Bycatch in marine fisheries

A review of the significant contributions in the peer-reviewed literature indicates that the discarding of marine fish known as bycatch remains one of the most significant problem facing fisheries managers. Bycatch has negative affects on marine biodiversity, is ripe with ethical and moral issues surrounding the waste of life from increased juvenile fish mortality, hinders commercial profitability and recreational satisfaction, increases management costs, and results in socio-cultural problems and conflicts. While appearing to have a simple conservation engineering solution, reducing or eliminating bycatch in marine fishing operations given the presently existing regulated open access management environment is demonstrated to actually be so complex that its effects can appear to be counter-intuitive. An ecosystem simulation model that explicitly incorporates the human and biological dimensions is used to evaluate proposed bycatch reduction regulations for two fishing fleets exploiting three out of seven species of fish, each with ten cohorts, in two resource areas. One of the fishing fleets is divided into two components representing commercial fishermen and recreational anglers. The seven fish species represent predator, prey, and competitor behaviors and one stock is treated as an endangered species. The results displayed in a series of figures demonstrate the potential unintended effects of simplistic management approaches and the need for a holistic and comprehensive approach to bycatch management. That is, an ecosystem model that explicitly incorporates socio-cultural and biophysical attributes into a common framework allows the magnitude and direction of behavioral responses to be predicted based on changes in governance or biophysical constraints to determine if management goals and objectives have been obtained through the use of quantitative metrics.

Estimating overall fish bycatch in U.S. commercial fisheries

Bycatch, or the unintended capture of fish, marine mammals, sea turtles, and seabirds by fishing gear, occurs to some degree in most fisheries. The recently released National Marine Fisheries Service’s (NMFS) U.S. National Bycatch Report provides information on bycatch in U.S. commercial fisheries by fishery and species. The report also provides national statistics in the form of national bycatch ratio and a national bycatch estimate. We describe the methods used to develop these statistics and compare them to similar studies. We conclude that the national bycatch ratio and national bycatch estimates developed by NMFS represent the best available information on bycatch in U.S. fisheries. However, given changes in bycatch management over time, as well as inter-annual variability in bycatch levels and a high percentage of fisheries for which data on bycatch are not currently available, we recommend that NMFS continue to support bycatch data collection and reporting efforts to improve the quality and quantity of bycatch data and estimates available to fisheries managers and scientists over time. This will enable NMFS to meet its requirements for bycatch reporting under the Magnuson-Stevens Act (MSA), as well as requirements for bycatch minimization under the MSA, Marine Mammal Protection Act, and Endangered Species Act.

Forestry Impacts on Freshwater Habitat of Anadromous Salmonids in the Pacific Northwest and Alaska: requirements for protection and restoration

This synthesis presents a science overview of the major forest management Issues involved in the recovery of anadromous salmonids affected by timber harvest in the Pacific Northwest and Alaska. The issues involve the components of ecosystem-based watershed management and how best to implement them, including how to: Design buffer zones to protect fish habitat while enabling economic timber production; Implement effective Best Management Practices (BMPs) to prevent nonpoint-source pollution; Develop watershed-level procedures across property boundaries to prevent cumulative impacts; Develop restoration procedures to contribute to recovery of ecosystem processes; and Enlist support of private landowners in watershed planning, protection, and restoration. Buffer zones, BMPs, cumulative impact prevention, and restoration are essential elements of what must be a comprehensive approach to habitat protection and restoration applied at the watershed level within a larger context of resource concerns in the river basin, species status under the Endangered Species Act (ESA), and regional environmental and economic issues (Fig. ES. 1). This synthesis 1) reviews salmonid habitat requirements and potential effects of logging; 2) describes the technical foundation of forest practices and restoration; 3) analyzes current federal and non-federal forest practices; and 4) recommends required elements of comprehensive watershed management for recovery of anadromous salmonids.

Threatened corals provide underexplored microbial habitats

Contemporary in-depth sequencing of environmental samples has provided novel insights into microbial community structures, revealing that their diversity had been previously underestimated. Communities in marine environments are commonly composed of a few dominant taxa and a high number of taxonomically diverse, low-abundance organisms. However, studying the roles and genomic information of these “rare” organisms remains challenging, because little is known about their ecological niches and the environmental conditions to which they respond. Given the current threat to coral reef ecosystems, we investigated the potential of corals to provide highly specialized habitats for bacterial taxa including those that are rarely detected or absent in surrounding reef waters. The analysis of more than 350,000 small subunit ribosomal RNA (16S rRNA) sequence tags and almost 2,000 nearly full-length 16S rRNA gene sequences revealed that rare seawater biosphere members are highly abundant or even dominant in diverse Caribbean corals. Closely related corals (in the same genus/family) harbored similar bacterial communities. At higher taxonomic levels, however, the similarities of these communities did not correlate with the phylogenetic relationships among corals, opening novel questions about the evolutionary stability of coral-microbial associations. Large proportions of OTUs (28.7–49.1%) were unique to the coral species of origin. Analysis of the most dominant ribotypes suggests that many uncovered bacterial taxa exist in coral habitats and await future exploration. Our results indicate that coral species, and by extension other animal hosts, act as specialized habitats of otherwise rare microbes in marine ecosystems. Here, deep sequencing provided insights into coral microbiota at an unparalleled resolution and revealed that corals harbor many bacterial taxa previously not known. Given that two of the coral species investigated are listed as threatened under the U.S. Endangered Species Act, our results add an important microbial diversity-based perspective to the significance of conserving coral reefs.

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

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

Combining stable isotopes and skeletal growth marks to detect habitat shifts in juvenile loggerhead sea turtles Caretta caretta

Understanding the phase and timing of ontogenetic habitat shifts underlies the study of a species’ life history and population dynamics. This information is especially critical to the conservation and management of threatened and endangered species, such as the loggerhead sea turtle Caretta caretta. The early life of loggerheads consists of a terrestrial egg and hatchling stage, a posthatchling and juvenile oceanic, pelagic feeding stage, and a juvenile neritic, primarily benthic feeding stage. In the present study, novel approaches were applied to explore the timing of the loggerhead ontogenetic shift from pelagic to benthic habitats. The most recent years of somatic growth are recorded as annual marks in humerus cross sections. A consistent growth mark pattern in benthic juvenile loggerheads was identified, with narrow growth marks in the interior of the bone transitioning to wider growth marks at the exterior, indicative of a sharp increase in growth rates at the transitional growth mark. This increase in annual growth is hypothesized to correlate with the ontogenetic shift from pelagic to benthic habitats. Stable isotopes of carbon and nitrogen just interior and exterior to the transitional growth mark, as well as stable isotopes from pelagic and benthic flora, fauna and loggerhead stomach contents, were analyzed to determine whether this transition related to a diet shift. The results clearly indicate that a dietary shift from oceanic/pelagic to neritic/benthic feeding corresponds to a transitional growth mark. The combination of stable isotope analysis with skeletochronology can elucidate the ecology of cryptic life history stages during loggerhead ontogeny.

Rapid assessment of stony coral richness and condition on Saba Bank, Netherlands Antilles

The benthic habitats of Saba Bank (17°25′N, 63°30′W) are at risk from maritime traffic, especially oil tankers (e.g., anchoring). To mitigate this risk, information is needed on the biodiversity and location of habitats to develop a zone use plan. A rapid survey to document the biodiversity of macro-algae, sponges, corals and fishes was conducted. Here we report on the richness and condition of stony coral species at 18 select sites, and we test for the effects of bottom type, depth, and distance from platform edge. Species richness was visually assessed by roving scuba diver with voucher specimens of each species collected. Coral tissue was examined for bleaching and diseases. Thirty-three coral species were documented. There were no significant differences in coral composition among bottom types or depth classes (ANOSIM, P>0.05). There was a significant difference between sites (ANOSIM, P<0.05) near and far from the platform edge. The number of coral species observed ranged from zero and one in algal dominated habitats to 23 at a reef habitat on the southern edge of the Bank. Five reef sites had stands of Acropora cervicornis, a critically endangered species on the IUCN redlist. Bleaching was evident at 82% of the sites assessed with 43 colonies bleached. Only three coral colonies were observed to have disease. Combining our findings with that of other studies, a total of 43 species have been documented from Saba Bank. The coral assemblage on the bank is representative and typical of those found elsewhere in the Caribbean. Although our findings will help develop effective protection, more information is needed on Saba Bank to create a comprehensive zone use plan. Nevertheless, immediate action is warranted to protect the diverse coral reef habitats documented here, especially those containing A. cervicornis.

Accelerating loss of seagrasses across the globe threatens coastal ecosystems

Coastal ecosystems and the services they provide are adversely affected by a wide variety of human activities. In particular, seagrass meadows are negatively affected by impacts accruing from the billion or more people who live within 50 km of them. Seagrass meadows provide important ecosystem services, including an estimated $1.9 trillion per year in the form of nutrient cycling; an order of magnitude enhancement of coral reef fish productivity; a habitat for thousands of fish, bird, and invertebrate species; and a major food source for endangered dugong, manatee, and green turtle. Although individual impacts from coastal development, degraded water quality, and climate change have been documented, there has been no quantitative global assessment of seagrass loss until now. Our comprehensive global assessment of 215 studies found that seagrasses have been disappearing at a rate of 110 square kilometers per year since 1980 and that 29% of the known areal extent has disappeared since seagrass areas were initially recorded in 1879. Furthermore, rates of decline have accelerated from a median of 0.9% per year before 1940 to 7% per year since 1990. Seagrass loss rates are comparable to those reported for mangroves, coral reefs, and tropical rainforests and place seagrass meadows among the most threatened ecosystems on earth.

Use of skeletochronological analysis to estimate the age of leatherback sea turtles Dermochelys coriacea in the western North Atlantic

Although growth rate and age data are essential for leatherback management, estimates of these demographic parameters remain speculative due to the cryptic life history of this endangered species. Skeletochronological analysis of scleral ossicles obtained from 8 captive, known-age and 33 wild leatherbacks originating from the western North Atlantic was conducted to characterize the ossicles and the growth marks within them. Ages were accurately estimated for the known-age turtles, and their growth mark attributes were used to calibrate growth mark counts for the ossicles from wild specimens. Due to growth mark compaction and resorption, the number of marks visible at ossicle section tips was consistently and significantly greater than the number visible along the lateral edges, demonstrating that growth mark counts should be performed at the tips so that age is not underestimated. A correction factor protocol that incorporated the trajectory of early growth increments was used to estimate the number of missing marks in those ossicles exhibiting resorption, which was then added to the number of observed marks to obtain an age estimate for each turtle. A generalized smoothing spline model, von Bertalanffy growth curve, and size-at-age function were used to obtain estimates of age at maturity for leatherbacks in the western North Atlantic. Results of these analyses suggest that median age at maturation for leatherbacks in this part of the world may range from 24.5 to 29 yr. These age estimates are much greater than those proposed in previous studies and have significant implications for population management and recovery.

Trends in counts of manatees Trichechus manatus latirostris from 1987 to 2006 in waters of Sarasota County, Florida, USA

To demonstrate the utility of distributional surveys for assessing relative abundance and trends in counts for a discrete area of coastline, aerial survey data from Sarasota County, Florida, USA, were analyzed for the years 1987 to 2006. The study area was divided into 3 regions: the Sarasota Bay Region (SBR; N = 353 surveys), Lemon Bay (N = 368), and the Myakka River (N = 209). Manatee counts varied significantly across seasons (p < 0.0001) for all 3 regions. Manatees within Sarasota County utilized open bays primarily in the warmer months. Such usage may have been influenced by resource availability. Conversely, usage of the Myakka River peaked in winter months when manatees seek warm-water refugia such as Warm Mineral Spring. Marginal means for yearly counts within Lemon Bay and the SBR increased significantly, beginning midway through the survey period (1996) until the early 2000s. In contrast, mean yearly counts within the Myakka River decreased over this time period. After record lows in 2003 for Lemon Bay and the Myakka River, and a considerable decline in 2004 for the SBR, mean yearly counts for all 3 regions showed an increasing trend over the remaining 2 yr of the study. Greater protection of manatee habitat and availability of forage coincided with the increase in numbers of manatees using Sarasota County waters during the 1990s, and the subsequent decline in numbers may be indicative of the increase in mortality in recent years due to watercraft collisions and severe red tide events.

Northeast Fisheries Observer Program manual, 2013

The National Marine Fisheries Service (NMFS) Northeast Fisheries Science Center (NEFSC) Fisheries Sampling Branch (FSB) collects, maintains, and distributes data for scientific and management purposes in the northwest Atlantic Ocean. FSB manages three separate but related observer programs: the Northeast Fisheries Observer Program (NEFOP), the Industry Funded Scallop (IFS) Observer Program, and the At Sea Monitoring (ASM) Program. For the purposes of this manual, “observers” refers to any observer/monitor working for the FSB. In 2011, FSB trained and deployed over 200 observers, provided coverage on a variety of fisheries, and completed over 15,000 sea days. Observed trips are required under many of the region's fishery management plans, and for some fisheries by other federal laws and authorities such as Amendment 16 and Framework 44, Magnuson-Stevens Fishery Conservation and Management Act, Marine Mammal Protection Act, the Endangered Species Act, the and the Sustainable Fisheries Act. The purpose of this guide is to provide FSB observers, as well as end users of NEFSC Observer Program data, with a detailed description of each data field collected. In addition to this manual, the NEFSC Observer Program Biological Sampling and Catch Estimation Manual provides summaries and tables intended to enable observers to quickly determine the correct sampling protocols and methods while at sea. This manual represents a revision of the data forms, collection procedures, and protocols described in the 1996 NEFSC Observer Program Manual. For documentation of other changes see Documentation of changes made to the NEFSC Fisheries Observer Program Manual, 2013.

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

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

Feasibility of using sea surface temperature imagery to mitigate cheloniid sea turtle–fishery interactions off the coast of northeastern USA

As sea turtles migrate along the Atlantic coast of the USA, their incidental capture in fisheries is a significant source of mortality. Because distribution of marine cheloniid turtles appears to be related, in part, to sea surface temperature (SST), the ability to predict water temperature over the continental shelf could be useful in minimizing turtle–fishery interactions. We analyzed 10 yr of advanced very high resolution radiometer (AVHRR) SST imagery to estimate the proportion of 18 spatial zones, nearshore and offshore of Hatteras, North Carolina, USA (35° N), to north of Cape Sable, Nova Scotia (44° N), at temperatures >10 to 15°C, by week. Detailed examples for 11°C, the temperature employed by some management actions in the study area, and for 14°C, the lowest temperature at which turtles were sighted by some studies in the area, demonstrate a predictable pattern of rapid warming in March and April, followed by rapid cooling in October and November, with nearshore waters warming more rapidly than those offshore. Of those loggerhead turtles Caretta caretta that stranded, were sighted, or were incidentally captured between Cape Hatteras, North Carolina, and Cape Cod, Massachusetts, those at lower latitudes occurred when 25% or more of the area reached a water temperature of 11°C, while those in the northern zones did not occur until 50% or more of the area had reached a water temperature of 14°C. This analysis provides a means of predicting marine cheloniid turtle presence, which can be helpful in regulating fisheries that seasonally interact with turtles.

Trade secrets: a ten year overview of the illegal import of sea turtle products into the United States

For more than 25 years all sea turtle products have been prohibited from international commerce by the 170-member nations of the Convention on International Trade in Endangered Species (CITES). Sea turtles continue to be threatened by direct take (including poaching) and illegal trade despite multi-national protection efforts. Although take may contribute significantly to sea turtle decline, illegal take is difficult to measure since there are few quantified records associated with legal fisheries and fewer still for illegal take (poaching). We can, however, quantify one portion of the illegal sea turtle trade by determining how many illegal products were seized at United States ports of entry over a recent 10-year period. The United States Fish and Wildlife Service (USFWS) oversees the import and export of wildlife and wildlife products, ensuring that wildlife trade complies with United States laws and international treaties. Additionally, the USFWS has legal authority to target suspected illegal wildlife activity through undercover and field investigations. In an effort to assess the scale of illegal sea turtle take and trade, we have conducted a 10-year (1994 – 2003) review of the law enforcement database maintained by the USFWS. This database tracks the number and type of wildlife cases, the quantity of seized products, and the penalties assessed against violators. These data are minimum estimates of the sea turtle products passing through the United States borders, as smuggled wildlife is oftentimes not detected.

Molecular methods for the genetic identification of salmonid prey from Pacific harbor seal (Phoca vitulina richardsi) scat

Twenty-six stocks of Pacific salmon and trout (Oncorhynchus spp.), representing evolutionary significant units (ESU), are listed as threatened or endangered under the Endangered Species Act (ESA) and six more stocks are currently being evaluated for listing. The ecological and economic consequences of these listings are large; therefore considerable effort has been made to understand and respond to these declining populations. Until recently, Pacific harbor seals (Phoca vitulina richardsi) on the west coast increased an average of 5% to 7% per year as a result of the Marine Mammal Protection Act of 1972 (Brown and Kohlman2). Pacific salmon are seasonally important prey for harbor seals (Roffe and Mate, 1984; Olesiuk, 1993); therefore quantifying and understanding the interaction between these two protected species is important for Morphobiologically sound management strategies. Because some Pacific salmonid species in a given area may be threatened or endangered, while others are relatively abundant, it is important to distinguish the species of salmonid upon which the harbor seals are preying. This study takes the first step in understanding these interactions by using molecular genetic tools for species-level identification of salmonid skeletal remains recovered from Pacific harbor seal scats.