Sampling Microbiomes Associated with Different Plant Compartments

Methods Mol Biol. 2021;2232:23-29. doi: 10.1007/978-1-0716-1040-4_2.


The microbiome is known to influence plant fitness and differs significantly between plant compartments. To characterize the communities associated with different plant compartments, it is necessary to separate plant tissues in a manner that is suitable for microbiome analysis. Here, we describe a standardized protocol for sampling the microbiomes associated with bulk soil, the apical and basal ectorhizosphere, the apical and ectorhizosphere, the rhizome, pseudostem, and leaves of Musa spp. The approach can easily be modified for work with other plants.

Keywords: Bacteria; Fungi; Microbiome; Plant; Rhizosphere; Sampling; Sequencing.

MeSH terms

  • Microbiota / genetics*
  • Molecular Biology / methods*
  • Musa / genetics
  • Musa / microbiology
  • Plant Leaves / genetics
  • Plant Leaves / microbiology*
  • Plant Roots / genetics
  • Plant Roots / microbiology
  • Rhizome / genetics*
  • Rhizome / microbiology