Fisheries Habitat Research Articles

Source and fate of inorganic solutes in the Gibbon River, Yellowstone National Park, Wyoming, USA: I. Low-flow discharge and major solute chemistry

The Gibbon River in Yellowstone National Park (YNP) is an important natural resource and habitat for fisheries and wildlife. However, the Gibbon River differs from most other mountain rivers because its chemistry is affected by several geothermal sources including Norris Geyser Basin, Chocolate Pots, Gibbon Geyser Basin, Beryl Spring, and Terrace Spring. Norris Geyser Basin is one of the most dynamic geothermal areas in YNP, and the water discharging from Norris is much more acidic (pH 3) than other geothermal basins in the upper-Madison drainage (Gibbon and Firehole Rivers). Water samples and discharge data were obtained from the Gibbon River and its major tributaries near Norris Geyser Basin under the low-flow conditions of September 2006. Surface inflows from Norris Geyser Basin were sampled to identify point sources and to quantify solute loading to the Gibbon River. The source and fate of the major solutes (Ca, Mg, Na, K, SiO 2, Cl, F, HCO 3, SO 4, NO 3, and NH 4) in the Gibbon River were determined in this study and these results may provide an important link in understanding the health of the ecosystem and the behavior of many trace solutes. Norris Geyser Basin is the primary source of Na, K, Cl, SO 4, and N loads (35–58%) in the Gibbon River. The largest source of HCO 3 and F is in the lower Gibbon River reach. Most of the Ca and Mg originate in the Gibbon River upstream from Norris Geyser Basin. All the major solutes behave conservatively except for NH 4, which decreased substantially downstream from Gibbon Geyser Basin, and SiO 2, small amounts of which precipitated on mixing of thermal drainage with the river. As much as 9–14% of the river discharge at the gage is from thermal flows during this period.

Global Review of the Physical and Biological Effectiveness of Stream Habitat Rehabilitation Techniques

AbstractThe degradation of inland aquatic habitats caused by decades of human activities has led to worldwide efforts to rehabilitate freshwater habitats for fisheries and aquatic resources. We reviewed published evaluations of stream rehabilitation techniques from throughout the world, including studies on road improvement, riparian rehabilitation, floodplain connectivity and rehabilitation, instream habitat improvement, nutrient addition, and other, less‐common techniques. We summarize current knowledge about the effectiveness of these techniques for improving physical habitat and water quality and increasing fish and biotic production. Despite locating 345 studies on effectiveness of stream rehabilitation, firm conclusions about many specific techniques were difficult to make because of the limited information provided on physical habitat, water quality, and biota and because of the short duration and limited scope of most published evaluations. Reconnection of isolated habitats, floodplain rehabilitation, and instream habitat improvement have, however, proven effective for improving habitat and increasing local fish abundance under many circumstances. Techniques such as riparian rehabilitation, road improvements (sediment reduction), dam removal, and restoration of natural flood regimes have shown promise for restoring natural processes that create and maintain habitats, but no long‐term studies documenting their success have yet been published. Our review demonstrates that the failure of many rehabilitation projects to achieve objectives is attributable to inadequate assessment of historic conditions and factors limiting biotic production; poor understanding of watershed‐scale processes that influence localized projects; and monitoring at inappropriate spatial and temporal scales. We suggest an interim approach to sequencing rehabilitation projects that partially addresses these needs through protecting high‐quality habitats and restoring connectivity and watershed processes before implementing instream habitat improvement projects.

Introduction to Water Use From Arctic Lakes: Identification, Impacts, and Decision Support1

Introduction to Water Use From Arctic Lakes: Identification, Impacts, and Decision Support¹

Restoring coastal habitat using marsh terracing: The effect of cell size on nekton use

Marsh terracing is used to restore coastal wetlands by converting shallow nonvegetated bottom to intertidal marsh. Terraces are constructed from excavated bottom sediments, and are commonly arranged in a checkerboard pattern of square cells with open corners to form terrace fields. In 1999, terrace cells of three sizes (large = 122 m sides with 1.30 ha ponds; medium = 61 m sides with 0.29 ha ponds; small = 30 m sides with 0.06 ha ponds) were incorporated into a restoration project constructed at Galveston Island State Park, Texas, USA. This restoration project provided an opportunity to examine how nekton populations and the cost effectiveness of terracing projects vary with cell size. We compared nekton density and biomass (as measures of habitat value) in marsh and open water habitat types among the three cell sizes of the terrace fields. We also compared the habitat value of these terrace fields with the area before project construction, with nearby nonvegetated bottom, and with natural marsh habitat. Nekton abundance and biomass increased substantially in the project area following restoration by marsh terracing. An analysis of post-construction samples detected few statistically significant differences in animal density and biomass among cell sizes or between the terraced areas and adjacent natural habitats. Within terrace cells, density, biomass, and species richness were generally higher in marsh vegetation than over nonvegetated bottom. Using these post-construction density data, GIS, and population models for selected fishery species, we show that populations of most fishery species increase as cell size decreases. However, as cell size decreases, the cost of terrace construction increases much faster than population size. Therefore, terrace fields constructed of medium or large cells would be more cost effective in providing fishery habitat than would terraces composed of small cells.

Management of Adverse Effects of a Public Water Supply Well Field on the Aquatic Habitat of a Stratified Drift Stream in Eastern Connecticut

A study was conducted to determine the effect of water withdrawals from the University of Connecticut's (Storrs) water supply wells on the fisheries habitat of the Fenton River adjacent to the well field. The study was designed to investigate the relationships between in-stream flow and selected fish habitat in the section of the Fenton River situated in the main zone of influence of the pumping field. With the aid of historical data, new data collection, and mathematical simulation modeling, the relation between the magnitude and timing of groundwater withdrawals on the stage and flow of water in the stream was derived. Fish sampling and habitat modeling were used to assess the effects of human influence on certain reaches of the Fenton River. Among the various water management scenarios studied, several are presented that would optimize water withdrawals, while minimizing adverse effects on the stream flow and in-stream habitat.

Ecological observations on the colonial ascidian Didemnum sp. in a New England tide pool habitat

The colonial ascidian Didemnum sp. has colonized northwestern Atlantic coastal habitats from southern Long Island, New York, to Eastport, Maine. It is also present in offshore habitats of the Georges Bank fishing grounds. It threatens to alter fisheries habitats and shellfish aquacultures. Observations in a tide pool at Sandwich, MA from December 2003 to February 2006 show that Didemnum sp. tolerates water temperatures ranging from ≤ 1 to > 24 °C, with daily changes of up to 11 °C. It attaches to pebbles, cobbles, and boulders, and it overgrows other tunicates, seaweeds, sponges, and bivalves. From May to mid July, colonies appear as small patches on the bottoms of rocks. Colonies grow rapidly from July to September, with some growth into December, and they range in color from pink to pale yellow to pale orange. Colony health declines from October through April, presumably in response to changes in water temperatures, and this degenerative process is manifested by color changes, by the appearance of small dark brown spots that represent clumps of fecal pellets in the colony, by scavenging by periwinkles, and by a peeling-away of colonies from the sides of cobbles and boulders. At Sandwich, colonies died that were exposed to air at low tide. The species does not exhibit this seasonal cycle of growth and decline in subtidal habitats (40–65 m) on the Georges Bank fishing grounds where the daily climate is relatively stable and annual water temperatures range from 4 to 15 °C. Experiments in the tide pool with small colony fragments (5 to 9 cm 2) show they re-attach and grow rapidly by asexual budding, increasing in size 6- to 11-fold in the first 15 days. Didemnum sp. at Sandwich has no known predators except for common periwinkles ( Littorina littorea) that graze on degenerating colonies in the October to April time period and whenever colonies are stressed by desiccation. The tendencies of the ascidian (1) to attach to firm substrates, (2) to rapidly overgrow other species, (3) to tolerate a wide temperature range, (4) to be free from predation, and (5) to spread by colony fragmentation combine to make it a potential threat to benthic marine habitats and aquacultures. Didemnum sp. is known to overgrow mussels, oysters, and sea scallops, and it likely envelops other bivalves too.

Modelling a single-species closed habitat fishery with spatial heterogeneity and time delay

A mathematical model describing a single species fishery is presented. The coupling effect of intra-species interaction delay of the harvested species and the spatial non-homogeneity of the aquatic environment is studied. The analysis is performed in a finite domain with the help of Neumann boundary value problem which resembles a closed-habitat fishery. Existence, uniqueness and regularity of solutions are demonstrated using the method of upper-lower solution pair. Stability criteria of the system is derived and interpreted from a bio-economic viewpoint.

Protecting marine biodiversity: a comparison of individual habitat quotas and marine protected areas

Fisheries managers in the United States are required to identify and mitigate the adverse impacts of fishing activity on essential fish habitat (EFH). There are additional concerns that the viability of sessile noncommercial species, animals that are habitat dependent and (or) are themselves constituents of fishery habitat, may be threatened by fishing activities. We propose a system of individual habitat quotas (IHQ) to achieve habitat conservation and species protection cost effectively. Individual quotas of habitat impact units would be distributed to fishers with an aggregate quota set to maintain a target habitat "stock". Using a dynamic, spatially explicit fishery simulation model, we explore the efficiency and effectiveness of an IHQ policy versus marine protected areas (MPAs) for conserving habitat-dependent, sessile species of unknown spatial distributions. Our findings indicate that an IHQ policy with a conservatively established habitat target is better suited to the protection of sessile nontarget species than a rotating or fixed MPA policy.

Impacts of urbanization on West Nose Creek: a Canadian experience

The lower reaches of West Nose Creek have been subject to urbanization since the 1970s, leading to channel widening and excessive erosion. This paper discusses what would likely happen if urbanization were allowed to continue in the same manner. Comparisons are presented of the channel width and depth for both the upstream rural and downstream urbanizing reaches. Estimates of the evolution of the creek were generated by linking the dominant discharge to the entire shape and volume of the hydrograph that the creek is subjected to rather than solely considering peak discharges. otential remedial measures and stormwater management philosophies are discussed in relationship to instream flow needs (IFNs) initiatives. IFNs are generally developed by relating the amount of suitable aquatic habitat to the quantity of flow. The emphasis has so far been on IFNs for large river systems. Unfortunately, none of the IFN approaches cover streams that are subject to significant urbanization. In urbanized streams the issue is not as much the impacts due to withdrawals but due to significantly increased runoff rates and volumes generated within the urban areas. Examples are provided how fisheries habitat is impacted by the changed hydrologic regime and changed stream morphology.

Frontiers in Seafloor Mapping and Visualization

Over the past few years there have been remarkable and concomitant advances in sonar technology, positioning capabilities, and computer processing power that have revolutionized the mapping, imaging and exploration of the seafloor. Future developments must involve all aspects of the “seafloor mapping system,” including, sonars, ancillary sensors (motion sensors, positioning systems, and sound speed sensors), platforms upon which they are mounted, and the products that are produced. Current trends in sonar development involve the use of innovative new transducer materials and the application of sophisticated processing techniques including focusing algorithms that dynamically compensate for the curvature of the wavefront in the nearfield and thus allow narrower beam widths (higher lateral resolution) at close ranges . Future developments will involve “hybrid”, phase-comparison/beam-forming sonars, the development of broad-band “chirp” multibeam sonars, and perhaps synthetic aperture multibeam sonars. The inability to monitor the fine-scale spatial and temporal variability of the sound speed structure of the water column is often a limiting factor in the production of accurate maps of the seafloor; improvements in this area will involve continuous monitoring devices as well as improved ocean models and perhaps tomography. Remotely Operated Vehicles (ROV’s) and particularly Autonomous Underwater Vehicles (AUV’s) will become more important as platforms for seafloor mapping systems. There will also be great changes in the products produced from seafloor mapping and the processing necessary to create them. New processing algorithms are being developed that take advantage of the density of multibeam sonar data and use statistically robust techniques to “clean” massive data sets very rapidly. A range of approaches are being explored to use multibeam sonar bathymetry and imagery to extract quantitative information about seafloor properties, including those relevant to fisheries habitat. The density of these data also enable the use of interactive 3-D visualization and exploration tools specifically designed to facilitate the interpretation and analysis of very large, complex, multi-component spatial data sets. If properly georeferenced and treated, these complex data sets can be presented in a natural and intuitive manner that allows the simple integration and fusion of multiple components without compromise to the quantitative aspects of the data and opens up new worlds of interactive exploration to a multitude of users.

Protecting Marine Biodiversity: A Comparison of Individual Habitat Quota (IHQs) and Marine Protected Areas

Fisheries managers in the United States are required to identify and mitigate the adverse impacts of fishing activity on essential fish habitat (EFH). There are additional concerns that the viability of noncommercial species, animals that are habitat dependent and/or are themselves constituents of fishery habitat may still be threatened. We consider a cap-and-trade system for habitat conservation, individual habitat quotas for fisheries, to achieve habitat conservation and species protection goals cost effectively. Individual quotas of habitat impact units (HIUs) would be distributed to fishers with an aggregate quota set to maintain a target habitat stock of EFH conservation. Using a dynamic, spatially explicit fishery simulation model we explore the efficiency and cost effectiveness of an IHQ policy versus alternative marine protected area (MPA) configurations, at reducing the risk of extinguishing a habitat dependent species of unknown spatial distribution. Our findings indicate that an IHQ policy with a conservatively established habitat target is better suited to the protection of non-target species than a rotating or fixed MPA policy.

Internal tide—shelf topography interactions as a forcing factor governing the large-scale distribution and burial fluxes of particulate organic matter (POM) in the Benguela upwelling system

This study investigates the role of internal tides in driving the sedimentation and re-suspension of biogenic POM on the Namibian shelf and give rise to stable 500–800 km long shore alternating bands of high and low POM concentrations. Temperature time series data (September 2000–March 2001) from the benthic boundary layer at three sites are used to hypothesise that the dominant forcing mechanism are internal tides and their interaction with the shelf break zones. Vertical displacements of the temperature structure by 100–150 m at the outer shelf break (depth 450 m) are shown to occur through out the 6-month time series. In contrast at non-shelf break sites the vertical displacements of temperature are negligible. The shear–stresses predicted landward of the shelf break zone from 100–150 m vertical displacements of the temperature structure are significantly higher (>0.1 Pa) than the critical shear–stresses which govern the re-suspension of biogenic particles and fine sediments (0.05–0.1 Pa). Short-term ADCP data was used to show that critical shear–stress distribution at the different POM areas is consistent with the predicted net accumulation and net erosional zones of POM across the Namibian shelf. This study hypothesises that the barotropic–baroclinic tidal coupling governs vertical particle flux dynamics whereas Ekman and inertial flows are thought to govern the horizontal advection scales that result in the observed POM distribution. The importance of this improved dynamical understanding has implications for both carbon burial efficiency as well as the variability in the suitability of benthic fisheries habitats.

Seagrass population dynamics and water quality in the Great Barrier Reef region: A review and future research directions

Seagrasses in the Great Barrier Reef region, particularly in coastal habitats, act as a buffer between catchment inputs and reef communities and are important habitat for fisheries and a food source for dugong and green turtle. Within the Great Barrier Reef region there are four different seagrass habitat types now recognised. The spatial and temporal dynamics of the different types of seagrass habitat is poorly understood. In general seagrass growth is limited by light, disturbance and nutrient supply, and changes to any or all of these limiting factors may cause seagrass decline. The capacity of seagrasses to recover requires either recruitment via seeds or through vegetative growth. The ability of seagrass meadows to recover from large scale loss of seagrass cover observed during major events such as cyclones or due to anthropogenic disturbances such as dredging will usually require regeneration from seed bank. Limited research into the role of pollutants on seagrass survival suggests there may be ongoing impacts due to herbicides, pesticides and other chemical contaminants. Further research and monitoring of seagrass meadow dynamics and the influence of changing water quality on these is needed to enhance our ability to manage seagrasses on the Great Barrier Reef.

HABITAT–FISHERY LINKAGES AND MANGROVE LOSS IN THAILAND

The article develops a dynamic model of habitat–fishery linkage in which the habitat is being converted. The basic model is applied to a case study of the impacts of mangrove deforestation on the artisanal marine demersal and shellfish fisheries in Thailand. The comparative static effects of a change in mangrove area on the long‐run equilibrium level of effort and fish stocks, as well as on the resulting market harvesting supply of the fishery, are determined. By estimating parameters through pooled timE‐series and cross‐sectional data over the 1983–96 period for the five coastal zones along the Gulf of Thailand and Andaman Sea, the welfare impacts of mangrove deforestation are estimated. Mangrove conversion is expected to be a function of the return to shrimp farming and the input costs to farming shrimp, plus exogenous economic factors. The resulting aggregate reduced‐form level of mangrove clearing by all farmers in coastal areas is empirically estimated across the five coastal zones in Thailand over 1983–96. The policy implications of the findings are discussed with respect to Thailand and the modeling of habitat–fishery linkages.

Toward a community coastal sediment transport modeling system: The second workshop

Models for transport and the long‐term fate of particles in coastal waters are essential for a variety of applications related to commerce, defense, public health, and the quality of the marine environment. Examples include: analysis of waste disposal and transport and the fate of contaminated materials; evaluation of burial rates for naval mines or archaeological artifacts; prediction of water‐column optical properties; analysis of transport and the fate of biological particles; prediction of coastal flooding and coastal erosion; evaluation of impacts of sea‐level or wave‐climate changes and coastal development; planning for construction and maintenance of navigable waterways; evaluation of habitat for commercial fisheries; evaluation of impacts of natural or anthropogenic changes in coastal conditions on recreational activities; and design of intakes and outfalls for sewage treatment, cooling systems, and desalination plants.

Age, growth and radiometric age validation of a deep-sea, habitat-forming gorgonian (Primnoa resedaeformis) from the Gulf of Alaska

Sustainable fisheries require (1) viable stock populations with appropriate harvest limits and (2) appropriate habitat for fish to survive, forage, seek refuge, grow and reproduce. Some deep-water habitats, such as those formed by deep-water stands of coral, may be vulnerable to fishing disturbance. The rate at which habitat can be restored is a critical aspect of fishery management. The purpose of this study was to characterize growth rates for a habitatforming deep-sea coral. Two nearly complete colonies of red tree coral (Primnoa resedaeformis) collected from waters off southeast Alaska were used for an analysis of age and growth characteristics. CAT scans revealed that colonies consisted of multiple settlement events, where older basal structures provided for settlement of new colonies. The decay of 210 Pb over the length of the colony was used to validate age estimates from growth ring counts. Age estimates were over 100 yr for sections near the heavily calcified base. Based on validated growth ring counts, growth of red tree coral ranged from 1.60 to 2.32 cm per year in height and was approximately 0.36 mm per year in diameter. These growth rates suggest that the fishery habitat created by red tree coral is extremely vulnerable to bottom fishing activities and may take over 100 years to recover.

Marsh terracing as a wetland restoration tool for creating fishery habitat

Terracing is a relatively new wetland-restoration technique used to convert shallow subtidal bottom to marsh. This method uses existing bottom sediments to form terraces or ridges at marsh elevation. A terrace field is constructed by arranging these ridges in some pattern that maximizes intertidal edge and minimizes fetch between ridges; the intertidal area is planted with marsh vegetation. We examined the habitat value of terracing for fishery species at Sabine National Wildlife Refuge, Louisiana (USA) in spring and fall 1999 by quantifying and comparing nekton densities in a 9-yr-old terrace field and nearby reference area using a 1-m2 drop sampler. Decapod crustaceans were more abundant than fishes, composing 62% and 95% of all organisms we collected in spring and fall, respectively. White shrimp Litopenaeus setiferus, daggerblade grass shrimp Palaemonetes pugio, blue crab Callinectes sapidus, and brown shrimp Farfantepenaeus aztecus accounted for 94% of all crustaceans, whereas 60% of all fishes were gulf menhaden Brevoortia patronus. Mean densities of white shrimp (fall), daggerblade grass shrimp, blue crab, and brown shrimp (spring) were significantly greater in terrace marsh than on non-vegetated bottom in the reference pond. Densities of most nekton on non-vegetated bottom were similar in the terrace field and the reference pond, but gulf menhaden and white shrimp had higher densities at terrace pond sites and brown shrimp (spring) were more abundant at reference pond sites. The pattern for biomass was similar to that for density in that the mean biomass of most species was significantly greater at terrace marsh sites than reference pond sites and similar at terrace and reference pond sites. Terrace marsh, however, was not functionally equivalent to natural marsh, as mean densities of daggerblade grass shrimp (fall), brown shrimp (spring), and blue crab and mean biomass of white shrimp (fall), striped mullet Mugil cephalus (spring), and spotted seatrout Cynoscion nebulosus (fall) were greater at reference marsh sites than terrace marsh sites. Using these density and biomass patterns and the percentage of marsh and pond area in the terrace field, we concluded that terrace fields support higher standing crops of most fishery species compared with shallow marsh ponds of similar size. Future restoration projects could include design changes to increase the proportion of marsh in a terrace field and enhance the habitat value of marsh terraces for fishery species.

Multibeam sonars: Applications for fisheries research

Multibeam sonars are rapidly becoming a standard tool for seafloor mapping in support of geological, geophysical, and engineering applications. More recently, the ability of multibeam sonars to provide high-resolution, large areal coverage, and potentially quantitative, coregistered, backscatter has been applied very successfully to problems of defining fisheries habitat. While most multibeam sonars are designed to gate out all midwater returns, newly developed systems now allow access to the full data stream and thus offer the possibility of application to studies of pelagic and demersal fisheries. Traditional acoustic approaches to fisheries issues have used single beam echo sounders that sample a relatively small volume of the water column within a survey area. Multibeam sonars provide a mechanism to greatly enhance both the resolution and the area of coverage. When combined with powerful new 3-D visualization techniques, they can offer immediate feedback on fish behavior as well as the critical question of vessel avoidance. If properly calibrated, multibeam sonars can provide the means for much more robust assessment of stock levels and perhaps even species identification.

Integrated Coastal Management in the Philippines: Testing New Paradigms

With fisheries declining, coral reefs battered, mangrove forests under threat, pollution levels rising, and coastal communities experiencing increased poverty, the Philippines faces severe challenges in managing its coastal resources. Coastal management efforts began in the Philippines more than 20 years ago through various community-based projects. Now, integrated coastal management is expanding in the country and holds the potential to reverse the trends. This article analyzes the situation in relation to new approaches for coastal management being undertaken through the Coastal Resource Management Project supported by the United States Agency for International Development implemented by the Department of Environment and Natural Resources. This project, drawing on the lessons generated by past and ongoing coastal management initiatives, is emphasizing integrated approaches to management over narrowly focused fisheries management and habitat protection efforts. It highlights the increasingly important role of local governments and the changing roles of national government to effectively support integrated coastal management. Multisectoral collaboration is explained as standard procedure to achieve outcomes that are broad based and sustainable. Local and national level activities are contrasted and shown as essential complements in building institutionalization of resources management within all levels of government. A practical result framework is explained for measuring relative success at the local government level of implementing best practices for coastal management. Finally, lessons being learned related to collaboration, level of focus, education, and communication; who is responsible; and expansion of the project are highlighted.

Development of a seagrass-fish habitat model?I: A Seagrass Residency Index for economically important species

Seagrass plays a major role in supporting the processes and function of the marine environment and is a key fisheries habitat, which provides nursery, feeding and breeding areas for fish and crustaceans. Seagrass beds also stabilise the seabed, trap sediments, reduce coastal erosion and provide the basis for the food chain through photosynthesis. The goal of this project is to establish a seagrass–fish habitat spatial model that will quantitatively assess the economic value of seagrass habitats, particularly for fisheries production and this paper describes a preliminary step in the model construction. With the help of fisheries scientists from the South Australian Research and Development Institute (SARDI), the functional relationship of some economically important species of fish, crustaceans and molluscs to seagrass habitats was investigated. As a result, a ‘seagrass residency index’ (SRI) fior some species has been estimated indicating the species most likely to be affected by changes in health and abundance of the seagrass beds in the coastal waters of South Australia. The information collected mainly relates to the periods of time spent amongst seagrass beds, sheltered reefs and open waters at different life stages of the fish: larval/juvenile, adult/feeding and adult/spawning. It was then hypothesized that the SRI would be a weighted sum of the averages of the estimated residence time at each stage. This paper describes how the SRI figures were calculated and outlines the intended use of the indices, in conjunction with other information, to assess the value of seagrass habitats. Copyright © 2000 John Wiley & Sons, Ltd.