Rapid in-situ phytoplankton monitoring to support marine aquaculture and long term climate science

Lead Research Organisation: Scottish Association For Marine Science
Department Name: Dunstaffnage Marine Laboratory


Phytoplankton form the base of the marine food web. Through their primary production they are crucial to carbon cycling. Some species that form "harmful algal blooms (HABs) are harmful to human health and/or finfish and shellfish aquaculture operations.
There are many thousands of species of phytoplankton. The diversity in responses of these to changing environmental conditions means that long term time series are required to understand the role of environment/climate in driving the productivity and biodiversity of our oceans.

Phytoplankton increases (blooms) can occur over short timescales (days). Should blooming species be harmful, rapid early warning is required for the aquaculture industry and its regulators to protect human health (from HAB generated toxins that are vectored to humans by shellfish) and minimise mortalities, as a consequence of other HAB genera, of farmed fish.
At present, the time and cost to analyse phytoplankton samples by microscopy or molecular methods prevents the high resolution monitoring required to a) understand climate effects and b) provide rapid early warning to the aquaculture industry and its regulators of HAB events.

A solution to this problem is the Imaging FlowCytobot (IFCB) https://mclanelabs.com/imaging-flowcytobot/ This is an in-situ automated submersible imaging flow cytometer that also generates images of phytoplankton in-flow.
The IFCB allow real time (every 20 minutes) monitoring of phytoplankton including HAB events. Once the instrument is "trained", images can be automatically classified to genus or even species level with accuracy comparable to that of human experts. Data are therefore comparable in quality with traditional microscope counts but are obtained at a much higher temporal resolution.

Data collection is achieved through a novel combination of flow cytometric and video technology to capture high resolution images of suspended particles. Laser induced fluorescence and light scattering from individual particles are measured and used to trigger targeted image acquisition; the optical and image data are then transmitted to shore in real time.

Images collected during this continuous monitoring are processed with automated image classification software.

The IFCB can be deployed from a raft or pier to track the progression of annual phytoplankton cycles or HAB events. It can also be configured to sample from shipboard underway seawater systems, allowing phytoplankton communities to be monitored continuously along cruise routes.

IFCBs have been used to collect data in a range of environments ranging from Florida to the Arctic with, e.g., the first harmful bloom so the shellfish biotoxin producing dinoflagellate Dinophysis being revealed by use of an IFCB (Campbell et al. 2010 J Phycol 46:60-75). IFCBs are now also being utilised for harmful algal bloom detection in Scandinavia and New Zealand.

At present, there is no IFCB or similar capability in the UK. This instrument will therefore provide a step change in the capability of UK environmental science to monitor phytoplankton and provide early warning of the HABs that impact aquaculture.

In this project we propose to purchase, train and deploy at IFCB in UK coastal waters allowing, for the first time, the production of the long term, temporally resolved data sets we require to understand the environmental control of phytoplankton and HABs in UK waters.

The instrument will ordinarily be located at the Marine Scotland Coastal Observatory in Shetland close (a major site of aquaculture). IFCB data will be made freely available in real time via our web portal (www.HABreports.org) in a similar manner to an instrument in the Gulf of Mexico http://toast.tamu.edu/IFCB111. Our own expert data interpretation will enhance its benefit for aquaculture practitioners. The IFCB will therefore provide a long term data resource for scientists, policy makers the aquaculture industry and its regulators.

Planned Impact

Rapid, routine phytoplankton enumeration will be of benefit to governmental policy makers, the aquaculture industry and its regulators. Impact will be demonstrated through the generation of HAB "alerts" for Shetland finfish and shellfish aquaculture that will help to minimise human health incidents, product recalls and allow mitigation to minimise fish kills.

Social/Economic benefit
HABs result in significant health and economic impacts. Their early warning reduces costs for aquaculture, potential health issues for consumers and increases social confidence in the safety of (healthy) seafood.

Specific benefits for each sector are expanded on below:

The Aquaculture Industry

Aquaculture is an economic pillar of the UK economy, with a production value of ~ £590 million (Black & Hughes, 2017). Production is dominated by Atlantic salmon, with shellfish aquaculture being a significant employer in rural communities. The sustainable expansion of the Scottish and UK aquaculture sector is necessary to meet the economic growth targets. A major constraint to this is the threat posed by HABs.

For finfish aquaculture HAB risk is related to fish kills that can cause massive financial loss. For example, a HAB in Chile in 2016 was estimated to have an economic cost of $800M with an event in Norway this year killing 1.3M fish with a value of £56M. A recent UK HAB caused the mortalities of thousands of salmon https://www.bbc.co.uk/news/uk-scotland-glasgow-west-48092422

HABs pose a different threat to the shellfish industry. Here, blooms of toxic species are ingested by shellfish where the toxins are retained and concentrated with a subsequent health risk to human consumers.

Industry requires early warning of HABs (Seafoood Shetland letter of support). With this information, they can make management decision such as deploying protective tarpaulins, reducing feeding, moving cages (fish farming), and early or delayed harvest or end product testing (shellfish farming).

Many HABs are advective in nature and cover an extended geographical area. Hence, a single IFCB will have widespread benefit. We therefore intend to deploy the IFCB in the Shetland islands (the epicentre of the UK's aquaculture production) for an extended period. As part of a previous BBSRC/NERC grant (BB/M025934/1) we developed a web site www.HABreports.org from which we disseminate information of HAB risk to the Scottish aquaculture industry. We will therefore use this as a means of disseminating the data and our interpretation of its HAB risk to aquaculture.


Due to the health risk to humans, regulatory monitoring occurs at shellfish farms. Regulators (Food Standards Scotland - FSS) monitor both HABs and biotoxins and close areas to harvesting if concentrations are elevated.
On cost grounds, regulatory monitoring occurs, at maximum, weekly. It is also not possible to monitor all farms. Sites are grouped into "pods" that are assumed to respond in a similar manner. Similar approaches are undertaken elsewhere. Our project, will for the first time, provide the high resolution data, required to understand phytoplankton variability and hence the suitability of this approach.
Given that a major limiting factor increased monitoring is the staff time cost of microscopy, we will also evaluate the potential for automated HAB identification in a regulatory framework (for example by analysing samples within a central laboratory that houses a bench mounted IFCB).

Policy Makers

In our Shetland deployment we will locate the IFCB at the Marine Scotland Science (project partner) sentinel monitoring site. This co-location will provide the combination of high resolution phytoplankton data and parallel environmental data (temperature, salinity, nutrients etc) to allow better UK response to policy drivers such as the Water framework Directive and the Marine Strategy Framework Directive, within which phytoplankton is a key indicator.
Description The IFCB was initially Scalloway in the Shetland Islands. Following completion of "training" it has been transferred to a Scottish Sea Farms marine fish farm to allow us to enumerate harmful and non harmful phytoplankton on a high temporal frequency. These data are streamed "live" on the web via www.HABreports.org to assist in real time risk assessment of the threat of harmful algal blooms and their associated biotoxins to aquaculture.
Exploitation Route We have received funding from Seafood Shetland to use the instrument operationally to provide HAB early warning for the aquaculture industry.

The instrument is now deployed at a Scottish Sea Farms aquaculture site and hence helps to support their mitigation measues against harmful algal bloom events
Sectors Agriculture, Food and Drink,Environment

URL http://www.HABreports.org
Description The capital equipment purchased through this grant has led to the establishment of closer links with the Scottish shellfish industry who will be the users of the data collected. We have obtained industry funding from Seafood Shetland to use the instrument operationally to provide HAB early warming for the aquaculture industry
First Year Of Impact 2021
Sector Agriculture, Food and Drink
Impact Types Economic

Description MSS/Data LAB IFCB PhD studentship
Amount £100,000 (GBP)
Organisation Marine Scotland Science (MSS) 
Sector Public
Country United Kingdom
Start 02/2021 
End 09/2024
Description Real time modelling and prediction of harmful algal blooms to minimise their impact on finfish aquaculture
Amount £218,000 (GBP)
Organisation Scottish Aquaculture Innovation Centre 
Sector Multiple
Country United Kingdom
Start 03/2021 
End 03/2023
Title Web based Harmful algal risk assessment methodology 
Description The web site www.HABreports.org has been develped to include a range of tools to report harmful algal and marine biotoxin risk to regulatory, industry and the general public 
Type Of Material Improvements to research infrastructure 
Year Produced 2017 
Provided To Others? Yes  
Impact the risk assessments provided are safeguarding humand health from shellfish biotoxins 
Description Seafood Shetland 
Organisation Seafood Shetland
Country United Kingdom 
Sector Private 
PI Contribution Production of harmful algal and biotoxin risk assessments for the Shetland aquaculture industry
Collaborator Contribution Facilitating access to the shellfish industry in Shetland, local knowledge
Impact improved shellfish safety, less finanical rish for the shellfish industry
Start Year 2015
Description ARCH UK webinar 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact A webinar as part of the ARCUK UK aquaculture series
Year(s) Of Engagement Activity 2020
URL https://www.aquaculturehub-uk.com/past-events/offaqua
Description Arabian Gulf HABs workshop 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation on HAB early warning and its potential for application in the Arabian Gulf
Year(s) Of Engagement Activity 2022
Description GlobalHAB Workshop on Early warning systems for Harmful Algal Blooms in the Arabian Gulf 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact workshop related to the development of of harmful algal bloom early wanring system for the Arabian Gulf
Year(s) Of Engagement Activity 2022
Description International conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact ICHA internatinal confernece LA Paz Mesxico (on line)
Year(s) Of Engagement Activity 2021
Description SAIC Farmed Fish Health Framework workshop 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Contribution to a SAIC hosted Farmed Fish Health Framework workshop
Year(s) Of Engagement Activity 2023
Description Salmon Scotland presentation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Presentation of harmful algal bloom early warning to the industry body Salmon Scotland and its member companies
Year(s) Of Engagement Activity 2022