Hierarchical Bayesian modelling of early detection surveillance for plant pest invasions

Early detection surveillance programs aim to find invasions of exotic plant pests and diseases before they are too widespread to eradicate. However, the value of these programs can be difficult to justify when no positive detections are made. To demonstrate the value of pest absence information provided by these programs, we use a hierarchical Bayesian framework to model estimates of incursion extent with and without surveillance. A model for the latent invasion process provides the baseline against which surveillance data are assessed. Ecological knowledge and pest management criteria are introduced into the model using informative priors for invasion parameters. Observation models assimilate information from spatio-temporal presence/absence data to accommodate imperfect detection and generate posterior estimates of pest extent. When applied to an early detection program operating in Queensland, Australia, the framework demonstrates that this typical surveillance regime provides a modest reduction in the estimate that a surveyed district is infested. More importantly, the model suggests that early detection surveillance programs can provide a dramatic reduction in the putative area of incursion and therefore offer a substantial benefit to incursion management. By mapping spatial estimates of the point probability of infestation, the model identifies where future surveillance resources can be most effectively deployed.     

Combined use of eDNA metabarcoding and video surveillance for the assessment of fish biodiversity

Monitoring communities of fish is important for the management and sustainability of fisheries and marine ecosystems. Baited remote underwater video systems (BRUVs) are among the most effective nondestructive techniques for sampling bony fishes and elasmobranchs (sharks, rays, and skates). However, BRUVs sample visually conspicuous biota; hence, some taxa are undersampled or not recorded at all. We compared the diversity of fishes characterized using BRUVs with diversity detected via environmental DNA (eDNA) metabarcoding. We sampled seawater and captured BRUVs imagery at 48 locales that included reef and seagrass beds inside and outside a marine reserve (Jurien Bay in Western Australia). Eighty-two fish genera from 13 orders were detected, and the community of fishes described using eDNA and BRUVs combined yielded >30% more generic richness than when either method was used alone. Rather than detecting a homogenous genetic signature, the eDNA assemblages mirrored the BRUVs’ spatial explicitness; differentiation of taxa between seagrass and reef was clear despite the relatively small geographical scale of the study site (∼35 km²). Taxa that were not sampled by one approach, due to limitations and biases intrinsic to the method, were often detected with the other. Therefore, using BRUVs and eDNA in concert provides a more holistic view of vertebrate marine communities across habitats. Both methods are noninvasive, which enhances their potential for widespread implementation in the surveillance of marine ecosystems.     

Modelling pheromone anemotaxis for biosecurity surveillance: Moth movement patterns reveal a downwind component of anemotaxis

Insect pheromone traps are becoming an increasingly important tool in biosecurity and pest surveillance, alerting managers to the presence of unwanted organisms. To expand the role of these traps beyond their present sentinel role, it is necessary to develop reliable operational models of local insect dispersal. Following the detection of an insect incursion using a pheromone trap, such models could simulate the dispersal of the insect from its emergence site to the point of detection, enabling biosecurity managers to estimate the most likely proximal source of the incursion. An individual-based moth movement model was developed to simulate observed patterns of moth movement in response to the presence or absence of a pheromone. Using parameters derived from a genetic algorithm, it was possible to fit a model based on the three behavioural components (upwind, upwind with zigzags and casting) described in insect anemotaxis theory to a subset of observed movement patterns (0-135° to the wind), but not to the whole spectrum of movement patterns. It appears that current insect anemotaxis theory is missing a downwind flight component. Whilst the frequency of downwind movements is small; their ground speed could lead to significant downwind displacement, having a disproportionately strong influence on a moth movement model, and hence projections of the likely source or target locations.     

A novel Vibrio sp. pathogen of the coral Pocillopora damicornis

A coral pathogen was isolated from the diseased tissue of Pocillopora damicornis in Zanzibar. The pathogenic bacterium, referred to as Vibrio coralyticus YB, was classified as a member of the genus Vibrio. Based on its 16S rDNA sequence, V. coralyticus is probably a new species. In controlled aquaria experiments at 26-29°C, inoculation of pure cultures of V. coralyticus YB either into the seawater or by direct contact onto the coral caused tissue lysis of P. damicornis fragments. At 29°C, lysis began as small white spots after 3-5 days, rapidly spreading so that by 2 weeks the entire tissue was destroyed, leaving only the intact bare skeleton. When an infected diseased coral was placed in direct contact with a healthy one, the healthy coral lysed in 2-4 days, further indicating that the disease was contagious. Inoculation with as few as 30 bacteria ml^-1 was sufficient to infect and lyse corals. Seawater temperature was a critical variable for the infectious process: infection and lysis occurred rapidly at 27-29°C, slowly at 26°C and was not observed at 25°C. The data suggest that the presence of V. coralyticus YB, even in low numbers, in seawater surrounding a coral reef will lead to tissue destruction of P. damicornis, when seawater temperatures rise.     

Environmental public health tracking: piloting methods for surveillance of environmentally related diseases in England and Wales

An effective environmental public health tracking system integrates data and intelligence on environmental hazards, exposures, and health outcomes to focus interventions on reducing the impact of environmental contamination on public health. Most work in this area in the UK has focused on assessing data on hazards that are relatively easy to obtain. However, most hazards will present no actual risk and information on exposure is required to make an effective risk assessment. Obtaining exposure data is technically challenging, expensive, and potentially raises ethical concerns. Consequently, the Health Protection Agency is exploring methods for targeting geographical zones for efficient detailed environmental assessment (including exposure assessment). This paper describes and assesses three methods (indirect standardization, statistical process control (SPC) and kernel density contouring) for the surveillance of potentially environmentally related diseases for this purpose. While the evaluation demonstrates the utility of the three methods, particularly SPC, the comparison was limited due to ethical approval issues.     

Differences in sensitivity to the fungal pathogen Batrachochytrium dendrobatidis among amphibian populations

Contributing to the worldwide biodiversity crisis are emerging infectious diseases, which can lead to extirpations and extinctions of hosts. For example, the infectious fungal pathogen Batrachochytrium dendrobatidis (Bd) is associated with worldwide amphibian population declines and extinctions. Sensitivity to Bd varies with species, season, and life stage. However, there is little information on whether sensitivity to Bd differs among populations, which is essential for understanding Bd‐infection dynamics and for formulating conservation strategies. We experimentally investigated intraspecific differences in host sensitivity to Bd across 10 populations of wood frogs (Lithobates sylvaticus) raised from eggs to metamorphosis. We exposed the post‐metamorphic wood frogs to Bd and monitored survival for 30 days under controlled laboratory conditions. Populations differed in overall survival and mortality rate. Infection load also differed among populations but was not correlated with population differences in risk of mortality. Such population‐level variation in sensitivity to Bd may result in reservoir populations that may be a source for the transmission of Bd to other sensitive populations or species. Alternatively, remnant populations that are less sensitive to Bd could serve as sources for recolonization after epidemic events.     

Life-history trade-offs influence disease in changing climates: strategies of an amphibian pathogen

Life-history trade-offs allow many animals to maintain reproductive fitness across a range of climatic conditions. When used by parasites and pathogens, these strategies may influence patterns of disease in changing climates. The chytrid fungus, Batrachochytrium dendrobatidis, is linked to global declines of amphibian populations. Short-term growth in culture is maximal at 17 degrees-25 degrees C. This has been used in an argument that global warming, which increases the time that amphibians spend at these temperatures in cloud-covered montane environments, has led to extinctions. Here we show that the amphibian chytrid responds to decreasing temperatures with trade-offs that increase fecundity as maturation rate slows and increase infectivity as growth decreases. At 17 degrees-25 degrees C, infectious zoospores encyst (settle and develop a cell wall) and develop into the zoospore-producing stage (zoosporangium) faster, while at 7 degrees-10 degrees C, greater numbers of zoospores are produced per zoosporangium; these remain infectious for a longer period of time. We modeled the population growth of B. dendrobatidis through time at various temperatures using delayed differential equations and observational data for four parameters: developmental rate of thalli, fecundity, rate of zoospore encystment, and rate of zoospore survival. From the models, it is clear that life-history trade-offs allow B. dendrobatidis to maintain a relatively high long-term growth rate at low temperatures, so that it maintains high fitness across a range of temperatures. When a seven-day cold shock is simulated, the outcome is intermediate between the two constant temperature regimes, and in culture, a sudden drop in temperature induces zoospore release. These trade-offs can be ecologically important for a variety of organisms with complex life histories, including pathogenic microorganisms. The effect of temperature on amphibian mortality will depend on the interaction between fungal growth and host immune function and will be modified by host ecology, behavior, and life history. These results demonstrate that B. dendrobatidis populations can grow at high rates across a broad range of environmental temperatures and help to explain why it is so successful in cold montane environments.     

Soil feedback of exotic savanna grass relates to pathogen absence and mycorrhizal selectivity

Enemy release of exotic plants from soil pathogens has been tested by examining plant-soil feedback effects in repetitive growth cycles. However, positive soil feedback may also be due to enhanced benefit from the local arbuscular mycorrhizal fungi (AMF). Few studies actually have tested pathogen effects, and none of them did so in arid savannas. In the Kalahari savanna in Botswana, we compared the soil feedback of the exotic grass Cenchrus biflorus with that of two dominant native grasses, Eragrostis lehmanniana and Aristida meridionalis. The exotic grass had neutral to positive soil feedback, whereas both native grasses showed neutral to negative feedback effects. Isolation and testing of root-inhabiting fungi of E. lehmanniana yielded two host-specific pathogens that did not influence the exotic C. biflorus or the other native grass, A. meridionalis. None of the grasses was affected by the fungi that were isolated from the roots of the exotic C. biflorus. We isolated and compared the AMF community of the native and exotic grasses by polymerase chain reaction-denaturing gradient gel elecrophoresis (PCR-DGGE), targeting AMF 18S rRNA. We used roots from monospecific field stands and from plants grown in pots with mixtures of soils from the monospecific field stands. Three-quarters of the root samples of the exotic grass had two nearly identical sequences, showing 99% similarity with Glomus versiforme. The two native grasses were also associated with distinct bands, but each of these bands occurred in only a fraction of the root samples. The native grasses contained a higher diversity of AMF bands than the exotic grass. Canonical correspondence analyses of the AMF band patterns revealed almost as much difference between the native and exotic grasses as between the native grasses. In conclusion, our results support the hypothesis that release from soil-borne enemies may facilitate local abundance of exotic plants, and we provide the first evidence that these processes may occur in arid savanna ecosystems. Pathogenicity tests implicated the involvement of soil pathogens in the soil feedback responses, and further studies should reveal the functional consequences of the observed high infection with a low diversity of AMF in the roots of exotic plants.     

Responses of a bacterial pathogen to phosphorus limitation of its aquatic invertebrate host

Host nutrition is thought to affect the establishment, persistence, and severity of pathogenic infections. Nutrient-deficient foods possibly benefit pathogens by constraining host immune function or benefit hosts by limiting parasite growth and reproduction. However, the effects of poor elemental food quality on a host's susceptibility to infection and disease have received little study. Here we show that the bacterial microparasite Pasteuria ramosa is affected by the elemental nutrition of its aquatic invertebrate host, Daphnia magna. We found that high food carbon:phosphorus (C:P) ratios significantly reduced infection rates of Pasteuria in Daphnia and led to lower within-host pathogen multiplication. In addition, greater virulent effects of bacterial infection on host reproduction were found in Daphnia-consuming P-deficient food. Poor Daphnia elemental nutrition thus reduced the growth and reproduction of its bacterial parasite, Pasteuria. The effects of poor host nutrition on the pathogen were further evidenced by Pasteuria's greater inhibition of reproduction in P-limited Daphnia. Our results provide strong evidence that elemental food quality can significantly influence the incidence and intensity of infectious disease in invertebrate hosts.     

Varying responses of northeastern North American amphibians to the chytrid pathogen Batrachochytrium dendrobatidis

Chytridiomycosis, caused by Batrachochytrium dendrobatidis (Bd), is widespread among amphibians in northeastern North America. It is unknown, however, whether Bd has the potential to cause extensive amphibian mortalities in northeastern North America as have occurred elsewhere. In the laboratory, we exposed seven common northeastern North American amphibian species to Bd to assess the likelihood of population-level effects from the disease. We exposed larval wood frogs (Lithobates sylvaticus) and postmetamorphic frogs of six other species to two different strains of Bd, a northeastern strain (JEL404) and a strain that caused die-offs of amphibians in Panama (JEL423), under ideal in vitro growth conditions for Bd. Exposed American toads (Anaxyrus americanus) all died; thus, this species may be the most likely to die from Bd-caused disease in the wild. Both Bd strains were associated with mortalities of wood frogs, although half the metamorphs survived. The Bd strain from Panama killed metamorphic green frogs (L. clamitans), whereas the northeastern strain did not, which means novel strains of Bd may lead to death even when local strains may not. No mortality was observed in four species (bullfrogs [L. catesbeianus], northern leopard frogs [L. pipiens], spring peepers [Pseudacris crucifer], and blue-spotted salamanders [Ambystoma laterale]) and in some individuals of green frogs and wood frogs that we exposed. This finding suggests these six species may be Bd vectors. Our results show that systematic exposures of amphibian species to Bd in the laboratory may be a good first step in the identification of species susceptible to Bd-caused declines and in directing regional conservation efforts aimed at susceptible species.     

Festering food: chytridiomycete pathogen reduces quality of Daphnia host as a food resource

When parasitic infections are severe or highly prevalent among prey, a significant component of the predator's diet may consist of parasitized hosts. However, despite the ubiquity of parasites in most food webs, comparisons of the nutritional quality of prey as a function of infection status are largely absent. We measured the nutritional consequences of chytridiomycete infections in Daphnia, which achieve high prevalence in lake ecosystems (>80%), and tested the hypothesis that Daphnia pulicaria infected with Polycaryum laeve are diminished in food quality relative to uninfected hosts. Compared with uninfected adults, infected individuals were smaller, contained less nitrogen and phosphorus, and were lower in several important fatty acids. Infected zooplankton had significantly shorter carapace lengths (8%) and lower mass (8-20%) than uninfected individuals. Parasitized animals contained significantly less phosphorus (16-18% less by dry mass) and nitrogen (4-6% less) than did healthy individuals. Infected individuals also contained 26-34% less saturated fatty acid and 31-42% less docosahexaenoic acid, an essential fatty acid that is typically low in cladocera, but critical to fish growth. Our results suggest that naturally occurring levels of chytrid infections in D. pulicaria populations reduce the quality of food available to secondary consumers, including planktivorous fishes, with potentially important effects for lake food webs.     

一株拮抗烟草青枯病菌的真菌的筛选与鉴定

为寻找烟草青枯病的生防微生物,研究采用平板涂布法从重庆烟田健康土壤中分离根际微生物,纯化后得到了59株真菌。用滤纸片法从中筛选出1株对青枯雷尔氏菌（Ralstonia solanacearum）有稳定拮抗效果的真菌,其抑菌圈为10.0 mm。其抑制活性优于或接近于近期发现的其他生防微生物。测定该株活性真菌的全细胞脂肪酸组成,进行菌落和分生孢子形态学观察,以及rDNA ITS区测序,结果表明：该菌株全细胞脂肪酸属性未被收录于TSBA6脂肪酸数据库,而根据形态学观察结果,以及对所获rDNA ITS区序列的分析,鉴定该株真菌为烟曲霉（Aspergillus fumigatus）。     

Importance of timely metadata curation to the global surveillance of genetic diversity

Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies produce large amounts of genome-scale genetic diversity data for wild populations, but most (87%) do not include the associated spatial and temporal metadata necessary for them to be reused in monitoring programs or for acknowledging the sovereignty of nations or Indigenous peoples. We undertook a distributed datathon to quantify the availability of these missing metadata and to test the hypothesis that their availability decays with time. We also worked to remediate missing metadata by extracting them from associated published papers, online repositories, and direct communication with authors. Starting with 848 candidate genomic data sets (reduced representation and whole genome) from the International Nucleotide Sequence Database Collaboration, we determined that 561 contained mostly samples from wild populations. We successfully restored spatiotemporal metadata for 78% of these 561 data sets (n = 440 data sets with data on 45,105 individuals from 762 species in 17 phyla). Examining papers and online repositories was much more fruitful than contacting 351 authors, who replied to our email requests 45% of the time. Overall, 23% of our email queries to authors unearthed useful metadata. The probability of retrieving spatiotemporal metadata declined significantly as age of the data set increased. There was a 13.5% yearly decrease in metadata associated with published papers or online repositories and up to a 22% yearly decrease in metadata that were only available from authors. This rapid decay in metadata availability, mirrored in studies of other types of biological data, should motivate swift updates to data-sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost to conservation science forever.     

Heterogeneity shapes invasion: host size and environment influence susceptibility to a nonnative pathogen.

Theoretical study of invasion dynamics has suggested that spatial heterogeneity should strongly influence the rate and extent of spreading organisms. However, empirical support for this prediction is scant, and the importance of understanding heterogeneity for real-world systems has remained ambiguous. This study quantified the influence of host and environmental heterogeneity on the dynamics of a 19-year disease invasion by the exotic and fatal pathogen, Phytophthora lateralis, within a stream population of its host tree, Port Orford cedar (Chamaecyparis lawsoniana). Using dendrochronology, we reconstructed the invasion history along a 1350-m length of infected stream, which serves as the only route of pathogen dispersal. Contrary to theoretical predictions, the temporal progression of the disease invasion was not related to a host's downstream spatial position, but instead was determined by two sources of heterogeneity: host size and proximity to the stream channel. These sources of heterogeneity influenced both the epidemic and endemic dynamics of this pathogen invasion. This analysis provides empirical support for the influence of heterogeneity on the invasion dynamics of a commercially important forest pathogen and highlights the need to incorporate such natural variability into both invasion theory and methods aimed at controlling future spread.     

Spatially constrained clustering and upper level set scan hotspot detection in surveillance geoinformatics

We discuss upper level set (ULS) scan as a type of spatially constrained clustering in relation to two ways of imposing the spatial constraint, retrospectively versus progressively. We show that ULS scan produces the same results both ways; whereas two popular clustering techniques, single-linkage and K-means, can yield different results when spatial constraints are imposed retrospectively versus progressively. The ULS scan approach examines spatially connected components of a tessellation as a threshold is moved from the highest level (value) in the data to the lowest level. When the variable of interest on the tessellation is a rate of incidence, then a significance test is available based on binomial or Poisson null models and Monte Carlo techniques. This is a common context for detecting hotspots of diseases in epidemiological work. We also discuss an approach for extending the univariate methodology to accommodate multivariate contexts. Received: September 2005 / Revised: February 2006 This material is based upon work supported by (i) the National Science Foundation under Grant No. 0307010, (ii) the United States Environmental Protection Agency under Grant No. CR-83059301 and (iii) the Pennsylvania Department of Health using Tobacco Settlement Funds under Grant No. ME 01324. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the agencies.     

Overlapping defense responses to water limitation and pathogen attack and their consequences for resistance to powdery mildew disease in garlic mustard, Alliaria petiolata

Plant responses to abiotic stress can alter their response to biotic stress. We examined changes in the activity of several defense proteins in response to powdery mildew infection of garlic mustard (Alliaria petiolata) in the greenhouse and in the field. Second, we examined the effects of water limitation on the same defense protein responses, as well as on total soluble protein and glucose concentration, plant growth, and powdery mildew disease development. Similar increases in the activity of peroxidase, chitinase, and β-1-3-glucanase were observed in leaves of plants with substantial powdery mildew disease in both greenhouse- and field-grown plants. In the greenhouse, activities of chitinase and peroxidase as well as total soluble protein and glucose concentrations generally increased with the degree of water limitation. In turn, leaf growth and powdery mildew symptom development decreased as the degree of water limitation increased. This study revealed that plant chemical responses to water limitation and powdery mildew disease can overlap to a large extent, which, in addition to changing microenvironmental conditions and other indicators of plant quality, may underlie the ability of water limitation to inhibit powdery mildew disease symptom development in this wild plant pathosystem.     

Using a Bayesian network to clarify areas requiring research in a host–pathogen system

Bayesian network analyses can be used to interactively change the strength of effect of variables in a model to explore complex relationships in new ways. In doing so, they allow one to identify influential nodes that are not well studied empirically so that future research can be prioritized. We identified relationships in host and pathogen biology to examine disease‐driven declines of amphibians associated with amphibian chytrid fungus (Batrachochytrium dendrobatidis). We constructed a Bayesian network consisting of behavioral, genetic, physiological, and environmental variables that influence disease and used them to predict host population trends. We varied the impacts of specific variables in the model to reveal factors with the most influence on host population trend. The behavior of the nodes (the way in which the variables probabilistically responded to changes in states of the parents, which are the nodes or variables that directly influenced them in the graphical model) was consistent with published results. The frog population had a 49% probability of decline when all states were set at their original values, and this probability increased when body temperatures were cold, the immune system was not suppressing infection, and the ambient environment was conducive to growth of B. dendrobatidis. These findings suggest the construction of our model reflected the complex relationships characteristic of host–pathogen interactions. Changes to climatic variables alone did not strongly influence the probability of population decline, which suggests that climate interacts with other factors such as the capacity of the frog immune system to suppress disease. Changes to the adaptive immune system and disease reservoirs had a large effect on the population trend, but there was little empirical information available for model construction. Our model inputs can be used as a base to examine other systems, and our results show that such analyses are useful tools for reviewing existing literature, identifying links poorly supported by evidence, and understanding complexities in emerging infectious‐disease systems.     

Infection and immunization trials of Asian seabass (Lates calcarifer) against fish pathogen Vibrio anguillarum

Vibriosis is one of the most prevalent fish diseases caused by bacteria belonging to the genus Vibrio sp. Fish disease will be controlled by proper vaccination trials and maintenance of fish form. Pathogenicity for Asian seabass (Lates calcarifer) against V anguillarum results in necrosis and haemorrhagic areas near the base of fins, exopthalmia and ulcers on the skin surface. Around 50, 100, 200 microl of formalin killed bacterial cells were injected (Intraperitoneal) to three different size (5-10, 20-30, 35-50 g) of seabass fishes respectively and control sere as saline were maintained separately. The Relative Percentage Survival (RPS) for vaccinated fishes was 60, 75, and 62.5 respectively and the vaccinations for 20-30 g fishes stay alive. These results stated that the vaccination for fishes with 20-30 g size may fabricate good immune response.     

Biosecurity threats: the design of surveillance systems,based on power and risk

We consider the problem of designing a surveillance system to detect a broad range of invasive species across a heterogeneous sampling frame. We present a model to detect a range of invertebrate invasives whilst addressing the challenges of multiple data sources, stratifying for differential risk, managing labour costs and providing sufficient power of detection. We determine the number of detection devices required and their allocation across the landscape within limiting resource constraints. The resulting plan will lead to reduced financial and ecological costs and an optimal surveillance system.