| 1. |
- Munk, P., et al.
(författare)
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Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance
- 2022
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019. We find regional patterns in resistomes, and these differ between subsets corresponding to drug classes and are partly driven by taxonomic variation. The genetic environments of 49 common ARGs are highly diverse, with most common ARGs carried by multiple distinct genomic contexts globally and sometimes on plasmids. Analysis of flanking sequence revealed ARG-specific patterns of dispersal limitation and global transmission. Our data furthermore suggest certain geographies are more prone to transmission events and should receive additional attention.
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| 2. |
- Harcourt, R., et al.
(författare)
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Animal-borne telemetry: An integral component of the ocean observing toolkit
- 2019
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Ingår i: Frontiers in Marine Science. - : Frontiers Media SA. - 2296-7745. ; 6:JUN
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Tidskriftsartikel (refereegranskat)abstract
- Animal telemetry is a powerful tool for observing marine animals and the physical environments that they inhabit, from coastal and continental shelf ecosystems to polar seas and open oceans. Satellite-linked biologgers and networks of acoustic receivers allow animals to be reliably monitored over scales of tens of meters to thousands of kilometers, giving insight into their habitat use, home range size, the phenology of migratory patterns and the biotic and abiotic factors that drive their distributions. Furthermore, physical environmental variables can be collected using animals as autonomous sampling platforms, increasing spatial and temporal coverage of global oceanographic observation systems. The use of animal telemetry, therefore, has the capacity to provide measures from a suite of essential ocean variables (EOVs) for improved monitoring of Earth's oceans. Here we outline the design features of animal telemetry systems, describe current applications and their benefits and challenges, and discuss future directions. We describe new analytical techniques that improve our ability to not only quantify animal movements but to also provide a powerful framework for comparative studies across taxa. We discuss the application of animal telemetry and its capacity to collect biotic and abiotic data, how the data collected can be incorporated into ocean observing systems, and the role these data can play in improved ocean management. © 2019 Harcourt, Sequeira, Zhang, Roquet, Komatsu, Heupel, McMahon, Whoriskey, Meekan, Carroll, Brodie, Simpfendorfer, Hindell, Jonsen, Costa, Block, Muelbert, Woodward, Weise, Aarestrup, Biuw, Boehme, Bograd, Cazau, Charrassin, Cooke, Cowley, de Bruyn, Jeanniard du Dot, Duarte, Eguíluz, Ferreira, Fernández-Gracia, Goetz, Goto, Guinet, Hammill, Hays, Hazen, Hückstädt, Huveneers, Iverson, Jaaman, Kittiwattanawong, Kovacs, Lydersen, Moltmann, Naruoka, Phillips, Picard, Queiroz, Reverdin, Sato, Sims, Thorstad, Thums, Treasure, Trites, Williams, Yonehara and Fedak.
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| 3. |
- Edwards, Robert A., et al.
(författare)
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Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
- 2019
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Ingår i: Nature Microbiology. - : Springer Science and Business Media LLC. - 2058-5276. ; 4:10, s. 1727-1736
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Tidskriftsartikel (refereegranskat)abstract
- Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
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| 4. |
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| 5. |
- Aarestrup, K., et al.
(författare)
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Survival and progression rates of anadromous brown trout kelts Salmo trutta during downstream migration in freshwater and at sea
- 2015
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Ingår i: Marine Ecology Progress Series. - : Inter-Research Science Center. - 0171-8630 .- 1616-1599. ; 535, s. 185-195
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Tidskriftsartikel (refereegranskat)abstract
- The marine migration of post-spawning anadromous fish remains poorly understood. The present study examined survival and progression rates of anadromous brown trout Salmo trutta L. after spawning (kelts) during downriver, fjord, and sea migration. Kelts (n = 49) were captured in the Danish River Gudenaa, tagged with acoustic transmitters and subsequently recorded by automatic receivers. Kelts spent on average 25 d moving down the 45 km river and through the brackish fjord. The fish entered the Kattegat Sea between 14 April and 30 May. Eighteen of the 49 kelts disappeared in the river and fjord during outward migration, likely due to mortality. Survival was not significantly related to gill Na+/K+-ATPase activity, suggesting that physiological adaptation to saltwater may be less critical for adults compared to juveniles (smolts). Of the 31 fish that entered the Kattegat Sea, 45% survived and returned to the fjord. The duration of the entire marine migration, from leaving to entering the river, was on average 163 d. The fish returned from the Kattegat Sea to the fjord between 22 July and 21 October. Upon return, the fish spent 1-90 d passing through Randers Fjord, with most individuals completing the reach within 4 d, suggesting that the kelts spent limited time foraging after returning to the fjord. The total survival during the entire marine migration, including the fjord, was a minimum of 29%. Our study provides data that are important for management of anadromous brown trout, and the high survival highlights that kelts may represent a valuable resource for both population reproduction and recreational fisheries.
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| 6. |
- Larsen, M. H., et al.
(författare)
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Effects of Emergence Time and Early Social Rearing Environment on Behaviour of Atlantic Salmon: Consequences for Juvenile Fitness and Smolt Migration
- 2015
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Ingår i: Plos One. - : Public Library of Science (PLoS). - 1932-6203. ; 10:3
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Tidskriftsartikel (refereegranskat)abstract
- Consistent individual differences in behaviour have been well documented in a variety of animal taxa, but surprisingly little is known about the fitness and life-history consequences of such individual variation. In wild salmonids, the timing of fry emergence from gravel spawning nests has been suggested to be coupled with individual behavioural traits. Here, we further investigate the link between timing of spawning nest emergence and behaviour of Atlantic salmon (Salmo salar), test effects of social rearing environment on behavioural traits in fish with different emergence times, and assess whether behavioural traits measured in the laboratory predict growth, survival, and migration status in the wild. Atlantic salmon fry were sorted with respect to emergence time from artificial spawning nest into three groups: early, intermediate, and late. These emergence groups were hatchery-reared separately or in co-culture for four months to test effects of social rearing environment on behavioural traits. Twenty fish from each of the six treatment groups were then subjected to three individual-based behavioural tests: basal locomotor activity, boldness, and escape response. Following behavioural characterization, the fish were released into a near-natural experimental stream. Results showed differences in escape behaviour between emergence groups in a net restraining test, but the social rearing environment did not affect individual behavioural expression. Emergence time and social environment had no significant effects on survival, growth, and migration status in the stream, although migration propensity was 1.4 to 1.9 times higher for early emerging individuals that were reared separately. In addition, despite individuals showing considerable variation in behaviour across treatment groups, this was not translated into differences in growth, survival, and migration status. Hence, our study adds to the view that fitness (i.e., growth and survival) and life-history predictions from laboratory measures of behaviour should be made with caution and ideally tested in nature.
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| 7. |
- Larsen, M. H., et al.
(författare)
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Reduced rearing density increases postrelease migration success of Atlantic salmon (Salmo salar) smolts
- 2016
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Ingår i: Canadian Journal of Fisheries and Aquatic Sciences. - : Canadian Science Publishing. - 0706-652X .- 1205-7533. ; 73:5, s. 804-810
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Tidskriftsartikel (refereegranskat)abstract
- The overall aim of this study was to investigate the effect of rearing density on the postrelease survival of Atlantic salmon (Salmo salar) smolts during seaward migration. Fish were either reared at conventional hatchery density or at one-third of conventional density. Three hundred 1-year-old smolts from each density treatment were individually tagged with passive integrated transponder tags and released 3.2 km upstream of a stationary antenna array in a natural stream. There were no significant differences in length, body mass, or condition between fish from the two density treatments during rearing in the hatchery. However, individuals reared at reduced density had less eroded dorsal fins and opercula relative to those from the high-density treatment. In the stream, the downstream migration success was 16% higher for fish reared at reduced density than for conspecifics kept at high density, but the timing of migration was similar for both groups. These novel results suggest that conventionally high rearing densities may reduce welfare and the postrelease migration success of hatchery-reared Atlantic salmon.
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| 8. |
- Nevoux, M., et al.
(författare)
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Environmental influences of life history strategies in partial anadromous brown trout (Salmo trutta, Salmonidae)
- 2019
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Ingår i: Fish and Fisheries. - : Wiley. - 1467-2960 .- 1467-2979. ; 20:6, s. 1051-1082
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Tidskriftsartikel (refereegranskat)abstract
- This paper reviews the life history of brown trout and factors influencing decisions to migrate. Decisions that maximize fitness appear dependent on size at age. In partly anadromous populations, individuals that attain maturity at the parr stage typically become freshwater resident. For individual fish, the life history is not genetically fixed and can be modified by the previous growth history and energetic state in early life. This phenotypic plasticity may be influenced by epigenetic modifications of the genome. Thus, factors influencing survival and growth determine life-history decisions. These are intra- and interspecific competition, feeding and shelter opportunities in freshwater and salt water, temperature in alternative habitats and flow conditions in running water. Male trout exhibit alternative mating strategies and can spawn as a subordinate sneaker or a dominant competitor. Females do not exhibit alternative mating behaviour. The relationship between growth, size and reproductive success differs between sexes in that females exhibit a higher tendency to migrate than males. Southern populations are sensitive to global warming. In addition, fisheries, aquaculture with increased spreading of salmon lice, introduction of new species, weirs and river regulation, poor water quality and coastal developments all threaten trout populations. The paper summarizes life-history data from six populations across Europe and ends by presenting new research questions and directions for future research.
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| 9. |
- Näslund, Joacim, 1985, et al.
(författare)
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Early enrichment effects on brain development in hatchery-reared Atlantic salmon (Salmo salar): no evidence for a critical period
- 2012
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Ingår i: Canadian Journal of Fisheries and Aquatic Sciences. - : Canadian Science Publishing. - 0706-652X .- 1205-7533. ; 69:9, s. 1481-1490
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Tidskriftsartikel (refereegranskat)abstract
- In hatcheries, fish are normally reared in barren environments, which have been reported to affect their phenotypic development compared with wild conspecifics. In this study, Atlantic salmon (Salmo salar) alevins were reared in conventional barren hatchery trays or in either of two types of structurally enriched trays. We show that increased structural complexity during early rearing increased brain size in all investigated brain substructures. However, these effects disappeared over time after transfer to barren tanks for external feeding. Parallel to the hatchery study, a group of salmon parr was released into nature and recaptured at smoltification. These stream-reared smolts developed smaller brains than the hatchery reared smolts, irrespective of initial enrichment treatment. These novel findings do not support the hypothesis that there is a critical early period determining the brain growth trajectory. In contrast, our results indicate that brain growth is plastic in relation to environment. In addition, we show allometric growth in brain substructures over juvenile development, which suggests that comparisons between groups of different body size should be made with caution. These results can aid the development of ecologically sound rearing methods for conservational fish-stocking programs.
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| 10. |
- Näslund, Joacim, 1985, et al.
(författare)
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Environment-dependent plasticity and ontogenetic changes in the brain of hatchery-reared Atlantic salmon
- 2017
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Ingår i: Journal of Zoology. - : Wiley. - 0952-8369 .- 1469-7998. ; 301:1, s. 75-82
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Tidskriftsartikel (refereegranskat)abstract
- Lowered rearing density has repeatedly been shown to increase the performance of hatchery-reared salmonids stocked into natural environments. One possible mechanism for this pattern could be that lower densities enhance brain development, which has been shown to be the case in other hatchery enhancement strategies, like environmental enrichment. Here, we investigated the size of the brain in hatchery-reared Atlantic salmon Salmo salar kept at standard (high) and reduced (low) tank densities. In contrast to our predictions, we found that fish reared at high density had larger dry mass of cerebellum and telencephalon, correcting for body size. No differences were detected for total brain mass. Furthermore, we found that the relative size of both telencephalon and cerebellum, in relation to total brain mass, changed with body size. Cerebellum increased in relative size with increased body size, while the opposite pattern was observed for telencephalon. Overall, these results reveal substantial brain plasticity depending on the surrounding environment as well as ontogenetic adaptive changes in the brain of the Atlantic salmon.
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