This post-fire study was conducted to characterize and observe fire induced changes in physical habitat parameters, water-quality conditions and macroinvertebrate assemblages in the Little Creek watershed, a tributary to Scotts Creek located in Cal Poly’s Swanton Pacific Ranch in Davenport, California. Pre-fire data was collected by a Cal Poly student, John Hardy, for his 2017 thesis. Post-burn bioassessment surveys for this study were repeated at four of the same study sites used by Hardy to provide comparisons to the California Stream Condition Index via a modified version of the State of California’s Surface Water Ambient Monitoring Program protocol. Macroinvertebrates were taxonomically identified to the family level. Commonly used bioassessment indices were utilized in conjunction with Stepwise regression and Analysis of Variance on both pre- and post-fire datasets to illustrate how physical habitat and water quality parameters changed after the fire and to determine the significance of collected environmental variables (stream shading, cross sectional area, and median particle size) as predictors of macroinvertebrate community structure. Despite most of Little Creek having moderate and high burn severities, it was found that physical habitat, water quality and benthic macroinvertebrate populations were not greatly disturbed by the 2020 CZU lighting complex fire. Proportions of highly disturbance/pollution sensitive taxa and increased following the wildfire and there was a dramatic shift from collector-gatherer to predator organisms. Comparison of pre- and post-fire data in this study showed fire having a minimal effect on the studied watershed. Difference in study goals and associated protocols used in the pre- and post-fire studies and the low water year following the wildfire, complicates statistical comparisons and poses threat to the validity of results. However, there is opportunity for further investigation about the ability of an ecosystem to successfully recover from natural disasters and disturbances, specifically when there is little human impact (or influence) on the ecosystem.

Remote sensing studies based on satellite and aerial imagery have improved our understanding of the morphology and distribution of several shallow reefs along the Red Sea Arabian coast and of the benthic assemblages associated to them (Bruckner et al., 2011; Bruckner et al., 2012; Rowlands et al., 2016). However, data concerning the deeper benthic assemblages' composition and spatial distribution in the central Red Sea are still missing. Using high-resolution acoustic technology and an underwater remotely operated vehicle (ROV), we aim to map, describe, and classify the reefs found in Thuwal's coastal area, filling the information gap by producing the first benthic habitat map of this area and making progress towards the evaluation of shallow and upper mesophotic benthic resources in the Saudi Arabian Red Sea. High-resolution acoustic data was collected using a multibeam echosounder system, which generated a bathymetric model. Based on this, the seafloor features were classified into 12 morphotypes following a visual assessment. Based on the morphotypes classification, 28 sites were visually selected for ground-truthing data acquisition and characterization of the substrate and benthic assemblages using a remotely operated vehicle equipped with an ultra-short baseline (USBL) positioning system. With the information obtained from the bathymetry data and the ROV video transects, a Top-Down approach in which we analyzed, categorized, and classified the data was used to create Thuwal's reefs benthic habitat map in which 23 different benthic habitat types were identified. This research uncovered previously poorly studied reef morphologies in the Red Sea and their associated benthic assemblages. Moreover, this work will help improve the understanding of the spatial distribution of benthic communities located on Thuwal's reefs, giving a baseline with the potential to provide fundamental information that can be used for mapping, management, conservation, and future research at other Red Sea reef sites in Saudi Arabia.

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

Central Appalachian headwater streams in coalfield areas are prone to mining disturbances, and compensatory mitigation is required in cases of documented impacts. Stream construction on reclaimed mines is a common mitigation strategy. Streams constructed as compensatory mitigation are meant to restore structural and functional attributes of headwater streams and are often evaluated by measuring structural ecosystem characteristics. However, replacement of stream ecosystem functions is essential for mitigation of mining disturbances from an ecosystem perspective. This research compared selected structural and functional measures in eight constructed streams on mined areas to those of four forested reference streams across two years. Three organic matter functions were evaluated: riparian litterfall input, leaf breakdown, and periphyton accrual. Constructed streams were typically warmer than reference streams and also had elevated specific conductance, elevated oxidized nitrogen concentrations, depressed benthic macroinvertebrate richness, and lower levels of canopy cover. Functionally, litterfall input and total leaf breakdown means for constructed streams were approximately 25% and 60% of reference means, respectively. Leaf breakdown in constructed streams appeared to be inhibited as a result of reduced processing by benthic macroinvertebrates as well as inhibition of microbial and physicochemical pathways. Constructed streams with total breakdown rates most similar to reference-stream levels had the coldest stream temperatures. Areal periphyton biomass, benthic algal standing crop, and senescent autotrophic organic matter in constructed streams were roughly quadruple, double, and quintuple those of reference streams, respectively. Indicator ratios also suggested stream-type differences in periphyton structure. Mean algal accrual was greater in constructed streams than in reference streams during leaf-on seasons. My results suggest that light is likely the primary factor driving accrual rate differences during summer and fall, but that temperature may also be important during fall. Planting a diverse assemblage of native riparian trees and ensuring their successful development can inhibit benthic irradiance and thermal energy inputs while providing similar quantity and quality of OM to constructed streams, thereby fostering replacement of reference-like OM functions in some streams. / Ph. D.

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.

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

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

Excessive sedimentation is a leading cause of aquatic life use impairments in Virginia. As required by the Clean Water Act, a total maximum daily load (TMDL) must be developed for impaired waters. When developing a TMDL for aquatic life use impairment where sediment has been identified as the primary pollutant, the target sediment load is often determined using a non-impaired reference watershed, i.e., the reference watershed approach (RWA). The RWA has historically been used in Virginia to establish TMDL target sediment loads because there is no numeric ambient water quality criterion for sediment. The difference between the sediment load generated by the reference watershed and the load generated by the impaired watershed is used to determine the sediment load reduction required to meet the TMDL target load in the impaired watershed. Recent quantification of the Chesapeake Bay TMDL based on Phase 5.3 of the Chesapeake Bay Watershed Model (CBWM) offers a simpler and potentially more consistent method of calculating target sediment loads for impaired watersheds within the Chesapeake Bay watershed. Researchers in the Biological Systems Engineering department at Virginia Tech have developed the "disaggregate method" (DM) which uses landuse inputs to, and pollutant load outputs from, the CBWM to determine pollutant load reductions needed in watersheds whose areas are smaller than the smallest modeling segments generally used in the CBWM. The DM uses landuse-specific unit area loads from two CBWM model runs (an existing condition run and TMDL target load run) and a finer-scale, locally assessed landuse inventory to determine sediment loads. The DM is simpler and potential more consistent than the reference watershed approach. This study compared the reference watershed approach and the disaggregate method in terms of required sediment load reduction. Three sediment-impaired watersheds (Long Meadow Run, Taylor Creek and Turley Creek) within the Chesapeake Bay watershed were used for the study. Study results showed that the TMDL development method used to determine sediment loads would have noticeable effects on resulting sediment-load reduction requirements. For Taylor Creek, the RWA required 20.4 times greater reductions in sediment load (tons/yr) when compared to the DM. The RWA also required 9.2 and 10.4 times greater reductions for Turley Creek and Long Meadow Run watersheds, respectively. On a percentage basis, the RWA for reduction Taylor Creek was 7.3 times greater than that called for by the DM. The RWA called for 4.4 and 4.6 times greater percent reductions for Turley Creek and Long Meadow Run watersheds, respectively. An ancillary objective of this research was to compare the sediment load reductions required for the impaired and their respective RWA-reference watersheds, using the DM. This comparison revealed that, both Taylor Creek and Turley Creek watersheds required less sediment load reduction than their respective reference watersheds, while the load reductions required for Long Meadow Run were slightly greater than its reference watershed. There are several issues associated with either the RWA or the DM for developing sediment TMDLs. Those issues are discussed in detail. Recommendations the need for further studies, based in questions raised by the research presented here are also discussed. / Master of Science