A comparison of the use of different swab materials for optimal diagnosis of amoebic gill disease (AGD) in Atlantic salmon (Salmo salar L.)

Routine gill swabbing is a non-destructive sampling method used for the downstream qPCR detection and quantitation of the pathogen Neoparamoeba perurans, a causative agent of amoebic gill disease (AGD). Three commercially available swabs were compared aiming their application for timelier AGD diagnosis (Calgiswab^® (calcium alginate fibre-tipped), Isohelix^® DNA buccal and cotton wool-tipped). Calcium alginate is soluble in most sodium salts, which potentially allows the total recovery of biological material, hence a better extraction of target organisms’ DNA. Thus, this study consisted of (a) an in vitro assessment involving spiking of the swabs with known amounts of amoebae and additional assessment of retrieval efficiency of amoebae from agar plates; (b) in vivo testing by swabbing of gill arches (second, third and fourth) of AGD-infected fish. Both in vitro and in vivo experiments identified an enhanced amoeba retrieval with Calgiswab® and Isohelix® swabs in comparison with cotton swabs. Additionally, the third and fourth gill arches presented significantly higher amoebic loads compared to the second gill arch. Results suggest that limiting routine gill swabbing to one or two arches, instead of all, could likely lead to reduced stress-related effects incurred by handling and sampling and a timelier diagnosis of AGD.     

Effect of an intensive mechanical removal effort on a population of non‐native rainbow trout Oncorhynchus mykiss in a South African headwater stream

1. Invasions by non‐native species can compromise the conservation value of otherwise pristine headwater streams. While both developed and developing countries recognize this threat, few of the latter have suitable budgets to implement control programmes.
2. This study assessed the effectiveness of a mechanical project to remove non‐native rainbow trout Oncorhynchus mykiss from a 6 km section of the upper Krom River, a small headwater stream in the Cederberg Mountains in South Africa's Cape Floristic Region (CFR).
3. From October 2013 to February 2014, 354 O. mykiss were removed by angling (58%), fyke netting (28%) and gill netting (14%). This resulted in a marked reduction, but not eradication, of the O. mykiss population (fish relative abundance decreased from 0.53 ± 0.09 fish per net per night in October 2013 to 0.21 ± 0.09 fish per net per night in February 2014). Following the cessation of manual removals, the relative abundance of O. mykiss had increased to 0.56 ± 0.18 fish per net per night by March 2016, suggesting that without sustained removal effort, the population will rapidly return to its pre‐removal abundance level.
4. Further work is needed to refine the methodology and test the effectiveness of mechanical removal of non‐native freshwater fish in a variety of ecological settings in the CFR. This approach holds potential for meeting the dual goals of reducing the ecological impacts of non‐native fishes and generating employment opportunities in line with the policy objectives of developing nations.

     

Variability in the performance of juvenile Chinook salmon is explained primarily by when and where they resided in estuarine habitats

Estuarine habitats provide rearing opportunities for the juvenile life stage of anadromous fishes. Because survival is positively correlated with juvenile performance, these estuarine habitats play an important role in population abundance and productivity. To provide information for the recovery of several depressed stocks of Chinook salmon in the Columbia River Basin, we sought to identify the factors that explain variability in performance. Using otolith‐derived estimates of juvenile somatic growth rate as an index of recent performance, we observed a negative nonlinear relationship between growth rate and day of year, and a decreasing and increasing trend of growth rate over the 8 years of this study and distance from the river mouth respectively. Using a generalised linear modelling approach, we found that variability in juvenile somatic growth rate was best explained by where and when individuals were collected, their body size, contaminant loads, stock of origin, and whether a fish was hatchery produced or unmarked. Lastly, we argue that a considerable improvement to the growth rate of juveniles in estuarine habitats is physiologically possible. The results of this 8‐year study provide a baseline of the performance of juvenile Chinook salmon to evaluate habitat restoration programs and to compare against future anthropogenic conditions.     

Ecoviability for ecosystem‐based fisheries management

Reconciling food security, economic development and biodiversity conservation is a key challenge, especially in the face of the demographic transition characterizing many countries in the world. Fisheries and marine ecosystems constitute a difficult application of this bio‐economic challenge. Many experts and scientists advocate an ecosystem approach to manage marine socio‐ecosystems for their sustainability and resilience. However, the ways by which to operationalize ecosystem‐based fisheries management (EBFM) remain poorly specified. We propose a specific methodological framework—viability modelling—to do so. We show how viability modelling can be applied using four contrasted case‐studies: two small‐scale fisheries in South America and Pacific and two larger‐scale fisheries in Europe and Australia. The four fisheries are analysed using the same modelling framework, structured around a set of common methods, indicators and scenarios. The calibrated models are dynamic, multispecies and multifleet and account for various sources of uncertainty. A multicriteria evaluation is used to assess the scenarios’ outcomes over a long time horizon with different constraints based on ecological, social and economic reference points. Results show to what extent the bio‐economic and ecosystem risks associated with the adoption of status quo strategies are relatively high and challenge the implementation of EBFM. In contrast, strategies called ecoviability or co‐viability strategies, that aim at satisfying the viability constraints, reduce significantly these ecological and economic risks and promote EBFM. The gains associated with those ecoviability strategies, however, decrease with the intensity of regulations imposed on these fisheries.     

Combined application of nitrogen and phosphorus to enhance nitrogen use efficiency and close the wheat yield gap on varying soils in semi‐arid conditions

A primary driver of the wheat yield gap in Australia and globally is the supply of nitrogen (N) and options to increase N use efficiency (NUE) are fundamental to closure of the yield gap. Co‐application of N with phosphorus (P) is suggested as an avenue to increase fertiliser NUE, and inputs of N and P fertiliser are key variable costs in low rainfall cereal crops. Within field variability in the response to nutrients due to soil and season offers a further opportunity to refine inputs for increased efficiency. The response of wheat to N fertiliser input (0, 10, 20, 40 and 80 kg N ha^‐1) under four levels of P fertiliser (0, 5, 10 and 20 kg P ha^?1) was measured on three key low rainfall cropping soils (dune, mid‐slope and swale) across a dune‐swale system in a low rainfall semi‐arid environment in South Australia, for three successive cropping seasons. Wheat on sandy soils produced significant and linear yield and protein responses across all three seasons, while wheat on a clay loam only produced a yield response in a high rainfall season. Responses to P fertiliser were measured on the sandy soils but more variable in nature and a consistent effect of increased P nutrition leading to increased NUE was not measured.     

Growth and maturation of three commercially important coral reef species from American Samoa

Fisheries Science - This study presents age-based life history information on three small-bodied species targeted in the American Samoan fishery: Chlorurus japanensis palecheek...     

Quantifying uncertainty in the wild‐caught fisheries goal of the Ocean Health Index

Sustainability indices are proliferating, both to help synthesize scientific understanding and inform policy. However, it remains poorly understood how such indices are affected by underlying assumptions of the data and modelling approaches used to compute indicator values. Here, we focus on one such indicator, the fisheries goal within the Ocean Health Index (OHI), which evaluates the sustainable provision of food from wild fisheries. We quantify uncertainty in the fisheries goal status arising from the (a) approach for estimating missing data (i.e., fish stocks with no status) and (b) reliance on a data‐limited method (catch‐MSY) to estimate stock status (i.e., B/B_MSY). We also compare several other models to estimate B/B_MSY, including an ensemble approach, to determine whether alternative models might reduce uncertainty and bias. We find that the current OHI fisheries goal model results in overly optimistic fisheries goal statuses. Uncertainty and bias can be reduced by (a) using a mean (vs. median) gap‐filling approach to estimate missing stock scores and (b) estimating fisheries status using the central tendency from a simulated distribution of status scores generated by a bootstrap approach that incorporates error in B/B_MSY. This multitiered approach to measure and describe uncertainty improves the transparency and interpretation of the indicator and allows us to better understand uncertainty around our OHI fisheries model and outputs for country‐level interpretation and use.     

Thirty years of change and the future of Alaskan fisheries: Shifts in fishing participation and diversification in response to environmental,regulatory and economic pressures

Heterogeneity in human responses and decision‐making can contribute to the resilience of social–ecological systems in the face of environmental, political and economic pressures. In fishery systems worldwide, the ability of harvesters to maintain a diverse portfolio of fishing strategies is important for building adaptive capacity. We used a case‐study approach to examine the complexity of factors that inhibit or promote diversification in fisheries of Alaska, one of the major fishing regions of the world. Through a combination of harvest records and literature review, we explored shifts in participation and portfolio diversity in Alaskan fisheries over three decades. The four case‐studies examined the responses of fishers, fleets and communities to multiple, intersecting pressures, including biological declines, market and price dynamics, fishery privatization and the 1989 Exxon Valdez oil spill. These cases illustrate how stressors acting at multiple scales can encourage or constrain opportunities for diversification, and that these opportunities may be spread inequitably across participants. Overall, we found evidence for reduced participation and increasing specialization in Alaskan commercial fisheries. While numerous factors explain these trends, policies like individual quota systems and the increasing cost of entry into fisheries are forcing consolidation at local to regional scales. A portfolio approach to managing fisheries that reduces barriers to diversification and includes broad representation of resource users and communities in management may help to maintain opportunity and choice for fishers.     

Annualized diameter and height growth equations for Pacific Northwest plantation-grown Douglas-fir, western hemlock, and red alder

Simulating the influence of intensive management and annual weather fluctuations on tree growth requires a shorter time step than currently employed by most regional growth models. High-quality data sets are available for several plantation species in the Pacific Northwest region of the United States, but the growth periods ranged from 2 to 12 years in length. Measurement periods of varying length complicate efforts to fit growth models because observed growth rates must be interpolated to a common length growth period or those growth periods longer or shorter than the desired model time step must be discarded. A variation of the iterative technique suggested by Cao [Cao, Q.V., 2000. Prediction of annual diameter growth and survival for individual trees from periodic measurements. Forest Sci. 46, 127–131] was applied to estimate annualized diameter and height growth equations for pure plantations of Douglas-fir, western hemlock, and red alder. Using this technique, fits were significantly improved for all three species by embedding a multi-level nonlinear mixed-effects framework (likelihood ratio test: p < 0.0001). The final models were consistent with expected biological behavior of diameter and height growth over tree, stand, and site variables. The random effects showed some correlation with key physiographic variables such as slope and aspect for Douglas-fir and red alder, but these relationships were not observed for western hemlock. Further, the random effects were more correlated with physiographic variables than actual climate or soils information. Long-term simulations (12–16 years) on an independent dataset using these annualized equations showed that the multi-level mixed effects models were more accurate and precise than those fitted without random effects as mean square error (MSE) was reduced by 13 and 21% for diameter and height growth prediction, respectively. The level of prediction error was also smaller than an existing similar growth model with a longer time step (ORGANON v8) as the annualized equations reduced MSE by 17 and 38% for diameter and height growth prediction, respectively. These models will prove to be quite useful for understanding the interaction of weather and silviculture in the Pacific Northwest and refining the precision of future growth model projections.     

Methacarn preserves mucus integrity and improves visualization of amoebae in gills of Atlantic salmon (Salmo salar L.)

Two aqueous fixation methods (modified Davidson's solution and modified Davidson's solution with 2% (w/v) Alcian blue) were compared against two non‐aqueous fixation methods (methacarn solution and methacarn solution with 2% (w/v) Alcian blue) along with the standard buffered formalin fixation method to (a) improve preservation of the mucous coat on Atlantic salmon, Salmo salar L., gills and (b) to examine the interaction between the amoebae and mucus on the gill during an infection with amoebic gill disease. Aqueous fixatives demonstrated excellent cytological preservation but failed to deliver the preservation of the mucus when compared to the non‐aqueous‐based fixatives; qualitative and semi‐quantitative analysis revealed a greater preservation of the gill mucus using the non‐aqueous methacarn solution. A combination of this fixation method and an Alcian blue/Periodic acid–Schiff staining was tested in gills of Atlantic salmon infected with amoebic gill disease; lectin labelling was also used to confirm the mucus preservation in the methacarn‐fixed tissue. Amoebae were observed closely associated with the mucus demonstrating that the techniques employed for preservation of the mucous coat can indeed avoid the loss of potential mucus‐embedded parasites, thus providing a better understanding of the relationship between the mucus and parasite.