Low Fish Densities Research Articles

Fecal microbiome analysis uncovers hidden stress effects of low stocking density on rainbow trout

BackgroundRecirculating aquaculture systems can cause chronic stress in fish when stocking density is too high. However, this study tested whether low stocking density can cause fish stress. Adult rainbow trout, with an average weight of 1.517 kg (± 0.39), were subjected to low (12 kg/m3 ± 0.94) and moderate (43 kg/m3 ± 2.03) stocking densities for 24 days in a recirculating system maintained at 15 °C. At the end of the experiment, fecal microbiome analysis was carried out using a 16S rRNA amplicon sequencing. Additionally, an untargeted plasma metabolomics analysis was conducted.ResultsThe moderate stocking density group harboured greater numbers of commensals, such as C. somerae, R. lituseburensis, and L. plantarum. In contrast, detrimental species such as S. putrifacens and P. putida were abundant in the low-stocking density fish. Functional microbiome profiling revealed vitamin B12 salvage and synthesis in moderate stocking densities, which may support intestinal tight junction function. Additionally, vitamin B1 biosynthesis pathways were more abundant in the moderate stocking density group, which may function towards oxidative energy metabolism and protect against oxidative stress. A complementary plasma metabolomics study, although done at slightly different stocking densities and duration, confirmed the presence of blood metabolic stress markers. Elevated levels of L-lactic acid and L-Norvaline, L-Valine, and L-glutamine, indicate low stocking density fish were under stress. Furthermore, a P4HA2 stress gene biomarker confirmed the occurrence of stress in low-density fish. This study suggests that low stocking density can induce stress in fish. Moreover, moderate stocking density leads to a distinct and beneficial fecal microbiome profile.ConclusionOur study highlights the potential benefits of optimizing the stocking density of fish in recirculating aquaculture systems. This can improve fish health and welfare, promoting a more resilient fecal microbiome.Graphical abstract

Multifractal fluctuations in zebrafish (Danio rerio) polarization time series.

In this work, we study the polarization time series obtained from experimental observation of a group of zebrafish (Danio rerio) confined in a circular tank. The complex dynamics of the individual trajectory evolution lead to the appearance of multiple characteristic scales. Employing the Multifractal Detrended Fluctuation Analysis (MF-DFA), we found distinct behaviors according to the parameters used. The polarization time series are multifractal at low fish densities and their average scales with . On the other hand, they tend to be monofractal, and their average scales with for high fish densities. These two regimes overlap at critical density , suggesting the existence of a phase transition separating them. We also observed that for low densities, the polarization velocity shows a non-Gaussian behavior with heavy tails associated with long-range correlation and becomes Gaussian for high densities, presenting an uncorrelated regime.

Modulation of growth performance, feed utilization, and physiological traits in redbelly Tilapia (Tilapia zillii) through environmental and sex-based interactions.

This study explored the combined influence of tank color, stocking density, and gender on Tilapia zillii's performance and well-being. In this 120-day trial, 320 T. zillii, each initially weighing 10.0 ± 0.1 g/fish, were distributed among 24 tanks. The experiment included eight distinct treatment combinations, varying tank color (blue and green), stocking density (10 and 30 fish/m3)and sex (monosexual and mixed). The results showed that blue tanks improved specific growth rate and condition factor, while green tanks were better for feed utilization. Density at 30 fish/m3 showed the highest mean values of final body weight and total length, weight gain (WG), and gain length. Mono-sex outperformed mixed-sex ones in WG and daily growth. Interactions between color, densityand sex were significant, affecting growth and feed utilization. Green tanks were best for protein profiles, while blue tanks excelled in glucose. A density of 10 fish/m3 yielded the highest protein profiles, and mono-sex fish had higher protein profiles. For lipid profiles, green tanks were superior, and density affected lipid profiles. Mixed-sex populations were best for certain lipid profile parameters. Interactions between these factors also played a significant role, making the biochemical profiles of T. zillii a complex interplay of various factors. The results explored that tank color, fish densityand sex influence the activity of nonspecific immune enzymes in the liver of T. zillii. Blue tanks and lower fish density led to higher nonspecific immune enzymes, while mono-sex fish exhibited more significant nonspecific immune enzymes. Complex interactions between these factors also influenced nonspecific immune enzyme activities. Blue tanks increased malondialdehyde (MDA) levels, while green tanks raised glutathione S-transferases (GST) and catalase (CAT) levels. Lower fish density led to higher MDA, while higher density increased GST and CAT. Mono-sex fish had more MDA and GST, while mixed-sex fish showed greater CAT levels. Complex interactions among these factors affected the antioxidant levels in T. zillii. In summary, our study suggests that rearing T. zillii in green tanks at higher densities (30 fish/m3) and in mono-sex conditions yields the best results in terms of growth and overall performance.

Flood pulses and fish species coexistence in tropical rivers - a theoretical food web model

AbstractFreshwater fish diversity reaches its zenith in large tropical rivers. Although the origins of this diversity have been relatively well studied, the mechanisms that maintain high fish diversity in tropical rivers remain largely unknown. It has been hypothesized that the annual flood pulse, a perennial feature of many lowland rivers in the tropics, reduces competitive exclusion and consequently promotes species coexistence. During the high-water season, superabundant allochthonous resources and relatively low fish density may reduce intra- and interspecific competition. During the low-water season on the other hand, resource availability is low and predation pressure high, offsetting competitive differences between species and controlling fish population sizes. Here, we tested the potential role of these mechanisms for species coexistence using a food web model where fish species exhibit strong differences in competition strength and compete for finite resources. We simulated fish interactions when a regular flood pulse was either present or absent. We found that extinction rates in the simulations without an annual flood pulse were consistently higher when compared to those with a flood pulse, indicating more species could coexist when a regular annual flood pulse is present. If the flood pulse is a relevant mechanism for fish species coexistence, as our model results suggest, then flood pulse changes could result in species extinctions and lower fish diversity. Deforestation, climate change, and the construction of large hydropower dams are current drivers of hydrological change across the tropics, increasing the urgency to understand the role of natural flooding regimes for the maintenance of tropical freshwater fish diversity.

Distinguishing the Effects of Water Volumes versus Stocking Densities on the Skeletal Quality during the Pre-Ongrowing Phase of Gilthead Seabream (Sparus aurata).

Gilthead seabream (Sparus aurata) production is a highly valued aquaculture industry in Europe. The presence of skeletal deformities in farmed gilthead seabream represents a major bottleneck for the industry leading to economic losses, negative impacts on the consumers' perception of aquaculture, and animal welfare issues for the fish. Although past work has primarily focused on the hatchery phase to reduce the incidence of skeletal anomalies, this work targets the successive pre-ongrowing phase in which more severe anomalies affecting the external shape often arise. This work aimed to test the effects of: (i) larger and smaller tank volumes, stocked at the same density; and (ii) higher and lower stocking densities maintained in the same water volume, on the skeleton of gilthead seabream fingerlings reared for ~63 days at a pilot scale. Experimental rearing was conducted with gilthead seabream juveniles (~6.7 ± 2.5 g), which were selected as 'non-deformed' based on external inspection, stocked at three different densities (Low Density (LD): 5 kg/m3; Medium Density (MD): 10 kg/m3; High Density (HD): 20 kg/m3) in both 500 L and 1000 L tanks. Gilthead seabream were sampled for growth performance and radiographed to assess the skeletal elements at the beginning and end of the experimental trial. Results revealed that (i) LD fish were significantly longer than HD fish, although there were no differences in final weights, regardless of the water volume; (ii) an increase in the prevalence of seabream exhibiting cranial and vertebral axis anomalies was found to be associated with increased density. These results suggest that farmers can significantly reduce the presence of some cranial and axis anomalies affecting pre-ongrown gilthead seabream by reducing the stocking density.

Physical and social enrichment influences the adaptability-related behaviors of black rockfish Sebastes schlegelii: An effect mediated by social behaviors, HPI axis and neurogenesis

Environmental enrichment is a promising method to increase fish ecological fitness in hatchery release and to improve fish welfare in the aquaculture industry. However, little is known about the effects of physical and social enrichment on fish behavioral development and the relevant regulatory mechanisms. To address this knowledge gap, a typical aquaculture fish, black rockfish Sebastes schlegelii, was exposed to contrasting environments (i.e., physically enriched environment vs. barren environment, and socially low-density environment vs. high-density environment) for six weeks. Subsequently, the adaptability-related behaviors and social interactions during the captive period were determined, and stress-related physiological parameters and neurogenesis-related gene markers were measured. In general, the fish from an enriched environment expressed significantly higher sheltering propensity and anti-predator ability while less risk-taking frequency than the fish from a barren environment. And meanwhile, the fish from a low-density environment presented significantly less risk-taking behavior and more anti-predator responses than high-density fish. A structurally barren environment significantly increased fish aggressive frequency and locomotor activity compared with an enriched environment, whereas the social environment did not affect fish social interactions. For physiological status, the hypothalamus-pituitary-interrenal (HPI) axis and corticosteroid receptor system activities of barren fish were significantly higher than those of enriched fish, and meanwhile, the high-density fish also presented significantly higher physiological stress than low-density fish. For neurogenesis processes, an enriched environment did not affect fish brain cell proliferation but increased telencephalon neuronal differentiation ratio and immature neuron number. In contrast, a low-density environment significantly stimulated cell proliferating activity in telencephalon but did not affect brain neuronal differentiation activity. These novel results verified the conspicuous effects of physical and social environments on the adaptability-related behaviors in aquaculture fish, and finally, we proposed a novel regulatory pathway for fish behavioral plasticity, i.e., environmental stimuli - social interactions - HPI axis - corticosteroid receptor system - neurogenesis - adaptability-related behaviors. These results may lay the foundations for restoring fishery resources and for improving fish welfare, add novel knowledge to fish biology and environmental enrichment framework, and help deeply understand the mechanisms of environmental effects on marine animal behaviors.

Long-term series demonstrate small-scale differences in trends within fish assemblages explained by climate variability

Over 30 years (1985–2018) of environmental monitoring data in the Belgian part of the North Sea allowed us to study common and individual species trends within three spatially distinct demersal and benthopelagic fish assemblages in relation to climate-related variability. A combination of multivariate (dynamic factor analysis) and univariate modelling techniques (Trendspotter and Spearman rank correlations) showed that the observed trends in fish densities in two coastal (mud and fine sand) assemblages were best explained by sea surface temperature (SST)-related variables and the Atlantic multidecadal oscillation winter index (AMOwinter). Higher fish densities seem to be linked with extreme cold winters in the year before (e.g. 1985, 1996, 2010), while warmer years may be linked to lower fish densities (fine sand assemblage) a few years later. Trends for the more offshore coarse sand fish assemblage were rather related to the North-Atlantic Oscillation index (NAO) (next to AMOwinter), coupled to the circulation and inflow of warmer saline waters through the English Channel. The temporal decrease in densities in this assemblage may partially reflect climate and subsequent biological regime shifts, as described for the broader North Sea region.At the species level, both positive, negative and varying trends in densities were noted, dependent on the fish assemblage. Overall, densities of most Lusitanean (warm water) species increased over the last decade, positively correlated with most SST-related variables and AMOwinter-values, indicating a northward expansion of their habitat range, which corroborates the findings of other studies. On the contrary, several Boreal (cold water) species were negatively correlated with SST and AMOwinter, with more or less stable trends in density between 1985 and 2000 followed by a decrease in the last decade, potentially explained by a relocation to deeper waters to cope with increasing seawater temperatures. For plaice Pleuronectes platessa, a commercially important species, a linear and significant decrease in length was observed over the 34-year period, most probably related to a combination of climatic influences and fishing induced selection. The current study shows that environmental, climate related drivers are important to explain part of the biological variability and should be taken into account when investigating the direct impact of human activities on the marine, demersal and benthopelagic ecosystem.

Could spatial heterogeneity in flow disturbance drive temporal stability of native–invasive species co‐occurrence in riverscapes?

Abstract Spatial heterogeneity of abiotic influences like disturbance in riverscapes could play an important role in dispersal‐aided community stability. We tested if higher spatial variability in conditions around river confluences caused by different flood disturbance regimes in branches could possibly influence the stability of a fish assemblage dominated by strong negative interactions between non‐native trout and native galaxiid fishes. We used field surveys to evaluate the effects of disturbance‐driven differences between river branches on fish densities and temporal variation in the relative abundance of galaxiids. Three repeated electrofishing surveys were conducted in two reaches of all branches of eight confluences in Canterbury, New Zealand. We found the differences in flood disturbance regimes between the two stream branches joining at a confluence were associated with higher mean fish abundance and more temporal stability in the relative abundance of native fish. Conversely, when flood disturbance conditions in the two streams joining were similar, resulting in a homogeneous confluence, fish abundance was lower and temporal variability was higher. For homogeneous confluences, strong interactions between native galaxiids and invasive trout probably produced lower fish densities where rivers with low flow disturbance met, whereas when two highly flow‐disturbed rivers met, environmental harshness probably lowered fish densities. By comparison, enhanced galaxiid temporal stability at confluences containing both disturbed and stable river branches probably reflected the combined effects of refugia from trout predation in disturbed branches and refugia from flooding in stable branches. Overall, these results are likely to reflect the combined effects of population‐specific responses to physical heterogeneity and spatially variable interspecific interactions. They may mean that river network configuration, and confluences especially, could influence community stability through a habitat portfolio effect. Furthermore, it will be worth investigating further whether preservation or restoration of differences in flow disturbance conditions in riverscapes encourages higher ecosystem resilience in the face of global change.

Modeling trophic webs in freshwater fishpond systems using Ecopath: towards better polyculture management

Freshwater pond polyculture faces many challenges in Europe. Appropriate tools must be developed to better understand and manage trophic interactions in pond ecosystems. The objective of our study was to understand the trophic interactions and make inference on the fish diet in common carp polyculture through a combination of experiments and trophic web modeling. We conducted an experiment in small fishponds of common carp polyculture reared with roach and perch and used Ecopath with Ecosim software to characterize the food web. Two replicates of 3 treatments were performed: a semi-extensive pond with low fish density and no formulated feed, an intensive pond with twice the fish density and formulated feed and an intensive pond coupled with a planted lagoon. Ten trophic groups were defined to describe the food web. The modeling procedure enabled us to estimate the diets of each trophic group. The fish diet in fed and non-fed treatments differed greatly since the carp fed mainly on formulated feed when available. The roach exhibited trophic plasticity by adapting their diet to the available resources. The benthic macroinvertebrates and zooplankton were preyed upon intensively; they became the limiting factors for fish production and depended on phytoplankton availability. Detritus and phytoplankton were the main sources of nutrients in all treatments but were not used efficiently. These results provide several insights for improving polyculture. In particular, they promote better management of zooplankton and macroinvertebrates as food sources for target species and a better balance in fish assemblages for more efficient use of resources.

Using Freshwater Bivalves (Corbicula Fluminea) to Alleviate Harmful Effects of Small-Sized Crucian Carp (Carassius Carassius) on Growth of Submerged Macrophytes during Lake Restoration by Biomanipulation

Increased recruitment of small-sized fish following biomanipulation by reducing the biomass of plankti-benthivorous fish, not least in (sub)tropical lakes, may deteriorate water quality and thereby potentially hamper the recovery of submerged macrophytes. Filter-feeding bivalves remove suspended particles from the water and may, thereby, somewhat or fully counteract this negative effect of the increasing abundance of small-sized fish. So far, only few studies have investigated the interactive effects of fish and bivalves on water clarity and macrophyte growth. We conducted a 2 × 2 factorial designed outdoor mesocosm experiment with two densities of small crucian carp Carassius carassius (low 10 g m−2 and high 40 g m−2) and two densities of bivalves Corbicula fluminea (low 204 g m−2 and high 816 g m−2). We found significant interactive effect of fish and bivalves on the growth of the macrophyte Vallisneria natans. In the low density bivalve regime, the relative growth rates, root mass, root:shoot ratio and number of tubers were 30.3%, 30.8%, 21.6% and 27.8% lower in the high than in the low density fish treatments, while the decrease was less pronounced in the high density bivalve regime: 1.2%, 8.7%, 2.1% and 13.3%, respectively. Thus, bivalves reduced the negative effects of fish, not least when bivalve density was high. The weaker effects of small fish on plants in the high- than in the low-density C. fluminea regime can be attributed to lower total suspended solids (TSS) and Chl a in the first week of the experiment. Better light conditions further stimulated the growth of benthic algae, potentially increasing the removal of nutrients from the water and reducing fish-driven resuspension of the sediment. In addition, high densities of C. fluminea also enriched the sediment total nitrogen (TN) and total phosphorus (TP) content, favouring plant growth as indicated by an increase in leaf tissue TN and TP contents. Our results demonstrate that filter-feeding bivalves can alleviate harmful effects of small fish by prolonging a clear-water state that facilitates submerged macrophyte growth. Addition of the bivalve C. fluminea can be a promising tool for the restoration of submerged macrophytes in shallow eutrophic lakes, in particular lakes containing small, rapidly reproducing fish that due to their small sizes are not capable of controlling the bivalves.

Observations of sperm storage in some deep-sea elasmobranchs

The presence of sperm storage was evaluated in several deep-sea elasmobranchs (Centrophorus squamosus, Centroselachus crepidater, Deania calcea, Brochiraja spinifera, Brochiraja asperula, Apristurus ampliceps, A. exsanguis, A. garricki and A. sinensis), all considered at risk to the impacts of fishing in New Zealand. Biological measurements of reproductive organs (e.g. follicle size and number, oviducal gland size, uterus width and gonad weight) were recorded in addition to conventional macroscopic maturity assessment measures. Histology was conducted on a sample of oviducal glands to investigate the occurrence of sperm storage. Sperm storage was confirmed in three of the nine species: Centroselachus crepidater, Centrophorus squamosus and Brochiraja asperula. To the best of our knowledge, these are the first observations of sperm storage for these genera, and the first in the family Centrophoridae. Sperm storage was observed in macroscopically mature females and also in some females considered macroscopically as maturing. The female reproductive tract may regress substantially between reproductive events to the extent that a mature fish is mis-classified as maturing, and would be consistent with long periods of resting between reproductive events. Alternatively, it is equally possible that aggrieve male mating behaviour results in premature copulation of maturing females. We summarise published occurrences of sperm storage in chondrichthyans, and conclude that sperm storage is most likely ubiquitous in chondrichthyans, and an adaptive benefit to traumatic mating behaviour, that may also be adaptive to low fish densities in the relatively unproductive environment of the deep-sea.

Evidence of Positive Phototaxis in Paddlefish: Implications for Larval Sampling

Paired lit and unlit quatrefoil traps were used to examine the photic response of Paddlefish Polyodon spathula yolk-sac larvae (YSL) and exogenous-feeding larvae (EFL) under controlled conditions in a hatchery. One lit and one unlit trap were placed in two identical circular raceways containing approximately 10,000 YSL and EFL for 20 2-min trials. Lit traps captured nearly 10x more larvae than unlit traps for each cohort and accounted for 91% and 94% of total catch for YSL and EFL, respectively. This is the first documentation of this photic response in Paddlefish. A slight increasing trend in capture with length was noted for YSL, whereas EFL demonstrated a strong decreasing trend in capture, indicating a possible behavioral shift at 15-16 mm TL. The high proportional catch of lit traps among 1-mm length classes evaluated (≥79%) suggests that Paddlefish exhibit positive phototaxis and light trapping for Paddlefish larvae <20 mm TL may have potential to substantially increase catches in the wild. More efficient capture of larval Paddlefish in the wild using lighted traps might prove useful for documenting the presence of reproduction, for initial indications of year class strength, and as a source of fish for rearing in hatcheries and repatriation to the wild. However, much remains to be evaluated in controlled and wild settings, including responses to different light emissions, lower fish density, and higher turbidities common in rivers when and where wild Paddlefish spawn.

Influence of Salinity on Predator–Prey Interactions between the Mosquitofish (Gambusia affinis) and Larvae of the Green Toad (Bufotes variabilis)

We investigated the effects of the Mosquitofish (Gambusia affinis) predation and increased salinity on larvae of the Green Toad (Bufotes variabilis) in two levels of fish density and two levels of salinity. The experiment was carried out within 28 days and included the following treatments: low fish density × low salinity, low fish density × high salinity, high fish density × low salinity, high fish density × high salinity, and a control treatment. Except for the impact of fish density and salinity on survival, B. variabilis was tolerant of both fish density and increased salinity and there was no interaction between fish density and increased salinity in term of growth and development. The green toad larvae treated in high salinity × high fish density revealed also malformations and abdominal edema.

음향을 이용한 추자도 바다목장 해역의 계절별 어군의 분포 조사

The purpose of this research is to investigate the distribution of seasonal fish schools in Chujado Marine Ranch Area. Acoustic surveys were conducted three times in May, August, and November 2019. The results of the survey were a low fish density in May and November while the highest density was recorded in August. In May and November, there were no fish schools, and small number of individual fish appeared. In August, a large fish schools was formed throughout the depths of the surveyed sea. The water temperature was the highest in August compared to May and November. It was found that the fish schools changes according to the time of day or night, the seasonal environment, water temperature, and the submarine topography. Regular and systematic investigation is necessary to construct a marine ranch suitable for the target sea area.

Impact of Vertically-Suspended Environmental Enrichment and Two Densities of Fish on Circular Tank Velocity Profiles

Vertically-suspended environmental enrichment has been shown to produce improvements in fish growth during hatchery rearing in circular tanks. This study documented the effects of a novel suspended structure on the velocity profile of a 3.63-m diameter circular tank containing juvenile landlocked fall Chinook salmon (Oncorhynchus tshawytscha) at two different densities (9.0 and 34.3 kg/m3). The addition of vertically-suspended structure to the tank significantly decreased velocities at nearly every sampling point, with velocities typically dropping from 15 cm/s without structure to less than 6 cm/s when structure was present. Fish density also significantly impacted in-tank velocities, with an inverse relationship observed between the density of fish and water velocity. Significant interactions were present among the presence or absence of structure and fish density. When structure and fish were absent, the velocity at the edge of the tank was 15.63 cm/s, which was significantly higher than the 4.75 cm/s velocity when both structure and the lower fish density were added, which was in turn significantly higher than the 2.29 cm/s velocity observed with structure and higher fish density. Despite the potentially unique features of this study, vertically-suspended environmental enrichment and the presence of fish clearly alter circular tank water velocities, which may at least partially explain the improvements in fish rearing performance observed with the use of suspended structure.

Changes in Relative Fish Density Around a Deployed Tidal Turbine during on-Water Activities

Global interest in mitigating climate change effects is a driver for the development of renewable energy sources. In-stream tidal power, a type of marine hydrokinetic (MHK) energy uses tidal currents to generate electricity and is one example of developing a renewable energy industry. Effects and impacts on fishes in areas of tidal power development are a consideration, and presently there are many unanswered questions in this field of research. Knowledge of how fish use these areas before and after device installation is essential to informing regulators for decision-making. We attempted a Before-After-Control-Impact (BACI) study design to compare an index of fish density near and away from an MHK tidal energy device deployed in Cobscook Bay, Maine. The index was mean volume backscattering strength (Sv) obtained from 24-hour stationary, down-looking hydroacoustic surveys. Data were collected several times per year at an “impact” site within 50–75 m of a device and at a “control” site approximately 1.6 km away, both before and after turbine installation in August 2012. Fish density was lowest in March surveys and highest in May surveys at both sites. One of four comparisons (August 2011/before vs. 2012/after) indicated an interaction of fish density with turbine installation. Operational status of the installed turbine and on-water activity disturbances (e.g., industry vessel and diving activities) varied at the impact site and possibly influenced results. Lower fish densities were observed during installation and maintenance periods than during normal device operation. The effects of construction activities must be separated from the effects of a deployed device to effectively implement a statistically rigorous assessment that could separate the effects of these different activities. This parsimonious approach and results were used for permit licensing by federal and state regulatory bodies at this site and others and can be used to consider regulatory adjustments during different phases of device operation and maintenance.

Low input of offshore areas to fisheries in a large tropical reservoir in Lao PDR

Nam Theun 2 is the largest neo-reservoir in Lao PDR that was impounded to produce electricity. The objective of this study was to assess the input of the offshore zone to the total fish production. Hydroacoustics in areas > 5 m deep were sampled during the cold-dry season for 2 consecutive years. Results showed low fish densities (200–300 ind. ha−1), low biomass ( < 1 kg ha−1) and fish of small sizes (approximately 6 cm) in deep zones. Fish stock in the pelagic zone was concentrated between 2 and 13 m depth. The low colonization by fish was corroborated by the small catches achieved by experimental fishing in this part of the reservoir. This study has highlighted the limited contribution of the pelagic zone of a large neo-reservoir to fish production (low density, low biomass and few commercial species) when the reservoir was at its maximal water level. This study suggests that future management actions should mainly focus on the littoral zone.

High fish density delays wound healing in Atlantic salmon (Salmo salar)

In this study, we look closer at how high fish densities influence wound repair mechanisms in post-smolt Atlantic salmon. The fish were wounded with a 5 mm skin punch biopsy needle and stocked at two different densities, a high fish density (100 kg/m3) treatment and a low fish density treatment (20 kg/m3) serving as the control. The healing wounds were followed for 57 days with samples taken 1, 3, 7, 14, 36, 43 and 57 days post wounding. The transcriptomic analysis suggests that high fish density enhance inflammation and represses cell proliferation, tissue secretion and collagen synthesis in the healing wounds. The histological analysis further showed delayed epidermal and dermal repair in the high fish density treatment compared to control. The overall wound contraction was also altered by the treatment. In conclusion, high fish density enhances immune responses and delay tissue repair, which ultimately results in delayed wound healing.

Real-time multiplex PCR for simultaneous detection of multiple species from environmental DNA: an application on two Japanese medaka species

Information about species distribution is crucial to ecological studies. Environmental DNA (eDNA) analysis has recently been used to estimate the distribution of aquatic organisms. Several analytical methods including metabarcoding and species-specific PCR are being used for eDNA analysis. However, when only a few species are targeted, metabarcoding is not cost-effective because of the wasted consumption of read due to amplification of non-target species DNA. On the other hand, species-specific PCR requires tests to be repeated multiple times resulting in consuming more DNA templates, and experimental consumables. Here we propose a methodological framework for simultaneously detecting a few species using real-time multiplex PCR. We developed the species-specific primer-probe sets for two species of Japanese medaka (Oryzias latipes and o. sakaizumii), and we used them in the real-time multiplex PCR. In aquarium experiment, even when the species abundances were biased, both species were simultaneously detected in all samples. In a field survey, eDNA analysis and capture survey produced consistent results in all sampling sites, including sites with low fish densities. eDNA analysis using real-time multiplex PCR can be easily applied to other aquatic organisms, enabling a more cost-effective distribution survey of multiple target organisms.

Habitat availability and ontogenetic shifts alter bottlenecks in size‐structured fish populations

For species that utilize different habitats throughout their life cycle, the habitat limitation at a given stage can act as a bottleneck on population abundance, impacting density-dependent processes such as individual growth and survival. We explore the influence of habitat limitation on population dynamics by developing a multi-stage population model based on lake-dwelling rainbow trout (Oncorhynchus mykiss) populations where adults occupy the lake habitat but use tributaries for spawning and juvenile rearing. The model details density-dependent ecological processes and ontogenetic habitat shifts, harvest mortality, and the impact of climate on growth. We ran model simulations using a range of early life stage habitat availabilities and climatic conditions representative of the native range of rainbow trout in Canada and compared the results to empirical data. The results suggest that (1) increases in early life stage habitat leads to increases in population abundance but, due to density-dependent processes, also results in slower growing stunted populations; (2) population bottlenecks can occur at any life stage, even at the adult stage if spawning and rearing habitats are abundant; (3) when the level of competition for early life stages is increased, inter-cohort competition can lead to population cycles. The model's conclusions are further reinforced by empirical data showing a similar trend in the relationship between fish density and maximum size and providing evidence that limited early life stage habitat leads to lower fish densities and larger fish size. We provide a model that links environmental conditions to population dynamics and is useful for fisheries management and habitat conservation decisions.