No description available.

There have been growing concerns over the decline of healthy river ecosystems and the severe consequences this decline could have on biodiversity, ecosystem services, and human well-being. These concerns have led to increased efforts in river restoration around the globe, which aim to improve the ecological health and functioning of rivers. The restoration is usually done by implementing strategies such as hydromorphological adaptation and flow management. These measures, nevertheless, do not guarantee the recovery of river ecosystems. This is because there are multiple factors contributing to the success of restoration projects, which can vary depending on the specific characteristics of each river system. Habitat modeling, one of the most widely used ecological quality assessment tools for rivers, has been applied in the evaluation of restoration projects. An aquatic ecosystem is complex, and its dynamic nature requires a comprehensive understanding of the interconnections between biotic and abiotic components. These components also have a high degree of spatial and temporal variability. Therefore, it is crucial that approaches and modeling techniques be tailored to capture this dynamic. In the assessment of river restoration, for instance, habitat modeling needs to account for the changes in flow patterns, sediment transport, water quality, and habitat availability/quality for the key indicator species that result from the restoration efforts. This study addresses the need for developing an integrated approach to habitat modeling, particularly for macrozoobenthos, an important indicator of river health that plays a crucial role in the functioning of aquatic ecosystems. The primary research objective is to improve the existing modeling framework (TRiMM) by focusing on three key aspects: 1) expanding the prediction factors of physical habitat that influence habitat suitability for macrozoobenthos; 2) integrating fuzzy algorithms in the suitability assignment process; 3) incorporating species' (re-)colonization capacity and habitat temporal variability into habitat connectivity assessment. The model adopts the fuzzy logic method in the habitat module to account for the interactions between various factors described in the habitat template (Poff & Ward, 1990). Moreover, the model considers both spatial and temporal changes in habitat parameters by running a transient simulation over a specific time period relevant to the life cycle requirements of the target species. This allows for a more accurate representation of the dynamic nature of river habitats and provides valuable insights into how they may change over time. Additionally, the model incorporates species' (re-)colonization potentials into habitat connectivity analysis by considering their dispersal capabilities. This helps in understanding how changes in habitat parameters can affect the overall connectivity of river habitats, which is crucial for assessing the resilience and sustainability of the systems. The proposed transient habitat modeling (TRiMM 2.0) is applied to two case studies of low-order rivers in Germany. The first case study focuses on a river that has been restored after a period of degradation. The habitat model was tested with sampling data, and the results reveal that the model improved when additional variables related to habitat were included. The second case study was a simulation of habitat suitability and connectivity in a hypothetical river reach. Hydraulic and morphological factors (water depth, velocity, temperature, and sediment) are simulated over a period of four years using SRH-2D. The simulation results showed that hydraulic and morphological factors had a significant impact on sediment characteristics, which in turn influenced habitat suitability and connectivity. This study also highlights the importance of considering multiple variables and their interactions when assessing river habitats. Additionally, the use of transient modeling provides information about long-term changes in habitat quality and connectivity.:Abstract Kurzfassung Contents List of figures List of tables Nomencature Acknowledgement List of publications 1. General introduction 1.1. Research motivation 1.2. Statement of research objectives 1.3. Structure of the dissertation 2. Macrozoobenthos and stream’s ecology 2.1. Macrozoobenthos and their habitat 2.2. Factors influencing the distribution of macrozoobenthos 2.2.1. Food sources 2.2.2. Water quality 2.2.3. Physical habitat 2.2.4. Colonization process 2.2.5. Presence of other species 2.3. Spatial scale and temporal variability 2.4. Conclusion 3. State of the art in river habitat modeling 3.1. Habitat modeling and river ecology assessment 3.2. Habitat modeling principles 3.2.1. Habitat suitability curves method 3.2.2. Fuzzy logic method 3.2.3. Generalized additive models 3.3. Existing benthos habitat modeling 3.3.1. PHABSIM 3.3.2. RHYHABSIM 3.3.3. BITHABSIM 3.3.4. CASiMiR 3.3.5. HABFUZZ 3.4. TRiMM and further development 3.5. Conclusion 4. Basis for the modeling concept and methodological framework 4.1. Physical habitat template 4.1.1. Streamflow regime 4.1.2. Substrate regime 4.1.3. Thermal regime 4.2. Habitat connectivity 4.3. Species colonization and habitat connectivity 4.4. Analysis scales 4.5. Conclusion 5. Transient river habitat modeling for macrozoobenthos – TRiMM 2.0 5.1. Habitat model description 5.2. Input data preparation 5.2.1. Field survey 5.2.2. Hydro-morphodynamic models 5.3. Habitat suitability calculation 5.4. Patch-building and patch dynamics analysis 5.5. Habitat connectivity calculation 5.6. Conclusion 6. Model applications 6.1. Case study 1: Simulation of habitat suitability for macrozoobenthos in a small restored stream (Saxony, Germany) Abstract 6.1.1. Introduction 6.1.2. Material and Method 6.1.3. Results 6.1.4. Discussion 6.1.5. Conclusion 6.2. Case study 2: Application of TRiMM 2.0 to simulate benthic habitat quality in a hypothetical reach of Zschopau river 6.2.1. Introduction 6.2.2. Methodology 6.2.3. Results 6.2.4. Discussion 6.2.5. Conclusion 7. Summary and future outlook 8. References

Measurements in paired stream reaches with and without livestock access in southwestern Virginia suggest that livestock exclusion practices installed on short, isolated stream reaches result in improved geomorphic and riparian vegetation condition, but do not significantly improve the benthic macroinvertebrate assemblage. Detailed longitudinal and cross-sectional surveys, pebble counts, and rapid geomorphic assessments were conducted on contiguous, paired stream reaches (5 pairs) with and without active livestock access across a range of time since livestock exclusion was implemented. In addition, bank characteristics were quantified by measuring groundcover biomass, shrub crown volume, tree density and diameter, soil bulk density, and particle-size analysis. Benthic macroinvertebrates were collected with a D-frame dip net and quantified using the Virginia Stream Condition Index (SCI), and other benthic macroinvertebrate metrics. We determined that: 1) small lengths of livestock exclusion can significantly increase channel depth and decrease the width to depth ratio, and increase groundcover vegetation growth, but do not significantly alter benthic macroinvertebrate assemblages; and, 2) qualitative geomorphic assessment results showed trends over time since exclusion (0 to greater than 50 years), but not in any of the other parameters evaluated. These observations suggest that a more targeted and holistic approach that addresses watershed-wide impacts must be implemented to restore aquatic habitat. (Key Words: CREP, stream channel morphology, livestock exclusion, agriculture, benthic macroinvertebrates, riparian buffers.) / Master of Science

Increased loading of dissolved ions (salinization) and trace elements from surface coal mining is a common alteration to headwater streams in the central Appalachian region. However, temporal and spatial trends of water quality and associated influences on biota in these stream systems have not been well-studied. To address this research need, I analyzed temporal trends in specific conductance, ion matrix, and benthic macroinvertebrate communities in 24 headwater streams, including 19 influenced by surface mining, from 2011-2019. There was limited evidence of recovery of water chemistry or macroinvertebrate communities in these streams, indicating lasting impacts from surface coal mining. Among benthic macroinvertebrates, Ephemeroptera and the scraper functional feeding group were most-impacted by chronic salinization in study streams. In addition, I analyzed spatial patterns of water chemistry in a subset of these streams using synoptic sampling of multiple constituents under baseflow and highflow conditions. Study results indicate that water chemistry is spatially dynamic and can be influenced by both groundwater dilution and inputs from tributaries. Lastly, I investigated patterns in selenium bioaccumulation across and within streams, from particulate matter to top trophic levels (i.e. fish and salamanders). I found that benthic macroinvertebrates had the highest concentrations of selenium in these ecosystems, with lower concentrations in salamander and fish species. However, there was limited evidence of longitudinal trends in bioaccumulation dynamics downstream of mining impacts. Collectively, this work indicates long-term (ca. decades) coal-mining influences but also highlights future research needs to better understand downstream impacts to water quality and biotic communities. / Master of Science / Surface coal mining affects water quality in central Appalachian headwater streams. However, long-term and downstream patterns of impacted water quality and potential effects on aquatic life have not been well-studied. To address this research need, I analyzed trends in water quality parameters and aquatic insect communities in 24 headwater streams from 2011-2019. There was limited evidence of recovery of water chemistry or aquatic life in these streams, indicating lasting impacts from surface coal mining. Certain aquatic insects including Ephemeroptera (mayflies) appear to be more impacted than others by long-term altered water quality. In addition to trends over time, I also analyzed downstream variation in water chemistry in a subset of these streams under baseflow conditions and after a rain event. Results indicate that water chemistry can vary greatly within a stream network and is influenced by tributary inputs and dilution from groundwater. Concentrations of the trace element selenium can also be elevated as a result of surface mining. This is of environmental concern because selenium can biomagnify, where concentrations increase in organisms higher in the food chain and can cause toxic effects. Here, I investigated selenium bioaccumulation patterns across organisms in the food chain and with distance downstream across six headwater streams. I found that aquatic insects had the highest concentrations of selenium, with lower concentrations in salamanders and fish. This work indicates that surface coal mining has longterm (ca. decades) effects on headwater streams, but also points to future research to better understand downstream impacts to water quality and aquatic life.

Of eleven commercial and state trout farms surveyed in Virginia, five farms were selected for intensive examination of effluent impacts during Fall 1994 and Summer 1995 to maximize effects of stream low flows and high temperature. Substrate embeddedness increased significantly downstream, but effluent settleable solids concentrations were always less than 0.1 ml/L. Total ammonia and nitrite levels increased downstream 0.1 - 0.7 mg/L and 0.003 - 0.01 mg/L respectively, but were well below recommended thresholds for lethal exposure. Dissolved oxygen levels were reduced downstream, but were typically > 6.5 mg/L. Effluent water temperatures, pH, nitrate, and total phosphorus concentrations did not differ from upstream levels. Downstream water quality was contingent on feed loading rates and the use of effluent settling ponds. Periphyton were enhanced up to tenfold (58 mg/cm² chlorophyll <i>a</i>) downstream of farms, but enrichment was localized to within 400 m. The richness and abundance of sensitive macroinvertebrate taxa (mayflies, stoneflies, and caddisflies) were reduced downstream and pollution-tolerant non-insect taxa (isopods and gastropods) increased. EPA Rapid Bioassessment Protocol (RBP) reflected moderately-impaired water quality downstream at farms A and C, and only slightly or unimpaired water quality at the other farms. The Index of Biotic Integrity (IBI), based on fish community metrics, did not correspond to the RBP, and reflected poor water quality at C and D. Low fish species richness and abundance in these headwater streams limited the usefulness of the IBI. The proposed general discharge permit for aquaculture in Virginia is discussed and trout farm management and design recommendations are presented. / Master of Science

The goal of the Aquatic Indicators of Land Condition (AILC) project is to develop analytical tools that integrate land condition information with stream condition for improved watershed management within the United States Bureau of Land Management (BLM). Based on the goal of the AILC, two objectives for this study were: to determine the effect of four GIS-derived distance measurements on potential relationships between common BLM landscape stressors (mining and grazing) and changes in benthic macroinvertebrate community structure; and to assess the effectiveness of individual questions on a commonly-used Bureau-wide qualitative stream assessment protocol, the proper functioning condition (PFC) assessment. The four GIS distance measurements assessed for biotic relevance included: straight-line distance, slope distance, flow length, and travel time. No significant relationships were found between the measured distance to stressor and macroinvertebrate community structure. However, the hydrological relevance of flow length and travel time are logically superior to straight-line and slope distance and should be researched further. Several individual questions in the PFC assessment had statistically significant relationships with the final reach ratings and with field-measured characteristics. Two of the checklist questions were significantly related to the number of cow droppings. This may indicate a useful and efficient measure of stream degradation due to grazing. The handling and use of the PFC assessment within the BLM needs further documentation and examination for scientific viability, and the addition of quantitative measurements to the PFC in determining restoration potential would be desirable. / Master of Science

Stream ecosystems can be influenced by cattle grazing in the riparian zone due to sediment input, nutrient loading, and soil compaction, which lead to alterations of macroinvertebrate and microbial activity. Recently government programs, such as the Conservation Reserve Enhancement Program (CREP), have provided funding for farmers to exclude cattle from streams and riparian zones. Funding for CREP is limited and does not allow for post exclusion assessment. The objectives for this study were; 1) to explore whether CREP and other cattle exclusion initiatives help restore functional integrity to streams; 2) and if they do, to evaluate the time required for integrity to be restored. I predicted leaf processing (a fundamental ecosystem level function) in streams would be influenced by excluding cattle from the riparian zone due to changes in nutrient availability, sediment abundance, shredding macroinvertebrates, and microbial activity. I tested this prediction by measuring leaf processing at sites that had cattle excluded for <1 to 15 years. Breakdown rates did not correspond linearly to time since cattle exclusion. This was probably due to the opposing effects of elevated sediment versus nutrients on leaf breakdown at recently grazed sites. Leaf breakdown and shredder density were strongly correlated with riparian vegetation density. This study suggests that in addition to cattle exclusion, reforestation of woody riparian vegetation may be essential to restore functional integrity to agricultural streams. / Master of Science

The Central Appalachian region is home to several resource-extraction industries, a host of globally unique aquatic wildlife species, and region-wide poverty. These overlapping circumstances make solving environmental issues in the region challenging. Of particular focus is the coal mining industry, both because of its prevalence and because of controversial methods of practice such as mountain top mining. One of the primary concerns in the region is the extirpation of sensitive aquatic macroinvertebrate species. Several studies have suggested the primary driver of this loss of biodiversity is due to increased conductivity in streams impacted by these mining practices. The reality is that several pollutant sources coexist in these Central Appalachian watersheds. Because of geographic isolation, many headwater communities lack proper sewerage and discharge directly into nearby waterways, compounding potential effects of upstream mining activities. Additionally, several legacy sites exist throughout the Appalachian region, both underground and surface mining in nature. To best mitigate ecological impacts of all of these pollutant types, relative contributions of each must be understood, as well as the nature of the pollution contributed by each. As a contribution towards this region-wide need for better information on pollution, the studies comprising this dissertation seek to better understand the composition of these different pollutant sources and their in-stream contributions to conductivity. The first paper found that these sources are indeed distinct in their inorganic ion make-up: surface coal mining was found to contribute primarily Ca, K, Ni, Se, and SO₄⁻², while untreated household waste (UHW) was primarily associated with P. HCO₃⁻ Mn, and Si were found to be associated with a legacy underground discharge. The second and third scientific studies included here analyzed conductivity's effect on Virginia Stream Condition Index (VSCI) versus other water quality and habitat parameters as well as the effect of specific ion suites on VSCI score. Findings indicated that excellent habitat extends species resilience against elevated conductivity, with passing VSCI scores found at conductivity in the 600-800 µs/cm range in cases of excellent habitat metric scores. Meanwhile, VSCI score suppression was highly related to surface mining-related inorganic ions (Ca, K, Mg, Ni, and SO₄⁻²), but also negatively correlated with ions related to UHW (P and Na). These results indicate the need for quantification of biological responses to specific ions in order to initiate targeted mitigate of pollutants in Central Appalachian watersheds. / Ph. D.

Prior studies have demonstrated Appalachian coal mining often causes elevated specific conductance (SC) in streams, and others have examined SC effects on benthic macroinvertebrate communities using point-in-time SC measurements. However, both SC and benthic macroinvertebrate communities exhibit temporal variation. Twelve Appalachian headwater streams with minimally impacted physical habitat and reference-quality physicochemical conditions (except elevated SC) were sampled ten to fourteen times each for benthic macroinvertebrates between June 2011 and November 2012. In situ loggers recorded SC at 15-minute intervals. Streams were classified by mean SC Level (Reference 17-142 S/cm, Medium 262-648 S/cm, and High 756-1,535 S/cm). Benthic macroinvertebrate community structure was quantified by the Virginia Stream Condition Index and other metrics. Structural metric differences among SC Levels and month of sampling were explored. Reference-SC streams exhibited significantly higher scores on most metrics, supporting previous findings that SC may act as a biotic stressor, even in streams lacking limitations from degradation of physical habitat or other physicochemical conditions. Temporal variation was greatest in Medium-SC streams, which had the most metrics exhibiting significant differences among months and the greatest range of monthly means for six metrics. Metrics involving % Plecoptera and/or % Trichoptera were not sensitive to elevated SC, as Leuctridae and Hydropsychidae exhibited increased abundance in streams with elevated SC. Best scores for benthic macroinvertebrate community metrics differed based on selected metric, SC Level, and month. Consequently, timing of sampling is important, particularly in streams with elevated SC because community metric scores may be impacted by dominant taxa life history patterns. / Master of Science

Cattle exclusion from streams is believed to improve riparian vegetation, in-stream habitat, and composition of aquatic organisms. Yet research on the effects of cattle exclusion have yielded conflicting results. The goal of this study was to examine relationships between physical habitat and benthic macroinvertebrate populations with increasing downstream distance from cattle-impacted stream segments, and determine which physical habitat and chemical water quality parameters are affected by cattle presence. Macroinvertebrates from 24 sites in Rockingham County, VA were used to calculate bioassessment metrics. Fourteen sites made up 4 longitudinal studies where improvement of biotic condition with distance from cattle impact was examined. Linear regression and multilevel modeling results indicated improving macroinvertebrate assemblage with increasing distance downstream from cattle-impacted reaches. Presence of riparian trees and distance from impact had a positive influence on bioassessment scores. A total of 39 stream sites in the Shenandoah Valley were classified using the Rapid Habitat Assessment (RHA) which is based on 10 visual evaluations of physical characteristics. Four of the ten RHA parameters, embeddedness, bank stability, vegetative protection, and riparian vegetative zone width, along with the total RHA score, were associated with cattle presence. This study found that a) RHA factors reflect direct cattle impacts on the riparian zone, but RHA has limitations as a general predictor of cattle impact, b) cattle influence on benthic macroinvertebrates extends hundreds of meters beyond the immediate pasture boundary, and c) improvement in Virginia Stream Condition Index can be predicted as a function of distance downstream. / Master of Science