Mesohaline estuarine regions in Louisiana play an important role in coastal ecosystems. To begin to understand how nektonic species and communities respond to environmental variables before habitat modification, I examined patterns of habitat use by fishes and decapod crustaceans in a seemingly pristine mesohaline system that drains into Bay Batiste, southeastern Louisiana. The study area was focused on a relatively unaltered core saltmarsh complex drained by intertidal and subtidal streams and it was representative of a larger surrounding system in terms of nekton community structure and associated environmental variables. Stratified monthly sampling (February November 2004) along a stream-order gradient examined changes in nekton abundance, species richness, and community structure within the study area. Analyses were based on a microhabitat approach used to characterize nekton responses to seasonal and spatial gradients of water depth, temperature, dissolved oxygen concentration, salinity, turbidity, bottom slope, stream width and distance to mouth. In 81 seine samples, 3757 individuals from 30 taxa were collected. Daggerblade grass shrimp was the numerically dominant species (72.7 %), followed by penaeid shrimp (13.4 %), bay anchovy (1.7 %) and inland silverside (1.7 %). Univariate ANOVAs detected the significant effects of stream order and season on nekton abundance and associated environmental variables. Greater numbers of nekton were mainly distributed in streams of low order. Kendalls W tests of ranked abundances indicated that nekton community structure was concordant among stream orders but not among seasons. Seasonal and spatial differences of environmental variables across stream orders and among seasons were attributed to the geomorphological and hydrological characteristics of the study area. A factor analysis resolved eight environmental variables into four orthogonal axes that explained 80 % of environmental variation. Factor one was interpreted as a stream-order axis, Factor two as a morphological axis, Factor three as a seasonal axis, and Factor four as a salinity axis. Differences in use of the four-dimensional factor space by dominant species reflected habitat selection, species residency status and seasonality of recruitment.

The development of reliable tools for identifying essential fish habitat (EFH) has proven problematic. Knowledge of the distribution and biomass of fishes over discrete habitat types is a prerequisite for effective use of EFH in the management of important commercial and recreational fish species. Resolution of the influence of habitat type and environmental factors on the distribution of fishes is confounded by limitations of traditional sampling gears. To date, hydroacoustic technology has been widely accepted as a tool for surveying fishery resources; however few studies have implemented acoustics in ultra shallow (<2 m) coastal waters. Efforts should be made to utilize hydroacoustics for quantifying changes in fish distributions within estuarine environments given the benefits provided through acoustic technology (e.g. ease of deployment, reduced sampling effort, and non-invasive sampling attributes). A technique was developed for acoustically sensing fishes in the shallow, turbid waters of Barataria Bay, Louisiana. A robust and lightweight remotely-controlled transducer platform was designed for deploying acoustic gear. Sources of scattering within the bay were identified through a series of exclosure net experiments designed to quantify potential effects of plankton and suspended solids on acoustic scattering. Analysis filters were developed to reduce the effects of bubble-induced noise, often observed during periods when wind speeds were greater than 4.5 m s^-1. Side-aspect acoustic target strength-length and target strength-weight relationships were derived for tethered individuals of bay anchovy (Anchoa mitchilli) and Gulf menhaden (Brevoortia patronus), with best fit models incorporating data from both species at the lateral perspective. Greater mean fish biomass and fish size were associated with higher salinity and oyster shell habitat in Barataria Bay when compared to nearby soft-bottom habitats. Results of acoustic mobile surveys of the Freeport Sulphur Mine Artificial Reef are presented and illustrate the flexibility and adaptability of the acoustic system for monitoring spatial and temporal changes in fish distributions. I conclude that acoustics can be successfully implemented as a complementary survey technique and can serve as a valuable tool to fishery managers for quantifying fish distributions associated with estuarine habitats.

Spartina alterniflora is a salt marsh macrophyte found from Canada to the Gulf of Mexico which often provides the dominant plant cover. Although S. alterniflora is well known for its high aboveground productivity, fifty to ninety percent of the total plant production occurs belowground. No previous studies address the seasonal variation of belowground biomass or the response of above-and belowground biomass to nutrients at the southern limits of its U. S. range. The objectives of this study were to: 1) document the seasonal variability of its above- and belowground biomass and test for responses to various combinations of N, P, and Fe supplements, 2) test the usefulness and variability of three functional indicators of nutrient use efficiency, resorption efficiency, resorption proficiency, and, 3) compare nutrient limitation controls in East coast and Gulf of Mexico salt marshes. Various combinations of N additions resulted in more aboveground biomass, higher stem densities and longer stem lengths, but had no effect on the amount of belowground biomass. No change in the aboveground biomass observed when P was added, but there was a decrease in the live belowground biomass. The average N : P molar ratios in the above- and belowground tissues, and three resorption indices supported the hypothesis that the accumulation of biomass aboveground was limited by N, and by P belowground. Higher soil respiration and a lower Eh are anticipated additional soil property changes with nutrient enrichment. The observations from these field trials formed a unified conclusion, which is that the widespread effects of coastal eutrophication leads to lower root and rhizome biomass, belowground production, and organic matter accumulation. The cumulative effects of increased nutrient loadings to salt marshes may be to decrease soil elevation and accelerate the conversion of emergent plant habitat to open water, particularly at the lower elevation range of the plant. These results support management actions supporting coastal marsh conservation through: 1) reducing nutrient loading to coastal zones and not diverting more nutrients to coastal marshes, 2) solving water quality problems with a multiple nutrient approach, and, 3) choosing monitoring metrics based on both belowground and aboveground plant production.

In the cycle of delta growth and decay, peat-forming wetlands span a time and space continuum. Later in the delta cycle, freshwater floating marshes become increasingly removed from external sediment subsidy and internal nutrient cycling controls plant productivity and organic matter accumulation. An interesting question is whether increased external nutrient loading can affect the basic processes that lead to peat formationplant production and organic matter decomposition. I conducted several field studies to understand whether belowground organic matter accumulation and decomposition were affected with increased nutrient exposure; in addition, the plant community was monitored over three years. A laboratory soil respiration experiment was run to determine potential limiting nutrients to microbial activity. After two years, there was a reduction of total belowground organic matter accumulation with increased nutrients; this partially resulted from reduced belowground root deposition coupled with accelerated root decomposition. This reduction in belowground accumulation, however, may be related also to the disappearance of a common plant of the community following fertilization, and not necessarily from a phenotypic shift in the allocation pattern by the dominant plant species. Fertilization accounted for an approximate doubling in aboveground biomass, accompanied by decreased stem density, and decreased species richness. Compared to other species, the grass, maidencane (Panicum hemitomon) responded most positively to increased nutrient availability at both sites, while at one site goldenrod (Solidago sempervirens) eventually captured a significant proportion of biomass. Nutrient resorption efficiency of nitrogen (N) and phosphorus (P) were both decreased with increased fertility. The degree of N- or P-limitation observed across coastal populations of P. hemitomon reflect the composite influences of site geology, water source, fire frequency, and the more conservative cycling of P compared to N. Plant community nutrient limitation may not be a reliable predictor of the type of nutrient limitation to soil microbes. Floating marshes have developed and are sustained under nutrient restricted conditions compared to other coastal marshes. Although floating marshes may function as nutrient sinks, a change in community and plant allocation pattern can be predicted with increased nutrient enrichment of these wetland types.

The primary impediment to the recovery of Gulf of Mexico (GOM) red snapper is believed to be high levels of bycatch of age 0 and age 1 individuals in shrimp trawls. Thus, conservation of GOM red snapper involves evaluating both habitat-specific function and effects of shrimp trawls on red snapper and the associated benthic ecosystem. The two goals of this study were to evaluate the effects commercial shrimp trawls have on juvenile red snapper life history parameters, on associated fish and invertebrate communities and their habitat, and to identify essential fish habitat (EFH) for red snapper by applying all four data quality levels specified by the National Marine Fisheries Service. Sampling with a suite of gear types occurred during quarterly cruises over a two-year period on the northern Gulf of Mexico continental shelf. Presence of commercial shrimp trawls had negative impacts on the benthic ecosystem at large. Red snapper were found to have truncated size distributions, slower growth rates in the fall, higher mortality rates, lower production potential, and different feeding dynamics, as revealed by differences in ä15N and ä34S, over habitats exposed to trawling. Differences in biotic communities, diversity indices, size structure, and habitat characteristics were also found between similar habitats in trawled versus non-trawled areas. Ontogenetic habitat shifts from low to higher relief habitats with increasing size and age were found for red snapper. Shell-rubble and reef habitats may be important for red snapper by providing protection from predators; however, the sand and mud habitat appears to be the most important for enhancing production and early life survival of age 0 fish based upon faster daily growth rates and higher production potential. Results of this study indicate the presence of commercial shrimp trawling negatively impacts the benthic ecosystem and post-settlement processes acting on age 0 red snapper. All habitats sampled in this study are important during some portion of the life history of red snapper. Thus, if shrimp closures are proposed in the GOM to enhance survival of age 0 and age 1 red snapper, then all habitat types sampled in this study will need to be protected.

With marshes deteriorating rapidly across the Louisiana coast, the role of seagrasses in sustaining fisheries has come into question. Seagrasses are known to shelter small fish from larger predators. Seagrasses also act as a foraging ground for commercially important species, including spotted seatrout. Thirty samples, fifteen from seagrass habitats and fifteen from bare substrate habitats, were collected inside Biloxi Marsh using a drop sampler in May 2005. After the passage of Hurricanes Cindy and Katrina on July 6, 2005 and August 29, 2005, respectively, the seagrasses in Biloxi Marsh were either uprooted, buried, or both. The May 2005 sites were re-sampled in August 2005 and May 2006 for comparison of pre- and post-hurricane communities. Multidimensional Scaling (MDS) analysis, followed by MANOVA was used to assess overall community structure and species composition, whereas canonical correlation was used to assess the influence of environmental variables on communities. Results show differences in seagrass and bare substrate communities prior to hurricane passage in May 2005. However, post-Cindy, the sites with remaining seagrass resembled the seagrass sites of May 2005, while those without seagrass resembled the bare sites of May 2005. After Cindy, canonical correlation analysis showed that the variables of bottom type, habitat type, month, salinity, turbidity, dry weight of seagrasses, Farfantepenaeus aztecus, Lucania parva, Palaemonetes pugio and Syngnathus scovelli loaded heavily on the first canonical variable, while habitat type, month, substrate, and Sphoeroides parvus loaded heavily on the second. Post-Katrina, all sites were bare, and thus resembled the bare substrate sites of May 2005. Post-Katrina canonical correlation revealed heavy loadings of bottom type, habitat type, year, salinity, dissolved oxygen, turbidity, dry weight, Anchoa mitchilli, Lucania parva, Mysidopsis spp., Palaemonetes pugio, and Syngnathus scovelli. Changes in community structure and species composition observed after the passage of Cindy and Katrina occurred only in seagrass stations that suffered either removal of seagrasses, influx of salt water from storm surges, or both. Additionally, dry weight of seagrasses and/or habitat type were the variables that loaded most heavily on the canonical variables, indicating that presence of seagrasses was the main factor leading to observed changes in community.

Developing organism-based metrics for assessing habitat quality is an important tool in conservation and restoration of aquatic habitats. The use of the RNA:DNA ratio as an early indicator of habitat effects on growth of nekton species has been suggested, but requires species-specific laboratory assessment prior to field application. We used food availability in laboratory treatments to simulate differences in habitat quality. Wild Gobiosoma bosc eggs were collected using nest-traps constructed of PVC pipe. Eggs from several different nests collected in the field were hatched in the lab, yielding larvae that were randomly assigned to three feeding treatments in two replicate tanks per treatment. Larvae were fed rotifers, Brachionus plicatilis, at densities of 20, 200, or 1200 l-1, in two trials lasting 10 and 8 days. Prey concentrations were measured every 8 hours and adjusted to nominal prey densities. One to five individuals from each tank, totaling 699 larvae, were sampled daily for nucleic acids. Wild larvae were collected using a light trap, and individuals were sampled identically to laboratory-reared fish to allow direct comparisons of growth and nucleic acid concentrations. Experimental fish exhibited significantly higher growth and lower mortality with increasing prey concentration. RNA:DNA ratios declined with age, length, and dry weight (DW) in all treatments. Wild larvae exhibited similar trends in nucleic acid accumulation as laboratory-reared fish. Ratios were lower in fish from higher prey concentrations when related to age, but showed no differences when related to SL, and were higher at higher prey concentration when related to DW. RNA:DNA ratios did not accurately reflect growth rate magnitudes (G d-1), but trends in growth and RNA:DNA were positively correlated. DNA:DW ratios proved to be a more accurate index of nutritional condition. I hypothesize that inherent growth patterns in larval Gobiosoma bosc largely prevent RNA:DNA from accurately reflecting nutritional condition, which has broad implications for use of this index in the field.

Matrix projection models and individual-based models (IBM) are commonly used for the analysis and management of fish populations. Matrix models break down the population into age or stage classes, while IBMs track individuals. I perform a series of quantitative comparisons between the predictions of the two modeling approaches using the IBM as the standard of comparison to demonstrate when individual variation, species interactions, and spatial heterogeneity adversely affect matrix model performance. I first evaluate the matrix approach for predicting yellow perch population responses when perch are involved in size-specific predator-prey interactions with walleye. I created density-dependent and stochastic age-structured and stage-within-age matrix models from an Oneida Lake walleye-yellow perch IBM, and then changed perch survival rates within the matrix models and IBM and compared their predicted responses. The matrix models simulated yellow perch responses reasonably well when density-dependent YOY survival was correctly defined. At least 20 years of data (IBM output) were needed to correctly estimate the density-dependent relationships in the matrix models. Second, I developed a 2-species matrix model by linking the elements between perch and walleye matrix models. The 2-species model simulated yellow perch prey responses reasonably well, but was unable to correctly predict walleye predator responses. Third, I developed a new IBM that simulated a 6-species tidal marsh community on a fine-scale spatial grid of habitat cells. The IBM was used to scale individual-level effects of lowered dissolved oxygen and habitat degradation to population-level responses, and used to estimate relatively simple stage-based matrix models for grass shrimp and gulf killifish populations. Equilibrium analysis of the simple matrix models was insufficient for predicting population responses. This study showed that stochastic, density-dependent matrix projection models were able to mimic density- dependent survival processes and species interactions relatively well, while equilibrium analysis of simple matrix models was inadequate. The matrix approach consistently had trouble estimating density-dependent and inter-specific growth relationships that were important for accurate model predictions. I recommend the use of IBMs and relatively complicated matrix models (stage-within-age, stochastic, density-dependent, multispecies) for simulation of fish population and community dynamics.

Water quality in the Chesapeake Bay and the Patuxent River has decreased since the 1950s due to an increase in nutrient loadings. Increased nutrient loads have caused an increase in the extent and duration of hypoxic conditions. Restoration via large-scale reductions in nutrient loadings is now underway. How reducing nutrient loadings will affect water quality is well predicted; however the effect on fish is generally unknown as most water quality models do not include trophic levels higher than zooplankton. I combined two water quality models with bay anchovy models (Anchoa mitchilli) to examine the effects of changes in nutrient loadings on anchovy survival and growth. An individual-based predation model was statically linked to Patuxent River watershed land-use and water quality models, and used to simulate the effects of changes in watershed land-use, Chesapeake Bay boundary condition nutrient loadings, and water year types on the summertime survival of daily anchovy egg and larval cohorts. I found that changes in Patuxent watershed land-use had little effect on egg and larval survival, while reduced nutrient loadings at the Chesapeake Bay boundary condition increased egg survival but reduced larval survival in June. The second analysis dynamically coupled a spatially-explicit, individual-based population dynamics model of juvenile and adult anchovy to the 3-dimensional Chesapeake Bay water quality model. Growth rates of individual anchovy within water quality model cells were calculated using a bioenergetics equation. Zooplankton densities from the water quality model provided prey for anchovy consumption, and anchovy consumption was an additional mortality term on zooplankton. Anchovy mortality was size-dependent. Anchovy movement depended on water temperature, dissolved oxygen, and zooplankton concentrations. Multi-year simulations with fixed annual recruitment were performed under decreased, baseline, and increased nutrient loadings scenarios. Increasing nutrient loadings had small effects on survival, but increased anchovy growth and therefore biomass. Anchovy growth exhibited compensatory density dependence. The results of both analyses showed that anchovy responses to changed nutrient loadings were complex and depended on life stage. Full-life cycle, spatially-explicit population models that are dynamically coupled to water quality models are needed to truly predict the effects of changes in nutrient loadings on fish populations.

Channel networks in tidal marshes serve as conduits for the exchange of water between the estuary and the marsh surface and form the spatial structure that regulates the flow of organisms, materials, and energy throughout the marsh system. Canal dredging creates channels with distinct linear shapes, and the artificial levee created from the dredged material creates âspoil banksâ along either side of the channel edge. Differences in morphology and adjacent marsh surface elevation between natural and dredged channel systems have not been well quantified, but may have important implications for the functioning of tidal channels as habitat for marsh-dependent species. I used GIS methods commonly applied to terrestrial landscape patterns, Light Detection and Ranging (LiDAR) data, and aerial orthophotographs to examine differences in the shape complexity of natural and dredged channel networks and to compare the elevation of the marsh adjacent to natural and dredged channels and productive and non-productive oil and gas wells in a tidal salt marsh in Louisiana. I examined the distribution of Spartina alterniflora, Geukensia demissa demissa, and Littoraria irrorata in relation to channel morphology, soil properties and elevation of the marsh edge at natural creeks, dredged canals, and open bay edges in order to correlate landscape patterns with ecological processes. Dredged canal networks were significantly less complex in shape. The elevation of the marsh within 30 m of the channel edge was highest along dredged channels. The marsh at distances greater than 30 m from dredged canals appears to be more broken up, but not lower in elevation than in natural systems. Densities of S. alterniflora and G. demissa were lower, and soil and leaf nitrogen were less in marsh adjacent to dredged canals. The age distribution of G. demissa populations provided evidence that structural differences between natural creeks and dredged canal systems influence the recruitment, growth, and mortality of mussels. This work demonstrates that landscape scale changes to tidal marshes have the potential to alter ecological processes at the microhabitat scale. Dredged canals may reduce the growth and productivity of plants and animals that are critical to maintaining coastal Louisianans marshes.