40 research outputs found
Automated real-time monitoring of commercial fish species using environmental DNA and an Environmental Sample Processor
No full textNovel DNA methods and instrumentation for species monitoring in fisheries
No full textMarine fish play a vital role for global food biosecurity and economy, whose continued productivity necessitates proper fisheries management. Successful management relies on the ability to accurately determine and monitor how many fish can be sustainably caught and subsequently ensure correct reporting of catches through fisheries surveillance. However, current monitoring of marine fish is expensive and limited to annual surveys, if conducted at all. Moreover, current fisheries surveillance is reliant on visual assessment of the catch, which make advantageous onboard bulk storage and processing methods illegal. Thus, tools to improve current monitoring and fisheries surveillance will benefit both commercial fisheries, management and conservation of marine fish stocks. This present thesis examines novel genetic methods and instruments as an alternative approach or supplement to established fisheries monitoring and surveillance techniques. Utilizing advanced genetic instrumentation and methodologies, the overarching goals of this PhD were to (1) examine the current knowledge, challenges and perspectives for using modern DNA monitoring and surveillance techniques in applications relevant to fisheries, (2) test a fully automated 2. Generation Environmental Sample Processor (2G ESP) for in-situ environmental DNA (eDNA) analysis, and (3) assess the ability of DNA based methods to identify and quantify species composition in complex bulk fisheries products. The thesis opens with a general introduction briefly describing the history and present state of genetic applications of relevance to species monitoring and surveillance in fisheries management (chapter I). The introduction extends to review relevant knowledge, contemporary instrumentation and methodological issues in order to put the content of the thesis into an overarching state of the art research context. Hereafter, four manuscripts are provided in chapter II-V. In chapter II we review the wealth studies which have revealed great potential but also challenges related to the use of eDNA in marine fish monitoring. In chapter III we demonstrate that a 2G ESP has the ability to perform autonomous, remote in situ eDNA analysis for real-time monitoring of fish. Further, in chapter IV we show how DNA based methods can detect and quantify proportions of marine fish from complex tissue mixtures in bulk fisheries products, such as fish silage and frozen fish blocks. Finally, chapter V describes and discusses the potential of genetic methods in relation to the European landing obligation in order to prevent, assess and control the catch of non-targeted species. Overall, this thesis presents the immense potential of modern genetics and the rapidly developing applications in marine fisheries, but also provides critical insights to strengths and weaknesses related to various methods and applications. Further, the thesis highlights the potential of using novel methodologies and instrumentation applicable to fisheries monitoring and surveillance. Of particular note, chapter III provides the first example of a fully autonomous eDNA analysis using the 2G ESP, a finding which has broad perspectives for future monitoring in remote and inaccessible marine areas.<br/
Kortlægning af udbredelsen af krebs og krebsepest i danske ferske vande
No full textDenne rapport beskriver resultaterne af en landsdækkende kortlægning af udbredelsen af krebs og krebsepest i Danmarks ferske vande. Projektet er udført i perioden 1. maj 2020 til 1. december 2021.Den primære undersøgelsesmetode, der er anvendt, er indsamling af vandprøver, som er blevet filtrerede og konserverede på stedet. Filtratet er efterfølgende anvendt til analyse for forekomst af DNA – såkaldt miljø-DNA eller eDNA – fra krebs og krebsepest. Der er indsamlet vandprøver fra vandløb og de dertil knyttede søer i hele landet inkl. otte større øer, hvor der findes væsentlige vandløb: Mors, Als, Ærø, Langeland, Lolland, Falster, Møn og Bornholm. Gennem analyse af disse indsamlede prøver, er udbredelsen af krebs og krebsepest på landsplan beskrevet. Herudover er der udført en mere detaljeret indsamling af vandprøver fra både vandløb og store samt små søer på fem udvalgte øer: Samsø, Als, Ærø, Langeland og Møn, for dels at beskrive omfanget af forekomst af krebs i Danmarks mange småsøer og dels at vurdere om en eller flere af de undersøgte øer egner sig som såkaldt safesite eller ”reservat” for flodkrebs (Astacus astacus). Ud af Danmarks ca. 900 selvstændige vandløb, blev det valgt at undersøge alle de vandløb, der har et hovedløb på mindst 10 km længde, for dem der er længere end 20 km med én prøve pr. 10 km. For kortere vandløb blev 50 % af dem, der har en længde mellem 5 og 10 km undersøgt samt 20 % af vandløbene med længde mellem 2 og 5 km. Vandløb < 2 km blev ikke undersøgt. Den anvendte teststrategi for de indsamlede prøver er følgende: alle de indsamlede prøver er blevet testet for forekomst af tre arter af ferskvandskrebs: flodkrebs, signalkrebs (Pacifastacus leniusculus) og galizisk sumpkrebs (Astacus leptodactylus). Alle prøver, der blev fundet positive for krebs, er efterfølgende blevet testet for forekomsten af krebsepest (Aphanomyces astaci), idet krebsepest er en obligat parasit, der ikke kan forventes at forekomme i vandområder uden en bestand af krebs, der kan være vært for parasitten. Endelig er en række udvalgte prøver fra vandløb blevet testet for forekomst af marmorkrebs (Procambarus virginalis) og Louisiana flodkrebs (Procambarus clarkii). I alt blev 838 stationer besøgt, heraf 635 beliggende i vandløb og 203 beliggende i søer. Det resulterede i indsamling af 768 prøver, hvor mellem 0,5 og 5 l vand blev filtreret. På en del stationer var mængden af partikler i vandet så stor, at filteret stoppede til inden målet på 5 l var nået. På 70 stationer var det slet ikke muligt at indsamle vandprøve, enten grundet udtørring eller fordi intensiv algevækst umuliggjorde filtrering fuldstændigt. I nogle tilfælde kunne der vælges et alternativ til udtørrede søer, mens det ikke var tilfældet for vandløb, idet de udtørrede vandløb primært var beliggende på Møn og Bornholm, hvor samtlige vandløb blev undersøgt. Analyse af de indsamlede vandprøver resulterede i sikker detektion af flodkrebs på 57 stationer beliggende i 35 vandsystemer, heraf 2 beliggende i søer, begge på Møn. Signalkrebs blev fundet på 106 stationer beliggende i 49 vandsystemer, heraf 3 beliggende i søer på Als. Galizisk sumpkrebs blev kun fundet på 6 stationer i 5 vandsystemer, 4 beliggende på Sjælland og én på Lolland. Krebsepest blev konstateret på 54 stationer beliggende i 21 vandsystemer. Der blev ikke konstateret forekomst af hverken marmorkrebs eller Louisiana flodkrebs i de 192 prøver, der blev analyseret for disse to arter.Generelt har det været muligt at påvise forekomst af krebs på lokaliteter, hvor der i forvejen var kendt forekomst af en af de tre fundne arter. Det kan derfor konkluderes, at eDNA er en velegnet metode til kortlægning af udbredelse af krebs og krebsepest i ferske vande. Kortlægningen har vist, at signalkrebs findes udbredt over hele landet og i dag må betegnes som den mest udbredte art af ferskvandskrebs i Danmark. Flodkrebs findes også i alle landsdele, men en del bestande er under pres fra signalkrebs og/eller krebsepest. For den galiziske sumpkrebs vedkommende, er udbredelsen primært afgrænset til Sjælland. Krebsepest findes udbredt over hele landet, primært i forbindelse med forekomst af signalkrebs
Den skeptiske optimist: Udfordringer og perspektiver i anvendelse af eDNA til marin monitering og fiskeriforvaltning
No full textSea lice (<i>Lepeophtherius salmonis</i>) detection and quantification around aquaculture installations using environmental DNA
No full textThe naturally occurring ectoparasite salmon lice (Lepeophtherirus salmonis) poses a great challenge for the salmon farming industry, as well as for wild salmonids in the Northern hemisphere. To better control the infestation pressure and protect the production, there is a need to provide fish farmers with sensitive and efficient tools for rapid early detection and monitoring of the parasitic load. This can be achieved by targeting L. salmonis DNA in environmental samples. Here, we developed and tested a new L. salmonis specific DNA-based assay (qPCR assay) for detection and quantification from seawater samples using an analytical pipeline compatible with the Environmental Sample Processor (ESP) for autonomous water sample analysis of gene targets. Specificity of the L. salmonis qPCR assay was demonstrated through in-silico DNA analyses covering sequences of different L. salmonis isolates. Seawater was spiked with known numbers of nauplii and copepodite free-swimming (planktonic) stages of L. salmonis to investigate the relationship with the number of marker gene copies (MGC). Finally, field samples collected at different times of the year in the vicinity of a salmon production farm in Western Norway were analyzed for L. salmonis detection and quantification. The assay specificity was high and a high correlation between MGC and planktonic stages of L. salmonis was established in the laboratory conditions. In the field, L. salmonis DNA was consequently detected, but with MGC number below that expected for one copepodite or nauplii. We concluded that only L. salmonis tissue or eDNA residues were detected. This novel study opens for a fully automatized L. salmonis DNA quantification using ESP robotic to monitor the parasitic load, but challenges remain to exactly transfer information about eDNA quantities to decisions by the farmers and possible interventions
The sceptical optimist: challenges and perspectives for the application of environmental DNA in marine fisheries
No full textApplication of environmental DNA (eDNA) analysis has attracted the attention ofresearchers, advisors and managers of living marine resources and biodiversity. The apparent simplicity and cost-effectiveness of eDNA analysis make it highly attractive as species distributions can be revealed from water samples. Further, species-specific analyses indicate that eDNA concentrations correlate with biomass and abundance, suggesting the possibility for quantitative applications estimating abundance and biomass of specific organisms in marine ecosystems, such as for stock assessment. However, the path from detecting occurrence of an organism to quantitative estimates is long and indirect, not least as eDNA concentration depends on several physical, chemical and biological factors which influence its production, persistence and transport in marine ecosystems. Here, we provide an overview of basic principles in relation to eDNA analysis with potential for marine fisheries application. We describe fundamental processes governing eDNA generation, breakdown and transport andsummarize current uncertainties about these processes. We describe five major challenges in relation to application in fisheries assessment, where there is immediate need for knowledge building in marine systems, and point to apparent weaknesses of eDNA compared to established marine fisheries monitoring methods. We provide an overview of emerging applications of interest to fisheries management and point to recent technological advances, which could improve analysis efficiency. We advise precaution against exaggerating the present scope for application of eDNA analysis in fisheries monitoring, but also argue that with informed insights into strengths andlimitations, eDNA analysis can become an integrated tool in fisheries assessment and managemen
Using eDNA to estimate biomass of bycatch in pelagic fisheries
No full textAbstract In recent years, the analysis of environmental DNA (eDNA) has significantly improved, allowing for high‐resolution species identification and possible biomass quantification from water samples. Fisheries management typically requires monitoring of catches, including precise information about bycatch quantities to make sound assessments of exploitation rates. Bycatch assessment is particularly challenging in large catches (>500 T), and the current practice of visual assessment of subsampled catches is time‐consuming, requires extensive labor, and often has low precision. We explored the feasibility for applying eDNA‐based methods for studying catch composition using the pelagic North Sea herring fishery with bycatch of mackerel as a case. First, we experimentally simulate a series of catches using a range of herring and mackerel weight proportions to establish relationships under real fisheries scenarios. The relationship is subsequently used to estimate the biomass of mackerel bycatch from eDNA from three herring catches, by sampling and comparing processing water both onboard ships and at the processing factory. All samples are analyzed using species‐specific quantitative PCR (qPCR). The experiments reveled a strong correlation between DNA and weight fractions characterized by a constant overrepresentation of mackerel DNA compared to expected mackerel weight. We found that eDNA‐based and visual methods applied to the same landing reflect the within catch variability in species composition alike, however, the methods can show disparity in total estimates of mackerel biomass. Accounting for haul mixing within total landed catches increases the precision of the factory and ship eDNA‐based estimates for the same catch. We show that eDNA‐based bycatch estimates provide coherent quantitative data, and likely improve quality and reduce costs of collecting fisheries‐dependent data and thereby contribute to securing sustainable fisheries
Marine mammal biodiversity around oil and gas platforms - Challenges and successes of long-term monitoring
No full textMonitoring, understanding, and communicating the impact of offshore oil and gas exploration and production (E&P) activities on marine mammal (MM) biodiversity can be challenging. Here, we share methods, results, and experiences accumulated during seven years of monitoring MM and underwater sound in a mature E&P activity area in the North-East Atlantic. We collected data on the distribution and behaviour of MM, their prey and changes associated with impulsive (e.g., seismic) and continuous (e.g., platform) sound generated by E&P operations. A program was created as an incentive for offshore staff to report systematically incidental MM sightings. Underwater acoustic recorders were placed around producing facilities and across a 3D seismic survey area before, during and after acquisition. A 2nd Generation Environmental Sample Processor (ESP) was deployed to collect and analyse environmental DNA (eDNA) from seawater to identify MM species and their potential prey. Monitoring data were shared with relevant stakeholders through publications in scientific journals, presentations at conferences and meetings, or through social media. Our data provided evidence of MM activity in the E&P activity area year-round. A total of eight species were sighted from platforms and vessels; harbour porpoise being the most common MM. Harbour porpoises were recorded as being within 800m of the platform three times more often than at stations further away. Near installations, acoustic data showed porpoises actively searched for prey whilst eDNA confirmed the presence of prey species - validating a strong reef-effect. Decrease in porpoise echolocation to 8-12 km from an active seismic vessel, is suggestive of a temporary displacement of animals in the corresponding area. There was no large scale or long-term displacement as harbour porpoises were detected again in the area few hours after airgun operations ended. The results indicate that despite elevated sound level in the E&P area, porpoise distribution appears to be linked to higher availability of prey around the artificial reef created by subsea O&G structures. The monitoring efforts generate valuable scientific knowledge, which form a sound basis to support management and regulation of E&P activities in Denmark. Additionally, several simultaneous tangible benefits resulted from the study such as staff awareness of biodiversity and increased stakeholder interactions. Results and methodologies may be used by HSE practitioners and O&G project managers to assess the potential impact of sound generated by O&G industry on marine mammals. Our success illustrates the value of long-term monitoring and should inspire and support HSE practitioners in their future environmental monitoring initiatives
