More than a hundred hydropower dams have already been built in the Amazon basin and numerous proposals for further dam constructions are under consideration. The accumulated negative environmental effects of existing dams and proposed dams, if constructed, will trigger massive hydrophysical and biotic disturbances that will affect the Amazon basin's floodplains, estuary and sediment plume. We introduce a Dam Environmental Vulnerability Index to quantify the current and potential impacts of dams in the basin. The scale of foreseeable environmental degradation indicates the need for collective action among nations and states to avoid cumulative, far-reaching impacts. We suggest institutional innovations to assess and avoid the likely impoverishment of Amazon rivers.

Coastline communities have experienced a marked increase in human populations over the last few decades. This increase in population places disproportionate pressure on coastal ecosystems to provide economic services to support local economies. At the same time, overuse of these services can aid in the destruction of the ecosystems responsible for them. Seagrass ecosystems are mainly found near coastlines, and are typically a chief provider of some of these economic goods and services. Many previous studies have documented the ecological functions of this seagrasses. Unfortunately, our increasing knowledge of seagrass structure and function has not been fully incorporated into economic models estimating their value. In this dissertation, I focus on the seagrass ecosystem in southern Biscayne Bay, and simultaneously study the ecological dynamics of the seagrass beds, and estimate its economic value. This value is based on recent ecological models in the literature as well as data I collected from the system. I focused on Biscayne Bay due to, 1) the relevance that this question had to the relationship between Biscayne Bay and the Miami metropolis, and 2) the lack of existing reliable models that explore this relationship in this area. More specifically, I became very interested in this question while working for Biscayne National Park, where such a model would have improved seagrass restoration work taking place there. I found that southern Biscayne Bay is dominated by Thalassia testudinum, with other seagrasses following a spatial pattern primarily determined by salinity and water column nutrient distribution. Syringodium filiforme was mostly found east of the islands, Halodule wrightii was mostly found near the shoreline, and Halophila engelmenii was spotted at only two of the 190 sites visited. T. testudinum distribution was largely unaffected by nutrient enrichment at all sites, but it appeared to induce severe herbivory further from the coastline. For the calendar year 2004, we deduced using a Total Ecosystems Valuation (TEV) model that seagrass ecosystems potentially contributed over $198 million US dollars to the local economy. We argue that a simultaneous understanding and use of both ecological and economic models is important for future conservation efforts of seagrass ecosystems.

Soil nitrogen availability to plants is a fundamental control on the structure and functioning of arctic tundra ecosystems. Despite recent evidence that biogeochemical and microbial dynamics during the non-growing season impact nitrogen availability to plants in tundra ecosystems, very little is known about soil microbial patterns and mechanisms for nutrient mobilization in the winter, spring and fall. In this dissertation I have examined the environmental and microbial controls on seasonal nitrogen mobilization in a widespread Canadian low arctic birch hummock tundra ecosystem. In particular, I have investigated the potential for increased winter snow depth and different above-ground vegetation-types to alter soil microbial community patterns and nutrient mobilization from organic matter into plant-available pools. First, I demonstrated that experimentally deepened winter snow altered soil microbial physiology during winter, defined as increased microbial carbon limitation to growth and activity. Second, I established that deepened snow enhanced spring nutrient mobilization during distinct environmental phases, producing large peaks in the soil microbial biomass and soil solution carbon, nitrogen and phosphorus during snow thaw. Third, I showed that laboratory predictions of early-spring air temperature freeze-thaw cycles promoting tundra soil nitrogen loss are not relevant, as the soil environment and soil biogeochemistry were relatively stable after snow melt and before plant growth began. Fourth, I demonstrated that microbial functional groups did not differ strongly under different tundra vegetation types, but higher quality shrub litter induced positive feedbacks on soil carbon availability and soil nitrogen mineralization in the late summer. Finally, I illustrated that annual patterns of tundra soil microbial community structure and composition were strongly linked to soil biogeochemistry and that significant shifts in fungal/bacterial ratios occur during snowmelt. This research suggests two broad conclusions: a) that soil microbial activity is responsive to changes in above-ground vegetation; and b) that seasonal changes in microbial community structure and microbial biochemistry are strongly correlated. Therefore, the synchronicity of microbial seasonal succession and plant species-specific timing of nitrogen uptake is a critical factor restricting the potential for ecosystem N losses at spring thaw and ultimately in supplying growth-limiting nutrients to plants in the following summer. / Thesis (Ph.D, Biology) -- Queen's University, 2009-09-25 23:29:53.103

abstract: Humans have dramatically increased phosphorus (P) availability in terrestrial and aquatic ecosystems. As P is often a limiting nutrient of primary production, changes in its availability can have dramatic effects on ecosystem processes. I examined the effects of calcium carbonate (CaCO3) deposition, which can lower P concentrations via coprecipitation of phosphate, on P availability in two systems: streams in the Huachuca Mountains, Arizona, and a stream, Río Mesquites, in Cuatro Ciénegas, México. Calcium carbonate forms as travertine in the former and within the microbialites of the latter. Despite these differences, CaCO3 deposition led to lowered P availability in both systems. By analyzing a three-year dataset of water chemistry from the Huachuca Mountain streams, I determined that P concentrations were negatively related to CaCO3 deposition rates. I also discovered that CaCO3 was positively correlated with nitrogen concentrations, suggesting that the stoichiometric effect of CaCO3 deposition on nutrient availability is due not only to coprecipitation of phosphate, but also to P-related constraints on biotic nitrogen uptake. Building from these observations, bioassays of nutrient limitation of periphyton growth suggest that P limitation is more prevalent in streams with active CaCO3 deposition than those without. Furthermore, when I experimentally reduced rates of CaCO3 deposition within one of the streams by partial light-exclusion, areal P uptake lengths decreased, periphyton P content and growth increased, and periphyton nutrient limitation by P decreased. In Río Mesquites, CaCO3 deposition was also associated with P limitation of microbial growth. There, I investigated the consequences of reductions in CaCO3 deposition with several methods. Calcium removal led to increased concentrations of P in the microbial biomass while light reductions decreased microbial biomass and chemical inhibition had no effect. These results suggest that CaCO3 deposition in microbialites does limit biological uptake of P, that photoautotrophs play an important role in nutrient acquisition, and, combined with other experimental observations, that sulfate reduction may support CaCO3 deposition in the microbialite communities of Río Mesquites. Overall, my results suggest that the effects of CaCO3 deposition on P availability are general and this process should be considered when managing nutrient flows across aquatic ecosystems. / Dissertation/Thesis / Doctoral Dissertation Biology 2015

In aquatic ecosystems, dissolved organic matter (DOM) is an important source of detrital energy on which microorganisms rely. However, its dynamics are not well understood in an ecological context. By isolating watershed sources, the work reported in this thesis has attempted to characterize the seasonal patterns of DOM in the hyporheic zone of a temperate stream and to find the likely sources that contribute to this pool of organic carbon. Hyporheic DOM characteristics described by UV spectroscopy indicated temporal rather than spatial dependence. Excitation-emission matrices (EEMs) showed that hyporheic DOM was mainly comprised of fulvic- and humic-like fluorescence with small amounts of protein-like fluorescence. Increases in dissolved organic carbon (DOC) concentrations from birch litter isolates were greater than those from cedar litter in early autumn, but less in late autumn. Although streambed biofilm was not significant in increasing DOC concentrations, it was also a source of protein-like fluorescence.

In aquatic ecosystems, dissolved organic matter (DOM) is an important source of detrital energy on which microorganisms rely. However, its dynamics are not well understood in an ecological context. By isolating watershed sources, the work reported in this thesis has attempted to characterize the seasonal patterns of DOM in the hyporheic zone of a temperate stream and to find the likely sources that contribute to this pool of organic carbon. Hyporheic DOM characteristics described by UV spectroscopy indicated temporal rather than spatial dependence. Excitation-emission matrices (EEMs) showed that hyporheic DOM was mainly comprised of fulvic- and humic-like fluorescence with small amounts of protein-like fluorescence. Increases in dissolved organic carbon (DOC) concentrations from birch litter isolates were greater than those from cedar litter in early autumn, but less in late autumn. Although streambed biofilm was not significant in increasing DOC concentrations, it was also a source of protein-like fluorescence.

Amazonian evergreen forests are of broad interest, attributable to their ecological, economic, aesthetic, and cultural importance. However, their fate under climate change remains uncertain, largely due to unclear mechanisms in regulating tropical photosynthetic metabolism. Understanding mechanistic controls on these dynamics across time scales (e.g. hours to years) is essential and a prerequisite for realistically predicting tropical forest responses to inter-annual and longer-term climate variation and change. Tropical forest photosynthesis can be conceptualized as being driven by two interacting causes: variation due to changes in environmental drivers (e.g. solar radiation, diffuse light fraction, and vapor pressure deficit) interacting with model parameters that govern photosynthetic behavior, and variation in photosynthetic capacity (PC) due to changes in the parameters themselves. In this thesis, I aim to reveal photosynthetic controls by addressing three fundamental but complementary questions: (1) What are the mechanisms by which the subtle tropical phenology exert controls on tropical photosynthetic seasonality? (2) How do the extrinsic and intrinsic controls regulate the photosynthesis processes at hourly to interannual time scales in an Amazonian evergreen forest? (3) Are there sufficiently consistent relations among leaf traits, ages, and spectra that allow a single model predict the leaf aging process of Amazonian evergreen trees? To address question 1, I firstly show that seasonal change in ecosystem-scale photosynthetic capacity (PC), rather than environmental drivers, is the primary driver of seasonality of gross primary productivity (GPP) at four Amazonian evergreen forests spanning gradients in rainfall seasonality, forest composition, and flux seasonality. Using novel near-surface camera-detected leaf phenology to drive a simple leaf-cohort canopy model at two of these sites, I further show that leaf ontogeny and demography explain the changes in ecosystem photosynthetic capacity. The coordination of new leaf growth and old leaf divestment (litterfall) during the dry season shifts canopy composition towards younger leaves with higher photosynthetic capacity, driving large seasonal increases (~27%) in ecosystem photosynthetic capacity. To address question 2, I used the 7-year eddy covariance (EC) measurements in an Amazonian tropical evergreen forest. I used a statistical model to partition the variability of 7-year EC-derived GPP into two main causes: variation due to changes in extrinsic environmental drivers and variation in intrinsic PC. The fitted model well predicts variability in EC-derived GPP at hourly (R²=0.71) to interannaul (R²=0.81) timescales. Attributing model predictions to causal factors at different timescales, I find that ~92% of the variability in modeled hourly GPP could be attributed to environmental driver variability, and ~5% to variability in PC. When aggregating the modeled GPP into the annual time-step, the attribution is reversed (only ~4% to environment and ~91% to PC). These results challenge conventional approaches for modeling evergreen forests, which neglect intrinsic controls on PC and assume that the primary photosynthetic control at both long and short timescales is due to changes in the hourly-to-diurnal environment on the physiological phenotype. This work thus highlights the importance of accounting for differential regulation of different components of GPP at different timescales, and of identifying the underlying feedbacks and adaptive mechanisms which regulate them. To address question 3, I explored the potential for a general spectrally based leaf age model across tropical sites and within the vertical canopy profiles using a phenological dataset of 1831 leaves collected at two lowland Amazonian forests in Peru (12 species) and Brazil (11 species). This work shows that a simple model (parameterized using only Peruvian canopy leaves) successfully predicts ages of canopy leaves from both Peru (R²=0.83) and Brazil (R²=0.77), but ages for Brazilian understory leaves with significantly different growth environment and leaf trait values have lower prediction accuracy (R²=0.48). Prediction accuracy for all Brazilian samples is improved when information on growth environment and leaf traits were added into the model (5% R² increase; R²=0.69), or when leaves from the full range of trait values are used to parameterize the model (15% R² increase; R²=0.79). This work shows that fundamental ecophysiological rules constrain leaf traits and spectra to develop consistently across species and growth environment, providing a basis for a general model associating leaf age with spectra in tropical forests. In sum, in this thesis, I (1) conceptualize photosynthesis as being driven by two interacting dynamics, extrinsic and intrinsic, (2) propose and validate a model for biological mechanisms that mediate seasonal dynamics of tropical forest photosynthesis, (3) assess and quantify the factors controlling tropical forest photosynthesis on timescales from hourly to interannual, and (4) develop a general model for monitoring leaf aging processes of tropical trees across sites and growth environments. The revealed mechanisms (and proposed models) in this thesis greatly improve our mechanistic understanding of the photosynthetic and phenological processes in tropical evergreen forests. Strategic incorporation of these mechanisms will improve ecological, evolutionary and earth system theories describing tropical forests structure and function, allowing more accurate representation of forest dynamics and feedbacks to climate in earth system models.

abstract: An understanding of the formation of spatial heterogeneity is important because spatial heterogeneity leads to functional consequences at the ecosystem scale; however, such an understanding is still limited. Particularly, research simultaneously considering both external variables and internal feedbacks (self-organization) is rare, partly because these two drivers are addressed under different methodological frameworks. In this dissertation, I show the prevalence of internal feedbacks and their interaction with heterogeneity in the preexisting template to form spatial pattern. I use a variety of techniques to account for both the top-down template effect and bottom-up self-organization. Spatial patterns of nutrients in stream surface water are influenced by the self-organized patch configuration originating from the internal feedbacks between nutrient concentration, biological patchiness, and the geomorphic template. Clumps of in-stream macrophyte are shaped by the spatial gradient of water permanence and local self-organization. Additionally, significant biological interactions among plant species also influence macrophyte distribution. The relative contributions of these drivers change in time, responding to the larger external environments or internal processes of ecosystem development. Hydrologic regime alters the effect of geomorphic template and self-organization on in-stream macrophyte distribution. The relative importance of niche vs. neutral processes in shaping biodiversity pattern is a function of hydrology: neutral processes are more important in either very high or very low discharge periods. For the spatial pattern of nutrients, as the ecosystem moves toward late succession and nitrogen becomes more limiting, the effect of self-organization intensifies. Changes in relative importance of different drivers directly affect ecosystem macroscopic properties, such as ecosystem resilience. Stronger internal feedbacks in average to wetter years are shown to increase ecosystem resistance to elevated external stress, and make the backward shifts (vegetation loss) much more gradual. But it causes increases in ecosystem hysteresis effect. Finally, I address the question whether functional consequences of spatial heterogeneity feed back to influence the processes from which spatial heterogeneity emerged through a conceptual review. Such feedbacks are not likely. Self-organized spatial patterning is a result of regular biological processes of organisms. Individual organisms do not benefit from such order. It is order for free, and for nothing. / Dissertation/Thesis / Doctoral Dissertation Biology 2015

abstract: Constructed treatment wetlands (CTW) have been a cost-efficient technological solution to treat different types of wastewater but may also be sources of emitters of methane (CH4) and nitrous oxide (N2O). Thus, my objective for this dissertation was to investigate CH4 and N2O fluxes via multiple pathways from the Tres Rios CTW located in Phoenix, AZ, USA. I measured gas fluxes from the CTW along a whole-system gradient (from inflow to outflow) and a within-marsh gradient (shoreline, middle, and open water sites). I found higher diffusive CH4 release in the summer compared to spring and winter seasons. Along the whole-system gradient, I found greater CH4 and N2O emission fluxes near the inflow compared to near the outflow. Within the vegetated marsh, I found greater CH4 emission fluxes at the vegetated marsh subsites compared to the open water. In contrast, N2O emissions were greater at the marsh-open water locations compared to interior marsh. To study the plant-mediated pathway, I constructed small gas chambers fitted to Typha spp. leaves. I found plant-mediated CH4 fluxes were greater near the outflow than near the inflow and that CH4 fluxes were higher from lower sections of plants compared to higher sections. Overall, Typha spp. emitted a mean annual daily flux rate of 358.23 mg CH4 m-2 d-1. Third, using a 30-day mesocosm experiment I studied the effects of three different drydown treatments (2, 7, 14 days) on the fluxes of CH4 and N2O from flooded CTW soils. I found that CH4 fluxes were not significantly affected by soil drydown events. Soils that were dry for 7 days shifted from being N2O sources to sinks upon inundation. As a result, the 7-day drydown soils were sinks while the 14-day drydown soils showed significant N2O release. My results emphasize the importance of studying ecological processes in CTWs to improve their design and management strategies so we can better mitigate their greenhouse gas emissions. / Dissertation/Thesis / Doctoral Dissertation Biology 2017

No description available.