Sea lice (Lepeophtherius salmonis) detection and quantification around aquaculture installations using environmental DNA

The 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.publishedVersio

Effects of chronic exposure to the water-soluble fraction of crude oil and in situ burn residue of oil on egg-bearing Northern shrimp (Pandalus borealis)

Oil spill clean-up measures using in situ burning can potentially result in seafloor contamination affecting benthic organisms. To mimic realistic exposure and measure effects, ovigerous Northern shrimp were continuously exposed for two weeks to the water-soluble fraction of oil coated on gravel followed by two weeks in clean seawater. North Sea crude oil (NSC) and field generated in situ burn residue (ISBR) of NSC were used (Low: 3 g/kg gravel, Medium: 6 g/kg gravel and High: 12 g/kg gravel). The concentrations of polyaromatic hydrocarbons (PAHs) in the water resulting from NSC were higher compared to ISBR. No mortality was observed in any treatment and overall moderate sublethal effects were found, mostly after exposure to NSC. Feeding was temporarily reduced at higher concentrations of NSC. PAH levels in hepatopancreas tissue were significantly elevated following exposure and still significantly higher at the end of the experiment in NSCHigh and ISBRHigh compared to control. Mild inflammatory response reactions and tissue ultrastructural alterations in gill tissue were observed in both treatments. Signs of necrosis occurred in ISBRHigh. No change in shrimp locomotory activity was noted from NSC exposure. However, ISBR exposure increased activity temporarily. Larvae exposed as pleopod-attached embryos showed significant delay in development from stage I to stage II after exposure to NSCHigh. Based on this study, oil-contaminated seafloor resulting from in situ burning clean-up actions does not appear to cause serious effects on bottom-living shrimp.publishedVersio

The One Ocean Expedition: Science and Sailing for the Ocean We Want

The One Ocean Expedition (OOE) was a 20-month long circumnavigation of the globe by the Norwegian sail training vessel Statsraad Lehmkuhl, and a recognised part of the UN decade of Ocean Science for Sustainable Development. The ship was equipped with modern instrumentation to collect high-quality data on ocean physics, chemistry, and biology. Many of the data series were available in near real time from an open repository. The scientific programme was executed along the sailing route of Statsraad Lehmkuhl, with occasional stops for stationary work. The aim of the data collection on board the vessel was to improve knowledge about the state of the world's ocean with regards to the distribution and diversity of organisms, environmental status, climate, and human pressures on the marine ecosystem. Another aim of the expedition was to educate ocean scientists and strengthen ocean literacy. The main types of instrumentation are sensors that measure continuously underway including echosounder, hydrophone, temperature and salinity probes, and various instruments that collect and analyse water sampled from an inlet in the ship's hull, including for environmental DNA and microplastic. Here, we describe the scientific instrumentation onboard Statsraad Lehmkuhl and present preliminary results from the Atlantic part of the expedition. While there are many challenges to using a sail ship for scientific purposes, there are also some key benefits as the vessel is quiet and has a low footprint. Furthermore, the use of a common set of instruments and procedures across the ocean also removes an uncertainty factor when comparing data between ocean areas.The One Ocean Expedition: Science and Sailing for the Ocean We WantpublishedVersio

The One Ocean Expedition: Science and Sailing for the Ocean We Want

Source at https://www.hi.no/hi.The One Ocean Expedition (OOE) was a 20-month long circumnavigation of the globe by the Norwegian sail training vessel Statsraad Lehmkuhl, and a recognised part of the UN decade of Ocean Science for Sustainable Development. The ship was equipped with modern instrumentation to collect high-quality data on ocean physics, chemistry, and biology. Many of the data series were available in near real time from an open repository. The scientific programme was executed along the sailing route of Statsraad Lehmkuhl, with occasional stops for stationary work. The aim of the data collection on board the vessel was to improve knowledge about the state of the world's ocean with regards to the distribution and diversity of organisms, environmental status, climate, and human pressures on the marine ecosystem. Another aim of the expedition was to educate ocean scientists and strengthen ocean literacy. The main types of instrumentation are sensors that measure continuously underway including echosounder, hydrophone, temperature and salinity probes, and various instruments that collect and analyse water sampled from an inlet in the ship's hull, including for environmental DNA and microplastic. Here, we describe the scientific instrumentation onboard Statsraad Lehmkuhl and present preliminary results from the Atlantic part of the expedition. While there are many challenges to using a sail ship for scientific purposes, there are also some key benefits as the vessel is quiet and has a low footprint. Furthermore, the use of a common set of instruments and procedures across the ocean also removes an uncertainty factor when comparing data between ocean areas

Kunnskapsstatus for bruk av molekylære verktøy i kartlegging og overvåkning av biologisk mangfold i marine miljø

Source at https://www.miljodirektoratet.no/publikasjoner/2021/juni-2021/kunnskapsstatus-for-bruk-av-molekylare-verktoy-i-kartlegging-og-overvakning-av-biologisk-mangfold-i-marine-miljo/Denne rapporten er bestilt av Miljødirektoratet fra NorBOL (Norwegian Barcode of Life), et nasjonalt nettverk av forskningsinstitusjoner som koordineres av NTNU Vitenskapsmuseet. Universitetsmuseet i Bergen har hatt prosjektledelsen. Rapporten gir en oppsummering av dagens status på DNA-basert metodikk som verktøy i kartlegging og overvåking av biologisk mangfold i det marine miljø. Fokus har vært på innsamlingsmetodikk og protokoller for DNA-analyser av arter og artsgrupper. Metodikken er evaluert opp mot kartleggings- og overvåkingsaktivitet i regi av Miljødirektoratet, og kommer med anbefalinger for videre framdrift for å ta metodikken i bruk i nasjonal kartlegging og overvåking. Rapporten har også en gjennomgang og evaluering av eksisterende referansemateriale og referansesekvenser for relevante arter og artsgrupper som inngår i Miljødirektoratets kartleggings- og overvåkingsaktivitet

Abundance and diversity of n-alkane and PAH-degrading bacteria and their functional genes – Potential for use in detection of marine oil pollution

Monitoring environmental status through molecular investigation of microorganisms in the marine environment is suggested as a potentially very effective method for biomonitoring, with great potential for automation. There are several hurdles to that approach with regards to primer design, variability across geographical locations, seasons, and type of environmental pollution. Here, qPCR analysis of genes involved in the initial activation of aliphatic and aromatic hydrocarbons were used in a laboratory setup mimicking realistic oil leakage at sea. Seawater incubation experiments were carried out under two different seasons with two different oil types. Degenerate primers targeting initial oxygenases (alkane 1-monooxygenase; alkB and aromatic-ring hydroxylating dioxygenase; ARHD) were employed in qPCR assays to quantify the abundance of genes essential for oil degradation. Shotgun metagenomics was used to map the overall community dynamics and the diversity of alkB and ARHD genes represented in the microbial community. The amplicons generated through the qPCR assays were sequenced to reveal the diversity of oil-degradation related genes captured by the degenerate primers. We identified a major mismatch between the taxonomic diversity of alkB and ARHD genes amplified by the degenerate primers and those identified through shotgun metagenomics. More specifically, the designed primers did not amplify the alkB genes of the two most abundant alkane degraders that bloomed in the experiments, Oceanobacter and Oleispira. The relative abundance of alkB sequences from shotgun metagenomics and 16S rRNA-based Oleispira-specific qPCR assay were better signals for oil in water than the tested qPCR alkB assay. The ARHD assay showed a good agreement with PAHs degradation despite covering only 25% of the top 100 ARHD genes and missing several abundant Cycloclasticus sequences that were present in the metagenome. We conclude that further improvement of the degenerate primer approach is needed to rely on the use of oxygenase-related qPCR assays for oil leakage detection

Numeric analysis of planktonic spatial patterns revealed by echograms

Observations of acoustic images made along a transect perpendicular to the Coast, off Villefranche-sur-Mer, allow one to recognize the hydrological zone corresponding to a surface density gradient characterizing the Ligurian Sea front (Mediterranean Sea). Combinations of statistical and geometrical parameters from the digitized echoes enable discrimination between different classes of patches in relation to the frontal structure during one transect recorded on December 20, 1990. Patch recognition is based on the extraction of the general trend of each column and each row of the digitized data matrix by Eigenvector filtering. Multivariate analysis (principal component analysis and discriminant analysis) run on a 650 patches × 19 variables matrix shows a high negative relation between statistic and geometric parameters of the patches. The two main discriminant parameters are shape and echo strength of patches. From the convergence of our results in the Ligurian front with those of previous works made in other frontal region, it is suggested that this method could be generalized for quantifying and standardizing studies of the patchiness of plankton

Numeric analysis of planktonic spatial patterns revealed by echograms

Observations of acoustic images made along a transect perpendicular to the Coast, off Villefranchesur-Mer, allow one to recognize the hydrological zone corresponding to a surface density gradient characterizing the Ligurian Sea front (Mediterranean Sea). Combinations of statistical and geometrical parameters from the digitized echoes enable discrimination between different classes of patches in relation to the frontal structure during one transect recorded on December 20, 1990. Patch recognition is based on the extraction of the general trend of each column and each row of the digitized data matrix by Eigenvector filtering. Multivariate analysis (principal component analysis and discriminant analysis) run on a 650 patches x 19 variables matrix shows a high negative relation between statistic and geometric parameters of the patches. The two main discriminant parameters are shape and echo strength of patches. From the convergence of our results in the Ligurian front with those of previous works made in other frontal region, it is suggested that this method could be generalized for quantifying and standardizing studies of the patchiness of plankton

Abundance and diversity of n-alkane and PAH-degrading bacteria and their functional genes – Potential for use in detection of marine oil pollution

Monitoring environmental status through molecular investigation of microorganisms in the marine environment is suggested as a potentially very effective method for biomonitoring, with great potential for automation. There are several hurdles to that approach with regards to primer design, variability across geographical locations, seasons, and type of environmental pollution. Here, qPCR analysis of genes involved in the initial activation of aliphatic and aromatic hydrocarbons were used in a laboratory setup mimicking realistic oil leakage at sea. Seawater incubation experiments were carried out under two different seasons with two different oil types. Degenerate primers targeting initial oxygenases (alkane 1-monooxygenase; alkB and aromatic-ring hydroxylating dioxygenase; ARHD) were employed in qPCR assays to quantify the abundance of genes essential for oil degradation. Shotgun metagenomics was used to map the overall community dynamics and the diversity of alkB and ARHD genes represented in the microbial community. The amplicons generated through the qPCR assays were sequenced to reveal the diversity of oil-degradation related genes captured by the degenerate primers. We identified a major mismatch between the taxonomic diversity of alkB and ARHD genes amplified by the degenerate primers and those identified through shotgun metagenomics. More specifically, the designed primers did not amplify the alkB genes of the two most abundant alkane degraders that bloomed in the experiments, Oceanobacter and Oleispira. The relative abundance of alkB sequences from shotgun metagenomics and 16S rRNA-based Oleispira-specific qPCR assay were better signals for oil in water than the tested qPCR alkB assay. The ARHD assay showed a good agreement with PAHs degradation despite covering only 25% of the top 100 ARHD genes and missing several abundant Cycloclasticus sequences that were present in the metagenome. We conclude that further improvement of the degenerate primer approach is needed to rely on the use of oxygenase-related qPCR assays for oil leakage detection.publishedVersio

Report from the Coral Workshop 31st of May–1st June 2010

Knowlcdge status and -gaps in coral biology and scnsitivity to drilling opcrations of cold-watcr corals (CWC). as wcll as cxamples of rnitigation actions raken by oil operators were presentcd at the "'OLF coral workshop"· held in Stavanger. Norway, 31 st of May and Ist of June 2010. The workshop was organized by the Norwegian Oil lndustry Association (OLF) and hostcd by the International Rescarch Institute or Stavanger (IRIS). Acona Wellpro has supported IRIS and OLF in the finalizing of this report from the workshop.OL