COMBINING HIGH-THROUGHPUT IMAGING AND AMPLICON SEQUENCING TO MONITOR EUKARYOTIC PLANKTON

• Main Author: MacNeil, Liam
• Other Authors: Department of Biology, Master of Science, Connie Lovejoy, Paul Bentzen, Maycira Costa, Thomas Trappenberg, Julie LaRoche, Not Applicable, Yes
• Language: English
• Published: 2021
• Subjects: Plankton Imaging; Holographic Microscopy; Environmental DNA; Amplicon Sequencing; Deep Learning; Automatic Classification; Newfoundland
• Online Access: http://hdl.handle.net/10222/80648

Microbial communities support ocean food webs and respond to the surrounding environment to varying degrees across different time scales. The eukaryotic plankton throughout the oceans are extraordinarily diverse but difficult to monitor using conventional tools. A next generation of ocean observations are possible but remain unrealized to monitor eukaryotic plankton directly from the ocean using high-throughput measurements. In this thesis, I apply digital holography and amplicon sequencing to describe diverse community compositions of micro-mesoplankton. First, I evaluate automatic classification of micro-mesoplankton from seawater and monocultures using a deployable digital in-line holographic microscope and state-of-the-art classification algorithms. Second, I quantify and barcode the micro-mesoplankton community across transects of the Newfoundland Shelf. These results confirm digital in-line holographic microscopes can yield rapid, high-quality plankton images under multiple in-situ conditions, that benchmark image recognition tools are highly transferrable to plankton images, and that paired high-throughput amplicon sequencing yields different, although complementary surveys.