Exploration of Hitherto-Uncultured Bacteria from the Rhizosphere

Leonard S. van Overbeek*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterAcademicpeer-review

3 Citations (Scopus)


Well-studied microorganisms commonly found in the rhizosphere are considered to play important roles in plant growth support. These microorganisms grow well in culture media as single-species cultures. However, the vast majority of the species present in soil and in the rhizosphere remain uncultured so far. Virtually nothing is known about their eventual interactions with plants and microorganisms indigenous to the rhizosphere and endosphere. Eventual occurrences of plant and microbe interactions may be studied with culture-independent technologies, like metagenomics. However, for experimentation in the rhizosphere, culturable representatives of hitherto uncultured are favored. This chapter focuses on Acidobacteria and Verrucomicrobia, two deep-rooting lineages in bacterial taxonomy because representatives of both phyla are fastidious in their growth. A few culturable representatives have been found so far in different natural ecosystems, including soils. Recently, culturable representatives of the two phyla were found in the rhizospheres of leek (Allium porrum) and potato (Solanum tuberosum), and their identities were different from the ones found in soils. Two representatives of Acidobacteria subdivision 8 (class Holophagae) were found in the leek rhizosphere, whereas in soil, representatives of subdivisions 1, 2, 3, 4, and 6 were found. Further, three taxonomically (based on 16S rRNA gene comparisons with public database sequences) distinguishable groups of Verrucomicrobia subdivision 1 were found in the rhizospheres of leek and potato, whereas in soil, culturable representatives of Verrucomicrobia subdivisions 2 and 3 (Spartobacteria) were found. Acidobacteria subdivision 8 and one particular subgroup of Verrucomicrobia subdivision 1 (whose genus was proposed as Candidatus genus Rhizophora) were shown to be present in the leek rhizosphere. Demonstrating rhizosphere competence will be the first step in the exploration of the roles of these groups in rhizospheres and endospheres of different plant species.

Original languageEnglish
Title of host publicationMolecular Microbial Ecology of the Rhizosphere
EditorsF.J. de Bruijn
PublisherJohn Wiley and Sons
Number of pages9
ISBN (Print)9781118296172
Publication statusPublished - 18 Mar 2013


  • Acidobacteria
  • Bacterial cultivation
  • Rhizosphere competence
  • Soil
  • Verrucomicrobia


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