Microbes, living on the boundary between the sediment and the water-column in lakes, can play a pivotal role in governing the magnitude and frequency of nutrient cycling. The purpose of this research was to focus on the role of benthic microalgae in regulating such processes and to identify spatial and temporal characteristics in their function. Approaches included the quantification of sediment nutrient concentrations (particularly P fractionation), estimates of equilibrium phosphate concentrations (EPC0) (resuspended and undisturbed sediment estimates), and assessment of the benthic microalgal community composition, biostabilisation capacity, and its ability to regulate diffusive-nutrient flux. This thesis highlighted the importance of biological regulation of benthic/pelagic nutrient cycling, especially the role of benthic microautotrophs. Release sensitive sediment-P fractions were observed to be highly variable (both with depth and season) and correlated well with indicators of benthic photosynthesis (e.g. DO, chlorophyll, pH). Understanding the seasonality of whole-system P partitioning can enhance future lake management programmes. EPC0 estimates were significantly higher during undisturbed as opposed to disturbed sediment conditions. Epipelon constituted < 17 % of the total sediment chlorophyll signal and was highest in the clearer winter months and at intermediate depths at which a trade off between wind-induced habitat disturbance and light limitation existed. In intact core experiments, the benthic microalgal community significantly reduced the diffusive nutrient (especially PO₄-P and SiO₂) flux. NH₄ -N release was highest under light conditions at high temperatures. The mechanisms for regulation included direct uptake, photosynthetic oxygenation of the sediment surface, and regulation of nitrification/denitrification processes. Sediment stability increased with colloidal carbohydrate concentration (extruded by benthic microbes) at 4.1 m water-depth but not at 2.1 m overlying water depth, probably indicating the role of habitat disturbance in shallow areas acting to reduce epipelic production. Additionally, in an ecosystem comparison, the nature and extent of the biotic mediation of sediment stability varied between freshwater and estuarine ecosystems.

Measuring the impact of physical disturbance on macrofaunal communities and sediment composition is important given the increased demand for the exploitation and disturbance of marine ecosystems. The aim of the present investigation was to provide a comprehensive study about the extent to which the disturbance (especially aggregate dredging) may affect benthic ecosystem function. The first part of the thesis concerns a field investigation of the impacts of dredging on the benthic community and related ecosystem function which was measured by different approaches including traditional methods based on benthic community structure and a more novel approach based on the functional traits of benthic organisms. The assessment was done by comparing dredged sites (Area 222, southeast England) with nearby undisturbed reference sites from the years 2001 to 2004 and in 2007. In general, low dredging intensity did not appear to impose great impacts on the benthic community and related ecosystem function compared to the higher intensity activity. Most of the analyses suggested that the community at the high dredging intensity site had yet to recover at the end of this study period. Among many factors related to the recovery of the benthic community was sediment composition where gravel deposits appeared to support a faster biological recovery. Meanwhile, the recovery of species with specific traits, such as tube-building and filter feeding also indicate a faster recovery for the whole community. The experimental work to determine different impacts of Hediste diversicolor on its surrounding depending on its relative size is discussed in Appendix 1.

<p>Arbuscular mycorrhizal fungi (AMF) are best known for their potential to help plants acquire nutrients, especially phosphorous. These microbes improve soil health by promoting soil aggregation and carbon sequestration, and further benefit plants by helping them withstand biotic and abiotic stress. Currently, there are 200 recognized species of AMF within the phylum Glomeromycota. Recent studies indicate that individual AMF species differ in the benefits they provide, with some even acting as parasites. Moreover, AMF community composition can be altered by soil and crop management practices, but the effect of these changes on the benefits conferred by AMF are still not well understood. Consequently, the goal of this study was to determine how two widely used crop management systems can alter the composition of AMF species, and affect the potential for these communities to promote the productivity and drought tolerance. To accomplish this goal, we collected AMF inoculum from a long-term crop systems trial comparing organic and conventional management for use in greenhouse trials where we subjected plants to drought. We collected AMF inoculum during mid-summer when differences between the two management systems were likely cause larger effects on AMF communities, and again in autumn after harvest to see if differences in AMF communities would persist. We determined AMF species composition using next generation sequencing. Results of this study confirm that soil-building practices commonly used in organic farming systems can improve soil health and increase the productivity of food-grade soybeans. They also demonstrate that AMF communities in Indiana croplands are highly diverse, and some of these taxa can improve soybean growth and help plants tolerate water stress. Although the overall diversity of AMF communities did not differ between the organic and conventional management systems in mid-summer, individual AMF taxa did differ between the systems, which were likely responsible for the greater tolerance to water stress observed when plants were amended with inoculum from the organic system. AMF communities present during autumn were significantly different between the two crop management systems, but did not result in differences in drought tolerance of soybeans, indicating that the loss of key AMF taxa in the organic system from the first relative to the second experiment was likely responsible. Finally, plants grown using inoculum from both crop management systems in autumn had greater tolerance to water stress than plants that received a AMF commercial inoculum. This provides further evidence that individual AMF species vary in the benefits they provide, and that the presence of a diverse consortium of AMF species is needed to optimize plant health and productivity in agricultural systems. Agricultural producers should consider incorporating soil-building practices that are commonly used in organic farming systems such as planting winter cover crops, to improve the health of their soil and enhance the productivity of their crops. <b></b></p> <br>

<p>Biological invasion has become a major threat to economy, ecology, global biodiversity and ecosystem function of aquatic ecosystems. The main aim of the thesis was to study the effects of the zebra mussel <i>(Dreissena polymorpha)</i>, a versatile invasive species, on phytoplankton dynamics and ecosystem function of lakes. </p><p>In a first attempt, I compared the density of <i>Dreissena</i> and the physicochemical data of ecosystems that it invaded among North American and European lakes to identify important factors in its invasion success. Secondly, I investigated the impact of zebra mussels on phytoplankton community composition in a natural lake. Thirdly, I evaluated whether zebra mussel feeding behavior were affected by the presence of predatory waterborne cues. Finally, I examined the effect of <i>Dreissena</i> on seston stoichiometry.</p><p>A Generalized Additive Model revealed that a joint effect of surface area, mean depth, total phosphorus and calcium concentrations can explain the variability in <i>Dreissena</i> density. Selective grazing by zebra mussels varied in relation to seasonal phytoplankton dynamics. Risk cues released by predators affected both feeding rate and prey selection of the mussels and had cascading indirect effects on phytoplankton biomass and community structure. I found that the flux in nutrients caused by differences in zebra mussel consumption lead to a variation in phytoplankton nutrient limitation.</p><p>The flexibility of zebra mussel feeding behavior and variation in susceptibility among phytoplankton groups to mussel ingestion indicate that invading zebra mussels could alter phytoplankton community composition of lakes and have important ecosystem consequences. The results of this thesis contribute to the growing evidence that predators indirectly affect resource dynamics and food web structure through their non-lethal effects on consumers. The results suggested that zebra mussel can indirectly both reduce and increase the energy transfer efficiency from primary producers to upper trophic levels in the pelagic and benthic food webs, respectively. </p>

There is growing concern that the worldwide loss in biodiversity will harm the stability of the ecosystems, and thereby, the carrying capacity and critical ecosystem services the biosphere provides. Phytoplankton (microalgae) in lakes and oceans are arguably the most important primary producers. They are responsible for approximately half of the earth's primary production. However, there is little research into what influences the biodiversity of phytoplankton communities and of those studies the mechanisms for coexistence of phytoplankton have so far almost exclusively been studied on ecological time scales. We, therefore, explored how biodiversity and biomass (a proxy to primary production) of phytoplankton communities respond to co-varied environmental drivers over evolutionary time scales. We model adaptive evolution of phytoplankton' resource use, with a non-dimensionalized model of negatively buoyant phytoplankton inhabiting a partially mixed one-dimensional water column using reaction-advection-diffusion equations. We show that a number of environmental drivers have novel effects on biodiversity and biomass on evolutionary timescales. In contrast with previous non-evolutionary work, we found that decreasing light attenuation or increasing resource use efficiency can result in decreased biomass of plankton communities and nutrient-poor environments. One novel driver of species diversity was the combination of low rates of diffusion with relatively intermediate rates of sinking promote species diversity. Furthermore, we show that the phytoplankton turnover rate affects environmental heterogeneity and is, therefore, a contributing driver to species diversity.The evolution of half saturation constants can produce a variety of biodiversity-ecosystem function patterns as two positive, one unimodal, and one negative association were found when comparing biodiversity-ecosystem function. Collectively, our analyses suggest that environmental drivers can have substantially different effects over evolutionary timescales than those effects ecological modeling has previously shown.

The prevalence of hypoxia in aquatic systems has increased in recent decades and climate change is expected to worsen the extent and severity of hypoxic phenomena worldwide. Moreover, aquatic hypoxia has produced adverse ecological consequences and stimulated research interest within the Laurentian Great Lakes. The physiological stress imposed by hypoxia reduces habitat quality for most aquatic biota and causes changes in patterns of resource use and food web dynamics. We conducted a review of the primary literature to identify trends in prevalence of Great Lakes hypoxia research and broadly classify the unique hypoxic conditions afflicting Great Lakes ecosystems. We found that the majority of research effort toward Great Lakes hypoxia is focused on the Lake Erie central basin. Our review further revealed that this does not characterize the breadth of hypoxic phenomena that occur throughout the Great Lakes region. We then utilized a long-term monitoring dataset provided by the U.S. Environmental Protection Agency Great Lakes National Program Office to quantify the impact of Lake Erie central basin hypoxia on habitat quality of several fish species. We found that bioenergetics-based growth-rate potential models have a potential application as the framework for the development of biological endpoints that measure the effects of hypoxia on aquatic biota. Finally, we utilized stable isotope analysis to look for broad spatial and temporal trends in resource utilization within distinct regions of the Lake Erie central basin, with hypoxia and large-scale hydrodynamic patterns serving as potential driving patterns for spatial differences.

No description available.

<p>This research focused on developing adaptable models and protocols for early warning systems for forecasting plant diseases and datasets. It compared the performance of deep learning models in predicting soybean rust disease outbreaks using three years of public epidemiological data and gridded weather data. The models selected were a dense network and a Long Short-Term Memory (LSTM) network. The objectives included evaluating the effectiveness of small citizen science datasets and gridded meteorological weather in sequential forecasting, assessing the ideal window size and important inputs, and exploring the generalizability of the model protocol and models to other diseases. The model protocol was developed using a soybean rust dataset. Both the dense and the LSTM networks produced accuracies of over 90% during optimization. When tested for forecasting, both networks could forecast with an accuracy of 85% or higher over various window sizes. Experiments on window size indicated a minimum input of 8 -11 days. Generalizability was demonstrated by applying the same protocol to a southern corn rust dataset, resulting in 87.8% accuracy. In addition, transfer learning and pre-trained models were tested. Direct transfer learning between disease was not successful, while pre training models resulted both positive and negative results. Preliminary results are reported for building generalizable disease models using epidemiological and weather data that researchers could apply to generate forecasts for new diseases and locations.</p>

Imidacloprid is a neonicotinoid pesticide used to protect against biting and sucking insects. Land managers rely on its systemic properties, however long-term studies investigating imidacloprid effects on ecosystem function are limited. This study investigated imidacloprid applications to Tsuga caroliniana and Tsuga canadensis over time and compared concentrations to measures of ecosystem function including soil respiration, microbial function, and invertebrate density. Results indicate that imidacloprid is persistent (p0.5). Microbial function and invertebrate density were not significantly different between control and treatment locations nor did imidacloprid concentrations correlate with ecosystem functional indicator activity (p>0.05). It is evident that imidacloprid does not affect ecosystem function over time, however care should be taken when applying it in sensitive locations where endemic, threatened, and endangered organisms reside.

No description available.