Aquatic Habitat Mapping within the Obed Wild and Scenic River for Threatened and Endangered Species Habitat Delineation

There is a need to define a more efficient and accurate approach to aquatic habitat mapping. Traditional approaches have focused on intense biological/non-biological sampling and observation analysis within specific and restrained scales. Therefore, an underwater video mapping system (UVMS) has been developed in efforts to identify federally protected aquatic species’ habitats within the Obed Wild and Scenic River (OBRI). The UVMS kayak apparatus provides georeferenced video footage correlated with GPS (global positioning systems) for GIS (geographic information systems) mapping applications. Based on its fluvial and geomorphological trends, OBRI was dissected quantitatively and integrated into databases for species-specific GIS habitat queries. Substrate type, depth, above water river characteristics (pool/riffle/run), and substrate embeddedness were extracted to access specific habitats. To better pinpoint optimal microhabitat locations, a physical habitat suitability model was developed to rank preferred habitat locales. Rankings were sequentially broken into five categories: optimal, sub-optimal, marginal, sub-marginal, and poor habitat criteria. Habitat suitability findings for the interested species habitats varied tremendously, favoring fish species. Spotfin chub, Erimonax monacha, optimal habitat was found to cover 22.14 km of river length within OBRI (30 % of OBRI’s spatial extent). The blackside dace, Phoxinus cumberlandensis, (38.9 km) and the duskytail darter, Etheostoma percnurum, (50.9 km) met optimal habitat conditions that yielded 51% and 69% of OBRI’s spatial extent, respectively. In general, optimal habitats for the six mussels were sporadically distributed and had low occurrences. Primarily, these mussel species prefer highly embedded areas with very specific depths and pool/riffle/run conditions. Cumberland elktoe, Alasmidonta atropurea, optimal habitat ranges spanned across 4.32 km (6% of OBRI’s spatial extent) with most of the habitat characteristics in OBRI being marginal. The purple bean, Villosa perpurpurea, optimal habitat was identified within 2.61 km of OBRI (3.5% of OBRI’s spatial extent). Most of the physical conditions of OBRI supplied poor to sub-marginal habitat for the purple bean, at least from a thalweg perspective. Only 385 m coincided with optimal habitat for the cumberland bean, Villosa trabalis, (0.5% of OBRI’s spatial extent) with most habitats in long sub-marginal reaches. Optimal habitats for the cumberlandian combshell, Epioblasma brevidens, the tan riffleshell, Epioblasma florentina walkeri, and the littlewing pearlymussel, Pegias fibula, were deficient, only occurring in 484 m, 276 m, and 252 m of OBRI, respectively (0.7%, 0.4%, and 0.3% of OBRI’s spatial extent). Marginal to sub-marginal habitats dominated the park for these three mussel species

Changes in the algal composition, bacterial metabolic activity and element content of biofilms developed on artificial substrata in the early phase of colonization

Changes in the algal composition and metabolic profiles of bacterial communities as well as the inorganic components were studied on artificial substrata during the early phase of biofilm formation under laboratory conditions in September 2002 and 2003. Sterile Perspex and polished quartz glass discs with a diameter of 3 cm were placed into a Perspex rack, which was immersed vertically in an aquarium containing water from a shallow soda lake. The temperature was kept constant and sufficient oxygen supply was provided. The samples were illuminated for 12 hours a day. Periphyton communities were sampled from 2 to 126 hours of exposure. In both experiments, the alteration of the number of algal species and cells as well as the carbon source utilization of microbial communities was logarithmic. In the two years, considerable differences were revealed in the magnitude of algal cell numbers. The proportion of benthic and planktonic algae showed an undulating pattern in the second experiment. One of the dominant benthic species was the diatom Achnanthidium minutissimum Kütz., while that of the planktonic, the cyanobacterium Microcystis aeruginosa Kütz. During the experiments an increase in the bacterial activities could be observed; the higher the microbial diversity and abundance that was detected, the more BIOLOG carbon sources were utilized. The examined element contents indicated interactions among algae and bacteria in the biofilms from the beginning of the colonization processes

Application of mineralogical, petrological and geochemical tools for evaluating the palaeohdrogeological evolution of the PADAMOT study sites

The role of Work Package (WP) 2 of the PADAMOT project – ‘Palaeohydrogeological Data Measurements’ - has been to study late-stage fracture mineral and water samples from groundwater systems in Spain, Sweden, United Kingdom and the Czech Republic, with the aim of understanding the recent palaeohydrogeological evolution of these groundwater systems. In particular, the project sought to develop and evaluate methods for obtaining information about past groundwater evolution during the Quaternary (about the last 2 million years) by examining how the late-stage mineralization might record mineralogical, petrographical and geochemical evidence of how the groundwater system may have responded to past geological and climatological changes. Fracture-flow groundwater systems at six European sites were studied: • Melechov Hill, in the Bohemian Massif of the Czech Republic: a shallow (0-100 m) dilute groundwater flow system within the near-surface weathering zone in fractured granitic rocks; • Cloud Hill, in the English Midlands: a (~100 m) shallow dilute groundwater flow system in fractured and dolomitized Carboniferous limestone; • Los Ratones, in southwest Spain: an intermediate depth (0-500 m) dilute groundwater flow system in fractured granitic rocks; • Laxemar, in southeast Sweden: a deep (0-1000 m) groundwater flow system in fractured granitic rocks. This is a complex groundwater system with potential recharge and flushing by glacial, marine, lacustrine and freshwater during the Quaternary; • Sellafield, northwest England: a deep (0-2000 m) groundwater flow system in fractured Ordovician low-grade metamorphosed volcaniclastic rocks and discontinuous Carboniferous Limestone, overlain by a Permo-Triassic sedimentary sequence with fracture and matrix porosity. This is a complex coastal groundwater system with deep hypersaline sedimentary basinal brines, and deep saline groundwaters in crystalline basement rocks, overlain by a shallow freshwater aquifer system. The site was glaciated several times during the Quaternary and may have been affected by recharge from glacial meltwater; • Dounreay, northeast Scotland: a deep (0-1400 m) groundwater flow system in fractured Precambrian crystalline basement overlain by fractured Devonian sedimentary rocks. This is within the coastal discharge area of a complex groundwater system, comprising deep saline groundwater hosted in crystalline basement, overlain by a fracture-controlled freshwater sedimentary aquifer system. Like Sellafield, this area experienced glaciation and may potentially record the impact of glacial meltwater recharge. In addition, a study has been made of two Quaternary sedimentary sequences in Andalusia in southeastern Spain to provide a basis of estimating the palaeoclimatic history of the region that could be used in any reconstruction of the palaeoclimatic history at the Los Ratones site: • The Cúllar-Baza lacustrine sequence records information about precipitation and palaeotemperature regimes, derived largely from the analysis of the stable isotope (δ18O and δ13C) signatures from biogenic calcite (ostracod shells). • The Padul Peat Bog sequence provided information on past vegetation cover and palaeogroundwater inputs based on the study of fossil pollen and biomarkers as proxies for past climate change. Following on from the earlier EC 4th Framework EQUIP project, the focus of the PADAMOT studies has been on calcite mineralization. Calcite has been identified as a late stage mineral, closely associated with hydraulically-conductive fractures in the present-day groundwater systems at the Äspö-Laxemar, Sellafield, Dounreay and Cloud Hill sites. At Los Ratones and Melechov sites late-stage mineralization is either absent or extremely scarce, and both the quantity and fine crystal size of any late-stage fracture mineralization relevant to Quaternary palaeohydrogeological investigations is difficult to work with. The results from the material investigated during the PADAMOT studies indicate that the fracture fillings at these sites are related to hydrothermal activity, and so do not have direct relevance as Quaternary indicators. Neoformed calcite has not been found at these two sites at the present depth of the investigations. Furthermore, the HCO3 - concentration in all the Los Ratones groundwaters is mainly controlled by complex carbonate dissolution. The carbonate mineral saturation indices do not indicate precipitation conditions, and this is consistent with the fact that neoformed calcite, ankerite or dolomite have not been observed petrographically

Freshwater Mussel Populations of the Monongahela River, PA and Evaluation of the ORSANCO Copper Pole Substrate Sampling Technique Using G.I.S. Interpolation with Geometric Means

Large river studies for freshwater mussel populations and habitat in the Monongahela River within Pennsylvania have been almost non-existent over the past century. Aquatic diversity and water quality have been impaired in the Monongahela River since the Industrial Revolution and early impoundments were constructed to control the river. To date, there have been no thorough mussel population studies conducted on the Pennsylvanian Monongahela River proper since A.E. Ortmann in 1919. The mussel population accounts for this large river system are invaluable accounts of the aquatic condition of the Monongahela River. Mussel populations and habitat within the river have diminished drastically during the 20 th century. Mussel populations and habitat were evaluated using SCUBA reconnaissance at 31 survey sites over 91 river miles. Survey methods included timed SCUBA searches for mussel populations and substrate consistency. Substrate habitat at each site was evaluated using diver reconnaissance and a modified version of the Ohio River Valley Water Sanitation Commission (ORSANCO) Copper Pole Substrate Sampling Protocol. Substrate sampling efficacy using the Copper Pole sampling technique was evaluated using benthic diagrams built using Inverse Distance Weighting with software ArcGIS 9.2. Results of this survey indicated seven (7) mussel species persist within the river with limited abundance compared to the 28 species accounted for in 1919. Habitat assessment techniques evaluated for use in large rivers illustrated an overestimation of substrate size. Paired T-test and Wilcoxon Signed-Rank analysis of Copper Pole Sampling versus diver reconnaissance of substrate size classes expressed significant differences of substrate geometric means. These data are presented to build on the ever growing research and evaluation of techniques used for large river ecosystem monitoring currently being developed in the field of river ecolog

The use of aerial imagery to map in-stream physical habitat related to summer distribution of juvenile salmonids in a Southcentral Alaskan stream

Thesis (M.S.) University of Alaska Fairbanks, 2011Airborne remote sensing (3-band multispectral imagery) was used to assess in-stream physical habitat related to summer distributions of juvenile salmonids in a Southcentral Alaskan stream. The objectives of this study were to test the accuracy of using remote sensing spectral and spatial classification techniques to map in-stream physical habitat, and test hypotheses of spatial segregation of ranked densities of juvenile chinook salmon Oncorhynchus tschwytscha, coho salmon O. kisutch, and rainbow trout O. mykiss, related to stream order and drainage. To relate habitat measured with remote sensing to fish densities, a supervised classification technique based on spectral signature was used to classify riffles, non-riffles, vegetation, shade, gravel, and eddy drop zones, with a spatial technique used to classify large woody debris. Combining the two classification techniques resulted in an overall user's accuracy of 85%, compared to results from similar studies (11-80%). Densities of juvenile salmonids was found to be significantly different between stream orders, but not between the two major drainages. Habitat data collected along a 500-meter stream reach were used successfully to map in-stream physical habitat for six river-kilometers of a fourth-order streams. The use of relatively inexpensive aerial imagery to classify in-stream physical habitats is cost effective and repeatable for mapping over large areas, and should be considered an effective tool for fisheries and land-use managers.Alaska Cooperative Fish and Wildlife Research Unit, University of Alaska Fairbanks, Alaska Department of Fish and Gam

Habitat Analysis by Hierarchical Scheme and Stream Geomorphology

A study was undertaken to classify eight stream reaches in the North Branch of the Potomac River watershed and determine if geomorphologic differences influenced the availability of fish habitat structure and fish density. Stream reaches were classified using Rosgen Level II (1996) methods, and fish habitat was determined using Hydraulic Channel Unit (HCU) classification based on a method modified from Bisson et al. (1982). Other habitat variables were also studied such as stream shading and physical habitat based on the Rapid Bioassessment Protocol (Barbour et al. 1999). Despite the differences in HCU density between sites, HCU density did not influence fish density in the study streams. HCU density appeared to be mainly controlled by slope. Fish densities were highest in the relatively unimpacted streams, as expected. However, the impacted streams also appeared to have sufficient physical fish habitat structure to support fishes historically found in these streams. Other confounding variables, such as acid mine drainage, may be controlling factors in inhibiting fish populations in the impacted streams

Application of airborne LiDAR bathymetry in Norway

New technologies in remote sensing provide opportunities for effectively sampling information on topography and bathymetry for large areas. With Airborne LiDAR Bathymetry (ALB) terrain and also the river bottom (bathymetry) can be measured with high accuracy. In this report we present our contributions to 1) validation, 2) flood risk analysis and mitigation, and 3) river restoration. All rivers could be classified to river types according to Hauer & Pulg (2018) from remote sensing data only. ALB data can be much faster than other surveying or mapping methods and has higher accuracy. Ecological information can be acquired from ALB data in higher resolution than with other methods, and also parameters like grain size and shelter have a high correlation with ALB derivates. The ALB datasets can be used for planning and assessing ecological and flood related questions from the desktop with a strongly reduced requirement for field work compared to data from other data sources, additionally giving a model verification with much higher accuracy and detail degree than other methods. ALB can therefore improve planning safety and speed up planning and modelling process for high- flow, low-flow, morphodynamics and ecological applications. The Lærdal flood case study shows that advances in remote sensing can be used to develop and model nature-based and integrated solutions for improving flood safety and ecological status.Application of airborne LiDAR bathymetry in NorwaypublishedVersio

Integrated Approaches in Water Quality Monitoring for River Health Assessment: Scenario of Malaysian River

Current practice of determining river water quality in Malaysia is based mainly on physicochemical components. Perhaps, owing to the lack of information on habitat requirements and ecological diversity of aquatic macroinvertebrates and on unearthly taxonomic key of benthic macroinvertebrates in this region makes it less popular than conventional methods. The study took place in three rivers in the state of Johor, Southern Peninsula of Malaysia, which exhibited different degrees of disturbances and physical properties, namely Sungai Ayer Hitam Besar, Sg Berasau, and Sg Mengkibol. Benthic macroinvertebrates were sampled using rectangular dipnet with frame dimension 0.5 m × 0.3 m. Although physicochemical elements such as water temperature, pH, and dissolved oxygen (DO) were measured using a YSI Professional Plus handheld multiparameter instrument, other parameters such as biochemical oxygen demand (BOD5), chemical oxygen demand (COD), total suspended solid (TSS), and ammoniacal nitrogen (NH3N) were tested using the procedure of APHA Standard Method. The study found that the status of water quality varies among the three rivers. A multivariate analysis, the canonical correspondence analysis (CCA), was applied to elucidate the relationships between biological assemblages of species and their environment using PAST (version 2) software. The present findings reveal that human-induced activities are the ultimate causes of the alteration in macroinvertebrate biodiversity

SPATIAL HETEROGENEITY OF NITROGEN CYCLING WITHIN AND ACROSS FRESHWATER ECOSYSTEMS

Dinitrogen (N2) fixation and denitrification are two nitrogen (N) cycling processes that despite differences in environmental requirements and constraints, co-occur in aquatic ecosystems. The overall goal of this dissertation was to evaluate how spatial heterogeneity of environmental variables 1) drive hot spots of N2 fixation, denitrification rates and gene abundances in streams, 2) facilitate co-occurrence of these processes across wetland – stream – lake interfaces, and 3) affect differences in microbial community composition in streams across U.S. ecoregions. We found hot spots of both processes within 7 stream reaches in Michigan and Idaho, but rates of N2 fixation were not directly related to relative gene abundances of nifH, while denitrification rates were related to relative gene abundances of nirS. Spatial heterogeneity of organic matter and dissolved oxygen concentrations were important predictors of rates of both processes. In a survey across 5 wetland – stream – lake interfaces of Lakes Superior and Huron, we found that rates of N2 fixation and denitrification occurred across stream, wetland and shallow lake habitats and that phosphorus (P) availability was important for predicting rates of both processes, while N availability was an important predictor of denitrification and carbon (C) availability was important predictor of N2 fixation. Finally, in a survey of microbial assemblages from 30 streams across 13 U.S. ecoregions, we found that microbial community composition differed across ecoregions in alpha diversity and relative Class abundances, but little of this variation was explained by environmental variables. Together, these studies show that N2 fixation and denitrification co-occurred in stream and coastal ecosystems and across spatial scales from stream reaches to ecoregions. However, rates and microbial community composition are not explained fully xii by differences in environmental variables on the microhabitat, cross-habitat, or ecoregion scale. N alone was not always an important predictor of the processes despite N being thought of as the best indicator of these processes in the past. Overall, these studies highlight the need to include both N2 fixation and denitrification measurements in biogeochemical studies for a better understanding of the complexity of N cycling in aquatic ecosystems

Visual pathways from the perspective of cost functions and multi-task deep neural networks

Vision research has been shaped by the seminal insight that we can understand the higher-tier visual cortex from the perspective of multiple functional pathways with different goals. In this paper, we try to give a computational account of the functional organization of this system by reasoning from the perspective of multi-task deep neural networks. Machine learning has shown that tasks become easier to solve when they are decomposed into subtasks with their own cost function. We hypothesize that the visual system optimizes multiple cost functions of unrelated tasks and this causes the emergence of a ventral pathway dedicated to vision for perception, and a dorsal pathway dedicated to vision for action. To evaluate the functional organization in multi-task deep neural networks, we propose a method that measures the contribution of a unit towards each task, applying it to two networks that have been trained on either two related or two unrelated tasks, using an identical stimulus set. Results show that the network trained on the unrelated tasks shows a decreasing degree of feature representation sharing towards higher-tier layers while the network trained on related tasks uniformly shows high degree of sharing. We conjecture that the method we propose can be used to analyze the anatomical and functional organization of the visual system and beyond. We predict that the degree to which tasks are related is a good descriptor of the degree to which they share downstream cortical-units.Comment: 16 pages, 5 figure