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Complex genetic architecture of the chicken Growth1 QTL region
Get PDFThe genetic complexity of polygenic traits represents a captivating and intricate facet of biological inheritance. Unlike Mendelian traits controlled by a single gene, polygenic traits are influenced by multiple genetic loci, each exerting a modest effect on the trait. This cumulative impact of numerous genes, interactions among them, environmental factors, and epigenetic modifications results in a multifaceted architecture of genetic contributions to complex traits. Given the well-characterized genome, diverse traits, and range of genetic resources, chicken (Gallus gallus) was employed as a model organism to dissect the intricate genetic makeup of a previously identified major Quantitative Trait Loci (QTL) for body weight on chromosome 1. A multigenerational advanced intercross line (AIL) of 3215 chickens whose genomes had been sequenced to an average of 0.4x was analyzed using genome-wide association study (GWAS) and variance-heterogeneity GWAS (vGWAS) to identify markers associated with 8-week body weight. Additionally, epistatic interactions were studied using the natural and orthogonal interaction (NOIA) model. Six genetic modules, two from GWAS and four from vGWAS, were strongly associated with the studied trait. We found evidence of both additive- and non-additive interactions between these modules and constructed a putative local epistasis network for the region. Our screens for functional alleles revealed a missense variant in the gene ribonuclease H2 subunit B (RNASEH2B), which has previously been associated with growth-related traits in chickens and Darwin’s finches. In addition, one of the most strongly associated SNPs identified is located in a non-coding region upstream of the long non-coding RNA, ENSGALG00000053256, previously suggested as a candidate gene for regulating chicken body weight. By studying large numbers of individuals from a family material using approaches to capture both additive and non-additive effects, this study advances our understanding of genetic complexities in a highly polygenic trait and has practical implications for poultry breeding and agriculture.publishedVersio
Emergence and dissemination of epidemic-causing OXA-244 carbapenemase-producing Escherichia coli ST38 through hospital sewage in Norway, 2020–2022
Get PDFBackground Population-based sewage surveillance has emerged as a promising approach for studying the prevalence of antibiotic resistance in pathogens. Aim To determine the temporal prevalence of cefotaxime-resistant Escherichia coli in sewage from five sewage treatment plants located in Bergen city, to determine whether ESBL- and carbapenemase-producing E. coli are consistently disseminated in the receiving environment through sewage. Method A total of 569 cefotaxime-resistant E. coli were isolated over a period of 19 months (August 2020 to February 2022) using ECC CHROMagar™ plates from 82 samples, antibiotic sensitivity profiles were determined, using Sensititre™ plates. The draft genome sequences were determined, using Illumina MiSeq-based sequencing. Complete genome sequences were determined, using Oxford Nanopore-based sequencing. Findings All 569 strains obtained from influent (N=461) and effluent (N=108) were multi-drug resistant. Most of the sequenced strains (52 of 61) carried blaCTX-M-15 (38.5%) and blaCTX-M-27 (34.6%). The most prevalent sequence types (STs) for ESBL-carrying strains were ST131 (32.8%) and ST38 (21.3%). All CTX-M-27-carrying ST131 strains belonged to clade A or C1, while CTX-M-15-harbouring strains were present in all the clades. Five OXA-244-producing ST38 strains, genetically similar to epidemic-causing strains from Western Norway, France and the Netherlands, were isolated only from raw and treated sewage of the treatment plant receiving hospital sewage. Conclusion This is the first study showing persistent dissemination of OXA-244-producing ST38 clones through sewage in Norway, demonstrating that hospital sewage is the likely source of OXA-244-producing ST38 clones reaching the receiving environment.publishedVersio
Life-history parameters of adult females of Merluccius capensis (Gadidae) off the south coast of South Africa
Get PDFThis study explores the life-history parameters of female Merluccius capensis off South Africa (N = 1819) during 2014–2016, including gonadosomatic index (GSI), length-at-maturity, length–weight relationships, and condition indices (relative condition [k] and Fulton's condition factor [K]). We detected weak indications of two peaks of spawning within the year, the first in austral autumn from March to May, whereas the other in austral spring around August. GSI was slightly higher in spring and autumn, though still low at all maturity stages (≤7%), though the opposite was true for the actively spawning stage (≥7%) as well as access to less such data during winter- and summertime. The length (L) at 50% maturity was around 38 cm (L50), though differences occurred between the two applied staging methods, histology and visual (macroscopic) classification, when L approached infinity. The latter method presented underestimated length at maturity values at the 75 and 95 percentiles (48 and 60 cm) compared to the corresponding percentiles given by histology (50 and 65 cm). There were trivial across-method differences in L50. However, we found a clear reduction in L50 in view of published information in prior years when this estimate was 48 (1985), 42 (2008), 53 (2011), and 24.8 (2015) cm. Overall, L explained 90% of the variation in whole body weight (W). As the bootstrapped, grand mean growth coefficient was b = 2.98, indicating a slight allometric growth function, there were no significant variations between years, though an isometric growth existed for 2016 with b = 3.0, whereas for 2014 and 2015 this b was 2.98 and 2.93, respectively. In terms of demography, females 60 cm. The relative condition index (k = 1) exhibited higher values than Fulton's K, which was 0.80. Overall, the maternal stock of M. capensis along the south coast seems to be in good condition and likely spawns throughout the year, but we found that the macroscopic data tend to give biased maturity ogives.publishedVersio
The Polar Front in the northwestern Barents Sea: structure, variability and mixing
Get PDFIn the northwestern Barents Sea the warm and salty Atlantic Water meets the cold and fresh Polar Water, forming a distinct thermohaline front, the Barents Sea Polar Front. Here we present the structure of the front, its variability and associated mixing using observations from two cruises conducted in October 2020 and February 2021 during the Nansen Legacy project in the region between the Hopen Trench and the Olga Basin. Ocean stratification, currents and turbulence data were obtained during seven ship transects across the Polar Front near 77° N, 30° E. These transects are complemented by four missions using ocean gliders, one of which was equipped with microstructure sensors to measure turbulence. Across the front, we observe warm (> 1 °C) and salty (> 35.0 g kg−1) Atlantic Water intruding below the colder (< 0 °C) and fresher (< 34.6 g kg−1) Polar Water, setting up a baroclinic front and geostrophic currents reaching 25 cm s−1, with estimated eastward transport of 0.2±0.6 Sv (1 Sv m3 s−1). We observe anomalous warm- and cold-water patches on the cold and warm side of the front, respectively, colocated with enhanced turbulence, where dissipation rates of turbulent kinetic energy range between 10−8 and 10−7 W kg−1. Short-term variability below the surface mixed layer arises from tidal currents and mesoscale eddies. While the effects of tidal currents are mainly confined to the bottom boundary layer, eddies induce significant shifts in the position of the front and alter the isopycnal slopes and the available potential energy of the front. Substantial water mass transformation is observed across the front, likely a result of eddy-driven isopycnal mixing. Despite the seasonal changes in the upper layers of the front (0–100 m) influenced by atmospheric forcing, sea ice formation and brine rejection, the position of the front beneath 100 m depth remained relatively unperturbed.publishedVersio
Temporal changes in visual organic enrichment indicators at an aquaculture site over mixed- and hard-bottom substrates
Get PDFNorway employs an environmental management system to assess benthic organic loading from aquaculture activities. Monitoring surveys, mostly performed through grab sampling, scrutinise responses to enrichment within soft-sediment macrofaunal communities. However, new methods and indicators of organic enrichment (IOE) need to be identified for mixed- and hard-bottom substrates. We used image characterisation to examine temporal changes in the abundance and coverage of benthic IOE on mixed- and hard-bottom substrates (organic pellets, sulphur-oxidising bacterial mats, opportunistic polychaete complexes [OPC], polychaete tube aggregations [PTA]) in relation to changes in organic deposition pressure through 1 yr of production at a rainbow trout farm on the western coast of Norway. Rates of organic deposition on the seafloor around the farm increased towards the end of the survey period as fish biomass increased. PTA were significantly associated with low levels of organic deposition and their abundance declined in 2 of the 3 study cages as the production cycle progressed. OPC coverage significantly increased with organic deposition and was greatest, 4 mo before the end of the production cycle. Organic pellet coverage closely followed the patterns of organic deposition on the seafloor, whereas bacterial mat coverage showed no relationship with deposition. Our findings provide new knowledge on the annual impact of organic enrichment on IOE beneath fish farms over mixed- and hard-bottom substrates, highlighting image characterisation methods as a means to improve benthic monitoring. This knowledge can contribute to the development of an environmental proxy to assess the enrichment stage around aquaculture farms placed over mixed- and hard-bottom areas.publishedVersio
Electronic tags reveal high migratory diversity within the largest Atlantic halibut (Hippoglossus hippoglossus) stock
Get PDFGrowing evidence suggests that complex spatial structure occurs within the Scotian Shelf and southern Grand Banks (SSGB) Atlantic halibut stock, yet large knowledge gaps remain about diversity of migratory and spawning behaviors. Here, 71 pop-up satellite archival tags were deployed on large Atlantic halibut (FL: 87–166 cm) between 2012 and 2020. Migration tracks were successfully reconstructed for 43 fish using a hidden Markov geolocation model, and temperature and depth time series were available for an additional nine fish (total n = 52). Five migratory behavior categories were identified: shelf residency, slope residency, shelf-channel migration, shelf-slope migration, and dispersal. High-resolution data for four of 20 physically recovered tags provided evidence of putative spawning behavior in deep channels on the continental shelf and along the continental slope between January and February. Additionally, four halibut displayed previously undocumented periods of sustained, oscillatory vertical movements along the continental slope between November and February. The high migratory diversity observed in this study provides support for the existence of multiple resident and migratory contingents in the SSGB stock in the apparent absence of significant genetic structure.publishedVersio
Characterization of nutrients and contaminants in fish sludge from Atlantic salmon (Salmo salar L.) production sites - A future resource
Get PDFA total of 47 fish sludge samples from commercial land-based Atlantic salmon (Salmo salar) farms in Norway were assessed for their nutrient composition, presence of various legacy contaminants and a wide spectrum of contaminants of emerging concern, veterinary medicines as well as selected salmonid pathogenic bacteria and virus. The aim was to document the levels of desirable and undesirable components in fish sludge in relation to a potential future use of sludge as invertebrate feed. The samples had variable, but relatively high protein and fat contents, indicating a high load of undigested feed in some of the sludge samples. Fatty acid analysis showed the presence of essential omega-3 fatty acids. In terms of undesirable substances, 43% and 84% of the sludge samples contained levels of arsenic and cadmium, respectively, which exceeded the EU Maximum Levels established for complete animal feed. The concentrations of copper, zinc, iron and aluminum were highly variable in the sludge samples. The concentrations of dioxins, sum PCB6, and chlorinated pesticides were all below the Maximum Levels for animal feed. Of the 18 per- and polyfluoroalkyl substances (PFAS) only one compound (L-PFOS) was present at measurable levels. None of the samples had detectable levels of veterinary medicines, salmonid virus or bacteria. Performing a suspect and non-target screening of the sludge samples identified 18 compounds, including four pharmaceuticals, plastic-related products and the UV filter benzophenone, warranting further investigations. Overall, the results from this study show that fish sludge is a nutrient-rich resource; however, undesirable substances, originating from the feed or from treatment of sludge may be present.publishedVersio
Pulse duration, frequency band, and sweep direction effects on crosstalk in wideband backscattering measurements
Get PDFMultiple broadband transducers are typically used to cover both a wide frequency range and fill in gaps resulting from sampling with multiple narrowband echosounders. Synchronized operation of these echosounders is preferred in many cases. Simultaneous operation of multiple broadband echosounders, even when using non-overlapping primary bands, can result in cross-channel interferences caused by nonlinear generation of sound and can contaminate backscattered signal. Decreasing the transmit power of channels with lower frequencies has been demonstrated as an effective technique for reducing the level of crosstalk. Reducing the transmit power inherently decreases the signal energy. Hence, the reduction in crosstalk also reduces signal-to-noise ratio and consequently observation range. Increasing the broadband pulse duration is an alternative to compensate for the reduced signal energy from lower transmit power. This paper examines the effects of increasing pulse duration on crosstalk through numerical modeling and field experiments. Raising the transmit power amplifies the higher-harmonic level more than the main band, while extending the pulse duration increases the levels of both main-band and higher harmonics the same amount. Additionally, the study explores the influence of frequency band and sweep direction on crosstalk.publishedVersio
Retention of prions in the polychaete Hediste diversicolor and black soldier fly, a Hermetia illucens, larvae after short-term experimental immersion and feeding with brain homogenate from scrapie infected sheep
Get PDFFinding alternative protein and lipid sources for aquafeeds is crucial for the sustainable growth of fed aquaculture. Upcycling industrial side streams and byproducts using extractive species can reduce waste and help reduce the sector's dependence on fish meal and fish oils. Polychaete worms (Hediste diversicolor) and black soldier fly (Hermetia illucens) larvae (BSFL) are promising candidates for converting waste materials into valuable protein and lipid sources. However, further research and evaluations are needed to ensure the safety and regulatory compliance of these alternative feed sources, especially regarding prions spreading potential in the unlikely case that prions would be introduced in the value chain via feedstocks. In the present investigation, BSFL and juvenile polychaetes that had received a massive dose of scrapie prions through immersion and oral inoculation were found to harbour detectable prions using an ultrasensitive amplification method known as PMCA. This observation suggests that both H. diversicolor and BSFL have the potential to serve as mechanical vectors for prions diseases. However, it is important to note that insects, lacking the prion protein gene, are incapable of propagating prions. Therefore, the quantity of prions present in the larvae will inevitably be lower than the amount of prions they encountered. This is the first study to report on the fate of prions through ingestion by these marine and terrestrial invertebrate species.publishedVersio
Low light exacerbates effects of marine heatwaves on seaweeds
Get PDFMarine heatwaves (MHWs) are becoming more frequent and intense. At the same time, diverse human activities are causing coastal darkening: increased turbidity and reduced light at the seafloor. Since both temperature and light are critical to the physiological and ecological performance of seaweeds—important habitat-formers and primary producers—these co-occurring stressors could have knock-on effects in coastal ecosystems. We tested the effects of MHWs under different irradiance levels on 3 brown seaweeds: the kelp Ecklonia radiata and 2 common understorey species, Zonaria turneriana and Lobophora variegata. The seaweeds were subjected to 15 d MHWs of different maximum intensities (25° and 28°C) at 2 reduced light levels (~40 and ~10 µmol m-2 s-1). Effects on cover of bleached tissue, biomass, maximum quantum yield and pigment concentrations were assessed. Temperature was the main cause of observed changes in seaweed condition, with strong negative effects of the most intense MHW (28°C) especially for tissue bleaching and maximum quantum yield. Low light had a minor effect at 19°C (background temperature) and in the moderate MHW treatment (25°C). However, at extreme temperatures (28°C), low light enhanced the negative effects on virtually all seaweed condition metrics. For all species, the negative effects of the most severe MHW persisted during the recovery period, during which temperatures were returned to background conditions. The compounding effect of high temperature and reduced light highlights the need to assess the interactive nature of multiple stressors with respect to the emerging threat of MHWs to reef ecosystems.publishedVersio