Analysis of Sample Frames and Subsampling Methods for Reef Fish Surveys

Introduction: The National Oceanic and Atmospheric Administration’s Biogeography Branch has conducted surveys of reef fish in the Caribbean since 1999. Surveys were initially undertaken to identify essential fish habitat, but later were used to characterize and monitor reef fish populations and benthic communities over time. The Branch’s goals are to develop knowledge and products on the distribution and ecology of living marine resources and provide resource managers, scientists and the public with an improved ecosystem basis for making decisions. The Biogeography Branch monitors reef fishes and benthic communities in three study areas: (1) St. John, USVI, (2) Buck Island, St. Croix, USVI, and (3) La Parguera, Puerto Rico. In addition, the Branch has characterized the reef fish and benthic communities in the Flower Garden Banks National Marine Sanctuary, Gray’s Reef National Marine Sanctuary and around the island of Vieques, Puerto Rico. Reef fish data are collected using a stratified random sampling design and stringent measurement protocols. Over time, the sampling design has changed in order to meet different management objectives (i.e. identification of essential fish habitat vs. monitoring), but the designs have always remained: • Probabilistic – to allow inferences to a larger targeted population, • Objective – to satisfy management objectives, and • Stratified – to reduce sampling costs and obtain population estimates for strata. There are two aspects of the sampling design which are now under consideration and are the focus of this report: first, the application of a sample frame, identified as a set of points or grid elements from which a sample is selected; and second, the application of subsampling in a two-stage sampling design. To evaluate these considerations, the pros and cons of implementing a sampling frame and subsampling are discussed. Particular attention is paid to the impacts of each design on accuracy (bias), feasibility and sampling cost (precision). Further, this report presents an analysis of data to determine the optimal number of subsamples to collect if subsampling were used. (PDF contains 19 pages)

Support for Integrated Ecosystem Assessments of NOAA’s National Estuarine Research Reserves System (NERRS), Volume II: Assessment of Ecological Condition and Stressor Impacts in Subtidal Waters of the North Carolina NERRS

A study was conducted to assess the status of ecological condition and potential human-health risks in subtidal estuarine waters throughout the North Carolina National Estuarine Research Reserve System (NERRS) (Currituck Sound, Rachel Carson, Masonboro Island, and Zeke’s Island). Field work was conducted in September 2006 and incorporated multiple indicators of ecosystem condition including measures of water quality (dissolved oxygen, salinity, temperature, pH, nutrients and chlorophyll, suspended solids), sediment quality (granulometry, organic matter content, chemical contaminant concentrations), biological condition (diversity and abundances of benthic fauna, fish contaminant levels and pathologies), and human dimensions (fish-tissue contaminant levels relative to human-health consumption limits, various aesthetic properties). A probabilistic sampling design permitted statistical estimation of the spatial extent of degraded versus non-degraded condition across these estuaries relative to specified threshold levels of the various indicators (where possible). With some exceptions, the status of these reserves appeared to be in relatively good to fair ecological condition overall, with the majority of the area (about 54%) having various water quality, sediment quality, and biological (benthic) condition indicators rated in the healthy to intermediate range of corresponding guideline thresholds. Only three stations, representing 10.5% of the area, had one or more of these indicators rated as poor/degraded in all three categories. While such a conclusion is encouraging from a coastal management perspective, it should be viewed with some caution. For example, although co-occurrences of adverse biological and abiotic environmental conditions were limited, at least one indicator of ecological condition rated in the poor/degraded range was observed over a broader area (35.5%) represented by 11 of the 30 stations sampled. In addition, the fish-tissue contaminant data were not included in these overall spatial estimates; however, the majority of samples (77% of fish that were analyzed, from 79%, of stations where fish were caught) contained inorganic arsenic above the consumption limits for human cancer risks, though most likely derived from natural sources. Similarly, aesthetic indicators are not reflected in these spatial estimates of ecological condition, though there was evidence of noxious odors in sediments at many of the stations. Such symptoms reflect a growing realization that North Carolina estuaries are under multiple pressures from a variety of natural and human influences. These data also suggest that, while the current status of overall ecological condition appears to be good to fair, long-term monitoring is warranted to track potential changes in the future. This study establishes an important baseline of overall ecological condition within NC NERRS that can be used to evaluate any such future changes and to trigger appropriate management actions in this rapidly evolving coastal environment. (PDF contains 76 pages)

Ongoing monitoring of Tortugas Ecological Reserve: Assessing the consequences of reserve designation

Over the past five years, a biogeographic characterization of Tortugas Ecological Reserve(TER) has been carried out to measure the post-implementation effects of TER as a refuge for exploited species. Our results demonstrate that there is substantial microalgal biomass at depths between 10 and 30 m in the soft sediments at the coral reef interface, and that this community may play an important role in the food web supporting reef organisms. In addition, preliminary stable isotope data, in conjunction with prior results from the west Florida shelf, suggest that the shallow water benthic habitats surrounding the coral reefs of TER will prove to be an important source of the primary production ultimately fueling fish production throughout TER. The majority of the fish analyzed so far have exhibited a C isotope signature consistent with a food web which relies heavily on benthic primary production. Fish counts indicate a marked increase in the abundance of large fish (>20 cm) within the Reserve relative to the Out and Park strata, across years. Faunal collections from open and protected soft bottom habitat near the northern boundary of Tortugas North strongly suggest that relaxation of trawling pressure has increased benthic biomass and diversity in this area of TER. These data, employing an integrated Before - After Control Impact (BACI) design at multiple spatial scales, will allow us to continue to document and quantify the post-implementation effects of TER. (PDF contains 58 pages)

U.S. Caribbean fish trap fishery costs and earnings study

Executive Summary: This study describes the socio-economic characteristics of the U.S. Caribbean trap fishery that encompasses the Commonwealth of Puerto Rico and Territory of the U.S. Virgin Islands. In-person interviews were administered to one hundred randomly selected trap fishermen, constituting nearly 25% of the estimated population. The sample was stratified by geographic area and trap tier. The number of traps owned or fished to qualify for a given tier varied by island. In Puerto Rico, tier I consisted of fishermen who had between 1-40 fish traps, tier II was made up of fishermen who possessed between 41 and 100 fish traps, and tier III consisted of fishermen who held in excess of 100 fish traps. In St. Thomas and St. John, tier I was composed of fishermen who held between 1 and 50 fish traps, tier II consisted of fishermen who had between 51-150 fish traps and tier III was made up of fishermen who had in excess of 150 fish traps. Lastly, in St. Croix, tier I was made up of fishermen who had less than 20 fish traps and tier II consisted of fishermen who had 20 or more fish traps. The survey elicited information on household demographics, annual catch and revenue, trap usage, capital investment on vessels and equipment, fixed and variable costs, behavioral response to a hypothetical trap reduction program and the spatial distribution of traps. The study found that 79% of the sampled population was 40 years or older. The typical Crucian trap fisherman was older than their Puerto Rican and St. Thomian and St. Johnian counterparts. Crucian fishermen’s average age was 57 years whereas Puerto Rican fishermen’s average age was 51 years, and St. Thomian and St. Johnian fishermen’s average age was 48 years. As a group, St. Thomian and St. Johnian fishermen had 25 years of fishing experience, and Puerto Rican and Crucian fishermen had 30, and 29 years, respectively. Overall, 90% of the households had at least one dependent. The average number of dependents across islands was even, ranging between 2.8 in the district of St. Thomas and St. John and 3.4 in the district of St. Croix. The percentage utilization of catch for personal or family use was relatively low. Regionally, percentage use of catch for personal or family uses ranged from 2.5% in St. Croix to 3.8% in the St. Thomas and St. John. About 47% of the respondents had a high school degree. The majority of the respondents were highly dependent on commercial fishing for their household income. In St. Croix, commercial fishing made up 83% of the fishermen’s total household income, whereas in St. Thomas and St. John and Puerto Rico it contributed 74% and 68%, respectively. The contribution of fish traps to commercial fishing income ranged from 51% in the lowest trap tier in St. Thomas and St. John to 99% in the highest trap tier in St. Croix. On an island basis, the contribution of fish traps to fishing income was 75% in St. Croix, 61% in St. Thomas and St. John, and 59% in Puerto Rico. The value of fully rigged vessels ranged from $400 to $250,000. Over half of the fleet was worth $10,000 or less. The St. Thomas and St. John fleet reported the highest mean value, averaging $58,518. The Crucian and Puerto Rican fleets were considerably less valuable, averaging $19,831 and $8,652, respectively. The length of the vessels ranged from 14 to 40 feet. Fifty-nine percent of the sampled vessels were at least 23 feet in length. The average length of the St. Thomas and St. John fleet was 28 feet, whereas the fleets based in St. Croix and Puerto Rico averaged 21 feet. The engine’s propulsion ranged from 8 to 400 horsepower (hp). The mean engine power was 208 hp in St. Thomas and St. John, 108 hp in St. Croix, and 77 hp in Puerto Rico. Mechanical trap haulers and depth recorders were the most commonly used on-board equipment. About 55% of the sampled population reported owning mechanical trap haulers. In St. Thomas and St. John, 100% of the respondents had trap haulers compared to 52% in Puerto Rico and 20% in St. Croix. Forty-seven percent of the fishermen surveyed stated having depth recorders. Depth recorders were most common in the St. Thomas and St. John fleet (80%) and least common in the Puerto Rican fleet (37%). The limited presence of emergency position indication radio beacons (EPIRBS) and radar was the norm among the fish trap fleet. Only 8% of the respondents had EPIRBS and only 1% had radar. Interviewees stated that they fished between 1 and 350 fish traps. Puerto Rican respondents fished on average 39 fish traps, in contrast to St. Thomian and St. Johnian and Crucian respondents, who fished 94 and 27 fish traps, respectively. On average, Puerto Rican respondents fished 11 lobster traps, and St. Thomian and St. Johnian respondents fished 46 lobster traps. None of the Crucian respondents fished lobster traps. The number of fish traps built or purchased ranged between 0 and 175, and the number of lobster traps built or bought ranged between 0 and 200. Puerto Rican fishermen on average built or purchased 30 fish traps and 14 lobster traps, and St. Thomian and St. Johnian fishermen built or bought 30 fish traps and 11 lobster traps. Crucian fishermen built or bought 25 fish traps and no lobster traps. As a group, fish trap average life ranged between 1.3 and 5 years, and lobster traps lasted slightly longer, between 1.5 and 6 years. The study found that the chevron or arrowhead style was the most common trap design. Puerto Rican fishermen owned an average of 20 arrowhead traps. St. Thomian and St. Johnian and Crucian fishermen owned an average of 44 and 15 arrowhead fish traps, respectively. The second most popular trap design was the square trap style. Puerto Rican fishermen had an average of 9 square traps, whereas St. Thomian and St. Johnian fishermen had 33 traps and Crucian fishermen had 2 traps. Antillean Z (or S) -traps, rectangular and star traps were also used. Although Z (or S) -traps are considered the most productive trap design, fishermen prefer the smaller-sized arrowhead and square traps because they are easier and less expensive to build, and larger numbers of them can be safely deployed. The cost of a fish trap, complete with rope and buoys, varied significantly due to the wide range of construction materials utilized. On average, arrowhead traps commanded $94 in Puerto Rico, $251 in St. Thomas and St. John, and $119 in St. Croix. The number of trips per week ranged between 1 and 6. However, 72% of the respondents mentioned that they took two trips per week. On average, Puerto Rican fishermen took 2.1 trips per week, St. Thomian and St. Johnian fishermen took 1.4 trips per week, and Crucian fishermen took 2.5 trips per week. Most fishing trips started at dawn and finished early in the afternoon. Over 82% of the trips lasted 8 hours or less. On average, Puerto Rican fishermen hauled 27 fish traps per trip whereas St. Thomian and St. Johnian fishermen and Crucian fishermen hauled 68 and 26 fish traps per trip, respectively. The number of traps per string and soak time varied considerably across islands. In St. Croix, 84% of the respondents had a single trap per line, whereas in St. Thomas and St. John only 10% of the respondents had a single trap per line. Approximately, 43% of Puerto Rican fishermen used a single trap line. St. Thomian and St. Johnian fishermen soaked their traps for 6.9 days while Puerto Rican and Crucian fishermen soaked their traps for 5.7 and 3.6 days, respectively. The heterogeneity of the industry was also evidenced by the various economic surpluses generated. The survey illustrated that higher gross revenues did not necessarily translate into higher net revenues. Our analysis also showed that, on average, vessels in the trap fishery were able to cover their cash outlays, resulting in positive vessel income (i.e., financial profits). In Puerto Rico, annual financial profits ranged from $4,760 in the lowest trap tier to $32,467 in the highest tier, whereas in St. Thomas and St. John annual financial profits ranged from $3,744 in the lowest tier to $13,652 in the highest tier. In St. Croix, annual financial profits ranged between $9,229 and $15,781. The survey also showed that economic profits varied significantly across tiers. Economic profits measure residual income after deducting the remuneration required to keep the various factors of production in their existing employment. In Puerto Rico, annual economic profits ranged from ($9,339) in the lowest trap tier to $ 8,711 in the highest trap tier. In St. Thomas and St. John, annual economic profits ranged from ($7,920) in the highest tier to ($18,486) in the second highest tier. In St. Croix, annual economic profits ranged between ($7,453) to $10,674. The presence of positive financial profits and negative economic profits suggests that higher economic returns could be earned from a societal perspective by redirecting some of these scarce capital and human resources elsewhere in the economy. Furthermore, the presence of negative economic earnings is evidence that the fishery is overcapitalized and that steps need to be taken to ensure the long-run economic viability of the industry. The presence of positive financial returns provides managers with a window of opportunity to adopt policies that will strengthen the biological and economic performance of the fishery while minimizing any adverse impacts on local fishing communities. Finally, the document concludes by detailing how the costs and earnings information could be used to develop economic models that evaluate management proposals. (PDF contains 147 pages)

Ecological condition of coastal ocean waters along the U.S. Western Continental Shelf: 2003

Executive Summary: The western National Coastal Assessment (NCA-West) program of EPA, in conjunction with the NOAA National Ocean Service (NOS), conducted an assessment of the status of ecological condition of soft sediment habitats and overlying waters along the western U.S. continental shelf, between the target depths of 30 and 120 m, during June 2003. NCA-West and NOAA/NOS partnered with the West Coast states (Washington (WA), Oregon (OR), and California (CA)), and the Southern California Coastal Water Research Project (SCCWRP) Bight ’03 program to conduct the survey. A total of 257 stations were sampled from Cape Flattery, WA to the Mexican border using standard methods and indicators applied in previous coastal NCA projects. A key study feature was the incorporation of a stratified-random sampling design with stations stratified by state and National Marine Sanctuary (NMS) status. Each of the three states was represented by at least 50 random stations. There also were a total of 84 random stations located within NOAA’s five NMSs along the West Coast including the Olympic Coast NMS (OCNMS), Cordell Bank NMS (CBNMS), Gulf of Farallones NMS (GFNMS), Monterey Bay NMS (MBNMS), and Channel Islands NMS (CINMS). Collection of flatfish via hook-and-line for fish-tissue contaminant analysis was successful at 50 EMAP/NCA-West stations. Through a collaboration developed with the FRAM Division of the Northwest Fisheries Science Center, fish from an additional 63 stations in the same region and depth range were also analyzed for fish-tissue contaminants. Bottom depth throughout the region ranged from 28 m to 125 m for most stations. Two slightly deeper stations from the Southern California Bight (SCB) (131, 134 m) were included in the data set. About 44% of the survey area had sediments composed of sands (< 20% silt-clay), about 47% was composed of intermediate muddy sands (20-80% silt-clay), and about 9% was composed of muds (> 80% silt-clay). The majority of the survey area (97%) had relatively low percent total organic carbon (TOC) levels of < 2%, while a small portion (< 1%) had high TOC levels (> 5%), in a range potentially harmful to benthic fauna. Salinity of surface waters for 92% of the survey area were > 31 psu, with most stations < 31 psu associated with the Columbia River plume. Bottom salinities ranged only between 31.6 and 34.4 psu. There was virtually no difference in mean bottom salinities among states or between NMS and non-NMS stations. Temperatures of surface water (range 8.5 -19.9 °C) and bottom water (range 5.8 -14.7 °C) averaged several degrees higher in CA in comparison to WA and OR. The Δσt index of watercolumn stratification indicated that about 31% of the survey area had strong vertical stratification of the water column. The index was greatest for waters off WA and lowest for CA waters. Only about 2.6 % of the survey area had surface dissolved oxygen (DO) concentrations ≤ 4.8 mg/L, and there were no values below the lower threshold (2.3 mg/L) considered harmful to the survival and growth of marine animals. Surface DO concentrations were higher in WA and OR waters than in CA, and higher in the OC NMS than in the CA sanctuaries. An estimated 94.3% of the area had bottom-water DO concentrations ≤ 4.8 mg/L and 6.6% had concentrations ≤ 2.3 mg/L. The high prevalence of DO from 2.3 to 4.8 mg/L (85% of survey area) is believed to be associated with the upwelling of naturally low DO water across the West Coast shelf. Mean TSS and transmissivity in surface waters (excluding OR due to sample problems) were slightly higher and lower, respectively, for stations in WA than for those in CA. There was little difference in mean TSS or transmissivity between NMS and non-NMS locations. Mean transmissivity in bottom waters, though higher in comparison to surface waters, showed little difference among geographic regions or between NMS and non-NMS locations. Concentrations of nitrate + nitrite, ammonium, total dissolved inorganic nitrogen (DIN) and orthophosphate (P) in surface waters tended to be highest in CA compared to WA and OR, and higher in the CA NMS stations compared to CA non-sanctuary stations. Measurements of silicate in surface waters were limited to WA and CA (exclusive of the SCB) and showed that concentrations were similar between the two states and approximately twice as high in CA sanctuaries compared to OCNMS or nonsanctuary locations in either state. The elevated nutrient concentrations observed at CA NMS stations are consistent with the presence of strong upwelling at these sites at the time of sampling. Approximately 93% of the area had DIN/P values ≤ 16, indicative of nitrogen limitation. Mean DIN/P ratios were similar among the three states, although the mean for the OCNMS was less than half that of the CA sanctuaries or nonsanctuary locations. Concentrations of chlorophyll a in surface waters ranged from 0 to 28 μg L-1, with 50% of the area having values < 3.9 μg L-1 and 10% having values > 14.5 μg L-1. The mean concentration of chlorophyll a for CA was less than half that of WA and OR locations, and concentrations were lowest in non-sanctuary sites in CA and highest at the OCNMS. Shelf sediments throughout the survey area were relatively uncontaminated with the exception of a group of stations within the SCB. Overall, about 99% of the total survey area was rated in good condition (<5 chemicals measured above corresponding effect range low (ERL) concentrations). Only the pesticides 4,4′-DDE and total DDT exceeded corresponding effect range-median (ERM) values, all at stations in CA near Los Angeles. Ten other contaminants including seven metals (As, Cd, Cr, Cu, Hg, Ag, Zn), 2-methylnaphthalene, low molecular weight PAHs, and total PCBs exceeded corresponding ERLs. The most prevalent in terms of area were chromium (31%), arsenic (8%), 2-methylnaphthalene (6%), cadmium (5%), and mercury (4%). The chromium contamination may be related to natural background sources common to the region. The 2-methylnaphthalene exceedances were conspicuously grouped around the CINMS. The mercury exceedances were all at non-sanctuary sites in CA, particularly in the Los Angeles area. Concentrations of cadmium in fish tissues exceeded the lower end of EPA’s non-cancer, human-health-risk range at nine of 50 EMAP/NCA-West and nine of 60 FRAM groundfish-survey stations, including a total of seven NMS stations in CA and two in the OCNMS. The human-health guidelines for all other contaminants were only exceeded for total PCBs at one station located in WA near the mouth of the Columbia River. Benthic species richness was relatively high in these offshore assemblages, ranging from 19 to 190 taxa per 0.1-m2 grab and averaging 79 taxa/grab. The high species richness was reflected over large areas of the shelf and was nearly three times greater than levels observed in estuarine samples along the West Coast (e.g NCA-West estuarine mean of 26 taxa/grab). Mean species richness was highest off CA (94 taxa/grab) and lower in OR and WA (55 and 56 taxa/grab, respectively). Mean species richness was very similar between sanctuary vs. non-sanctuary stations for both the CA and OR/WA regions. Mean diversity index H′ was highest in CA (5.36) and lowest in WA (4.27). There were no major differences in mean H′ between sanctuary vs. nonsanctuary stations for both the CA and OR/WA regions. A total of 1,482 taxa (1,108 to species) and 99,135 individuals were identified region-wide. Polychaetes, crustaceans and molluscs were the dominant taxa, both by percent abundance (59%, 17%, 12% respectively) and percent species (44%, 25%, 17%, respectively). There were no major differences in the percent composition of benthic communities among states or between NMSs and corresponding non-sanctuary sites. Densities averaged 3,788 m-2, about 30% of the average density for West Coast estuaries. Mean density of benthic fauna in the present offshore survey, averaged by state, was highest in CA (4,351 m-2) and lowest in OR (2,310 m-2). Mean densities were slightly higher at NMS stations vs. non-sanctuary stations for both the CA and OR/WA regions. The 10 most abundant taxa were the polychaetes Mediomastus spp., Magelona longicornis, Spiophanes berkeleyorum, Spiophanes bombyx, Spiophanes duplex, and Prionospio jubata; the bivalve Axinopsida serricata, the ophiuroid Amphiodia urtica, the decapod Pinnixa occidentalis, and the ostracod Euphilomedes carcharodonta. Mediomastus spp. and A. serricata were the two most abundant taxa overall. Although many of these taxa have broad geographic distributions throughout the region, the same species were not ranked among the 10 most abundant taxa consistently across states. The closest similarities among states were between OR and WA. At least half of the 10 most abundant taxa in NMSs were also dominant in corresponding nonsanctuary waters. Many of the abundant benthic species have wide latitudinal distributions along the West Coast shelf, with some species ranging from southern CA into the Gulf of Alaska or even the Aleutians. Of the 39 taxa on the list of 50 most abundant taxa that could be identified to species level, 85% have been reported at least once from estuaries of CA, OR, or WA exclusive of Puget Sound. Such broad latitudinal and estuarine distributions are suggestive of wide habitat tolerances. Thirteen (1.2%) of the 1,108 identified species are nonindigenous, with another 121 species classified as cryptogenic (of uncertain origin), and 208 species unclassified with respect to potential invasiveness. Despite uncertainties of classification, the number and densities of nonindigenous species appear to be much lower on the shelf than in the estuarine ecosystems of the Pacific Coast. Spionid polychaetes and the ampharetid polychaete Anobothrus gracilis were a major component of the nonindigenous species collected on the shelf. NOAA’s five NMSs along the West Coast of the U.S. appeared to be in good ecological condition, based on the measured indicators, with no evidence of major anthropogenic impacts or unusual environmental qualities compared to nearby nonsanctuary waters. Benthic communities in sanctuaries resembled those in corresponding non-sanctuary waters, with similarly high levels of species richness and diversity and low incidence of nonindigenous species. Most oceanographic features were also similar between sanctuary and non-sanctuary locations. Exceptions (e.g., higher concentrations of some nutrients in sanctuaries along the CA coast) appeared to be attributable to natural upwelling events in the area at the time of sampling. In addition, sediments within the sanctuaries were relatively uncontaminated, with none of the samples having any measured chemical in excess of ERM values. The ERL value for chromium was exceeded in sediments at the OCNMS, but at a much lower percentage of stations (four of 30) compared to WA and OR non-sanctuary areas (31 of 70 stations). ERL values were exceeded for arsenic, cadmium, chromium, 2- methylnaphthalene, low molecular weight PAHs, total DDT, and 4,4′-DDE at multiple sites within the CINMS. However, cases where total DDT, 4,4′-DDE, and chromium exceeded the ERL values were notably less prevalent at CINMS than in non-sanctuary waters of CA. In contrast, 2-methylnaphthalene above the ERL was much more prevalent in sediments at the CINMS compared to non-sanctuary waters off the coast of CA. While there are natural background sources of PAHs from oil seeps throughout the SCB, this does not explain the higher incidence of 2-methylnaphthalene contamination around CINMS. Two stations in CINMS also had levels of TOC (> 5%) potentially harmful to benthic fauna, though none of these sites exhibited symptoms of impaired benthic condition. This study showed no major evidence of extensive biological impacts linked to measured stressors. There were only two stations, both in CA, where low numbers of benthic species, diversity, or total faunal abundance co-occurred with high sediment contamination or low DO in bottom water. Such general lack of concordance suggests that these offshore waters are currently in good condition, with the lower-end values of the various biological attributes representing parts of a normal reference range controlled by natural factors. Results of multiple linear regression, performed using full model procedures to test for effects of combined abiotic environmental factors, suggested that latitude and depth had significant influences on benthic variables regionwide. Latitude had a significant inverse influence on all three of the above benthic variables, i.e. with values increasing as latitude decreased (p< 0.01), while depth had a significant direct influence on diversity (p < 0.001) and inverse effect on density (p <0.01). None of these variables varied significantly in relation to sediment % fines (at p< 0.1), although in general there was a tendency for muddier sediments (higher % fines) to have lower species richness and diversity and higher densities than coarser sediments. Alternatively, it is possible that for some of these sites the lower values of benthic variables reflect symptoms of disturbance induced by other unmeasured stressors. The indicators in this study included measures of stressors (e.g., chemical contaminants, eutrophication) that are often associated with adverse biological impacts in shallower estuarine and inland ecosystems. However, there may be other sources of humaninduced stress in these offshore systems (e.g., bottom trawling) that pose greater risks to ambient living resources and which have not been captured. Future monitoring efforts in these offshore areas should include indicators of such alternative sources of disturbance. (137pp.) (PDF contains 167 pages)

Hydroacoustic surveys: a non-destructive approach to monitoring fish distributions at National Marine Sanctuaries

The science of fisheries acoustics and its applicability to resource management have evolved over the past several decades. This document provides a basic description of fisheries acoustics and recommendations on using this technology for research and monitoring of fish distributions and habitats within sanctuaries. It also describes recent efforts aimed at applying fisheries acoustics to Gray’s Reef National Marine Sanctuary (GRNMS) (Figure 1). Historically, methods to assess the underwater environment have included net trawls, diver censuses, hook and line, video, sonar and other techniques deployed in a variety of ways. Fisheries acoustics, using active sonar, relies on the physics of sound traveling through water to quantify the distribution of biota in the water column. By sending a signal of a given frequency through the water column and recording the time of travel and the strength of the reflected signal, it is possible to determine the size and location of fish and estimate biomass from the acoustic backscatter. As a fisheries assessment tool, active hydroacoustics technology is an efficient, non-intrusive method of mapping the water column at a very fine spatial and temporal resolution. It provides a practical alternative to bottom and mid-water trawls, which are not allowed at GRNMS. Passive acoustics, which uses underwater hydrophones to record man-made and natural sounds such as fish spawning calls and sounds produced by marine mammals for communication and echolocation, can provide a useful, complementary survey tool. This report primarily deals with active acoustics, although the integration of active and passive acoustics is addressed as well. (PDF contains 32 pages)

Long-Term Monitoring of Ecological Conditions In Gray’s Reef National Marine Sanctuary: Comparison of soft-bottom benthic assemblages and contaminant levels in sediments and biota in Spring 2000 and 2005

As part of an ongoing program of benthic sampling and related assessments of sediment quality at Gray’s Reef National Marine Sanctuary (GRNMS) off the coast of Georgia, a survey of soft-bottom benthic habitats was conducted in spring 2005 to characterize condition of macroinfaunal assemblages and levels of chemical contaminants in sediments and biota relative to a baseline survey carried out in spring 2000. Distribution and abundance of macrobenthos were related foremost to sediment type (median particle size, % gravel), which in turn varied according to bottom-habitat mesoscale features (e.g., association with live bottom versus flat or rippled sand areas). Overall abundance and diversity of soft-bottom benthic communities were similar between the two years, though dominance patterns and relative abundances of component species were less repeatable. Seasonal summer pulses of a few taxa (e.g., the bivalve Ervilia sp. A) observed in 2000 were not observed in 2005. Concentrations of chemical contaminants in sediments and biota, though detectable in both years, were consistently at low, background levels and no exceedances of sediment probable bioeffect levels or FDA action levels for edible fish or shellfish were observed. Near-bottom dissolved oxygen levels and organic-matter content of sediments also have remained within normal ranges. Highly diverse benthic assemblages were found in both years, supporting the premise that GRNMS serves as an important reservoir of marine biodiversity. A total of 353 taxa (219 identified to species) were collected during the spring 2005 survey. Cumulatively, 588 taxa (371 identified to species) have been recorded in the sanctuary from surveys in 2000, 2001, 2002, and 2005. Species Accumulation Curves indicate that the theoretical maximum should be in excess of 600 species. Results of this study will be of value in advancing strategic science and management goals for GRNMS, including characterization and long-term monitoring of sanctuary resources and processes, as well as supporting evolving interests in ecosystem-based management of the surrounding South Atlantic Bight (SAB) ecosystem. (PDF contains 46 pages)

1979 Ecological study of fishes and the water quality characteristics of Florida Bay, Everglades National Park, Florida

Fish collections under varying ecological conditions were made by trawling and seining, monthly and quarterly in depths of <1 m to depths of 3 m of the Florida Bay portion of Everglades National Park, Florida. From May 1973 through September 1976, a total of 182,530 fishes representing 128 species and 50 families were taken at 27 stations. An additional 21 species were identified from sportfish-creel surveys and supplemental observations. Most of the species collected were juveniles of species that occur as adults in the Florida Bay creel census survey, or were small species that were seasonal residents. Marked temporal and spatial abundance of the catches was observed. The greatest numbers and biomass of the fishes occurred in the wet season (summer/fall), whereas lowest numbers and biomass appeared during the dry season (winter/spring) The greatest abundance and diversity of fishes was found in western Florida Bay followed by eastern and central Bay regions respectively. Overall, five species comprised 75% of the numerical total while eleven species made up 75% of the total biomass. Collections were dominated numerically by anchovies (Engraulidae), especially Anchoa mitchilli, in western Florida Bay. Mojarras (Gerridae), mostly silver jenny Eucinostomus gula, and porgies (Sparidae), especially pinfish Lagodon rhomboides, dominated numerically in central and eastern portions of the Bay, respectively. Except for salinity, other measured physico-chemical parameters (water temperature, pH, dissolved oxygen, and turbidity) showed no variation beyond ranges considered normal for shallow, tropical marine environments. Salinity varied from 0 to 66 ppt near the mainland. Nearshore hypersaline conditions (>45 ppt) persisted for nearly 2 years during the 1974 - 1975 severe drought period. Significant reductions in fish abundance/diversity were observed in relation to hypersaline conditions. Bay-wide macrobenthic communities were mapped (presence/absence) and were primarily comprised of turtle grass (Thalassia), shoalgrass [(Diplanthera = (Halodule)], and/or green algae Penicillus. Seasonal dieoff of seagrasses was observed in north-central Florida Bay. (PDF contains 107 pages)

Results of a fish health survey of North Biscayne Bay, June 1976-June 1977

Fish were collected weekly in Biscayne Bay using a monofilament gill net set from a small skiff during 20-30 minute intervals. Although weekly sampling took place for 2.5 years, only the data from samples collected from June 1976 to June 1977 were used in this document. Abnormal external conditions of fins and body were observed on each fish and recorded. Fish were returned immediately to their habitats. Fish collected in the time period for this study numbered 3,765 and included 32 species. Of these, 16 species, totaling 3,556 fish, were caught in sufficient numbers (20 or more) to warrant data analysis. Only 3 of the 16 species could be considered relatively unafflicted: Aetobatus narinari (spotted eagle ray), Diodon hystrix (porcupinefish), and Selene vomer (lookdown). More than 80% of the examined specimens of these three species were unaffected. Less than 20% of the specimens of Diapterus plumieri (striped mojarra), Micropogonias undulatus (Atlantic croaker), and Pogonias cromis (black drum) displayed normal conditions. The three most afflicted species were Diapterus plumieri, striped mojarra; Micropogonias undulatus, Atlantic croaker; and Pogonias cromis, black drum. Only 7, 3, and 7% respectively showed no external evidence of disease. Data described in this document were originally tabulated in the mid-1970s, remained unpublished, and are no longer available. This document was based on archived unpublished text, a data summary table, and figures. Most of the text and cited references were the ones used in the original manuscript and no attempt was made to update them. (PDF contains 44 pages)

Endocrine disruption in fish: An assessment of recent research and results

This report provides an assessment of recent investigations into endocrine disruption in fresh and saltwater species of fish. Most work to date has concen-trated on reproductive endocrine disruption. Laboratory studies have shown a variety of synthetic and natural chemicals including certain industrial intermediates, PAHs, PCBs, pesticides, dioxins, trace elements and plant sterols can interfere with the endocrine system in fish. The potency of most of these chemicals, however, is typically hundreds to thousands of times less than that of endog-enous hormones. Evidence of environmental endocrine disruption ranges from the presence of female egg proteins in males and reduced levels of endogenous hormones in both males and females, to gonadal histopathologies and intersex (presence of ovotestes) fish. Overt endocrine disruption in fish does not appear to be a ubiquitous environmental phenomenon, but rather more likely to occur near sewage treatment plants, pulp and paper mills, and in areas of high organic chemical contamination. However, more wide-spread endocrine disruption can occur in rivers with smaller flows and correspondingly large or numerous wastewater inputs. Some of the most severe examples of endocrine disruption in fish have been found adjacent to sewage treatment plants. Effects are thought to be caused prima-rily by natural and synthetic estrogens and to a lesser extent by the degradation products of alkylphenol poly-ethoxylate surfactants. Effects found in fish near pulp and paper mills include reduced levels of estrogens and androgens as well as masculinization of females, and has been linked to the presence of β-sitosterol, a plant sterol. Effects seen in areas of heavy industrial activity typically include depressed levels of estrogens and androgens as well as reduced gonadal growth, and may be linked to the presence of PAHs, PCBs, and possibly dioxins. At this time, however, there is no clear indication that large populations of fish are being seriously impacted as a result of endocrine disruption, although additional work is needed to address this possibility. (PDF contains 63 pages)

Cruise Report 72-S-4: Big Game Fish Investigations

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The Indonesian ornamental fish trade: case studies and options for improving livelihoods while promoting sustainability in Banggai and Banyuwangi

The four main objectives of this case study are: 1. Understanding market chains: an overview of the market chain from Indonesian reefs to international retail, with greater detail for case study sites. 2. Identifying poor people in the market chains: including people involved in the chain of custody and others who may be indirectly involved or impacted. 3. Understanding the influence of the marine ornamentals trade on the livelihoods of poor people: the case study looks specifically for underlying as well as obvious factors contributing to poverty reduction, and identify examples of better practice for poverty reduction in the marine ornamentals trade, including examples of positive livelihood outcomes from participation of poor people. 4. Identifying recommendations to improve poor people’s livelihoods. (PDF contains 286 pages)

A comparison of seafloor habitats and associated benthic fauna in areas open and closed to bottom trawling along the central California Continental Shelf

Executive Summary: A number of studies have shown that mobile, bottom-contact fishing gear (such as otter trawls) can alter seafloor habitats and associated biota. Considerably less is known about the recovery of these resources following such disturbances, though this information is critical for successful management. In part, this paucity of information can be attributed to the lack of access to adequate control sites – areas of the seafloor that are closed to fishing activity. Recent closures along the coast of central California provide an excellent opportunity to track the recovery of historically trawled areas and to compare recovery rates to adjacent areas that continue to be trawled. In June 2006 we initiated a multi-year study of the recovery of seafloor microhabitats and associated benthic fauna inside and outside two new Essential Fish Habitat (EFH) closures within the Cordell Bank and Gulf of the Farallones National Marine Sanctuaries. Study sites inside the EFH closure at Cordell Bank were located in historically active areas of fishing effort, which had not been trawled since 2003. Sites outside the EFH closure in the Gulf of Farallones were located in an area that continues to be actively trawled. All sites were located in unconsolidated sands at equivalent water depths. Video and still photographic data collected via a remotely operated vehicle (ROV) were used to quantify the abundance, richness, and diversity of microhabitats and epifaunal macro-invertebrates at recovering and actively trawled sites, while bottom grabs and conductivity/temperature/depth (CTD) casts were used to quantify infaunal diversity and to characterize local environmental conditions. Analysis of still photos found differences in common seafloor microhabitats between the recovering and actively trawled areas, while analysis of videographic data indicated that biogenic mound and biogenic depression microhabitats were significantly less abundant at trawled sites. Each of these features provides structure with which demersal fishes, across a wide range of size classes, have been observed to associate. Epifaunal macro-invertebrates were sparsely distributed and occurred in low numbers in both treatments. However, their total abundance was significantly different between treatments, which was attributable to lower densities at trawled sites. In addition, the dominant taxa were different between the two sites. Patchily-distributed buried brittle stars dominated the recovering site, and sea whips (Halipteris cf. willemoesi) were most numerous at the trawled site though they occurred in only five of ten transects. Numerical classification (cluster analysis) of the infaunal samples also revealed a clear difference between benthic assemblages in the recovering vs. trawled areas due to differences in the relative abundances of component species. There were no major differences in infaunal species richness, H′ diversity, or J′ evenness between recovering vs. trawled site groups. However, total infaunal abundance showed a significant difference attributable to much lower densities at trawled sites. This pattern was driven largely by the small oweniid polychaete Myriochele gracilis, which was the most abundant species in the overall study region though significantly less abundant at trawled sites. Other taxa that were significantly less abundant at trawled sites included the polychaete M. olgae and the polychaete family Terebellidae. In contrast, the thyasirid bivalve Axinopsida serricata and the polychaetes Spiophanes spp. (mostly S. duplex), Prionospio spp., and Scoloplos armiger all had significantly to near significantly higher abundances at trawled sites. As a result of such contrasting species patterns, there also was a significant difference in the overall dominance structure of infaunal assemblages between the two treatments. It is suggested that the observed biological patterns were the result of trawling impacts and varying levels of recovery due to the difference in trawling status between the two areas. The EFH closure was established in June 2006, within a month of when sampling was conducted for the present study, however, the stations within this closure area are at sites that actually have experienced little trawling since 2003, based on National Marine Fishery Service trawl records. Thus, the three-year period would be sufficient time for some post-trawling changes to have occurred. Other results from this study (e.g., similarly moderate numbers of infaunal species in both areas that are lower than values recorded elsewhere in comparable habitats along the California continental shelf) also indicate that recovery within the closure area is not yet complete. Additional sampling is needed to evaluate subsequent recovery trends and persistence of effects. Furthermore, to date, the study has been limited to unconsolidated substrates. Ultimately, the goal of this project is to characterize the recovery trajectories of a wide spectrum of seafloor habitats and communities and to link that recovery to the dynamics of exploited marine fishes. (PDF has 48 pages.)