Teleosts exhibit extensive diversity of sex determination (SD) systems and mechanisms, providing the opportunity to study the evolution of SD and sex chromosomes. Here we sequenced the genome of the common lumpfish (Cyclopterus lumpus Linnaeus), a species of increasing importance to aquaculture, and identified the SD region and master SD locus using a 70 K single nucleotide polymorphism array and tissue‐specific expression data. The chromosome‐level assembly identified 25 diploid chromosomes with a total size of 572.89 Mb, a scaffold N50 of 23.86 Mb and genome annotation‐predicted 21,480 protein‐coding genes. Genome‐wide association analysis located a highly sex‐associated region on chromosome 13, suggesting that anti‐Müllerian hormone (AMH) is the putative SD factor. Linkage disequilibrium and heterozygosity across chromosome 13 support a proto‐XX/XY system, with an absence of widespread chromosome divergence between sexes. We identified three copies of AMH in the lumpfish primary and alternate haplotype assemblies localized in the SD region. Comparison to sequences from other teleosts suggested a monophyletic relationship and conservation within the Cottioidei. One AMH copy showed similarity to AMH/AMHY in a related species and was also the only copy with expression in testis tissue, suggesting this copy may be the functional copy of AMH in lumpfish. The two other copies arranged in tandem inverted duplication were highly similar, suggesting a recent duplication event. This study provides a resource for the study of early sex chromosome evolution and novel genomic resources that benefits lumpfish conservation management and aquaculture.
This report documents the fishery, assessment, and management of lumpfish (Cyclopterus lumpus) across its distribution range. Targeting lumpfish for their roe on a large scale began in the 1950s in Iceland and Norway and then in Canada in the 1970s and Greenland in the 1990s. When the fishery began, there were few regulations, but limits on vessel size, mesh size, number of nets, and length of the fishing season were gradually implemented over time. Worldwide landings have varied from ca. 2000 to 8000 tonnes of roe between 1977 and 2016. Iceland and Canada accounted for >80% of the landings until 2000. After 2013, Greenland and Iceland accounted for >94%. All countries except Iceland show a decreasing trend in the number of boats participating in the fishery, which is related to several factors: the monetary value of the roe, changes in the abundance of lumpfish, and increasing age of artisanal fishers. Each country has a different combination of data available for assessment from basic landings and fishing effort data to more detailed fishery independent survey indices of abundance. The management of total catch also differs, with an effort-controlled fishery in Iceland and Canada, a total allowable catch (TAC) per boat in Norway, and TAC per area in Greenland. Population abundance is above management targets in Iceland and Norway, but the status is less clear in Greenland and around Denmark/Sweden and appears to be depleted around Canada. Certification by the Marine Stewardship Council was instrumental in the adoption of a management plan in Greenland; however, benefits to the fishers remain unclear. Aspects surrounding the biology of lumpfish, which is poorly understood and requires investigation, include growth rate, natural mortality, and population differentiation. In addition, there is concern about the potential impacts that the recent escalation in production of lumpfish for use as cleaner fish in the aquaculture industry could have on the wild population.
In both shaker-flask and mesocosm-scale experiments, a commercial oleophilic bioremediation agent containing biostimulation (nutrients) and bioaugmentation (bacterial inocula) properties was more effective in enhancing oil biodegradation rates than that of no treatment and/or periodic inorganic nutrient addition. However, similar results were not obtained from a subsequent 129-day field trial conducted in a sand beach environment. In this case, periodic additions of inorganic nutrients, with and without the commercial bioremediation agent, enhanced the number of heterotrophic bacteria and microbial respiration rates within the oiled sediments. The commercial product appeared to elevate the number of oil-degrading bacteria within the oiled sediment between days 17 and 89. However, the addition of inorganic nutrients alone, on a periodic basis, was the most effective means of enhancing the extent of oil biodegradation within the residual oil and of reducing sediment toxicity. By retaining residual oil and altering the physical and chemical characteristics of the treated sediment, the oleophilic product suppressed both the rate and extent of oil loss by tidal activity and biodegradation. This is not to say that the use of the product was ineffective in protecting the environment or was detrimental to it; the product does enhance natural biodegradation rates, and it limits the transport of beached oil to more sensitive areas. This study clearly illustrates the complexity associated with the selection of bioremediation agents, the need for improved experimental protocols for evaluating the performance and toxicity of bioremediation agents, and the potential of nutrient enrichment as a bioremediation strategy.
Natural biodegradation rates of oil within the marine environment are partly controlled by surface availability, as microbial attack primarily occurs at the oil-water interface. Therefore, increasing the surface area of residual oil by the addition of fine oleophilic particles may prove to be an effective bioremediation strategy. Considering commercial availability and cost, heat-treated peat was identified to be a promising particle source as it has high oil absorption properties and does not compete with oil as an alternative carbon source to oil-degrading bacteria. A preliminary laboratory experiment conducted with a respirometry system demonstrated the feasibility of nutrient and peat additions to enhance the metabolic activity of bacteria within oil-contaminated sand beach sediments. Field trials were conducted with similar peat and nutrient concentrations in a north-temperate beach environment with weathered Scotian Light crude oil over a 138-day period. The rates of microbial respiration and productivity were enhanced significantly above unoiled and oiled control sediments with the addition of inorganic nutrients with and without peat amendments. Treatment of sediments with inorganic nutrients and peat did not increase the toxicity of the residual oil. Gas chromatography/mass spectroscopy analysis was used to quantify bioremediation success by normalizing the loss of individual components to the conserved marker 17?(H), 21?H)-hopane. While there is evidence of a stimulatory effect with the addition of peat, results suggest that nutrient availability in the interstitial water limited optimal rates of oil bioremediation.
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