Locating the microbes along the maize root system under nitrogen limitation: a root phenotypic approach
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Updated: Sep 11, 2025
An Optimized Rhizobox Protocol to Visualize Root Growth and Responsiveness to Localized Nutrients
Published on: October 22, 2018
Tania Galindo-Castañeda1, Elena Kost1, Elena Giuliano1
1Institute of Agricultural Sciences, Department of Environmental Systems Science, ETH Zurich, 8092 Zurich, Switzerland.
Background:
A major challenge in agriculture is the low nitrogen (N) uptake efficiency of crops, which poses environmental and economic costs. Root adaptive architectural and anatomical phenotypes in synergy with root microbes could be a promising approach to improve plant N uptake. However, little is known about such synergies. Here, we aimed to characterize the spatial distribution of the root prokaryotes of maize (Zea mays) under low N in 30-L mesocosms, where root architecture and anatomy are freely expressed, searching for correlations between prokaryotic genus abundance and ten phenotypes.
Methods:
We studied the root prokaryotic community of 4-week-old plants growing in 30-L mesocosms under low N using two sandy soil mixtures. We collected root, rhizosphere and bulk soil samples at various locations, including depths (0-20, 20-70, 70-150 cm), root classes (lateral and axial) and root types (seminal and crown). We measured plant growth response to low N availability and performed 16S rRNA gene metabarcoding on extracted DNA.
Key Results:
Sampling location was the third most important factor after soil mixture and compartment, explaining ∼5 % of the variance in root prokaryotic diversity. Seminal roots (0-20 cm depth), shallow crown roots (0-20 cm) and deep crown roots (20-150 cm) showed well-separated root microbial communities. Lateral root branching density (LRBD) explained 10 % of this variance in the rhizosphere and the root tissue. We identified prokaryotic genera specific to depth, soil-root compartment, root class and type under LN. Moreover, architectural phenotypes LRBD and lateral root length significantly correlated with the abundance of 37 genera.
Conclusions:
We highlight the importance of sampling location and architectural traits that may be associated with the microbial cycling of soil N. The exploration of synergies between root traits and microbes that participate in the N cycle has the potential to increase sustainability in agriculture.
