Salmon Farming Research Articles

Pseudomonas aphyarum sp. nov., Pseudomonas fontis sp. nov., Pseudomonas idahonensis sp. nov. and Pseudomonas rubra sp. nov., isolated from in, and around, a rainbow trout farm.

During a large-scale bacterial culturing effort of biofilms in the vicinity of a rainbow trout aquaculture facility in Idaho, USA, 10 isolates were identified as having pathogen-inhibiting activity and were characterized further. These isolates were shown to be Gram-negative, rod-shaped bacteria belonging to the genus Pseudomonas. Whole-genome comparisons and multi-locus sequence analysis using four housekeeping genes (16S rRNA, gyrA, rpoB and rpoD) showed that these 10 isolates clustered into four distinct species groups. These comparisons also indicated that these isolates were below the established species cutoffs for the genus Pseudomonas. Further phenotypic characterization using API 20NE, API ZYM and Biolog GENIII assays and chemotaxonomic analysis of cellular fatty acids were carried out. Based on the genomic, physiological and chemotaxonomic properties of these isolates, we concluded that these strains composed four novel species of the genus Pseudomonas. The proposed names are as follows: Pseudomonas aphyarum sp. nov. consisting of strains ID233, ID386T and ID387 with ID386T (=DSM 114641T=ATCC TSD-305T) as the type strain; Pseudomonas rubra sp. nov. consisting of strains ID291T, ID609 and ID1025 with ID291T (=DSM 114640T=ATCC TSD-303T) as the type strain; Pseudomonas idahonensis sp. nov. consisting of strains ID357T and ID1048 with ID357T (=DSM 114609T=ATCC TSD-304T) as the type strain; and Pseudomonas fontis sp. nov. consisting of strains ID656T and ID681 with ID656T (=DSM 114610T=ATCC TSD-306T) as the type strain.

Assessment of the biochemical status of Parasalmo mykiss walbaum in trout farming conditions as a basis for the development of a natural adaptogen based on green microalgae

Increasing the output of aquaculture products is an important condition for supporting food security in Russia and ensuring the socio-economic development of the regions. One of the key factors for the sustainable functioning of trout farms is the timely and effective prevention of the occurrence and spread of diseases in farmed fish [8,10]. The purpose of the presented study was to monitor the condition of rainbow trout based on the assessment of biochemical and morphological blood parameters in age dynamics to identify critical periods and develop an adaptogen from green microalgae for the correction of metabolic processes. In the presented study, the hematological status of rainbow trout was studied in the conditions of the fisheries of the Republic of Karelia. The study was conducted in the summer in 4 age groups. During the research, it was revealed that the age of trout significantly affects the biochemical blood levels studied. As a result of the research, it was revealed that in the studied animals with age there is a significant increase in such biochemical parameters as ALT, Total protein, albumin, and urea. Thus, during the monitoring of the biochemical status of rainbow trout under aquaculture conditions, it was found that the condition of the fish’s body worsens with age, which is reflected in the biochemical parameters of the blood, such as total protein, albumin, and urea. In this case, green microalgae Chlorella can act as a natural adaptogen that normalizes blood biochemical parameters due to the high content of available carotenoids. It has been established that the pigments chlorophyll a (6.68 mg/g) and carotenoids (3.36%) accumulate in noticeable quantities in the biomass of.

The fate of nitrogen in the Zarin-Gol River receiving trout farm effluent

This study investigated the Zarrin-Gol River ecosystem in Iran to trace organic matter in the food web and evaluate the impact of aquaculture farm effluent using stable isotopes of nitrogen (δ15N) and carbon (δ13C). Using a previously-developed model (Islam 2005), we estimated that a trout farm in the vicinity released 1.4 tons of nitrogen into the river. This was comparable to an estimated total nutrient load of 2.1 tons of nitrogen for the six-month fish-rearing period based on a web-based constituent load estimator (LOADEST). A model estimate of river nitrogen concentration at the time of minimum river discharge (100 L/s) was 2.74 mg/L. Despite relatively high nitrogen loading from the farm, isotope data showed typical food web structure. Several biological groups had elevated δ13C or δ15N values, but there was limited evidence for the entry of organic matter from the trout farm into the food web, with sites above and below trout farms having inconsistent patterns in 15N enrichment. By coupling nitrogen load modeling with stable isotope analysis we showed that stable isotopes might not be effective tracers of organic matter into food webs, depending on surrounding land use and other point sources of nutrients. The Zarrin-Gol River ecosystem, like other basins with high human population density, remains vulnerable to eutrophication in part due to trout farm effluent.

A social and ethical game-changer? An empirical ethics study of CRISPR in the salmon farming industry

The genome editing technology CRISPR is described as a technological game-changer because of its flexibility and precision, and as an ethical game-changer due to its ability to engineer traits in living organisms without crossing species, avoiding a significant objection to genetically modified organisms (GMOs). In salmon farming, applications of CRISPR in breeding hold the promise of handling environmental and fish welfare challenges yet require social acceptance. Adopting an empirical bioethics framework, this stakeholder interview study shows that respecting species borders is important, but not decisive, for acceptance among Norwegian stakeholders. The main objections are based on moral reflections about technology use and outcomes. These reflections combine principles and pragmatic deliberations of moral costs and benefits, suggesting that CRISPR applications with environmentally and ethically significant benefits can be socially acceptable. This indicates that the game-changing potential of CRISPR relies on the characteristics of the editing and the context in which the application takes place.

Genetic selection for reduced parasite load in Atlantic salmon: Zero-sum game or a tool for group-level protection against sea lice?

Sea lice are copepod ectoparasites of major importance in salmonid aquaculture. Under controlled challenge testing, individual lice count has moderate heritability and has been suggested as a trait in genetic selection for parasite control, under the assumption that selection for reduced individual parasite burden provides group-level protection against the parasite. Recent studies indicate that genetic variation of lice count in Atlantic salmon is mostly explained by variation in initial infestation, rather than ability to limit parasite burden after infestation. Results from a selection experiment are presented, with two Atlantic salmon (Salmo salar) lines divergently selected for low/high parasite burden, showing substantial between-strain difference under common-garden testing. An experiment was performed where the final generation of the divergently selected salmon lines were challenge tested separately to assess potential for group-level protection against sea lice. The results showed that, despite the two groups being clearly different under common garden testing, the line difference was not significant when tested separately, i.e., no evidence for group-level protection. However, in a follow-up experiment, using a more realistic lice challenge model under water-flow, expected to be less favorable for the parasite, significant group-level differences were found, albeit smaller than under common garden testing. The results show that the potential for group-level protection is lower than suggested by within-group genetic variation in lice count, and more so for environments giving the parasites easy access to hosts. These results cast some doubt about the efficacy of selective breeding for reduced lice count as a tool for group-level parasite control in densely populated fish farm environments.

The role of salmon aquaculture eco-certification in corporate social responsibility and the delivery of ecosystem services and disservices

Aquaculture eco-certification is especially relevant in salmon farming where it has emerged as a popular corporate social responsibility (CSR) strategy, providing global standards that can be applied to a globally traded commodity. However, eco-certification is just one of many CSR strategies used to address seafood sustainability at the corporate level. CSR is important for company image, but it is not clear whether or how these strategies contribute to sustainability outcomes. This paper applies an ecosystem services framework to an analysis of sustainability reporting from top salmon farming companies to identify links between eco-certification, other CSR strategies, and the delivery of ecosystem services. Although eco-certification was used to indicate commitment to sustainability practices across all companies, other CSR strategies, especially practices, power, and partnership, were more frequently and explicitly connected to the delivery of ecosystem services. Results show that individual CSR strategies including eco-certification are not isolated but interact and work in concert to manage the supply of ecosystem services.

Description of spatiotemporal patterns of infectious salmon anemia virus (ISAV) detections in marine Atlantic Salmon farms in Newfoundland and Labrador.

The objectives of this study were to describe spatiotemporal patterns of infectious salmon anemia virus (ISAV) detections in marine salmonid production sites in the province of Newfoundland and Labrador in Canada. Infectious salmon anemia virus surveillance data between 2012 and 2020 from the province of Newfoundland and Labrador were used. Data comprised a total of 94 sampling events from 20 Atlantic Salmon Salmo salar production sites in which ISAV was detected. Using linear regression models, factors influencing time to detection (days from stocking to first ISAV detection) and time to depopulation (days from first detection to production site depopulation) were investigated. Based on 28 unique cases, site-level annual incidence risk of ISAV detection ranged from 3% to 29%. The proportion of ISAV detection by PCR in fish samples ranged from 2% to 45% annually. Overall, ISAV variants from the European clade were more common than variants from the North American clade. The type of ISAV clade, detections of ISAV in nearest production sites based on seaway distances, and year of infectious salmon anemia cases were not associated with time to first ISAV detection. Time to depopulation for sites infected with the ISAV-HPRΔ variant was not associated with ISAV North American or European clades. Our results contribute to the further understanding of the changing dynamics of infectious salmon anemia detections in Newfoundland and Labrador since its first detection in 2012 and will likely assist in the design of improved disease surveillance and control programs in the province.

Prioritized imputed sequence variants from multi-population GWAS improve prediction accuracy for sea lice count in Atlantic salmon (Salmo salar)

Sea lice infestation is one of the major fish health problems that occurs during the grow-out phase in Atlantic salmon (Salmo salar) aquaculture. In this study, we integrated different genomic approaches, including whole-genome sequencing (WGS), genotype imputation and meta-analysis of genome-wide association studies (GWAS), to identify single-nucleotide polymorphisms (SNPs) associated with sea lice count in Atlantic salmon. Different sets of trait-associated SNPs were prioritized and compared against randomly chosen markers, based on the accuracy of genomic predictions for the trait. Lice count phenotypes and dense genotypes of five breeding populations challenged with sea lice were used. Genotype imputation was applied to increase SNP density of challenged animals to WGS level. The summary statistics from GWAS of each population were then combined in a meta-analysis to increase the sample size and improve the statistical power of associations. Eight different genotyping scenarios were considered for genomic prediction: 70K_array: 70 K standard genotyping panel; 70K_priori: 70 K SNPs with the highest p-values identified in the meta-analysis; 30K_priori: 30 K SNPs with the highest p-values identified in the meta-analysis; WGS: SNPs imputed to whole-genome sequencing level. The remaining four scenarios were the same SNP sets with a linkage disequilibrium (LD) pruning filter: 70K_array_LD; 70K_priori_LD; 30K_priori_LD and WGS_LD. Genomic prediction accuracy was evaluated using a five-fold cross-validation scheme in two different populations which were excluded from the meta-analysis to remove possible validation-reference bias. Results showed significant genetic variation for the number of sea lice in Atlantic salmon across populations, with heritabilities ranging from 0.06 to 0.24. The meta-analysis identified several SNPs associated with sea lice resistance, mainly in Ssa03 and Ssa09 chromosomes. Genomic prediction using the GWAS-based prioritized SNPs showed higher accuracy compared to the standard SNP array in most of scenarios; achieving up to 57% increase in accuracy. Accuracy of prioritized scenarios was higher for the 70K_priori than the 30K_priori. The use of WGS data in genomic prediction presented marginal or negative accuracy gain compared to the standard SNP array. The LD-pruning filter presented no benefits, reducing accuracy in most scenarios. Overall, our study demonstrated the potential of prioritized imputed sequence variants from multi-population GWAS meta-analysis to improve prediction accuracy for sea lice counts in Atlantic salmon. The findings suggest that incorporating WGS data and prioritized SNPs from GWAS meta-analysis can accelerate the genetic progress of selection for polygenic traits in salmon aquaculture.

A modeling study of the impact of treatment policies on the evolution of resistance in sea lice on salmon farms.

Salmonid aquaculture is an important source of nutritious food with more than 2 million tonnes of fish produced each year (Food and Agriculture Organisation of the United Nations, 2019). In most salmon producing countries, sea lice represent a major barrier to the sustainability of salmonid aquaculture. This issue is exacerbated by widespread resistance to chemical treatments on both sides of the Atlantic. Regulation for sea lice management mostly involves reporting lice counts and treatment thresholds, which depending on interpretation may encourage preemptive treatments. We have developed a stochastic simulation model of sea lice infestation including the lice life-cycle, genetic resistance to treatment, a wildlife reservoir, salmon growth and stocking practices in the context of infestation, and coordination of treatment between farms. Farms report infestation levels to a central organisation, and may then cooperate or not when coordinated treatment is triggered. Treatment practice then impacts the level of resistance in the surrounding sea lice population. Our simulation finds that treatment drives selection for resistance and coordination between managers is key. We also find that position in the hydrologically-derived network of farms can impact individual farm infestation levels and the topology of this network can impact overall infestation and resistance. We show how coordination and triggering of treatment alongside varying hydrological topology of farm connections affects the evolution of lice resistance, and thus optimise salmon quality within socio-economic and environmental constraints. Network topology drives infestation levels in cages, treatments, and hence treatment-driven resistance. Thus farmer behaviour may be highly dependent on hydrologically position and local level of infestation.

Greenhouse gas emission reduction opportunities for the Norwegian salmon farming sector - can they outweigh growth?

Norwegian farmed Atlantic salmon is a nutritious type of food in increasing demand and although production has stagnated and is faced by various challenges, it is likely to continue to expand in the future. We present results from a detailed greenhouse gas emission assessment of the most important Norwegian farmed salmon export products along with improvement measures. By scaling up both baseline results and reduction opportunities, based on growth projections, we estimate current and future emissions of the sector as a whole. We show that export of gutted salmon to Europe by truck dominates Norwegian salmon exports, not only in volume and value, but also in emissions, followed by export of fresh gutted salmon and fillets to Asia and fillets to the US by air. The cumulative greenhouse gas emissions are dominated by feed production followed by emissions from overseas airfreighting of fresh products. The five most important emission reduction measures, based only on existing technology and without particular order were 1) slightly increased feed efficiency, 2) increased utilization of side streams occurring in secondary processing after export, 3) seafreight to market instead of road and air, 4) higher energy efficiency and cleaner energy sources, and 5) changed feed composition. Collectively, they have the potential to reduce greenhouse gas emissions of current production by 60%, from 5.2 to 2.1 million tonnes of CO2e, assuming the same relative importance of each supply chain.This implies that a medium growth-scenario, representing more than a doubling of the volume of salmon farmed to 3.3 million tonnes, would be possible while reducing total sector emissions by 16% if the improvement measures were fully implemented. For larger reductions, either lower growth or more ambitious implementation of improvement measures is needed. Although greenhouse gas emissions are often linked to resource efficiency and wider sustainability, this is not always the case, and it is important to avoid shifting burdens from climate to e.g. eutrophication or biodiversity impacts. However, many environmental impacts of salmon farming are centered around feed efficiency, and even problems with welfare, escapees, and in part eutrophication are reflected in lower feed efficiency resulting in higher greenhouse gas emissions. In addition to the systematic collection of robust data for more continuous monitoring of greenhouse gas emission performance over time, we therefore recommend identifying additional indicators to monitor to ensure the sector develops not only towards climate neutrality but also towards broader sustainability.

Impact and recovery of water quality in a river with salmon aquaculture

AbstractFreshwater aquaculture can have negative impacts on chemical, physical and biological water quality. To contextualise the impact that these activities may have, a case study site in Ireland was monitored for 1 year. The study aims were to investigate the impact of freshwater aquaculture on water quality (biological, physical, and chemical) and the degree of the impact and recovery in water quality, within 1000 m downstream of a salmon smolt hatchery. The hatchery was monitored, at four locations (upstream, 10, 100, and 1,000 m downstream of the discharge point). Data on macroinvertebrate, macrophyte, hydromorphology and chemical characteristics were collected. Results for the physical monitoring indicated no significant changes in hydromorphology between up and downstream sites. Chemical water quality did decrease downstream in terms of nitrogen (N) and phosphorus (P). The greatest concentrations in N and P were found at 1000 m though it is likely additional contributions from agriculture impacted this site. Dissolved oxygen was steady throughout the monitoring campaign with a 13% variance between upstream and downstream locations. Changes in biological indices were statistically significant for taxa at all downstream sites. There were positive trends which indicated a degree of recovery in biotic indices.

Drying treatment for sludges of the Chilean salmon farming industry and its potential as an agricultural soil amendment

ABSTRACT Organic waste generation in aquaculture worldwide requires circular economy approaches. The revalorization of wastes in the Chilean salmon industry could be a potential soil amendment. We investigated the thermo-drying process on salmon sludge, evaluating it as an alternative to reusing in horticulture. The chemical characterization of untreated sludge (wet sludges: WS) and dried sludges (DS) were evaluated with thermogravimetry, IR spectroscopy, and fluorescence. Additionally, the germination index of the DS was determined in L. sativa, R. sativus, and S. lycopersicum. The results show that DS reduces salinity, ammonium content, and pathogens compared to WS. During the thermic process, there were no significant decreases in organic matter, phosphorus, potassium, and humic and fulvic substances. The high salinity in DS inhibited seed germination. This research constituted a novel contribution to studying the DS as a strategy for horticultural production. In the same way, the drying technology for salmon sludge favored the management of wastes, contributing to the circular economy in both the agricultural and aquaculture sectors. However, we recommend considering that excessive incorporation of DS into germination substrates or direct application into the soil could affect the crop’s performance due to its high salinity.

Upcycling of carbon, nitrogen, and phosphorus from aquaculture sludge using the polychaete Hediste diversicolor (OF Müller, 1776) (Annelida: Nereididae)

IntroductionFocusing on circular bioeconomy and finding solutions for managing finite and scarce resources such as phosphorus are issues that need to be addressed across sectors to attain food security. Land-based aquaculture of Atlantic salmon (Salmo salar L.) smolt and post-smolt results in a large output of aquaculture sludge. These nutrient-rich side streams from aquaculture production constitute a valuable resource for cultivation of polychaetes Hediste diversicolor. The aim of this study was to evaluate the capacity of H. diversicolor to upcycle carbon (C), nitrogen (N), and phosphorus (P) contained in aquaculture sludge from Norwegian salmon production.Material and methodsWe investigated the effect of two diets, smolt sludge and post-smolt sludge, which were supplied at four different feed levels, on the gain of C, N, and P in H. diversicolor and established uptake rates for the upcycling of these nutrients. Additionally, we examined how different feed composition (type of diet) and supply (feel level) influenced C, N, and P content as well as the elemental ratios of H. diversicolor.Results and discussionPolychaetes fed with both types of sludge were shown to incorporate C, N, and P from their diets into biomass. Incorporation of C, N, and P in polychaete biomass was highest at the highest feed levels, following specific growth rates. Uptake of diet C, N, and P into polychaete biomass was similar for both diets and across feed levels. On average, C and N uptake rates amounted to 2–10% and 2–15%, respectively, while values for P uptake were lower at 0.5–1.5%. C, N, and P content of polychaetes was not affected by different diets or feed levels while the C:N ratio increased with increasing feed supply. Overall, we found that H. diversicolor can successfully take up nutrients contained in aquaculture sludge and thus can be beneficial for upcycling of side streams from Atlantic salmon production.

Evolutionary predictions for a parasite metapopulation: Modelling salmon louse resistance to pest controls in aquaculture.

Pests often evolve resistance to pest controls used in agriculture and aquaculture. The rate of pest adaptation is influenced by the type of control, the selective pressure it imposes, and the gene flow between farms. By understanding how these factors influence evolution at the metapopulation level, pest management strategies that prevent resistance from evolving can be developed. We developed a model for the metapopulation and evolutionary dynamics of the salmon louse (Lepeophtheirus salmonis), which is a major parasite affecting salmon aquaculture. Different management scenarios were simulated across a network of salmon farms covering half of Norway, and their effects on louse epidemiology and evolution were investigated. We compared louse controls that differed in how they were deployed through time (discrete vs. continuous), how they impacted the louse life cycle, and in their overall efficacy. We adjusted the strength of selection imposed by treatments, the dominance effect of the resistant allele, and the geographic location at which resistance originated. Continuously acting strategies (e.g., louse-resistant salmon) were generally more effective than discrete strategies at controlling lice, especially when they increased louse mortality during early developmental stages. However, effective strategies also risked imposing frequent and/or strong selection on lice, thus driving rapid adaptation. Resistant alleles were more likely to be lost through genetic drift when they were recessive, had a low-fitness advantage, or originated in low-farm-density areas. The north-flowing current along the Norwegian coastline dispersed resistant genes from south to north, and limited gene flow in the opposite direction. We demonstrate how evolutionary models can produce quantitative predictions over large spatial and temporal scales and for a range of pest control scenarios. Quantitative outputs can be translated into practical management decisions applied at a regional level to minimise the risk of resistance developing.

Trout Production in District Ganderbal – An Analysis of Economic Challenges

The present study carried during the year 2022-23, worked on the impact of the introduction of genetically improved strains of rainbow trout on the economy of the fish farmers, in comparison to the normal strains. The economy of 40 farmers in groups of 20 Normal stock (NS) and Genetically Improved Stock (GIS) each was conducted and interviewed using a pre-tested questionnaire. The investigation showed that fixed capital investment on sample farm was Rs.1.25 lakh per raceway in both the set ups. The major share of investment was for the construction of raceway, which accounted for 68.53% of total investment on sample farms. The share of total variable cost was 58.37% in NS and 48.50 in GIS per cent and fixed cost was 41.62 in NS and 51.49 in GIS group. Feed was the major cost component accounting for about 46.43 per cent of the total cost in NS, while as it was reduced to 37.15% in GIS, thereby encouraging as a key factor in deciding profitability of trout farming. Resource use efficiency showed that feed was overutilized while labor was under-utilized in NS, while as it was optimally utilized in GIS group. The returns to scale in trout production of 1.25 indicates increasing returns to scale in trout production. High price of feed and seed are found to be the major constraints in trout culture. The B-C ratio worked out to be 1.37 in NS group and 1.87 in GIS group, indicating the economic feasibility of trout farming in the Kashmir valley, and better economic profile of farmers farming GIS strain.

Descriptive analyses of bacterial communities in marine sediment microcosms spiked with fish wastes, emamectin benzoate, and oxytetracycline

In marine sediments surrounding salmon aquaculture sites, organic matter (OM) enrichment has been shown to influence resident bacterial community composition; however, additional effects on these communities due to combined use of the sea-lice therapeutant emamectin benzoate (EMB) and the widely used antibiotic oxytetracycline (OTC) are unknown. Here, we use sediment microcosms to assess the influence of OM, EMB, and OTC on benthic bacterial communities. Microcosms consisted of mud or sand sediments enriched with OM (fish and feed wastes) and spiked with EMB and OTC at environmentally-relevant concentrations. Samples were collected from initial matrices at the initiation of the trial and after 110 days for 16 S rRNA gene sequencing of the V3-V4 region and microbiome profiling. The addition of OM in both mud and sand sediments reduced alpha diversities; for example, an average of 1106 amplicon sequence variants (ASVs) were detected in mud with no OM addition, while only 729 and 596 ASVs were detected in mud with low OM and high OM, respectively. Sediments enriched with OM had higher relative abundances of Spirochaetota, Firmicutes, and Bacteroidota. For instance, Spirochaetota were detected in sediments with no OM with a relative abundance range of 0.01–1.2%, while in sediments enriched with OM relative abundance varied from 0.16% to 26.1%. In contrast, the addition of EMB (60 ng/g) or OTC (150 ng/g) did not result in distinct taxonomic shifts in the bacterial communities compared to un-spiked sediments during the timeline of this experiment. EMB and OTC concentrations may have been below effective inhibitor concentrations for taxa in these communities; further work should explore gene content and the presence of antibiotic resistance genes (ARGs) in sediment-dwelling bacteria.

Overview on the Biosecurity Measures of Salmonid Fish Farms: A Case Study in Italy

Italy is one of the main European producers of trout fish, and the most important producing area is the Autonomous Province of Trento (APT) in the North East. The objective of the study was to obtain a snapshot of the trout farms of the APT by identifying biosecurity factors, objectifying them, and classifying the establishments accordingly. Data from 62 salmonid farms were collected using a national checklist in which biosecurity elements were identified and assessed using the method of expert elicitation. The purpose was to evaluate the levels of biosecurity of a trout farm in order to rank the risk of introduction and spread of infectious fish diseases. The main critical factors identified during this study were as following: (i) cleaning and disinfection of the cargo truck; (ii) regular collection, storage, and disposal of dead fish; (iii) presence of anti-bird nets; (iv) use of dedicated equipment for the different sectors of the farm; and (v) presence of external areas dedicated to the loading of dead fish.

Co-Occurrence Between Salmon Farming, Alien American Mink (Neogale vison), and Endangered Otters in Patagonia

The southern river otter (Lontra provocax) and the marine otter (Lontra felina) are endangered species that inhabit Chile. In southern Chile, both species cohabit with the American mink (Neogale vison), an invasive exotic species. The Chilean aquaculture industry has grown exponentially since the late 1980s, with salmon farming taking place from central Chile to the Patagonian fjords and channels. This study assessed co-occurrence between otters, mink, and aquaculture in Patagonia by (1) distributing a survey among workers, fisheries personnel, and aquaculture inspectors concerning observations of otters and mink inside or around aquaculture facilities and outcomes; and (2) a geographical assessment of distribution overlap between known otter territory and salmon farming-registered facilities. We recorded the first anecdotal evidence of interaction, described as co-occurrence, among native otters, American mink, and salmon aquaculture in Patagonia, which varied among seasons and seems to be increasing. We also recorded evidence of difficulty in recognition of the three mustelids among respondents. There is a geographically extended interaction between otters and salmon farms in Chile. The evidence of interaction among alien American mink, native endangered otters, and aquaculture is an early alarm for human–wildlife conflict, and further studies are recommended to ensure native otter conservation.

The Atlantic salmon microbiome infected with the sea louse Caligus rogercresseyi reveals tissue-specific functional dysbiosis

The microbiota plays functional roles in almost all living organisms, influencing metabolism, defense, and nutrition. Conventionally, parasitism is defined as a bipartite interaction between host and parasites, where both organisms display molecular responses mainly associated with the immune system. However, the microbial community is another relevant factor that can interact during the parasite infection in fish farming. Therefore, this study aimed to characterize the Atlantic salmon microbiota's dynamics, correlation, and functional potential in skin and gut tissues during the sea louse Caligus rogercresseyi parasitism. The findings showed that the parasitism reduced the alpha and beta diversity in infested salmon's microbiota. This reduction favored the tissue-specific occurrence of opportunistic bacterial pathogens. Notably, Photobacterium was identified primarily on the skin, and Vibrio was predominant in the gut microbiota of infested individuals. Cluster analysis of full-length 16S rRNA sequencing suggested that C. rogercresseyi could be a vector for transmitting Tenacibaculum and Vibrio species. Network analysis evidenced that parasitism also perturbs the correlation of the skin and gut microbiota, revealing fewer associations in infested individuals. Finally, a contrasting effect on the functional potential of the skin and gut microbiome was found. Herein, the parasitism increased the biosynthetic processes and reduced degradation pathways in the skin; meanwhile, the opposite trend was observed in the gut microbiome. Overall, our results evidenced that sea lice parasitism induces tissue-specific functional dysbiosis and provides novel evidence about the harmful effects of sea lice in salmon aquaculture.

Transcriptome analysis revealed immune responses in the kidney of Atlantic salmon (Salmo salar) co-infected with sea lice (Lepeophtheirus salmonis) and infectious salmon anemia virus

Sea lice (Lepeophtheirus salmonis) and infectious salmon anemia virus (ISAv) are two of the most important pathogens in Atlantic salmon (Salmo salar) farming and typically cause substantial economic losses to the industry. However, the immune interactions between hosts and these pathogens are still unclear, especially in the scenario of co-infection. In this study, we artificially infected Atlantic salmon with sea lice and ISAv, and investigated the gene expression patterns of Atlantic salmon head kidneys in response to both lice only and co-infection with lice and ISAv by transcriptomic analysis. The challenge experiment indicated that co-infection resulted in a cumulative mortality rate of 47.8 %, while no mortality was observed in the lice alone infection. We identified 240 differentially expressed genes (DEGs) under the lice alone infection, of which 185 were down-regulated and 55 were up-regulated, while a total of 994 DEGs were identified in the co-infection, of which 206 were down-regulated and 788 were significantly up-regulated. The pathway enrichment analysis revealed that single-infection significantly suppressed the innate immune system (e.g., the complement system), whereas co-infection induced a strong immune response, leading to the activation of immune-related signaling pathways such as Toll-like receptors and NOD-like receptors pathways, as well as significant upregulation of genes related to the activation of interferon and MH class I protein complex. Our results provide the first global transcriptomic study of gene expression in the Atlantic salmon head kidney in response to co-infection with sea lice and ISAv, and provided the baseline knowledge for understanding the immune responses during co-infection.