Improved estimates of digestion correction factors and passage rates for harbor seal (Phoca vitulina) prey in the northeast Atlantic

Diet composition in pinnipeds is widely estimated using hard prey remains recovered from feces. To estimate the size and number of prey represented in fecal samples accurately, digestion correction factors (DCFs) must be applied to measurements and counts of fish otoliths and cephalopod beaks. In this study, 101 whole prey feeding trials were conducted with six harbor seals (Phoca vitulina) and 18 prey species. We derived species‐ and grade‐specific estimates of digestion coefficients (DCs) and species‐specific recovery rates (RRs) to account for partial and complete digestion, respectively. Greater than 98% of otoliths were passed within three days of consumption. RRs were smallest for Atlantic salmon smolts (RR = 0.306, SE = 0.031) and increasingly larger for sandeels (RR = 0.494, SE = 0.017), flatfish (RR = 0.789, SE = 0.033), and large gadoids (RR = 0.944, SE = 0.034). Species‐specific otolith width DCs were smallest for Trisopterus species (DC = 1.14, SE = 0.015) and increasingly larger for flatfish (DC = 1.27, SE = 0.045), large gadoids (DC = 1.32, SE = 0.067) and sandeels (DC = 1.57, SE = 0.035). RRs were similar to those from gray seals (Halichoerus grypus), but harbor seal species‐ and grade‐specific DCs were generally smaller. Differences in partial and complete digestion rates among prey species and between seal species highlight the importance of applying DCFs when reconstructing diet.     

Juvenile salmon in estuaries: comparisons between North American Atlantic and Pacific salmon populations

All anadromous fishes, including juvenile salmon, encounter estuarine habitats as they transition from riverine to marine environments. We compare the estuarine use between juvenile Atlantic salmon (Salmo salar) in the Penobscot River estuary and Pacific salmon (Oncorhynchus spp.) in the Columbia River estuary. Both estuaries have been degraded by anthropogenic activities. Atlantic and Pacific salmon populations in both basins rely heavily on hatchery inputs for persistence. Pacific salmon, as a group, represent a continuum of estuarine use, from species that move through rapidly to those that make extensive use of estuarine habitats. While Atlantic salmon estuarine use is predominantly similar to rapidly moving Pacific salmon, they can exhibit nearly the entire range of Pacific salmon estuarine use. Both slow and rapidly migrating Atlantic and Pacific salmon actively feed in estuarine environments, consuming insect and invertebrate prey. Interactions between juvenile salmon and estuarine fish communities are poorly understood in both estuaries, although they experience similar avian and marine mammal predators. Estuaries are clearly important for Atlantic and Pacific salmon, yet our understanding of this use is currently insufficient to make informed judgments about habitat quality or overall estuary health. This review of salmonid migration through and residency within estuaries identifies actions that could hasten restoration of both Atlantic and Pacific salmon populations.     

Diet composition and food consumption rate of harbor porpoises (Phocoena phocoena) in the western Baltic Sea

Stomach content composition and prey‐specific consumption rates of juvenile and adult harbor porpoises (Phocoena phocoena) were estimated from a data set including 339 stomachs collected over a 32 yr period (1980–2011) in the western Baltic Sea. The stomach contents were mainly hard parts of fish prey and in particular otoliths. The bias originating from differential residence time of otoliths in the stomachs was addressed by use of a recently developed approach. Atlantic cod and herring were the main prey of adults, constituting on average 70% of the diet mass. Juvenile porpoises also frequently consumed gobies. Here, the mass contribution by gobies was on average 25%, which was as much as cod. Other species such as whiting, sprat, eelpout, and sandeels were of minor importance for both juveniles and adults. The diet composition differed between years, quarters, and porpoise acquisition method. Yearly consumption rates for porpoises in the western Baltic Sea were obtained in three scenarios on the daily energy requirements of a porpoise in combination with an estimate including the 95% CLs of the porpoise population size. Cod of age groups 1 and 2 and intermediate‐sized herring suffered the highest predation from porpoises.     

Otolith shape discriminates between juvenile Atlantic salmon, Salmo salar L., and brown trout, Salmo trutta L.

Otoliths of Atlantic salmon, Salmo salar L., are more slender than the otoliths of brown trout, Salmo trutta L. Discriminant analysis on otolith measurements of juvenile Atlantic salmon and brown trout from four river systems revealed a discriminant function which distinguished more than 94% of the cases. This function was tested by using data from a fifth river with cohabiting Atlantic salmon and brown trout: all Atlantic salmon and 91 % of the brown trout were correctly classified.     

A captive feeding study with the Pacific harbor seal (Phoca vitulina richardii): Implications for scat analysis

Seven prey species ( n _total > 2,700) were fed to seven captive male Pacific harbor seals ( Phoca vitulina richardii ) in 177 experimental meals to quantify biases associated with scat analysis and current consumption models. Hard parts from an individual meal were recovered in an average of 3.8 ± 1.8 scats (range 1–10; mean ± SD). Overall, 57.7 ± 33.2% of otoliths and 89.5 ± 15.5% of squid beaks were recovered. Recovery rates varied, and prey with smaller, fragile otoliths were recovered in lesser quantities than prey with larger, robust otoliths. Recovery rates of all prey except pink salmon were improved by a mean of 31.7% when all diagnostic structures were included in estimates. Estimated recovery of pink salmon was 9.5 times that fed seals based on the all-structure technique. Mean length reduction of recovered otoliths was 20.4 ± 10.1%. Correction factors calculated from average length reduction improved length estimates for all fish species. Grade-specific length correction factors (gLCFs) reduced variability in all of the estimates and significantly improved estimates of prey with highly eroded otoliths including Pacific hake and shortbelly rockfish. The Biomass Reconstruction (BR) model accurately predicted biomass consumption within 4% of known consumption, whereas estimates based on frequency of occurrence were inaccurate.     

Stable isotope analyses of otoliths in identification of hatchery origin of Atlantic salmon (Salmo salar) in Maine

We conducted stable oxygen and carbon isotope analyses for otoliths of Atlantic salmon (Salmo salar), in an attempt to develop a reference database on isotopic variability among private and federal hatcheries in Maine which currently support the salmon aquaculture industry and recovery of endangered populations. During the first phase of our study, we collected 40–50 sagittal otoliths of juvenile Atlantic salmon from each of the five hatcheries and analyzed for stable oxygen and carbon isotope ratios (¹⁸O/¹⁶O or δ¹⁸O, and ¹³C/¹²C or δ¹³C). Combination of δ¹⁸O and δ¹³C signatures in otoliths showed that the five hatcheries can be clearly separated and chemically distinguished. By identifying stable isotopic variations of otoliths from different hatchery settings, we were able to establish some isotopic criteria or standards to assign a likelihood that an individual Atlantic salmon came from a specific hatchery within the reference database. If successful, a diagnostic tool that can provide definitive information on identification of the hatchery origin could serve as a novel marking technique, and the chemical method may provide a more effective alternative to DNA analysis for mixed stocks. Overall our isotopic data from otoliths support the hypothesis that there are detectable differences between the five hatcheries, and multiple statistical analyses indicated that we can correctly distinguish individual Atlantic salmon into a hatchery with high confidence.     

Diet partitioning in sympatric Atlantic salmon and brown trout in streams with contrasting riparian vegetation

Prey intake by Atlantic salmon Salmo salar and brown trout Salmo trutta was measured across different riparian vegetation types: grassland, open canopy deciduous and closed canopy deciduous, in upland streams in County Mayo, Western Ireland. Fishes were collected by electrofishing while invertebrates were sampled from the benthos using a Surber sampler and drifting invertebrates collected in drift traps. Aquatic invertebrates dominated prey numbers in the diets of 0+ year Atlantic salmon and brown trout and 1+ year Atlantic salmon, whereas terrestrial invertebrates were of greater importance for diets of 1+ and 2+ year brown trout. Terrestrial prey biomass was generally greater than aquatic prey for 1+ and 2+ year brown trout across seasons and riparian types. Prey intake was greatest in spring and summer and least in autumn apart from 2+ year brown trout that sustained feeding into autumn. Total prey numbers captured tended to be greater for all age classes in streams with deciduous riparian canopy. Atlantic salmon consumed more aquatic prey and brown trout more terrestrial prey with an ontogenetic increase in prey species richness and diversity. Atlantic salmon and brown trout diets were most similar in summer. Terrestrial invertebrates provided an important energy subsidy particularly for brown trout. In grassland streams, each fish age class was strongly associated with aquatic, mainly benthic invertebrates. In streams with deciduous riparian canopy cover, diet composition partitioned between conspecifics with older brown trout associated with surface drifting terrestrial invertebrates and older Atlantic salmon associated with aquatic invertebrates with a high drift propensity in the water column and 0+ year fish feeding on benthic aquatic invertebrates. Deciduous riparian canopy cover may therefore facilitate vertical partitioning of feeding position within the water column between sympatric Atlantic salmon and brown trout. Implications for riparian management are discussed.     

Feeding and prey-selection of wild Atlantic salmon post-smolts

The diet of post-smolt Atlantic salmon Salmo salar caught in the Trondheimsfjord and Frohavet in central Norway, based on stomach contents analysis, showed a gradual change during migration from the river to the estuary, fjord and coastal areas. Post-smolts caught in the estuary had eaten intertidal gammarid amphipods, while post-smolts caught further seawards preyed upon available marine prey such as Calanus spp., adult euphausiids and fish larvae. The frequency of adult insects was high in all post-smolt stomachs. The gradual change in diet suggested that feeding conditions in the early marine phase were important for post-smolt survival and growth. With the exception of the copepods, there was no overall similarity between species composition of the plankton samples and the stomach contents. Although the hypothesis that the post-smolts are opportunistic feeders cannot be rejected, the composition of the stomach contents suggests a possible selectivity of advantageous prey.     

Do Low-Mercury Terrestrial Resources Subsidize Low-Mercury Growth of Stream Fish? Differences between Species along a Productivity Gradient

Low productivity in aquatic ecosystems is associated with reduced individual growth of fish and increased concentrations of methylmercury (MeHg) in fish and their prey. However, many stream-dwelling fish species can use terrestrially-derived food resources, potentially subsidizing growth at low-productivity sites, and, because terrestrial resources have lower MeHg concentrations than aquatic resources, preventing an increase in diet-borne MeHg accumulation. We used a large-scale field study to evaluate relationships among terrestrial subsidy use, growth, and MeHg concentrations in two stream-dwelling fish species across an in-stream productivity gradient. We sampled young-of-the-year brook trout (Salvelinus fontinalis) and Atlantic salmon (Salmo salar), potential competitors with similar foraging habits, from 20 study sites in streams in New Hampshire and Massachusetts that encompassed a wide range of aquatic prey biomass. Stable isotope analysis showed that brook trout used more terrestrial resources than Atlantic salmon. Over their first growing season, Atlantic salmon tended to grow larger than brook trout at sites with high aquatic prey biomass, but brook grew two-fold larger than Atlantic salmon at sites with low aquatic prey biomass. The MeHg concentrations of brook trout and Atlantic salmon were similar at sites with high aquatic prey biomass and the MeHg concentrations of both species increased at sites with low prey biomass and high MeHg in aquatic prey. However, brook trout had three-fold lower MeHg concentrations than Atlantic salmon at low-productivity, high-MeHg sites. These results suggest that differential use of terrestrial resource subsidies reversed the growth asymmetry between potential competitors across a productivity gradient and, for one species, moderated the effect of low in-stream productivity on MeHg accumulation.     

Functions of restored wetlands for juvenile salmon in an industrialized estuary

The Duwamish estuary is an industrialized waterway located in Seattle, WA, USA. Despite a history of habitat loss, naturally produced juvenile Chinook salmon use the estuary. In addition to experiencing degraded habitat in the estuary, wild salmon growth may be affected by competition with more than three million hatchery fish released yearly into the river. Restoring habitat to benefit salmon in the Duwamish River is a priority for trustees of public resources, and a number of wetland restoration sites have been created there. We tested the function of restored sites in the Duwamish estuary for juvenile Chinook salmon by comparing fish densities from enclosure nets or beach seines at three paired restored/un-restored sites and by applying environmental and diet data to a bioenergetics model. We also examined temporal and diet overlap of wild juvenile Chinook salmon with other salmon species and with hatchery-reared Chinook salmon using non-metric multidimensional scaling (NMDS). At a brackish upstream site with a relatively large opening to the river, we found higher densities of juvenile Chinook salmon at the restored site. NMDS results indicated that juvenile Chinook salmon fed on different taxa at the restored sites than at the reference sites. However, modeled growth was similar at restored and reference sites. Co-occurring juvenile chum and Chinook salmon fed differently, with chum eating smaller prey, and Chinook salmon eating larger prey. Co-occurring hatchery and wild juvenile Chinook salmon had similar diets, indicating that they may compete for prey. However, modeled growth was positive and did not differ between hatchery and wild fish, suggesting that food was not limiting. Bioenergetics models indicated that overall juvenile Chinook salmon growth potential at the brackish water site was consistently higher than at more saline sites. Our results suggest that restoration sites in the Duwamish estuary that have larger access openings and are located in brackish water may have increased function over other configurations.     

Influence of growth and temperature on strontium deposition in the otoliths of Atlantic salmon

Sr : Ca ratios measured in the otoliths of sea‐caged Atlantic salmon Salmo salar showed distinct seasonal peaks that were unrelated to water temperature and somatic growth, suggesting other factors have a greater influence on strontium deposition. Atlantic salmon remained in the sea‐cages for two seasons, or equivalent to two‐seawinter fish in the wild and were subjected to seasonally varying temperatures. Water temperature appeared to be inversely related to the Sr : Ca ratios, but this relationship was statistically not significant. Furthermore, water temperature could not explain the distinct increase in the strontium during the second year. The intensity of the Sr peaks increased in the second season while average winter water temperatures were consistent between years. Additionally, strontium deposition in the otoliths was unrelated to somatic growth. Somatic growth, as evidenced by circuli spacings on the scales, was largely invariant and therefore could not explain the observed peaks. Though not explicitly measured, the data are consistent with the notion that strontium deposition is a function of maturity state in Atlantic salmon.     

Effect of diet on otolith composition in Pomatomus saltatrix, an estuarine piscivore

To test the hypothesis that elemental composition of otoliths (sagittae) could be influenced by differences in natural prey type, young‐of‐the‐year bluefish Pomatomus saltatrix were captured immediately after their migration from oceanic waters into mid‐Atlantic Bight estuaries and fed either shrimp, Crangon septemspinosa and Palaemonetes spp. or fish Menidia menidia under similar temperature and salinity regimes in two separate 60 day experiments. Unlimited rations of fish and shrimp prey were provided in the first experiment which led to differences in bluefish growth rate between the two prey treatments; fish prey was limited in the second experiment to ensure that growth rates of bluefish in the two prey treatments were similar. Concentrations of seven elements in bluefish otoliths were determined using solution‐based inductively coupled plasma mass spectrometry (ICPMS). There was no significant effect of diet on five of the seven elements examined (Na, Mg, K, Ca and Mn). The levels of Sr and Ba in the otoliths of shrimp‐fed bluefish, however, were significantly higher than fish‐fed bluefish in both experiments. Concentrations of Ba in shrimp‐fed bluefish otoliths were double that found in fish‐fed bluefish. The results suggest that diet can explain some of the variation in otolith chemistry previously attributed to physical and chemical properties of the water.     

Molecular Genetic Analysis of Stomach Contents Reveals Wild Atlantic Cod Feeding on Piscine Reovirus (PRV) Infected Atlantic Salmon Originating from a Commercial Fish Farm

In March 2012, fishermen operating in a fjord in Northern Norway reported catching Atlantic cod, a native fish forming an economically important marine fishery in this region, with unusual prey in their stomachs. It was speculated that these could be Atlantic salmon, which is not typical prey for cod at this time of the year in the coastal zone. These observations were therefore reported to the Norwegian Directorate of Fisheries as a suspected interaction between a local fish farm and this commercial fishery. Statistical analyses of genetic data from 17 microsatellite markers genotyped on 36 partially-degraded prey, samples of salmon from a local fish farm, and samples from the nearest wild population permitted the following conclusions: 1. The prey were Atlantic salmon, 2. These salmon did not originate from the local wild population, and 3. The local farm was the most probable source of these prey. Additional tests demonstrated that 21 of the 36 prey were infected with piscine reovirus. While the potential link between piscine reovirus and the disease heart and skeletal muscle inflammation is still under scientific debate, this disease had caused mortality of large numbers of salmon in the farm in the month prior to the fishermen''s observations. These analyses provide new insights into interactions between domesticated and wild fish.     

Predation on hatchery-reared and wild smolts of Atlantic salmon, Salmo salar L., in the estuary of River Orkla, Norway

Predation on wild and hatchery-reared Atlantic salmon smolts was studied in the estuary of River Orkla. Cod and saithe congregating in the estuary were the most serious predators on smolts. There was no difference between the mortality rates of wild and hatchery-reared smolts. Predation by cod was estimated at 20%. No evidence was found to indicate selective predation on the smallest wild and hatchery-reared smolts.     

Diet estimation in California sea lions,Zalophus californianus

We performed a captive feeding experiment using California sea lions to assess biases associated with estimating pinniped diet using scats and spews. Sea lions were fed nine of their natural prey species: anchovy, sardine, Pacific mackerel, jack mackerel, hake, steelhead smolts, shortbelly rockfish, pink salmon, and market squid. Recovery percentages varied among prey species using otoliths and were improved for adult salmon and sardine using the all‐structure method. Numerical and graded length correction factors provided better estimates of number and size of prey consumed. Four models used to determine the proportions of prey species consumed by a sea lion population were tested. The all‐structure method and variable biomass reconstruction model, in conjunction with numerical and graded length correction factors, provided more accurate estimates than without. We provide numerical correction factors for all prey species, including correction factors for specific salmon bones: vertebrae, branchials, radials, teeth, gill rakers, and hypurals.     

Statistical analysis on otolith data of anadromous fishes

Stable oxygen and carbon isotope (δ¹⁸O and δ¹³C) analyses of otoliths are becoming increasingly common in fisheries science and management. However, little is known about the statistical properties of isotopic data and few attempts have been made to explore appropriate statistical methods that could be used for otolith data analysis. In this paper, we present a pilot study on δ¹⁸O and δ¹³C data from otoliths of two anadromous fish species, Atlantic salmon (Salmo salar) and Pacific sockeye salmon (Oncorhynchus nerka). The results indicated that the salmon otolith data were not normally distributed, so that linear discriminant function analysis and commonly-used statistical tests such as ANOVA and the t-test may not be appropriate. Using non-parametric k-sample nearest neighbor discriminant analysis, we were able to discriminate with high accuracy among five hatcheries for Atlantic salmon and the origins of wild and hatchery sockeye salmon. Analyses also indicated that the sample sizes required to estimate δ¹⁸O and δ¹³C means based on the different sources of variability (between group or within group) and precision levels (≤ ±5.0 %) were not large. These results and conclusions not only address the statistical considerations of isotopic data from otoliths, but also have practical importance for fisheries management as well.     

Spatial variability of trace elements in fish otoliths: comparison with dietary items and habitat constituents in seagrass meadows

Juvenile trumpeters Pelates sexlineatus , two main prey items (amphipods and polychaetes) and seagrass constituents (detritus, young and old leaves of Zostera capricorni ) were collected from two sites within six estuaries, to compare the spatial variability of elemental composition (Li, Mn, Sr, Cd, Ba and Pb). Average elemental values were lower in the fish otoliths except for Sr. Significant differences in elemental composition of otoliths were detected among estuaries (Mn and Pb). Spatial differences in concentrations of Cd were found in amphipods and polychaetes; the latter also showed differences for Ba and Pb. Detritus and Z. capricorni leaves showed appreciable spatial differences for most of the elements. Spatial variability between sites was generally high. There were differences in the multivariate composition of trace elements found in the otoliths of fish among estuaries. One estuary was consistently separated from the other estuaries in the ordinations. Significant correlations were detected between concentrations of Mn in otoliths and concentrations in prey, Z. capricorni and detritus. A significant relationship was also detected between Pb in otoliths and detritus. There were significant correlations between concentrations of Mn, Sr and Ba in detritus and that in otoliths. The study demonstrated that trophic transfer and habitat constituents may be considered as a potential source for some of the elemental accumulation in fish otoliths.     

Otolith calcification in Atlantic salmon parr, Salmo salar L. and its relation to photoperiod and calcium metabolism

Otolith calcification in Atlantic salmon parr, Salmo salar , was investigated using a radioisotope of calcium, ⁴⁵Ca. Otolith calcification was found to be entrained to light-dark cycles in salmon parr, calcium accumulation on to otoliths declining at night and resuming at dawn. The decline in Otolith calcification at night coincided with a diel decline in plasma calcium concentration. The influence of extracellular calcium on otolith increment formation was considered by inducing hypocalcemia. Induced hypocalcemia resulted in a short-term net loss of calcium from the otolith. The results are discussed in relation to previous studies of the role of extracellular calcium in otolith formation.     

Flexible foraging techniques in breeding Cormorants Phalacrocorax carbo and Shags Phalacrocorax aristotelis: benthic or pelagic feeding?

A total of 8772 dive durations were recorded during 117 diving bouts in five Cormorants Phalacrocorax carbo and five Shags Phalacrocorax aristotelis breeding at the Chausey Islands, France. Diet of the birds was assessed by analysis of 526 pellets containing 13,016 otoliths. Radio-tracking data indicated that Cormorants fed exclusively on pelagic fish during social fishing (5% of the trips) and executed 11% pelagic and 60% benthic dives during the remaining 95% of the trips. In Shags, 44% of all trips were pelagic, and the remaining 56% included 9% pelagic and 67% benthic dives. The proportions of benthic to pelagic dives varied widely between dive sequences of single birds and between individuals and sexes in both species. The prey spectrum of the Cormorants contained both pelagic (29%) and benthic fish (67%) and confirmed considerable flexibility in foraging. In Shags, birds may adjust their diving patterns to accommodate the behaviour of their main prey, sandeels Ammodytidae (87% of all prey). We propose that the wetability of plumage may explain this flexibility.     

Fractionation of δ15N and δ13C for Atlantic salmon and its intestinal cestode Eubothrium crassum

Stable isotopes of nitrogen (δ¹⁵N) and carbon (δ¹³C) were measured for Atlantic salmon Salmo salar and their intestinal cestode, Eubothrium crassum , sharing the same diet. Atlantic salmon muscle tissues were enriched in ¹⁵N and depleted in ¹³C compared to their prey (sprat Sprattus sprattus sprattus ) and their intestinal cestode. There was no significant difference in δ¹⁵N or δ¹³C between E. crassum and the sprat. Differences in nutrient uptake and intestine physiology between Atlantic salmon and E. crassum are discussed, as well as how these may give rise to different fractionations of stable isotopes between a host and its parasites. Furthermore, Atlantic salmon contained a significantly higher lipid content than their prey, which may partly explain differences in δ¹³C values between the host and its cestode. In addition, cestodes inhabiting lipid-rich hosts were also lipid rich. Larger Atlantic salmon were enriched in ¹⁵N compared to smaller fish. Cestodes inhabiting large hosts were also enriched in ¹⁵N compared to parasites living in smaller hosts. The last two results were explained by larger fish possibly feeding from a higher trophic level, or from larger and older prey, that resulted in both a higher lipid content and an enrichment in ¹⁵N.