A PCR diagnostic assay for rapid detection of plant pathogenic pseudomonads

Molecular detection of phytopathogens is increasingly being applied to identify regulated organisms at the border in many parts of the world. However, even with molecular tests, complete phenotyping and identification of a strain is often time consuming and sometimes inconclusive. In this study, a leaf-based pathogenicity test was used to separate pseudomonads into two groups, Group A containing pathogens, and Group B containing saprotrophs. Comparative genomics of 56 pseudomonad genomes from different plant hosts (including 29 strains from kiwifruit) agreed with kiwifruit pathogenicity test results, placing pathogens into Group A and saprotrophs into Group B. Sixteen loci were found unique to Group A. A PCR assay was developed for amplification of one of these loci, the trehalose phosphatase gene. The generation of this 655 bp amplicon was associated with production of water-soaked lesions on inoculated kiwifruit leaves by pseudomonads in Group A. This test was validated for further strains from all seven pathogenic Pseudomonas phylogroups, non-pathogenic pseudomonads, and other bacterial genera. The sensitivity of the PCR was comparable to the limit of recovery of pseudomonads by culturing. This simple PCR assay could be used as part of a testing pipeline at the border and for general surveillance for screening plants with and without symptoms, offering the potential to detect uncharacterized pseudomonads that may pose a biosecurity risk. The method was shown to be able to rapidly identify pathogens cultured from plant material with symptoms, or, more importantly, to detect pathogens directly from plant tissue.     

Time-delayed influence of urban landscape change on the susceptibility of koalas to chlamydiosis

Context

Infectious diseases are important in the dynamics of many wildlife populations, but there is limited understanding of how landscape change influences susceptibility to disease.

Objectives

We aimed to quantify the time-delayed influence of spatial and temporal components of landscape change and climate variability on the prevalence of chlamydiosis in koala (Phascolarctos cinereus) populations in southeast Queensland, Australia.

Methods

We used data collected over 14 years (n = 9078 records) from a koala hospital along with time-lagged measures of landscape change and rainfall to conduct spatial and temporal analyses of the influence of landscape and environmental variables on prevalence of chlamydiosis and koala body condition.

Results

Areas with more suitable habitat were associated with higher levels of disease prevalence and better body condition, indicating that koalas were less likely to be impacted by chlamydiosis. More intact landscapes with higher proportions of total habitat are associated with a reduction in prevalence of chlamydiosis and a decrease in body condition. Increased annual rainfall contributed to a decrease in prevalence of chlamydiosis and an increase in body condition. Urbanization was associated with an increase in disease, however the effects of urban landscape change and climate variability on chlamydiosis may not manifest until several years later when overt disease impacts the population via effects upon body condition and reproductive success.

Conclusions

Our study highlights the importance of effects of landscape change and climate variability on disease prevalence in wildlife. This recognition is essential for long-term conservation planning, especially as disease often interacts with other threats.

     

Sirius: a mechanistic model of wheat response to environmental variation

Sirius is a wheat simulation model that calculates biomass production from intercepted photosynthetically active radiation (PAR) and grain growth from simple partitioning rules. Leaf area index (LAI) is developed from a thermal time sub-model. Phenological development is calculated from the mainstem leaf appearance rate and final leaf number, with the latter determined by responses to daylength and vernalisation. Effects of water and N deficits are calculated through their influences on LAI development and radiation-use efficiency. This paper describes the model and its validation using data from independent and near independent experiments at Lincoln, New Zealand, and Rothamsted, UK. Despite there being no calculation of tiller dynamics or grain number, the model accurately simulated the behaviour of crops exposed to a wide range of conditions. We conclude that the accurate prediction of phenological development and LAI is much more important for grain yield prediction than are the components of yield. Although grain population is not a necessary step in yield calculation in Sirius, the model proved useful in investigating the effects of stress in setting grain number. The analysis showed that the influence of stress on partitioning of biomass to the ear during pre-anthesis ear growth was much more important in determining grain number than was the effect on biomass accumulation during the same phase.     

Aquaculture of the sand star,Astropecten indicus Döderlein, 1888, as a step toward the sustainable aquaculture of harlequin shrimp,Hymenocera picta Dana, 1852

Ornamental harlequin shrimp, Hymenocera picta, are commonly maintained on live comet sea stars, Linckia multifora. In Thailand, both species are commonly collected from the wild, raising concerns regarding the sustainability of such practices. As a step toward the sustainable aquaculture of both, methods of their culture and nutrition were investigated. Under captive conditions, harlequin shrimp readily predate, and can be maintained upon the astropectinid sand star Astropecten indicus as an alternative live feed during periods when comet sea stars are unavailable. Wild A. indicus subsequently spawned multiple times shortly after their collection; the eggs (300 μm diameter) were transferred to static aquaria. Following the appearance of planktonic bipinnaria, larval sea stars were fed a 50:50 Chaetoceros calcitrans and Isochrysis galbana diet. Eleven days post-transfer, brachiolaria stages began to settle; stages were then fed concentrated I. galbana. When specimens measured 1–2 mm in diameter, they were transferred onto an in-house formulated Amphiprion diet (>50% protein, >16% lipid). Sea stars were graded regularly; they matured and spawned after 6 months. Populations were maintained for more than three successive generations, demonstrating their ready culture under captive conditions, representing the first harvestable aquaculture of a sea star as a step toward supporting the sustainable culture of a primary, marine species.     

Fine‐scale population structure and connectivity of bottlenose dolphins,Tursiops truncatus,in European waters and implications for conservation

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Dynamic changes in American lobster suitable habitat distribution on the Northeast U.S. Shelf linked to oceanographic conditions

American lobster (Homarus americanus) supports one of the most valuable regional fisheries in the United States, with its abundance and distribution profoundly influenced by environmental conditions. To explain how lobster distribution has changed over time and assess the role of environmental variables on these changes, we used random forest classification and regression tree models to estimate occupancy and biomass in two seasonal periods. The occupancy models were fit to static and dynamic variables, which yielded model fits with AUC scores of 0.80 and 0.78 for spring and fall, respectively. Biomass models were fit with the same data and resulted in models explaining 61% and 63% of the spring and fall biomass variance, respectively. Significant variables scored in the formation of the regression trees were secondary productivity (i.e., zooplankton), bathymetry characteristics, and temperature. American lobster suitable habitat has changed regionally; habitat has increased in the Gulf of Maine and declined in Southern New England. There is also evidence of declining habitat along the inshore margin of the Gulf of Maine, which has been accompanied by a shift in occupancy probability offshore. Habitat suitability results from the random forest models provide insights on the structure and function of lobster habitat and context to understand recent population trends.     

改善管理方法控制猪的传染性疾病

20世纪90年代在英国出现新的猪病如PMWS／PDNS,迫使人们开始重新评估现有的生产系统,疫苗已经不能解决所有问题,养猪场必须采用改进管理方法来控制疾病。如PRRS,离开了综合饲养管理,疫苗仍然不起作用。本文涵盖各种控制疾病的基本饲养管理方法,每个场则须针对各自情况采用合适的方法。     

Decadal changes (1996–2006) in coastal ecosystems of the Chagos archipelago determined from rapid assessment

• 1. The atolls and islands comprising Chagos are a biodiversity hotspot of global conservation significance in a remote part of the central Indian Ocean.
• 2. This study examines the condition of the archipelago's coastal ecosystems by rapid environmental assessment at 21 sites/islands, which were also investigated a decade earlier using the same methodology. Major changes in ecosystem structure and environmental disturbance were determined.
• 3. Coral fish abundance was significantly lower in 2006 than 1996. Decrease in the physical structural complexity of the reefs, as a result of coral bleaching and mortality induced by the 1998 warming event, may have been a contributing factor.
• 4. Evidence of collecting/fishing was significantly greater in 2006 than 1996. This is attributed mainly to an illegal fishery for holothurians (sea cucumbers), which has expanded over recent years and now exerts substantial pressure on the resource. The significant decline observed in beach wood, a readily accessible fuel for fishing camps, is consistent with this.
• 5. Solid waste on islands was high (median 2 to 20 items m^?1 beach) in both 1996 and 2006. Potentially harmful biological impacts, determined from other studies, include entanglement, toxic effects and provision of transport for invasives or other ‘hitchhiker’ species.
• 6. Significantly higher bird abundances were recorded in protected areas than ‘unprotected’ areas, attributed mainly to absence of predation by rats.
• 7. Rapid assessment augments more comprehensive ecosystem investigations. It provides a valuable snapshot of environmental conditions based upon a broad suite of features (ecosystems and disturbances) determined, concurrently, within the same site inspection quadrats and using the same scale of assessment.

Copyright © 2009 John Wiley & Sons, Ltd.     

Occurrence of killer whales in Scottish inshore waters: temporal and spatial patterns relative to the distribution of declining harbour seal populations

• 1. Sightings of killer whales around Shetland were recorded between 1991 and 2006 and for the whole of Scotland for 2007. The data were used to investigate temporal patterns in killer whale occurrence around Shetland and spatial patterns in occurrence around Scotland.
• 2. There was a strong seasonal peak in sightings around Shetland during June–July, coinciding with the harbour seal pupping season.
• 3. There was no clear trend in annual sightings around Shetland between 1991 and 2006.
• 4. Killer whales were sighted most frequently around Shetland and the Pentland Firth as well as around Mull and the Treshnish Isles.
• 5. These findings are discussed in terms of potential impacts upon local declining harbour seal populations and future research requirements.

Copyright © 2009 John Wiley & Sons, Ltd.