m-CAFEs researchers studied microbial communities at different zones of the roots in three different types of growth containers: conventional pots, tubes, and standardized fabricated ecosystems (EcoFABs), designed to mimic conditions of a natural environment. The goal was to characterize microbial communities on the tips of the roots, the soil at the base of the roots and regular bulk soil that was not in the rhizosphere environment.
The team found that the microbes found in the bulk soil compared to the microbes in the rhizosphere were distinct from each other, indicating that microbes are recruited from bulk soil outside of the rhizosphere onto the root surface–as early as 14 days into plant growth. Another key finding was that genes associated with different metabolic pathways and root colonization were more abundant in root tips than those associated with nutrient-limitations and environmental stress, implying the absence of easily available and stable carbon and nutrients in bulk soil relative to roots. The study also shows that using different growth containers with different shapes, volumes and sizes had no observed effect on the microbial composition throughout the roots.
“The root exudates, the substances released by roots, along different parts of roots is considered an important parameter in rhizosphere dynamics, systematic and standardized studies probing this deeper are lacking especially in the early critical stages of plant growth,” said Chakraborty.
This study reveals key information on rhizosphere microbiology, which is a hotbed of carbon and nutrient transformations in all ecosystems. Closing the knowledge gap related to this environment and the microbes associated with it is essential to building our understanding of biogeochemical and carbon cycling.
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Lawrence Berkeley National Laboratory
Acharya, S.M., Yee, M.O., Diamond, S. et al. Fine scale sampling reveals early differentiation of rhizosphere microbiome from bulk soil in young Brachypodium plant roots. ISME COMMUN. 3, 54 (2023). https://doi.org/10.1038/s43705-023-00265-1