A high-throughput assay for quantifying phenotypic traits of microalgae

High-throughput methods for phenotyping microalgae are in demand across a
variety of research and commercial purposes. Many microalgae can be
readily cultivated in multi-well plates for experimental studies which can
reduce overall costs, while measuring traits from low volume samples can
reduce handling. Here we develop a high-throughput quantitative phenotypic
assay (QPA) that can be used to phenotype microalgae grown in multi-well
plates. The QPA integrates 10 low-volume, relatively high-throughput trait
measurements (growth rate, cell size, granularity, chlorophyll a, neutral
lipid content, silicification, reactive oxygen species accumulation, and
photophysiology parameters: ETRmax, Ik, and alpha) into one workflow. We
demonstrate the utility of the QPA on Thalassiosira spp., a cosmopolitan
marine diatom, phenotyping six strains in a standard nutrient rich
environment (f/2 media) using the full 10-trait assay. The multivariate
phenotypes of strains can be simplified into two dimensions using
principal component analysis, generating a trait-scape. We determine that
traits show a consistent pattern when grown in small volume compared to
more typical large volumes. The QPA can thus be used for quantifying
traits across different growth environments without requiring exhaustive
large-scale culturing experiments, which facilitates experiments on trait
plasticity. We confirm that this assay can be used to phenotype newly
isolated diatom strains within 4 weeks of isolation. The QPA described
here is highly amenable to customisation for other traits or unicellular
taxa and provides a framework for designing high-throughput experiments.
This method will have applications in experimental evolution, modelling,
and for commercial applications where screening of phytoplankton traits is
of high importance.