Fate and effects of drilling wastes in a shallow estuarine mesocosm

To address concerns expressed about the possible effect of drilling mud discharges on shallow, low-energy estuarine ecosystems, a 12 month study was designed to detect alterations in water quality and sediment geochemistry. Each drilling mud used in the study and sediments from the study site were analyzed in the laboratory for chemical and physical characteristics. Potential water quality impacts were simulated by the EPA-COE elutriation test procedure. Mud toxicity was measured by acute and chronic bioassays with Mysidopsis bahia, Mercenaria mercenaria, and Nereis virens.^ For the field study, a relatively pristine, shallow (1.2 m) estuary (Christmas Bay, TX) without any drilling activity for the last 30 years was chosen for the study site. After a three month baseline study, three stations were selected. Station 1 was an external control. At each treatment station (2, 3), mesocosms were constructed to enclose a 3.5 m$\sp3$ water column. Each treatment station included an internal control site also. Each in situ mesocosm, except the controls, was successively dosed at a mesocosm-specific dose (1:100; 1:1,000; or 1:10,000 v/v) with 4 field collected drilling muds (spud, nondispersed, lightly-treated, and heavily-treated lignosulfonate) in sequential order over 1.5 months. Twenty-four hours after each dose, water exchange was allowed until the next treatment. Station 3 was destroyed by a winter storm. After the last treatment, the enclosures were removed and the remaining sites monitored for 6 months. One additional site was similarly dosed (1:100 v/v) with clean dredged sediment from Christmas Bay for comparison between dredged sediments and drilling muds.^ Results of the analysis of the water samples and field measurements showed that water quality was impacted during the discharges, primarily at the highest dose (1:100 v/v), but that elevated levels of C, Cr (T,F), Cr$\sp{+3}$ (T, F), N, Pb, and Zn returned to ambient levels before the end of the 24 hour exposure period or immediately after water exchange was allowed (Al, Ba(T), Chlorophyll ABC, SS, %T). Barium, from the barite, was used as a geochemical tracer in the sediments to confirm estimated doses by mass balance calculations. Barium reached a maximum of 166x background levels at the high dose mesocosm. Barium levels returned to ambient or only slightly elevated levels at the end of the 6 month monitoring period due to sediment deposition, resuspension, and bioturbation. QA/QC results using blind samples consisting of lab standards and spiked samples for both water and sediment matrices were within acceptable coefficients of variation.^ In order to avoid impacts on water quality and sediment geochemistry in a shallow estuarine ecosystem, this study concluded that a minimal dilution of 1:1,000 (v/v) would be required in addition to existing regulatory constraints. ^

Proposed estuarine sanctuary grant award for Padilla Bay, Skagit County, Washington, to State of Washington /

At head of title: United States Department of Commerce draft environmental impact statement.

Physiological performance measures and tolerance limits of estuarine indicator species in south Florida

Current water management practices in South Florida have negatively impacted many species inhabiting Florida Bay. Variable and high salinity has been identified as a key stressor in these estuaries. The Comprehensive Everglades Restoration Plan (CERP) includes water redistribution projects that will restore natural freshwater flows to northeastern Florida Bay. My studies focused on the following central theme and hypotheses: Biological performance measures (i.e., growth, reproduction, survival), behavior (i.e., habitat preference and locomotor behavior) and diversity of estuarine fish will be controlled by changes in salinity and water quality that will occur as a result of the restoration of freshwater flow to the bay. A series of acute and subchronic physiological toxicity studies were conducted to determine the effects of salinity changes on the life stages (embryo/larval, juvenile, adult) and fecundity of four native estuarine fish (Cyprinodon variegatus, Floridichthys carpio, Poecilia latipinna, and Gambusia holbrooki). Fish were exposed to a range of salinity concentrations (freshwater to hypersaline) based on salinity profiles in the study areas. Growth (length, weight) and survival were measured. Salinity trials included both rapid and gradual change events. Results show negative effects of acute, abrupt salinity changes on fish survival, development and reproductive success as a result of salinity stress. Other studies targeted reproduction and critical embryo-larval/neonate development as key areas for detecting long-term population effects of salinity change in Florida Bay. Adults of C. variegates and P. latipinna were also examined for behavioral responses to pulsed salinity changes. These responses include changes in swimming performance, locomotor behavior and zone preference. Finally, an ecological risk assessment was conducted for adverse salinity conditions in northeastern Florida Bay. Using the U.S. EPA's framework, the risk to estuarine fish species diversity was assessed against regional salinity profiles from a 17-year database. Based on the risk assessment, target salinity profiles for these areas are recommended for managers.^

Spatial patterns of fish communities along two estuarine gradients in southern Florida

In tropical and subtropical estuaries, gradients of primary productivity and salinity are generally invoked to explain patterns in community structure and standing crops of fishes. We documented spatial and temporal patterns in fish community structure and standing crops along salinity and nutrient gradients in two subtropical drainages of Everglades National Park, USA. The Shark River drains into the Gulf of Mexico and experiences diurnal tides carrying relatively nutrient enriched waters, while Taylor River is more hydrologically isolated by the oligohaline Florida Bay and experiences no discernable lunar tides. We hypothesized that the more nutrient enriched system would support higher standing crops of fishes in its mangrove zone. We collected 50 species of fish from January 2000 to April 2004 at six sampling sites spanning fresh to brackish salinities in both the Shark and Taylor River drainages. Contrary to expectations, we observed lower standing crops and density of fishes in the more nutrient rich tidal mangrove forest of the Shark River than in the less nutrient rich mangrove habitats bordering the Taylor River. Tidal mangrove habitats in the Shark River were dominated by salt-tolerant fish and displayed lower species richness than mangrove communities in the Taylor River, which included more freshwater taxa and yielded relatively higher richness. These differences were maintained even after controlling for salinity at the time of sampling. Small-scale topographic relief differs between these two systems, possibly created by tidal action in the Shark River. We propose that this difference in topography limits movement of fishes from upstream marshes into the fringing mangrove forest in the Shark River system, but not the Taylor River system. Understanding the influence of habitat structure, including connectivity, on aquatic communities is important to anticipate effects of construction and operational alternatives associated with restoration of the Everglades ecosystem.

Dynamics of ecosystem metabolism and flocculent detritus transport in estuarine Taylor River

Estuaries and estuarine wetlands are ecologically and societally important systems, exhibiting high rates of primary production that fuel offshore secondary production. Hydrological processes play a central role in shaping estuarine ecosystem structure and function by controlling nutrient loading and the relative contributions of marine and terrestrial influences on the estuary. The Comprehensive Everglades Restoration Plan includes plans to restore freshwater delivery to Taylor Slough, a shallow drainage basin in the southern Everglades, ultimately resulting in increased freshwater flow to the downstream Taylor River estuary. The existing seasonal and inter-annual variability of water flow and source in Taylor River affords the opportunity to investigate relationships between ecosystem function and hydrologic forcing. Estimates of aquatic ecosystem metabolism, derived from free-water, diel changes in dissolved oxygen, were combined with assessments of wetland flocculent detritus quality and transport within the context of seasonal changes in Everglades hydrology. Variation in ecosystem gross primary production and respiration were linked to seasonal changes in estuarine water quality using multiple autoregression models. Furthermore, Taylor River was observed to be net heterotrophic, indicating that an allochthonous source of carbon maintained ecosystem respiration in excess of autochthonous primary production. Wetland-derived detritus appears to be an important vector of energy and nutrients across the Everglades landscape; and in Taylor River, is seasonally flushed into ponded segments of the river where it is then respired. Lastly, seasonal water delivery appears to govern feedbacks regulating water column phosphorus availability in the Taylor River estuary.

Does landscape context affect habitat value? The importance of seascape ecology in back-reef systems

Seascape ecology provides a useful framework from which to understand the processes governing spatial variability in ecological patterns. Seascape context, or the composition and pattern of habitat surrounding a focal patch, has the potential to impact resource availability, predator-prey interactions, and connectivity with other habitats. For my dissertation research, I combined a variety of approaches to examine how habitat quality for fishes is influenced by a diverse range of seascape factors in sub-tropical, back-reef ecosystems. In the first part of my dissertation, I examined how seascape context can affect reef fish communities on an experimental array of artificial reefs created in various seascape contexts in Abaco, Bahamas. I found that the amount of seagrass at large spatial scales was an important predictor of community assembly on these reefs. Additionally, seascape context had differing effects on various aspects of habitat quality for the most common reef species, White grunt Haemulon plumierii. The amount of seagrass at large spatial scales had positive effects on fish abundance and secondary production, but not on metrics of condition and growth. The second part of my dissertation focused on how foraging conditions for fish varied across a linear seascape gradient in the Loxahatchee River estuary in Florida, USA. Gray snapper, Lutjanus griseus, traded food quality for quantity along this estuarine gradient, maintaining similar growth rates and condition among sites. Additional work focused on identifying major energy flow pathways to two consumers in oyster-reef food webs in the Loxahatchee. Algal and microphytobenthos resource pools supported most of the production to these consumers, and body size for one of the consumers mediated food web linkages with surrounding mangrove habitats. All of these studies examined a different facet of the importance of seascape context in governing ecological processes occurring in focal habitats and underscore the role of connectivity among habitats in back-reef systems. The results suggest that management approaches consider the surrounding seascape when prioritizing areas for conservation or attempting to understand the impacts of seascape change on focal habitat patches. For this reason, spatially-based management approaches are recommended to most effectively manage back-reef systems.

Relating Freshwater Flow with Estuarine Water Quality in the Southern Everglades Mangrove Ecotone

Florida Bay is more saline than it was historically, and reduced freshwater flows may lead to more phosphorus inputs to the mangrove ecotone from the marine end-member. This is important given plans to restore freshwater flow into eastern Florida Bay. We investigated the relationships between salinity, nutrients, and hydrologic variables in the mangrove ecotone of Taylor Slough. We expected that total phosphorus (TP) would increase with salinity, reflecting a downstream marine source, while total nitrogen (TN) would increase with flow in the mangrove ecotone. Despite expectations of increased flows improving the ecological health of lower Taylor Slough and Florida Bay, total nitrogen (TN) and total phosphorus (TP) dynamics may shift in response to new conditions of flow and salinity as well as organic carbon, N, and P availability. Our results showed that TP concentrations are more discharge-driven while TN is more variable and potentially derived from different sources along the flow path from the freshwater Everglades marshes to Florida Bay. Increased flow of freshwater through Taylor Slough will likely decrease TP concentrations in this historically oligotrophic and P-limited ecosystem. However, more studies along the mangrove ecotone is needed to understand how increased flows will affect nitrogen dynamics relative to phosphorus.

Spatial and temporal interaction between sediment and microphytobenthos in a temperate estuarine macro-intertidal bay

Intertidal flats of the estuarine macro-intertidal Baie des Veys (France) were investigated to identify spatial features of sediment and microphytobenthos (MPB) in April 2003. Gradients occurred within the domain, and patches were identified close to vegetated areas or within the oyster-farming areas where calm physical conditions and biodeposition altered the sediment and MPB landscapes. Spatial patterns of chl a content were explained primarily by the influence of sediment features, while bed elevation and compaction brought only minor insights into MPB distribution regulation. The smaller size of MPB patches compared to silt patches revealed the interplay between physical structure defining the sediment landscape, the biotic patches that they contain, and that median grain-size is the most important parameter in explaining the spatial pattern of MPB. Small-scale temporal dynamics of sediment chl a content and grain-size distribution were surveyed in parallel during 2 periods of 14 d to detect tidal and seasonal variations. Our results showed a weak relationship between mud fraction and MPB biomass in March, and this relationship fully disappeared in July. Tidal exposure was the most important parameter in explaining the summer temporal dynamics of MPB. This study reveals the general importance of bed elevation and tidal exposure in muddy habitats and that silt content was a prime governing physical factor in winter. Biostabilisation processes seemed to behave only as secondary factors that could only amplify the initial silt accumulation in summer rather than primary factors explaining spatial or long-term trends of sediment changes.

Soil organic carbon stocks in estuarine and marine mangrove ecosystems are driven by nutrient colimitation of P and N

Mangroves play an important role in carbon sequestration, but soil organic carbon (SOC) stocks differ between marine and estuarine mangroves, suggesting differing processes and drivers of SOC accumulation. Here, we compared undegraded and degraded marine and estuarine mangroves in a regional approach across the Indonesian archipelago for their SOC stocks and evaluated possible drivers imposed by nutrient limitations along the land-to-sea gradients. SOC stocks in natural marine mangroves (271–572 Mg ha-1 m-1 were much higher than under estuarine mangroves (100–315 Mg ha-1 m-1 with a further decrease caused by degradation to 80–132 Mg ha-1 m-1. Soils differed in C/N ratio (marine: 29–64; estuarine: 9–28), δ15N (marine: 0.6 to 0.7‰; estuarine: 2.5 to 7.2‰), and plant-available P (marine: 2.3–6.3 mg kg-1; estuarine: 0.16–1.8 mg kg-1). We found N and P supply of sea-oriented mangroves primarily met by dominating symbiotic N2 fixation from air and P import from sea, while mangroves on the landward gradient increasingly covered their demand in N and P from allochthonous sources and SOM recycling. Pioneer plants favored by degradation further increased nutrient recycling from soil resulting in smaller SOC stocks in the topsoil. These processes explained the differences in SOC stocks along the land-to-sea gradient in each mangrove type as well as the SOC stock differences observed between estuarine and marine mangrove ecosystems. This first large-scale evaluation of drivers of SOC stocks under mangroves thus suggests a continuum in mangrove functioning across scales and ecotypes and additionally provides viable proxies for carbon stock estimations in PES or REDD schemes.

Abrupt shifts in the Gironde fish community: an indicator of ecological changes in an estuarine ecosystem

For decades, global climate change has directly and indirectly affected the structure and function of ecosystems. Abrupt changes in biodiversity have been observed in response to linear or sudden modifications to the environment. These abrupt shifts can cause long-term reorganizations within ecosystems, with communities exhibiting new functional responses to environmental factors. Over the last 3 decades, the Gironde estuary in southwest France has experienced 2 abrupt shifts in both the physical and chemical environments and the pelagic community. Rather than describing these shifts and their origins, we focused on the 3 inter-shift periods, describing the structure of the fish community and its relationship with the environment during these periods. We described fish biodiversity using a limited set of descriptors, taking into account both species composition and relative species abundances. Inter-shift ecosystem states were defined based on the relationship between this description and the hydro-physico-chemical variables and climatic indices defining the main features of the environment. This relationship was described using generalized linear mixed models on the entire time series and for each inter-shift period. Our results indicate that (1) the fish community structure has been significantly modified, (2) environmental drivers influencing fish diversity have changed during these 3 periods, and (3) the fish-environment relationships have been modified over time. From this, we conclude a regime shift has occurred in the Gironde estuary. We also highlight that anthropogenic influences have increased, which re-emphasizes the importance of local management in maintaining fish diversity and associated goods and services within the context of climate change.

Sea otter predation and the distribution of bivalve prey in the Elkhorn Slough National Estuarine Research Reserve

The California sea otter population is gradually expanding in size and geographic range and is consequently invading new feeding grounds, including bays and estuaries that are home to extensive populations of bivalve prey. One such area is the Elkhorn Slough, where otters have apparently established a spring and summer communal feeding and resting area. In anticipation of future otter foraging in the slough, an extensive baseline database on bivalve densities, size distributions, biomasses, and burrow depths has been established for three potential bivalve prey species, Saxidomus nuttalli, Tresus nutallii, and Zirphaea pilsbryi. In 1986, the Elkhorn Slough otters were foraging predominately at two areas immediately east and west of the Highway 1 bridge (Skipper's and the PG&E Outfall). Extensive subtidal populations of Saxidomus nuttalli and Tresus nuttallii occur in these areas. Shell records collected at these study areas indicated that sea otters were foraging selectively on Saxidomus over Tresus. The reason for this apparent preference was not clear. At the Skipper's study site, 51% of the shell record was composed of Saxidomus, yet this species accounted for only 16% of the in situ biomass, and only 39% of the available clams. Tresus represented 49% of the shell record at Skipper's, yet this species accounted for 84% of the in situ biomass and 61% of the available clams. There was no difference in mean burrow depth between the two species at this site so availability does not explain the disparity in consumption. At the PG&E Outfall, Saxidomus represents 66% of the in situ biomass and 81% of the available clams, while Tresus accounts for 34% of the in situ biomass and 19% of the available clams. Saxidomus accounts for 96% of the shell record at this site vs. 4% for Tresus, again indicating that the otters were preying on Saxidomus out of proportion to their density or biomass. High densities and biomasses of a third species, Zirphaea pilsbryi, occur in areas where sea otters were observed to be foraging, yet no cast-off Zirphaea shells were found. Although it is possible this species was not represented in the shell record because the otters were simply chewing up the shells, it is more likely this species is avoided by sea otters. There were relatively few sea otters in the Elkhorn Slough in 1986 compared to the previous two years. This, coupled with high bivalve densities, precluded any quantitative comparison of bivalve densities before and after the 1986 sea otter occupation. Qualitative observations made during the course of this study, and quantitative observations from previous studies indicate that, after 3 years, sea otters are not yet significantly affecting bivalve densities in the Elkhorn Slough.

Does Landscape Context Affect Habitat Value? The Importance of Seascape Ecology in Back-reef Systems

Seascape ecology provides a useful framework from which to understand the processes governing spatial variability in ecological patterns. Seascape context, or the composition and pattern of habitat surrounding a focal patch, has the potential to impact resource availability, predator-prey interactions, and connectivity with other habitats. For my dissertation research, I combined a variety of approaches to examine how habitat quality for fishes is influenced by a diverse range of seascape factors in sub-tropical, back-reef ecosystems. In the first part of my dissertation, I examined how seascape context can affect reef fish communities on an experimental array of artificial reefs created in various seascape contexts in Abaco, Bahamas. I found that the amount of seagrass at large spatial scales was an important predictor of community assembly on these reefs. Additionally, seascape context had differing effects on various aspects of habitat quality for the most common reef species, White grunt Haemulon plumierii. The amount of seagrass at large spatial scales had positive effects on fish abundance and secondary production, but not on metrics of condition and growth. The second part of my dissertation focused on how foraging conditions for fish varied across a linear seascape gradient in the Loxahatchee River estuary in Florida, USA. Gray snapper, Lutjanus griseus, traded food quality for quantity along this estuarine gradient, maintaining similar growth rates and condition among sites. Additional work focused on identifying major energy flow pathways to two consumers in oyster-reef food webs in the Loxahatchee. Algal and microphytobenthos resource pools supported most of the production to these consumers, and body size for one of the consumers mediated food web linkages with surrounding mangrove habitats. All of these studies examined a different facet of the importance of seascape context in governing ecological processes occurring in focal habitats and underscore the role of connectivity among habitats in back-reef systems. The results suggest that management approaches consider the surrounding seascape when prioritizing areas for conservation or attempting to understand the impacts of seascape change on focal habitat patches. For this reason, spatially-based management approaches are recommended to most effectively manage back-reef systems.

Development of molecular approaches to assess the diversity and abundance of marine nematodes assemblages for assessment of Good Environmental Status of the estuarine and marine ecosystems

In Europe, the concerns with the status of marine ecosystems have increased, and the Marine Directive has as main goal the achievement of Good Environmental Status (GES) of EU marine waters by 2020. Molecular tools are seen as promising and emerging approaches to improve ecosystem monitoring, and have led ecology into a new era, representing perhaps the most source of innovation in marine monitoring techniques. Benthic nematodes are considered ideal organisms to be used as biological indicator of natural and anthropogenic disturbances in aquatic ecosystems underpinning monitoring programmes on the ecological quality of marine ecosystems, very useful to assess the GES of the marine environment. dT-RFLP (directed Terminal-Restriction Fragment Length Polymorphism) allows to assess the diversity of nematode communities, but also allows studying the functioning of the ecosystem, and combined with relative real-time PCR (qPCR), provides a high-throughput semi-quantitative characterization of nematode communities. These characteristics make the two molecular tools good descriptors for the good environmental status assessment. The main aim of this study is to develop and optimize the dT-RFLP and qPCR in Mira estuary (SW coast, Portugal). A molecular phylogenetic analysis of marine and estuarine nematodes is being performed combining morphological and molecular analysis to evaluate the diversity of free-living marine nematodes in Mira estuary. After morphological identification, barcoding of 18S rDNA and COI genes are being determined for each nematode species morphologically identified. So far we generated 40 new sequences belonging to 32 different genus and 17 families, and the study has shown a good degree of concordance between traditional morphology-based identification and DNA sequences. These results will improve the assessment of marine nematode diversity and contribute to a more robust nematode taxonomy. The DNA sequences are being used to develop the dT-RFLP with the ability to easily process large sample numbers (hundreds and thousands), rather than typical of classical taxonomic or low throughput molecular analyses. A preliminary study showed that the digest enzymes used in dT-RFLP for terrestrial assemblages separated poorly the marine nematodes at taxonomic level for functional group analysis. A new digest combination was designed using the software tool DRAT (Directed Terminal Restriction Analysis Tool) to distinguished marine nematode taxa. Several solutions were provided by DRAT and tested empirically to select the solution that cuts most efficiently. A combination of three enzymes and a single digest showed to be the best solution to separate the different clusters. Parallel to this, another tool is being developed to estimate the population size (qPCR). An improvement in qPCR estimation of gene copy number using an artificial reference is being performed for marine nematodes communities to quantify the abundance. Once developed, it is proposed to validate both methodologies by determining the spatial and temporal variability of benthic nematodes assemblages across different environments. The application of these high-throughput molecular approaches for benthic nematodes will improve sample throughput and their implementation more efficient and faster as indicator of ecological status of marine ecosystems.

Using information criteria to select the correct variance–covariance structure for longitudinal data in ecology

1. Ecological data sets often use clustered measurements or use repeated sampling in a longitudinal design. Choosing the correct covariance structure is an important step in the analysis of such data, as the covariance describes the degree of similarity among the repeated observations. 2. Three methods for choosing the covariance are: the Akaike information criterion (AIC), the quasi-information criterion (QIC), and the deviance information criterion (DIC). We compared the methods using a simulation study and using a data set that explored effects of forest fragmentation on avian species richness over 15 years. 3. The overall success was 80.6% for the AIC, 29.4% for the QIC and 81.6% for the DIC. For the forest fragmentation study the AIC and DIC selected the unstructured covariance, whereas the QIC selected the simpler autoregressive covariance. Graphical diagnostics suggested that the unstructured covariance was probably correct. 4. We recommend using DIC for selecting the correct covariance structure.

Elicitator : an expert elicitation tool for regression in ecology

Expert elicitation is the process of retrieving and quantifying expert knowledge in a particular domain. Such information is of particular value when the empirical data is expensive, limited, or unreliable. This paper describes a new software tool, called Elicitator, which assists in quantifying expert knowledge in a form suitable for use as a prior model in Bayesian regression. Potential environmental domains for applying this elicitation tool include habitat modeling, assessing detectability or eradication, ecological condition assessments, risk analysis, and quantifying inputs to complex models of ecological processes. The tool has been developed to be user-friendly, extensible, and facilitate consistent and repeatable elicitation of expert knowledge across these various domains. We demonstrate its application to elicitation for logistic regression in a geographically based ecological context. The underlying statistical methodology is also novel, utilizing an indirect elicitation approach to target expert knowledge on a case-by-case basis. For several elicitation sites (or cases), experts are asked simply to quantify their estimated ecological response (e.g. probability of presence), and its range of plausible values, after inspecting (habitat) covariates via GIS.