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Item Trichophycin A, a cytotoxic linear polyketide isolated from a Trichodesmium thiebautii bloom(MDPI, 1/6/2017) Bertin, Matthew J.; Wahome, Paul G.; Zimba, Paul V.; He, Haiyin; Moeller, Peter D. R.In an effort to isolate and characterize bioactive secondary metabolites from Trichodesmium thiebautii blooms, collected cyanobacteria biomass was subjected to bioassay-guided extraction and fractionation using the human colon cancer cell line HCT-116, resulting in the isolation and subsequent structure characterization of a linear polyketide trichophycin A (1). The planar structure of 1 was completed using 1D and 2D NMR spectroscopy and high-resolution electrospray ionization mass spectrometry (HRESIMS). Trichophycin A was moderately toxic against the murine neuroblastoma cell line Neuro-2A (EC50: 6.5 μM) and HCT-116 cells (EC50: 11.7 μM). Trichophycin A was significantly more cytotoxic than the previously isolated polyketides trichotoxin A and trichotoxin B. These cytotoxicity observations suggest that toxicity may be related to the polyol character of these polyketide compounds.Item DISTRIBUTION AND DIVERSITY OF OCTOCORALS IN THE GULF OF MEXICO(11/11/2014) Etnoyer, Peter; T. C. ShirleyOctocorals are broadly distributed throughout the world’s oceans, from the shallow intertidal zone to deeper than 5800 meters. Fishermen refer to large colonies as ‘trees’. This is appropriate because colonies provide complex structural habitat for associated species, they are broadly distributed, and they are threatened by industrial practices, such as bottom trawling. Below the warm water layer (50 – 70 m deep), octocorals are presumed to be cosmopolitan in the West Atlantic, with a broadly homogenous distribution. This creates a problem for conservation and management because it is difficult to justify conservation of one place, if all others are the same. This dissertation tested the null hypothesis of no difference in octocoral assemblages at the three spatial scales (referred to as basin, region, and site scale) through meta-analysis of two large, original datasets. The first was 1881 records of octocoral occurrences in the Gulf of Mexico from cruise reports and museums. The second was 8495 seafloor images from six outer continental shelf banks, and one site between banks, in the northwestern Gulf region. Univariate, multivariate, and spatial analysis techniques were used to compare genera, depth zones, regions, and banks within a Geographic Information System framework.Octocoral assemblages in the Gulf of Mexico differed significantly between depth zones and regions, but there was no difference in diversity between depth zones less than 800 m, due to species replacement. Composition of octocoral assemblages varied significantly between sites, and hotspots for richness and abundance were evident within sites. Null hypotheses of no difference between banks, depth zones, and regions were rejected with confidence. The findings support the broad distribution of octocorals in the Gulf of Mexico, but not homogeneity of octocoral assemblages. Based on these results, place-based conservation of deep octocoral habitat is justified, because some sites have higher diversity and abundance of octocorals than others.Item A Field Guide to Ward Island(1995) Hickman, Graham C.Item Biological productivity associated with the serpulid reefs of Baffin Bay, Texas(1997-08) Hardegree, Beau; McKee, David A.; Prouty, Jennifer S.; Tunnell, John W.; Dunton, Kenneth H.The upper Laguna Madre and Baffin Bay-complex has long been noted for its abundant finfish populations despite its generally persistent hypersaline condition. The purpose of this present study was to determine the contribution of the serpulid worm reefs to the productivity of Baffin Bay. The primary focus of this thesis was to test the hypothesis that fish were larger and found in higher concentrations near the serpulid worm reefs in Baffin Bay, and to quantify the abundances of potential prey items associated with the reefs. In addition, I measured the productivity (by O2 evolution) of the epiphytic algae growing on the reefs and compared it to published seagrass studies in the upper Laguna Madre. Lastly, I examined the dependence of consumers on carbon fixed by these primary producers using stable carbon isotope ratios as tracers. A total of 5,396 individuals representing 35 fish species, were collected by trammel net during the study. Seven fish species (Mugil cephalus = 27.3 o/q Pogonias cromis = 20.2 %, Cynoscion nebulosus = 15.2 %, Leiostomus xanthurus = 12.1 %, Arius felis = 10.7 %, Lagodon rhomboides = 2.3 %, and Sciaenops ocel/atus = 1.1 %) comprised 89.0 % of the total catch. The overall ichythyofaunal catch rate was not significantly different between reef and non-reef sites and only a seasonal effect in the catch rate data was observed. Seasonal differences can be explained by the recruitment of fish into the bay in Spring and Summer. These seasonal peaks can be attributed to three species: Arius felis, Pogonias cromis, and Leiostomus xanthurus. No strong evidence was found to support the hypothesis that larger fish congregate around the serpulid worm reefs.Item Development of a green fluorescent protein-based laboratory curriculum(IUMBM Journals, 2005-01) Larkin, PatrickA laboratory curriculum has been designed for an undergraduate biochemistry course that focuses on the investigation of the green fluorescent protein (GFP). The sequence of procedures extends from analysis of the DNA sequence through PCR amplification, recombinant plasmid DNA synthesis, bacterial transformation, expression, isolation, and characterization of the protein by SDS-PAGE. A survey of participants found that the majority of them were performing most of these procedures for the first time and that participants found the exercises enjoyable and considered them a significant aid to their understanding of biochemistry, cell biology, and molecular genetics.Item Optimization of 12 chiral analytes with 8 polymeric surfactants(Oxford Academic, 2008-10-01) Billiot, Eugene; Billiot, Fereshteh; Warner, IsiahThis manuscript discusses the results of studies that were performed to determine optimum capillary electrophoresis (CE) conditions for the enantiomeric resolution of twelve chiral analytes with eight amino acid based polymeric surfactants. The parameters that were optimized include pH, buffer type, and concentration of surfactant. The results indicated that the optimum conditions for enantiomeric separations with the amino acid based polymeric surfactants examined in this study using CE were analyte dependent, not surfactant dependent. In other words, the optimum conditions for a particular analyte were the same for all the amino acid based polymeric surfactants examined in this study. The results of these studies indicate that when using a large group of related amino acid based polymeric surfactants only a few surfactants need to be optimized for each analyte under study. These studies were limited to anionic surfactants that contain the amino acids glycine, L-alanine, L-valine, and L-leucine only. No inference can be necessarily drawn about surfactants containing other types of amino acids such as threonine and serine, which contain extra heteroatoms, or phenylalanine that has an aromatic moiety.Item Habitat use patterns of newly settled southern flounder, paralichthys lethostigma, in Aransas–Copano Bay, Texas(Springer, 2008-10-31) Nañez-James, Suraida E.; Stunz, Gregory; Holt, Scott A.Southern flounder Paralichthys lethostigma populations have been declining in Texas during the past 25 years. Despite their economic importance, little is known about their juvenile habitat requirements. We examined habitat use patterns of newly settled southern flounder in three zones at varying distances from the Aransas Pass inlet in Aransas–Copano Bay by measuring densities using a beam trawl in replicate estuarine habitat types in each zone. Highest abundance occurred near the inlet in vegetated sandy areas and was lowest in nonvegetated muddy bottom in regions furthest from the inlet. We also examined a 25-year fisheries data set from Texas Parks and Wildlife Department to evaluate long-term spatiotemporal recruitment patterns in Aransas–Copano Bay. These data showed generally low recruitment during the past 25 years with highest abundance near the inlets. Our results support the importance of vegetated habitat types, especially those near tidal passes, and suggest a long-term decline in recruitment densities of southern flounder.Item Role of science-based and adaptive management in allocating environmental flows to the Nueces estuary, Texas, use(WIT Press, 2009-06) Montagna, Paul A.; Hill, Erin M.; Moulton, B.The Nueces River System has been subject to adaptive management since construction of the Choke Canyon Reservoir in 1982. A special condition required the City of Corpus Christi to provide not less than 185 million cubic meters (151,000 ac-ft) of water per year to the Nueces Estuary through a combination of spills, releases, and return flows to maintain ecological health and productivity of living marine resources. However, no releases were made and salinities in Nueces Bay increased to hypersaline conditions during the drought period of 1988–1990 and the estuary was inverted where fresher water entered the delta on high tides. In contrast, the bay historically supported populations of shrimp and oysters generally requiring salinities in the range of 10–20 ppt. Beginning in May 1990, the Texas Water Commission issued a series of Orders requiring the City to meet the special conditions contained in their water right permit and provide for freshwater inflows to the estuary. Since 1990, a series of restoration activities, monitoring and experimental studies, and Order amendments has resulted in a stakeholder driven process that increased environmental health while providing a sustainable water supply to the region. However, with climate change and continued development, more changes are likely to occur in the future. The lesson learned is that the goal of achieving consensus can occur with a blend and balance of science and a stakeholder decision process. Keywords: freshwater inflow, wetlands, marsh, shellfish, dams, water resources.Item The effect of boat propeller scarring intensity on genetic variation in a subtropical seagrass species(De Gruyter, 2009-12-15) Larkin, Patrick; Heideman, Krista L.; Burfeind, Dana; Stunz, Gregory; Larkin, Patrick; Heideman, Krista L.; Burfeind, Dana; Stunz, GregoryWe report here the effect of one form of disturbance, boat propeller scarring, on genetic variation in the subtropical seagrass Halodule wrightii. We developed an amplified fragment length polymorphism assay to measure genetic var-aition in plots representing four levels of scarring intensity: reference (0% scarring), low (1–5%), moderate (5–15%) and severe (>15%). Although we found severely scarred plots to have the lowest, and moderately scarred plots to have the highest, mean genetic diversity estimates (He,P), differences among scarring levels were found to be non-significant(as0.05). Analysis of molecular variance also showed no significant effect of scarring intensity. While propeller scar-ring can cause significant habitat loss, scarring intensities of up to 20% may not yet have seriously affected those factors (population size, flowering density, recruitment, gene flow)that strongly influence population genetic variation. The relatively recent occurrence of this type of disturbance, how-ever, could mean that any long-term effects have yet to detectedItem Seagrass response to wastewater inputs: Implementation of a seagrass monitoring program in two Texas estuaries(2011-02-25) Cammarata, KirkThe study protocol followed a recent proposal by Dunton and Pulich to the Seagrass Monitoring Work Group (Landscape Monitoring and Biological Indicators for Seagrass Conservation in Texas Coastal Waters, draft, Dunton et al. 2007) and included three components: 1) landscape monitoring using high resolution color aerial photography, 2) seagrass condition and water quality indicators, and 3) seagrass epiphyte fluorescence analysis. Findings from the third objective are presented here.Item Existence of a unique solution to a quasilinear elliptic equation(Elsevier, 2011-03-29) Denny, DianeThe purpose of this paper is to prove the existence of a unique classical solution u(x) to the quasilinear elliptic equation −∇ · (a(u)∇u) + v · ∇u = f , where u(x0) = u0 at x0 ∈ Ω and where n · ∇u = g on the boundary ∂Ω. We prove that if the functions a, f , v, g satisfy certain conditions, then a unique classical solution u(x) exists. Applications include stationary heat/diffusion problems with convection and with a source/sink, where the value of the solution is known at a spatial location x0 ∈ Ω, and where n · ∇u is known on the boundary.Item MERIS retrieval of water quality components in the turbid Albemarle Pamlico sound estuary, USA(MDPI, 2011-04-01) Sokoletsky, Leonid G.; Lunetta, Ross S.; Wetz, Michael S.; Paerl, Hans W.Two remote-sensing optical algorithms for the retrieval of the water quality components (WQCs) in the Albemarle-Pamlico Estuarine System (APES) were developed and validated for chlorophyll a (Chl). Both algorithms were semi-empirical because they incorporated some elements of optical processes in the atmosphere, water, and air/water interface. One incorporated a very simple atmospheric correction and modified quasi-single-scattering approximation (QSSA) for estimating the spectral Gordon’s parameter, and the second estimated WQCs directly from the top of atmosphere satellite radiance without atmospheric corrections. A modified version of the Global Meteorological Database for Solar Energy and Applied Meteorology (METEONORM) was used to estimate directional atmospheric transmittances. The study incorporated in situ Chl data from the Ferry-Based Monitoring (FerryMon) program collected in the Neuse River Estuary (n = 633) and Pamlico Sound (n = 362), along with Medium Resolution Imaging Spectrometer (MERIS) satellite imagery collected (2006–2009) across the APES; providing quasi-coinciding samples for Chl algorithm development and validation. Results indicated a coefficient of determination (R2) of 0.70 and mean-normalized root-mean-squares errors (NRMSE) of 52% in the Neuse River Estuary and R2 = 0.44 (NRMSE = 75 %) in the Pamlico Sound—without atmospheric corrections. The simple atmospheric correction tested provided on performance improvements. Algorithm performance demonstrated the potential for supporting long-term operational WQCs satellite monitoring in the APES.Item Differences between two estimates of air-sea turbulent heat fluxes over the Atlantic Ocean(AGU, 2011-09-23) Santorelli, A.; Pinker, R. T.; Bentamy, Anas; Katsaros, K. B.; Drennan, W. M.; Mestas Nuñez, Marcos; Carton, J. A.[1] Uncertainties in turbulent ocean-atmosphere heat flux estimates, both among the estimates and between them and ground truth, suggest that further comparisons are needed. We analyze estimates from the French Research Institute for Exploitation of the Sea (IFREMER) and the Woods Hole Oceanographic Institution's Objectively Analyzed air-sea Fluxes (WHOI OAFlux). The IFREMER products are based on satellite observations and the WHOI OAFlux ones on data from satellites, buoys, and ships assimilated into numerical analyses. We focus on the Atlantic sector (70°W–30°E, 45°S–45°N) during 1996–2005, where the variables that enter the bulk formulae for computing fluxes (wind speed, sea surface and air temperature, and specific humidity) can be evaluated against buoys in the Prediction and Research Moored Array in the Atlantic (PIRATA). Since WHOI assimilates PIRATA observations, we have added two independent buoy data sets: FETCH and ROMEO. To examine how each variable contributes to the difference between estimated and buoy fluxes, the method of Bourras (2006) is applied. His so-called Q terms showed that specific air humidity and air temperature contributed the most to the biases of IFREMER latent and sensible heat fluxes, respectively, at both independent buoys. For WHOI OAFlux products, deviations from FETCH values were mainly due to wind speed and sea surface temperature differences, while in comparison with ROMEO fluxes, WHOI OAFlux biases were primarily due to specific humidity and sea surface temperature estimates. Modified estimates of turbulent fluxes with the IFREMER approach using the 10 m specific humidity and air temperature products of Jackson et al. (2009) show significant improvement in three test cases at PIRATA buoys.Item Development of gene expression markers of acute heat-light stress in reef-building corals of the genus porites(PLOS ONE, 2011-10-26) Kenkel, Carly; Aglyamova, Galina; Alamaru, Ada; Bhagooli, Ranjeet; Capper, Roxana; Cunning, Ross; deVillers, Amanda; Haslun, Joshua; Hédouin, Laetitia; Keshavmurthy, Shashank; Kuehl, Kristin A.; Mahmoud, Huda; McGinty, Elizabeth S.; Montoya Maya, Phanor Hernando; Palmer, Caroline V.; Pantile, Raffaella; Sánchez, Juan A.; Schils, Tom; Silverstein, Rachel N.; Squiers, Logan B.; Tang, Pei-Ciao; Goulet, Tamar; Matz, Mikhail; Kenkel, Carly; Aglyamova, Galina; Alamaru, Ada; Bhagooli, Ranjeet; Capper, Roxana; Cunning, Ross; deVillers, Amanda; Haslun, Joshua; Hédouin, Laetitia; Keshavmurthy, Shashank; Kuehl, Kristin A.; Mahmoud, Huda; McGinty, Elizabeth S.; Montoya Maya, Phanor Hernando; Palmer, Caroline V.; Pantile, Raffaella; Sánchez, Juan A.; Schils, Tom; Silverstein, Rachel N.; Squiers, Logan B.; Tang, Pei-Ciao; Goulet, Tamar; Matz, MikhailCoral reefs are declining worldwide due to increased incidence of climate-induced coral bleaching, which will have widespread biodiversity and economic impacts. A simple method to measure the sub-bleaching level of heat-light stress experienced by corals would greatly inform reef management practices by making it possible to assess the distribution of bleaching risks among individual reef sites. Gene expression analysis based on quantitative PCR (qPCR) can be used as a diagnostic tool to determine coral condition in situ. We evaluated the expression of 13 candidate genes during heat-light stress in a common Caribbean coral Porites astreoides, and observed strong and consistent changes in gene expression in two independent experiments. Furthermore, we found that the apparent return to baseline expression levels during a recovery phase was rapid, despite visible signs of colony bleaching. We show that the response to acute heat-light stress in P. astreoides can be monitored by measuring the difference in expression of only two genes: Hsp16 and actin. We demonstrate that this assay discriminates between corals sampled from two field sites experiencing different temperatures. We also show that the assay is applicable to an Indo-Pacific congener, P. lobata, and therefore could potentially be used to diagnose acute heat-light stress on coral reefs worldwide.Item Static inflation and deflation pressure–volume curves from excised lungs of marine mammals(The Company of Biologists, 2011-11-15) Fahlman, Andreas; Loring, Stephen; Ferrigno, Massimo; Moore, Colby; Early, Greg; Niemeyer, Misty; Lentell, Betty; Wenzel, Frederic; Joy, Ruth; Moore, Michael J.Excised lungs from eight marine mammal species [harp seal (Pagophilus groenlandicus), harbor seal (Phoca vitulina), gray seal (Halichoerus grypush), Atlantic white-sided dolphin (Lagenorhynchus acutus), common dolphin (Delphinus delphis), Risso's dolphin (Grampus griseus), long-finned pilot whale (Globicephala melas) and harbor porpoise (Phocoena phocoena)] were used to determine the minimum air volume of the relaxed lung (MAV, N=15), the elastic properties (pressure–volume curves, N=24) of the respiratory system and the total lung capacity (TLC). Our data indicate that mass-specific TLC (sTLC, l kg–1) does not differ between species or groups (odontocete vs phocid) and agree with that estimated (TLCest) from body mass (Mb) by applying the equation: TLCest=0.135 Mb0.92. Measured MAV was on average 7% of TLC, with a range from 0 to 16%. The pressure–volume curves were similar among species on inflation but diverged during deflation in phocids in comparison with odontocetes. These differences provide a structural basis for observed species differences in the depth at which lungs collapse and gas exchange ceases.Item Estimated tissue and blood N2 levels and risk of decompression sickness in deep-, intermediate-, and shallow-diving toothed whales during exposure to naval sonar(Frontiers, 2012-05-10) Kvadsheim, Petter H; Miller, P. J. O.; Tyack, P. L.; Sivle, Lise Doksæter; Lam, F. P. A.; Fahlman, AndreasNaval sonar has been accused of causing whale stranding by a mechanism which increases formation of tissue N2 gas bubbles. Increased tissue and blood N2 levels, and thereby increased risk of decompression sickness (DCS), is thought to result from changes in behavior or physiological responses during diving. Previous theoretical studies have used hypothetical sonar-induced changes in both behavior and physiology to model blood and tissue N2 tension (PN2), but this is the first attempt to estimate the changes during actual behavioral responses to sonar. We used an existing mathematical model to estimate blood and tissue N2 tension (PN2) from dive data recorded from sperm, killer, long-finned pilot, Blainville’s beaked, and Cuvier’s beaked whales before and during exposure to Low- (1–2 kHz) and Mid- (2–7 kHz) frequency active sonar. Our objectives were: (1) to determine if differences in dive behavior affects risk of bubble formation, and if (2) behavioral- or (3) physiological responses to sonar are plausible risk factors. Our results suggest that all species have natural high N2 levels, with deep diving generally resulting in higher end-dive PN2 as compared with shallow diving. Sonar exposure caused some changes in dive behavior in both killer whales, pilot whales and beaked whales, but this did not lead to any increased risk of DCS. However, in three of eight exposure session with sperm whales, the animal changed to shallower diving, and in all these cases this seem to result in an increased risk of DCS, although risk was still within the normal risk range of this species. When a hypothetical removal of the normal dive response (bradycardia and peripheral vasoconstriction), was added to the behavioral response during model simulations, this led to an increased variance in the estimated end-dive N2 levels, but no consistent change of risk. In conclusion, we cannot rule out the possibility that a combination of behavioral and physiological responses to sonar have the potential to alter the blood and tissue end-dive N2 tension to levels which could cause DCS and formation of in vivo bubbles, but the actually observed behavioral responses of cetaceans to sonar in our study, do not imply any significantly increased risk of DCS.Item The relative roles of salinity stratification and nutrient loading in seasonal hypoxia in Corpus Christi Bay, Texas(2012-10-09) Nelson, Kevin K.; Montagna, Paul A.Hypoxia (low dissolved oxygen concentration) is known to occur in the southeast corner of Corpus Christi Bay, Texas, USA each summer since its discovery in 1988. In 2006, ongoing field research discovered that the hypoxia area has a greater extent spatially and temporally than previously thought. Although it was known that hypoxia was associated with salinity stratification, it was not until 2007 that it was discovered that salty water from both Oso Bay and Laguna Madre were contributing to this stratification. This is interesting because there are three wastewater treatment plants that empty into Oso Creek and to Oso Bay, so there is a source of nutrients as well as salt. The purpose of the current study was to determine the spatial and temporal extent of hypoxia, to explore the role of nutrients and bay currents in the formation and frequency of hypoxia, to determine what, if any role small rain events play in the formation of hypoxia, and to test the feasibility of disseminating the data collected in this study and others to the public via the use of a standardized database schema and web services. Hypoxia was found to begin as early as the first week of June, and occur as late as the last week of August, i.e. stops when wind stops. Hypoxic conditions can extend from Ward Island to Shamrock Island, and area estimated to cover 80 km2. Nutrient concentrations are not at high levels however, ammonium levels are higher in the hypoxic zone, likely due to anaerobic remineralization of organic matter. Even small-scale rain events appear to flush nutrients from Oso Bay however, this does not appear to affect hypoxia in Corpus Christi Bay. Differences in acoustic opacity, current velocity, and current direction, and salinity between the bottom waters and those above may all be contributing to stratification, known to cause hypoxia. Hypoxia also appears to be influenced by the fortnightly lunar cycle, bathymetry, and bottom composition. Attempts to transform data from this project into a standard database schema were successful. However, not all of the complexities of biological nomenclature, multivariate data structures, and laboratory information requirements could be met with the system under study.Item Changes in dive behavior during naval sonar exposure in killer whales, long-finned pilot whales, and sperm whales(Frontier, 2012-10-11) Sivle, Lise Doksæter; Kvadsheim, Petter H; Fahlman, Andreas; Lam, F. P. A.; Tyack, P. L.; Miller, P. J. O.Anthropogenic underwater sound in the environment might potentially affect the behavior of marine mammals enough to have an impact on their reproduction and survival. Diving behavior of four killer whales (Orcinus orca), seven long-finned pilot whales (Globicephala melas), and four sperm whales (Physeter macrocephalus) was studied during controlled exposures to naval sonar [low frequency active sonar (LFAS): 1–2 kHz and mid frequency active sonar (MFAS): 6–7 kHz] during three field seasons (2006–2009). Diving behavior was monitored before, during and after sonar exposure using an archival tag placed on the animal with suction cups. The tag recorded the animal's vertical movement, and additional data on horizontal movement and vocalizations were used to determine behavioral modes. Killer whales that were conducting deep dives at sonar onset changed abruptly to shallow diving (ShD) during LFAS, while killer whales conducting deep dives at the onset of MFAS did not alter dive mode. When in ShD mode at sonar onset, killer whales did not change their diving behavior. Pilot and sperm whales performed normal deep dives (NDD) during MFAS exposure. During LFAS exposures, long-finned pilot whales mostly performed fewer deep dives and some sperm whales performed shallower and shorter dives. Acoustic recording data presented previously indicates that deep diving (DD) is associated with feeding. Therefore, the observed changes in dive behavior of the three species could potentially reduce the foraging efficiency of the affected animals.Item Hyperspectral analysis of seagrass in Redfish Bay, Texas(2012-11-07) Wood, John S.; James Gibeaut; John W. TunnellRemote sensing using multi- and hyperspectral imaging and analysis has been used in resource management for quite some time, and for a variety of purposes. In the studies to follow, hyperspectral imagery of Redfish Bay is used to discriminate between species of seagrasses found below the water surface. Water attenuates and reflects light and energy from the electromagnetic spectrum, and as a result, subsurface analysis can be more complex than that performed in the terrestrial world. In the following studies, an iterative process is developed, using ENVI image processing software and ArcGIS software. Band selection was based on recommendations developed empirically in conjunction with ongoing research into depth corrections, which were applied to the imagery bands (a default depth of 65 cm was used). Polygons generated, classified and aggregated within ENVI are reclassified in ArcGIS using field site data that was randomly selected for that purpose. After the first iteration, polygons that remain classified as `Mixed' are subjected to another iteration of classification in ENVI, then brought into ArcGIS and reclassified. Finally, when that classification scheme is exhausted, a supervised classification is performed, using a `Maximum Likelihood' classification technique, which assigned the remaining polygons to the classification that was most like the training polygons, by digital number value. Producer's Accuracy by classification ranged from 23.33 % for the `MixedMono' class to 66.67% for the `Bare' class; User's Accuracy by classification ranged from 22.58% for the `MixedMono' class to 69.57% for the `Bare' classification. An overall accuracy of 37.93% was achieved. Producers and Users Accuracies for Halodule were 29% and 39%, respectively; for Thalassia, they were 46% and 40%. Cohen's Kappa Coefficient was calculated at .2988. We then returned to the field and collected spectral signatures of monotypic stands of seagrass at varying depths and at three sensor levels: above the water surface, just below the air/water interface, and at the canopy position, when it differed from the subsurface position. Analysis of plots of these spectral curves, after applying depth corrections and Multiplicative Scatter Correction, indicates that there are detectable spectral differences between Halodule and Thalassia species at all three positions. Further analysis indicated that only above-surface spectral signals could reliably be used to discriminate between species, because there was an overlap of the standard deviations in the other two positions. A recommendation for wavelengths that would produce increased accuracy in hyperspectral image analysis was made, based on areas where there is a significant amount of difference between the mean spectral signatures, and no overlap of the standard deviations in our samples. The original hyperspectral imagery was reprocessed, using the bands recommended from the research above (approximately 535, 600, 620, 638, and 656 nm). A depth raster was developed from various available sources, which was resampled and reclassified to reflect values for water absorption and water scattering, which were then applied to each band using the depth correction algorithm. Processing followed the iterative classification methods described above. Accuracy for this round of processing improved; overall accuracy increased from 38% to 57%. Improvements were noted in Producer's Accuracy, with the `Bare' vi classification increasing from 67% to 73%, Halodule increasing from 29% to 63%, Thalassia increasing slightly, from 46% to 50%, and `MixedMono' improving from 23% to 42%. User's Accuracy also improved, with the `Bare' class increasing from 69% to 70%, Halodule increasing from 39% to 67%, Thalassia increasing from 40% to 7%, and `MixedMono' increasing from 22.5% to 35%. A very recent report shows the mean percent cover of seagrasses in Redfish Bay and Corpus Christi Bay combined for all species at 68.6%, and individually by species: Halodule 39.8%, Thalassia 23.7%, Syringodium 4%, Ruppia 1% and Halophila 0.1%. Our study classifies 15% as `Bare', 23% Halodule, 18% Thalassia, and 2% Ruppia. In addition, we classify 5% as `Mixed', 22% as `MixedMono', 12% as `Bare/Halodule Mix', and 3% `Bare/Thalassia Mix'. Aggregating the `Bare' and `Bare/species' classes would equate to approximately 30%, very close to what this new study produces. Other classes are quite similar, when considering that their study includes no `Mixed' classifications. This series of research studies illustrates the application and utility of hyperspectral imagery and associated processing to mapping shallow benthic habitats. It also demonstrates that the technology is rapidly changing and adapting, which will lead to even further increases in accuracy. Future studies with hyperspectral imaging should include extensive spectral field collection, and the application of a depth correction.Item Linking ecological function and ecosystem service values of estuarine habitat types associated with a barrier island system(2012-11-15) Francis, Jeffrey M.; Fox, Joe M.; David W. YoskowitzEcosystem services are benefits humans receive as a function of natural processes. Many current studies seek to express these benefits as an economic value per unit of habitat type without quantifying the ecological functions that allow for the provision of ecosystem services. This study is designed to model each habitat type in an effort to explicitly link the major estuarine habitat types of Mustang Island (oyster reefs, seagrass meadows, and intertidal salt marsh) to their contribution to Nitrogen cycling services. First, a dynamic biomass model of each foundational species was created using Simile, a declarative modeling framework. Second, a monthly snapshot of Nitrogen captured in living biomass was used to quantify the contribution of each species to the Nitrogen cycling services. Finally, the amount of Nitrogen captured in living biomass was valued using a replacement cost approach. An effort was also made to link the provision of recreational fishing services provided by each aforementioned habitat type by partitioning travel costs and license sales weighted by the density of fish found in each habitat type. It was found that oyster reefs of Mustang Island contribute $173,000 yr-1, seagrass meadows contribute $12,054,095 yr-1, and intertidal salt marshes contribute $5,242,755 yr-1 in potential Nitrogen cycling services. The total value of recreational fishing services within the study site was calculated to be $83.8 million dollars yr-1. A portion of the total value was then attributed to each habitat type: Marsh edge: $2 million; Seagrass meadows: $81 million; and Oyster: $81,000 thousand. These efforts have been made to translate ecological function into economic benefit to improve communication among a wide variety of stakeholders that are more likely to understand economic value. Further refinement of both the models and the economic data necessary to support them, will have the potential to improve the applicability and results of these tools. These results, and the modeling framework through which they are calculated, provide a platform to evaluate management relevant scenarios in a simple, flexible manner that may be adjusted and transferred to other study sites given appropriate local data.