A History of Benthic Research in the NMFS Northeast Fisheries Science Center

The Northeast Fisheries Science Center of NOAA's National Marine Fisheries Service has a long history of research on benthic invertebrates and habitats in support of the management of living marine resources. These studies began in the 1870's under Spencer F. Baird's guidance as part of an effort to characterize the Nation's fisheries and living marine resources and their ecological interactions. This century and a quarter of research has included many benthic invertebrate studies, including community characterizations, shellfish biology and culture, pathology, ecosystem energy budget modeling, habitat evaluations, assessments of human impacts, toxic chemical bioaccumulation in demersal food webs, habitat or endangered species management, benthic autecology, systematics (to define new species and species population boundaries), and other benthic studies. Here we review the scope of past and current studies as a background for strategic research planning and suggest areas for further research to support NOAA's goals of sustainable fisheries management, healthy coastal ecosystems, and protected species populations.

Annual report 2006 - North Pacific Marine Science Organization (PICES). Fifteenth meeting, Yokohama, Japan, October 13-22, 2006

◾ Report of Opening Session (p. 1) ◾ Report of Governing Council (p. 15) ◾ Report of the Finance and Administration Committee (p. 47) ◾ Reports of Science Board and Committees: Science Board Inter-sessional Meeting (p. 63); Science Board (p. 73); Biological Oceanography Committee (p. 87); Fishery Science Committee (p. 95); Marine Environmental Quality Committee (p. 105); MONITOR Technical Committee (p. 115); Physical Oceanography and Climate Committee (p. 125); Technical Committee on Data Exchange (p. 133) ◾ Reports of Sections, Working and Study Groups: Section on Carbon and Climate (p. 139); Section on Ecology of Harmful Algal Blooms in the North Pacific (p. 143); Working Group 18 on Mariculture in the 21st Century - The Intersection Between Ecology, Socio-economics and Production (p. 147); Working Group 19 on Ecosystem-Based Management Science and its Application to the North Pacific (p. 151); Working Group 20 on Evaluations of Climate Change Projections (p. 157); Working Group 21 on Non-indigenous Aquatic Species (p. 159); Study Group to Develop a Strategy for GOOS (p. 165) ◾ Reports of the Climate Change and Carrying Capacity Scientific Program: Implementation Panel on the CCCC Program (p. 169); CFAME Task Team (p. 175); MODEL Task Team (p. 181) ◾ Reports of Advisory Panels: Advisory Panel for a CREAMS/PICES Program in East Asian Marginal Seas (p. 187); Advisory Panel on Continuous Plankton Recorder Survey in the North Pacific (p. 193); Advisory Panel on Iron Fertilization Experiment in the Subarctic Pacific Ocean (p. 197); Advisory Panel on Marine Birds and Mammals (p. 201); Advisory Panel on Micronekton Sampling Inter-calibration Experiment (p. 205) ◾ Summary of Scientific Sessions and Workshops (p. 209) ◾ Membership List (p. 259) ◾ List of Participants (p. 277) ◾ List of PICES Acronyms (p. 301) ◾ List of Acronyms (p. 303)

Annual report 2007 - North Pacific Marine Science Organization (PICES). Sixteenth meeting, Victoria, Canada, October 26-November 5, 2007

Report of Opening Session (p. 1). Report of Governing Council (p. 15). Report of the Finance and Administration Committee (p. 65). Reports of Science Board and Committees: Science Board Inter-Sessional Meeting (p. 83); Science Board (p. 93); Biological Oceanography Committee (p. 105); Fishery Science Committee (p. 117); Marine Environmental Quality Committee (p. 129); Physical Oceanography and Climate Committee (p. 139); Technical Committee on Data Exchange (p. 145); Technical Committee on Monitoring (p. 153). Reports of Sections, Working and Study Groups: Section on Carbon and Climate (p. 161); Section on Ecology of Harmful Algal Blooms in the North Pacific (p. 167); Working Group 19 on Ecosystem-based Management Science and its Application to the North Pacific (p. 173); Working Group 20 on Evaluations of Climate Change Projections (p. 179); Working Group 21 on Non-indigenous Aquatic Species (p. 183); Study Group to Develop a Strategy for GOOS (p. 193); Study Group on Ecosystem Status Reporting (p. 203); Study Group on Marine Aquaculture and Ranching in the PICES Region (p. 213); Study Group on Scientific Cooperation between PICES and Non-member Countries (p. 225). Reports of the Climate Change and Carrying Capacity Program: Implementation Panel on the CCCC Program (p. 229); CFAME Task Team (p. 235); MODEL Task Team (p. 241). Reports of Advisory Panels: Advisory Panel for a CREAMS/PICES Program in East Asian Marginal Seas (p. 249); Advisory Panel on Continuous Plankton Recorder Survey in the North Pacific (p. 253); Advisory Panel on Iron Fertilization Experiment in the Subarctic Pacific Ocean (p. 255); Advisory Panel on Marine Birds and Mammals (p. 261); Advisory Panel on Micronekton Sampling Inter-calibration Experiment (p. 265). 2007 Review of PICES Publication Program (p. 269). Guidelines for PICES Temporary Expert Groups (p. 297). Summary of Scientific Sessions and Workshops (p. 313). Report of the ICES/PICES Conference for Early Career Scientists (p. 355). Membership (p. 367). Participants (p. 387). PICES Acronyms (p. 413). Acronyms (p. 415).

Historical knowledge of sharks: ancient science, earliest American encounters, and American science, fisheries, and utilization

In western civilization, the knowledge of the elasmobranch or selachian fishes (sharks and rays) begins with Aristotle (384–322 B.C.). Two of his extant works, the “Historia Animalium” and the “Generation of Animals,” both written about 330 B.C., demonstrate knowledge of elasmobranch fishes acquired by observation. Roman writers of works on natural history, such as Aelian and Pliny, who followed Aristotle, were compilers of available information. Their contribution was that they prevented the Greek knowledge from being lost, but they added few original observations. The fall of Rome, around 476 A.D., brought a period of economic regression and political chaos. These in turn brought intellectual thought to a standstill for nearly one thousand years, the period known as the Dark Ages. It would not be until the middle of the sixteenth century, well into the Renaissance, that knowledge of elasmobranchs would advance again. The works of Belon, Salviani, Rondelet, and Steno mark the beginnings of ichthyology, including the study of sharks and rays. The knowledge of sharks and rays increased slowly during and after the Renaissance, and the introduction of the Linnaean System of Nomenclature in 1735 marks the beginning of modern ichthyology. However, the first major work on sharks would not appear until the early nineteenth century. Knowledge acquired about sea animals usually follows their economic importance and exploitation, and this was also true with sharks. The first to learn about sharks in North America were the native fishermen who learned how, when, and where to catch them for food or for their oils. The early naturalists in America studied the land animals and plants; they had little interest in sharks. When faunistic works on fishes started to appear, naturalists just enumerated the species of sharks that they could discern. Throughout the U.S. colonial period, sharks were seldom utilized for food, although their liver oil or skins were often utilized. Throughout the nineteenth century, the Spiny Dogfish, Squalus acanthias, was the only shark species utilized in a large scale on both coasts. It was fished for its liver oil, which was used as a lubricant, and for lighting and tanning, and for its skin which was used as an abrasive. During the early part of the twentieth century, the Ocean Leather Company was started to process sea animals (primarily sharks) into leather, oil, fertilizer, fins, etc. The Ocean Leather Company enjoyed a monopoly on the shark leather industry for several decades. In 1937, the liver of the Soupfin Shark, Galeorhinus galeus, was found to be a rich source of vitamin A, and because the outbreak of World War II in 1938 interrupted the shipping of vitamin A from European sources, an intensive shark fishery soon developed along the U.S. West Coast. By 1939 the American shark leather fishery had transformed into the shark liver oil fishery of the early 1940’s, encompassing both coasts. By the late 1940’s, these fisheries were depleted because of overfishing and fishing in the nursery areas. Synthetic vitamin A appeared on the market in 1950, causing the fishery to be discontinued. During World War II, shark attacks on the survivors of sunken ships and downed aviators engendered the search for a shark repellent. This led to research aimed at understanding shark behavior and the sensory biology of sharks. From the late 1950’s to the 1980’s, funding from the Office of Naval Research was responsible for most of what was learned about the sensory biology of sharks.

Age determination manual of the Alaska Fisheries Science Center Age and Growth Program

The Age and Growth Program at the Alaska Fisheries Science Center is tasked with providing age data in order to improve the basic understanding of the ecology and fisheries dynamics of Alaskan fish species. The primary focus of the Age and Growth Program is to estimate ages from otoliths and other calcified structures for age-structured modeling of commercially exploited stocks; however, the program has recently expanded its interests to include numerous studies on topics ranging from age estimate validation to the growth and life history of non-target species. Because so many applications rely upon age data and particularly upon assurances as to their accuracy and precision, the Age and Growth Program has developed this practical guide to document the age determination of key groundfish species from Alaskan waters. The main objective of this manual is to describe techniques specific to the age determination of commercially and ecologically important species studied by the Age and Growth Program. The manual also provides general background information on otolith morphology, dissection, and preparation, as well as descriptions of methods used to measure precision and accuracy of age estimates. This manual is intended not only as a reference for age readers at the AFSC and other laboratories, but also to give insight into the quality of age estimates to scientists who routinely use such data.

National Centers for Coastal Ocean Science Coastal Ecosystem Assessment Program: a manual of methods

Environmental managers strive to preserve natural resources for future generations but have limited decision-making tools to define ecosystem health. Many programs offer relevant broad-scale, environmental policy information on regional ecosystem health. These programs provide evidence of environmental condition and change, but lack connections between local impacts and direct effects on living resources. To address this need, the National Oceanic and Atmospheric Administration/National Ocean Service (NOAA/NOS) Cooperative Oxford Laboratory (COL), in cooperation with federal, state, and academic partners, implemented an integrated biotic ecosystem assessment on a sub-watershed 14-digit Hydrologic Unit Code (HUD) scale in Chesapeake Bay. The goals of this effort were to 1) establish a suite of bioindicators that are sensitive to ecosystem change, 2) establish the effects of varying land-use patterns on water quality and the subsequent health of living resources, 3) communicate these findings to local decision-makers, and 4) evaluate the success of management decisions in these systems. To establish indicators, three sub-watersheds were chosen based on statistical analysis of land-use patterns to represent a gradient from developed to agricultural. The Magothy (developed), Corsica (agricultural), and Rhode (reference) Rivers were identified. A random stratified design was developed based on depth (2m contour) and river mile. Sampling approaches were coordinated within this structure to allow for robust system comparisons. The sampling approach was hierarchal, with metrics chosen to represent a range from community to cellular level responses across multiple organisms. This approach allowed for the identification of sub-lethal stressors, and assessment of their impact on the organism and subsequently the population. Fish, crabs, clams, oysters, benthic organisms, and bacteria were targeted, as each occupies a separate ecological niche and may respond dissimilarly to environmental stressors. Particular attention was focused on the use of pathobiology as a tool for assessing environmental condition. By integrating the biotic component with water quality, sediment indices, and land- use information, this holistic evaluation of ecosystem health will provide management entities with information needed to inform local decision-making processes and establish benchmarks for future restoration efforts.

Marine cage culture and the environment: twenty-first century science informing a sustainable industry

Technological innovation has made it possible to grow marine finfish in the coastal and open ocean. Along with this opportunity comes environmental risk. As a federal agency charged with stewardship of the nation’s marine resources, the National Oceanic and Atmospheric Administration (NOAA) requires tools to evaluate the benefits and risks that aquaculture poses in the marine environment, to implement policies and regulations which safeguard our marine and coastal ecosystems, and to inform production designs and operational procedures compatible with marine stewardship. There is an opportunity to apply the best available science and globally proven best management practices to regulate and guide a sustainable United States (U.S.) marine finfish farming aquaculture industry. There are strong economic incentives to develop this industry, and doing so in an environmentally responsible way is possible if stakeholders, the public and regulatory agencies have a clear understanding of the relative risks to the environment and the feasible solutions to minimize, manage or eliminate those risks. This report spans many of the environmental challenges that marine finfish aquaculture faces. We believe that it will serve as a useful tool to those interested in and responsible for the industry and safeguarding the health, productivity and resilience of our marine ecosystems. This report aims to provide a comprehensive review of some predominant environmental risks that marine fish cage culture aquaculture, as it is currently conducted, poses in the marine environment and designs and practices now in use to address these environmental risks in the U.S. and elsewhere. Today’s finfish aquaculture industry has learned, adapted and improved to lessen or eliminate impacts to the marine habitats in which it operates. What progress has been made? What has been learned? How have practices changed and what are the results in terms of water quality, benthic, and other environmental effects? To answer these questions we conducted a critical review of the large body of scientific work published since 2000 on the environmental impacts of marine finfish aquaculture around the world. Our report includes results, findings and recommendations from over 420 papers, primarily from peer-reviewed professional journals. This report provides a broad overview of the twenty-first century marine finfish aquaculture industry, with a targeted focus on potential impacts to water quality, sediment chemistry, benthic communities, marine life and sensitive habitats. Other environmental issues including fish health, genetic issues, and feed formulation were beyond the scope of this report and are being addressed in other initiatives and reports. Also absent is detailed information about complex computer simulations that are used to model discharge, assimilation and accumulation of nutrient waste from farms. These tools are instrumental for siting and managing farms, and a comparative analysis of these models is underway by NOAA.

A biogeographic asssessment of seabirds, deep sea corals and ocean habitats of the New York Bight: science to support offshore spatial planning

This report provides a compilation of new maps and spatial assessments for seabirds, bathymetry, surficial sediments, deep sea corals, and oceanographic habitats in support of offshore spatial planning led by the New York Department of State Ocean and Great Lakes Program. These diverse ecological themes represent priority information gaps left by past assessments and were requested by New York to better understand and balance ocean uses and environmental conservation in the Atlantic. The main goal of this report is to translate raw ecological, geomorphological and oceanographic data into maps and assessments that can be easily used and understood by coastal managers involved in offshore spatial planning. New York plans to integrate information in this report with other ecological, geophysical and human use data to obtain a broad perspective on the ocean environment, human uses and their interactions. New York will then use this information in an ecosystem-based framework to coordinate and support decisions balancing competing demands in their offshore environment, and ultimately develop a series of amendments to New York’s federally approved Coastal Management Program. The targeted users of this report and the compiled spatial information are New York coastal managers, but other State and federal decision-makers, offshore renewable energy development interests and environmental advocates will also find the information useful. In addition, the data and approaches will be useful to regional spatial planning initiatives set up by the Mid-Atlantic Regional Council on the Ocean (MARCO) and federal regional planning bodies for coastal and marine spatial planning.

National Centers for Coastal Ocean Science (NCCOS) research highlights in the Chesapeake Bay

The Chesapeake Bay is the largest estuary in the United States. It is a unique and valuable national treasure because of its ecological, recreational, economic and cultural benefits. The problems facing the Bay are well known and extensively documented, and are largely related to human uses of the watershed and resources within the Bay. Over the past several decades as the origins of the Chesapeake’s problems became clear, citizens groups and Federal, State, and local governments have entered into agreements and worked together to restore the Bay’s productivity and ecological health. In May 2010, President Barack Obama signed Executive Order number 13508 that tasked a team of Federal agencies to develop a way forward in the protection and restoration of the Chesapeake watershed. Success of both State and Federal efforts will depend on having relevant, sound information regarding the ecology and function of the system as the basis of management and decision making. In response to the executive order, the National Oceanic and Atmospheric Administration’s National Centers for Coastal Ocean Science (NCCOS) has compiled an overview of its research in Chesapeake Bay watershed. NCCOS has a long history of Chesapeake Bay research, investigating the causes and consequences of changes throughout the watershed’s ecosystems. This document presents a cross section of research results that have advanced the understanding of the structure and function of the Chesapeake and enabled the accurate and timely prediction of events with the potential to impact both human communities and ecosystems. There are three main focus areas: changes in land use patterns in the watershed and the related impacts on contaminant and pathogen distribution and concentrations; nutrient inputs and algal bloom events; and habitat use and life history patterns of species in the watershed. Land use changes in the Chesapeake Bay watershed have dramatically changed how the system functions. A comparison of several subsystems within the Bay drainages has shown that water quality is directly related to land use and how the land use affects ecosystem health of the rivers and streams that enter the Chesapeake Bay. Across the Chesapeake as a whole, the rivers that drain developed areas, such as the Potomac and James rivers, tend to have much more highly contaminated sediments than does the mainstem of the Bay itself. In addition to what might be considered traditional contaminants, such as hydrocarbons, new contaminants are appearing in measurable amounts. At fourteen sites studied in the Bay, thirteen different pharmaceuticals were detected. The impact of pharmaceuticals on organisms and the people who eat them is still unknown. The effects of water borne infections on people and marine life are known, however, and the exposure to certain bacteria is a significant health risk. A model is now available that predicts the likelihood of occurrence of a strain of bacteria known as Vibrio vulnificus throughout Bay waters.