Browsing by Subject "aquaculture"

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  • Harrison, Jesse P.; Chronopoulou, Panagiota-Myrsini; Salonen, Iines S.; Jilbert, Tom; Koho, Karoliina A. (2021)
    Metabarcoding analyses of bacterial and eukaryotic communities have been proposed as efficient tools for environmental impact assessment. It has been unclear, however, to which extent these analyses can provide similar or differing information on the ecological status of the environment. Here, we used 16S and 18S rRNA gene metabarcoding to compare eutrophication-induced shifts in sediment bacterial and eukaryotic community structure in relation to a range of porewater, sediment and bottom-water geochemical variables, using data obtained from six stations near a former rainbow trout farm in the Archipelago Sea (Baltic Sea). Shifts in the structure of both community types were correlated with a shared set of variables, including porewater ammonium concentrations and the sediment depth-integrated oxygen consumption rate. Distance-based redundancy analyses showed that variables typically employed in impact assessments, such as bottom water nutrient concentrations, explained less of the variance in community structure than alternative variables (e.g., porewater NH4+ inventories and sediment depth-integrated O2 consumption rates) selected due to their low collinearity (up to 40 vs. 58% of the variance explained, respectively). In monitoring surveys where analyses of both bacterial and eukaryotic communities may be impossible, either 16S or 18S rRNA gene metabarcoding can serve as reliable indicators of wider ecological impacts of eutrophication.
  • Tiedje, James M.; Wang , Fang; Manaia, Celia M.; Virta, Marko; Sheng, Hongjie; Ma, Liping; Zhang , Tong; Topp, Edward (2019)
    Antibiotic resistance and its environmental component are gaining more attention as part of combating the growing healthcare crisis. The One Health framework, promulgated by many global health agencies, recognizes that antimicrobial resistance is a truly inter-domain problem in which human health, animal agriculture, and the environment are the core and interrelated components. This prospectus presents the status and issues relevant to the environmental component of antibiotic resistance, namely, the needs for advancing surveillance methodology: the environmental reservoirs and sources of resistance, namely, urban wastewater treatment plants, aquaculture production systems, soil receiving manure and biosolid, and the atmosphere which includes longer range dispersal. Recently, much work has been done describing antibiotic resistance genes in various environments; now quantitative, mechanistic, and hypothesis-driven studies are needed to identify practices that reduce real risks and maintain the effectiveness of our current antibiotics as long as possible. Advanced deployable detection methods for antibiotic resistance in diverse environmental samples are needed in order to provide the surveillance information to identify risks and define barriers that can reduce risks. Also needed are practices that reduce antibiotic use and thereby reduce selection for resistance, as well as practices that limit the dispersal of or destroy antibiotic-resistant bacteria or their resistance genes that are feasible for these varied environmental domains.
  • Topp, Edward; Larsson, D. G. Joakim; Miller, Daniel N.; Van den Eede, Chris; Virta, Marko P. J. (2018)
    A roundtable discussion held at the fourth International Symposium on the Environmental Dimension of Antibiotic Resistance (EDAR4) considered key issues concerning the impact on the environment of antibiotic use in agriculture and aquaculture, and emissions from antibiotic manufacturing. The critical control points for reducing emissions of antibiotics from agriculture are antibiotic stewardship and the pre-treatment of manure and sludge to abate antibiotic-resistant bacteria. Antibiotics are sometimes added to fish and shellfish production sites via the feed, representing a direct route of contamination of the aquatic environment. Vaccination reduces the need for antibiotic use in high value (e.g. salmon) production systems. Consumer and regulatory pressure will over time contribute to reducing the emission of very high concentrations of antibiotics from manufacturing. Research priorities include the development of technologies, practices and incentives that will allow effective reduction in antibiotic use, together with evidence-based standards for antibiotic residues in effluents. All relevant stakeholders need to be aware of the threat of antimicrobial resistance and apply best practice in agriculture, aquaculture and pharmaceutical manufacturing in order to mitigate antibiotic resistance development. Research and policy development on antimicrobial resistance mitigation must be cognizant of the varied challenges facing high and low income countries.
  • Kotta, Jonne; Futter, Martyn; Kaasik, Ants; Liversage, Kiran; Rätsep, Merli; Barboza, Francisco R.; Bergström, Lena; Bergström, Per; Bobsien, Ivo; Díaz, Eliecer; Herkül, Kristjan; Jonsson, Per R.; Korpinen, Samuli; Kraufvelin, Patrik; Krost, Peter; Lindahl, Odd; Lindegarth, Mats; Lyngsgaard, Maren Moltke; Mühl, Martina; Sandman, Antonia Nyström; Orav-Kotta, Helen; Orlova, Marina; Skov, Henrik; Rissanen, Jouko; Šiaulys, Andrius; Vidakovic, Aleksandar; Virtanen, Elina (Elsevier, 2020)
    Science of The Total Environment
    Eutrophication is a serious threat to aquatic ecosystems globally with pronounced negative effects in the Baltic and other semi-enclosed estuaries and regional seas, where algal growth associated with excess nutrients causes widespread oxygen free “dead zones” and other threats to sustainability. Decades of policy initiatives to reduce external (land-based and atmospheric) nutrient loads have so far failed to control Baltic Sea eutrophication, which is compounded by significant internal release of legacy phosphorus (P) and biological nitrogen (N) fixation. Farming and harvesting of the native mussel species (Mytilus edulis/trossulus) is a promising internal measure for eutrophication control in the brackish Baltic Sea. Mussels from the more saline outer Baltic had higher N and P content than those from either the inner or central Baltic. Despite their relatively low nutrient content, harvesting farmed mussels from the central Baltic can be a cost-effective complement to land-based measures needed to reach eutrophication status targets and is an important contributor to circularity. Cost effectiveness of nutrient removal is more dependent on farm type than mussel nutrient content, suggesting the need for additional development of farm technology. Furthermore, current regulations are not sufficiently conducive to implementation of internal measures, and may constitute a bottleneck for reaching eutrophication status targets in the Baltic Sea and elsewhere. Highlights • Mussel farming is a viable internal measure to address Baltic Sea eutrophication. • Rates of nutrient removal depend on salinity at the regional scale and food availability at the local scale. • Cost effectiveness of nutrient removal by mussel farming depends also on farm type. • Total farm area needed for achieving HELCOM nutrient reduction targets is realistic.
  • Nguyen, Nguyen H.; Rastas, Pasi M. A.; Premachandra, H. K. A.; Knibb, Wayne (2018)
    The genetic resources available for the commercially important fish species Yellowtail kingfish (YTK) (Seriola lalandi) are relative sparse. To overcome this, we aimed (1) to develop a linkage map for this species, and (2) to identify markers/variants associated with economically important traits in kingfish (with an emphasis on body weight). Genetic and genomic analyses were conducted using 13,898 single nucleotide polymorphisms (SNPs) generated from a new high-throughput genotyping by sequencing platform, Diversity Arrays Technology (DArTseq (TM)) in a pedigreed population comprising 752 animals. The linkage analysis enabled to map about 4,000 markers to 24 linkage groups (LGs), with an average density of 3.4 SNPs per cM. The linkage map was integrated into a genome-wide association study (GWAS) and identified six variants/SNPs associated with body weight (P <5e(-8)) when a multi-locus mixed model was used. Two out of the six significant markers were mapped to LGs 17 and 23, and collectively they explained 5.8% of the total genetic variance. It is concluded that the newly developed linkage map and the significantly associated markers with body weight provide fundamental information to characterize genetic architecture of growth-related traits in this population of YTK S. lalandi.
  • Ruuskanen, Jutta (Helsingin yliopisto, 2020)
    Arapaima gigas is one of the world’s largest freshwater fishes and it is native to the Amazon region. The species is over-exploited and sustainable long-term conservation strategies are needed to maintain the genetic diversity of the species. The aim of this study was to analyze the genetic diversity of Peruvian Arapaima gigas populations. The microsatellite data was collected as a part of a three-year project by the Regional Government of San Martín (GORESAM) and Finnish Game and Fisheries Research Institute (FGFRI). The data consisted of 15 microsatellite loci and 324 samples from three populations, Iquitos, Paiche, and Pucallpa. The samples for Iquitos and Pucallpa were collected from populations in the Amazon basin. Samples of Paiche were collected from a captive population in a fish farming research center. The average numbers of alleles and genotypes ranged between 1.9-3.3 and 2.5-4.6, respectively. Population Pucallpa showed the highest average level of heterozygosity (0.41), whereas the lowest level was observed in population Iquitos (0.25). There were altogether 13 loci which showed a statistically significant excess of heterozygosity, and nine loci with significant deficiency of heterozygosity across the three populations. The FIS-values were in accordance with most of the significant deviations indicating the excess or deficiency of heterozygosity. The average FIT-value (0.226) indicated a slight increase of homozygotes. Populations Iquitos and Paiche were on a state of Hardy-Weinberg equilibrium, but population Pucallpa showed a statistically significant deviation from the state of equilibrium. The pairwise FST-values ranged between 0.169-0.373, and they indicate that the three studied populations are genetically different. In addition, the values of Nei’s genetic distance (D) and full-pedigree likelihood analysis indicate a genetic differentiation between the populations. The number of migrants (Nm) between the three populations was estimated based on the mean frequency of private alleles (p(1) = 0.085) and the mean sample size (108 individuals). The number of migrants was 0.273 after the correction for sample size. The genetic diversity within and between the Peruvian populations resembles the results obtained in other studies of Arapaima gigas in the Amazon basin. Sustainable fish farming could offer a solution in maintaining the genetic diversity of the species.
  • Karlson, Bengt; Andersen, Per; Arneborg, Lars; Cembella, Allan; Eikrem, Wenche; John, Uwe; West, Jennifer Joy; Klemm, Kerstin; Kobos, Justyna; Lehtinen, Sirpa; Lundholm, Nina; Mazur-Marzec, Hanna; Naustvoll, Lars; Poelman, Marnix; Provoost, Pieter; De Rijcke, Maarten; Suikkanen, Sanna (Elsevier, 2021)
    Harmful Algae 102 (2021), 101989
    Harmful algal blooms (HAB) are recurrent phenomena in northern Europe along the coasts of the Baltic Sea, Kattegat-Skagerrak, eastern North Sea, Norwegian Sea and the Barents Sea. These HABs have caused occasional massive losses for the aquaculture industry and have chronically affected socioeconomic interests in several ways. This status review gives an overview of historical HAB events and summarises reports to the Harmful Algae Event Database from 1986 to the end of year 2019 and observations made in long term monitoring programmes of potentially harmful phytoplankton and of phycotoxins in bivalve shellfish. Major HAB taxa causing fish mortalities in the region include blooms of the prymnesiophyte Chrysochromulina leadbeateri in northern Norway in 1991 and 2019, resulting in huge economic losses for fish farmers. A bloom of the prymesiophyte Prymnesium polylepis (syn. Chrysochromulina polylepis) in the Kattegat-Skagerrak in 1988 was ecosystem disruptive. Blooms of the prymnesiophyte Phaeocystis spp. have caused accumulations of foam on beaches in the southwestern North Sea and Wadden Sea coasts and shellfish mortality has been linked to their occurrence. Mortality of shellfish linked to HAB events has been observed in estuarine waters associated with influx of water from the southern North Sea. The first bloom of the dictyochophyte genus Pseudochattonella was observed in 1998, and since then such blooms have been observed in high cell densities in spring causing fish mortalities some years. Dinoflagellates, primarily Dinophysis spp., intermittently yield concentrations of Diarrhetic Shellfish Toxins (DST) in blue mussels, Mytilus edulis, above regulatory limits along the coasts of Norway, Denmark and the Swedish west coast. On average, DST levels in shellfish have decreased along the Swedish and Norwegian Skagerrak coasts since approximately 2006, coinciding with a decrease in the cell abundance of D. acuta. Among dinoflagellates, Alexandrium species are the major source of Paralytic Shellfish Toxins (PST) in the region. PST concentrations above regulatory levels were rare in the Skagerrak-Kattegat during the three decadal review period, but frequent and often abundant findings of Alexandrium resting cysts in surface sediments indicate a high potential risk for blooms. PST levels often above regulatory limits along the west coast of Norway are associated with A. catenella (ribotype Group 1) as the main toxin producer. Other Alexandrium species, such as A. ostenfeldii and A. minutum, are capable of producing PST among some populations but are usually not associated with PSP events in the region. The cell abundance of A. pseudogonyaulax, a producer of the ichthyotoxin goniodomin (GD), has increased in the Skagerrak-Kattegat since 2010, and may constitute an emerging threat. The dinoflagellate Azadinium spp. have been unequivocally linked to the presence of azaspiracid toxins (AZT) responsible for Azaspiracid Shellfish Poisoning (AZP) in northern Europe. These toxins were detected in bivalve shellfish at concentrations above regulatory limits for the first time in Norway in blue mussels in 2005 and in Sweden in blue mussels and oysters (Ostrea edulis and Crassostrea gigas) in 2018. Certain members of the diatom genus Pseudo-nitzschia produce the neurotoxin domoic acid and analogs known as Amnesic Shellfish Toxins (AST). Blooms of Pseudo-nitzschia were common in the North Sea and the Skagerrak-Kattegat, but levels of AST in bivalve shellfish were rarely above regulatory limits during the review period. Summer cyanobacteria blooms in the Baltic Sea are a concern mainly for tourism by causing massive fouling of bathing water and beaches. Some of the cyanobacteria produce toxins, e.g. Nodularia spumigena, producer of nodularin, which may be a human health problem and cause occasional dog mortalities. Coastal and shelf sea regions in northern Europe provide a key supply of seafood, socioeconomic well-being and ecosystem services. Increasing anthropogenic influence and climate change create environmental stressors causing shifts in the biogeography and intensity of HABs. Continued monitoring of HAB and phycotoxins and the operation of historical databases such as HAEDAT provide not only an ongoing status report but also provide a way to interpret causes and mechanisms of HABs.
  • Hinchliffe, Steve; Butcher, Andrea; Rahman, Muhammad Meezanur; Guilder, James; Tyler, Charles; Verner-Jeffries, David (2021)
    Improved biosecurity and livestock disease control measures in low resource settings are often regarded as beneficial for agricultural productivity, rural incomes, global health, and sustainability. In this paper we present data from a study of shrimp and prawn aquaculture in Bangladesh to argue that this relationship is not as straightforward as it would seem. Analysing quantitative and qualitative data from a multi‐method field study involving 300 “missing middle” farmers, we demonstrate the importance of socio‐economic and ecological conditions to any disease management strategy. We describe how a technical programme to introduce “disease‐free” seed faltered partly as a result of the farmers' tendency to offset disease and livelihood risks by frequently re‐stocking their ponds. Changes to seed provision were accompanied by calls to alter farmers' livestock production practices. Paradoxically, these changes exposed farmers to more intense risks, potentially locking them into unsustainable disease management practices. The analysis emphasises that vernacular farming practices should be considered as key assets rather than barriers to disease management strategies, and that closer attention be paid to value chain and other risks as drivers of unsustainable practices.
  • Pulkkinen, Katja; Ketola, Tarmo; Laakso, Jouni; Mappes, Johanna; Sundberg, Lotta-Riina (2022)
    Phenotypic variation is suggested to facilitate the persistence of environmentally growing pathogens under environmental change. Here, we hypothesized that the intensive farming environment induces higher phenotypic variation in microbial pathogens than natural environment, because of high stochasticity for growth and stronger survival selection compared to the natural environment. We tested the hypothesis with an opportunistic fish pathogen Flavobacterium columnare isolated either from fish farms or from natural waters. We measured growth parameters of two morphotypes from all isolates in different resource concentrations and two temperatures relevant for the occurrence of disease epidemics at farms and tested their virulence using a zebrafish (Danio rerio) infection model. According to our hypothesis, isolates originating from the fish farms had higher phenotypic variation in growth between the morphotypes than the isolates from natural waters. The difference was more pronounced in higher resource concentrations and the higher temperature, suggesting that phenotypic variation is driven by the exploitation of increased outside-host resources at farms. Phenotypic variation of virulence was not observed based on isolate origin but only based on morphotype. However, when in contact with the larger fish, the less virulent morphotype of some of the isolates also had high virulence. As the less virulent morphotype also had higher growth rate in outside-host resources, the results suggest that both morphotypes can contribute to F. columnare epidemics at fish farms, especially with current prospects of warming temperatures. Our results suggest that higher phenotypic variation per se does not lead to higher virulence, but that environmental conditions at fish farms could select isolates with high phenotypic variation in bacterial population and hence affect evolution in F. columnare at fish farms. Our results highlight the multifaceted effects of human-induced environmental alterations in shaping epidemiology and evolution in microbial pathogens.
  • Vehviläinen, Harri; Kause, Antti; Kuukka-Anttila, Hanna; Koskinen, Heikki; Paananen, Tuija (2012)