Understanding sedimentation impacts to benthic macroinvertebrates in headwater, mountain streams is a top priority of watershed management programs in the Chattahoochee National Forest. Five studies involving the analysis of historical, biological survey data and current data were conducted to improve our understanding of macroinvertebrate response to sedimentation and to support the development of biological information for sediment load models to be applied in the Chattooga River watershed. An initial analysis of historical data involving a composited, macroinvertebrate reach-scale sample revealed weak relationships between assemblage metrics and sedimentation, which was similar to results of two recent macroinvertebrate studies that found biological ratings of good or excellent with reported physical impact attributed to sedimentation. Those findings and field reconnaissance in the Chattooga River watershed revealed that patchy, coarse sands may be the primary issue of concern regarding sedimentation impact to benthic macroinvertebrates. Therefore, a modified sampling approach was used to investigate relationships of macroinvertebrates and environmental conditions that included micro-habitat patches containing coarse sands, a product of erosion associated with Southern Blue Ridge, silicate parent geology. At the microhabitat, patch scale, flow velocity was the main environmental factor associated with a macroinvertebrate assemblage gradient, and was significantly correlated with percent deposited sediment across 264 samples. The high dominance of just a few macroinvertebrate genera, and the majority lack of individual macroinvertebrate associations with dominant substrate types may suggest that the dominant macroinvertebrates utilize a multi-microhabitat portion of the streambed at any given time, which may be due to the homogenization of streambeds due to sand (providing ease of movement) and its immobility (low bedload volume and sand patch shift). Because flow was the only significantly correlated environmental variable on an assemblage gradient produced by ordination (and was individually correlated with dominant substrate and percent deposited sediment), a subsequent study was conducted to determine macroinvertebrate sensitivity to deposited sediments among two flow-differentiated habitat types. Results showed that more taxa were related to a gradient of percent deposited sediment in fast water habitats, and no taxa were positively correlated with percent deposited sediment. Indicator species analysis found a number of taxa that were associated with a four-level grouping of percent deposited sediment levels. Therefore, a final study involved calculating deposited sediment tolerance values using indicator species associations and individual cumulative abundances across percent deposited sediment levels. The final index developed from cumulative abundances showed a relationship with deposited sediment within the range 0 – 30%, and that low range was due to the low deposited sediment levels at which all 50% cumulative abundances fell (1 - 10%). The sedimentation index produced from indicator species analysis produced a reach-scale index that was related to percent pool embeddedness. Key findings from these studies are: (1) sand is the primary deposited sediment type, with most streambed comprised of cobble-sand substrate, (2) few taxa are associated with deposited sand substrate, (3) there are high numbers of a relatively few dominant taxa across samples and streams, (4) macroinvertebrate response to deposited sediments is greatest in fast water habitats, and (5) the developed sedimentation biotic index is a potential, assemblage-level indicator of increasing sedimentation in these headwater systems. The functional and habit organization of the four most dominant taxa determined in recent studies suggest that they may be utilizing sand patches for crawling and collecting food, therefore structurally adapting to long-term, press disturbances due to historical and contemporary anthropogenic activities and natural erosion. In addition, macroinvertebrate assemblage composition in these streams indicates overall good "health" and suggests streambed stability in the presence of a large portion of coarse sand. However, an important question that remains involves sand movement along streambeds and the ecological consequences of continued sediment inputs to these headwater systems. / Ph. D.

Although sediment is a natural component of stream ecosystems, excess sediment presents a threat to natural freshwater ecosystems. Sediment management is complicated because sediment can be dissolved in the water column, suspended as particles in the water column, or rest on the bottom of the stream bed, and can move between these forms (e.g. bedded sediment can be resuspended). Each form of sediment affects aquatic life in a specific way. To manage stream sediment in a way that protects aquatic life, we need to understand the ways different forms of sediment affect living things, and we need to be able to predict how sediment changes form under different stream conditions (for example, during high water events). To improve our understanding of these things, the studies in this dissertation set out to: (1) identify how often sediment is specifically mentioned as the primary pollutant “stressor” of the benthic macroinvertebrate community (primarily aquatic insects); (2) determine which forms of sediment have the largest negative impacts on aquatic insects in Virginia and what levels of sediment may cause harm; and (3) measure the changes of sediment between suspended and bedded forms in a small stream to provide information needed to restore the health of stream ecosystems. An inventory of published US Clean Water Act Total Maximum Daily Load (TMDL) reports, which states write to identify their impaired waters and their plans to improve those waters, revealed that sediment is an important stressor in over 70% of waters that have altered aquatic insect communities. If the language used to describe how waters are evaluated and what is causing the impairments were standardized among states, data collected under the Clean Water Act could be more broadly used to help understand water quality issues and ways to address them. Analysis of 10 years of Virginia Department of Environmental Quality sediment and aquatic insect community data collected within 5 ecoregions of the state indicates that a combination of 9 sediment parameters reflecting dissolved, suspended, and bedded forms explains between 20.2% and 76.4% of the variability in the health of the aquatic insect community within these regions. Embeddedness, which measures how much larger particles such as gravel and cobble are buried by finer particles like sand; and conductivity, which is a measure of dissolved salts in the water column, both have substantial impacts on the aquatic insect community. Sensitivity thresholds for embeddedness and conductivity indicate the levels of these parameters above which 5% of insect families are absent from a stream; therefore, these levels are considered protective of 95% of the insect community. Thresholds for embeddedness are 68% for the 5 combined ecoregions, 65% for the Mountain bioregion (comprised of Central Appalachian, Ridge and Valley, and Blue Ridge ecoregions), and 88% for the Piedmont bioregion (comprised of Northern Piedmont and Piedmont ecoregions). Thresholds for conductivity are 366 µS/cm for combined ecoregions, 391 µS/cm for the Mountain bioregion, and 136 µS/cm for the Piedmont bioregion. These thresholds can be used by water quality professionals to identify waters with sediment impairments and can be used to help identify appropriate stream restoration goals. A study of sediment movement within the channel of a small stream indicated average transport speeds of ~ 0.21 m/s during floods with peak flows of ~ 55 L/s. The use of rare earth elements (REE) to trace sediment particles revealed individual particle transport distances ranging from 0 m to >850 m. Deposition on a unit area basis was greater in the stream channel than on the floodplain, and the movement of sediment from the stream bed to the water column and back again during sequential floods was evident. Approximately 80% of the tracer was deposited within the first 66 m of the reach. This information can aid the development of models that predict the impact of stream restoration practices on in-stream habitat and improve predictions on the time it will take between the initiation of stream restoration projects and when we see improvements in the biological community. / PHD / Although sediment is a natural component of stream ecosystems, excess sediment presents a threat to natural freshwater ecosystems. Sediment management is complicated because sediment can be dissolved in the water column, suspended as particles in the water column, or rest on the bottom of the stream bed, and can move between these forms (e.g. bedded sediment can be resuspended). Each form of sediment affects aquatic life in a specific way. To manage stream sediment in a way that protects aquatic life, we need to understand the ways different forms of sediment affect living things, and we need to be able to predict how sediment changes form under different stream conditions (for example, during high water events). To improve our understanding of these things, the studies in this dissertation set out to: (1) identify how often sediment is specifically mentioned as the primary pollutant “stressor” of the benthic macroinvertebrate community (primarily aquatic insects); (2) determine which forms of sediment have the largest negative impacts on aquatic insects in Virginia and what levels of sediment may cause harm; and (3) measure the changes of sediment between suspended and bedded forms in a small stream to provide information needed to restore the health of stream ecosystems. An inventory of published US Clean Water Act Total Maximum Daily Load (TMDL) reports, which states write to identify their impaired waters and their plans to improve those waters, revealed that sediment is an important stressor in over 70% of waters that have altered aquatic insect communities. If the language used to describe how waters are evaluated and what is causing the impairments were standardized among states, data collected under the Clean Water Act could be more broadly used to help understand water quality issues and ways to address them. Analysis of 10 years of Virginia Department of Environmental Quality sediment and aquatic insect community data collected within 5 ecoregions of the state indicates that a combination of 9 sediment parameters reflecting dissolved, suspended, and bedded forms explains between 20.2% and 76.4% of the variability in the health of the aquatic insect community within these regions. Embeddedness, which measures how much larger particles such as gravel and cobble are buried by finer particles like sand; and conductivity, which is a measure of dissolved salts in the water column, both have substantial impacts on the aquatic insect community. Sensitivity thresholds for embeddedness and conductivity indicate the levels of these parameters above which 5% of insect families are absent from a stream; therefore, these levels are considered protective of 95% of the insect community. Thresholds for embeddedness are 68% for the 5 combined ecoregions, 65% for the Mountain bioregion (comprised of Central Appalachian, Ridge and Valley, and Blue Ridge ecoregions), and 88% for the Piedmont bioregion (comprised of Northern Piedmont and Piedmont ecoregions). Thresholds for conductivity are 366 µS/cm for combined ecoregions, 391 µS/cm for the Mountain bioregion, and 136 µS/cm for the Piedmont bioregion. These thresholds can be used by water quality professionals to identify waters with sediment impairments and can be used to help identify appropriate stream restoration goals. A study of sediment movement within the channel of a small stream indicated average transport speeds of ~ 0.21 m/s during floods with peak flows of ~ 55 L/s. The use of rare earth elements (REE) to trace sediment particles revealed individual particle transport distances ranging from 0 m to >850 m. Deposition on a unit area basis was greater in the stream channel than on the floodplain, and the movement of sediment from the stream bed to the water column and back again during sequential floods was evident. Approximately 80% of the tracer was deposited within the first 66 m of the reach. This information can aid the development of models that predict the impact of stream restoration practices on in-stream habitat and improve predictions on the time it will take between the initiation of stream restoration projects and when we see improvements in the biological community.

Bioassessment is the concept of evaluating the ecological condition of habitats by surveying the resident assemblages of living organisms. Conducting bioassessment with benthic macroinvertebrates is still evolving and continues to be refined. There are strongly divided opinions about study design, sampling methods, laboratory analyses, and data analysis. Two issues that are currently being debated about study design for bioassessment in streams were examined here: 1) what habitats within streams should be sampled; 2) and is it necessary to identify organisms to the species level? The influence of habitat sampling design and level of taxonomic identification on the interpretation of ecological conditions of ten small streams in western Virginia was examined. Cattle watering and grazing heavily affected five of these streams (impaired sites). The other five streams, with no recent cattle activity or other impact by man, were considered to be reference sites because they were minimally impaired and represented best attainable conditions. Inferential and non-inferential statistical analyses concluded that multiple habitat sampling design was more effective than a single habitat design (riffle only) at distinguishing impaired conditions, regardless of taxonomic level. It appeared that sampling design (riffle habitat versus multiple habitats) is more important than taxonomic identification level for distinguishing reference and impaired ecological conditions in this bioassessment study. All levels of taxonomic resolution, which were studied, showed that the macroinvertebrate assemblages at the reference and impaired sites were very different and the assemblages at the impaired sites were adversely affected by perturbation. This study supported the sampling of multiple habitats and identification to the family level as a design for best determining the ecological condition of streams in bioassessment. / Master of Science

Acid mine drainage (AMD) results from the oxidation of pyretic mineralogy, exposed by mining operations to oxygen and water. This reaction produces sulfuric acid and liberates heavy metals from the surrounding mineralogy and impairs water quality and freshwater communities. The U.S. Army Corps of Engineers has begun an ecosystem restoration project to remediate the abandoned mine land (AML) impacts to the North Fork Powell River (NFP) and is utilizing the ecotoxicological rating (ETR) system to delineate these affects to focus restoration efforts. The ETR was developed to summarize the integrative data into a single number ranging from 0 to 100, which is descriptive of the environmental integrity of a sampling station. The ETR is conceptualized to work as an academic grading scale (0 through 100), rating reference stations with A's (90-100) and B's (80-89) and impacted stations with C's (70-80), D's (60-70) and failures (F = 60). Two rounds of ETR investigations have evaluated seven headwater tributaries to the NFP including investigations of Ely and Puckett's Creek from 1997 and 1998. This thesis contains the results of the second series of ETR investigations at 41 stations in Cox Creek, Jone's Creek, Reed's Creek, Summers Fork, Straight Creek, and areas in the NFP. Eight stations were recommended for reclamation; CC 03, JCRF2 02, JCRF2 01, RCPS 09B, RCPS 11B, SULF 01, SU 02, and SU 01. Summers Fork was the most severely impacted watershed of the second round of ETR investigations. An effort to streamline the ETR to the most ecologically predictive parameters was successful in creating a system more time and cost efficient then the initial ETRs and exclusive of benthic macroinvertebrate surveys. The Modified ETR streamlined the ETR to just 5 parameters including; mean conductivity, mean Asian clam survival, mean aluminum (Al) and manganese (Mn) in the water column, and mean habitat score to describe the AMD impacts to small headwater streams. Also, an investigation was conducted to determine the mode of toxicity, (i.e., exposures to metal contaminated surface waters or sediments) by which Al and iron (Fe) dominated AMD impairs benthic macroinvertebrate communities. It was found that water column exposures both within and beyond the zone of pH depression are the most likely mode by which AMD impairs the benthic macroinvertebrate communities of the NFP. / Master of Science

Benthic macroinvertebrate diversity influences stream food web dynamics, nutrient cycling and material exchange between the benthos and the water column. Stream bioassessment has moved to the forefront of water quality monitoring in terms of benthic macroinvertebrate diversity in the recent past. The objectives of this study were to determine optimum subsample size and level of taxonomic resolution necessary to accurately and precisely describe macroinvertebrate diversity in streams flowing in the Piedmont province of the James River watershed in Virginia. Forty-nine sampling sites were selected from streams within the Piedmont Physiographic Province of the James River watershed. Ten sites were randomly selected to have all macroinvertebrates in the sample identified to the genus level whenever possible. Optimum subsampling intensities and Virginia Stream Condition Index (VSCI) metrics and scores were determined. For samples with the total number of individuals at less than 500, the genus level of taxonomy provided lower overall optimum subsampling intensities. However, for samples with total individuals over 1000, optimum subsampling intensities at the genus level of taxonomy were higher than the family level for more than 50% of the metrics. For both family and genus levels of taxonomy, the majority of optimum subsampling intensities were well over 50% of the total individuals in the sample, with some as high as 100% of the individuals. While optimum subsampling intensities were valuable in comparing family and genus level taxonomy, they are not reasonable for stream bioassessment protocols; the cost:benefit ratio would be highly unbalanced. A minimum subsample size of 200 individuals is optimum for determining VSCI scores, while optimum taxonomic resolution is dependent on several factors. Thus, the level of taxonomic resolution for a particular study should be determined by the study objectives, level of site impairment and sample size.

Taxpayer dollars can be used more efficiently by land management agencies to monitor streams if agency-wide monitoring protocols are adopted. To address this issue, the Bureau of Land Management (BLM) developed the National Aquatic Monitoring Framework (NAMF) to implement standardized assessments of stream condition and trend in the Western United States. As one of the first applications of the NAMFI sought to develop and apply an analytical framework to determine the biological condition of streams, extent of in stream stressors and their impact on biological condition, and anthropogenic sources of stressors in Northeast California and Northwest Nevada over three years at a cost of $80,000. I measured biological, chemical, and physical attributes to determine the condition of stream sat 70 spatially distributed random locations. I found 45% of BLM stream km in the study area have degraded biology, 68% have excessive total nitrogen (TN), 43% have canopy cover below expected conditions, and 37% have excessive total phosphorus (TP). Excessive TN and TP and degraded riparian complexity (RC) were most strongly related to degraded biological conditions. The occurrence of excess TN and TP was most associated with livestock grazing. RC was identified as a stressor, but was not associated with land uses. This study provides an example of the data and analytical approach needed to help the BLM adaptively manage streams and rivers in compliance with federal regulations while efficiently using taxpayer dollars.

Stream temperature (ST) is a primary determinant of individual stream species distributions and community composition. Moreover, thermal modifications associated with urbanization, agriculture, reservoirs, and climate change can significantly alter stream ecosystem structure and function. Despite its importance, we lack ST measurements for the vast majority of USA streams. To effectively manage these important systems, we need to understand how STs vary geographically, what the natural (reference) thermal condition of altered streams was, and how STs will respond to climate change. Empirical ST models, if calibrated with physically meaningful predictors, could provide this information. My dissertation objectives were to: (1) develop empirical models that predict reference- and nonreference-condition STs for the conterminous USA, (2) assess how well modeled STs represent measured STs for predicting stream biotic communities, and (3) predict potential climate-related alterations to STs. For objective 1, I used random forest modeling with environmental data from several thousand US Geological Survey sites to model geographic variation in nonreference mean summer, mean winter, and mean annual STs. I used these models to identify thresholds of watershed alteration below which there were negligible effects on ST. With these reference-condition sites, I then built ST models to predict summer, winter, and annual STs that should occur in the absence of human-related alteration (r2 = 0.87, 0.89, 0.95, respectively). To meet objective 2, I compared how well modeled and measured ST predicted stream benthic invertebrate composition across 92 streams. I also compared predicted and measured STs for estimating taxon-specific thermal optima. Modeled and measured STs performed equally well in both predicting invertebrate composition and estimating taxon-specific thermal optima (r2 between observation and model-derived optima = 0.97). For objective 3, I first showed that predicted and measured ST responded similarly to historical variation in air temperatures. I then used downscaled climate projections to predict that summer, winter, and annual STs will warm by 1.6 °C - 1.7 °C on average by 2099. Finally, I used additional modeling to identify initial stream and watershed conditions (i.e., low heat loss rates and small base-flow index) most strongly associated with ST vulnerability to climate change.

A goal of the U.S. Environmental Protection Agency is to develop protocols applicable to coral reefs to distinguish between the effects of local water quality and those associated with regional to global environmental change. One test case is the current-dominated southeast coast of Florida where the Delray Outfall delivers 30 million gallons per day (114,000 cubic meters per day) of secondary-treated sewage into the ocean. Five study sites were established at depths between 15 and 18 m, and at distances between 1 and 18 km distance from the outfall, where the Stony Coral Rapid Bioassessment Protocol (RBP) was conducted to determine coral cover and selected other parameters. During sampling, 29 surface sediment samples were collected that I analyzed with respect to sediment texture, foraminiferal assemblages, and sediment constituents. Most samples were characterized by fine sands with <2% mud. A total of 77 genera of foraminifers were identified, averaging 28 genera per sample. Abundances of foraminiferal shells varied among samples by more than an order of magnitude (83 to 1010 shells per g sediment). The Foraminifera in Reef Assessment and Monitoring (FORAM) Index was calculated from the foraminiferal data, yielding values of 3 or more for all sites, with 26 of the 29 test sites yielding values >4, indicating that water quality should support coral growth. Sediment constituent analyses revealed that the sediments were overwhelmingly dominated by unidentifiable fragments (60%), with molluscan debris second (20%), and calcareous algae third (4.5%); larger foraminiferal shells and coral fragments together made up < 5.5%. The resulting sediment constituent (SEDCON) Index was consistently <2, indicating that erosional processes dominate over sediment production along the sampled shelf area. Results provided by the FORAM and SEDCON indices are consistent with results for stony coral based on the RBP. Stony coral cover was low at all sites, <2%, indicating that coral occurs in the area but neither dominates the benthos nor builds reefs. No relationship was observed between any parameter and distance from the Delray Outfall. However, both the RBP and FORAM Index indicated poorest conditions at the Horseshoe site, suggesting unidentified stressors in that vicinity.

<p>By concentrating materials and increasing the speed with which rainfall is conveyed off of the landscape, nearly all forms of land use change lead to predictable shifts in the hydrologic, thermal, and chemical regimes of receiving waters that can lead to the local extirpation of sensitive aquatic biota. In Central Appalachian river networks, alkaline mine drainage (AlkMD) derived from mountaintop removal mining for coal (MTM) noticeably simplifies macroinvertebrate communities. In this dissertation, I have used this distinct chemical regime shift as a platform to move beyond current understanding of chemical pollution in river networks. In Chapter Two, I applied a new model, the Hierarchical Diversity Decision Framework (HiDDeF) to a macroinvertebrate dataset along a gradient of AlkMD. By using this new modeling tool, I showed that current AlkMD water quality standards allow one-quarter of regional macroinvertebrates to decline to half of their maximum abundances. In Chapter Three, I conducted a field study in the Mud River, WV to understand how AlkMD influences patterns in aquatic insect production. This work revealed roughly 3-fold declines in annual production of sensitive taxa throughout the year in reaches affected by AlkMD. These declines were more severe during summer base flow when pollutant concentrations were higher, thereby preventing sensitive organisms from completing their life cycles. Finally, in Chapter Four I described the idea of chemical fragmentation in river networks by performing a geospatial analysis of chemical pollution in Central Appalachia. In this work I showed that the ~30% of headwaters that remain after MTM intensification over the last four decades support ~10% of macroinvertebrates not found in mined reaches. Collectively my work moves beyond the simple tools used to understand the static, local consequences of chemical pollution in freshwater ecosystems.</p> / Dissertation