STREAM Journal, Vol. 6, No. 1, pp 1-21. Jan-March 2007

CONTENTS: Approaches to understanding pond-dike systems in Asia: the POND-LIVE project approach, by Dave Little, Marc Verdegem and Roel Bosma. The contribution of fish ponds to nutrient cycling in integrated farming systems, by P.N. Muendo, J.J. Stoorvogel and Marc Verdegem. Improving the contribution of fishfarming to livelihoods in Northeast Thailand, by Chittra Arjinkit, Roel Bosma, Danai Turongrouang. Benefits of pond-dike systems in Bangladesh, by M.S. Kabir, M.A. Wahab and Marc Verdegem. Common carp increases rohu production in farmers ponds, by Mohammad Mustafizur Rahman, Md. Abdul Wahab and Marc C.J. Verdegem. Improving pond-dike farming systems in the Mekong delta, Vietnam; the Can Tho approach, by Dang Kieu Nhan, Le Thanh Duong, Le Thanh Phong, Roel H. Bosma and Marc C.J. Verdegem. Fuzzy pathways for farm development in Vietnam, by Roel H. Bosma, Le Thanh Phong, and Dang Kieu Nhan.

Some effects of tropical storm Agnes on water quality in the Patuxent River estuary

A post Agnes study emphasizing environmental factors...weekly sampling at eight stations from 28 June to August 30, 1972. Spatial and temporal changes in the distribution of many factors, e.g., salinity, dissolved oxygen (DO), seston, particulate carbon and nitrogen, inorganic and organic fractions of dissolved nitrogen and phosphorus, and chlorophyll a were studied and compared to earlier extensive records. Patterns shown by the present data were compared especially with a local heavy storm that occurred in the Patuxent drainage basin during July 1963. Some interesting correlations were observed in the data. (PDF has 39 pages.)

Some effects of Hurricane Agnes on water quality in the Patuxent River Estuary

A post-Agnes study that emphasized environmental factors was carried out on the Patuxent River estuary with weekly sampling at eight stations from 28 June t o 30 August 1972. Spatial and temporal changes in the distribution of many factors , e.g., salinity , dissolved oxygen, seston, particulate carbon and nitrogen, inorganic and organic fractions of dissolved nitrogen and phosphorus, and chlorophyll a were studied and compared t o extensive earlier records. Patterns shown by the present data were compared especially with a local heavy storm that occurred in the Patuxent drainage basin during July 1969. Estimates were made of the amounts of material contributed via upland drainage. A first approximation indicated that 14.8 x l0 (3) metric tons of seston were contributed t o the head of the estuary between 21 and 24 June. (PDF contains 46 pages)

Aquaculture Asia, Vol.13, No.4, pp.1-51, October-December 2008

Editorial An increasingly secure future for wastewater-fed aquaculture in Kolkata, India? by Peter Edwards. First culture-based fisheries growth cycle in Lao PDR is overwhelmingly encouraging, by Sena De Silva. Revival of abandoned shrimp farms in Krishna District of Andhra Pradesh, by National Centre for Sustainable Aquaculture (NaCSA). Growth of forward and backward industries linked with aquaculture in Kolleru Lake area, Andhra Pradesh, India, by A. K. Roy, G. S. Saha, P. Kumaraiah and N. Sarangi Effective marketing strategies for economic viability of prawn farming in Kuttanad, India, by Ranjeet K. and B. Madhusoodana Kurup. Applications of nutritional biotechnology in aquaculture, by S.D. Singh, S.K. Nayak, M. Sekar and B.K. Behera. Some technical and management aspects of catfish hatcheries in Hong Ngu district, Dong Thap province, Vietnam, by H. P. Hung, N. T. T. An, N. V. Trieu, D. T. Yen, U. Na-Nakorn, Thuy T. T. Nguyen. Nodavirus: An emerging threat to freshwater prawn farming, by Biju Sam Kamalam, J., Saravanan, S. and Ajith Stalin, J.L. Asia-Pacific Marine Finfish Aquaculture Network Magazine: Asian seabass farming: Brainstorming workshop and training in India. Comparative study for broodstock management of grey mullet (Mugil cephalus L.) in cages and earthen ponds with hormone treatment, by Nani Gopal Das, Md. Shahadat Hossain, Sushanta Bhattacharjee and Prabal Barua. Cultivation of gilthead sea bream (Sparus auratus L.) in low saline inland water of the southern part of Israel desert, by Samuel Appelbaum and A. Jesu Arockia Raj. Mariculture development opportunities in SE Sulawesi, Indonesia, by La Ode M. Aslan, Hotman Hutauruk, Armen Zulham,Irwan Effendy, Mhummaed Atid, Michael Phillips, Lars Olsen, Brendan Larkin, Sena S De Silva, Geoff Gooley. Improved hatchery and grow-out technology for marine finfish. NACA Newsletter

Using forecasts to protect Federal facilities in the path of Hurricane Isabel

Hurricane Isabel made landfall as a Category 2 Hurricane on 18 September 2003, on the North Carolina Outer Banks between Cape Lookout and Cape Hatteras, then coursed northwestward through Pamlico Sound and west of Chesapeake Bay where it downgraded to a tropical storm. Wind damage on the west and southwest shores of Pamlico Sound and the western shore of Chesapeake Bay was moderate, but major damage resulted from the storm tide. The NOAA, National Ocean Service, National Centers for Coastal Ocean Sciences, Center for Coastal Fisheries and Habitat Research at Beaufort, North Carolina and the Center for Coastal Environmental Health and Biomedical Research Branch at Oxford, Maryland have hurricane preparedness plans in place. These plans call for tropical storms and hurricanes to be tracked carefully through NOAA National Weather Service (NWS) watches, warnings, and advisories. When a hurricane watch changes to a hurricane warning for the areas of Beaufort or Oxford, documented hurricane preparation plans are activated. Isabel exacted some wind damage at both Beaufort and Oxford. Storm tide caused damage at Oxford, where area-wide flooding isolated the laboratory for many hours. Storm tide also caused damage at Beaufort. Because of their geographic locations on or near the open ocean (Beaufort) or on or near large estuaries (Beaufort and Oxford), storm tide poses a major threat to these NOAA facilities and the safety of federal employees. Damage from storm surge and windblown water depends on the track and intensity of a storm. One tool used to predict storm surge is the Sea, Lake, and Overland Surges from Hurricanes (SLOSH) model of the NWS, which provides valuable surge forecasts that aid in hurricane preparation.

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)

Magnitude and Extent of Contaminated Sediment and Toxicity in Chesapeake Bay

INTRODUCTION: This report summarizes the results of NOAA's sediment toxicity, chemistry, and benthic community studies in the Chesapeake Bay estuary. As part of the National Status and Trends (NS&T) Program, NOAA has conducted studies to determine the spatial extent and severity of chemical contamination and associated adverse biological effects in coastal bays and estuaries of the United States since 1991. Sediment contamination in U.S. coastal areas is a major environmental issue because of its potential toxic effects on biological resources and often, indirectly, on human health. Thus, characterizing and delineating areas of sediment contamination and toxicity and demonstrating their effect(s) on benthic living resources are viewed as important goals of coastal resource management. Benthic community studies have a history of use in regional estuarine monitoring programs and have been shown to be an effective indicator for describing the extent and magnitude of pollution impacts in estuarine ecosystems, as well as for assessing the effectiveness of management actions. Chesapeake Bay is the largest estuarine system in the United States. Including tidal tributaries, the Bay has approximately 18,694 km of shoreline (more than the entire US West Coast). The watershed is over 165,000 km2 (64,000 miles2), and includes portions of six states (Delaware, Maryland, New York, Pennsylvania, Virginia, and West Virginia) and the District of Columbia. The population of the watershed exceeds 15 million people. There are 150 rivers and streams in the Chesapeake drainage basin. Within the watershed, five major rivers - the Susquehanna, Potomac, Rappahannock, York and James - provide almost 90% of the freshwater to the Bay. The Bay receives an equal volume of water from the Atlantic Ocean. In the upper Bay and tributaries, sediments are fine-grained silts and clays. Sediments in the middle Bay are mostly made of silts and clays derived from shoreline erosion. In the lower Bay, by contrast, the sediments are sandy. These particles come from shore erosion and inputs from the Atlantic Ocean. The introduction of European-style agriculture and large scale clearing of the watershed produced massive shifts in sediment dynamics of the Bay watershed. As early as the mid 1700s, some navigable rivers were filled in by sediment and sedimentation caused several colonial seaports to become landlocked. Toxic contaminants enter the Bay via atmospheric deposition, dissolved and particulate runoff from the watershed or direct discharge. While contaminants enter the Bay from several sources, sediments accumulate many toxic contaminants and thus reveal the status of input for these constituents. In the watershed, loading estimates indicate that the major sources of contaminants are point sources, stormwater runoff, atmospheric deposition, and spills. Point sources and urban runoff in the Bay proper contribute large quantities of contaminants. Pesticide inputs to the Bay have not been quantified. Baltimore Harbor and the Elizabeth River remain among the most contaminated areas in the Unites States. In the mainstem, deep sediment core analyses indicate that sediment accumulation rates are 2-10 times higher in the northern Bay than in the middle and lower Bay, and that sedimentation rates are 2-10 times higher than before European settlement throughout the Bay (NOAA 1998). The core samples show a decline in selected PAH compounds over the past several decades, but absolute concentrations are still 1 to 2 orders of magnitude above 'pristine' conditions. Core data also indicate that concentrations of PAHs, PCBs and, organochlorine pesticides do not demonstrate consistent trends over 25 years, but remain 10 times lower than sediments in the tributaries. In contrast, tri-butyl-tin (TBT) concentrations in the deep cores have declined significantly since it=s use was severely restricted. (PDF contains 241 pages)

Organic Contaminant Analytical Methods of the National Status and Trends Program: 2000-2006

This document describes the analytical methods used to quantify core organic chemicals in tissue and sediment collected as part of NOAA’s National Status and Trends Program (NS&T) for the years 2000-2006. Organic contaminat analytical methods used during the early years of the program are described in NOAA Technical Memoranda NOS ORCA 71 and 130 (Lauenstein and Cantillo, 1993; Lauenstein and Cantillo, 1998) for the years 1984-1992 and 1993-1996, respectively. These reports are available from our website (http://www.ccma.nos.gov) The methods detailed in this document were utilized by the Mussel Watch Project and Bioeffects Project, which are both part of the NS&T program. The Mussel Watch Project has been monitoring contaminants in bivalves and sediments since 1986 and is the longest active national contaminant monitoring program operating in U.S. costal waters. Approximately 280 Mussel Watch sites are sampled on a biennial and decadal timescale for bivalve tissue and sediment respectively. Similarly, the Bioeffects Assessment Project began in 1986 to characterize estuaries and near coastal environs. Using the sediment quality triad approach that measures; (1) levels of contaminants in sediments, (2) incidence and severity of toxicity, and (3) benthic macrofaunal conmmunities, the Bioeffects Project describes the spatial extent of sediment toxicity. Contaminant assessment is a core function of both projects. These methods, while discussed here in the context of sediment and bivalve tissue, were also used with other matricies including: fish fillet, fish liver, nepheloid layer, and suspended particulate matter. The methods described herein are for the core organic contaminants monitored in the NS&T Program and include polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), butyltins, and organochlorines that have been analyzed consistently over the past 15-20 years. Organic contaminants such as dioxins, perfluoro compounds and polybrominated biphenyl ethers (PBDEs) were analyzed periodically in special studies of the NS&T Program and will be described in another document. All of the analytical techniques described in this document were used by B&B Laboratories, Inc, an affiliate of TDI-Brook International, Inc. in College Station, Texas under contract to NOAA. The NS&T Program uses a performance-based system approach to obtain the best possible data quality and comparability, and requires laboratories to demonstrate precision, accuracy, and sensitivity to ensure results-based performance goals and measures. (PDF contains 75 pages)

Establishing National Ocean Service Priorities for Estuarine, Coastal, and Ocean Modeling: Capabilities, Gaps, and Preliminary Prioritization Factors

This report was developed to help establish National Ocean Service priorities and chart new directions for research and development of models for estuarine, coastal and ocean ecosystems based on user-driven requirements and supportive of sound coastal management, stewardship, and an ecosystem approach to management. (PDF contains 63 pages)

Fish Habitat Utilization Patterns and Evaluation of the Efficacy of Marine Protected Areas in Hawaii: Integration of NOAA Digital Benthic Habitat Mapping and Coral Reef Ecological Studies

Over the past four decades, the state of Hawaii has developed a system of eleven Marine Life Conservation Districts (MLCDs) to conserve and replenish marine resources around the state. Initially established to provide opportunities for public interaction with the marine environment, these MLCDs vary in size, habitat quality, and management regimes, providing an excellent opportunity to test hypotheses concerning marine protected area (MPA) design and function using multiple discreet sampling units. NOAA/NOS/NCCOS/Center for Coastal Monitoring and Assessment’s Biogeography Team developed digital benthic habitat maps for all MLCD and adjacent habitats. These maps were used to evaluate the efficacy of existing MLCDs for biodiversity conservation and fisheries replenishment, using a spatially explicit stratified random sampling design. Coupling the distribution of habitats and species habitat affinities using GIS technology elucidates species habitat utilization patterns at scales that are commensurate with ecosystem processes and is useful in defining essential fish habitat and biologically relevant boundaries for MPAs. Analysis of benthic cover validated the a priori classification of habitat types and provided justification for using these habitat strata to conduct stratified random sampling and analyses of fish habitat utilization patterns. Results showed that the abundance and distribution of species and assemblages exhibited strong correlations with habitat types. Fish assemblages in the colonized and uncolonized hardbottom habitats were found to be most similar among all of the habitat types. Much of the macroalgae habitat sampled was macroalgae growing on hard substrate, and as a result showed similarities with the other hardbottom assemblages. The fish assemblages in the sand habitats were highly variable but distinct from the other habitat types. Management regime also played an important role in the abundance and distribution of fish assemblages. MLCDs had higher values for most fish assemblage characteristics (e.g. biomass, size, diversity) compared with adjacent fished areas and Fisheries Management Areas (FMAs) across all habitat types. In addition, apex predators and other targeted resources species were more abundant and larger in the MLCDs, illustrating the effectiveness of these closures in conserving fish populations. Habitat complexity, quality, size and level of protection from fishing were important determinates of MLCD effectiveness with respect to their associated fish assemblages. (PDF contains 217 pages)

Extreme events and ecological forecasting

Almost all extreme events lasting less than several weeks that significantly impact ecosystems are weather related. This review examines the response of estuarine systems to intense short-term perturbations caused by major weather events such as hurricanes. Current knowledge concerning these effects is limited to relatively few studies where hurricanes and storms impacted estuaries with established environmental monitoring programs. Freshwater inputs associated with these storms were found to initially result in increased primary productivity. When hydrographic conditions are favorable, bacterial consumption of organic matter produced by the phytoplankton blooms and deposited during the initial runoff event can contribute to significant oxygen deficits during subsequent warmer periods. Salinity stress and habitat destruction associated with freshwater inputs, as well as anoxia, adversely affect benthic populations and fish. In contrast, mobile invertebrate species such as shrimp, which have a short life cycle and the ability to migrate during the runoff event, initially benefit from the increased primary productivity and decreased abundance of fish predators. Events studied so far indicate that estuaries rebound in one to three years following major short-term perturbations. However, repeated storm events without sufficient recovery time may cause a fundamental shift in ecosystem structure (Scavia et al. 2002). This is a scenario consistent with the predicted increase in hurricanes for the east coast of the United States. More work on the response of individual species to these stresses is needed so management of commercial resources can be adjusted to allow sufficient recovery time for affected populations.

Ecological forecasting: new tools for coastal and marine ecosystem management

Policy makers, natural resource managers, regulators, and the public often call on scientists to estimate the potential ecological changes caused by both natural and human-induced stresses, and to determine how those changes will impact people and the environment. To develop accurate forecasts of ecological changes we need to: 1) increase understanding of ecosystem composition, structure, and functioning, 2) expand ecosystem monitoring and apply advanced scientific information to make these complex data widely available, and 3) develop and improve forecast and interpretative tools that use a scientific basis to assess the results of management and science policy actions. (PDF contains 120 pages)

Fish assemblages and benthic habitats of Buck Island Reef National Monument (St. Croix, U.S. Virgin Islands) and the surrounding seascape: A characterization of spatial and temporal patterns

Since 1999, NOAA’s Biogeography Branch of the Center for Coastal Monitoring and Assessment (CCMA-BB) has been working with federal and territorial partners to characterize, monitor, and assess the status of the marine environment around northeastern St. Croix, U.S. Virgin Islands. This effort is part of the broader NOAA Coral Reef Conservation Program’s (CRCP) National Coral Reef Ecosystem Monitoring Program (NCREMP). With support from CRCP’s NCREMP, CCMA conducts the “Caribbean Coral Reef Ecosystem Monitoring project” (CREM) with goals to: (1) spatially characterize and monitor the distribution, abundance, and size of marine fauna associated with shallow water coral reef seascapes (mosaics of coral reefs, seagrasses, sand and mangroves); (2) relate this information to in situ fine-scale habitat data and the spatial distribution and diversity of habitat types using benthic habitat maps; (3) use this information to establish the knowledge base necessary for enacting management decisions in a spatial setting; (4) establish the efficacy of those management decisions; and (5) develop data collection and data management protocols. The monitoring effort in northeastern St. Croix was conducted through partnerships with the National Park Service (NPS) and the Virgin Islands Department of Planning and Natural Resources (VI-DPNR). The geographical focal point of the research is Buck Island Reef National Monument (BIRNM), a protected area originally established in 1961 and greatly expanded in 2001; however, the work also encompassed a large portion of the recently created St. Croix East End Marine Park (EEMP). Project funding is primarily provided by NOAA CRCP, CCMA and NPS. In recent decades, scientific and non-scientific observations have indicated that the structure and function of the coral reef ecosystem around northeastern St. Croix have been adversely impacted by a wide range of environmental stressors. The major stressors have included the mass Diadema die off in the early 1980s, a series of hurricanes beginning with Hurricane Hugo in 1989, overfishing, mass mortality of Acropora corals due to disease and several coral bleaching events, with the most severe mass bleaching episode in 2005. The area is also an important recreational resource supporting boating, snorkeling, diving and other water based activities. With so many potential threats to the marine ecosystem and a dramatic change in management strategy in 2003 when the park’s Interim Regulations (Presidential Proclamation No. 7392) established BIRNM as one of the first fully protected marine areas in NPS system, it became critical to identify existing marine fauna and their spatial distributions and temporal dynamics. This provides ecologically meaningful data to assess ecosystem condition, support decision making in spatial planning (including the evaluation of efficacy of current management strategies) and determine future information needs. The ultimate goal of the work is to better understand the coral reef ecosystems and to provide information toward protecting and enhancing coral reef ecosystems for the benefit of the system itself and to sustain the many goods and services that it offers society. This Technical Memorandum contains analysis of the first six years of fish survey data (2001-2006) and associated characterization of the benthos (1999-2006). The primary objectives were to quantify changes in fish species and assemblage diversity, abundance, biomass and size structure and to provide spatially explicit information on the distribution of key species or groups of species and to compare community structure inside (protected) versus outside (fished) areas of BIRNM. (PDF contains 100 pages).

A Biogeographic Assessment off North/Central California: To Support the Joint Management Plan Review for Cordell Bank, Gulf of the Farallones, and Monterey Bay National Marine Sanctuaries: Phase I - Marine Fishes, Birds and Mammals.

In the spring of 2001, NOAA’s National Marine Sanctuary Program (NMSP) and National Centers for Coastal Ocean Science (NCCOS), in consultation with the National Marine Fisheries Service (NMFS), launched a 24-month effort to define and assess biogeographic patterns of selected marine species found within and adjacent to the boundaries of three west coast National Marine Sanctuaries. These sanctuaries, Monterey Bay, Gulf of the Farallones, and Cordell Bank are conducting a joint review process to update sanctuary management plans. The management plans for these sanctuaries have not been updated for over ten years and the status of the natural resources and their management issues in and around the sanctuaries may have changed. In addition, significant accomplishments in research and resource assessments have been made within the region. Thus, it is important to incorporate new and expanding knowledge into the revised management plans for these Sanctuaries.

Ecological linkages: Marine and estuarine ecosystems of Central and Northern California

Three of California’s four National Marine Sanctuaries, Cordell Bank, Gulf of the Farallones, and Monterey Bay, are currently undergoing a comprehensive management plan review. As part of this review, NOAA’s National Marine Sanctuary Program (NMSP) has collaborated with NOAA’s National Centers for Coastal Ocean Science (NCCOS) to conduct a biogeographic assessment of selected marine resources using geographic information system (GIS) technology. This report complements the analyses conducted for this effort by providing an overview of the physical and biological characteristics of the region. Key ecosystems and species occurring in estuarine and marine waters are highlighted and linkages between them discussed. In addition, this report describes biogeographic processes operating to affect species’ distributional patterns. The biogeographic analyses build upon this background to further understanding of the biogeography of this region. (PDF contaons 172 pages)