At Crabby Creek, an urbanized watershed in northeast Chester County, Pennsylvania, an NaCl tracer test was conducted in 2010 to assess changes in hyporheic flow from a 2009 tracer test around the same stream restoration J-Hook. This project compares the 2009 and 2010 tracer test breakthrough curves and geophysical time-lapse resistivity surveys. This project also compares elevation cross sections and tile probing from 2009 and 2010, both measured upstream and downstream from the J-Hook. To confirm areas of lingering tracer seen in the time-lapse resistivity profiles, sediment cores using the freeze core method were taken to measure pore water for tracer. This project also measured diurnal temperature flux through the streambed at several locations along the sample site to model vertical water and heat flux. The breakthrough graphs constructed from the conductivity of the well water samples shows similar hyporheic flow characteristics from 2009 to 2010. The time-lapse resistivity profiles show an area of lingering tracer upstream from the J-Hook in 2010 that is similar in shape and location to an area upstream from the J-Hook in the 2009 profiles. However, an area of lingering tracer downstream from the J-Hook present in 2009 as a round feature on the profile is now a thin linear feature. The freeze cores show tracer present in the pore water after the end of the tracer injection in the stream sediment, confirming areas of lingering tracer seen in the time-lapse resistivity profiles. The grain size analysis of the freeze cores and the comparison to the 2009 cores taken at Crabby Creek show similar grain size distribution upstream from the J-Hook. Downstream from the J-Hook the grain size analysis shows a redistribution of sediment. Upstream from the J-Hook the tile probe shows both shallower and deeper bedrock, a redistribution of sediment but no net erosion. Downstream from the restoration structure, however, the tile probe data show a sediment loss of 20 cm. Elevation cross section surveys from 2009 and 2010 confirm what the tile probing found, a loss of sediment downstream but not upstream from the J-Hook. Temperature modeling of heat flux through the sediment shows that the diurnal temperature distribution can be accounted for without vertical flux. Thus, the immobile regions upstream and downstream from the J-Hook seem to be related to sediment distribution rather than hydrologic gradient differences. The significance of this study shows the need to use multiple techniques to characterize the immobile zone as a part of hyporheic flow. The immobile zone is an important area of chemical reactions in the streambed. At Crabby Creek the central J-Hook inhibits net erosion patterns upstream from the structure, allowing for the continued presence of an immobile zone. Downstream from the central J-Hook the erosion of the streambed sediment led to a decrease in size and location of the immobile zone. The disturbance of sediment around restoration structures influences the development of a healthy hyporheic flow and needs to be studied for future restoration of impaired streams and riparian corridors. / Geology

We investigated the transport of dissolved arsenic in groundwater, surface water and the hyporheic zone in a stream-aquifer system influenced by an abandoned arsenopyrite mine. Mine tailing piles consisting of a host of arsenic-bearing minerals including arsenopyrite and scorodite remain adjacent to the stream and represent a continuous source of arsenic. Arsenic loads from the stream, springs, and groundwater were quantified at the study reach on nine dates from January to August 2005 and a mass-balance approach was used to determine hyporheic retention. Arsenic loading from the groundwater was the dominate source of arsenic to the stream, while loads from springs represented a substantial proportion of the total arsenic load during spring. Arsenic loads in surface and groundwater were significantly elevated during summer. Elevated temperatures during summer may lead to increased arsenic loading by increasing dissolution rate of arsenic source minerals and/or increases in microbially-mediated dissolution processes. The hyporheic zone was shown to be retaining arsenic in the upstream-most sub-reach. Retention most likely occurs through the sorption of dissolved arsenic onto hyporheic sediments. In downstream sub-reaches, hyporheic sediments are derived from mine-tailing piles which have high arsenic content. The hyporheic zone in these sub-reaches was shown to be releasing dissolved arsenic. The historic influence of mining activity has resulted in multiple sources of arsenic to the stream which has increased arsenic contamination of the surface waters. / Master of Science

A principal ecological role proposed for the hyporheic zone is as a refugium that promotes benthic invertebrate survival during adverse conditions in the surface stream. Whilst a growing body of work has examined use of this hyporheic refugium during hydrological extremes (spates, streambed drying), little research has considered variation in refugium use over prolonged periods including contrasting conditions of surface flow. In this thesis, benthic invertebrate use of the hyporheic refugium is considered at monthly intervals over a five-month period of variable surface flow, at nine sites in two groundwater-dominated streams, the River Lathkill (Derbyshire) and the River Glen (Lincolnshire). Conditions identified as potential triggers of refugium use included a flow recession and a high-magnitude spate on the Lathkill, and small spates and a decline in flow preceding localised streambed drying on the Glen. During flow recession, reductions in submerged habitat availability and concurrent increases in benthic population densities were dependent on channel morphology. An unusual paired benthic-hyporheic sampling strategy allowed the type of refugium use (active migration, passive inhabitation) to be inferred from changes in hyporheic abundance and the hyporheic proportion of the total population. Using this approach, evidence of active migrations into the hyporheic zone use was restricted to two instances: firstly, Gammarus pulex (Amphipoda: Crustacea) migrated in response to habitat contraction and increased benthic population densities; secondly, migrations of Simuliidae (Diptera) were associated with low-magnitude spates. Refugium use was site-specific, with refugial potential being highest at sites with downwelling water and coarse sediments. A conceptual model describing this spatial variability in the refugial capacity of the hyporheic zone is developed for low flow conditions. In some cases, hyporheic refugium use was apparently prevented by disturbance-related factors (rapid onset, high magnitude) regardless of the refugial potential of the sediments. The extension of the hyporheic zone's refugial role to include low flows highlights the need to explicitly protect the integrity of hydrologic exchange in river rehabilitation schemes. However, the limited capacity of the hyporheic refugium emphasizes the additional importance of maintaining habitat heterogeneity including multiple instream refugia.

No description available.

The feedbacks between hydrology and biogeochemical cycling of nitrogen (N) are of critical importance to global bioavailable N budgets. Human activities are dramatically increasing the amount of bioavailable N in the biosphere, which is causing increasingly frequent and severe impacts on ecosystems and human welfare. Streams are important features in the landscape for N cycling, because they integrate many sources of terrestrially derived N and control export to downgradient systems via internal source and sink processes. N transformations in stream ecosystems are typically very complex due to spatiotemporal variability in the factors controlling N biogeochemistry. Thus, it is difficult to predict if a particular stream system will function as a net source or sink of bioavailable N. A key location for N transformations in stream ecosystems is the hyporheic zone, where stream and ground waters mix. The hyporheic zone can be a source of bioavailable N via nitrification or a sink via denitrification. These N transformations are regulated by the physical and biogeochemical conditions of hyporheic zones. Natural heterogeneity in streams leads to unique combinations of both the physical and biogeochemical conditions which in turn result in unique N source and sink conditions. This dissertation investigates the relationships between physical and biogeochemical controls and the resulting fate of bioavailable N in hyporheic zones. The key physical factor investigated is the supply rate of solutes which is a function of transport processes - advection and dispersion, and transport conditions - hydraulic conductivity and flowpath length. Different physical conditions result in different characteristic residence times of water and solutes in hyporheic zones. The key biogeochemical factors investigated are the dynamics of oxygen (O₂), labile dissolved organic carbon (DOC), and inorganic bioavailable N (NH₄⁺ and NO₃⁻). This dissertation uses ¹⁵N isotope experiments, numerical modeling of coupled transport of the bioavailable N species, O₂ and DOC, and a suite of geophysical measurements to identify the key linkages between hydrological and biogeochemical controls on N transformations in hyporheic zones. Specifically, it was determined that the conditions governing the fate of hyporheic N are both the physical transport and reaction kinetics – the residence time of water and the O2 uptake rate. An important scaling relationship is developed by relating the characteristic timescales of residence time and O₂ uptake. The resulting dimensionless relationship, the Damköhler number for O₂, is useful for scaling different streams hyporheic zones and their role on stream N source – sink dynamics. More generally, these investigations demonstrate that careful consideration and quantification of hydrological processes can greatly inform the investigation of aquatic biogeochemical dynamics and lead to the development of process-based knowledge. In turn, this process-based knowledge will facilitate more robust approaches to quantifying and predicting biogeochemical cycles and budgets. / Graduation date: 2012 / Access restricted to the OSU Community at author's request from Sept. 21, 2011 - March 21, 2012

The hyporheic interstitial was recognized as an integral zone within the aquatic ecosystem bearing important functions for both adjacent compartments, surface and ground water, about 50 years ago. Since then, rather disciplinary works gained knowledge on the organismic community of this ecotone, its spatial extent, the role of distinct parameters such as hydrology and morphology, temporal characteristics, process dynamics, the role for stream or groundwater quality and restoration measures. However, a systematic study on the risks to the hyporheic functions was missing to date. This thesis combined existing methods in order to gather an integrated set of information allowing for the assessment of the ecotonal status. This approach was applied to investigate the functional behavior towards stressors like increasing nutrient and fine sediment input into a rather pristine environment. An interdisciplinary risk assessment and the establishment of adapted measures was called for as land-use scenarios for the studied catchment area indicated progressive onland erosion. Therefore firstly, an integrated monitoring scheme was drawn up and conducted at three sites along a river that underlay a stressor gradient such as mentioned before. Secondly, the data sets were analysed in order to evaluate the status of the hyporheic funtions at the riffles. Thirdly, a coupled surface-subsurface modelling approach was set up to further study the impact of the stressors on the ecotonal integrity. And fourthly, an interdisciplinary consideration combined with studies on the catchments sediment budget and the rivers ecological status was applied to identify measures for the restoration and protection of the aquatic ecosystem. The analysis of the data gathered with the help of the established monitoring scheme revealed that elevated nutrient or fine sediment input lead to biological or physical clogging, respectively, with consequences for the hyporheic zone functions. The surface - ground water connectivity was either lowered in summer months, when biofilm growth was highest, or permanently, as fine sediment particles infiltrated into the interstices of the riverbed sediment. Scouring did not seem to take place as high amounts of fine particles were found in the matrix after discharge events of snowmelt and summer precipitation. With respect to the biogeochemical regulation function, biofilm material appeared to provide an autochthonous carbon source boosting microbial substance turnover. The sediment underneath the physical clogged layer was cut off from carbon and oxygen rich surface water and thus was not reactive. However, the enhanced surface area provided by the fine sediment within the topmost sediment layer seemed to support microbial processing. The inclusion of the results of a study concerning the ecological status at the investigated reaches lead to the deduction that biological clogging at the present degree was not affecting habitat quality. Whereas the physical clogging had tremendeous and lasting effects on the macroinvertebrate community which carries to the conclusion that sediment management within the studied catchment is of uttermost importance. A scenario analysis reflecting distinct clogging degrees and types with a calibrated model of a studied riffle within a pristine reach proved the observed loss of hydrologic connectivity due to physical and biological clogging. Further, a treshold of oxygen consumption rates above which the reproduction of salmonid fish would be unsuccessful was identified for the settings of the middle reaches. In summer month with low discharge it seemed to be likely that this treshold might be reached. Following, a dynamic discharge may be decisive to protect the ecotonal integrity. The integration with the outcome of an investigation regarding the sediment sources within the catchment allowed for two suggestions. On the one hand, river bank restoration and protection within the middle reaches need to be prioritised, and on the other hand, the conservation of the natural vegetation at the steep slopes within the mountaineous areas need to be undertaken in order to secure the pristine aquatic environment of this area. Hyporheic zone research of the last decade was driven by testing hypotheses on the functional significance of distinct spatial and temporal configurations in the field and by new modelling approaches. However, data on the quantification of the ecological impact of clogging processes were lacking. The thesis contributed to the systemic understanding of the hyporheic zone being affected by physical and biological clogging and new field data within a degrading pristine environment were generated, accessible for further hyporheic research. The interdisciplinarity enabled comprehensive statements for the usage of an Integrated Water Resources Management plan.

Amostras de diferentes espécies de Phreatobius foram coletadas para obtenção de dados moleculares potencialmente informativos do gene nuclear RAG-2 para resolver as relações filogenéticas do gênero. Apresento resultados de sequências. Os dados de Phreatobius foram combinados com sequências equivalentes de representantes de várias outras famílias de Siluriformes, e analisados via máxima parcimônia (total de 966 pares de base de RAG-2 para 176 táxons). As análises resultaram em 172 árvores com 5213 passos. O resultado do consenso estrito indica fortemente que Phreatobius forma um grupo monofilético (sustentado por 33 sinapomorfias moleculares) com Pseudopimelodidae e Pimelodidae, e Conorhynchos + Heptapteridae. Hipóteses anteriores posicionando Phreatobius exclusivamente com Heptapteridae não foram sustentadas. Os resultados apresentados requerem que Phreatobius seja alocado na sua própria família, Phreatobiidae (disponível em nível subfamiliar). Uma revisão taxonômica de Phreatobiidae mostra que existem ao menos sete espécies, das quais apenas três descritas: Phreatobius cisternarum, Phreatobius dracunculus, Phreatobius sanguijuela, Phreatobius sp. "Anapixi", Phreatobius sp. "Jaú", Phreatobius sp. Tarumanzinho", Phreatobius sp. "Viruá". A hipótese de relações filogenéticas dentro de Phreatobiidae mostra que Phreatobius cisternarum é grupo-irmão do clado composto por (Phreatobius sp. "Viruá" (P. dracunculus + Phreatobius sp. "Tarumanzinho")). O mapeamento filogenético demonstra que o hábito subterrâneo evoluiu uma única vez na família e o ambiente freático foi invadido duas vezes. / Samples from different species of Phreatobius were collected in order to obtain molecular data from nuclear RAG-2 gene sequence potentially informative to resolve phylogenetic relationships of the genus. The data on Phreatobiidae were combined with equivalent sequence information from representatives of several other siluriform families, and analyzed by maximum parsimony (a total of 966 bp RAG-2 for 176 taxa). The analyses resulted in 172 trees, with 5213 steps. The strict consensus results strongly indicate that Phreatobius forms a monophyletic group (supported by 33 molecular synapomorphies) with Pseudopimelodidae, Pimelodidae, and Conorhynchos + Heptapteridae. Previous hypotheses aligning Phreatobius exclusively with Heptapteridae were not supported. Results herein presented requires that Phreatobius be allocated in its own family, as Phreatobiidae (already available at subfamilial level). A taxonomic revision of Phreatobiidae shows that at least seven species exist, only three of which currently described: Phreatobius cisternarum, Phreatobius dracunculus, Phreatobius sanguijuela, Phreatobius sp. "Anapixi", Phreatobius sp. "Jaú", Phreatobius sp. Tarumanzinho", Phreatobius sp. "Viruá". A hypothesis of relationships within Phreatobiidae shows that P. cisternarum is sister-group of a clade composed of (P. sp. "Viruá" (P. dracunculus + P. sp. "Tarumanzinho")). Phylogenetic mapping shows that subterranean habit has evolved once in the family and the phreatic environment was invaded twice.

I studied nine streams near Grand Teton National Park, Wyoming, covering a land use gradient (urban, agricultural, and forested) to assess influences of land use on denitrification rates and hyporheic exchange. I hypothesized denitrification in the hyporheic zone is governed by availability of chemical substrates and hydrologic transport. I tested this hypothesis by coupling measurements of denitrification potentials in hyporheic sediments with a 2-storage zone solute transport model. Denitrification potentials were lowest on average in hyporheic sediments from forested streams and highest from agricultural streams. Modeling results suggest, on average, agricultural sites are transport-limited by having the slowest exchange rate with hyporheic zone and longest transport before entering storage. Land use influences the capacity for hyporheic denitrification in two ways 1) agricultural and urban practices supply substrates that build the microbial potential for denitrification and 2) agricultural and urban activities alter channel form and substrates, limiting hyporheic exchange.

In the present doctoral work we have developed and tested a model for dissolved oxygen (DO) transfer from water to underlying flat and cohesive sediment beds populated with DO-absorbing bacteria. The model couples Large-Eddy Simulation (LES) of turbulent transport in the water-column, a biogeochemical model for DO transport and consumption in the sediment, and Darcy’s Law for the pore water-driven solute dispersion and advection. The model’s predictions compare well against experimental data for low friction-Reynolds numbers (Re). The disagreement for higher Re is investigated by progressively increasing the complexity of the model. A sensitivity analysis shows that the sediment-oxygen uptake (or demand, SOD) is approximately proportional to the bacterial content of the sediment layer, and varies with respect to fluid dynamics conditions, in accordance to classic high-Schmidt-number mass-transfer laws. The non- linear transport dynamics responsible for sustaining a statistically steady SOD are investigated by temporal- and-spatial correlations and with the aid of instantaneous visualizations: the near-wall coherent structures modulate the diffusive sublayer, which exhibits complex spatial and temporal filtering behaviours; its slow and quasi-periodic regeneration cycle determines the streaky structure of the DO field at the sediment-water interface (SWI), retained in the deeper layers of the porous medium. Oxygen depletion dynamics are then simulated by preventing surface re-areation with turbulent mixing driven by an oscillating low-speed current — an idealization of hypolimnetic DO depletion in the presence of a non-equilibrium periodic forcing. The oxygen distribution exhibits a self-similar pattern of decay with, during the deceleration phase, oscillations modulated by the periodic ejection of peaks of high turbulent mass flux (pumping oxygen towards the SWI), generated at the edge of the diffusive sublayer at the end of the acceleration phase. These fronts of highly turbulent mixing propagate away from the SWI, at approximately constant speed, in layers of below-average oxygen concentration. Finally, the model has been tested in a real geophysical framework, reproducing published in-situ DO measurements of a transitional flow in the bottom boundary layer of lake Alpnach. A simple model for the SOD is then derived for eventual inclusion in RANSE biogeochemical management-type models for similar applications. / Thesis (Ph.D, Mechanical and Materials Engineering) -- Queen's University, 2012-07-04 11:13:24.936

Thesis (M.S.)--Oregon State University, 2010. / Printout. Includes bibliographical references (leaves 113-118). Also available on the World Wide Web.