Accelerated high-throughput imaging and phenotyping system for small organisms

Abstract

Studying the complex web of interactions in biological communities requires large multifactorial experiments with sufficient statistical power. Automation tools reduce the time and labor associated with setup, data collection, and analysis in experiments that untangle these webs. We developed tools for high-throughput experimentation (HTE) in duckweeds, small aquatic plants that are amenable to autonomous experimental preparation and image-based phenotyping. We showcase the abilities of our HTE system in a study with 6,000 experimental units grown across 2,000 treatments. These automated tools facilitated the collection and analysis of time-resolved growth data, which revealed finer dynamics of plant-microbe interactions across environmental gradients. Altogether, our HTE system can run experiments with up to 11,520 experimental units and can be adapted for other small organisms.

The Duckbot: A system for automated imaging and manipulation of duckweed

“…We moreover conduct our growth assays in 24-well plates, wherein a similar problem recurs: fronds can quickly become overcrowded within wells, particularly for the larger Spirodela polyrhiza and Lemna minor duckweeds. In pursuit of high-throughput experimental systems, similar growth experiments have been conducted using Lemna minor duckweed in smaller 96-well plates [ 14 ]. The tradeoff between overcrowding and large-scale experimental design is therefore under active negotiation by duckweed researchers.…”

“…In addition, small size, preference for free-floating aquatic growth, and fast growth rates relative to other angiosperms facilitate laboratory research by allowing the use of labware designed for cultivation of microscopic organisms and higher-throughput approaches. Those possibilities have been demonstrated in work characterizing physiological parameters for 39 different genotypes from across the family [ 13 ] as well as recent work developing machine automated pipelines for high-throughput studies of duckweed-microbe interactions [ 14 ]. Many species in the family flower rarely or have never been observed flowering [ 15 ]; this hampers use of traditional plant genetics approaches based on crosses.…”

“…The power of workflow automation for duckweed phenotyping as a means to address complex multi-organismal and environmental interactions was recently demonstrated by Kose et al [ 14 ]. They used a hardware combination of an Opentrons OT-2 liquid handling robot, bespoke transfer loops, and a robotic camera gantry within a walk-in growth chamber to carry out experiments involving 6000 duckweed units tracked over 10 days.…”

“…In this work, we leverage the Jubilee’s tool-changing ability to demonstrate a multi-tool experimental workflow. Scientists have always built their own tools to meet research needs; we are interested in exploring how to support more custom automation workflows such as those described by Kose et al [ 14 ].…”

Comparative Phytotoxicity of Metallic Elements on Duckweed Lemna gibba L. Using Growth- and Chlorophyll Fluorescence Induction-Based Endpoints

“…Recent studies have adapted duckweed tests in multi-well plates (usually 6-, 12- or 24-well plates) using a smaller volume of test medium for 3–7 days [ 19 , 24 , 26 , 27 , 28 ]. Such small-scale, multi-well-plate-based experiments can be managed in a limited space and with fewer resources, promising a potential alternative to standard toxicity testing [ 29 , 30 , 31 ]. So far, however, most multi-well-plate-based studies with duckweeds have focused on small sets of toxicants and/or on narrow concentration ranges.…”