The hidden side of interaction: microbes and roots get together to improve plant resilience

Figures & data

Figure 1. The hidden root microbiome, a vast spectrum of microorganisms involved in interactions with roots and the rhizosphere.

Figure 2. Conceptual diagram of the hidden soil interactome and its consequences for plant nutrition (

) and defense (

). A: plant alone, B: plant + Plant Growth Promoting Rhizobacteria, C: plant + Arbuscular Mycorrhizal Fungi, D: plant + Plant Growth Promoting Rhizobacteria + Arbuscular Mycorrhizal Fungi.

Table 1. Root phenotyping tools with a potential for studying root-microbe interactions. AMF: AM fungi.

Tool	Type of Phenotyping	Application	Reference
Rhizotrons	2D	Traditional nondestructive 2D imaging	Atkinson et al. 2019
Minirhizotrons	2D	High-resolution imaging of root dynamics in field conditions	Bauer et al. 2022
RhizoTubes	2D	Dynamic root phenotyping, high-quality imaging	Jeudy et al. 2016
WinRHIZO™	2D & AMF colonization analysis	Global root measurements (diameter, length, area), root topology, estimation of AMF colonization	Deguchi et al. 2017
EZ-Rhizo	2D	Global root measurements (diameter, length, area), root topology	Armengaud et al. 2009
RhizoVision Explorer	2D	Global root measurements (diameter, length, area), root topology	Seethepalli et al. 2021
GrowScreen-PaGe	2D	High-throughput phenotyping of shoot and root growth under different conditions	Gioia et al. 2016
X-ray CT	3D	Monitoring root system growth over time, nondestructive imaging	Pfeifer et al. 2015
Magnetic resonance imaging (MRI)	3D	Monitoring root system growth over time, nondestructive imaging	Pflugfelder et al. 2017
Trouvelot Method, Grid-line Intersect Method	AMF colonization analysis	Microscopical observations of AMF colonization	Trouvelot et al. 1986 Giovannetti and Mosse 1980
AMFinder	AMF colonization analysis	Automatic identification and quantification of AMF using computer vision and neural networks	Evangelisti et al. 2021
TAIM	AMF colonization analysis	Web-based application using machine learning for AMF colonization rate calculation	Muta et al. 2023
Machine Learning-based method	AMF colonization analysis	High efficiency and correlation with traditional methods for AMF colonization assessment	Sciascia et al. 2023
qPCR with universal AMF primer set	AMF colonization analysis	High-throughput molecular tool for AMF colonization assessment in roots	Corona Ramírez et al. 2023
Standardized Quantitative Analysis for nodule	Nodule quantification analysis	Standardized representation and calculation of nodulation degree	Remmler et al. 2014
SNAP	Nodule quantification analysis	Nodule quantification on soybean roots using deep learning for detection and segmentation	Jubery et al. 2021

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