Computer vision to expand monitoring and accelerate assessment of coastal fish (CoastVision)

Funding agency: The Research Council of Norway, Researcher Project for Scientific Renewal, Oceans Program
Project period: 2021-2025
Project leader: Kim Halvorsen
Project participants: Morten Goodwin, Diana Perry, Suzanne Alonzo, Cigdem Beyan, Holly Kindsvater, Howard Browman, Anne Berit Skiftesvik, Vaneeda Allken, Ketil Malde, Krisitan Knausgård

Project summary
Effective monitoring and management of coastal ecosystems is limited by observation methods. Underwater cameras are increasingly being used to monitor and study coastal fish communities; a major bottleneck for upscaling their use is dependence on human experts for image and video analysis. CoastVision will use the power of deep learning to refine and extend a computer vision pipeline for detecting, classifying and sizing the key fish species in shallow water coastal ecosystems, facilitating a transition to fully automated video analysis. Our models will be trained on data sets from several different surveys, ensuring cost-efficient development of routines that will be widely applicable. Computer vision for re-identifying (re-ID) individuals solely based on their unique visible features will also be developed. This novel aspect of CoastVision could ultimately provide new opportunities to obtain detailed knowledge about behaviour and population dynamics in wild fish populations, with minimal negative impact on animals and habitats and at a low cost. Our focal species for re-ID are Atlantic cod, ballan wrasse and corkwing wrasse, commercially important species with complex, high-contrast skin patterns. To generate the necessary training data for re-ID we will use synchronized radio frequency identification and camera systems. CoastVision’s automated video analysis pipeline will be integrated into ongoing ecosystem surveys and case studies whose main objective is to better understand the factors that affects the reproduction, recruitment and survival of commercially important coastal species. As such, CoastVision will contribute to independent, but complementary, research objectives. The project will advance the international research front for applied machine learning in marine ecology, which ultimately can revolutionize our ability to observe, understand and respond to ecological change at scales far more refined than is currently possible.

Novel tools and knowledge for a future with no lice infestations in Norwegian aquaculture

Funding agency: The Research Council of Norway, Collaborative projects to meet challenges in society and business Program.
Project period: 2021-2024
Project leader: Nicholas Robinson (NOFIMA)
Workpackage leader for semiochemical WP: Aleksei Krasnov (NOFIMA) – Howard Browman, Anne Berit Skiftesvik and David Fields are participants in this WP.
Project summary
The overall aim of this project is to identify compounds (semiochemicals) that are associated with Atlantic salmon susceptibility and resistance to the parasitic copepodids Lepeophtheirus salmonis and Caligus elongatus and to develop tools that can be applied to boost Atlantic salmon resistance and reduce lice infestation in Norway. We have previously established that there is substantial genetic variation in susceptibility to L. salmonis within farmed Norwegian Atlantic salmon populations and also detected some compounds released by the skin of Atlantic salmon that are associated with this variation. However the mechanisms triggering the release of these compounds, and their underlying genetic basis is still unknown. This project will identify host-specific semiochemicals (kairomones that attract and/or allomones that deter lice) within the Atlantic salmon population associated with the level of lice parasitisation, test whether measurement of semiochemical production could provide an accurate and more ethical phenotype (without challenge testing) for breeding to boost resistance, identify and test feed additives that could potentially block semiochemical attractant production or boost mucosal secretion of semiochemicals repelling lice and test for additional effects on the reproductive capacity of the lice and its epidemiology that might be derived from breeding for resistance. The research objectives and results of this project will integrate with those of a separate research project funded by FHF, and utilise results from our previous projects, to enhance genomic selection and prioritise candidate genes for manipulation via feed additives to produce salmon with full or high resistance. Outcomes will include improved fundamental knowledge of lice resistance mechanisms and development of tools that can be applied to boost genetic and non-genetic resistance to sea lice.

CrispResist – Harnessing cross-species variation in sea lice resistance to transform Norwegian salmon farming

Funding agency: Fiskeri- og havbruksnæringens forskningsfinansiering AS
Project period: 2021-2024
Project leader: Nicholas Robinson (NOFIMA)
Workpackage leader for semiochemical WP: Aleksei Krasnov (NOFIMA) – Howard Browman, Anne Berit Skiftesvik and David Fields are participants in this WP.
Project summary
Elaborate and document the potential for utilising genetic traits and mechanisms of salmon lice resistance in Pacific salmon as tools to achieve an Atlantic salmon with high or full salmon lice resistance – Identify and document genes and mechanisms responsible for the difference in salmon lice resistance between salmonid species – Elaborate and document the potential for utilising the identified genetic traits and mechanisms of salmon lice resistance as tools to achieve an Atlantic salmon with high or full salmon lice resistance – Conduct a risk evaluation on the possibilities for, and consequences of salmon lice adapting to Atlantic salmon with salmon lice resistance.

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2TEM – Transcriptomic tool to determine European Eel marine residency for use in monitoring and management

Funding agency: The Nordic Council of Ministers, Nordic Working Group for Oceans and Coastal Areas
Project period: 2020-2022
Project leader: Caroline Durif
Co-investigators: Jonna Tomkiewicz, Francesca Bertolini, Mehis Rohtla, Josefin Sundin
Project summary
The continental distribution of European eel covers Europe and North Africa, while reproduction takes place in the Sargasso Sea. The growth phase is typically assumed to be in freshwater (FW). However, otolith microchemistry has revealed alternate life histories where some individuals skip the FW phase or change habitats between FW and saltwater (SW) during their growth phase. This remains poorly understood because such analyses are costly and sampling lethal. Therefore, management of this endangered species currently ignores the contingent of SW eels. Our objective is to develop a non-lethal tool based on gene expression, measuring specific RNA levels in a blood sample, to determine recent SW-FW life-history. This tool may also provide information about eel pathogen, fat and contaminant levels. This methodology can serve as benchmark for the development of similar tools also for other fish species.

Assessing the effects of offshore wind turbine facilities on fish early life stages

Funding agency: The Institute of Marine Research, North Sea Program.
Project period: 2020-2024
Project leader: Howard Browman
Co-investigators: Anne Berit Skiftesvik, Caroline Durif, Alessandro Cresci
Project summary
The need to reduce fossil fuel emissions to combat global climate change has motivated a rapid development and expansion of sources of renewable energy, including large offshore wind farms (OWFs). To date, assessments of the potential effects of OWFs on marine organisms – needed to inform stakeholders and managers – have focused mainly on the construction phase – that is, on pile-driving. Very few studies have assessed lethal or sublethal effects of operational noise from OWFs, or electromagnetic fields (EMFs) from the subsea power cables that carry the energy produced from offshore to land. Besides a very small number of studies on the effects of simulated operational noise and static magnetic fields on fish embryos and hatching larvae, there is no information at all on the impacts of OWFs on the early life history stages of fish that either reside in or pass through OWFs. More effort is needed to investigate the possible impacts of OWFs on ichthyoplankton, particularly larval migratory behaviour or dispersal ecology.
Recruitment in commercially important fish is related, at least in part, to whether the early life stages disperse to areas that are suitable for survival. Dispersal of ichthyoplankton is determined by the combined effect of oceanographic features, active swimming, and directed orientation behavior. Active and directed orientation has recently been reported in the larvae of several commercially important species such as Atlantic haddock, Atlantic herring, saithe and European glass eel. Larvae use this ability to orient during their long-distance migrations and during dispersal from spawning grounds to nursery areas. We have also observed that exposure to very low levels of oil residues reduces the swimming speed and disrupts the orientation of Atlantic haddock larvae, demonstrating that sub-lethal effects of anthropogenic stressors can be subtle.
Measure and model the sound and EMFs associated with OWFs, and at various distances from the wind turbines, to establish realistic exposure levels for experimental and field work.
Assess the potential impacts of sound and EMFs associated with OWFs on the ability of the early life stages of fish to disperse, orient, and navigate in their environment.
Apply the information produced to develop a first-order risk assessment.

ZoopSeis – Effects of seismic sound on zooplankton

Funding agency: The Research Council of Norway, MARINFORSK Program.
Project period: 2020-2023
Project leader: Karen de Jong
Co-investigators: Lise Doksæter Sivle, Nils Olav Handegard, Howard Browman, David Fields, Anne Berit Skiftesvik+++
Project summary
Anthropogenic noise from seismic surveys has been documented to affect fish and marine mammals both in terms of physical injury and changes in behaviour. However, data on lower taxa are scarce. Two recent studies show highly contradicting results. A study by McCauley et al. (2017) indicates that seismic blasts may kill various species of zooplankton in Australia at distances of up to 1200 m from an airgun, while another study (Fields et al. 2019) reports no mortality or sublethal effect at distances >10m from a seismic blast in Norway. These highly contradictory results suggest that effects may be variable and highly dependent on species and geographic area. To predict at what ranges a seismic survey can impact zooplankton populations, a thorough understanding of the mechanism behind such effects is crucial. In this project, we will use a combination of modelling and laboratory to address what forces can induce injury and mortality in zooplankton, and at what ranges from a seismic survey such forces could be strong enough to have a lasting impact. We will focus on direct mortality, reproductive output and predator avoidance to assess both immediate and delayed effects. In addition, we will use field studies to verify predicted effects on natural population and to assess the potential for avoidance. The results will be used to provide advice on how to minimize the negative impact of seismic surveys in areas with high zooplankton concentrations.

MAREEL – The importance of the marine habitat for the critically endangered European eel

Funding agencies: The Research Council of Norway, MARINFORSK Program + The Institute of Marine Research, Coastal Ecosystems Program.
Project period: 2018-2021
Project leader: Caroline Durif
Co-investigators: Howard Browman, Anne Berit Skiftesvik, Even Moland, Eva Thorstad, Francoise Daverat, Michael Arts, Janet Koprivnikar, Michael Power, Leif Asbjørn Vøllestad.

Project summary
     The European eel, (Anguilla anguilla) is semi-catadromous: it spawns in the sea but spends most of its life in freshwater (FW). Some individuals either skip the FW phase or shift habitat throughout the growth phase of their life history. Despite habitat shifting sometimes being a dominant trait at high latitudes, little is known about eels that remain in marine habitats (saltwater (SW) residency). A. anguilla is currently red listed as critically endangered. Causes for the decline are associated mainly with FW residency: dams and power plants, parasites and elevated contaminant levels. Although the proximate and ultimate drivers of FW vs. SW residency are unknown, residing in SW, or shifting habitats, may confer considerable advantages. To test whether eels that have lived in the marine environment are fitter and have a better chance at reproduction than FW eels, we will investigate condition, growth, length and age at maturation of eels caught in different salinity environments along a latitudinal gradient in Norway. The salinity history of eels will be retraced using microchemistry analyses on otoliths and compared with back-calculated growth rates. Their overall condition will be linked to the parasite load, their fatty acid (FA) profile and their long-term dietary patterns obtained by stable isotope analysis (SIA). Once FA and SIA profiles are established, we will use these proxies to infer the salinity histories of a larger sample of eels at different latitudes along the Norwegian coast. We will investigate seasonal movements of eels between SW and FW, using tags and fixed monitoring station. Habitat use in the sea (behavior, depth, effect of the swimbladder parasite) will be investigated using acoustic telemetry. This project will provide unique knowledge on the determinants of diadromy and on the SW and “shifting” life history strategies of eels that will contribute to worldwide efforts to conserve this ancient species. MAREEL will explore the drivers of catadromy vs. marine residency in the Norwegian subpopulation of the European eel.
     MAREEL’s objectives are: 1) To understand the factors that drive European eels to either colonize freshwater systems or remain in saltwater systems or shift habitat by determining their relative ecological advantage in terms of growth, fatty acid profiles, dietary pattern and parasite load; 2) To identify patterns in the different life-history strategies of eels (saltwater, freshwater, or habitat shifting), for example along a latitudinal gradient 3) To determine the proximate drivers (environmental and biological) of migrations between freshwater and saltwater. 4) To characterize habitat use of eel in marine waters and investigate the effect of the swimbladder parasite on their swimming behavior.

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Fine-scale interactions in the plankton – empirical observations to parameterize trophodynamic and dispersal models

Funding agency: Institute of Marine Research, Marine Processes and Human Impact Program
Project period: 2021 – 2025
Project leader: Howard Browman
Co-investigators: Anne Berit Skiftesvik, David Fields, Caroline Durif

Project summary
This is a long-term project in which we make behavioural and physiological observations of ichthyoplankton and zooplankton, in the laboratory and in situ, with the aim of delivering empirical relationships on vital rates, swimming and orientation for parameterization of various components of ecosystem and trophic interaction models. For the laboratory-based observations, we use microrespirometry, electrophysiology, microspectrophotmetry, flumes, plankton kriesel tanks, a plankton grazing wheel, a magnetic coil system to manipulate the field orientation and strength to which organisms are exposed, and silhouette and schlieren imaging for behavioural observations of swimming and escape response kinematics. For the in situ work, we use Drifting in situ Chambers, passive acoustics and tagging.

Capacity for adaptation to multiple climate change drivers in sub-Arctic invertebrates

Funding agencies: Institute of Marine Research, Marine Processes and Human Activity Program + Fram Centre for High North Research Centre for Climate and the Environment
Project period: 2018 – 2021
Project leader: Howard Browman
Co-investigators: Haakon Hop, Anne Berit Skiftesvik, Caroline Durif, David Fields, Neel Aluru

Project summary
Marine cladocerans (Podon spp. and/or Evadne spp.) will be used as a model to investigate the relative roles of genetic and epigenetic mechanisms in determining the adaptation capacity of marine populations to CO2 and temperature. Cladocerans are widely used as models to study the evolutionary basis of phenotypic plasticity because they reproduce clonally (asexually) and sexually, which offers a unique opportunity to assess the relative contributions of the epigenetic (in clonal populations) and genetic (in sexually reproducing populations) mechanisms underlying adaption to environmental drivers, and their molecular basis.


The effects of photo-induced toxicity of polycyclic aromatic hydrocarbon on the escape performance and foraging behaviour of larval fish

Funding agency: The Institute of Marine Research, Marine Processes and Human Activity Program
Project period: 2018-2021
Project leaders: Bridie Jean Marie Allan and Sonnich Meier
Co-investigators: Howard Browman, Caroline Durif, Anne Berit Skiftesvik, Elin Sørhus, Carey Donald, Valeriya Komyakova, Olav Sigurd Kjesbu, Arild Folkvord

Project summary
This project will use laboratory exposures of polycyclic aromatic hydrocarbon (PAHs) and ultraviolet radiation (UV), as well as simulations of predation events and foraging opportunities, to answer three main questions:
• Does PAH exposure affect the anti-predator behaviour of haddock, cod and herring?
• Does PAH exposure affect the foraging behaviour of haddock, cod and herring?
• Does photo-induced toxicity of PAHs increase any observed behavioral effects?

Population dynamics of wild wrasse populations along the Norwegian coast

Funding agency: Norwegian Directorate of Fisheries + the Institute of Marine Research, Coastal Ecosystems Program
Project period: 2020 – 2024
Project Leader: Anne Berit Skiftesvik
Co-investigators: Howard Browman, Caroline Durif, Kim Halvorsen

Project summary
To assess the population dynamics and status of wrasse populations that are now exploited for use as cleanerfish on salmon farms.