Box 1 Recommended improvements in current methodological practices and areas for methodological advancements for root sampling and rhizosphere removal methods in the rhizosphere microbiome research field

Recommendations for root and rhizosphere sampling approaches

1. Match sampling schemes to research questions

  Pooled sampling net impacts on/of the rhizosphere microbiome; encompassing and coarse rhizosphere microbiome characterization

  Separated sampling functional root-microbe relationships; targeted and variation-minimized rhizosphere microbiome characterization

2. Select functionally-explicit methods based on traits with putative functional linkage (e.g., root branching order)

3. Report how and why root sampling and rhizosphere removal methodologies were selected

4. Report in discussion how root sampling schemes may have influenced interpretation of results (e.g., false negatives)

Research priorities for methodological advancement

1. Simplified exudate measurement methods

2. Identification of root traits with functional links to rhizosphere microbiomes

3. Consequences of variable rhizosphere removal methods for rhizosphere microbiome characterization

4. Standardized methods and language for characterizing gradients within the rhizosphere and/or regions of the rhizosphere