Pine wilt disease and the pinewood nematode

Pine wilt disease (PWD) is one of the most damaging events affecting conifer forests (in particular Pinus spp.), in the Far East (Japan, China and Korea), North America (USA and Canada) and, more recently, in the European Union (Portugal). In Japan it became catastrophic, damaging native pine species (Pinus thunbergii and P. densiflora), and becoming the main forest problem, forcing some areas to be totally replaced by other tree species. The pine wilt nematode (PWN) Bursaphelenchus xylophilus, endemic, with minor damage, to North America, was introduced in Japan in the early XX century and then spread to Asia (China and Korea) in the 1980s. In 1999 it was detected for the first time in Portugal, where, due to timely detection and immediate government action, it was initially (1999-2008) contained to a small area 30 km SE of Lisbon. In 2008, the PWN spread again to central Portugal, the entire country now being classified as “affected area”. Being an A1 quarantine pest, the EU acted to avoid further PWN spreading and to eradicate it, by actions including financial support for surveyes and eradication, annual inspections and research programs. Experience from control actions in Japan included aerial spraying of insecticides to control the insect vector (the Cerambycid beetle Monochamus alternatus), injection of nematicides to the trunk of infected trees, slashing and burning of large areas out of control, beetle traps, biological control and tree breeding programs. These actions allowed some positive results, but also unsuccessful cases due to the PWN spread and virulence. Other Asian countries also followed similar strategies, but the nematode is still spreading in many regions. In Portugal, despite lower damage than Asia, PWD is still significant with high losses to the forestry industry. New ways of containing PWD include preventing movement of contaminated wood, cutting symptomatic trees and monitoring. Despite a national and EU legislative body, no successful strategy to control and eventually eradicate the nematode and the disease will prevail without sound scientific studies regarding the nematode and vector(s) bioecology and genetics, the ecology and ecophysiology of the pine tree species, P. pinaster and P. pinea , as well as the genomics and proteomics of pathogenicity (resistance/ susceptibility).

Modelling the Minho river plume intrusion into the rias baixas

The Minho River, situated 30 km south of the Rias Baixas is the most important freshwater source flowing into the Western Galician Coast (NW of the Iberian Peninsula). This discharge is important to determine the hydrological patterns adjacent to its mouth, particularly close to the Galician coastal region. The buoyancy generated by the Minho plume can flood the Rias Baixas for long periods, reversing the normal estuarine density gradients. Thus, it becomes important to analyse its dynamics as well as the thermohaline patterns of the areas affected by the freshwater spreading. Thus, the main aim of this work was to study the propagation of the Minho estuarine plume to the Rias Baixas, establishing the conditions in which this plume affects the circulation and hydrographic features of these coastal systems, through the development and application of the numerical model MOHID. For this purpose, the hydrographic features of the Rias Baixas mouths were studied. It was observed that at the northern mouths, due to their shallowness, the heat fluxes between the atmosphere and ocean are the major forcing, influencing the water temperature, while at the southern mouths the influence of the upwelling events and the Minho River discharge were more frequent. The salinity increases from south to north, revealing that the observed low values may be caused by the Minho River freshwater discharge. An assessment of wind data along the Galician coast was carried out, in order to evaluate the applicability of the study to the dispersal of the Minho estuarine plume. Firstly, a comparative analysis between winds obtained from land meteorological stations and offshore QuikSCAT satellite were performed. This comparison revealed that satellite data constitute a good approach to study wind induced coastal phenomena. However, since the numerical model MOHID requires wind data with high spatial and temporal resolution close to the coast, results of the forecasted model WRF were added to the previous study. The analyses revealed that the WRF model data is a consistent tool to obtain representative wind data near the coast, showing good results when comparing with in situ wind observations from oceanographic buoys. To study the influence of the Minho buoyant discharge influence on the Rias Baixas, a set of three one-way nested models was developed and implemented, using the numerical model MOHID. The first model domain is a barotropic model and includes the whole Iberian Peninsula coast. The second and third domains are baroclinic models, where the second domain is a coarse representation of the Rias Baixas and adjacent coastal area, while the third includes the same area with a higher resolution. A bi-dimensional model was also implemented in the Minho estuary, in order to quantify the flow (and its properties) that the estuary injects into the ocean. The chosen period for the Minho estuarine plume propagation validation was the spring of 1998, since a high Minho River discharge was reported, as well as favourable wind patterns to advect the estuarine plume towards the Rias Baixas, and there was field data available to compare with the model predictions. The obtained results show that the adopted nesting methodology was successful implemented. Model predictions reproduce accurately the hydrodynamics and thermohaline patterns on the Minho estuary and Rias Baixas. The importance of the Minho river discharge and the wind forcing in the event of May 1998 was also studied. The model results showed that a continuous moderate Minho River discharge combined with southerly winds is enough to reverse the Rias Baixas circulation pattern, reducing the importance of the occurrence of specific events of high runoff values. The conditions in which the estuarine plume Minho affects circulation and hydrography of the Rias Baixas were evaluated. The numerical results revealed that the Minho estuarine plume responds rapidly to wind variations and is also influenced by the bathymetry and morphology of the coastline. Without wind forcing, the plume expands offshore, creating a bulge in front of the river mouth. When the wind blows southwards, the main feature is the offshore extension of the plume. Otherwise, northward wind spreads the river plume towards the Rias Baixas. The plume is confined close to the coast, reaching the Rias Baixas after 1.5 days. However, for Minho River discharges higher than 800 m3 s-1, the Minho estuarine plume reverses the circulation patterns in the Rias Baixas. It was also observed that the wind stress and Minho River discharge are the most important factors influencing the size and shape of the Minho estuarine plume. Under the same conditions, the water exchange between Rias Baixas was analysed following the trajectories particles released close to the Minho River mouth. Over 5 days, under Minho River discharges higher than 2100 m3 s-1 combined with southerly winds of 6 m s-1, an intense water exchange between Rias was observed. However, only 20% of the particles found in Ria de Pontevedra come directly from the Minho River. In summary, the model application developed in this study contributed to the characterization and understanding of the influence of the Minho River on the Rias Baixas circulation and hydrography, highlighting that this methodology can be replicated to other coastal systems.

DPSIR framework application supported by integrated watershed modeling for irrigation from Alqueva dam (Portugal) on Guadiana river estuary

Dissertação de mest., Gestão da Água e da Costa, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2009

Organic-walled dinoflagellate cysts in recent sediments from the Guadiana river estuary, South-East Portugal

Dissertação de Mestrado, Biologia Marinha, Faculdade de Ciências do Mar e do Ambiente, Universidade do Algarve, 2007

The function and future of the LOICS basins approach in promoting integrated coastal zone & watershed management with an emphasis on developing countries

Dissertação de Mestrado, Gestão da Água e da Costa, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2010

Ecology of the early life-history stages of shad Alosa fallax fallax (Lacépède, 1803) in the River Mira, with a note on Alosa spp. larvae in the River Guadiana

Tese dout., Ecologia, Universidade do Algarve, 2006

Our Past Betrays Us: Collective Memory, Homicide and Southern Lynching

Thesis (Master's)--University of Washington, 2013

A Community-Level, Mesoscale Analysis of Fish Assemblage Structure in Shoreline Habitats of a Large River Using Multivariate Regression Trees.

The mesoscale (100–102 m) of river habitats has been identified as the scale that simultaneously offers insights into ecological structure and falls within the practical bounds of river management. Mesoscale habitat (mesohabitat) classifications for relatively large rivers, however, are underdeveloped compared with those produced for smaller streams. Approaches to habitat modelling have traditionally focused on individual species or proceeded on a species-by-species basis. This is particularly problematic in larger rivers where the effects of biological interactions are more complex and intense. Community-level approaches can rapidly model many species simultaneously, thereby integrating the effects of biological interactions while providing information on the relative importance of environmental variables in structuring the community. One such community-level approach, multivariate regression trees, was applied in order to determine the relative influences of abiotic factors on fish assemblages within shoreline mesohabitats of San Pedro River, Chile, and to define reference communities prior to the planned construction of a hydroelectric power plant. Flow depth, bank materials and the availability of riparian and instream cover, including woody debris, were the main variables driving differences between the assemblages. Species strongly indicative of distinctive mesohabitat types included the endemic Galaxias platei. Among other outcomes, the results provide information on the impact of non-native salmonids on river-dwelling Galaxias platei, suggesting a degree of habitat segregation between these taxa based on flow depth. The results support the use of the mesohabitat concept in large, relatively pristine river systems, and they represent a basis for assessing the impact of any future hydroelectric power plant construction and operation. By combing community classifications with simple sets of environmental rules, the multivariate regression trees produced can be used to predict the community structure of any mesohabitat along the reach.

Geographic and host factors shape the evolution of a newly recognized subgroup within the U genogroup of the fish rhabdovirus IHNV

Thesis (Master's)--University of Washington, 2015

The new suburban history, New Urbanism and the spaces in between

A review article of three recent books on suburbanization and suburbia in the USA: Andrew Friedman, Covert Capital: Landscapes of Denial and the Making of the US Empire in the Suburbs of Northern Virginia. Berkeley, Los Angeles: University of California Press, 2013. 416pp. £19.95 pbk. Elaine Lewinnek, The Working Man's Reward: Chicago's Early Suburbs and the Roots of American Sprawl. Oxford and New York: Oxford University Press, 2014. 239pp. 20 b&w illustrations. £30.99 hbk. Benjamin Ross, Dead End: Suburban Sprawl and the Rebirth of American Urbanism. Oxford and New York: Oxford University Press, 2014. 249pp. £20.99 hbk.

Biodiversity of amoebae and amoebae-resisting bacteria in a drinking water treatment plant

The complex ecology of free-living amoebae (FLA) and their role in spreading pathogenic microorganisms through water systems have recently raised considerable interest. In this study, we investigated the presence of FLA and amoebae-resisting bacteria (ARB) at various stages of a drinking water plant fed with river water. We isolated various amoebal species from the river and from several points within the plant, mostly at early steps of water treatment. Echinamoeba- and Hartmannella-related amoebae were mainly recovered in the drinking water plant whereas Acanthamoeba- and Naegleria-related amoebae were recovered from the river water and the sand filtration units. Some FLA isolates were recovered immediately after the ozonation step, thus suggesting resistance of these microorganisms to this disinfection procedure. A bacterial isolate related to Mycobacterium mucogenicum was recovered from an Echinamoeba-related amoeba isolated from ozone-treated water. Various other ARB were recovered using co-culture with axenic Acanthamoeba castellanii, including mycobacteria, legionella, Chlamydia-like organisms and various proteobacteria. Noteworthy, a new Parachlamydia acanthamoebae strain was recovered from river water and from granular activated carbon (GAC) biofilm. As amoebae mainly multiply in sand and GAC filters, optimization of filter backwash procedures probably offers a possibility to better control these protists and the risk associated with their intracellular hosts

Pathogen-induced hatching and population-specific life-history response to water-borne cues in brown trout (Salmo trutta)

Hatching is an important niche shift, and embryos in a wide range of taxa can either accelerate or delay this life-history switch in order to avoid stage-specific risks. Such behavior can occur in response to stress itself and to chemical cues that allow anticipation of stress. We studied the genetic organization of this phenotypic plasticity and tested whether there are differences among populations and across environments in order to learn more about the evolutionary potential of stress-induced hatching. As a study species, we chose the brown trout (Salmo trutta; Salmonidae). Gametes were collected from five natural populations (within one river network) and used for full-factorial in vitro fertilizations. The resulting embryos were either directly infected with Pseudomonas fluorescens or were exposed to waterborne cues from P. fluorescens-infected conspecifics. We found that direct inoculation with P. fluorescens increased embryonic mortality and induced hatching in all host populations. Exposure to waterborne cues revealed population-specific responses. We found significant additive genetic variation for hatching time, and genetic variation in trait plasticity. In conclusion, hatching is induced in response to infection and can be affected by waterborne cues of infection, but populations and families differ in their reaction to the latter.

Larval habitat associations with human land uses, roads, rivers, and land cover for Anopheles albimanus, A. pseudopunctipennis, and A. punctimacula (Diptera: Culicidae) in coastal and highland Ecuador

Larval habitat for three highland Anopheles species: Anopheles albimanus Wiedemann, Anopheles pseudopunctipennis Theobald, and Anopheles punctimacula Dyar and Knab was related to human land uses, rivers, roads, and remotely sensed land cover classifications in the western Ecuadorian Andes. Of the five commonly observed human land uses, cattle pasture (n = 30) provided potentially suitable habitat for A. punctimacula and A. albimanus in less than 14% of sites, and was related in a principal components analysis (PCA) to the presence of macrophyte vegetation, greater surface area, clarity, and algae cover. Empty lots (n = 30) were related in the PCA to incident sunlight and provided potential habitat for A. pseudopunctipennis and A. albimanus in less than 14% of sites. The other land uses surveyed (banana, sugarcane, and mixed tree plantations; n = 28, 21, 25, respectively) provided very little standing water that could potentially be used for larval habitat. River edges and eddies (n = 41) were associated with greater clarity, depth, temperature, and algae cover, which provide potentially suitable habitat for A. albimanus in 58% of sites and A. pseudopunctipennis in 29% of sites. Road-associated water bodies (n = 38) provided potential habitat for A. punctimacula in 44% of sites and A. albimanus in 26% of sites surveyed. Species collection localities were compared to land cover classifications using Geographic Information Systems software. All three mosquito species were associated more often with the category “closed/open broadleaved evergreen and/or semi-deciduous forests” than expected (P ≤ 0.01 in all cases), given such a habitat’s abundance. This study provides evidence that specific human land uses create habitat for potential malaria vectors in highland regions of the Andes.