Survey protocol for invasive species

This protocol was developed by the Biogeography Branch of NOAA’s Center for Coastal Monitoring and Assessment to support invasive species research by the Papahānaumokuākea Marine National Monument. The protocol’s objective is to detect Carijoa riisei and Hypnea musciformis in deepwater habitats using visual surveys by technical divers. Note: This protocol is designed to detect the presence or absence of invasive species. A distinct protocol is required to collect information on abundance and impact, or monitor changes over time.

Manual for the Sampling Design Tool for ArcGIS

The Biogeography Branch’s Sampling Design Tool for ArcGIS provides a means to effectively develop sampling strategies in a geographic information system (GIS) environment. The tool was produced as part of an iterative process of sampling design development, whereby existing data informs new design decisions. The objective of this process, and hence a product of this tool, is an optimal sampling design which can be used to achieve accurate, high-precision estimates of population metrics at a minimum of cost. Although NOAA’s Biogeography Branch focuses on marine habitats and some examples reflects this, the tool can be used to sample any type of population defined in space, be it coral reefs or corn fields.

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.

Distribution of persistent organic contaminants in canyons and on the continental shelf off central California

The National Status and Trends (NS&T) Program has conducted studies to determine the spatial extent and severity of chemical contamination and associated adverse biological effects in coastal bays and estuaries of the United States since 1991. Sediment contamination in U.S. coastal areas is a major environmental issue because of its potential toxic effects on biological resources and often, indirectly, on human health. Thus, characterizing and delineating areas of sediment contamination and toxicity and demonstrating their effect(s) on benthic living resources are therefore important goals of coastal resource management at NOAA. The National Centers for Coastal Ocean Science, and the Office of National Marine Sanctuaries, in cooperation with the U.S. Geological Survey (USGS), University of California Moss Landing Marine Lab (MLML), and the Monterey Bay Aquarium Research Institute (MBARI), conducted ecosystem monitoring and characterization studies within and between marine sanctuaries along the California coast in 2002 and 2004 on the NOAA RV McArthur. One of the objectives was to perform a systematic assessment of the chemical and physical habitats and associated biological communities in soft bottom habitats on the continental shelf and slope in the central California region. This report addresses the magnitude and extent of chemical contamination, and contaminant transport patterns in the region. Ongoing studies of the benthic community are in progress and will be reported in an integrated assessment of habitat quality and the parameters that govern natural resource distributions on the continental margin and in canyons in the region.

Estado de conservación de la ictiofauna arrecifal en sitios de buceo turístico de cuatro regiones del Archipiélago Sabana-Camagüey, Cuba.

Los peces constituyen uno de los atractivos principales en los arrecifes coralinos para el buceo turístico, por lo cual resulta necesario monitorear su abundancia y valores estéticos. El objetivo de esta investigación fue evaluar el estado de conservación de las asociaciones de peces arrecifales en cuatro de los principales polos turísticos del Archipiélago Sabana-Camagüey, Cuba en el año 2010. Se muestrearon 23 sitios de buceo turísticos en áreas adyacentes a las regiones de Varadero (5 sitios), cayos de Villa Clara (6 sitios), Cayo Coco (6 sitios) y Santa Lucia (6 sitios). En cada uno de ellos se realizaron seis réplicas de censos visuales de todas las especies de peces en recorridos lineales de 50 m de largo por 2 m de ancho, ocupando un área total de 600 m2. El puntaje más alto de conservación lo presentó los cayos de Villa Clara (37), siguiéndole en orden decreciente Cayo Coco (35), y con valores más bajos Varadero (24) y Santa Lucia (22). Los puntajes de las cuatro regiones fueron inferiores a los encontrados en otros arrecifes de Cuba y el Caribe. Los valores de Varadero y Santa Lucia se correspondieron con los de arrecifes de hábitats degradados y sometidos a explotación pesquera. En general, en la mayoría de las regiones predominaron peces de talla pequeña (<20 cm) pertenecientes a las familias Pomacentridae y Labridae y hubo poca abundancia de peces carnívoros y herbívoros de mediana (20-40 cm) y gran talla (>40 cm). ABSTRACT Fish are one of the main attractions on coral reefs for diving tourism; therefore, it is necessary to monitor their condition and aesthetic values. The objective of this research was to evaluate the status of reef fish assemblages in four tourist areas of Sabana-Camaguey Archipelago, Cuba in 2010. Twentythree tourist diving sites were sampled in adjacent areas to regions of Varadero (five sites), Villa Clara keys (6 sites), Coco key (6 sites) and Santa Lucia (6 sites). In each region, six replicated visual census of all fish species were conducted along belt transects of 50 m length and 2 m width, occupying a total area of 600 m2. The highest conservation score was obtained by Villa Clara keys (37), followed in decreasing order by Coco key (35), and with lower values Varadero (24) and St. Lucia (22). The scores of the four regions were lower than the values of other Cuban and Caribbean reefs. The values of Varadero and Santa Lucia corresponded to reefs with degraded habitats and subject to overfishing. In general, small fish (< 20 cm) from families Pomacentridae and Labridae, and low abundance of carnivore and herbivore fish of middle (20-40 cm) and large size (> 40 cm) predominated in most regions.

Lobster trap debris in the Florida Keys National Marine Sanctuary: distribution, abundance, density, and patterns of accumulation

The fishery for spiny lobster Panulirus argus in the Florida Keys National Marine Sanctuary is well chronicled, but little information is available on the prevalence of lost or abandoned lobster traps. In 2007, towed-diver surveys were used to identify and count pieces of trap debris and any other marine debris encountered. Trap debris density (debris incidences/ha) in historic trap-use zones and in representative benthic habitats was estimated. Trap debris was not proportionally distributed with fishing effort. Coral habitats had the greatest density of trap debris despite trap fishers’ reported avoidance of coral reefs while fishing. The accumulation of trap debris on coral emphasizes the role of wind in redistributing traps and trap debris in the sanctuary. We estimated that 85,548 ± 23,387 (mean ± SD) ghost traps and 1,056,127 ± 124,919 nonfishing traps or remnants of traps were present in the study area. Given the large numbers of traps in the fishery and the lack of effective measures for managing and controlling the loss of gear, the generation of trap debris will likely continue in proportion to the number of traps deployed in the fishery. Focused removal of submerged trap debris from especially vulnerable habitats such as reefs and hardbottom, where trap debris density is high, would mitigate key habitat issues but would not address ghost fishing or the cost of lost gear.

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.

Translocation as a strategy to rehabilitate the queen conch (Strombus gigas) population in the Florida Keys

Queen conch (Strombus gigas) stocks in the Florida Keys once supported commercial and recreational fisheries, but overharvesting has decimated this once abundant snail. Despite a ban on harvesting this species since 1985, the local conch population has not recovered. In addition, previous work has reported that conch located in nearshore Keys waters are incapable of spawning because of poor gonadal condition, although reproduction does occur offshore. Queen conch in other areas undergo ontogenetic migrations from shallow, nearshore sites to offshore habitats, but conch in the Florida Keys are prevented from doing so by Hawk Channel. The present study was initiated to determine the potential of translocating nonspawning nearshore conch to offshore sites in order to augment the spawning stock. We translocated adult conch from two nearshore sites to two offshore sites. Histological examinations at the initiation of this study confirmed that nearshore conch were incapable of reproduction, whereas offshore conch had normal gonads and thus were able to reproduce. The gonads of nearshore females were in worse condition than those of nearshore males. However, the gonadal condition of the translocated nearshore conch improved, and these animals began spawning after three months offshore. This finding suggests that some component of the nearshore environment (e.g., pollutants, temperature extremes, poor food or habitat quality) disrupts reproduction in conch, but that removal of nearshore animals to suitable offshore habitat can restore reproductive viability. These results indicate that translocations are preferable to releasing hatchery-reared juveniles because they are more cost-effective, result in a more rapid increase in reproductive output, and maintain the genetic integrity of the wild stock. Therefore, translocating nearshore conch to offshore spawning aggregations may be the key to expediting the recovery of queen conch stocks in the Florida Keys.

Diet shifts of juvenile red snapper (Lutjanus campechanus) with changes in habitat and fish size

We examined the diets and habitat shift of juvenile red snapper (Lutjanus campechanus) in the northeast Gulf of Mexico. Fish were collected from open sand-mud habitat (little to no relief), and artificial reef habitat (1-m3 concrete or PVC blocks), from June 1993 through December 1994. In 1994, fish settled over open habitat from June to September, as shown by trawl collections, then began shifting to reef habitat — a shift that was almost completed by December as observed by SCUBA visual surveys. Stomachs were examined from 1639 red snapper that ranged in size from 18.0 to 280.0 mm SL. Of these, 850 fish had empty stomachs, and 346 fish from open habitat and 443 fish from reef habitat contained prey. Prey were identified to the lowest possible taxon and quantified by volumetric measurement. Specific volume of particular prey taxa were calculated by dividing prey volume by individual fish weight. Red snapper shifted diets with increasing size. Small red snapper (<60 mm SL) fed mostly on chaetognaths, copepods, shrimp, and squid. Large red snapper (60–280 mm SL) shifted feeding to fish prey, greater amounts of squid and crabs, and continued feeding on shrimp. We compared red snapper diets for overlapping size classes (70–160 mm SL) of fish that were collected from both habitats (Bray-Curtis dissimilarity index and multidimensional scaling analysis). Red snapper diets separated by habitat type rather than fish size for the size ranges that overlapped habitats. These diet shifts were attributed to feeding more on reef prey than on open-water prey. Thus, the shift in habitat shown by juvenile red snapper was reflected in their diet and suggested differential habitat values based not just on predation refuge but food resources as well.

Multidirectional movements of sportfish species between an estuarine no-take zone and surrounding waters of the Indian River Lagoon, Florida

We examined movement patterns of sportfish that were tagged in the northern Indian River Lagoon, Florida, between 1990 and 1999 to assess the degree of fish exchange between an estuarine no-take zone (NTZ) and surrounding waters. The tagged f ish were from seven species: red drum (Sciaenops ocellatus); black drum (Pogonias cromis); sheepshead (Archosargus probatocephalus); common snook (Centropomus undecimalis); spotted seatrout (Cynoscion nebulosus); bull shark (Carcharhinus leucas); and crevalle jack (Caranx hippos). A total of 403 tagged fish were recaptured during the study period, including 65 individuals that emigrated from the NTZ and 16 individuals that immigrated into the NTZ from surrounding waters of the lagoon. Migration distances between the original tagging location and the sites where emigrating fish were recaptured were from 0 to 150 km, and these migration distances appeared to be influenced by the proximity of the NTZ to spawning areas or other habitats that are important to specific life-history stages of individual species. Fish that immigrated into the NTZ moved distances ranging from approximately 10 to 75 km. Recapture rates for sportfish species that migrated across the NTZ boundary suggested that more individuals may move into the protected habitats than move out. These data demonstrated that although this estuarine no-take reserve can protect species from fishing, it may also serve to extract exploitable individuals from surrounding fisheries; therefore, if the no-take reserve does function to replenish surrounding fisheries, then increased egg production and larval export may be more important mechanisms of replenishment than the spillover of excess adults from the reserve into fishable areas.

Radiometric validation of age, growth, and longevity for the blackgill rockfish (Sebastes melanostomus)

As nearshore fish populations decline, many commercial fishermen have shifted fishing effort to deeper continental slope habitats to target fishes for which biological information is limited. One such fishery that developed in the northeastern Pacific Ocean in the early 1980s was for the blackgill rockfish (Sebastes melanostomus), a deep-dwelling (300−800 m) species that congregates over rocky pinnacles, mainly from southern California to southern Oregon. Growth zone-derived age estimates from otolith thin sections were compared to ages obtained from the radioactive disequilibria of 210Pb, in relation to its parent, 226Ra, in otolith cores of blackgill rockfish. Age estimates were validated up to 41 years, and a strong pattern of agreement supported a longevity exceeding 90 years. Age and length data fitted to the von Bertalanffy growth function indicated that blackgill rockfish are slow-growing (k= 0.040 females, 0.068 males) and that females grow slower than males, but reach a greater length. Age at 50% maturity, derived from previously published length-at-maturity estimates, was 17 years for males and 21 years for females. The results of this study agree with general life history traits already recognized for many Sebastes species, such as long life, slow growth, and late age at maturation. These traits may undermine the sustainability of blackgill rockfish populations when heavy fishing pressure, such as that which occurred in the 1980s, is applied.

Impact of hatchery releases on the recreational fishery for Pacific threadfin (Polydactylus sexfilis) in Hawaii

The Pacific threadfin (Polydactylus sexfilis) is considered one of the premier Hawaiian food fishes but even with catch limits, seasonal closures, and size limits, catches have declined dramatically since the 1960s. It was identified as the top candidate species for stock enhancement in Hawaii, based on the decline in stocks, high market value, and importance of the fishery. In the stock enhancement program for Pacific threadfin, over 430,000 fingerlings of various sizes were implanted with coded wire tags and released in nursery habitats along the windward coast of Oahu between 1993 and 1998. Because few Pacific threadfin were present in creel surveys conducted between 1994 and 1998, Oahu fishermen were offered a $10 reward for each threadfin that was caught (for both hatchery-reared and wild fish). A total of 1882 Pacific threadfin were recovered from the reward program between March 1998 and May 1999, including 163 hatchery-reared fish, an overall contribution of 8.7% to the fishery. Hatchery-reared fish accounted for as high as 71% of returns in the release areas. Hatchery-reared fish were recovered on average 11.5 km (SD=9.8 km) from the release site, although some had moved as far away as 42 km. Average age for recovered hatchery-reared fish was 495 days; the oldest was 1021 days. Cultured Pacific threadfin juveniles survived and recruited successfully to the recreational fishery, accounting for 10% of fishermen’s catches on the windward side of Oahu. Recruitment to the fishery was highest for the 1997 release year; few juveniles from earlier releases were observed. Presence of a few large, fully developed females in the recreational fishery suggested that hatchery-reared fish can survive, grow, and reproductively contribute to the population. Implementation of an enhancement program that is focused on juveniles and perhaps large females, as part of an integrated fishery management strategy, could speed the recovery of this fish population.

Seasonal distribution, abundance, and growth of young-of-the-year Atlantic croaker (Micropogonias undulatus) in Delaware Bay and adjacent marshes

We examined the spatial and temporal distribution, abundance, and growth of young-of-the-year (YOY) Atlantic croaker (Micropogonias undulatus) in Delaware Bay, one of the northernmost estuaries in which they consistently occur along the east coast of the United States. Sampling in Delaware Bay and in tidal creeks in salt marshes adjacent to the bay with otter trawls, plankton nets and weirs, between April and November 1996–99, collected approximately 85,000 YOY. Ingress of each year class into the bay and tidal creeks consistently occurred in the fall, and the first few YOY appeared in August. Larvae as small as 2–3 mm TL were collected in September and October 1996. Epibenthic individuals <25 mm TL were present each fall and again during spring of each year, but not in 1996 when low water temperatures in January and February apparently caused widespread mortality, resulting in their absence the following spring and summer. In 1998 and 1999, a second size class of smaller YOY entered the bay and tidal creeks in June. When YOY survived the winter, there was no evidence of growth until after April. Then the YOY grew rapidly through the summer in all habitats (0.8–1.4 mm/d from May through August). In the bay, they were most abundant from June to August over mud sediments in oligohaline waters. They were present in both subtidal and intertidal creeks in the marshes where they were most abundant from April to June in the mesohaline portion of the lower bay. The larger YOY began egressing out of the marshes in late summer, and the entire year class left the tidal creeks at lengths of 100–200 mm TL by October or November when the next year class was ingressing. These patterns of seasonal distribution and abundance in Delaware Bay and the adjacent marshes are similar to those observed in more southern estuaries along the east coast; however, growth is faster—in keeping with that in other northern estuaries.

Age-validation of a leopard shark (Triakis semifasciata) recaptured after 20 years

On 10 July 1999, vertebrae bearing an oxytetracycline (OTC) time mark were retrieved from a tagged leopard shark (Triakis semifasciata) recaptured in San Francisco Bay, CA, after being at liberty for almost 20 years. An additional long-term leopard shark tag return was received in June 2001, for which growth information (but not vertebrae) was obtained. The first recapture is significant in that it represents the longest at-liberty period for an age-validated (OTC-injected) shark, extends and completes age validation for this species, spanning all age classes up to its estimated average maximum age, and provides an example of the persistence of the OTC time mark in an elasmobranch at liberty for almost 20 years. The recaptured leopard shark made in 2001 also provides valuable information on long-term growth from time of release to time of recapture. Findings are documented here so that other researchers are aware that validation is complete for this species, to present pertinent evidence of considerable interannual variability in growth in this species, and to report observations on processing difficulties relating to the ephemeral nature of the 20-yr-old OTC mark.

Demographic assessment of the blue crab (Callinectes sapidus) in Chesapeake Bay using extractable lipofuscins as age markers

The blue crab (Callinectes sapidus) plays an important economic and ecological role in estuaries and coastal habitats from the Gulf of Mexico to the east coast of North America, but demographic assessments are limited by length-based methods. We applied an alternative aging method using biochemical measures of metabolic byproducts (lipofuscins) sequestered in the neural tissue of eyestalks to examine population age structure. From Chesapeake Bay, subsamples of animals collected from the 1998–99 (n=769) and 1999–2000 (n=367) winter dredge surveys were collected and lipofuscin was measured. Modal analysis of the lipofuscin index provided separation into three modes, whereas carapace-width data collected among the same individuals showed two broad modes. Lipofuscin modal analysis indicated that most adults (carapace width >120 mm) were <2 years old. The results indicate that use of extractable lipofuscin can provide a more accurate and better resolved estimation of demographic structure of blue crab populations in the field than size alone.