Assessing the suitability of a non-lethal biopsy punch for sampling fish muscle tissue

Non-lethal sampling for assessment of mitochondrial function does not affect metabolic rate and swimming performance

A fundamental issue in the metabolic field is whether it is possible to understand underlying mechanisms that characterize individual variation. Whole-animal performance relies on mitochondrial function as it produces energy for cellular processes. However, our lack of longitudinal measures to evaluate how mitochondrial function can change within and among individuals and with environmental context makes it difficult to assess individual variation in mitochondrial traits. The aims of this study were to test the repeatability of muscle mitochondrial metabolism by performing two biopsies of red muscle, and to evaluate the effects of biopsies on whole-animal performance in goldfish Carassius auratus. Our results show that basal mitochondrial respiration and net phosphorylation efficiency are repeatable at 14-day intervals. We also show that swimming performance (optimal cost of transport and critical swimming speed) was repeatable in biopsied fish, whereas the repeatability of individual oxygen consumption (standard and maximal metabolic rates) seemed unstable over time. However, we noted that the means of individual and mitochondrial traits did not change over time in biopsied fish. This study shows that muscle biopsies allow the measurement of mitochondrial metabolism without sacrificing animals and that two muscle biopsies 14 days apart affect the intraspecific variation in fish performance without affecting average performance of individuals. This article is part of the theme issue 'The evolutionary significance of variation in metabolic rates'.

A non-lethal stable isotope analysis of valued freshwater predatory fish using blood and fin tissues as alternatives to muscle tissue

Stable isotope analysis (SIA) is widely used to study trophic ecology and food webs in aquatic ecosystems. In the case of fish, muscle tissue is generally preferred for SIA, and the method is lethal in most cases. We tested whether blood and fin clips can be used as non-lethal alternatives to muscle tissue for examining the isotopic composition of two freshwater predatory fish, European catfish (Silurus glanis) and Northern pike (Esox lucius), species of high value for many freshwater systems as well as invasive species in many others. Blood samples from the caudal vein, anal fin clips, and dorsal muscle obtained by biopsy punch were collected from four catfish and pike populations (14-18 individuals per population). Subsequently, these samples were analyzed for δ13C and δ15N. The effects of alternative tissues, study site, and fish body mass on the isotopic offset were investigated. Both species showed a correlation between the isotopic offset and the tissue type, as well as the study site, but no significant relationship with the body mass. The isotopic offsets between tissues were used to calculate the conversion equations. The results demonstrated that both blood and fin clips are suitable and less invasive alternative to muscle in SIA studies focused on European catfish and Northern pike. Blood provided better correspondence to muscle isotope values. However, our results clearly demonstrated that isotopic offsets between tissues vary significantly among populations of the same species. Therefore, obtaining a muscle biopsy from several individuals in any population is advisable to gain initial insights and establish a possible population-specific inter-tissue conversion.

Non-lethal sampling method for the analysis of white muscle fatty acid profiles in European sea bass (Dicentrarchus labrax)

This study presents a novel non-lethal sampling method for assessing fatty acid (FA) composition in juvenile European sea bass (Dicentrarchus labrax) using subcutaneous white muscle biopsies. This research aimed to evaluate the suitability of the biopsy for FA analysis using two lipid extraction protocols and comparing them to a lethal routine method. The results showed that a mass of fresh tissue as low as 1.4 mg provided good quality FA chromatograms for both reserve and membrane lipids. Although the biopsy method displayed high variability in terms of FA quantity among intra-individual replicates, it showed good FA profile repeatability in both reserve and membrane lipids. The study highlights the potential of this non-lethal approach for studying FA dynamics in fish, with its application being particularly promising for ecological and experimental studies. However, careful biopsy implementation is recommended to account for potential lipid droplet and lipid distribution variability within the tissue.

Analysis of Selenium in Fish Tissue: An Interlaboratory Study on Weight Constraints

Environmental monitoring programs that target fish tissues for selenium (Se) analysis present unique sampling and analytical challenges. Selenium monitoring programs ideally focus on egg/ovary sampling but frequently sample multiple tissues with varying lipid content, often target small-bodied fish species because of their small home ranges, and require reporting in units of dry weight. In addition, there is a growing impetus for nonlethal tissue sampling in fish monitoring. As a result, Se monitoring programs often generate low-weight tissue samples of varying lipid content, which challenges analytical laboratories to quantify tissue Se concentrations accurately, precisely, and at desired detection limits. The objective of the present study was to stress-test some conventional analytical techniques used by commercial laboratories in terms of their ability to maintain data quality objectives (DQOs) in the face of sample weight constraints. Four laboratories analyzed blind a suite of identical samples, and data were compared against a priori DQOs for accuracy, precision, and sensitivity. Data quality tended to decrease with decreasing sample weight, particularly when samples were less than the minimum weights requested by the participating laboratories; however, effects of sample weight on data quality were not consistent among laboratories or tissue types. The present study has implications for accurately describing regulatory compliance in Se monitoring programs, highlighting some important considerations for achieving high data quality from low-weight samples. Environ Toxicol Chem 2023;42:2119-2129. © 2023 SETAC.

Comparison of Two Total Mercury Screening and Assessment Methods in Fishes: Biopsy Punch and Dried Muscle Samples

Rapid and effective quantification of total mercury concentrations ([THg]) in fish muscle is an important part of ongoing monitoring to provide reliable and near real-time public health guidance. Methods for quantifying THg in fish muscle frequently require the use of large sample mass and numerous preparation steps. Wet (aka fresh weight) biopsy punch samples of fish muscle have been used to quantify THg directly, without drying and homogenization. Both methods have advantages and disadvantages. We compare the use of fresh weight biopsy punches for quantifying THg to using larger, dried homogenized samples. The [THg] determination for the two sampling methods was EPA method 7473. Three separate biopsy punch samples and a large muscle sample were taken from each fish and analyzed on a Direct Mercury Analyzer. There were no statistical differences between mean log transformed wet weight [THg] from biopsy punches and homogenized muscle across all samples or within individual species. Similarly, across the range of [THg] (7.5-612.7 ng/g ww), linear regression of [THg] from biopsy punch and homogenized muscle samples was not different from a 1:1 linear relationship. Linear regression statistics of [THg] with fish fork length produced similar results for both biopsy punch and homogenized muscle samples. However, the coefficient of variation among biopsy punch replicates for individual fish was frequently above the acceptable threshold of 15%. We recommend biopsy punches be used as an effective tool for broad-scale rapid monitoring of fish resources for Hg, while homogenized muscle samples be used for fine-scale ecological and health questions.

Carbonic anhydrase in elasmobranchs and implications of the current climate change scenario

The enzyme carbonic anhydrase (CA) has well-known functions in acid-base balance, respiratory gas exchange, and osmoregulation in teleost fishes. However, studies concerning the role of CA in elasmobranchs are still scarce. Therefore, the aim of this study is to present the current status of CA studies in sharks and rays, as well as to identify gaps and emerging needs, in order to guide future studies. This review is organized according to the main roles of CA, with further considerations on climate change and CA effects indicated as paramount, as strategies in the face of climate change can be crucial for species response. The literature review revealed a reduction in publications on CA over the years. In addition, a historical research differentiation is noted, where the first assessments on the subject addressed investigations on basic CA functions, while the most recent studies present a comparative approach among species as well as interdisciplinary discussions, such as ecology and phylogeny. Considering that most elasmobranchs are threatened, future studies should prioritize non-lethal methodologies, in addition to expanding studies to climate change effects on CA.

A glimpse into the trophic ecology of deep-water sharks in an important crustacean fishing ground

Deep-water sharks are among the most vulnerable deep-water taxa because of their extremely conservative life-history strategies (i.e., late maturation, slow growth, and reproductive rates), yet little is known about their biology and ecology. Thus, this study aimed at investigating the trophic ecology of five deep-water shark species, the birdbeak dogfish (Deania calcea), the arrowhead (D. profundorum), the smooth lanternshark (Etmopterus pusillus), the blackmouth catshark (Galeus melastomus) and the knifetooth dogfish (Scymnodon ringens) sampled onboard a crustacean bottom-trawler off the south-west coast of Portugal. We combined carbon and nitrogen stable isotopes with RNA and DNA (RD) ratios to investigate the main groups of prey assimilated by these species and their nutritional condition, respectively. Stable isotopes revealed overall small interspecific variability in the contribution of different taxonomic groups to sharks' tissues, as well as in the origin of their prey. S. ringens presented higher δ¹⁵ N and δ¹³ C values than the other species, suggesting reliance on bathyal cephalopods, crustaceans and teleosts; the remaining species likely assimilated bathy-mesopelagic prey. The RD ratios indicated that most of the individuals had an overall adequate nutritional condition and had recently eaten. This information, combined with the fact that stable isotopes indicate that sharks assimilated prey from the local or nearby food webs (including commercially important shrimps), suggests a potential overlap between this fishing area and their foraging grounds, which requires further attention.

Experimentally derived biochemical modelling parameters to improve understanding of aquaculture's effect on marine food webs

To construct robust biogeochemical models for application to marine-based aquaculture settings, careful selection of appropriate model parameters is necessary. This study used an experimental approach to establish biomarkers of farm and marine-derived organic matter, and to derive isotopic turnover rates, and trophic discrimination factors specific to aquaculture associated food webs. A shift towards a farm-derived resource base resulted in consumer tissues more depleted in the carbon-13 isotope (indicated by more negative δ¹³C values) and a higher proportion of oleic acid, linoleic acid, and alpha-linoleic acid in the fatty acid profile of consumers over time. Measured trophic discrimination factors between dietary sources and consumer tissues demonstrated high variability among species and tissue types, ranging from -0.25‰ to 0.82‰ for Δ¹³C and from -0.77‰ to 6.8‰ for Δ¹⁵N. Stable isotope half-lives were also diverse among species and tissue types, ranging from <7 days to 462 days. Results demonstrated that construction of robust models for tracing assimilation of farm-derived organic matter through marine food webs requires the use of taxa and tissue specific parameters. Turnover rates have applications for understanding assimilative capacity of communities and for managing populations within the ecological footprint of farms.

Non-Lethal Sampling Supports Integrative Movement Research in Freshwater Fish

Freshwater ecosystems and fishes are enormous resources for human uses and biodiversity worldwide. However, anthropogenic climate change and factors such as dams and environmental contaminants threaten these freshwater systems. One way that researchers can address conservation issues in freshwater fishes is via integrative non-lethal movement research. We review different methods for studying movement, such as with acoustic telemetry. Methods for connecting movement and physiology are then reviewed, by using non-lethal tissue biopsies to assay environmental contaminants, isotope composition, protein metabolism, and gene expression. Methods for connecting movement and genetics are reviewed as well, such as by using population genetics or quantitative genetics and genome-wide association studies. We present further considerations for collecting molecular data, the ethical foundations of non-lethal sampling, integrative approaches to research, and management decisions. Ultimately, we argue that non-lethal sampling is effective for conducting integrative, movement-oriented research in freshwater fishes. This research has the potential for addressing critical issues in freshwater systems in the future.

The use of non-lethal sampling for transcriptomics to assess the physiological status of wild fishes

Fishes respond to different abiotic and biotic stressors through changes in gene expression as a part of an integrated physiological response. Transcriptomics approaches have been used to quantify gene expression patterns as a reductionist approach to understand responses to environmental stressors in animal physiology and have become more commonly used to study wild fishes. We argue that non-lethal sampling for transcriptomics should become the norm for assessing the physiological status of wild fishes, especially when there are conservation implications. Processes at the level of the transcriptome provide a "snapshot" of the cellular conditions at a given time; however, by using a non-lethal sampling protocol, researchers can connect the transcriptome profile with fitness-relevant ecological endpoints such as reproduction, movement patterns and survival. Furthermore, telemetry is a widely used approach in fisheries to understand movement patterns in the wild, and when combined with transcriptional profiling, provides arguably the most powerful use of non-lethal sampling for transcriptomics in wild fishes. In this review, we discuss the different tissues that can be successfully incorporated into non-lethal sampling strategies, which is particularly useful in the context of the emerging field of conservation transcriptomics. We briefly describe different methods for transcriptional profiling in fishes from high-throughput qPCR to whole transcriptome approaches. Further, we discuss strategies and the limitations of using transcriptomics for non-lethally studying fishes. Lastly, as 'omics' technology continues to advance, transcriptomics paired with different omics approaches to study wild fishes will provide insight into the factors that regulate phenotypic variation and the physiological responses to changing environmental conditions in the future.

Evaluating the effect of dorsal muscle biopsies on adult Atlantic salmon growth and marine return rates

Increasing conservation and animal-welfare concerns have driven the development of non-lethal sampling of fish populations, with the use of muscle tissue biopsies now being routinely applied as a sampling method in the wild. Crucial to the success of non-lethal sampling, however, is an evaluation of the short- and long-term consequences of the treatment and ultimately the determination of how these may affect organism mortality and other fitness-related traits. The current study evaluated the use of a dorsal muscle biopsies on post-spawned Atlantic salmon emigrating to sea and undertaking a 2-month long-feeding migration before returning to spawn. Using mark-recapture, return rates and growth were compared between fish that were biopsied and externally tagged, and a control group tagged only with external tags. The biopsy treatment showed no lasting effects on fish as estimated from the two key fitness-related parameters. Results, therefore, suggest the technique can be more widely applied to gather information on marine migrating Atlantic salmon and other anadromous fishes that can be intercepted as they descend and ascend rivers during seasonal migrations. Coupled with modern tagging technologies, the use of biopsies may facilitate an improved understanding of movement and its consequences in terms of feeding patterns and growth.

Detection of Betanodavirus in experimentally infected European seabass (Dicentrarchus labrax, Linnaeus 1758) using non-lethal sampling methods

One of the major disease threats affecting the Mediterranean aquaculture industry is viral encephalopathy and retinopathy (VER). The target organs for Betanodavirus detection are the brain and eyes, obtained through lethal sampling. This study aimed to evaluate the efficacy and suitability of non-lethal samples for detecting Betanodavirus in European seabass (Dicentrarchus labrax). European seabass juveniles were infected with Betanodavirus, by either an intramuscular injection or immersion (10⁷ TCID₅₀ /ml and 10⁶ TCID₅₀ /ml, respectively), and samples collected 7, 15 and 30 days post-infection (dpi). The brain was collected as a lethal sample, and gills, caudal fin and blood as non-lethal tissues for detecting Betanodavirus by quantitative reverse transcription PCR (RT-qPCR). The presence of virus in non-lethal tissues was inconsistent, with lower viral loads than in the brain. For blood, higher viral loads were detected in intramuscular-infected fish at 15 dpi until the end of the challenge. Serum antibodies against Betanodavirus were assessed using an enzyme-linked immunosorbent assay (ELISA). Antibodies were detected as early as 7 dpi, with higher mean antibody titres at 15 and 30 dpi. The presence of Betanodavirus-specific antibodies indicates that this is a suitable evaluation method for detecting early stages of the infection.

Prevalence of pelagic dependence among coral reef predators across an atoll seascape

Coral reef food webs are complex, vary spatially and remain poorly understood. Certain large predators, notably sharks, are subsidized by pelagic production on outer reef slopes, but how widespread this dependence is across all teleost fishery target species and within atolls is unclear.

North Malé Atoll (Maldives) includes oceanic barrier as well as lagoonal reefs. Nine fishery target predators constituting ca. 55% of the local fishery target species biomass at assumed trophic levels 3–5 were selected for analysis. Data were derived from carbon (δ¹³C), nitrogen (δ¹⁵N) and sulphur (δ³⁴S) stable isotopes from predator white dorsal muscle samples, and primary consumer species representing production source end‐members.

Three‐source Bayesian stable isotope mixing models showed that uptake of pelagic production extends throughout the atoll, with predatory fishes showing equal planktonic reliance between inner and outer edge reefs. Median plankton contribution was 65%–80% for all groupers and 68%–88% for an emperor, a jack and snappers.

Lagoonal and atoll edge predators are equally at risk from anthropogenic and climate‐induced changes, which may impact the linkages they construct, highlighting the need for management plans that transcend the boundaries of this threatened ecosystem.

Mercury Contamination in Riverine Sediments and Fish Associated with Artisanal and Small-Scale Gold Mining in Madre de Dios, Peru

Artisanal and small-scale gold mining (ASGM) in Madre de Dios, Peru, continues to expand rapidly, raising concerns about increases in loading of mercury (Hg) to the environment. We measured physicochemical parameters in water and sampled and analyzed sediments and fish from multiple sites along one ASGM-impacted river and two unimpacted rivers in the region to examine whether Hg concentrations were elevated and possibly related to ASGM activity. We also analyzed the 308 fish samples, representing 36 species, for stable isotopes (δ¹⁵N and δ¹³C) to estimate their trophic position. Trophic position was positively correlated with the log-transformed Hg concentrations in fish among all sites. There was a lack of relationship between Hg concentrations in fish and either Hg concentrations in sediments or ASGM activity among sites, suggesting that fish Hg concentrations alone is not an ideal bioindicator of site-specific Hg contamination in the region. Fish Hg concentrations were not elevated in the ASGM-impacted river relative to the other two rivers; however, sediment Hg concentrations were highest in the ASGM-impacted river. Degraded habitat conditions and commensurate shifts in fish species and ecological processes may influence Hg bioaccumulation in the ASGM-impacted river. More research is needed on food web dynamics in the region to elucidate any effects caused by ASGM, especially through feeding relationships and food sources.