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Anthropic impacts adversely affect the productivity, integrity, connectivity, and resilience of riverine ecosystems, with widespread cumulative effects on the biota and biodiversity. The natural flow regime is a fundamental driver of physical and chemical processes, determining the morphological profile of the river systems and sustaining the complex network of ecological interactions and biological patterns. Therefore, in order to reach the environmental goals required by the binding legislation, and achieve a sustainable use of water resources, it is urgent to understand the mechanisms behind changes in the structure of biological communities along gradients of human disturbances which affect the flow regime. Indicators based on macroinvertebrates are widely used to assess the ecological status of water bodies, given their sensitivity/tolerance to pollution. However, in Alpine running waters, where chemical quality is less impacted than in lowland rivers, it is particularly important and valuable to detect the hydro-morphological alterations, and to discriminate them from chemical degradation, based on the responses of benthic macroinvertebrates to such multiple stressors. Therefore, this thesis aims at: i) examining the taxonomic and functional responses of macroinvertebrate communities to the different anthropogenic pressures acting on river systems; ii) evaluating the taxa/functional traits which mostly discriminate between hydrological and morphological alterations, and chemical degradation, to support effective bioindication methods. Focus of the research is to assess the macroinvertebrate community responses to the alterations caused by flow regulation and morphological alterations, which include water abstraction, diversion, stocking and the intermittent release of water from hydropower plants, banks artificialization and construction of weirs, dams, and other structures, each of these with environmental consequences of different scale and magnitude, such as the interruption of the longitudinal continuity, residual flow release and hydropeaking. The first part of this thesis is based on two empirical field studies, following respectively a manipulative and a mensurative approach, and focuses on changes in the taxonomic and functional composition due to river regulation and hydrological alterations. The first study, conducted in a set of seminatural streamside experimental flumes, simulates a residual flow stretch by reducing the discharge of the downstream sections (treatment) to 50% of the discharge of the upstream sections (control). Even within the short-term of our experiment (i.e., 3 weeks from the beginning of the simulation), we successfully simulated a small run-of-the river water abstraction and we recorded substantial changes in the EPT (Ephemeroptera, Plecoptera and Trichoptera) benthic assemblages. In fact, we observed shifts in functional (rather than taxonomic) EPT community composition over time, likely due to the active drift, from a typically rheophile to a more limnophile one as a response to the stress imposed by the flow reduction, related to decrease of flow. In the second study, we investigated the effectiveness of a hydropeaking mitigation measure on flow and biotic components, in a case study of hydropeaking reduction on a 10-km reach of the Noce Stream, a unique approach for Alpine streams to date. The hydrological analysis conducted applying two hydropeaking quantification indices (HP1 and HP2 of Carolli et al., 2015, and the COSH method by Sauterleute & Charmasson. 2014) confirmed a partial mitigation of the hydropeaking in the stretch. As a consequence of the change in hydrological regime, we observed a different taxonomic and functional recovery in the benthic and hyporheic communities. In fact, macrobenthos was negatively affected by the reduced dilution of point and diffuse pollution; conversely, the hyporheic communities showed an increase in diversity and abundance of interstitial taxa, especially those exclusive to the hyporheic zone, likely due to changes in the interstitial space availability, brought by a reduction of clogging caused by fine sediments which were previously released with each hydropeaking wave. The second part of the thesis is based on large dataset analysis where expert knowledge has been integrated with machine learning and data-based approaches: the focus of thesis shifts towards a holistic approach, extending the investigation to the entire watershed of the Trentino Province by including macroinvertebrate field data collected between 2009 and 2019 from 160 sampling sites, distributed over 90 rivers and streams. Based on the expertise of field operators from the local Environment Agency (APPA), and the quality indices currently used according to the Water Framework Directive (WFD), all the APPA stream sites were classified according to the presence of known hydrological, morphological, and chemical alterations, including the co-occurrence of two or more alteration types; sites in pristine conditions were also identified. Seasonality, stream order and type, and other stream characteristics associated with the elevation gradient are important in flow-ecology investigation, and for this reason were included in the analysis. Moreover, these features are proxies for other variables which are closely related with the structure of the benthic community, such as current velocity, organic matter availability and substrate composition, and can also be related to the probability of expecting the presences of small hydropower plants and/or a diffuse or localized pollution sources. This second section of the thesis is divided into two parts: the first part describes the initial overall qualitative and quantitative analysis, which was conducted to determine to which extent a functional diversity-based approach better recognizes patterns in the benthic community compared to the WFD diversity indices. The second part describes the machine learning approach which we used to examine the degree to which a-priori expert classification matched data-driven classification based on the taxonomic and functional composition of benthic macroinvertebrates across different binary classification disturbances. A Random Forest analysis was performed independently on benthic-macroinvertebrate abundance (expressed as number of individuals per m2) and their functional compositions. The majority of stream sites were a-priori classified as impacted by either one or a combination of anthropogenic alterations (80%), with only 16% of sites in reference or pristine conditions. We observed high variability in benthic community assemblages, likely due to complex environmental interactions and caused by the cumulative/synergic effect of different alterations that negatively affect the discrimination between stressor-specific responses. The overall results of these large-dataset based analyses showed relevant outcomes, the main one being the good discrimination of unaltered sites from the altered ones, but a low discriminating power for the types of alteration (hydrological, morphological, pollution pf combination of two or three of them) based on taxonomic and functional composition of the benthic communities. The functional parameters directly related to the stream longitudinal preference, microhabitat preferences, flow velocity, hydrological and thermal regime, and food availability in the river network, well the most suitable to identify any type of river degradation. A further step in the detection of significant indicator taxa/traits was achieved with the machine learning approach, which resulted in robust and dependable predictive models, that identified the specific taxa and traits related to different stressors, thus representing a promising tool to support environmental assessment and water management. Overall, this thesis contributes to the identification of appropriate indicators based on macroinvertebrates taxonomic and functional sensitivity to different specific stressors, to use in the assessment of the Ecological Status of streams in mountain areas, with relevant outcomes for the water management of Alpine running waters, with particular regard to the definition of environmental flows, and to the mitigation of hydropeaking.

Competing paradigms of community assembly emphasize different mechanisms for predicting patterns in biogeography. Niche assembly emphasizes the role of environmental gradients as filters that organize a metacommunity by locally selecting colonizers with similar functional traits, whereas dispersal assembly emphasizes the importance of source pool characteristics and dispersal limitation in organizing a metacommunity. In this study, I developed a framework that uses spatially explicit patterns in taxonomic and functional measures of community composition as diagnostics for community assembly processes for benthic macroinvertebrates in headwater streams in the southern Appalachians. Distance decay in taxonomic and functional similarity was used to determine the scales at which taxonomic turnover occurred within functional niches. Trait-neutral models of community composition were used as null models to assess which functional traits were the best candidates to explain how community composition was influenced by environmental gradients: an assessment of niche-based community assembly. Regional scale patterns suggested that niche-based community assembly was the dominant mechanism organizing community composition in headwater streams at local scales (<30km). Therefore, I compared how well trait-neutral models identified functional traits as relevant to community sorting against how well observed trait distributions correlated with environmental variation at a local scale, in the Ray Branch catchment (<10km study extent). Functional traits exhibiting non-random distributions within the Ray Branch watershed were most strongly correlated with environmental variation. Lastly, I assessed how the influences of niche and dispersal assembly on benthic macroinvertebrate community composition were affected by disturbance (shelterwood logging). Environmental variables defining the habitat template, and macroinvertebrate community composition, were measured before and after the disturbance; and path analysis was used to quantify the disturbance effect. The relationship between environmental variation and functional composition increased following logging, indicating disturbance augmented the influence of environmental filters, and consequently, the importance of niche-based community assembly. My dissertation provides the framework for a novel assessment of taxonomic and functional community composition data to infer the types of ecological dynamics that organize communities in the landscape. Additionally, this work provides a theoretical basis for assessing how dominant ecological processes change, in predictable ways, in response to changes in the habitat template. / Ph. D.

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.

I investigated the baseline benthic macroinvertebrate community in relation to the environmental conditions in a section of Smith Creek, north of Harrisonburg, VA, prior to restoration. Quantitative benthic macroinvertebrate and environmental samples were collected in April and September 2006 from the Bruce Farm (BR) section of Smith Creek and the nearby Mixed Use (MU) section of Mountain Run. BR had been heavily used for cattle grazing for decades and suffered from sediment, nutrients, and lack of a forested riparian zone. MU had a forested riparian zone, but still received nutrient and sediment inputs from upstream cattle grazing. Visual habitat assessments were performed in September 2006 and were compared to quantitative measures. Benthic macroinvertebrate densities and taxa richness were greater at BR (total density for combined seasons = 52,438; taxa richness for both seasons = 84) than MU (total density for combined seasons = 3,982 and taxa richness for both seasons = 63). Biological environmental variables related to nutrients and growth of plants on rocks (ash-free dry mass, chlorophyll a, epilithic biomass) influenced the benthic macroinvertebrate assemblage more than physical environmental variables related to the substrate composition (% fines, % gravel, Trask's sorting coefficient). Visual habitat estimates were not as effective as quantitative measures of habitat for explaining the benthic macroinvertebrate assemblage. / Master of Science

Surface coal-mining is a source of selenium (Se) contamination in streams of the Appalachian coalfields. Selenium dynamics in aquatic systems are complex and largely controlled by site-specific factors, but have been understudied in Appalachian headwater streams. In this study, we evaluated the degree and dynamics of Se enrichment and bioaccumulation in headwater streams influenced by coal-mining. Based on Se concentrations in macroinvertebrates collected from 23 headwater streams, nine sites were selected for further study: three reference streams with no history of coal-mining, and six streams influenced by coal mining. Mining-influenced streams were further separated into high-Se and low-Sestreams based on macroinvertebrate tissue Se concentrations. Water-column, sediment, biofilm, leaf detritus, and prey and predator macroinvertebrates were collected and analyzed for Se concentration during two sample periods, Sept. - Oct. 2015 and Feb.-March 2016. Selenium concentrations in all media were found to be elevated in mining-influenced over reference streams and in high-Se over low-Se streams. Selenium dynamics, enrichment in particulate media (sediment, biofilm and leaf detritus) and trophic transfer of Se to prey from particulate media and to predators from prey, did not exhibit major differences among streams of differing Se levels. Water column Se concentrations were predicative of Se concentrations in macroinvertebrate tissues. Findings from this study indicate headwater streams influenced by coal-mining are capable of a high degree of Se bioaccumulation in macroinvertebrate populations. / Master of Science

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

This study was carried out to characterize ponds and aquaculture systems, and also to determine both the potential and actual impacts of pond aquaculture effluents on receiving stream quality in the Ashanti and Brong Ahafo regions of Ghana. Water, fish and macroinvertebrate samples were collected from upstream, downstream and nearby reference streams of, and questionnaires administered to, 32 farms. Total settleable solids were higher in ponds than reference streams (p = 0.0166); suspended solids was higher in ponds than reference streams (p = 0.0159) and upstream (p = 0.0361); and total phosphorus was higher in ponds than reference (p = 0.0274) and upstream (p = 0.0269). Total nitrogen was most clearly higher in ponds than all other locations: p = 0.0016, 0.0086 and 0.0154 for the differences between ponds and reference, upstream, and downstream respectively. BOD5 level was also higher in ponds than all locations (p = 0.0048, 0.0009, and 0.0012 respectively). Also, non-guarding fish species were more abundant in reference streams than downstream (p = 0.0214) and upstream (p = 0.0251), and sand-detritus spawning fish were less predominant in reference streams than upstream (p = 0.0222) and marginally less in downstream locations (p = 0.0539). A possible subsidy-stress response within study streams was also observed. Hence, ponds are potential sources of these water quality variables to receiving streams. Effluent-receiving streams, generally, were not much different from reference streams in terms of most the metrics of community structure and function used in the comparisons. Hence, even though receiving streams in Central Ghana may not be severely impacted by aquaculture effluents at the moment, the management of pond effluents will determine the scale of future impact. Vegetable, cereal, and livestock farming could serve as additional sources of fecal streptococci and coliform bacteria and nutrient-enrichment within the study area, besides aquaculture, and so these industries must also be included in efforts to minimize pollution of these streams. / 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

Road construction and maintenance throughout the country continues to be one of the largest contributors of sediment pollution to aquatic systems. Though impacts of road networks on aquatic systems can be potentially severe, little work has been performed to evaluate the effect that road spatial location within a watershed has on water quality. To address this issue from a quantitative perspective, a "Road Impact Factor" protocol was designed to identify potential erosion-prone segments of road networks based on road gradient, spatial location based on hydrologic flow length, surface composition, and water control installations. The protocol was developed for two regions in Central Idaho and Eastern Oregon. We then used the hydrologic travel time procedure, developed for use in the Hydrologic Engineering Center Hydrologic Modeling System (HEC-HMS) runoff and routing model, in order to characterize the spatial distribution of potential road runoff impacts within the study areas. Ten macroinvertebrate metrics sensitive to sedimentation (i.e. % Intolerant Taxa, Hilsenhoff Biotic Index, etc.) were analyzed to test the significance of the spatial distribution of Road Impact Factors. These 10 metrics were analyzed under the hypothesis that values will be lower for those study areas that have a higher degree of road impact and a lower distance between the road segments and stream reaches. Results of a quadrant analysis and hierarchical clustering analysis showed hypothesized trends for several metrics in Idaho, though the trends were not strong. No trends were observed in Oregon. The variability in results is likely due to limitations of the input datasets. / Master of Science