Staphylococcal scalded skin syndrome (SSSS) is a life-threatening skin condition caused by Staphylococcus aureus (SA) strains producing exfoliative toxin. Most SSSS cases are associated with Exfoliative Toxin A, encoded by the eta gene and carried by a temperate bacteriophage phiETA (ΦETA). An estimated ~10% of strains containing ΦETA are methicillin-resistant SA (MRSA), raising questions about the factors associated with ΦETA susceptibility. Our study investigates the lysogenization susceptibility of ΦETA in a set of SA strains through lysogenic challenges. To this end, we first isolate phage lysates from a known epidemic strain containing eta. In lysogenic challenge assays, we demonstrate that MRSA strains are resistant to ΦETA acquisition. All the 4/89 (4.5%) strains that were successfully lysogenized with ΦETA were characterized as methicillin-susceptible SA (MSSA). While lysogenic conversion did not modify other phenotypic markers, it increased the biofilm production, indicating potential fitness advantages conferred by ΦETA lysogenization. We also hypothesized that phage sequences in challenged strains may provide immunity against ΦETA, thus prophage presence and diversity may correlate with ΦETA susceptibility. Among the 89 strains tested, we bioinformatically identified that 54 of them contained at least one intact prophage sequence. Interestingly, all successfully lysogenized strains lacked intact prophages in their native state which contradicts the poly-lysogenic nature of SA. Additionally, the enhancement of biofilm formation after lysogenic conversion by ΦETA could be associated with pathogenesis of SSSS, increased invasiveness and even emergence of clinically relevant strains. Further studies are needed to explain the genetic and transcriptional basis of phenotypic changes. Together, our results underscore the vital role of ΦETA prophages in shaping SA diversity and clinical outcomes. This study highlights the necessity of investigating the molecular mechanisms associated with bacteriophage lysogenization and host range expansion.

Increases in atmospheric C have resulted in concerns about global warming and interest in finding means to sequester atmospheric C through land management strategies. The purpose of this study was to (i) compare changes in mineral soil C after a 30-year interval and (ii) examine the role of inorganic-N, soil texture, and topography in these changes. Soil samples were collected at permanently identified points on the Camp Branch Watershed, a second growth oak forest on the Cumberland Plateau in central Tennessee, in July of 1976 and archived. These points were re-sampled in July of 2006 and both archived and new samples of the 0 to 10 cm increment of the mineral soil were analyzed for C and N using the same procedures. Paired comparisons revealed changes in C and N were distinct to each of the 8 soil series. Comparison of 2006 samples to 1976 samples indicated changes in C concentration ranged from -13.1% to +12.0%. Changes in C mass ranged from -11.3% to +8.3%. Increases in C were most closely associated with increases in the C/total-N ratio. C was positively correlated to exchangeable inorganic-N in 1976 (r2 = 0.387) and 2006 (r2 = 0.107). Regression analysis revealed C increased with increasing azimuth and decreasing elevation in 1976 (r2 = 0.140). C was predicted only by clay content in 2006 (r2 = 0.079) and exhibited a negative relationship. Since topography was no longer a predictor of mineral soil C in 2006, we speculate that changes in forest cover also influenced changes in mineral soil C. / Master of Science

Forests play an important role in the net ecosystem exchange of CO2 in terrestrial ecosystems. Soil respiration is often the major source of CO2 in forests and is greatly influenced by climatic variability and management practices. Spatial and temporal variations of soil respiration have been examined in a chronosequence (60, 30, 15, and 1 year-old) of temperate, afforested, white pine (Pinus strobus) forest stands in Southern Ontario, Canada, in order to investigate any age related differences. Spatial and temporal variations of soil respiration in a 74 year-old boreal, mixed-wood forest in Central Ontario, was also studied and compared with results from the 60 year-old, temperate, white pine, forest stand, in order to investigate any climate related differences. Soil CO2 flux, temperature, and moisture were measured for one year (June 2003 to May 2004, inclusive, for the chronosequence study, and August 2003 to July 2004, inclusive, for the boreal-temperate study). In all stands, temporal variability of soil respiration followed the seasonal pattern of soil temperature, reaching a minimum in winter and maximum in summer. Temporal variability of soil temperature was able to explain 80 to 96% of the temporal variability in soil respiration at all stands. Spatial variability in soil respiration was also observed at all stands and the degree of this variability was seasonal, following the seasonal trend of mean daily soil respiration. Spatial variability of some soil chemical properties was highly correlated with the spatial variability of soil respiration, while litter thickness was not. The location of soil respiration measurement with respect to tree trunks may also help to explain some of the spatial variability in soil respiration. Across the chronosequence, the highest mean daily CO2 efflux was observed during the growing season for the 15 year-old-stand (5.2 ± 1.3 to 0.4 ± 0.2 μmol CO2 m^-2 s^-1), which was comparable to the 60 year-old-stand (4.9 ± 1.3 to 0.2 ±0.1 μmol CO2 m^-2 s^-1), but higher than the 30 year (3.8 ± 0.9 to 0.2 ± 0.0 μmol CO2 m^-2 s^-1) and 1 year (2.9 ± 0.9 to 0.3 ± 0.3 μmol CO2 m^-2 s^-1) old stands. From boreal-temperate comparison, it was observed that mean daily soil respiration rates for the boreal stand (6.9 ± 1.7 to 0.5 ±0.1 μmol CO2 m^-2 s^-1) were higher during the growing season compared to the 60 year-old temperate forest stand. Understanding temporal and spatial variability of soil respiration and how it is controlled is essential to improving forest ecosystem carbon budget assessments, and subsequently, the global carbon budget. This study will contribute direct observations necessary for improving and validating forest ecosystem CO2 exchange models. / Thesis / Master of Science (MSc)

Global biodiversity protection requires the development of protected areas that include representative samples of different ecosystems and their associated biodiversity (Dudley 1992, Scott et al. 2001a). I compared long-term decline and protection of forests in three major biomes; boreal, temperate and tropical. I found that forests in the temperate biome are less abundant and less protected than forests in the boreal and tropical biomes. I conducted regional analyses for five continents on the degree of protection of temperate forests across naturally occurring geographic and elevational ranges. My results indicate that protected temperate forests do not represent the full geographic and elevational range of naturally occurring temperate forests. Bias in location, elevation and slope of protected areas are present at both the regional and global scale. Better protection of temperate forests is needed if the diversity and resources associated with these forests types across their geographic range is to be preserved.

The soil organic carbon (C) pool is estimated to contain at least three times as much organic C as is stored in vegetation. However, the processes controlling below-ground C dynamics are poorly understood, representing a key uncertainty in ecosystem models. Soil respiration rate (Rs) is a large component of the forest carbon cycle, however the factors that control it are still poorly understood, and those affecting autotrophic (Ra) and heterotrophic (Rh) respiration rates differ and vary in space and time. A variety of direct (i.e. soil and ingrowth cores) and indirect (i.e. rhizotron and minirhizotron) methods exist for obtaining estimates of fine root (< 2 mm diameter) production, with the consequence that there is a high variability in root biomass estimates between root studies. In this thesis I aim to contribute towards a better understanding of processes governing below-ground C dynamics. In particular I focus on: 1) the spatial and seasonal variability of Rs and drivers; 2) the uncertainty on fine root C pool measurement methods; 3) comparing novel datasets of Rs, fine root biomass and girth increment, with outputs from the SPA v2 model. To determine the dominant controls and spatial heterogeneity of Rs, I measured Rs and key biotic and abiotic drivers seasonally, in a Quercus robur forest in southern England. Measurements were made quarterly in three plots, each with measurement points arranged according to a spatial sampling design, enabling any spatial autocorrelation to be detected. Rs drivers were categorised into plant (i.e. leaf area index, weighted tree proximity (i.e. mean dbh within 4 m of a point), and fine root biomass), physical (i.e. soil moisture, soil temperature and soil bulk density) and substrate (i.e. litter depth and organic layer depth) factors. I explore: 1) what the dominant controls of Rs are and whether they change during the growing season; 2) whether micro-topography and stand structure are correlated with drivers, and influence the spatial variability of Rs, thereby simplifying up-scaling processes; 3) if physical drivers of Rs are spatially more homogeneous than plant drivers and the availability of substrate. I found no clear seasonal difference in drivers, with Rs consistently responding to litter depth, bulk density and soil moisture. The only significant response of Rs to micro-topography and tree factor was in August and September respectively and physical factors were found to be the most spatially homogeneous. Rs measurements were non-normally distributed, with ‘hotspots’ of particularly high fluxes found that remained stable throughout the measurement campaign. These findings suggest that the seasonal and spatial variability and distribution of Rs and its main drivers should be considered at the sampling design stage, to avoid bias for up-scaling non-linear processes. To address the uncertainties associated with determining fine root biomass change, we compared the measurement error for five methodologies (four indirect and one direct) in a Pinus contorta and Quercus robur forest during 2010. Rhizotron and ingrowth measurements were taken during 2010 and fine root standing crop was measured in 2009. Root length against the rhizotron screens was measured using novel software (ORIDIS), developed as part of a collaboration here in Edinburgh. The software was developed to increase precision and reduce the cost and processing time of rhizotron measurements. Differences in final cumulative root ingrowth for each conversion method ranged between 20.7g-2 - 245.0 g m-2 in the oak forest and 89.7 g m-2 - 273.0 g m-2 in the pine forest. The study found that indirect measurements of root length had less operator error than indirect measurements of root diameter. Direct methods of determining root growth using ingrowth cores also showed a seasonal trend; however artefacts may have been introduced into the method, from the affect of severing roots and changing soil conditions. To test the representation of below-ground processes in an ecosystem model, I validate modelled dynamics using default SPA v2 parameters, against independent CO2 flux and C pool datasets. The flux data were of eddy covariance and automatic chamber measurements, partitioned into root (Rroot), mycorhizal (Rmyc) and microbial heterotrophic (Rh) components. The biometric measurements were of foliage, fine root biomass and woody biomass increment. The key findings of this study were that: 1) SPA outputs compare well to ecosystem scale measurements of NEE and GPP. However, model-data mismatch occurs for fine root and wood C allocation; 2) the timing of fine root C allocation is 53 days too late and the turnover rate of fine roots 17 times too high; 3) the timing of modelled below-ground Rh and Ra could be improved by separating above and below-ground Ra and including individual root, mychorrizae and microbial C pools. The thesis concludes by discussing the implications of each chapter for our understanding and capability to model below-ground C dynamics. I find that the key challenge for measuring individual below-ground C pools and fluxes is ensuring that the measurements are spatially representative and avoid bias. The key challenge for modelling below-ground C dynamics is ensuring processes sufficiently reflect reality, when the sparse data that exist for corroboration, capture multiple processes. I explore the possibilities of further research that could be conducted, as a result of this work.

Despite the long time since the introduction and spread of pine plantations in southern hemisphere countries there has been no study of the suitability of this exotic and novel type of vegetation on the native avifauna. This thesis aims to add understanding of this habitat replacement and its effects on the forest bird community. This research included a series of studies to assess the quality of mature pine plantations for the forest avifauna in comparison to what is in native forests. The first two studies determine the effects on the forest bird community of the fragmentation and replacement of native forest in a gradient of substitution. The results showed a direct relationship between level of substitution and loss of functional diversity, and that fragmentation predicts the bird assemblage in pine stands. The next two studies used data from an intensive ringing season to assess differences in the condition of populations inhabiting each habitat. Birds, in general, were found in better condition in native fragments than in pine plantations. Moreover, a despotic distribution was determined for a migrant species and a gradient in habitat quality was found in relation to proximity to native forest. The next two studies used information from a nest-box survey set in a gradient of sites with substitution of native forest. The results showed that the type of forest cover and their proportion in the landscape may affect the breeding performance of some species. Finally, in the last study I evaluated the foraging niche of bird species in each habitat. Compared with native forest, niche breath reduced while the niche overlap increased in pine plantations for most species. The results suggest that pine plantations are poor quality habitat for the bird community and that the substitution of native forests increases selective pressure.

Because of the multiple values and services that trees deliver to society, agroforestry is increasingly interpreted as an agricultural innovation that can help to address challenges in modern agriculture. Despite its potential opportunities in Flanders, many farmers remain skeptical though, resulting in adoption rates that are lagging behind. Therefore the objective of this thesis is to gain a better understanding of the unfavorable environment for agroforestry adoption and development making use of a farming systems research approach (FSR). In Chapter 2 we explain FSR as our general research approach, which implies the consideration of three key characteristics, i.e. systems thinking, interdisciplinarity and a participatory approach. Taking into account the general FSR characteristics, Chapter 3, 4 and 5 “diagnose” the agroforestry implementation gap more in detail. In chapter 3, we gain some first insights by assessing farmers’ intentions to engage in agroforestry and by giving an overview of the current agroforestry acreage in Flanders. In Chapter 4, we use the Agricultural Innovation Systems concept as general framework to identify the different stakeholders and their respective roles, and to give an overview of the different merits and failures with respect to agroforestry development. Afterwards Chapter 5 elucidates the different perspectives that exist on agroforestry systems among Flemish stakeholders, and links them with general discourses on agriculture in Flanders. Diagnostic analyses were followed up by design exercises in Chapter 6, which looks into different instruments that may give economic incentives to farmers to adopt agroforestry. Taking into account the gathered insights, we present in the main discussion chapter five development pathways to further stimulate agroforestry adoption and development: (1) the science and technology pathway, which stands for investing in research, especially targeting the productivity and compatibility of agroforestry systems, and this in active collaboration with farmers; (2) the market and financial pathway, which implies the creation of market mechanisms in which landscape and biodiversity aspects are valued, while stimulating private investments and consumer demand; (3) the policy and institutional pathway, which aims for the creation of a fully-fledged legal landscape for agroforestry, which is clear and steadfast into the future, and which should be complemented with an attractive and effective subsidy program; (4) the educational and organizational pathway, which stimulates the use of multiple communication and education channels to inform the relevant actors and familiarize them with agroecological practices and their benefits for society; and (5) the social and behavioral pathway, which encourages strengthening the dialogue between influential groups to restore mutual confidence, build up common visions, and open up collaboration opportunities. Through further systemic, interdisciplinary and participatory research, the identified development pathways should be translated into concrete action plans to eliminate adoption barriers and close the agroforestry implementation gap in Flanders. / Doctorat en Sciences agronomiques et ingénierie biologique / info:eu-repo/semantics/nonPublished

The meiofauna of a mangrove forest in the River Barwon estuary was studied by means of surveys and field experiments. Distinctive assemblages of meiofauna were described from the sediment and pneumatophores of the ecosystem. Fine resolution of phytal habitats was demonstrated, and particular assemblages of meiofauna were characteristic within habitat provided by dominant epibionts. Distribution of the meiofauna within leaf litter revealed high turnover rates of nematodes, and some factors controlling detrital assemblages were assessed. The vertical profile of sedimentary meiofauna was examined, and changes in abundance were related to the tychopelagic habit of many taxa at high tide. Dispersal within the water column was confirmed by pelagic trapping, and colonisation of mimic pneumatophores was investigated. The amount of algal cover, effects of grazing by gastropods, and rugosity of the colonised surface were shown to influence meiofauna colonisation of mimic pneumatophores. Establishment and persistence of patchy distributions of meiofauna at scales of less than 10 m in an intertidal environment was demonstrated, and it was concluded that this was due to the dynamic nature of assemblages rather than their integrity.

<p>Human activities are increasingly altering the ways in which energy and elements cycle within and move between ecosystems. Through fossil fuel combustion and the use of synthetic fertilizers we continue to expose much of the biosphere to new rates and ratios of essential element supply. We are also shifting climate patterns on local, regional and global scales in ways that affect reaction rates and residence times of elements within ecosystems. Even the simplest ecosystems are usually too complex to predict many of the potential consequences that human activities will have on their sustained functioning. Because of this, we often monitor ecosystems as integrated wholes, looking to explain processes that account for important patterns observed across space and time. This dissertation consists of 3 data chapters, all of which use the small watershed ecosystem as the principal unit of study for understanding how human activities have altered element cycling in temperate forests in the southern Appalachian Mountains. </p><p>In Chapter 2, we present results from repeated synoptic surveys of streamwater chemistry for ~30 watersheds spanning one of the largest nitrogen (N) deposition gradients in North America, located within the Great Smoky Mountains National Park. We primarily focus on patterns in dissolved organic matter (DOM) concentrations and composition across the N gradient, with particular attention given to dissolved organic nitrogen (DON). DON dominates the global flux of N between terrestrial and aquatic systems, yet we have little understanding of how this prevailing N form responds to human N pollution. We found that DON concentrations often declined significantly with increasing catchment N loading and, through laboratory bioavailability assays, found that when N limitation is alleviated increased microbial demand for labile carbon (C) may drive this pattern. We use these findings to suggest a new hypothesis for the potential responses of DON to anthropogenic N pollution that accounts for the dual role that DON plays in both C and N cycles. </p><p>Chapter 3 is an extension of Chapter 2, in which we attempt to assess the role of DON as either a C or N source within an entire stream reach through a series of independent manipulations of labile C and inorganic N availabilities. In the second order reach of Walker Branch, a well-studied stream in eastern Tennessee, we performed a series of progressive (i.e., sequentially increasing concentrations), kinetic (i.e., very short duration), enrichments of acetate and nitrate on two successive days during April of 2009 before the tree canopy emerged and when in-stream algal production was high. In this system and on these short timescales, we were unable to elicit the same responses observed at sites across the chronic N deposition gradient in Chapter 2. We did, however, observe that DOM processing and composition was significantly altered. Using fluorescence characterization of DOM, we found that adding acetate displaced heterotrophic demand for terrestrially derived DOM. Conversely, nitrate additions stimulated production of highly bioavailable autochthonous DOM within the stream channel, which resulted in an indirect displacement of demand for terrestrially derived DOM. Understanding DOM dynamics in streams has long been a priority for stream ecologists because it represents an important energy and nutrient source fueling stream metabolism. Our results provide new insight into the processes controlling DOM concentrations and composition in Walker Branch, as well as demonstrate the potential of this method for future investigations of DOM in stream ecosystems. </p><p>Chapter 4 deviates from the preceding chapters' focus on N availability and ecosystem DOM dynamics, instead assessing the role of climate change on long-term streamwater concentrations and fluxes from the West Fork of the Walker Branch watershed. At this site, mean annual temperatures have increased by ~2&#730;C, while mean annual precipitation and runoff have declined by ~20% and >40%, respectively, since 1989. We use weekly streamwater samples to assess trends in concentrations and fluxes for 9 different solutes over this period and, using wet deposition data, also evaluate changes in approximate watershed input-output budgets. The observed change in runoff was accompanied by a change in the proportional contributions of different soil flowpaths to streamflow generation through time, with deep groundwater playing an increasingly important role in recent years. Solutes that increase in concentration deeper in the soil profile exhibited significant increases in streamwater concentrations through time, while solutes with higher concentrations in soil solution in the upper profile decreased in concentration. Nutrient solutes, which exhibit much less variation across soil flowpaths, typically display large seasonal patterns in streamwater concentrations that are driven by in-stream biological uptake. However, most nutrient solutes exhibited little or no trend in concentrations through time, indicating that the biological controls on these solutes have remained relatively unaltered by the observed changes in climate over the 20-year period. On shorter timescales, changes in the frequency or severity of multi-year droughts, as well as changes in the frequency or intensity of storms that disrupt in-stream uptake, can have large impacts on watershed input-output budgets of nutrient solutes even if the effects do not manifest as linear trends through time. Our results demonstrate the important role that changing climates can have on watershed element cycles, illustrating that climate effects can manifest through either changes in hydrologic regime or through changing biogeochemical process rates. </p><p>Taken together, these chapters illustrate that human activities are indirectly but substantially changing biogeochemical cycles in temperate forests throughout the Southern Appalachians. Ecosystem structure and function depends on the ways in which energy and elements move within and between ecosystems. We rely on the sustained integrity of ecosystems for their many services and, because of this, it is essential that we understand ecosystem responses to current and future human impacts.</p> / Dissertation

This thesis attempted to determine whether precipitation at CFB Borden, Ontario Canada is derived from recycled or marine source water using δ18O and to explore the enrichment of leaf water in three temperate forest trees. The d-excess values and rainfall intensity were used as indicators of recycled water and were found to suggest that precipitation at Borden is not derived from recycled water. The leaves of ash, aspen and maple showed significant enrichment in δ18O over xylem water. Maple leaves were significantly more enriched over the leaves of ash and aspen (p-value = 0.0019), despite source water not being significantly different (p-value = 0.1782). Modelling leaf water demonstrated the need for the inclusion of the Peclet effect in the steady state model for ash and aspen leaves, however for maple, the Peclet effect is insignificant. The non-steady state model used measured values of δET, which were uncertain and lead to poor model predictions. / NSERC Strategic Project #351040