Microfabrication of a Chamber for High-Resolution, In Situ Imaging of the Whole Root for Plant–Microbe Interactions

Abstract

Fabricated ecosystems (EcoFABs) offer an innovative approach to in situ examination of microbial establishment patterns around plant roots using nondestructive, high-resolution microscopy. Previously high-resolution imaging was challenging because the roots were not constrained to a fixed distance from the objective. Here, we describe a new ‘Imaging EcoFAB’ and the use of this device to image the entire root system of growing Brachypodium distachyon at high resolutions (20×, 40×) over a 3-week period. The device is capable of investigating root–microbe interactions of multimember communities. We examined nine strains of Pseudomonas simiae with different fluorescent constructs to B. distachyon and individual cells on root hairs were visible. Succession in the rhizosphere using two different strains of P. simiae was examined, where the second addition was shown to be able to establish in the root tissue. The device was suitable for imaging with different solid media at high magnification, allowing for the imaging of fungal establishment in the rhizosphere. Overall, the Imaging EcoFAB could improve our ability to investigate the spatiotemporal dynamics of the rhizosphere, including studies of fluorescently-tagged, multimember, synthetic communities.

Plant phenotyping relevance

植物根系全体を高解像度・経時的に撮像するための新規チャンバーを開発し、その撮像性能と用途を示しており、表現型取得法が研究の中心である。

Code and data availability

The paper's computational analysis (K-means clustering and segmentation/cell counting of the 40× multispectral root image) is explicitly stated to have its environment, code, and parent data file available in the Supplementary Materials, hosted at the MDPI S1 link. Additionally, the 3D-printing-ready Imaging EcoFAB 3D-