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.

<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

The American chestnut tree (Castanea dentata) is a deciduous tree that largely exists in the eastern United States along the Appalachian Mountain range. Approximately 100 years ago, a fungal pathogen (Cryphonectria parasitica) decimated chestnut populations, resulting in the loss of billions of trees. Disease-resistant American chestnut populations have been developed, but the introgression of wild adaptive diversity into these breeding populations will be necessary to develop locally adapted and disease resistant chestnut trees for reintroduction. In this dissertation, I presented our findings which addressed previous gaps in knowledge regarding the population genomics of wild and backcross American chestnut populations. I 1) estimated the genomic diversity, population structure, and demographic history of remnant wild American chestnut populations; 2) revealed the genomic basis of local climate adaptation in American chestnut, developed a novel method to make tree sampling estimates for germplasm conservation, and defined unique seed zones for American chestnut based on climate and genotype, and 3) determined the amount of wild adaptive diversity captured by the backcross breeding program and made recommendations for their replanting region. These results will inform the development of a breeding plan for the introgression of adaptive diversity into backcross and transgenic chestnut populations. / Doctor of Philosophy / The American chestnut tree (Castanea dentata) is a deciduous tree that largely exists in the eastern United States along the Appalachian Mountain range. Approximately 100 years, a fungal disease (Cryphonectria parasitica) decimated chestnut populations, resulting in the loss of billions of trees. The American Chestnut Foundation developed disease-resistant American chestnut backcross trees by breeding American chestnut trees with Chinese chestnut trees (Castanea mollissima). These trees will need additional breeding with wild American chestnut trees so that their offspring will have both the disease-resistant traits and the adaptations to the local environment where they will be replanted. This is important, because trees that are both disease-resistant and locally adapted will be most likely to survive and thrive in their replanting location. However, a comprehensive evaluation of the genomic basis for local adaptation in American chestnut populations is lacking. In this dissertation, I presented our findings which addressed previous gaps in knowledge regarding the population genomics of wild and backcross American chestnut populations. I 1) estimated the genomic diversity, number of unique populations, and population size changes over time in wild American chestnut; 2) revealed the genes related to local adaptation in American chestnut, developed a novel method to make tree sampling estimates for conserving wild American chestnut diversity, and defined unique seed zones (areas within the species range that have unique adaptations to environment) for American chestnut based on climate (ie, precipitation and temperature values) and genotype (DNA), and 3) determined the amount of wild genomic diversity related to local adaption captured by the backcross breeding program and made recommendations for their replanting region. These results will inform the development of a breeding plan of wild American chestnut with backcross and transgenic chestnut populations to create locally adapted and disease-resistant chestnut populations for reintroduction.

No description available.

Light spectra distributions were measured in two different montane forests: temperate and tropical. Spectral light measurements were made in different sized canopy gaps in the conifer forest at H. J. Andrews Experimental Forest in Oregon, USA. Researchers at Oregon State University created these gaps of 20 m, 30 m, and 50 m in diameter. In the tropical cloud forest, spectral light measurements were made in two plots that were permanently established at La Mucuy Parque Nacional in Venezuela, in collaboration with researchers at Universidad de Los Andes. In both studies, spectra and distributions of physiologically active light were analyzed: red, far-red, R/FR ratio, and blue light.

No description available.

Changes in the productivity of temperate forests have important implications for atmospheric carbon dioxide (CO2) concentrations, and many efforts have focused on methods to monitor both gross and net primary productivity in temperate forests. Remotely sensed vegetation indices provide spatially extensive measures of vegetation activity, and the Enhanced Vegetation Index (EVI) has been widely linked to photosynthetic activity of vegetation. Networks of tree ring width (TRW) chronologies provide ground-based estimates of annual net carbon (C) uptake in forests, and time series of EVI and TRW may capture common productivity signals. Robust correlations between mean TRW and EVI may enhance spatial extrapolations of TRW-based productivity estimates, ultimately improving understanding of spatio-temporal variability in forest productivity. The research presented in this thesis investigates potential empirical relationships between networks of TRW chronologies and time series of Landsat EVI and Landsat-based phenological metrics in the Northeast United States. We hypothesized that mean TRW is positively correlated with mean monthly EVI during the growing season, EVI integrated over the growing season, and growing season length. Results indicate that correlations between TRW and EVI are largely not significant in this region. The complex response of tree growth to a variety of limiting climatic factors in temperate forests may decouple measures of TRW growth and canopy reflectance. However, results also indicate that there may be important lag effects in which EVI affects mean TRW during the following year. These findings may improve understanding of links between C uptake and growth of tree stems over large spatial scales.

Forests ecosystems cover about 30% of the Earth’s land surface, corresponding to an area of roughly 42 million km2 globally. Forests play an important role in the global carbon cycle by exchanging carbon dioxide (CO2) with the atmosphere. Annually, forests act to effectively sequester large amounts of anthropogenically-emitted CO2 from the atmosphere through photosynthetic processes. Through the unparalleled increase of CO2 emissions over the past century and the subsequent climatic inconsistencies due to global climate change, the carbon sink-capacity of the world’s forests remains uncertain. Furthermore, since increasing temperatures have been shown to extend the vegetative growing season in forests, phenological responses to this change are of particular interest. In an effort to effectively assess the future carbon sequestration potential of forests, a better understanding of the climatic controls on phenology, and its influence on carbon processes, is needed. The eddy covariance (EC) technique is a stand-level, in-situ, method used widely to assess the net CO2 exchange across the canopy-atmosphere interface. Together with meteorological data, the sequestration of CO2 and the subsequent ecosystem productivity can be quantified over various time scales (half-hours to decades). This dissertation reports results from field observations of EC measured fluxes that were used to study the climatic impacts on forest phenology and the resulting carbon dynamics in southern Ontario, Canada. The study sites, part of the Turkey Point Observatory, consisted of two similarly-aged, temperate, North American forests growing under similar climatic and edaphic conditions: the 80-year old (in 2019) white pine plantation (coniferous evergreen) and 90+ year-old, naturally-regenerated, white oak (deciduous broadleaf) forest. These forests were studied from 2012 to 2017, using the EC technique, digital phenological cameras, and remote-sensing measurements. At the deciduous broadleaf forest, mid-summer (July and August) meteorological conditions were the key period in determining the annual carbon sink-strength of the site, acting to regulate the interannual variability in carbon uptake. The forest experienced higher net ecosystem productivity (+NEP; carbon sink) when soil temperatures ranged from 15 to 20°C and vapor pressure deficit was 0.7 and 1.2 kPa. From 2012 to 2016, the forest remained a net annual sink, with mean NEP of 206 ± 92 g C m-2 yr-1, similar to that of other North American deciduous forests. Spring and autumn phenological transition dates were calculated for each year (2012 to 2017) from measured EC data and digital camera greenness indices. The timing of spring and autumn transition dates were impacted by seasonal changes in air temperature and other meteorological variables. Contrary to past studies, an earlier growing season start did not equate to increased annual carbon uptake. In autumn, a later end to the deciduous forest growing season negatively impacted the net carbon uptake of the forest, as ecosystem respiration (RE) outweighed the gains of photosynthesis. The digital camera indices failed to capture the peak dates of photosynthesis, but accurately measured the spring and autumn transition dates, which may be useful in future remote sensing applications. A comparison of the two forests from 2012 to 2017 found the coniferous forest to have higher but more variable annual NEP (218 ± 109 g C m-2 yr-1) compared to that of the deciduous broadleaf forest (200 ± 83 g C m-2 yr-1). Similarly, the mean annual evapotranspiration (ET) was higher (442 ± 33 mm yr-1) at the coniferous forest compared to that of the broadleaf forest (388 ± 34 mm yr-1). The greatest difference between years resulted from the response to heat and drought. During drought years, deciduous carbon and water fluxes were less sensitive to changes in temperature or water availability compared to the evergreen forest. Carotenoid sensitive vegetative indices and the red-edge chlorophyll index were shown to effectively capture seasonal changes in photosynthesis phenology within both forests via proximal remote sensing measurements during the 2016 growing season. Satellite vegetative indices were highly correlated to EC photosynthesis, but significant interannual variability resulted from either meteorological inputs or the heterogeneous landscapes of the agriculturally-dominated study area. This dissertation improved our understanding of the dynamics of carbon exchange within the northeastern North American deciduous forest ecozone, through the examination of climatic variability and its impact on carbon and phenology. This dissertation also contributed to efforts being made to better evaluate the impact of species composition on carbon dynamics in geographically similar forests. Moreover, the use of the digital phenological camera observations and remote sensing techniques to complement and better understand the fluxes observed with the EC method was innovative and may help other researchers in future studies. / Dissertation / Doctor of Philosophy (PhD)

Forest fragmentation is a pervasive consequence of human land use that creates novel forest boundaries in place of contiguous, intact forest. Boundary forests, or edges, experience environmental conditions distinct from the forest interior driven by lateral exposure to adjacent non-forest land cover. Forest edges tend to be hotter, drier and experience increased wind turbulence and atmospheric deposition with significant consequences for ecosystem processes and biogeochemical cycling. Much of what we know about forest edge structure and function derives from tropical forest research, despite prolific fragmentation in temperate forests. Building on recent field studies of temperate forest edges in the northeastern United States (US), I combine measurements from the US national forest inventory (NFI) with remotely-sensed maps of forest area to characterize broad patterns in the extent and impacts of fragmentation on temperate forest ecology. Using the US NFI to identify forest edges across a 20-state region, I report increased biomass and growth of edge forests compared their interior counterparts. I then compare the prevalence of forest edges in the US NFI and commonly-used forest maps to very-high-resolution land-cover maps, and I demonstrate that conventional methods of forest characterization systematically undercount and exclude forest edge area. Finally, I synthesize these findings to quantify aboveground carbon (C) cycling in New England using a novel approach that partitions forest C fluxes into forest edge and interior categories. I find that forest edges are disproportionately vulnerable to land-use conversion and are a critical component of both forest C uptake and emissions. Accounting for elevated growth rates in forest edges increases estimates of the net forest C sink in New England by 8.6% (4.36 Tg C). My dissertation research demonstrates the need to better understand the extent and effects of fragmentation in temperate forests, provides support for the treatment of forest edges as a distinct system, and highlights the need to include forest edges in current and future C accounting.