Accelerated High-throughput Imaging and Phenotyping System for Small Organisms

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2023 Jul 21

PMID 37478145

Authors

Talha Kose

Tiago F Lins

Jessie Wang

Anna M OBrien

David Sinton

Megan E Frederickson

Affiliations

Soon will be listed here.

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.

Citing Articles

Community interactions among microbes give rise to host-microbiome mutualisms in an aquatic plant.

Laurich J, Lash E, OBrien A, Pogoutse O, Frederickson M mBio. 2024; 15(7):e0097224.

PMID: 38904411 PMC: 11324027. DOI: 10.1128/mbio.00972-24.

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

Subbaraman B, de Lange O, Ferguson S, Peek N PLoS One. 2024; 19(1):e0296717.

PMID: 38261570 PMC: 10805289. DOI: 10.1371/journal.pone.0296717.

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

Irfan M, Meszaros I, Szabo S, Olah V Plants (Basel). 2024; 13(2).

PMID: 38256768 PMC: 10821045. DOI: 10.3390/plants13020215.

References

Song C, Von Ahn S, Rohr R, Saavedra S . Towards a Probabilistic Understanding About the Context-Dependency of Species Interactions. Trends Ecol Evol. 2020; 35(5):384-396. DOI: 10.1016/j.tree.2019.12.011. View

Appenroth K, Sree K, Bog M, Ecker J, Seeliger C, Bohm V . Nutritional Value of the Duckweed Species of the Genus (Lemnaceae) as Human Food. Front Chem. 2018; 6:483. PMC: 6215809. DOI: 10.3389/fchem.2018.00483. View

Acosta K, Appenroth K, Borisjuk L, Edelman M, Heinig U, Jansen M . Return of the Lemnaceae: duckweed as a model plant system in the genomics and postgenomics era. Plant Cell. 2021; 33(10):3207-3234. PMC: 8505876. DOI: 10.1093/plcell/koab189. View

Cox Jr K, Manchego J, Meyers B, Czymmek K, Harkess A . Automated imaging of duckweed growth and development. Plant Direct. 2022; 6(9):e439. PMC: 9510441. DOI: 10.1002/pld3.439. View

Chamberlain S, Bronstein J, Rudgers J . How context dependent are species interactions?. Ecol Lett. 2014; 17(7):881-90. DOI: 10.1111/ele.12279. View

David A, Thapa-Magar K, Menges E, Searcy C, Afkhami M . Do plant-microbe interactions support the Stress Gradient Hypothesis?. Ecology. 2020; 101(8):e03081. DOI: 10.1002/ecy.3081. View

Kehe J, Kulesa A, Ortiz A, Ackerman C, Thakku S, Sellers D . Massively parallel screening of synthetic microbial communities. Proc Natl Acad Sci U S A. 2019; 116(26):12804-12809. PMC: 6600964. DOI: 10.1073/pnas.1900102116. View

Cao W, Zhou J, Yuan Y, Ye H, Nguyen H, Chen J . Quantifying Variation in Soybean Due to Flood Using a Low-Cost 3D Imaging System. Sensors (Basel). 2019; 19(12). PMC: 6630946. DOI: 10.3390/s19122682. View

Lasfar S, Monette F, Millette L, Azzouz A . Intrinsic growth rate: a new approach to evaluate the effects of temperature, photoperiod and phosphorus-nitrogen concentrations on duckweed growth under controlled eutrophication. Water Res. 2007; 41(11):2333-40. DOI: 10.1016/j.watres.2007.01.059. View

10.

Olah V, Hepp A, Irfan M, Meszaros I . Chlorophyll Fluorescence Imaging-Based Duckweed Phenotyping to Assess Acute Phytotoxic Effects. Plants (Basel). 2021; 10(12). PMC: 8707530. DOI: 10.3390/plants10122763. View

11.

Birk S, Chapman D, Carvalho L, Spears B, Andersen H, Argillier C . Impacts of multiple stressors on freshwater biota across spatial scales and ecosystems. Nat Ecol Evol. 2020; 4(8):1060-1068. DOI: 10.1038/s41559-020-1216-4. View

12.

Nguyen B, Graham P, Rochman C, Sinton D . A Platform for High-Throughput Assessments of Environmental Multistressors. Adv Sci (Weinh). 2018; 5(4):1700677. PMC: 5908365. DOI: 10.1002/advs.201700677. View

13.

Das Choudhury S, Samal A, Awada T . Leveraging Image Analysis for High-Throughput Plant Phenotyping. Front Plant Sci. 2019; 10:508. PMC: 6491831. DOI: 10.3389/fpls.2019.00508. View

14.

Jones D, Atkinson B, Ware A, Sturrock C, Bishopp A, Wells D . Preparation, Scanning and Analysis of Duckweed Using X-Ray Computed Microtomography. Front Plant Sci. 2021; 11:617830. PMC: 7820725. DOI: 10.3389/fpls.2020.617830. View

15.

Vasseur F, Bresson J, Wang G, Schwab R, Weigel D . Image-based methods for phenotyping growth dynamics and fitness components in . Plant Methods. 2018; 14:63. PMC: 6060534. DOI: 10.1186/s13007-018-0331-6. View

16.

Shears N, Ross P . Toxic cascades: multiple anthropogenic stressors have complex and unanticipated interactive effects on temperate reefs. Ecol Lett. 2010; 13(9):1149-59. DOI: 10.1111/j.1461-0248.2010.01512.x. View

17.

Yang Y, Guo Y, OBrien A, Lins T, Rochman C, Sinton D . Biological Responses to Climate Change and Nanoplastics Are Altered in Concert: Full-Factor Screening Reveals Effects of Multiple Stressors on Primary Producers. Environ Sci Technol. 2020; 54(4):2401-2410. DOI: 10.1021/acs.est.9b07040. View

18.

Yang W, Feng H, Zhang X, Zhang J, Doonan J, Batchelor W . Crop Phenomics and High-Throughput Phenotyping: Past Decades, Current Challenges, and Future Perspectives. Mol Plant. 2020; 13(2):187-214. DOI: 10.1016/j.molp.2020.01.008. View

19.

Ge X, Pereira F, Mitteregger M, Berry D, Zhang M, Hausmann B . SRS-FISH: A high-throughput platform linking microbiome metabolism to identity at the single-cell level. Proc Natl Acad Sci U S A. 2022; 119(26):e2203519119. PMC: 9245642. DOI: 10.1073/pnas.2203519119. View

20.

OBrien A, Yu Z, Pencer C, Frederickson M, LeFevre G, Passeport E . Harnessing plant-microbiome interactions for bioremediation across a freshwater urbanization gradient. Water Res. 2022; 223:118926. DOI: 10.1016/j.watres.2022.118926. View