the top. The functional role of the lower crown of trees is a key question to address the impact of defoliation caused by foliar pathogens. Methods A 2 year artificial defoliation experiment was performed using two genotypes of grafted Pinus radiata to investigate the effects of lower-crown defoliation on carbon (C) assimilation and allocation. Grafts received one of the following treatments in consecutive years: control–control, control–defoliated, defoliated–control and defoliated–defoliated. Results No upregulation of photosynthesis either biochemically or through stomatal control was observed in response to defoliation. The root:shoot ratio and leaf mass were not affected by any treatment, suggesting prioritization of crown regrowth following defoliation. In genotype B, defoliation appeared to impose C shortage and caused reduced above-ground growth and sugar storage in roots, while in genotype A, neither growth nor storage was altered. Root C storage in genotype B decreased only transiently and recovered over the second growing season. Conclusions In genotype A, the contribution of the lower crown to the whole-tree C uptake appears to be negligible, presumably conferring resilience to foliar pathogens affecting the lower crown. Our results suggest that there is no C limitation after lower-crown defoliation in P. radiata grafts. Further, our findings imply genotype-specific defoliation tolerance in P. radiata.

International audience; The emergence of Phytophthora pluvialis as a foliar pathogen of Douglas fir in New Zealand and the Pacific Northwest United States has raised questions about its interaction with the widespread Swiss needle cast (SNC) disease. During Spring 2017, we repeatedly sampled 30 trees along an environmental gradient in each region and 292 additional trees in a longitudinal transect to assess the P. pluvialis epidemic and the association between P. pluvialis and Nothophaeocryptopus gaeumannii, which are causal agents of SNC. Both pathogens were consistently more abundant in the host’s exotic environment in New Zealand. In both areas, the two pathogens co-exist in different spatial scales for regions and needles. The relative abundance of both pathogens was negatively correlated in the Pacific Northwest, where both presumably have co-existed for longer. Our findings confirmed the interaction of P. pluvialis and N. gaeumannii as foliar pathogens of Douglas fir and suggest a within-site spatial variation in the Pacific Northwest.

International audience; Understanding the epidemiology of infectious diseases in a host population is a major challenge in forestry. Radiata pine plantations in New Zealand are impacted by a foliar disease, red needle cast (RNC), caused by Phytophthora pluvialis. This pathogen is dispersed by water splash with polycyclic infection affecting the lower part of the tree canopy. In this study, we extended an SI (Susceptible-Infectious) model presented for RNC to analyse the key epidemiological drivers. We conducted two experiments to empirically fit the extended model: a detached-needle assay and an in vivo inoculation. We used the detached-needle assay data to compare resistant and susceptible genotypes, and the in vivo inoculation data was used to inform sustained infection of the whole plant. We also compared isolations and real-time quantitative PCR (qPCR) to assess P. pluvialis infection. The primary infection rate and the incubation time were similar for susceptible and resistant genotypes. The pathogen death rate was 2.5 times higher for resistant than susceptible genotypes. Further, external proliferation of mycelium and sporangia were only observed on 28% of the resistant ramets compared to 90% of the susceptible ones. Detection methods were the single most important factor influencing parameter estimates of the model, giving qualitatively different epidemic outputs. In the early stages of infection, qPCR proved to be more efficient than isolations but the reverse was true at later points in time. Isolations were not influenced by the presence of lesions in the needles, while 19% of lesioned needle maximized qPCR detection. A primary infection peak identified via qPCR occurred at 4 days after inoculation (dai) with a secondary peak observed 22 dai. Our results have important implications to the management of RNC, by highlighting the main differences in the response of susceptible and resistant genotypes, and comparing the most common assessment methods to detect RNC epidemics.

Phytophthora pluvialis and Phytophthora kernoviae are the causal agents of important needle diseases on Pinus radiata in New Zealand. Little is known about the epidemiology of the diseases, making the development of control strategies challenging. To investigate the seasonality and climatic drivers of sporulation, inoculum traps, consisting of pine fascicles floating on water in plastic containers, were exchanged fortnightly at five sites in P. radiata plantations between February 2012 and December 2014. Sections of needle baits were plated onto selective media and growth of Phytophthora pluvialis and P. kernoviae recorded. To explore the generalizability of these data, they were compared to detection data for both pathogens from the New Zealand Forest Health Database (NZFHDB). Further, equivalent analyses on infection of Rhododendron ponticum by P. kernoviae in Cornwall, UK allowed the comparison of the epidemiology of P. kernoviae across different host systems and environments. In New Zealand, inoculum of P. pluvialis and P. kernoviae was detected between January–December and March–November, respectively. Inoculum of both species peaked in abundance in late winter. The probability of detecting P. pluvialis and P. kernoviae was greater at lower temperatures, while the probability of detecting P. pluvialis also increased during periods of wet weather. Similar patterns were observed in NZFHDB data. However, the seasonal pattern of infection by P. kernoviae in the UK was the opposite of that seen for sporulation in New Zealand. Phytophthora kernoviae was likely limited by warmer and drier summers in New Zealand, but by colder winter weather in the UK. These results emphasize the importance of considering both environmental drivers and thresholds in improving our understanding of pathogen epidemiology.

International audience; Climate change is expected to increase the frequency and duration of drought in many parts of New Zealand. This may affect the natural lifecycles of plant pathogens, influence host predisposition to infection or disease expression, shift the natural ranges of the pathogens, and alter the rate of genetic change in pathogen populations. Collectively, these influences are likely to affect a range of pathosystems of significant economic importance to New Zealand’s productive sectors. We undertook analyses of potential drought impacts on several diseases of plants important to New Zealand: pea root rot (caused by Aphanomyces euteiches), onion white rot (Sclerotium cepivorum), wheat take-all (Gaeumannomyces graminis var. tritici), wheat crown rot (Fusarium spp.), brassica black leg (Leptosphaeria maculans), grapevine black foot (Ilyonectria/Dactylonectria spp.), kiwifruit sclerotinia rot (Sclerotinia sclerotiorum), and radiata pine red needle cast (Phytophthora pluvialis). For most pathosystems, increased drought is expected to increase disease expression. However, drought may reduce the severity of some diseases, such as Scelerotina rot of kiwifruit and red needle cast of radiata pine. To exemplify how drought can affect different components of the host-pathogen-environment interaction, a case study on red needle cast of radiata pine is presented. We recommend that land-based productive sectors need to better prepare for the deleterious impacts or beneficial opportunities of increased drought for plant diseases in New Zealand.

International audience; Phytophthora pluvialis is associated with early defoliation and shoot dieback in Douglas-fir in Oregon and New Zealand. In 2013, P. pluvialis was described from mixed tanoak-Douglas-fir forests in the Pacific Northwest and concurrently recognized as the main causal agent of red needle cast (RNC) in New Zealand radiata pine plantations. Little is known about its infection cycle and impact on host physiology. P. pluvialis studies in Douglas-fir are challenging due to the ubiquitous presence of the endophyte Phaeocryptopus gaeumannii, which produces similar symptoms and premature defoliation with persistent needle wetness, known as Swiss needle cast (SNC). Nonetheless, our study showed P. pluvialis infection in the presence of SNC. Exclusive expression of P. pluvialis is difficult to achieve as both diseases are promoted by high humidity. Here we established a ‘dry leaf’ strategy to suppress SNC when inoculating Douglas-fir needles for RNC studies. Sheltering plants along with drip irrigation to avoid needle wetness during the P. gaeumannii sporulation period suppressed its development in the new season flush. The diminished endophyte inoculum enabled bias-reduced studies of P. pluvialis impacts on Douglas-fir without the confounding effects of stomatal blockage and premature defoliation caused by P. gaeumannii.