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Iberian oak decline caused by Phytophthora cinnamomi: A spatiotemporal analysis incorporating the effect of host heterogeneities at landscape scale
Abstract
The pathogen Phytophthora cinnamomi is considered a main driver of Iberian oak decline (IOD), a forest disease which decimates holm oaks (Quercus ilex) and cork oaks (Quercus suber) in a multipurpose, silvo‐pastoral and seminatural ecosystem of 3.1 million hectares in the south‐west of Europe. Little is known about the spatial dynamics of Phytophthora cinnamomi and how forest stand characteristics affect the IOD epidemic. Here, we analyse IOD spread over several decades in one such ecosystem by means of a multilevel approach based on (a) identification of diseased sites via repeated aerial imagery at landscape scale, (b) confirmation by subsampling of soil and roots, and iii) an epidemic model accounting for host population heterogeneities. We use a 'self‐exciting' spatiotemporal point process with two additive risk components: an epidemic component represents the inoculum pressure from nearby disease foci, and a background component describes sporadic disease transmission over larger distances or from unobserved sources. Both risk components are found to increase over time, and a lagged power‐law spatial kernel provides the best fit for the observed disease pattern. We estimate that 49% of the secondary infections triggered by a primary source occur within a distance of 250 m. Our results also highlight the role of density and diversity of the host population; we find that the rate of sporadic infections in silvo‐pastoral systems (dehesas) is lower than in forests, and higher in mixed stands and shrub encroached oak lands than in pure stands. These results have direct implications for IOD management, for example the estimated spatial kernel may guide the definition of suitable target areas for localized control measures and help to quantify their success. Our results also suggest that silviculture treatments aimed at controlling the density and species composition of oak stands, as well as the abundance of shrubs, are crucial to the containment of IOD.
... In the Mediterranean woodlands, the oomycete Phytophthora cinnamomi infects the roots of oaks [6] and shrubs [7,8] with the abundance of the parasite contributing to tree death along with other factors [9]. The ecological dynamics of the oomycete are adapted to variations in temperature and humidity across seasons and their abundance and spread will therefore be driven by climate change [10] and originate from recognised disease loci and through sporadic transmission of disease over longer distances [11]. 2 The significance of remote sensing for Earth's surface has grown considerably since the introduction of early weather satellites like Landsat and Nimbus. These satellites have revolutionized the observation of forest and crop canopies through the utilization of visible and infrared imaging, enabling the analysis of light reflection, absorption, and transmission by plant leaves. ...
... On the abaxial side of the leaves, no notable differences are present except for occasional spikes of noise. On the 11 adaxial side, most of the differences within the NIR plateau diminish, with the exception of the band ranging from 750 nm to 820 nm. However, a new development arises in the range of pigments, specifically between 620 nm and 700 nm, where differences between the two groups are apparent. ...
Cork oak tree (Quercus suber L.) symbolises Montado landscape in Portugal and is a central element in the country's social and economic history. In recent decades, the loss of thousands of cork oaks has been reported, revealing the ongoing decline of these agro-forestry ecosystems. This emblematic tree of the Mediterranean Basin is host to the soil-born root pathogen Phytophthora cinnamomi, an active cork oak decline driver. In this framework, the early diagnosis of trees infected by the oomycete by non-invasive methods should contribute to the sustainable management of cork oak ecosystems and motivated this work. Using leaf reflectance spectroscopy it was possible to distinguish plants inoculated with P. cinnamomi from non-inoculated plants in a long course assay and to argue about the factors contributing to this differentiation. Spectral acquisitions in the visible-near infrared (400–1100 nm) were performed at 63, 78, 91, 126 and 248 days after inoculation (DAI), on the abaxial and adaxial faces of the leaves, and the spectral data was arranged in a three-way array of samples × wavelengths × days. The separation of the two plant groups were attributed to variations in water content (4v (O−H)) and/or a shift in the red edge and to structural modifications in the epidermal layer and/or the mesophyll of the leaves observed in the visible range. These spectral signatures can assist in the field identification of cork oaks that are interacting with P. cinnamomi.
... As a result of climate change, predisposing factors like successive droughts, temperature, and humidity are thought to be the major attributed factors implicated in the decline of oak worldwide 3,4,7,8,[13][14][15][16][17][18][19][20][21][22][23][24][25][26] . The present study aimed at epidemiological modeling of the charcoal disease on oak forests in the Zagros habitat, west of Iran. ...
The first national-wide epidemiological modeling of oak charcoal disease in the Zagros forest of Iran is presented. We estimate that the areas prone to epidemic development can be predicted by a combination of massive on-site data analysis and machine-learning approaches. Data collected on the affected trees in an area of 3.1 M ha of oak forests and different bioclimatic/environmental variables and host distribution data were implemented in disease predictive modeling. To my knowledge, the first holistic survey in the field of plant pathology in Iran.
... However, a substantial portion of this region is devoted to agro-silvo-pastoral uses which hamper regeneration and drive trees towards an aging state. For years the decay of cork oak forests has had deleterious effects on cork productivity (Acacio et al. 2021;Cardillo et al. 2021;Vogiatzakis et al. 2020). To overcome this, over the last few decades of the twentieth century the European Union invested substantially in funding restocking of cork oak on abandoned arable farming land (Duque-Lazo et al. 2018). ...
Virgin cork is a little-known, sustainable and relatively scarce raw material. However, its global output is expected to increase substantially as recent cork oak plantations are stripped for the first time. The work described here aimed to examine the factors underlying the mechanical properties of granulated cork, most particularly the type of cork (virgin or reproduction), and to develop a technique to deliver fast and accurate assessments of the effects of said factors. A batch of virgin cork was boiled, dried, ground and graded following standard granule classification procedures according to size and density. The resulting granulates were then compared with equivalent commercial-grade reproduction cork granulates. Physical variables (tapped density and moisture content) were measured and elastic recovery and Young’s modulus were used as proxies for mechanical properties. Image analysis was used to study the size, shape and colour of the cork particles. ANOVA results show significant effects of particle size, density class, type of cork and first and second order interactions between most variables. Density class clearly reached the highest level of significance, whereas the type of cork was less critical. A very strong correlation was found between granulates’ elastic recovery and their tapped density (R² = 0.98; RMSE < 1%). Likewise, greyscale imaging revealed a good adjustment between tapped density and grey level (R² = 0.84; RMSE = 24 g·l⁻¹). The primary conclusion was that the differences between virgin and standard cork granulates are small and should have no effect on less demanding applications. Image analysis is likely to prove useful in further, more in-depth studies.
... In Western Australia, for example, it was estimated that more than 40% of the described plant species were susceptible to P. cinnamomi (Shearer et al., 2004). Severe impacts were also observed on chestnut stands in the United States and Europe and native oak species in Europe (Brasier et al., 1993;Cardillo et al., 2021;Diogo et al., 2022;Prigigallo et al., 2015). Another important example in forestry is the invasive species P. ramorum, which is responsible for sudden oak death in North America (LeBoldus et al., 2022;Rizzo et al., 2002) and sudden larch death in the UK (Brasier & Webber, 2010). ...
Forests are threatened by many natural stressors intensified by climate change and anthropogenic activities, which tend to increase their susceptibility to pests and pathogens. Consequently, oomycete‐related forest decline or dieback cases are increasing in natural, urban, and agricultural landscapes. It is in this context that Christmas tree growers from Southern Québec, Canada, are experiencing root rot problems, with reported incidences up to 25%. In a previous study, seven Phytophthora spp. were associated with this root rot problem, but the overall diversity of oomycetes has not yet been investigated. Hence, in this study, we use a metabarcoding approach to provide an overview of the diversity, richness, and composition of the oomycete community in fir plantations compared to surrounding natural forests. We showed that the P. cryptogea cluster, P. europaea cluster, P. sansomeana , and P. chlamydospora cluster were significantly more abundant in soils collected from plantations under diseased trees and confirmed that the P. europaea cluster (including P. abietivora ) was most frequently associated with trees showing Phytophthora root rot‐like symptoms. Finally, we report that land use (anthropogenic activities) shapes oomycete diversity, while plantations can act as a gateway for invading natural forests. In fact, the results presented here suggested that the P. europaea cluster might already have crossed this boundary and that other species might follow, advocating the importance of improved surveillance of oomycete diversity in various environments.
... These pests and diseases are associated with Iberian oak decline that affects both cork and holm oaks (Tiberi et al., 2016). In particular, the presence of Phytophthora cinnamomi Rands. is considered the principle cause of the Iberian oak decline (Brasier, 1996;Cardillo et al., 2021;de Sampaio e Paiva Camilo-Alves et al., 2013). However, if the incidence of pests and diseases in this stand were sustained over time, it could be interpreted that, if the stand is in good condition and the populations are kept in balance, the presence of these diseases and pests will not reduce tree vigor and the trees will remain in good health state. ...
Good knowledge of the factors that influence cork quality and the health of forests is essential when making decisions regarding the management of productive cork oak forests. The quality of cork planks depends on: plank thickness, plank porosity and the presence of anomalies. So far, no studies have evaluated cork quality based on cork anomalies, partly due to the difficulty of obtaining adequate data. In 1985, it was developed the first Cork Quality Field Assessment Plan (CQFAP) to provide information about the quality of harvested cork by collecting data of very high quality. This work analyzes the anomalies present in 2049 cork sampling units collected from ten stands under the CQFAP for the period 1986–2012 in three consecutive cork stripping cycles. Data on diseases, pests and stripping damages are also analyzed in the 654 trees where cork sampling units were collected in the third stripping cycle. Additionally, mean monthly temperature and precipitation values for the 35 years covering the three stripping periods were calculated. A progressive deterioration of cork quality was observed in the sampled cork oak stands. It was found a positive relationship between cork thickness and temperature indicating that the cork growing period could be extended when temperatures are moderate. Sampled cork oaks were more affected by Cerambycidae attacks and Coraebus undatus indicating their prevalent nature. The presence of Coraebus undatus were higher in stands with good health status. The studied diseases were Biscogniauxia mediterranea, Phytophthora sp. and fungi of the family Botryosphaeriaceae, finding a not previously reported correlation between the presence of Crematogaster scutellaris and the three studied diseases. Stripping damages increase with smaller cork thickness but climate is not a decisive factor for a proper stripping. Although having room for improvement, the CQFAP is proving to be an effective tool for assessing the quality of cork, the health status of cork oak forests and the evolution of these forests over time. The information provided could be also used to identify places worthy of further studying. The main recommendation for improving the CQFAP would be to monitor the same trees in each consecutive sampling for properly monitoring cork thickness and the presence of defects to be used as a proxy for tree health. Regarding forest management, the main recommendations would be to extend the length of stripping cycles to enhance cork production, and to use the new tools and systems for cork stripping to reduce damage.
... Mediterranean oak forest dynamics mirror the impact of anthropogenic factors and environmental variables over time, with the expectation of a more pronounced decline in the long term [5][6][7]. Canopy defoliation, dry peripheral branches, black spots, and exudations on the trunk are visually observable symptoms used for decline prognostics, sometimes complemented by the identification of Phytophthora cinnamomi in the rhizosphere of trees and the adjacent soils [8,9]. This oomycete invades the roots of the cork oak leading to cell death of the infected tissues, triggering a localized and distal defence response [10][11][12]. ...
Cork oak decline in Mediterranean forests is a complex phenomenon, observed with remarkable frequency in the southern part of the Iberian Peninsula, causing the weakening and death of these woody plants. The defoliation of the canopy, the presence of dry peripheral branches, and exudations on the trunk are visible symptoms used for the prognosis of decline, complemented by the presence of Phytophthora cinnamomi identified in the rhizosphere of the trees and adjacent soils. Recently, a large proteomic dataset obtained from the leaves of cork oak plants inoculated and non-inoculated with P. cinnamomi has become available. We explored it to search for an optimal set of proteins, markers of the biological pattern of interaction with the oomycete. Thus, using published data from the cork oak leaf proteome, we mathematically modelled the problem as an α, β-k-Feature Set Problem to select molecular markers. A set of proteins (features) that represent dominant effects on the host metabolism resulting from pathogen action on roots was found. These results contribute to an early diagnosis of biochemical changes occurring in cork oak associated with P. cinnamomi infection. We hypothesize that these markers may be decisive in identifying trees that go into decline due to interactions with the pathogen, assisting the management of cork oak forest ecosystems.
... While its center of origin has recently been demonstrated to be Southeast Asia (Shakya et al., 2021), the presence of disease symptoms typical of P. cinnamomi infections has been reported in Europe as early as the XIX century (Bergot et al., 2004). This pathogen has been demonstrated as main causal agent of the severe decline of Q. suber in Spain, Portugal and Italy (Robin et al., 1998;Camilo-Alves et al., 2013;Scanu et al., 2013;Moricca et al., 2016;Avila et al., 2017;Jung et al., 2018;Seddaiu et al., 2020;Cardillo et al., 2021). Infection of P. cinnamomi occurs predominantly through the roots, from where it spreads upwards to the trunk leading to the formation of bleeding collar lesions (Bergot et al., 2004;Jung et al., 2018). ...
Phytophthora cinnamomi Rands is a cosmopolite pathogen of woody plants which during the last couple of centuries has spread all over the world from its center of origin in Southeast Asia. In contrast to Chinese cork oak (Quercus variabilis Blume) forests native to Asia, which are generally healthy despite the presence of the pathogen, the populations of Cork oaks (Quercus suber L.) in Europe have been severely decimated by P. cinnamomi. The present study aims at identifying the differences in the early proteomic and metabolomic response of these two tree species that lead to their differences in susceptibility to P. cinnamomi. By using micropropagated clonal plants, we tried to minimize the plant-to-plant differences in the defense response that is maximized by the high intraspecific genetic variability inherent to the Quercus genus. The evolution on the content of Phytophthora proteins in the roots during the first 36 h after inoculation suggests a slower infection process in Q. variabilis plants. These plants displayed a significant decrease in sugars in the roots, together with a downregulation of proteins related to carbon metabolism. In the leaves, the biggest changes in proteomic profiling were observed 16 h after inoculation, and included increased abundance of peroxidases, superoxide dismutases and glutathione S-transferases in Q. variabilis plants, which probably contributed to decrease its susceptibility to P. cinnamomi.
... Rigorous analysis of fuel dynamics could be worthwhile across several P. cinnamomi-impacted forests where additional environmental factors can modify wildfire and/ or disease to result in interactive effects. In the southern Iberian Peninsula, P. cinnamomi is widespread, impactful, and actively spreading [30,61,66]; this region is also simultaneously experiencing shifting rural demographics which appear to increase vegetation density and accumulate fuel (Fig. 2) [67,68]. In combination, these two landscape changes could result in increased fire impacts. ...
Purpose of Review
I aim to contextualize wildfire-disease interactions with the goal of building a better understanding of where these may be of ecological importance and problems for sustainable forest management.
Recent Findings
While wildfire-disease interactions have been documented, they are not well represented in the ecological literature, probably because they require considerable effort or serendipity to rigorously quantify. Examples of disease-fire interactions are relatively limited and tend to be clearer in systems where fire and disease are management problems. The most resolved systems include Phytophthora pathogens although wildfire-disease interactions are not limited to these pathogens. Documented interactions encompass a range of effects which include the magnification of problems associated with each disturbance. Wildfire-disease interactions are also likely to shape basic ecological function in systems where both wildfire and disease are common but not necessarily critical management problems. Climate change has altered the fundamental controls on both fire and disease suggesting it will also alter the magnitude and likelihood (occurrence or detection) of disease-fire interactions.
Summary
I present a framework for linking wildfire-disease interactions and highlight the importance of host community/fuels structure on linking and mediating these interactions. I provide a series of examples where understanding interactive effects, interfacing with climate change, and the magnitude of changes to wildfire and disease intensification are of practical value and/or advance basic ecological knowledge. While much remains to be understood about these interactions, I make the argument that, in some cases, management can address both problems simultaneously.
The cork oak tree (Quercus suber L.) symbolizes the Montado landscape in Portugal and is a central element in the country’s social and economic history. In recent decades, the loss of thousands of cork oaks has been reported, revealing the ongoing decline of these agroforestry ecosystems. This emblematic tree of the Mediterranean Basin is host to the soil-born root pathogen Phytophthora cinnamomi, an active cork oak decline driver. In this framework, the early diagnosis of trees infected by the oomycete by non-invasive methods should contribute to the sustainable management of cork oak ecosystems, which motivated this work. Gas exchange and visible/near-infrared (400–1100 nm) reflectance spectroscopy measurements were conducted on leaves of both control and P. cinnamomi inoculated plants. These measurements were taken at 63, 78, 91, 126, and 248 days after inoculation. Additionally, at the end of the experiment, biochemical assays of pigments, sugars, and starch were performed. The spectroscopic measurements proved effective in distinguishing between control and inoculated plants, while the standard gas exchange and biochemistry data did not exhibit clear differences between the groups. The spectral data were examined both daily and globally, utilizing the PARAFAC method applied to a three-way array of samples × wavelengths × days. The separation of the two plant groups was attributed to variations in water content (4v (O−H)); shifts in the spectra red edge; and structural modifications in the epidermal layer and leaves’ mesophyll. These spectral signatures can assist in the field identification of cork oaks that are interacting with P. cinnamomi.
Phytophthora cinnamomi is one of the most important plant pathogens in the world, causing root rot in more than a thousand plant species. This observational study was carried out on a P. cinnamomi infected heathland of Erica umbellata used as goat pasture. The patterns and shapes of disease foci and their distribution were described in a spatial and temporal context using an aerial photograph record. A set of topographic traits was selected on the basis of a disease dynamic hypothesis and their effects on observed spatial disease patterns were analyzed. Incipient infections situated in flat terrain expanded as compact circular front patterns with a low growth rate. On slopes, disease patches developed more rapidly down slope, forming parabolic shapes. The axis direction of the parabolas was highly correlated with terrain aspect, while the parabolic amplitude was associated with land curvature and slope. New secondary foci appeared over the years producing an accelerated increase of the affected surface. These new foci were observed in sites where disease density was higher or near sites more frequently visited by animals such as the stable or the forage crop. In contrast, a smaller number of disease foci occur in areas which animals are reluctant to visit, such as where they have a short range of vision. Our results suggest that 1) the growth of existing P. cinnamomi foci is controlled by a combination of root-to-root contact and water flows, 2) the increase in the diseased area arises mainly from the multiplication of patches, 3) the formation of new foci is mediated by long-distance transport due to the movement of animals and humans along certain preferential pathways, and 4) geomorphology and topography traits are associated with the epidemiology of this soil-borne pathogen.
The availability of geocoded health data and the inherent temporal structure of communicable diseases have led to an increased interest in statistical models and software for spatio-temporal data with epidemic features. The open source R package surveillance can handle various levels of aggregation at which infective events have been recorded: individual-level time-stamped geo-referenced data (case reports) in either continuous space or discrete space, as well as counts aggregated by period and region. For each of these data types, the surveillance package implements tools for visualization, likelihoood inference and simulation from recently developed statistical regression frameworks capturing endemic and epidemic dynamics. Altogether, this paper is a guide to the spatio-temporal modeling of epidemic phenomena, exemplified by analyses of public health surveillance data on measles and invasive meningococcal disease.
Biological invasions, resulting from deliberate and unintentional species transfers of insects, fungal and oomycete organisms, are a major consequence of globalization and pose a significant threat to biodiversity. Limiting damage by non-indigenous forest pathogens requires an understanding of their current and potential distributions, factors affecting disease spread, and development of appropriate management measures. In this review, we synthesize innate characteristics of invading organisms (notably mating system, reproduction type, and dispersal mechanisms) and key factors of the host population (namely host diversity, host connectivity, and host susceptibility) that govern spread and impact of invasive forest pathogens at various scales post-introduction and establishment. We examine spread dynamics for well-known invasive forest pathogens, Hymenoscyphus fraxineus (T. Kowalski) Baral, Queloz, Hosoya, comb. nov., causing ash dieback in Europe, and Cryphonectria parasitica, (Murr.) Barr, causing chestnut blight in both North America and Europe, illustrating the importance of host variability (diversity, connectivity, susceptibility) in their invasion success. While alien pathogen entry has proven difficult to control, and new biological introductions are indeed inevitable, elucidating the key processes underlying host variability is crucial for scientists and managers aimed at developing effective strategies to prevent future movement of organisms and preserve intact ecosystems.
Disease ecology is a new approach to the understanding of the spread and dynamics of pathogens in natural and man-made environments. Defining and describing the ecological niche of the pathogens is one of the major tasks for ecological theory, as well as for practitioners preoccupied with the control and forecasting of established and emerging diseases. Niche theory has been periodically revised, not including in an explicit way the pathogens. However, many progresses have been achieved in niche modeling of disease spread, but few attempts were made to construct a theoretical frame for the ecological niche of pathogens. The paper is a review of the knowledge accumulated during last decades in the niche theory of pathogens and proposes an ecological approach in research. It quest for new control methods in what concerns forest plant pathogens, with a special emphasis on fungi like organisms of the genus Phytophthora. Species of Phytophthora are the most successful plant pathogens of the moment, affecting forest and agricultural systems worldwide, many of them being invasive alien organisms in many ecosystems. The hyperspace of their ecological niche is defined by hosts, environment and human interference, as main axes. To select most important variables within the hyperspace, is important the understanding of the complex role of pathogens in the ecosystems as well as for control programs. Biotic relationships within ecosystem of host-pathogen couple are depicted by ecological network and specific metrics attached to this. The star shaped network is characterized by few high degree nodes, by short path lengths and relatively low connectivity, premises for a rapid disturbance spread.
The dilution effect, that high host species diversity can reduce disease risk, has attracted much attention in the context of global biodiversity decline and increasing disease emergence. Recent studies have criticized the generality of the dilution effect and argued that it only occurs under certain circumstances. Nevertheless, evidence for the existence of a dilution effect was reported in about 80% of the studies that addressed the diversity–disease relationship, and a recent meta-analysis found that the dilution effect is widespread. We here review supporting and critical studies, point out the causes underlying the current disputes. The dilution is expected to be strong when the competent host species tend to remain when species diversity declines, characterized as a negative relationship between species’ reservoir competence and local extinction risk. We here conclude that most studies support a negative competence–extinction relationship. We then synthesize the current knowledge on how the diversity–disease relationship can be modified by particular species in community, by the scales of analyses, and by the disease risk measures. We also highlight the complex role of habitat fragmentation in the diversity–disease relationship from epidemiological, evolutionary and ecological perspectives, and construct a synthetic framework integrating these three perspectives. We suggest that future studies should test the diversity–disease relationship across different scales and consider the multiple effects of landscape fragmentation.
Wild boar (Sus scrofa) populations in many areas of the Palearctic including the Iberian Peninsula have grown continuously over the last century. This increase has led to numerous different types of conflicts due to the damage these mammals can cause to agriculture, the problems they create in the conservation of natural areas, and the threat they pose to animal health. In the context of both wildlife management and the design of health programs for disease control, it is essential to know how wild boar are distributed on a large spatial scale. Given that the quantifying of the distribution of wild species using census techniques is virtually impossible in the case of large-scale studies, modeling techniques have thus to be used instead to estimate animals’ distributions, densities, and abundances. In this study, the potential distribution of wild boar in Spain was predicted by integrating data of presence and environmental variables into a MaxEnt approach. We built and tested models using 100 bootstrapped replicates. For each replicate or simulation, presence data was divided into two subsets that were used for model fitting (60% of the data) and cross-validation (40% of the data). The final model was found to be accurate with an area under the receiver operating characteristic curve (AUC) value of 0.79. Six explanatory variables for predicting wild boar distribution were identified on the basis of the percentage of their contribution to the model. The model exhibited a high degree of predictive accuracy, which has been confirmed by its agreement with satellite images and field surveys. © 2014 Ministerio de Agricultura Pesca y Alimentacion. All Rights Reserved.
The availability of geocoded health data and the inherent temporal structure of communicable diseases have led to an increased interest in statistical models and software for spatio-temporal data with epidemic features. The open source R package surveillance can handle various levels of aggregation at which infective events have been recorded: individual-level time-stamped geo-referenced data (case reports) in either continuous space or discrete space, as well as counts aggregated by period and region. For each of these data types, the surveillance package implements tools for visualization, likelihoood inference and simulation from recently developed statistical regression frameworks capturing endemic and epidemic dynamics. Altogether, this paper is a guide to the spatio-temporal modeling of epidemic phenomena, exemplified by analyses of public health surveillance data on measles and invasive meningococcal disease.
Phytophthora is a genus of aquatic plant pathogens well known as disease agents in agri-culture and forestry. They are water molds, Oomycetes, with swimming zoospores and thick-walled resting spores. Many species are benign in coevolved plant communities, but given the opportunity of introduction to new hosts in new environments, new opportunities for dispersal, or unexpected sexual recombination, they are causing dramatic epidemics in forests around the world. Phytophthora ramorum (cause of sudden oak death in western North America and also damaging in Europe) provides a current example, dramatically illustrating the potential of these pathogens for rapid ecological (and economic) damage. Phytophthora cinnamomi and P. lateralis are also alien to Europe and North America but with different epidemiological strategies. By comparing these three related pathogens and the different consequences of their invasions, some predictions for the future of our forests are possible.
Invasive pathogens are becoming increasingly important in forested ecosystems, yet they are often difficult to study because of their rapid transmission. The rate and extent of pathogen spread are thought to be partially controlled by variation in host characteristics, such as when host size and location influence susceptibility. Few host-pathogen systems, however, have been used to test this prediction. We used Port Orford cedar (Chamaecyparis lawsoniana), a foundation tree species in riparian areas of California and Oregon (USA), and the invasive oomycete Phytophthora lateralis to assess pathogen impacts and the role of host characteristics on invasion. Across three streams that had been infected for 13–18 years by P. lateralis, we mapped 2241 trees and determined whether they had been infected using dendrochronology. The infection probability of trees was governed by host size (diameter at breast height [DBH]) and geomorphic position (e.g., active channel, stream bank, floodplain, etc.) similarly across streams. For instance, only 23% of trees ,20 cm DBH were infected, while 69% of trees !20 cm DBH were infected. Presumably, because spores of P. lateralis are transported downstream in water, they are more likely to encounter well-developed root systems of larger trees. Also because of this water-transport of spores, differences in infection probability were found across the geomorphic positions: 59% of cedar in the active channel and the stream bank (combined) were infected, while 23% of trees found on higher geomorphic types were infected. Overall, 32% of cedar had been infected across the three streams. However, 63% of the total cedar basal area had been killed, because the greatest number of trees, and the largest trees, were found in the most susceptible positions. In the active channel and stream bank, 91% of the basal area was infected, while 46% was infected across higher geomorphic positions. The invasion of Port Orford cedar populations by P. lateralis causes profound impacts to population structure and the invasion outcome will be governed by the heterogeneity found in host size and location. Models of disease invasion will require an understanding of how heterogeneity influences spread dynamics to adequately predict the outcome for host populations.
Feral pigs have long been implicated as potential vectors in the spread of the devastating plant pathogen Phytophthora cinnamomi due to their rooting and wallowing activities which may predispose them as vectors of infested soil. In this study, we aim to determine whether feral pigs have the potential to act as vectors of plant pathogens such as P. cinnamomi through their feeding activity. The typically omnivorous diet of feral pigs may also lead to the passage of P. cinnamomi infected plant material through their digestive system. This study investigates the potential for feral pigs to pass viable P. cinnamomi in their faeces following the ingestion of millet seeds, pine plugs and Banksia leptophilia roots inoculated with P. cinnamomi. Recovery rates of P. cinnamomi from the millet seeds, pine plugs and B. leptophilia roots following a single ingested bolus were 33.2, 94.9 and 10.4 %, respectively supported by quantitative PCR analysis. These results demonstrate that P. cinnamomi remain viable within infected plant material following passage through the pig digestive tract, although the digestive processes reduce the pathogen’s viability. An inverse relationship was observed between the viability of infected material and passage time, suggesting that partially digested plant material provides protection for P. cinnamomi against the adverse environmental conditions of the pig digestive tract. Phytophthora cinnamomi remained viable for up to 7 days in larger pieces of colonised woody plant material such as the pine plugs. A plant infection trial using passaged P. cinnamomi colonised pine plugs showed that even material that remained in the digestive tract for 7 days was capable of infecting and killing healthy plants, susceptible to P. cinnamomi. This study provides compelling evidence that feral pigs have the ability to transport viable P. cinnamomi in their digestive tract.
This study determined spatio-temporal invasion dynamics of Phytophthora cinnamomi, examined differences between disease centres and inferred mechanisms of invasion. Patch disease extension was measured from aerial photographs of three Banksia woodland areas infested with P. cinnamomi. Disease extension was also determined from the fronts of six disease centres in Banksia woodland biomes and a disease front in Eucalyptus marginata forest. A localised, salient, disjunct pattern of spatial variation in upslope disease extension that occurred in all disease centres between years was probably due to growth of P. cinnamomi in major lateral roots and infection of plants by root to root contact. The square root of the area invaded was significantly related to year after first assessment (R
2 = 0.59–0.97). Linear rates of disease extension from baselines with years after first assessment ranged from 0.1 ± 0.07 and 1.46 ± 0.39 m/year. Differences in P. cinnamomi isolation frequency, community structure and measured variables in different soils did not indicate reasons for the variation in rate of invasion between Banksia woodland disease centres. Management options to limit invasion will depend on whether disease extension is the result of unrestricted movement of infectious propagules in overland and subsurface flows, or relatively restricted growth through roots and root to root contact. The hierarchy of factors affecting the invasive success of P. cinnamomi is discussed.
Epidemiology involves the study of the temporal, spatial, and spatio-temporal dynamics of disease in populations, and the utilization of results of experiments and surveys to describe, understand, compare, and predict epidemics. Such understanding and description of epidemics can lead directly to the development and evaluation of efficient control strategies and tactics. Mathematical and statistical models are key tools of the epidemiologist. Recent advances in statistics, including linear and nonlinear mixed models, are allowing a more appropriate matching of data type and experimental (or survey) design to the statistical model used for analysis, in order to meet the objectives of the investigator. Coupled ordinary and partial differential equations, as well as simpler growth-curve equations, are especially useful deterministic models for representing plant disease development in fields in time and space over single seasons or many years, and their use can lead to appraisal of control strategies through metrics such as the basic reproduction number, a summary parameter that may be calculated for many general epidemic scenarios. Recently, compelling arguments have been made for the use of Bayesian decision theory in developing and evaluating real-time disease prediction rules, based on measured disease or weather conditions and either empirical or mechanistic models for disease or control intervention. Through some simple calculations of predictor accuracy and (prior) probability of an epidemic (or the need for control), the success of any predictor can be quantified in terms of the estimated probability of random observations being epidemics when predicted to be epidemics or not epidemics. Overall, despite the many contributions in epidemiology over the past four decades, more effort is still needed to convince those outside of epidemiology to more fully use epidemiological results and insights into the development and evaluation of disease controls.
Short-time human travel behaviour can be described by a power law with respect to distance. We incorporate this information in space-time models for infectious disease surveillance data to better capture the dynamics of disease spread. Two previously established model classes are extended, which both decompose disease risk additively into endemic and epidemic components: a spatio-temporal point process model for individual-level data and a multivariate time-series model for aggregated count data. In both frameworks, a power-law decay of spatial interaction is embedded into the epidemic component and estimated jointly with all other unknown parameters using (penalised) likelihood inference. Whereas the power law can be based on Euclidean distance in the point process model, a novel formulation is proposed for count data where the power law depends on the order of the neighbourhood of discrete spatial units. The performance of the new approach is investigated by a reanalysis of individual cases of invasive meningococcal disease in Germany (2002-2008) and count data on influenza in 140 administrative districts of Southern Germany (2001-2008). In both applications, the power law substantially improves model fit and predictions, and is reasonably close to alternative qualitative formulations, where distance and order of neighbourhood, respectively, are treated as a factor. Implementation in the R package surveillance allows the approach to be applied in other settings.
Mortality events in cork and holm oaks have occurred in the Mediterranean basin since the beginning of the XX century, but severity of decline increased during the 1980s. By that time, the exotic soil borne pathogen Phytophthora cinnamomi was often recovered from declining stands and since then it has been considered the main factor associated with decline. This work analyses data concerning P. cinnamomi surveys in cork and holm oaks trees, pathogenicity tests carried out in controlled experiments, studies about the influence of site characteristics in tree decline and approaches to control the disease. Results of field surveys showed that the pathogen is widespread and pathogenicity tests suggested that host susceptibility to the pathogen is moderate when seedlings are in appropriate watering conditions, particularly cork oaks. Occurrence of decline is also associated with soil characteristics that interfere with root expansion and water retention. We assessed the relative importance of each factor involved in decline and revised the role of P. cinnamomi in cork and holm oak decline.
Understanding biological invasions requires information on the history of spatial spread, as well as measures of landscape and biotic features that control habitat invasibility. Because invasive species often spread quickly over large areas, attaining these two sets of information simultaneously is uncommon. We studied the spread of a fatal nonnative root pathogen, Phytophthora lateralis, across a heterogeneous landscape of its host, Port Orford cedar (Chamaecyparis lawsoniana ). Within our 37-km2 study area in southwestern Oregon and northwest California, Port Orford cedar populations are generally restricted to riparian zones along creeks. The pathogen is spread between watersheds in two ways: (1) by spore-infested material being dislodged from vehicles, and (2) by animals or people moving infested mud (i.e., via foot traffic). Using dendrochronological techniques, we determined the date of infection for dead cedars and reconstructed spread history across our study area from 1977 to 1999. Twenty-six of the 36 (72%) separate infection events we identified were caused by dispersal via vehicles along roads, and the remainder by foot traffic. Survival analysis demonstrated that cedar populations in creeks crossed by roads were more likely to be infected than those creeks that were not crossed by roads. Also, a comparison of minimum dispersal distances showed infections that moved via road moved significantly farther than those vectored by foot traffic, and the distance infection traveled declined significantly through time. We also coupled our spread history with measures of landscape and host features, including abundance of potential host trees, the distance from the road surface to the nearest potential host, length of road in immediate contact with the riparian zone, catchment area (a measure of stream flow), elevation, slope, and solar ra- diation. Our results show that catchment area, host abundance, and proximity to the nearest tree are significantly and positively associated with infection risk. Our study demonstrates that increased connectivity between invasible sites created by the presence of roads can increase invasion success of a plant pathogen. We also document that successful pathogen invasion can be governed by both physical landscape features and attributes of host plant
Aims
The importance of soil properties as determinants of tree vitality and Phytophthora cinnamomi root infections was analysed.
Methods
The study comprised 96 declining stands in western Spain, where declining and non-declining holm oak (Quercus ilex L.) trees were sampled. Soil properties (soil depth, Ah horizon thickness, texture, pH, redox potential, soil bulk density and N-NH4+ and N-NO3− concentrations) and P. cinnamomi infections were assessed.
Results
Tree mortality rates increased with low soil bulk densities, which were also associated with more P. cinnamomi-infected trees. Occurrence of infected trees was higher in fine textured soils and in thick Ah horizons. Fine textured soils favoured trees, but with the presence of P. cinnamomi their health status deteriorated. Soil under declining trees had higher N-NO3−/N-NH4+ ratio values than under non-declining trees. Additional soil properties changes associated to grazing were not related to decline and P. cinnamomi infections.
Conclusions
The implications of P. cinnamomi in holm oak decline and the influence of soil properties as contributors to pathogen activity were demonstrated. Fine soil textures and thick Ah horizons, usually favourable for vigour and vitality of trees growing in the Mediterranean climate, were shown to be disadvantageous soil properties if P. cinnamomi was present. Fine soil textures and thick Ah horizons are frequently related with higher levels of soil moisture, which increase the inoculum of the pathogen and favours root infection. Grazing does not seem to be directly linked to Q. ilex health status or P. cinnamomi root rot.
During one spring season, 12 Phytophthora species, two Phytophthora hybrids, three Halophytophthora species and three Phytopythium species, were isolated from 48 waterways across Western Australia. The waterways were sampled using nylon mesh bags containing leaf baits of up to six different plant species and were isolated by plating necrotic lesions on these onto Phytophthora-selective agar media. Phytophthora species were isolated from all except one waterway. Of the Phytophthora species isolated, eight are
known while the remaining four are undescribed taxa. Six of the Phytophthora species and the two hybrids are from clade 6. The two hybrids and P. inundata were the predominant species recovered. Recoveries from different plant leaf baits varied with the best two baits being Pittosporum undulatum and Banksia attentuata; and from these two combined all Phytophthora species were isolated. There was a marked difference in the Phytophthora diversity in the waterways from different regions. This is the first comprehensive study
from Australia to examine the Phytophthora communities in waterways, and advances our understanding of the role of these oomycetes in natural and anthropized ecosystems.
The dynamics of infectious diseases can be affected by genetic diversity within host populations, species diversity within host communities, and diversity among communities. In principle, diversity can either increase or decrease pathogen transmission and disease risk. Theoretical models and laboratory experiments have demonstrated that a dilution effect (decreased disease risk with increasing diversity) can occur under a wide range of conditions. Field studies of plants, aquatic invertebrates, amphibians, birds, and mammals demonstrate that the phenomenon indeed does occur in many natural systems. A dilution effect is expected when (a) hosts differ in quality for pathogens or vectors; (b) higher quality hosts tend to occur in species-poor communities, whereas lower quality hosts tend to occur in more diverse communities; and (c) lower quality hosts regulate abundance of high-quality hosts or of vectors, or reduce encounter rates between these hosts and pathogens or vectors. Although these conditions char...
Soil-borne species of Phytophthora were isolated from 19 of 30 examined oak forest areas in Italy. The frequency of isolated Phytophthora spp. (35.2%) was significantly correlated with soil pH and longitude of the sites. Eleven Phytophthora species were detected. Phytophthora cambivora, P. cinnamomi and P. cactorum were recovered from sites in central and southern Italy whereas P. quercina was isolated in the northern and central part of the country. Phytophthora citricola occurred all over Italy. Phytophthora quercina was the only species significantly associated with declining oak trees.
Les Phytophthora dans les chênaies d'Italie et leur association avec les chênes dépérissants
Des Phytophthora ont été isolés du sol dans 19 sites parmi 30 sites analysés dans des chênaies italiennes. La fréquence d'isolement de Phytophthora spp. (35,2%) était corrélée significativement avec le pH du sol et la longitude des sites. Onze espèces de Phytophthora ont été trouvées. Phytophthora cambivora, P. cinnamomi et P. cactorum ont été trouvés dans le centre et le sud de l'Italie et le P. quercina dans le nord et le centre. Phytophthora citricolaétait présent dans l'ensemble de l'Italie. Phytophthora quercinaétait la seule espèce associée significativement avec des chênes dépérissants.
Vorkommen von Phytophthora Arten in Eichenbeständen in Italien und deren Bezug zu absterbenden Eichen
Bodenbürtige Phytophthora Arten wurden in 19 von 30 untersuchten Eichenbeständen in Italien isoliert. Die Korrelationen zwischen der Häufigkeit der isolierten Phytophthora spp. und dem Boden pH sowie der geographischen Länge der Standorte waren statistisch signifikant. Phytophthora cambivora, P. cinnamomi und P. cactorum wurden an Standorten in Zentral- und Süditalien nachgewiesen, während P. quercina in Zentral- und Norditalien vorhanden waren. Phytophthora citricola kam in ganz Italien vor. Phytophthora quercina war die einzige Arte mit einer deutlichen Vergesellschaftung mit absterbenden Eichen.
Dehesas are the most widespread agroforestry systems in Europe, where they cover 3.1 million hectares. They are multipurpose open woodlands, mostly created by clearing the natural forests, where livestock rearing, cereal cropping, cork and firewood harvesting, and hunting are combined. In dehesas, trees can be seen as “ecosystem engineers”, as they allow the maintenance of grass production in poor soils under a semiarid climate. We summarize the most outstanding results on both the effect of trees on the production and quality of the understorey (crop and native grasses) and also on the consequences of reduced tree density for the physiological condition and production of trees. The ecological basis of tree-understorey interactions is explained based on spatial distribution and use of above and belowground resources. Dehesas have been considered habitats to be preserved because they maintain a high biological diversity including several globally endangered animal species. They are considered an example of sustainable land use, although their conservation has been threatened in the last few decades. Excessive tree cutting, including complete elimination in some cases, has taken place as a consequence of increased mechanisation and stocking rates. This has caused a lack of natural regeneration and tree death in over-aged stands. We make a critical analysis of the ecological stability and sustainability of the system following four different approaches related to current problems: (i) historical evolution of the dehesa range, (ii) soil degradation and erosion, (iii) plot and farm-level factors precluding tree regeneration, and (iv) economic profitability of the dehesas. From these analyses, we derive a number of recommendations for dehesa management aimed at ensuring both its multifunctional role and its sustainability. The critical role of the shrub understorey for the ecological function, nutritional contribution and biodiversity is emphasized.
In a series of growth cabinet, glasshouse and field experiments, tissue samples from living clonal Eucalyptus marginata (jarřah) were incubated immediately after sampling on agar (NARPH) selective for Phytophthora. Phytophthora cinnamomi was recovered 3–6 months after inoculation from 50% of samples with lesions and 30% of symptomless samples. However, up to
11% of samples with and without lesions and from which P. cinnamomi was not initially isolated contained viable pathogen. This was shown by removing tissue which had not produced any growth
of P. cinnamomi on NARPH plates, cutting it into smaller sections, washing in sterile deionised water repeatedly for 9 days, and replating.
Plating stem or bark tissue directly onto NARPH produced false-negative results for nine P. cinnarnomi isolates and six jarrah clones. The behaviour of the pathogen indicates that it could be present as dormant structures, such
as chlamydospores, that need to be induced to germinate. Alternatively, fungistatic compounds in the tissue needed to be removed
to allow the pathogen to grow. These results have important implications for disease diagnosis and management, disease-free
certification and quarantine clearance.
Additional keywordscollar rot–dieback–hemibiotroph–necrotroph–recovery–root rot–fungistasis
Mediterranean agroforestry landscapes, dehesas, experience significant structural changes that affect their ability to support habitats for a rich biodiversity. The goal of this study is to provide quantitative information on loss, fragmentation, and alteration of holm oak (Quercus ilex) stands over a 42-year period, based on two sites in the lowlands of Cáceres province, Spain. Aerial photography and orthoimages from 1956, 1984, and 1998 were processed in a geographic information system (GIS). Important changes in demography and land-use were rural depopulation, abandonment of traditional agricultural activities, and a sharp increase in livestock stocking levels. These were related to intensification and extensification of land-uses determined by national and EU agricultural policies. Results of the land cover analysis indicated that dehesas suffered an annual 0.27% and 0.04% decrease in cover in the two sites. From 1984 loss rate had markedly accelerated (0.83% and 0.30%). Most dehesas were lost by shrub encroachment or conversion to open grassland. Fragmentation through roads increased by 28% and 45%, while rural buildings decreased by 17% and 50% from 1956 to 1998. Mean tree density decreased from 1956 to 1984, but a recovery was found since 1984. Significant factors determining stand densities in most time points were altitude (related with different land-uses and geological substrates), ownership, and proximity to villages. This suggests that stand structure is controlled both by human interventions and ecological settings. The findings support the view that opposite trends of land abandonment and intensification of land-uses arise in most northern Mediterranean countries as an effect of the EU Common Agricultural Policy.
Mathematical models of infectious diseases can provide important insight into our understanding of epidemiological processes, the course of infection within a host, the transmission dynamics in a host population, and formulation or implementation of infection control programs. We present a framework for modeling the dynamics of infectious diseases in discrete time, based on the theory of matrix population models. The modeling framework presented here can be used to model any infectious disease of humans or wildlife with discrete disease states, irrespective of the number of disease states. The model allows rigorous estimation of important quantities, including the basic reproduction ratio of the disease (R0) and growth rate of the population (λ), and permits quantification of the sensitivity of R0 and λ to model parameters. The model is amenable to rigorous experimental design, and when appropriate data are available, model parameters can be estimated using statistically robust multi-state capture-mark-recapture models. Methods for incorporating the effects of population density, prevalence of the disease, and stochastic forces on model behavior also are presented.
A novel point process model continuous in space-time is proposed for quantifying the transmission dynamics of the two most common meningococcal antigenic sequence types observed in Germany 2002-2008. Modeling is based on the conditional intensity function (CIF), which is described by a superposition of additive and multiplicative components. As an epidemiological interesting finding, spread behavior was shown to depend on type in addition to age: basic reproduction numbers were 0.25 (95% CI 0.19-0.34) and 0.11 (95% CI 0.07-0.17) for types B:P1.7-2,4:F1-5 and C:P1.5,2:F3-3, respectively. Altogether, the proposed methodology represents a comprehensive and universal regression framework for the modeling, simulation, and inference of self-exciting spatiotemporal point processes based on the CIF. Usability of the modeling in biometric practice is promoted by an implementation in the R package surveillance.
Increase in abiotic and biotic stress driven by global change threatens forest ecosystems and challenges understanding of mechanisms producing mortality. Phytophthora spp. like P. cinnamomi (PHYCI) are among the most lethal pathogens for many woody species including Quercus spp. Dynamics of biotic agents and their hosts are complex and influenced by climatic conditions. We analysed radial growth trends of dead and live adult Quercus ilex trees from agrosilvopastoral open woodlands under intense land-use. A pronounced warming trend since the 1980s has coincided in these woodlands with high oak mortality rates generally attributed to PHYCI. Yet, tree mortality and latency of the pathogen could be expressed at variable time spans, whereas, like many other forests worldwide, tree death could also be explained by other factors like drought. PHYCI was isolated from roots of all dead oaks from one region. Trees were younger than generally believed and ages of dead trees ranged between 38 and 230 years. Growth of dead trees reached a tipping point after two-year extraordinary droughts in 1980 and 1990. These dates set the start of growth declines up to 30 years before tree death. Live trees did not exhibit any recent growth decline. Tree growth was highly sensitive to climatic variability associated with water stress and climate-growth relationships suggested phenological changes since the 1980s. Live and dead trees showed differences in their sensitivity to moisture availability and temperature. The sensitivity of growth to climate was related to site environmental conditions. Simulated gross and net primary productivity were higher in live sites with less atmospheric demand for water. Tree death was not sudden but a slow multiannual process as expressed by radial growth declines likely triggered by drought. Regardless of the causal agent or mechanism, the observed mortality affected trees exhibiting negative drought and land-use legacies.
The decade of the fifties of the twentieth century triggered huge changes in land use and management in ecosystems worldwide, including the iconic Mediterranean ecosystems known as dehesas. In this study, we have quantified the changes in dehesa landscape status within a geographic area of 200,000 km² covering mainly the Spanish dehesa range over the last 60 years. We focused on changes of two important dehesa elements: tree density and live stocking rates. Tree density and tree cover change were measured via remote sensing in 29 sample plots (16 km² each) and selected from the plot-monitoring network of Spanish Rural Landscapes (SISPARES). Live stocking (cattle, sheep, and pig) rates data were obtained from the National Statistical Institute of Spain and were used to assess the entire study area. During the 1950–80s, tree density and cover declined significantly (by 18% and 13%, respectively). By the 1960s, sheep was predominant over cattle in all provinces; pigs had higher stocking rates than in the following decades. However, during the 1970–80s, sheep and pig stocking rate declined drastically (by 90% and 70%, respectively) in just 20 years. In contrast, cattle stocking rate increased progressively since the 1960s, reaching a 60% increment by the 2000s. At the municipality level, we observed similar trends. Our multi-scaled analysis explains the impact of social, political, and economic factors on the conservation status of the main dehesa territory within Spain. We conclude that it is necessary to ensure the effectiveness of these systems through sustainable activities to avoid negative consequences of poor management practices which threaten dehesa perpetuation.
When a species colonizes an area that it has not previously inhabited, it is called an "invasion", and it can result in the extinction of endemic species. The increase in numbers of humans travelling the world presents opportunities for invasions by organisms and the spread of diseases such as rabies and smallpox. Using the large amount of data from studies in pest control and epidemiology, it is possible to construct mathematical models that can predict which species will become invaders, which habitats are susceptible to invasion, and the biological impact. This book presents a clear and accessible introduction to the modeling of biological invasions. It demonstrates the latest theories and models, and includes data and examples from various case studies showing how these models can be applied to problems from deadly human diseases to the spread of weeds.
The present book is based on an earlier one published in Japan (in Japanese) by one of the authors (N.S.), entitled Mathematical modeling for biological invasions (University of Tokyo Press, 1992); this English edition, however, results from the collaboration between two authors. The original Japanese edition is aimed primarily at university undergraduate and graduate students, and its purpose is to introduce to them some of the pioneering works in biological invasion as well as some mathematical models developed by the authors. Necessarily, discussions on many relevant theories, field data, and their references were curtailed in favor of conciseness. For this English edition, we have included more field data, updated some theoretical results according to the latest findings, and rewritten much of the text with a wider audience, including field researchers and scholars, in mind.
One of the most destructive of all tree root pathogens, the oomycete fungus P. cinnamomi, is associated with mortality and decline of Quercus suber and Q. ilex in the Mediterranean region. The symptoms and distribution of this decline are described. It is soil borne and requires warm, wet soils to infect roots. Together with drought, it may be a major predisposing factor in the Iberian oak decline. Its possible role in this decline including its interaction with drought is discussed, and a generalised working hypothesis of decline is presented. The potential influence of climate warming on the activity of P. cinnamomi is also considered.
The Eurasian wild boar (Sus scrota) is growing in numbers and has been expanding its distribution in Europe from some decades ago. This increasing trend, in some circumstances, leads to conflicts involving several sectors, among others, agriculture damages, conservation problems and health risks. The disease-related conflicts are especially relevant; wild boar was raised as a potential host for numerous pathogens provoking economic losses to the livestock industry. In a wildlife management context, reliable indicators of wild boar abundance at large spatial scales are highly demanded. Thus, our main aim was to handle hunting bag data available for the 2006-2007 to 2009-2010 hunting seasons in order to develop a predictive model able to account for wild boar abundance in overall mainland Spain. For modelling, the response variable was the number of wild boars annually hunted per 100 km(2) in each hunting estate, as a well-established wild boar abundance index. Using data for 6280 hunting estates (similar to 44% of the study area), and 21 ecogeographical predictors (geography, climate and land cover), we modelled the species abundance by means of generalized linear models with a negative binomial distribution. Three analytical approaches were comparatively assessed, which differed in how the five bioregions considered in the Spanish Wildlife Disease Surveillance Scheme were considered in modelling. In terms of predictive performance on independent datasets, the approach in which five independent models were adjusted (one per bioregion) achieved the highest scores. These models were used to predict wild boar abundance in overall mainland Spain by using UTM 10 x 10 km squares (n=5245) and municipalities (n = 8050) as territorial units, in order to enhance the representativeness of the model at national scale and their usefulness in epidemiological studies, respectively. The pattern for wild boar abundance obtained in this study enlarges the knowledge of this species in mainland Spain. The analytical procedure developed here is valuable in itself, and it can be considered to model the spatial patterns of wild boar - or other relevant species - elsewhere, which is information highly demanded for wildlife managers in general and epidemiologists in particular.
J.L. (2012). Spatial analysis of risks posed by root rot pathogen, Phytophthora cinnamomi: implications for disease management. Proceedings of the Linnean Society of New South Wales 134, B147-B179. Phytophthora cinnamomi, a soil-borne pathogen that infects the roots of plants, is listed as a Key Threatening Process under Commonwealth and NSW state biodiversity legislation due to its deleterious effects on native fl ora. In warm temperate eastern Australia, the disease may cause insidious declines in plant species that have slow rates of population turnover, and thereby threaten their long term persistence. Phytophthora cinnamomi has been known to occur in Royal National Park since the 1970s and systematic surveys for the pathogen were carried out a decade ago. Development of effective management strategies to mitigate the impacts of the disease requires information on the spatial distribution of risks posed by the disease. In this study, we use limited disease survey data to identify areas that are most at risk. We propose and apply a simple risk model in which risks of disease impact are proportional to the product of habitat suitability for the pathogen and abundance of susceptible biota. We modelled habitat suitability of the pathogen from available survey data and found that soil landscapes and topographic variables were the strongest predictors. Susceptible fl ora were concentrated on sandstone plateaus. Disease risks were greatest on the sandstone plateaus and lowest in the shale gullies with intermediate levels of risk on shale ridges and the coastal sand plain. The outcomes of this spatially explicit risk assessment will help inform the development of management strategies and priorities for the disease in the Park. Our approach lends itself to broader application to conservation planning in other landscapes and to other threats to biodiversity. Manuscript received 11 January 2012, accepted for publication 2 May 2012.
Resistant annual and herbaceous perennial plant species were identified as key hosts which allow Phytophthora cinnamomi to persist on severely impacted black gravel sites within the Eucalyptus marginata (jarrah) forest of southwest Western Australia. Of the annual and herbaceous perennial plant species present on black gravel sites, 15 out of 19 species were found to be hosts of P. cinnamomi, and 10 of these were symptomless hosts. In particular, the native annual Trachymene pilosa and the two native herbaceous perennials Stylidium diuroides and Chamaescilla corymbosa were commonly found to be hosts of the pathogen. Species from 12 new genera including three from new families (Crassulaceae, Droseraceae and Primulaceae) are reported for the first time to be hosts of P. cinnamomi. The species from which P. cinnamomi was recovered were the native species: Chamaescilla corymbosa, Crassula closiana, Drosera erythrorhiza, Hydrocotyle callicarpa, Levenhookia pusilla, Paracaleana nigrita, Podotheca angustifolia, Pterochaeta paniculata, Rytidosperma caespitosum, Siloxerus multiflorus, Stylidium diuroides and Trachymene pilosa, and the introduced annual weeds Hypochaeris glabra, Lysimachia arvensis and Pentameris airoides.
An increasing decline and mortality of cork oak trees have been recently observed in central Italy and Sardinia Island. Following surveys conducted in three declining cork oak forests, a Phytophthora species was consistently isolated from soil samples collected from trees displaying different level of decline. Based on morphological features, growth rates at different temperatures and analysis of DNA sequences of the ITS region, all isolates were identified as Phytophthora cinnamomi Rands. This pathogen caused large brownish lesions on inoculated freshly cut branches of cork oak. It was re-isolated from all infected tissues. These findings represent the first report of P. cinnamomi on cork oak trees in Italy.
Removal of living plants from an area of Eucalyptus marginata (jarrah) forest on black gravel sites infested with Phytophthora cinnamomi significantly reduced subsequent pathogen recovery. Vegetation, including trees and annual and herbaceous perennial plants, was killed on the sites by herbicide application. To determine whether this treatment efficiently eliminated P. cinnamomi, soil samples were seasonally collected and baited to test for the presence of the pathogen. There were no recoveries on treated sites in autumn, 28 months after removal of all vegetation by herbicide application. To test whether this was the result of the complete elimination of the pathogen or whether inoculum remained, regrowth on sites was not controlled after this period leading to the re-establishment of annual and herbaceous perennial species, some of which are hosts of P. cinnamomi. Recovery of P. cinnamomi after plant regrowth on the formerly treated sites indicated that for complete pathogen removal, sites need to remain free of vegetation for longer than 28 months. Overall, however, this study confirms that the pathogen is a weak saprophyte, and withdrawal of host material for a period of time may make eventual rehabilitation of these sites possible.
Invasive soil-borne pathogens are a major threat to forest ecosystems worldwide. The newly discovered soil pathogen, Phytophthora 'taxon Agathis' (PTA), is a serious threat to endemic kauri (Agathis australis: Araucar-iaceae) in New Zealand. This study examined the potential for feral pigs to act as vectors of PTA. We investigated whether snouts and trotters of feral pigs carry soil contaminated with PTA, and using these results determined the probability that feral pigs act as a vector. We screened the soil on trotters and snouts from 457 pigs for PTA using various baiting techniques and molecular testing. This study detected 19 species of plant pathogens in the soil on pig trotters and snouts, including a different Phytophthora species (Phytophthora cinnamomi). However, no PTA was isolated from the samples. A positive control experiment showed a test sensitivity of 0–3% for the baiting methods and the data obtained were used in a Bayesian probability modelling approach. This showed a posterior probability of 35–90% (dependent on test sensitivity scores and design prevalence) that pigs do vector PTA and estimated that a sample size of over 1000 trotters would be required to prove a negative result. We conclude that feral pigs cannot be ruled out as a vector of soil-based plant pathogens and that there is still a high probability that feral pigs do vector PTA, despite our negative results. We also highlight the need to develop a more sensitive test for PTA in small soil samples associated with pigs due to unreliable detection rates using the current method.
This article discusses several classes of stochastic models for the origin times and magnitudes of earthquakes. The models are compared for a Japanese data set for the years 1885–1980 using likelihood methods. For the best model, a change of time scale is made to investigate the deviation of the data from the model. Conventional graphical methods associated with stationary Poisson processes can be used with the transformed time scale. For point processes, effective use of such residual analysis makes it possible to find features of the data set that are not captured in the model. Based on such analyses, the utility of seismic quiescence for the prediction of a major earthquake is investigated.
The susceptibility to Phytophthora cinna-momi of four crops (wheat, oat, vetch, and yellow lupin) commonly planted in rangeland ecosystems in southern Spain was evaluated. By means of in vitro infection experiments, the presence of the pathogen into the roots of yellow lupin (symptomatic) and vetch (asymptomatic) was observed, but never into wheat and oat roots (asymptomatic). It was also demonstrated that yellow lupin stimulated the production of zoospores of P. cinnamomi. Vetch, wheat and oat did not stimulate zoospore production. Under controlled conditions, only yellow lupin induced an increase in the number of viable chlamydospores in the soil. We concluded that the cul-ture of wheat, oat, and vetch in rangelands did not influence the epidemiology of the Quercus root disease, even when asymptomatically-infected vetch is grown, and these crops can constitute an alternative to the culture of yellow lupin in rangeland ecosystems affected by Quercus root rot.
Part 1 Theory: perspectives of biological invasions examples of invasions measures of areal expansion poopulation growth diffusion. Part 2 Applications and interpretation: parameter estimation and ecological boundry conditions simulating biological invasions birds invading Europe and America the stochastic structure of the wave front of rabies in Central Europe interpreting biological invasions.
Phytophthora ramorum and Phytophthora kernoviae are recently discovered invasive Phytophthoras causing leaf necrosis and shoot tip dieback mostly on ornamental and forest understorey species, but also cause bleeding cankers on stems of a wide range of tree species. Sporulation occurs only on infected shoots or fruits and foliage so foliar hosts are central to the disease epidemiology. In field trials to assess infection in trap plants exposed to natural inoculum of P. ramorum and P. kernoviae on rhododendron in south west England, it was discovered that leaves of the trap plants (Rhododendron‘Cunninghams White’) and holm oak (Quercus ilex) were asymptomatically infected and supported sporulation of both pathogens. More than half the rhododendron trap plants exposed to inoculum of P. kernoviae became infected compared with approximately a third of those exposed to P. ramorum in a natural situation. Approximately one third of the infections were detected from asymptomatic foliage for both pathogens. The significance of these findings for plant health regulation based on visual inspection as a measure to prevent introduction and dissemination of both these pathogens is explored and research gaps identified.
The combination of soil infestation with Phytophthora cinnamomi and repetitive flooding was studied on 1-year-old plants of Quercus ilex (holm oak) and Q. suber (cork oak). In a second experiment, using 2-year-old plants of the same species and of red oak (Q. rubra), the soil infestation was followed by two drought-rewatering cycles. Oak predawn leaf water potential (PLWP) and stomatal conductance (gs) were monitored during both experiments. Root infection, root loss, wilting and mortality were assessed at the end of the experiments. Q. ilex exhibited the highest susceptibility to P. cinnamomi, and Q. rubra the lowest. Root infections caused by P. cinnamomi were more severe in the flooding than in the drought experiment. The most noticeable effect of the infection on plant water relations was a decrease in stomatal conductance. This occurred at different times after inoculation, varying with species susceptibility and experiment. Inoculation with P. cinnamomi induced a decrease of PLWP in Q. ilex plants, and in some Q. suber plants exhibiting a severe root loss. The results further showed that the relationship between PLWP and gs was modified by infection with P. cinnamomi. The combination of flooding and infection with P. cinnamomi acted synergistically on the water relations of Q. ilex. By contrast, there was no significant increase in disease severity due to the postinoculation water stress imposed on the oaks.
The capacity of Phytophthora ramorum to colonize the inner bark of 18 native and two exotic tree species from the Iberian Peninsula was tested. Living logs were wound-inoculated in a growth chamber with three isolates belonging to the EU1 and two to the NA1 clonal lineages of P. ramorum. Most of the Quercus species ranked as highly susceptible in experiments carried out in summer, with mean lesion areas over 100 cm2 in Q. pubescens, Q. pyrenaica, Q. faginea and Q. suber and as large as 273 cm2 in Q. canariensis, ca. 40 days after inoculation. Quercus ilex ranked as moderately susceptible to P. ramorum, forming lesions up to 133 cm2 (average 17·2 cm2). Pinus halepensis and P. pinea were highly susceptible, exhibiting long, narrow lesions; but three other pine species, P. pinaster, P. nigra and P. sylvestris, were resistant to slightly susceptible. No significant difference in aggressiveness was found between the isolates of P. ramorum. In addition, there was evidence of genetic variation in susceptibility within host populations, and of significant seasonal variation in host susceptibility in some Quercus species. The results suggest a high risk of some Iberian oaks to P. ramorum, especially in forest ecosystems in southwestern Spain, where relict populations of Q. canariensis grow amongst susceptible understory species such as Rhododendron ponticum and Viburnum tinus. One isolate of P. cinnamomi used as positive control in all the inoculations was also highly aggressive to Iberian oaks and Eucalyptus dalrympleana.
The viability of 1-year-old holm oak (Quercus ilex) seedlings in a soil naturally infected with Phytophthora cinnamomi was studied during 2 consecutive years in a plot located in south-western Spain. In both years, total mortality during autumn and winter was not noticeable (<2.1%). In spring, mortality levels were higher (8.3-4.6%), especially the first year. A steep increase in total mortality occurred in summer, both in the first (11.4%) and second (24.2%) year, but mortality attributable to P. cinnamomi was 1.9 and 7.6%, respectively. Thus, 2 years after planting, total cumulative mortality was 43.4%, and that attributable to P. cinnamomi 9.6% (i.e. 22.1% of total mortality). Fungus-derived mortality followed a spatially aggregated pattern in the reforestation plot, suggesting a clustered distribution of the inoculum in the soil. Furthermore, mortality by P. cinnamomi was also associated with nearness of infected adult trees in the plot. Results obtained are discussed in the framework of seasonal water deficit, P. cinnamomi damage, weed competition and sanitation techniques to be used in declined holm oak stands in Spain.
Although decline of cork (Quercus suber) and holm oak trees (Quercus rotundifolia) has been described in Portugal in the late years of the 19th century, its development has become a motive of high concern during the last two decades. The presence of Phytophthora cinnamomi in cork and holm oak stands was surveyed in four different regions of the country (Trás-os-Montes, Alentejo, Ribatejo and Algarve) during 1995–98. Tree decline severity, sudden death and site characteristics were assessed in 56 sites representing varied conditions. The pathogen was isolated from oak roots and rhizosphere samples in 27 of those places. Other plant species from natural vegetation were sampled in three active disease centres. This survey showed that 56% of the surveyed species of shrub flora were infected with P. cinnamomi, which was detected mainly on species belonging to the families Ericaceae, Cistaceae and Leguminosae. Recovery of P. cinnamomi was more frequent in shallow soils (Leptosols and complex Leptosols and Luvisols). These soils are more common in the south (Algarve), where decline has a high impact. Soils with low fertility and low mineral nutrient levels, particularly phosphorus, seemed to favour infection. Site aspect and topographic tree situation were also evaluated. Sites facing south showed higher occurrence of P. cinnamomi, which was also more frequent in slopes and valleys than on hilltops. In Algarve, a relationship could be established between the crown status and the presence of P. cinnamomi in roots and rhizosphere. Different morphotypes of P. cinnamomi could be distinguished in vitro, and their occurrence in the field was correlated with particular site characteristics. Further research needs and management strategies to limit the extension of the disease are discussed.
Oak decline that was affecting three holm oak sites in the province of Huelva (south-western Spain) was studied during 1998-1999. The syndromes of dieback and sudden death have been observed and, in both cases, foliar symptoms were associated with root rot. Characterization of the fungal isolates from necrotic roots led us to identify Phytophthora cinnamomi A2 as consistently associated with the disease. The optimum growth temperatures of these isolates were very high (30 C). Inoculation tests under controlled conditions demonstrated the pathogenicity of the isolates on holm and cork oak seedlings. None of the other biotic factors of Mediterranean oak decline that have been previously described were found in the present study and so, in this case, the forest decline model does not seem to be necessary in order to explain the disease observed. The defoliation and mortality of the oaks was primarily caused by P. cinnamomi, although sonic abiotic factors such as alternating periods of drought and wet weather in the region may play an important role.
A central challenge to studying emerging infectious diseases (EIDs) is a landscape dilemma: Our best empirical understanding of disease dynamics occurs at local scales, whereas pathogen invasions and management occur over broad spatial extents. The burgeoning field of landscape epidemiology integrates concepts and approaches from disease ecology with the macroscale lens of landscape ecology, enabling examination of disease across spatiotemporal scales in complex environmental settings. We review the state of the field and describe analytical frontiers that show promise for advancement, focusing on natural and human-altered ecosystems. Concepts fundamental to practicing landscape epidemiology are discussed, including spatial scale, static versus dynamic modeling, spatially implicit versus explicit approaches, selection of ecologically meaningful variables, and inference versus prediction. We highlight studies that have advanced the field by incorporating multiscale analyses, landscape connectivity, and dynamic modeling. Future research directions include understanding disease as a component of interacting ecological disturbances, scaling up the ecological impacts of disease, and examining disease dynamics as a coupled human-natural system.
Within the scope of a research project on the condition of roots of declining oaks (Quercus robur, Quercus petraea), samples of fine roots and surrounding soil, specimens of stripe cankers on the stem base, and samples of stream water were examined for the presence of Phytophthora species using both baiting methods and selective agar media. At 27 sites in Germany (Bavaria, Rheinland-Pfalz, Schleswig-Holstein), Switzerland, Hungary, Italy and Slovenia the following species were isolated (mainly from soil): Phytophthora citricola, Phytophthora cactorum, Phytophthora cambivora, Phytophthora gon-apodyides, Phytophthora undulata, a species with affinity to Phytophthora drechsleri, and two additional species with close affinity to the Phytophthora cactorum group. Moreover, Pythium group P, Pythium anandrum, Pythium chamaehyphon, and many other Pythium species that have not yet been identified could be recovered. In a soil infestation test most isolates induced dieback of long root tips and necrotic lesions in the root cortex and at the root collar of Quercus robur seedlings. All Phytophthora species tested and Pythium group P caused cortical necrosis after stem inoculation of young Quercus robur trees. It could be shown in vitro that Phytophthora gonapodyides and Pythium group P were able to produce a wilting toxin. Nitrogen input and climatic changes are discussed as predisposing factors for root damage observed in the field.
Modern, powerful techniques for the residual analysis of spatial-temporal
point process models are reviewed and compared. These methods are applied to
California earthquake forecast models used in the Collaboratory for the Study
of Earthquake Predictability (CSEP). Assessments of these earthquake
forecasting models have previously been performed using simple, low-power means
such as the L-test and N-test. We instead propose residual methods based on
rescaling, thinning, superposition, weighted K-functions and deviance
residuals. Rescaled residuals can be useful for assessing the overall fit of a
model, but as with thinning and superposition, rescaling is generally
impractical when the conditional intensity $\lambda$ is volatile. While
residual thinning and superposition may be useful for identifying spatial
locations where a model fits poorly, these methods have limited power when the
modeled conditional intensity assumes extremely low or high values somewhere in
the observation region, and this is commonly the case for earthquake
forecasting models. A recently proposed hybrid method of thinning and
superposition, called super-thinning, is a more powerful alternative.
Ecology Letters (2011) 14: 1108–1116
Empirical evidence suggests that biodiversity loss can increase disease transmission, yet our understanding of the ‘diversity-disease hypothesis’ for generalist pathogens in natural ecosystems is limited. We used a landscape epidemiological approach to examine two scenarios regarding diversity effects on the emerging plant pathogen Phytophthora ramorum across a broad, heterogeneous ecoregion: (1) an amplification effect exists where disease risk is greater in areas with higher plant diversity due to the pathogen’s wide host range, or (2) a dilution effect where risk is reduced with increasing diversity due to lower competency of alternative hosts. We found evidence for pathogen dilution, whereby disease risk was lower in sites with higher species diversity, after accounting for potentially confounding effects of host density and landscape heterogeneity. Our results suggest that although nearly all plants in the ecosystem are hosts, alternative hosts may dilute disease transmission by competent hosts, thereby buffering forest health from infectious disease.