Structural microhabitat use by endemic cyprinids in a Mediterranean‐type river: Implications for restoration practices

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Recommendations for monitoring freshwater fishes in river restoration plans: A wasted opportunity for assessing impact

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Physical habitat,eco‐hydraulics and river design: a review and re‐evaluation of some popular concepts and methods

• 1. Improved linkage between physical characteristics of rivers and biological performance or potential is a recurrent theme in contemporary river survey, management and design. This paper examines the degree to which flow biotopes and functional habitats may be differentiated with respect to physical habitat delimiters, i.e. flow depth, velocity and Froude number.
• 2. Re‐examination of published data demonstrates only very broad associations between biotopes, functional habitats and ‘low’, ‘medium’ and ‘high’ bands in the chosen physical habitat delimiter. The associations are also not consistent between different delimiters.
• 3. Re‐analysis is complicated by considerations of research design and methodology. Further studies are required with greater control on the circumstances of observation (particularly flow stage and seasonality), which explicitly control for variance within and between different river cases, and which adopt more consistent terminology.
• 4. Field data for a single river reach at low and high flows indicate that use of the Froude number, in particular, requires careful interpretation. Very different velocity and depth combinations can exhibit similar Froude numbers. This may obscure important contrasts, such as those between channel margin and channel centreline environments.
• 5. Field data also reveal that the flow characteristics of even basic (riffle or pool) units of channel morphology exhibit strong stage‐dependence. There are also significant variations when channel margins are isolated from the definitions of the bedforms or analysis of the data. Current practice which seeks to simplify field survey to channel cross‐section transects is therefore likely to be misleading.
• 6. Given these difficulties, attempts to link biotopes with ecological response appear premature. Further research might, however, be directed to identifying possible associations between combinations of flow types and bedforms or functional habitats. In this sense, the biotope concept may be more profitably employed as one of several surrogate measures for potential biodiversity.

Copyright © 2006 John Wiley & Sons, Ltd.     

A new large‐scale and cost‐effective restoration method for cold‐water coral gardens

1. Gorgonians dwelling on the Mediterranean continental shelf are among the most frequent fishing bycatch taxa. These species display several traits, such as long lifespans and slow growth, which make them very vulnerable to the impacts caused by fishing activities with far‐reaching and long‐lasting effects.
2. Hence, restoration and mitigation actions are crucial to enhance and speed up the natural recovery of damaged cold‐water coral gardens. Given the growing concern to develop effective and affordable restoration actions, the present study aims to propose and technically validate a new large‐scale and cost‐effective restoration method.
3. This technique, named ‘badminton method', consists of attaching bycatch Eunicella cavolini colonies to cobble supports and returning them to the continental shelf by gently throwing the gorgonian transplants directly from a boat.
4. Two consecutive field experiments were conducted in order to find the best cobble type support and gorgonian size to be used: first, to evaluate the landing efficiency of gorgonian transplants at different depths (from 5 to 30 m) and second, to evaluate their capability to maintain a correct position over time.
5. Natural cobbles with large gorgonians attached were the best option. Field results and modelling approaches suggest that the transplants would correctly land on the continental shelf seabed in a predicted area of around 60 m². Moreover, they would successfully maintain an upright position ensuring gorgonian survival over time.
6. The success of this method highlights the feasibility of large‐scale and low‐cost restoration actions with promising results for the conservation and recovery of cold‐water coral gardens.

     

Re‐introduction of structurally complex wood jams promotes channel and habitat recovery from overwidening: Implications for river conservation

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Sampling techniques for burbot in a western non‐wadeable river

Burbot, Lota lota (L.), populations are declining throughout much of their native distribution. Although numerous aspects of burbot ecology are well understood, less is known about effective sampling techniques for burbot in lotic systems. Occupancy models were used to estimate the probability of detection () for three gears (6.4‐ and 19‐mm bar mesh hoop nets, night electric fishing), within the context of various habitat characteristics. During the summer, night electric fishing had the highest estimated detection probability for both juvenile (, 95% C.I.; 0.35, 0.26–0.46) and adult (0.30, 0.20–0.41) burbot. However, small‐mesh hoop nets (6.4‐mm bar mesh) had similar detection probabilities to night electric fishing for both juvenile (0.26, 0.17–0.36) and adult (0.27, 0.18–0.39) burbot during the summer. In autumn, a similar overlap between detection probabilities was observed for juvenile and adult burbot. Small‐mesh hoop nets had the highest estimated probability of detection for both juvenile and adult burbot (0.46, 0.33–0.59), whereas night electric fishing had a detection probability of 0.39 (0.28–0.52) for juvenile and adult burbot. By using detection probabilities to compare gears, the most effective sampling technique can be identified, leading to increased species detections and more effective management of burbot.     

Fish use of ecohydraulic‐based mesohabitat units in a low‐gradient Illinois stream: implications for stream restoration

• 1. A classification scheme for ecohydraulic‐based mesohabitat units was developed for a summer low‐flow period. Mesohabitat unit designations were based on the integration of three‐dimensional channel hydraulics, geomorphic maintenance processes of bed morphology, and biological resource needs of fish. Ecological relevance of the units was evaluated by a study of fish mesohabitat use patterns, and species relationships to feeding guild. By portraying the stream as a mosaic of hydraulic habitat patches that provide specific biotic resource needs, this study's aim was to advance how ecological information may be incorporated into the stream restoration design process.
• 2. Nine mesohabitat units were designated, including pool‐front, ‐mid, and ‐rear units, scour pool, simple and complex riffles, glide, submerged point bar, and channel expansion marginal deadwater. Physical habitat structure differed among the nine mesohabitat units by length, water depth, and bed slope and complexity. Fish were collected in specific unit volumes by use of prepositioned areal electrofishing devices, in which distinct patterns of fish mesohabitat use were observed.
• 3. A key finding was the differences in fish assemblages among the pool units, in which fish densities were greatest in the pool‐front and scour pool units. Also, fish density in the pool‐front unit was positively correlated with pool entrance slope. Biomass was greatest in the pool‐front and ‐mid units, and it was correlated with maximum mid‐pool depth. Density and biomass were generally lowest in the pool‐rear unit. Other unique relationships were also observed among the mesohabitat units.
• 4. Based on feeding guild, patterns of fish mesohabitat use were observed for this summer low‐flow period; insectivores dominantly used pool‐front and scour pool units, herbivores dominantly used complex riffle units, and piscivores used pool‐front and ‐mid units.
• 5. Useful ecological information was derived from fish species‐habitat relationships observed in this study, linking mesohabitat units with species requirements for food resources. Such findings support advancements to ecological design strategies for stream restoration that promote hydraulic habitat diversity.

Copyright © 2008 John Wiley & Sons, Ltd.     

A bird's‐eye view of reservoirs in the Mississippi Basin tips a need for large‐scale coordination

Reservoirs are mostly managed at local scales as spatially independent units. A basin‐scale perspective may increase awareness at a broader scope and generate insight not evident at local scales. We examined the array of reservoir attributes and fisheries in the Mississippi Basin to identify management opportunities. The basin is the third largest in the world and includes over 1,700 reservoirs >100 ha, the most of any river basin. Our bird's‐eye view shows a piecemeal approach where reservoirs are mostly administered at the local level. Basin‐wide or catchment coordination to holistically address problems that recur across the basin is mostly lacking. A basin‐wide coordination arrangement could facilitate various facets of reservoir management. We reviewed governance arrangements in major river basins across the globe and concluded that the basin‐wide administrative layer we encourage for the Mississippi Basin may already exist in some basins but may not be directly applicable everywhere.     

River dolphin distribution in regulated river systems: implications for dry‐season flow regimes in the Gangetic basin

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Desktop classification of inland wetlands for systematic conservation planning in data‐scarce countries: mapping wetland ecosystem types,disturbance indices and threatened species associations at country‐wide scale

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A quantitative method for detecting ammonia‐oxidizing bacteria in coastal aquaculture systems

There is a need to quantify autotrophic nitrifiers in coastal aquaculture systems for evolving a bioremediation strategy. Autotrophic nitrifiers are extremely slow‐growing organisms, which cannot be detected by traditional methods as they are notoriously difficult to culture. Molecular techniques based on functional genes could be deployed for the detection of nitrifiers. Ammonia monooxygenase (amoA), that catalyses the oxidation of ammonia to hydroxylamine in the rate‐determining step of nitrification is largely unique to ammonia‐oxidizing bacteria (AOB). In the present study, a quantitative real‐time polymerase chain reaction assay targeting amoA was developed to estimate AOB population size in coastal soil, ammonia‐removing bioaugmentors and the solid matrix. To achieve this objective, different set of primers and a dual labelled probe have been designed for SYBR Green and TaqMan real‐time assays. The abundance of AOB ranged from 10⁴ to 10⁶ order of magnitude in the samples. In the present study, biofilm formation of the consortium of nitrifying bacteria onto bagasse has also been quantified. The results demonstrate that the developed method is a rapid and sensitive tool for the quantitative detection of nitrifying bacteria in aquatic and related environment. This helps in making the bioremediation approach for ammonia removal by immobilization of nitrifying bacteria onto the natural substrate.     

A Strategy for Sperm Cryopreservation of Atlantic Salmon,Salmo salar,for Remote Commercial‐scale High‐throughput Processing

Sperm cryopreservation is an essential tool for long‐term storage of genetic resources for aquaculture fishes. The goal of this study was to develop an efficient and streamlined protocol for high‐throughput processing for sperm cryopreservation in Atlantic salmon, Salmo salar. The objectives were to evaluate: (1) osmolality of blood serum for determining extender osmolality, (2) effects of extenders for fresh sperm dilution and refrigerated storage, (3) effects of methanol and dimethyl sulfoxide (DMSO) on fresh sperm motility, and (4) motility and fertility after thawing. In this study, sperm samples were collected at a hatchery site in Canada and shipped to a freezing site located 2200 miles (3550 km) away in the USA. Evaluation of three extenders indicated that Mounib solution was suitable for diluting dry sperm for sample processing. Ten percent of methanol or DMSO was less toxic to sperm cells than was 15% within 30 min. Further testing with methanol at 5, 10, and 15%, and sperm solution : extender dilutions (v:v) of 1:1, 1:3, and 1:19 (at concentrations of 5 × 10⁷, 3 × 10⁸, and 1 × 10⁹ cells/mL) indicated that methanol at 5 and 10% showed less toxicity to fresh sperm within 1 h at sperm:extender dilutions of 1:1 and 1:3. Post‐thaw motility of sperm cryopreserved with 10% methanol was significantly higher than that with 10% DMSO, and fertility reflected those results (0–1% in DMSO vs. 38–55% in methanol). Further evaluation of sperm cryopreservation with 10 and 15% methanol at sperm dilution ratios of 1:1, 1:3, and 1:19 indicated that post‐thaw motility in 10% methanol was significantly higher than that in 15% methanol, and post‐thaw fertility in 10% methanol at 1:1 and 1:3 dilution ratios had fertilization rates similar to that of fresh sperm controls. Sperm samples from 12 males cryopreserved with 10% methanol showed male‐to‐male variation in post‐thaw motility (0–36%). Overall, a simplified standard protocol was established for cryopreservation of shipped sperm of Atlantic salmon using extender without egg yolk and yielded satisfactory post‐thaw motility and fertilization rates. This procedure can be readily adopted by aquaculture facilities to take advantage of high‐throughput cryopreservation capabilities at remote service centers. Most importantly, this approach lays the groundwork for an alternative commercial model for commercial‐scale production, quality control, and development of industrial standards. Control of male variability and sperm quality remain important considerations for future work.     

Evaluating the efficacy of small‐scale marine protected areas for preserving reef health: A case study applying emerging monitoring technology

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A gleam of hope for the critically endangered Isoëtes malinverniana: Use of small‐scale translocations to guide conservation planning

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Fishing operations and adaptive strategies of small‐scale fishers: insights for fisheries management in data‐poor situations

Small‐scale fisheries' management is complex given its multigear, multispecies nature; despite this, fishing effort has usually been controlled by nominal units, ignoring changes in effective fishing effort. This study aimed to understand the adaptive strategies of small‐scale fishers in San Felipe, Yucatan, Mexico through an analysis of their fishing operations. Minor changes in trip numbers among three seasons were observed, but increases in fishing time, depth and travel costs from one season to another at the operational level were found. It was also evident that high value species at the beginning of the season were gradually replaced by low‐value finfish as the season progresses. The results provide insights for new adaptive management strategies according to fisher's adaptive responses. For instance, using boats or fishing trips as fishing effort units in Yucatan may not be the most appropriated unit for management, as fishers adapt their strategies at different levels.     

A decision support tool for response to global change in marine systems: the IMBER‐ADApT Framework

Global change is occurring now, often with consequences far beyond those anticipated. Although there is a wide range of assessment approaches available to address‐specific aspects of global change, there is currently no framework to identify what governance responses have worked and where, what has facilitated change and what preventative options are possible. To respond to this need, we present an integrated assessment framework that builds on knowledge learned from past experience of responses to global change in marine systems, to enable decision‐makers, researchers, managers and local stakeholders to: (i) make decisions efficiently; (ii) triage and improve their responses; and (iii) evaluate where to most effectively allocate resources to reduce vulnerability and enhance resilience of coastal people. This integrated assessment framework, IMBER‐ADApT is intended to enable and enhance decision‐making through the development, a typology of case‐studies providing lessons on how the natural, social and governance systems respond to the challenges of global change. The typology is developed from a database of case‐studies detailing the systems affected by change, responses to change and, critically, an appraisal of these responses, generating knowledge‐based solutions that can be applied to other comparable situations. Fisheries, which suffer from multiple pressures, are the current focus of the proposed framework, but it could be applied to a wide range of global change issues. IMBER‐ADApT has the potential to contribute to timely, cost‐effective policy and governing decision‐making and response. It offers cross‐scale learning to help ameliorate, and eventually prevent, loss of livelihoods, food sources and habitat.     

A novel multiplex RT‐qPCR method based on dual‐labelled probes suitable for typing all known genotypes of viral haemorrhagic septicaemia virus

Viral haemorrhagic septicaemia (VHS) is a notifiable fish disease, whose causative agent is a rhabdovirus isolated from a wide range of fish species, not only in fresh but also in marine and brackish waters. Phylogenetic studies have identified four major genotypes, with a strong geographical relationship. In this study, we have designed and validated a new procedure – named binary multiplex RT‐qPCR (bmRT‐qPCR) – for simultaneous detection and typing of all four genotypes of VHSV by real‐time RT‐PCR based on dual‐labelled probes and composed by two multiplex systems designed for European and American/Asiatic isolates, respectively, using a combination of three different fluorophores. The specificity of the procedure was assessed by including a panel of 81 VHSV isolates covering all known genotypes and subtypes of the virus, and tissue material from experimentally infected rainbow trout, resulting in a correct detection and typing of all strains. The analytical sensitivity was evaluated in a comparative assay with titration in cell culture, observing that both methods provided similar limits of detection. The proposed method can be a powerful tool for epidemiological analysis of VHSV by genotyping unknown samples within a few hours.     

Primary fisheries management: a minimum requirement for provision of sustainable human benefits in small‐scale fisheries

The social and economic importance of small‐scale fisheries is frequently under‐valued, and they are rarely effectively managed. There is now growing consensus on how these fisheries could be managed for sustainability and to minimize the risks of crossing undesirable thresholds. Using a concept developed in health care, these approaches have been referred to as primary fisheries management. By encouraging the use of best‐available information in a precautionary way, the approaches will facilitate sustainable use and should therefore be encouraged, but they accept high scientific and implementation uncertainties as unavoidable because of limited management and enforcement resources and capacity. It is important to recognize that this limitation will result in social costs, because application of a precautionary approach in the face of high uncertainties will require forgoing potential sustainable benefits. Acceptance of primary fisheries management as a final and sufficient goal could therefore add a further constraint on the possibility of fishing communities escaping the poverty trap. Primary fisheries management should be seen as a first and minimum target for fisheries where there is currently no or inadequate management, but the longer‐term goal should still be well informed and adaptive management that strives for optimal benefits, referred to here as tertiary management.     

Efficacy of Netminder® silicone release coating for biofouling reduction in bay scallop grow‐out and comparative effects on scallop survival,growth and reproduction

Netminder^®, a water‐based silicone barrier release coating, was highly effective in reducing biofouling of lantern nets during grow‐out/overwintering of bay scallops, Argopecten irradians irradians, in a large‐scale restoration programme in New York, USA. Compared with untreated nets, scallops held in Netminder^®‐coated nets experienced reduced survival after 8 months, probably due to higher loads of epibionts on their shells. However, this was countered by higher reproductive and overall condition of scallops in treated vs. untreated nets; there were no consistent differences in shell growth in different net treatments. Although further testing is recommended under a wider range of conditions, we conclude that for the purposes of our scallop restoration work, coating nets with Netminder^® would eliminate the need for a gear change in spring, thus reducing labour costs; the coating process should be refined so that Velcro closures of nets do not become sealed shut.