Sediment quality triad assessment in Kachemak Bay: characterization of soft bottom benthic habitats and contaminant bioeffects assessment condensed. A NOAA/NOS/NCCOS/CCMA Special Report

A baseline environmental characterization of the inner Kachemak Bay, Alaska was conducted using standardized National Status and Trends Bioeffects Program methods. Three sites near the village of Port Graham were also sampled for comparison. Concentrations of over 120 organic and metallic contaminants were analyzed. Ambient toxicity was assessed using two bioassays. A detailed benthic community condition assessment was performed. Habitat parameters (e.g. depth, salinity, temperature, dissolved oxygen, sediment grain size, and organic carbon content) that influence species and contaminant distribution were also measured at each sampling site. The following is the synopsis of findings • Sediments were mostly mixed silt and sand with pockets of muddy zones. Organic compounds (PAHs, DDTs, PCBs, chlorinated pesticides) were detected throughout the bay but at relatively low concentrations. With some exceptions, metals concentrations were relatively low and probably reflect the input of glacial runoff. • Homer Harbor had elevated concentrations of metallic and organic contaminants. Concentrations of organic contaminants measured were five to ten times higher in the harbor sites than in the open bay sites. Tributyltin was elevated in Homer Harbor relative to the other areas. • There was no evidence of residual PAHs attributable to oil spills, outside of local input in the confines of the harbor. • The benthic community is very diverse. Specific community assemblages were distributed based on depth and water clarity. Species richness and diversity was lower in the eastern end of the bay in the vicinity of the Fox River input. Abundance was also generally lower in the eastern portion of the study area, and in the intertidal areas near Homer. The eastern portions of the bay are stressed by the sediment load from glacial meltwater. • Significant toxicity was virtually absent. • The benthic fauna at Port Graham contained a significant number of species not found in Kachemak Bay. • Selected metal concentrations were elevated at Port Graham relative to Kachemak Bay, probably due to local geology. Organic contaminants were elevated at a site south of the village.

Age, growth and mortality of the toadfish, Halobatrachus didactylus (Schneider, 1801) (Pisces: Batrachoididae), in the Bay of Cádiz (southwestern Spain)

Age, growth and mortality of the toadfish, Halobatrachus didactylus, were determined by examination of the whole sagittal otoliths of fish sampled in the Bay of Cádiz (southwestern Spain) from March 1999 to March 2000. A total of 844 specimens (425 males, 416 females, and 3 of indeterminate sex), ranging from 95 to 470 mm in total length were examined. Eighty-nine percent of the otoliths could be read allowing an age estimation. The opaque zone was formed between April and May coincident with the maximum reproductive peak, while the translucent zone formed mainly in summer-fall (June to December). Maximum ages for males and females were 12 and 10 years, respectively. The samples were dominated by 2- to 6-year-old specimens. Males matured at an age of approximately 2 years and females at 3 years. Fish total length and otolith radius were closely related. The von Bertalanffy growth curve was used to describe growth. The parameters were derived from back-calculated length-at-age. Significant differences in the growth parameters were found between sexes. Although the growth analysis revealed that this species is slow-growing, males reached larger sizes than females. Females appeared to experience higher natural mortality rates than males.

Predicting the distribution of Vibrio vulnificus in Chesapeake Bay

Vibrio vulnificus is a gram-negative pathogenic bacterium endemic to coastal waters worldwide, and a leading cause of seafood related mortality. Because of human health concerns, understanding the ecology of the species and potentially predicting its distribution is of great importance. We evaluated and applied a previously published qPCR assay to water samples (n = 235) collected from the main-stem of the Chesapeake Bay (2007 – 2008) by Maryland and Virginia State water quality monitoring programs. Results confirmed strong relationships between the likelihood of Vibrio vulnificus presence and both temperature and salinity that were used to develop a logistic regression model. The habitat model demonstrated a high degree of concordance (93%), and robustness as subsequent bootstrapping (n=1000) did not change model output (P > 0.05). We forced this empirical habitat model with temperature and salinity predictions generated by a regional hydrodynamic modeling system to demonstrate its utility in future pathogen forecasting efforts in the Chesapeake Bay.

Report of the special session of "Chesapeake Bay Ecological Forecasting: Moving Ecosystem Modeling from Research to Operation" of the 2010 Chesapeake Modeling Symposium

Moving ecosystem modeling from research to applications and operations has direct management relevance and will be integral to achieving the water quality and living resource goals of the 2010 Chesapeake Bay Executive Order. Yet despite decades of ecosystem modeling efforts of linking climate to water quality, plankton and fish, ecological models are rarely taken to the operational phase. In an effort to promote operational ecosystem modeling and ecological forecasting in Chesapeake Bay, a meeting was convened on this topic at the 2010 Chesapeake Modeling Symposium (May, 10-11). These presentations show that tremendous progress has been made over the last five years toward the development of operational ecological forecasting models, and that efforts in Chesapeake Bay are leading the way nationally. Ecological forecasts predict the impacts of chemical, biological, and physical changes on ecosystems, ecosystem components, and people. They have great potential to educate and inform not only ecosystem management, but also the outlook and opinion of the general public, for whom we manage coastal ecosystems. In the context of the Chesapeake Bay Executive Order, ecological forecasting can be used to identify favorable restoration sites, predict which sites and species will be viable under various climate scenarios, and predict the impact of a restoration project on water quality.

Microbial community analysis of Acropora palamata mucus swabs, water and sediment samples from Hawksnest Bay, St. John, U.S. Virgin Islands

Colonies of the scleractinian coral Acropora palmata, listed as threatened under the US Endangered Species Act in 2006, have been monitored in Hawksnest Bay, within Virgin Islands National Park, St. John, from 2004 through 2010 by scientists with the US Geological Survey, National Park Service, and the University of the Virgin Islands. The focus has been on documenting the prevalence of disease, including white band, white pox (also called patchy necrosis and white patches), and unidentified diseases (Rogers et al., 2008; Muller et al., 2008). In an effort to learn more about the pathologies that might be involved with the diseases that were observed, samples were collected from apparently healthy and diseased colonies in July 2009 for analysis. Two different microbial assays were performed on Epicentre Biotechnologies DNA swabs containing A. palmata coral mucus, and on water and sediment samples collected in Hawksnest Bay. Both assays are based on polymerase chain reaction (PCR) amplification of portions of the small rRNA gene (16S). The objectives were to determine 1) if known coral bacterial pathogens Serratia marcescens (Acroporid Serratiosis), Vibrio coralliilyticus (temperature-dependent bleaching, White Syndrome), Vibrio shiloi (bleaching, necrosis), and Aurantimonas coralicida (White Plague Type II) were present in any samples, and 2) if there were any differences in microbial community profiles of each healthy, unaffected or diseased coral mucus swab. In addition to coral mucus, water and sediment samples were included to show ambient microbial populations. In the first test, PCR was used to separately amplify the unique and diagnostic region of the 16S rRNA gene for each of the coral pathogens being screened. Each pathogen test was designed so that an amplified DNA fragment could be seen only if the specific pathogen was present in a sample. A positive result was indicated by bands of DNA of the appropriate size on an agarose gel, which separates DNA fragments based on the size of the molecule. DNA from pure cultures of each of the pathogens was used as a positive control for each assay.

Impact of the invasive colonial tunicate Didemnum vexillum on the recruitment of the bay scallop (Argopecten irradians irradians) and implications for recruitment of the sea scallop (Placopecten magellanicus) on Georges Bank

The invasive colonial tunicate Didemnum vexillum has become widespread in New England waters, colonizing large areas of shell-gravel bottom on Georges Bank including commercial sea scallop (Placopecten magellanicus) grounds. Didemnum vexillum colonies are also fouling coastal shellfish aquaculture gear which increases maintenance costs and may affect shellfish growth rates. We hypothesized that D. vexillum will continue to spread and may affect shellfish larval settlement and survival. We conducted a laboratory experiment to assess interactions between larval bay scallops (Argopectin irradians irradians) and D. vexillum. We found that larval bay scallops avoid settling on D. vexillum colonies, possibly deterred by the low pH of the tunicate’s surface tissue. The results of this study suggest that widespread colonization of substrata by D. vexillum could affect scallop recruitment by reducing the area of quality habitats available for settlement. We propose that the bay scallop can serve as a surrogate for the sea scallop in estimating the negative impact D. vexillum could have on the recruitment of sea scallops on Georges Bank.

Sediment Quality Triad assessment in Kachemak Bay: characterization of soft bottom benthic habitats and contaminant bioeffects assessment

A baseline environmental characterization of the inner Kachemak Bay, Alaska was conducted using the sediment quality triad approach based on sediment chemistry, sediment toxicity, and benthic invertebrate community structure. The study area was subdivided into 5 strata based on geophysical and hydrodynamic patterns in the bay (eastern and western intertidal mud flats, eastern and western subtidal, and Homer Harbor). Three to seven locations were synoptically sampled within each stratum using a stratified random statistical design approach. Three sites near the village of Port Graham and two sites in the footprint of a proposed Homer Harbor expansion were also collected for comparison. Concentrations of over 120 organic and metallic contaminants were analyzed. Ambient toxicity was assessed using two amphipod bioassays. A detailed benthic community condition assessment was performed. Habitat parameters (depth, salinity, temperature, dissolved oxygen, sediment grain size, and organic carbon content) that influence species and contaminant distribution were also measured at each sampling site. Sediments were mostly mixed silt and sand; characteristic of high energy habitats, with pockets of muddy zones. Organic compounds (PAHs, DDTs, PCBs, cyclodienes, cyclohexanes) were detected throughout the bay but at relatively low concentrations. Tributyltin was elevated in Homer Harbor relative to the other strata. With a few exceptions, metals concentrations were relatively low and probably reflect the input of glacial runoff. Relative to other sites, Homer Harbor sites were shown to have elevated concentrations of metallic and organic contaminants. The Homer Harbor stratum however, is a deep, low energy depositional environment with fine grained sediment. Concentrations of organic contaminants measured were five to ten times higher in the harbor sites than in the open bay sites. Concentration of PAHs is of a particular interest because of the legacy of oil spills in the region. There was no evidence of residual PAHs attributable to oil spills, outside of local input, beyond the confines of the harbor. Concentrations were one to ten times below NOAA sediment quality guidelines. Selected metal concentrations were found to be relatively elevated compared to other data collected in the region. However, levels are still very low in the scale of NOAA’s sediment quality guidelines, and therefore appear to pose little or no ecotoxicity threat to biota. Infaunal assessment showed a diverse assemblage with more than 240 taxa recorded and abundances greater than 3,000 animals m-22 in all but a few locations. Annelid worms, crustaceans, snails, and clams were the dominant taxa accounting for 63 %, 19%, 5%, and 7 % respectively of total individuals. Specific benthic community assemblages were identified that were distributed based on depth and water clarity. Species richness and diversity was lower in the eastern end of the bay in the vicinity of the Fox River input. Abundance was also generally lower in the eastern portion of the study area, and in the intertidal areas near Homer. The eastern portions of the bay are stressed by the sediment load from glacial meltwater. Significant toxicity was virtually absent. Conditions at the sites immediately outside the existing Homer Harbor facility did not differ significantly from other subtidal locations in the open Kachemak Bay. The benthic fauna at Port Graham contained a significant number of species not found in Kachemak Bay. Contaminant conditions were variable depending on specific location. Selected metal concentrations were elevated at Port Graham and some were lower relative to Kachemak Bay, probably due to local geology. Some organic contaminants were accumulating at a depositional site.

Domoic acid contamination within eight representative species from the benthic food web of Monterey Bay, California, USA

Benthic food webs often derive a significant fraction of their nutrient inputs from phytoplankton in the overlying waters. If the phytoplankton include harmful algal species like Pseudo-nitzschia australis, a diatom capable of producing the neurotoxin domoic acid (DA), the benthic food web can become a depository for phycotoxins. We tested the general hypothesis that DA contaminates benthic organisms during local blooms of P. australis, a widespread toxin producer along the US west coast. To test for trophic transfer and uptake of DA into the benthic food web, we sampled 8 benthic species comprising 4 feeding groups: filter feeders (Emerita analoga and Urechis caupo); a predator (Citharichthys sordidus); scavengers (Nassarius fossatus and Pagurus samuelis) and deposit feeders (Neotrypaea californiensis, Dendraster excentricus and Olivella biplicata). Sampling occurred before, during and after blooms of P. australis in Monterey Bay, CA, USA during 2000 and 2001. DA was detected in all 8 species, with contamination persisting over variable time scales. Maximum DA levels in N. fossatus (674 ppm), E. analoga (278 ppm), C. sordidus (515 ppm), N. californiensis (145 ppm), P. samuelis (56 ppm), D. excentricus (15 ppm) and O. biplicata (3 ppm) coincided with P. australis blooms, while DA levels in U. caupo remained above 200 ppm (max. = 751 ppm) throughout the study period. DA in 6 species exceeded levels thought to be safe for higher level consumers (i.e. ≥20 ppm) and thus is likely to have deleterious effects on marine birds, sea lions and the endangered California sea otter, known to prey upon these benthic species.

Leaf growth of the seagrass Syringodium filiforme in outer Florida Bay, Florida

Leaf growth of the seagrass Syringodium filiforme (Kütz., 1860) was determined using a new technique based on the growth of emergent leaves (EL method) and compared to the more labor intensive repeated measurements (RM) and demographic allometric age reconstruction techniques (DA). All three techniques were used to compare leaf growth dynamics of plants with different morphologies at two sites, a shallow water (0.5 m) banktop and an adjacent deeper water (1.5 m) environment in outer Florida Bay, Florida. Leaf formation rates (Leaf Plastochrone Interval or PI) determined using the EL and RM methods were nearly identical, with means of 20 and 21 d leaf–1 at both sites, significantly faster than the 30 d leaf–1 calculated using the DA method. The EL method produced the highest estimate of leaf growth, 1.8 and 1.9 cm d–1 at the 0.5 m and 1.5 m sites, respectively, followed by the RM method (1.3 and 1.3 cm d–1) and the DA method (1.0 and 1.1 cm d–1). None of the methods detected differences in leaf PI, leaf growth or leaf fragmentation rates between sites. However, leaves at the 1.5 m site typically retained intact leaf tips longer than those at the 0.5 m site, and total leaf lifespan was longer at the 1.5 m site. Based on these results and the amount of field and laboratory work required by each of the methods, the new EL method is the preferred technique for monitoring leaf growth in S. filiforme.

Prevalence of brevetoxins in prey fish of bottlenose dolphins in Sarasota Bay, Florida

Blooms of the brevetoxin-producing dinoflagellate Karenia brevis have been linked to high mortality of bottlenose dolphins Tursiops truncatus on Florida’s Gulf of Mexico coast. A clear understanding of trophic transfer of brevetoxin from its algal source up the food web to top predators is needed to assess exposure of affected dolphin populations. Prey fish constitute a means of accumulating and transferring brevetoxins and are potential vectors of brevetoxin to dolphins frequently exposed to K. brevis blooms. Here we report results of brevetoxin analyses of the primary fish species consumed by long-term resident bottlenose dolphins inhabiting Sarasota Bay, Florida. Fish collected during K. brevis blooms in 2003 to 2006 were analyzed by competitive enzyme-linked immunosorbent assay (ELISA) and had brevetoxin concentrations ranging from 4 to 10844 ng PbTx-3 eq g–1 tissue. Receptor binding assay (RBA) and liquid chromatography–mass spectrometry (LC-MS) analysis confirmed toxicity and the presence of parent brevetoxins and known metabolites. Fish collected in the absence of K. brevis blooms tested positive for brevetoxin by ELISA and RBA, with concentrations up to 1500 ng PbTx-3 eq g–1 tissue. These findings implicate prey fish exposed to K. brevis blooms as brevetoxin vectors for their dolphin predators and provide a critical analysis of persistent brevetoxin loads in the food web of dolphins repeatedly exposed to Florida red tides.

Characterizing Jobos Bay, Puerto Rico: a watershed modeling analysis and monitoring plan

Land-based pollution is commonly identified as a major contributor to the observed deterioration of shallow-water coral reef ecosystem health. Human activity on the coastal landscape often induces nutrient enrichment, hypoxia, harmful algal blooms, toxic contamination and other stressors that have degraded the quality of coastal waters. Coral reef ecosystems throughout Puerto Rico, including Jobos Bay, are under threat from coastal land uses such as urban development, industry and agriculture. The objectives of this report were two-fold: 1. To identify potentially harmful land use activities to the benthic habitats of Jobos Bay, and 2. To describe a monitoring plan for Jobos Bay designed to assess the impacts of conservation practices implemented on the watershed. This characterization is a component of the partnership between the U.S. Department of Agriculture (USDA) and the National Oceanic and Atmospheric Administration (NOAA) established by the Conservation Effects Assessment Project (CEAP) in Jobos Bay. CEAP is a multi-agency effort to quantify the environmental benefits of conservation practices used by private landowners participating in USDA programs. The Jobos Bay watershed, located in southeastern Puerto Rico, was selected as the first tropical CEAP Special Emphasis Watershed (SEW). Both USDA and NOAA use their respective expertise in terrestrial and marine environments to model and monitor Jobos Bay resources. This report documents NOAA activities conducted in the first year of the three-year CEAP effort in Jobos Bay. Chapter 1 provides a brief overview of the project and background information on Jobos Bay and its watershed. Chapter 2 implements NOAA’s Summit to Sea approach to summarize the existing resource conditions on the watershed and in the estuary. Summit to Sea uses a GIS-based procedure that links patterns of land use in coastal watersheds to sediment and pollutant loading predictions at the interface between terrestrial and marine environments. The outcome of Summit to Sea analysis is an inventory of coastal land use and predicted pollution threats, consisting of spatial data and descriptive statistics, which allows for better management of coral reef ecosystems. Chapters 3 and 4 describe the monitoring plan to assess the ecological response to conservation practices established by USDA on the watershed. Jobos Bay is the second largest estuary in Puerto Rico, but has more than three times the shoreline of any other estuarine area on the island. It is a natural harbor protected from offshore wind and waves by a series of mangrove islands and the Punta Pozuelo peninsula. The Jobos Bay marine ecosystem includes 48 km² of mangrove, seagrass, coral reef and other habitat types that span both intertidal and subtidal areas. Mapping of Jobos Bay revealed 10 different benthic habitats of varying prevalence, and a large area of unknown bottom type covering 38% of the entire bay. Of the known benthic habitats, submerged aquatic vegetation, primarily seagrass, is the most common bottom type, covering slightly less than 30% of the bay. Mangroves are the dominant shoreline feature, while coral reefs comprise only 4% of the total benthic habitat. However, coral reefs are some of the most productive habitats found in Jobos Bay, and provide important habitat and nursery grounds for fish and invertebrates of commercial and recreational value.

A geo-referenced benthic habitat survey in support of natural resource management: Port Graham Bay, Alaska

The impact of recent changes in climate on the arctic environment and its ecosystems appear to have a dramatic affect on natural populations (National Research Council Committee on the Bering Sea Ecosystem 1996) and pose a serious threat to the continuity of indigenous arctic cultures that are dependent on natural resources for subsistence (Peterson D. L., Johnson 1995). In the northeast Pacific, winter storms have intensified and shifted southward causing fundamental changes in sea surface temperature patterns (Beamish 1993, Francis et al. 1998). Since the mid 1970’s surface waters of the central basin of the Gulf of Alaska (GOA) have warmed and freshened with a consequent increase in stratification and reduced winter entrainment of nutrients (Stabeno et al. 2004). Such physical changes in the structure of the ocean can rapidly affect lower trophic levels and indirectly affect fish and marine mammal populations through impacts on their prey (Benson and Trites 2002). Alaskan natives expect continued and perhaps accelerating changes in resources due to global warming (DFO 2006).and want to develop strategies to cope with their changing environment.

Recruitment and spawning-stock biomass distribution of bay anchovy (Anchoa mitchilli) in Chesapeake Bay

Recruitment of bay anchovy (Anchoa mitchilli) in Chesapeake is related to variability in hydrological conditions and to abundance and spatial distribution of spawning stock biomass (SSB). Midwater-trawl surveys conducted for six years, over the entire 320-km length of the bay, provided information on anchovy SSB, annual spatial patterns of recruitment, and their relationships to variability in the estuarine environment. SSB of anchovy varied sixfold in 1995–2000; it alone explained little variability in young-of-the-year (YOY) recruitment level in October, which varied ninefold. Recruitments were low in 1995 and 1996 (47 and 31 Z 109) but higher in 1997–2000 (100 to 265 Z 109). During the recruitment process the YOY population migrated upbay before a subsequent fall-winter downbay migration. The extent of the downbay migration by maturing recruits was greatest in years of high freshwater input to the bay. Mean dissolved oxygen (DO) was more important than freshwater input in controlling distribution of SSB and shifts in SSB location between April– May (prespawning) and June–August (spawning) periods. Recruitments of bay anchovy were higher when mean DO was lowest in the downbay region during the spawning season. It is hypothesized that anchovy recruitment level is inversely related to mean DO concentration because low DO is associated with high plankton productivity in Chesapeake Bay. Additionally, low DO conditions may confine most bay anchovy spawners to the downbay region, where production of larvae and juveniles is enhanced. A modified Ricker stock-recruitment model indicated density-compensatory recruitment with respect to SSB and demonstrated the importance of spring-summer DO levels and spatial distribution of SSB as controllers of bay anchovy recruitment.

Growth, mortality, and hatchdate distributions of larval and juvenile spotted seatrout (Cynoscion nebulosus) in Florida Bay, Everglades National Park

Life history aspects of larval and, mainly, juvenile spotted seatrout (Cynoscion nebulosus) were studied in Florida Bay, Everglades National Park, Florida. Collections were made in 1994−97, although the majority of juveniles were collected in 1995. The main objective was to obtain life history data to eventually develop a spatially explicit model and provide baseline data to understand how Everglades restoration plans (i.e. increased freshwater flows) could influence spotted seatrout vital rates. Growth of larvae and juveniles (<80 mm SL) was best described by the equation loge standard length = –1.31 + 1.2162 (loge age). Growth in length of juveniles (12–80 mm SL) was best described by the equation standard length = –7.50 + 0.8417 (age). Growth in wet weight of juveniles (15–69 mm SL) was best described by the equation loge wet-weight = –4.44 + 0.0748 (age). There were no significant differences in juvenile growth in length of spotted seatrout in 1995 between three geographical subdivisions of Florida Bay: central, western, and waters adjacent to the Gulf of Mexico. We found a significant difference in wet-weight for one of six cohorts categorized by month of hatchdate in 1995, and a significant difference in length for another cohort. Juveniles (i.e. survivors) used to calculate weekly hatchdate distributions during 1995 had estimated spawning times that were cyclical and protracted, and there was no correlation between spawning and moon phase. Temperature influenced otolith increment widths during certain growth periods in 1995. There was no evidence of a relationship between otolith growth rate and temperature for the first 21 increments. For increments 22–60, otolith growth rates decreased with increasing age and the extent of the decrease depended strongly in a quadratic fashion on the temperature to which the fish was exposed. For temperatures at the lower and higher range, increment growth rates were highest. We suggest that this quadratic relationship might be influenced by an environmental factor other than temperature. There was insufficient information to obtain reliable inferences on the relationship of increment growth rate to salinity.

A habitat-use model to determine essential fish habitat for juvenile brown shrimp (Farfantepenaeus aztecus) in Galveston Bay, Texas

A density prediction model for juvenile brown shrimp (Farfantepenaeus aztecus) was developed by using three bottom types, five salinity zones, and four seasons to quantify patterns of habitat use in Galveston Bay, Texas. Sixteen years of quantitative density data were used. Bottom types were vegetated marsh edge, submerged aquatic vegetation, and shallow nonvegetated bottom. Multiple regression was used to develop density estimates, and the resultant formula was then coupled with a geographical information system (GIS) to provide a spatial mosaic (map) of predicted habitat use. Results indicated that juvenile brown shrimp (<100 mm) selected vegetated habitats in salinities of 15−25 ppt and that seagrasses were selected over marsh edge where they co-occurred. Our results provide a spatially resolved estimate of high-density areas that will help designate essential fish habitat (EFH) in Galveston Bay. In addition, using this modeling technique, we were able to provide an estimate of the overall population of juvenile brown shrimp (<100 mm) in shallow water habitats within the bay of approximately 1.3 billion. Furthermore, the geographic range of the model was assessed by plotting observed (actual) versus expected (model) brown shrimp densities in three other Texas bays. Similar habitat-use patterns were observed in all three bays—each having a coefficient of determination >0.50. These results indicate that this model may have a broader geographic application and is a plausible approach in refining current EFH designations for all Gulf of Mexico estuaries with similar geomorphological and hydrological characteristics.