Palmyra Atoll coral reef habitat mapping completion report

The United States Coral Reef Task Force (USCRTF) was established in 1998 by Presidential Executive Order 13089 to lead U.S. efforts to preserve and protect coral reef ecosystems. Current, accurate, and consistent maps greatly enhance efforts to preserve and manage coral reef ecosystems. With comprehensive maps and habitat assessments, coral reef managers can be more effective in designing and implementing a variety of conservation measures, including: • Long-term monitoring programs with accurate baselines from which to track changes; • Place-based conservation measures such as marine protected areas (MPAs); and • Targeted research to better understand the oceanographic and ecological processes affecting coral reef ecosystem health. The National Oceanic and Atmospheric Administration’s (NOAA) National Ocean Service (NOS) is tasked with leading the coral ecosystem mapping element of the U.S. Coral Reef Task Force (CRTF) under the authority of the Presidential Executive Order 13089 to map and manage the coral reefs of the United States.

Coral health and disease in the Pacific: vision for action

Shallow coral reefs in the IndoPacific contain the highest diversity of marine organisms in the world, with approximately 1500 described species of fish, over 500 species of scleractinian corals, and an estimated 1-10 million organisms yet to be characterized (Reaka-Kudla et al. 1994). These centers of marine biodiversity are facing significant, multiple threats to reef community and habitat structure and function, resulting in local to wide-scale regional damage. Wilkinson (2004) characterized the major pressures as including (1) global climate change, (2) diseases, plagues and invasive species, (3) direct human pressures, (4) poor governance and lack of political will, and (5) international action or inaction. Signs that the natural plasticity of reef ecosystems has been exceeded in many areas from the effects of environmental (e.g., global climate change) and anthropogenic (e.g., land use, pollution) stressors is evidenced by the loss of 20% of the world’s coral reefs (Wilkinson 2004). Predictions are that another 24% (Wilkinson 2006) are under imminent risk of collapse and an additional 26% are under a longer term threat from reduced fitness, disease outbreaks, and increased mortality. These predictions indicate that the current list of approximately 30-40 fatal diseases impacting corals will expand as will the frequency and extent of “coral bleaching” (Waddell 2005; Wilkinson 2004). Disease and corallivore outbreaks, in combination with multiple, concomitant human disturbances are compromising corals and coral reef communities to the point where their ability to rebound from natural disturbances is being lost.

Nocturnal fish movement and trophic flow across habitat boundaries in a coral reef ecosystem (SW Puerto Rico)

Few studies have quantified the extent of nocturnal cross-habitat movements for fish, or the influence of habitat adjacencies on nutrient flows and trophodynamics. To investigate the patterns of nocturnal cross-boundary movements of fish and quantify trophic connectivity, fish were sampled at night with gillnets set along the boundaries between dominant habitat types (coral reef/seagrass and mangrove/seagrass) in southwestern Puerto Rico. Fish movement across adjacent boundary patches were equivalent at both coral reefs and mangroves. Prey biomass transfer was greater from seagrass to coral reefs (0.016 kg/km) and from mangroves to seagrass (0.006 kg/km) but not statistically significant, indicating a balance of flow between adjacent habitats. Pelagic species (jacks, sharks, rays) accounted for 37% of prey biomass transport at coral reef/seagrass and 46% at mangrove/seagrass while grunts and snappers accounted for 7% and 15%, respectively. This study indicated that coral reefs and mangroves serve as a feeding area for a wide range of multi-habitat fish species. Crabs were the most frequent prey item in fish leaving coral reefs while molluscs were observed slightly more frequently than crabs in fish entering coral reefs. For most prey types, biomass exported from mangroves was greater than biomass imported. The information on direction of fish movement together with analysis of prey data provided strong evidence of ecological linkages between distinct adjacent habitat types and highlighted the need for greater inclusion of a mosaic of multiple habitats when attempting to understand ecosystem function including the spatial transfer of energy across the seascape.

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.

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.

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.

Demersal groundfish densities in trawlable and untrawlable habitats off Washington: implications for the estimation of habitat bias in trawl surveys

Demersal groundfish densities were estimated by conducting a visual strip-transect survey via manned submersible on the continental shelf off Cape Flattery, Washington. The purpose of this study was to evaluate the statistical sampling power of the submersible survey as a tool to discriminate density differences between trawlable and untrawlable habitats. A geophysical map of the study area was prepared with side-scan sonar imagery, multibeam bathymetry data, and known locations of historical NMFS trawl survey events. Submersible transects were completed at randomly selected dive sites located in each habitat type. Significant differences in density between habitats were observed for lingcod (Ophiodon elongatus), yelloweye rockfish (Sebastes ruberrimus), and tiger rockfish (S. nigrocinctus) individually, and for “all rockfish” and “all flatfish” in the aggregate. Flatfish were more than ten times as abundant in the trawlable habitat samples than in the untrawlable samples, whereas rockfish as a group were over three times as abundant in the untrawlable habitat samples. Guidelines for sample sizes and implications for the estimation of the continental shelf trawl-survey habitat-bias are considered. We demonstrate an approach that can be used to establish sample size guidelines for future work by illustrating the interplay between statistical sampling power and 1) habitat specific-density differences, 2) variance of density differences, and 3) the proportion of untrawlable area in a habitat.

Shortspine thornyhead (Sebastolobus alascanus) abundance and habitat associations in the Gulf of Alaska

Shortspine thornyhead (Sebastolobus alascanus) abundance was estimated from 107 video transects at 27 stations recorded from a research submersible in 1991 off southeast Alaska at depths ranging from 165 to 355 m. Numbers of invertebrates in seven major taxa were estimated, as was substrate type. Thornyhead abundance ranged from 0 to 7.5/100 m2, with a mean of 1.22/100 m2, and was positively correlated with depth and amount of hard substrate. Invertebrate abundances were not significantly correlated with numbers of thornyheads. Shortspine thornyhead abundance estimates from this study were several times higher than estimates produced by bottom trawl surveys off southeast Alaska in 1990 and 1993, the two years of survey that encompassed the submersible transects; however, the trend of increasing abundance with depth was similar in the trawl surveys and in the submersible transects, suggesting that trawl surveys systematically underestimate abundance of shortspine thornyheads

Integration of submersible transect data and high-resolution multibeam sonar imagery for a habitat-based groundfish assessment of Heceta Bank, Oregon

In the face of dramatic declines in groundfish populations and a lack of sufficient stock assessment information, a need has arisen for new methods of assessing groundfish populations. We describe the integration of seafloor transect data gathered by a manned submersible with high-resolution sonar imagery to produce a habitat-based stock assessment system for groundfish. The data sets used in this study were collected from Heceta Bank, Oregon, and were derived from 42 submersible dives (1988–90) and a multibeam sonar survey (1998). The submersible habitat survey investigated seafloor topography and groundfish abundance along 30-minute transects over six predetermined stations and found a statistical relationship between habitat variability and groundfish distribution and abundance. These transects were analyzed in a geographic information system (GIS) by using dynamic segmentation to display changes in habitat along the transects. We used the submersible data to extrapolate fish abundance within uniform habitat patches over broad areas of the bank by means of a habitat classification based on the sonar imagery. After applying a navigation correction to the submersible-based habitat segments, a good correlation with major boundaries on the backscatter and topographic boundaries on the imagery were apparent. Extrapolation of the extent of uniform habitats was made in the vicinity of the dive stations and a preliminary stock assessment of several species of demersal fish was calculated. Such a habitat-based approach will allow researchers to characterize marine communities over large areas of the seafloor.

Movements, behavior, and habitat selection of bigeye tuna (Thunnus obesus) in the eastern equatorial Pacific, ascertained through archival tags

Ninety-six bigeye tuna (88– 134 cm fork length) were caught and released with implanted archival (electronic data storage) tags near fish-aggregating devices (FADs) in the equatorial eastern Pacific Ocean (EPO) during April 2000. Twenty-nine fish were recaptured, and the data from twenty-seven tags were successfully downloaded and processed. Time at liberty ranged from 8 to 446 days, and data for 23 fish at liberty for 30 days or more are presented. The accuracy in geolocation estimates, derived from the light level data, is about 2 degrees in latitude and 0.5 degrees in longitude in this region. The movement paths derived from the filtered geolocation estimates indicated that none of the fish traveled west of 110°W during the period between release and recapture. The null hypothesis that the movement path is random was rejected in 17 of the 22 statistical tests of the observed movement paths. The estimated mean velocity was 117 km/d. The fish exhibited occasional deep-diving behavior, and some dives exceeded 1000 m where temperatures were less than 3°C. Evaluations of timed depth records, resulted in the discrimination of three distinct behaviors: 54.3% of all days were classified as unassociated (with a floating object) type-1 behavior, 27.7% as unassociated type-2 behavior, and 18.7% as behavior associated with a floating object. The mean residence time at floating objects was 3.1 d. Data sets separated into day and night were used to evaluate diel differences in behavior and habitat selection. When the fish were exhibiting unassociated type-1 behavior (diel vertical migrations), they were mostly at depths of less than 50 m (within the mixed layer) throughout the night, and during the day between 200 and 300 m and 13° and 14°C. They shifted their average depths in conjunction with dawn and dusk events, presumably tracking the deep-scattering layer as a foraging strategy. There were also observed changes in the average nighttime depth distributions of the fish in relation to moon phase.