Novel and Emerging Capabilities that Can Provide a Holistic Understanding of the Plant Root Microbiome

• Esther Singer^{1 2 †}
• John P. Vogel^{1 2 3}
• Trent Northen^{1 2}
• Christopher J. Mungall²
• Thomas E. Juenger⁴

¹Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720

²Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720

³Department of Plant and Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720

⁴The University of Texas at Austin, 2415 Speedway, Austin, TX 78712

Published Online:18 Jan 2021

https://doi.org/10.1094/PBIOMES-05-20-0042-RVW

Abstract

In recent years, the root microbiome (i.e., microorganisms growing inside, on, or in close proximity to plant roots) has been shown to play an important role in plant health and productivity. Despite its importance, the root microbiome is challenging to study because of its complexity, heterogeneity, and subterranean location. Fortunately, root microbiome research has seen a tremendous influx of novel technologies (e.g., imaging tools, robotics, and molecular analyses), experimental platforms (e.g., micro- and mesocosms), and data integration, modeling, and prediction tools in the past decade that have greatly increased our ability to dissect the complex network of interactions between above- and belowground environmental parameters, plants, bacteria, and fungi that dictate soil and broader ecosystem health. Herein, we discuss methods that are currently used in root microbiome research and that can be expanded to phytobiome research in general ranging from laboratory studies to mesocosm-scale studies and, finally, to field studies; evaluate their relevance to ecosystem studies; and discuss future root microbiome research directions.