Recent publication reveals new insights into plant-microbe interactions in early developmental stages of plants

Northen Lab researchers Spencer Diamond, Peter Andeer, and Trent R. Northen and collaborators from the Lawrence Berkeley National Laboratory and the University of California, Berkeley, recently co-authored an International Society for Microbial Ecology (ISME) Communications paper: “Fine scale sampling reveals early differentiation of rhizosphere microbiome from bulk soil in young Brachypodium plant roots.” This research utilized fabricated ecosystems (EcoFABs: to investigate spatial differences in the microbiome along the length of young plant roots, which was previously unexplored. EcoFABs are sterile devices developed in the Northen Lab that enable controlled microbiome studies under conditions where they can be imaged and sampled.

Photo shows EcoFAB 1.0 version with model grass plant. A newer version, EcoFAB 2.0, was recently developed and includes design changes allowing standardization and compatibility with automated systems (EcoFAB 2.0:
Fig. 4: Shows several metabolic pathway genes detected in different rhizosphere locations, including root base, root tip, and bulk soil, as well as across various container types, which included EcoFABs, conventional pots, and plastic tubes.

The results of this research revealed that container type had no significant impact on microbial community composition and no distinct spatial differences in microbiome composition along roots were observed. This is an important result showing that rhizosphere communities grown in soil filled EcoFAB devices are comparable to those observed in more conventional devices. Both microbial community composition and metabolic pathways were found to be altered in the bulk soil versus root soils, where pathways associated with root colonization and substrate utilization were more prevalent in root tip soils. Together these results demonstrate the utility of the EcoFAB devices in studying plant-microbe interactions.

To learn more, read the full article here.

Acharya, S.M., Yee, M.O., Diamond, S., Andeer, P.F., Baig, N.F., Aladesanmi, O.T., Northen, T.R., Banfield, J.F., Chakraborty, R. Fine scale sampling reveals early differentiation of rhizosphere microbiome from bulk soil in young Brachypodium plant roots. ISME COMMUN. 3, 54 (2023).