Current approaches and future directions for rhizosphere microbiome sampling methodologies

May 18, 2022




Suzanne M. Fleishman
PhD Candidate in Ecology
Intercollege Graduate Degree Program in Ecology
Departments of Plant Science and Ecosystem Science and Management
The Pennsylvania State University, USA


The rhizosphere is a nexus for plant-microbe interactions that shape plant health. There has been exponential growth in research focused on the root-associated microbiome, yet crucial questions remain unanswered, including how to identify microbes of key importance for plant function and the mechanisms by which roots structure their microbial communities. Addressing these questions requires estimating microbiome composition and diversity with methodological approaches that take into account the underlying functional and spatial heterogeneity of individual roots within a root system.

Over the past 4 years, research from our group has found that both root traits, such as root order and color, and spatial location of roots can structure root microbial assemblages to varying degrees. Even so, roots growing within one centimeter of one another can have drastically different microbial composition. This webinar will be structured by our systematic review of root sampling and rhizosphere removal methods, discussing the current trends and gaps in understanding. It will also briefly cover key findings from multiple studies linking within root system functional and spatial heterogeneity to rhizosphere microbiomes. These approaches were then applied to give a nuanced understanding of how the rhizosphere microbiomes of wine grapevines are impacted by concurrent growth with a grass groundcover across the soil profile to 1-meter. The webinar will end with a discussion of areas of methodological development that will advance the field.


  • King, W. L., Yates, C. F., Guo, J., Fleishman, S. M., Trexler, R. V., Centinari, M., Bell, T. H., and Eissenstat, D. M. 2021. The hierarchy of root branching order determines bacterial composition, microbial carrying capacity and microbial filtering. Communications biology 4(1):483.