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Frontiers in Microbiology




823109 (1-7)


As primary producers, phytoplankton play an integral role in global biogeochemical cycles through their production of oxygen and fixation of carbon. They also provide significant ecosystem services, by supporting secondary production and fisheries. Phytoplankton biomass and diversity have been identified by the Global Ocean Observing System (GOOS) as Essential Ocean Variables (EOVs), properties that need to be monitored to better understand and predict the ocean system. Phytoplankton identification and enumeration relies on the skills and expertise of highly trained taxonomic analysts. The training of new taxonomic analysts is intensive and requires months to years of supervised training before an analyst is able to independently and consistently apply identification skills to a sample. During the COVID-19 pandemic, access to laboratories was greatly restricted and social distancing requirements prevented supervised training. However, access to phytoplankton imaging technologies such as the Imaging FlowCytobot (IFCB), FlowCam, and PlanktoScope, combined with open online taxonomic identification platforms such as EcoTaxa, provided a means to continue monitoring, research, and training activities remotely when in-person activities were restricted. Although such technologies can not entirely replace microscopy, they have a great potential for supporting an expansion in taxonomic training, monitoring, surveillance, and research capacity. In this paper we highlight a set of imaging and collaboration tools and describe how they were leveraged during laboratory lockdowns to advance research and monitoring goals. Anecdotally, we found that the use of imaging tools accelerated the training of new taxonomic analysts in our phytoplankton analysis laboratory. Based on these experiences, we outline how these technologies can be used to increase capacity in taxonomic training and expertise, as well as how they can be used more broadly to expand research opportunities and capacity.


© 2022 Clayton, Gibala-Smith, Mogatas, Flores-Vargas, Marciniak, Wigginton and Mulholland.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (CC BY 4.0). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Article states: "The original contributions presented in the study are included in the article/supplementary material, further inquiries can be directed to the corresponding author."

Corresponding author: Sophie Clayton (ORCiD: 0000-0001-7473-4873)

Original Publication Citation

Clayton, S., Gibala-Smith, L., Mogatas, K., Flores-Vargas, C., Marciniak, K., Wigginton, M., & Mulholland, M. R. (2022). Imaging technologies build capacity and accessibility in phytoplankton species identification expertise for research and monitoring: Lessons learned during the COVID-19 pandemic. Frontiers in Microbiology, 13, 1-7, Article 823109.


0000-0001-7473-4873 (Clayton), 0000-0001-8819-189X (Mulholland)


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