Extensive Overlap of Tropical Rainforest Bacterial Endophytes between Soil, Plant Parts, and Plant Species


The extent to which distinct bacterial endophyte communities occur between different plant organs and species is poorly known and has implications for bioprospecting efforts. Using the V3 region of the bacterial 16S ribosomal RNA (rRNA) gene, we investigated the diversity patterns of bacterial endophyte communities of three rainforest plant species, comparing leaf, stem, and root endophytes plus rhizosphere soil community. There was extensive overlap in bacterial communities between plant organs, between replicate plants of the same species, between plant species, and between plant organ and rhizosphere soil, with no consistent clustering by compartment or host plant species. The non-metric multidimensional scaling (NMDS) analysis highlighted an extensively overlapping bacterial community structure, and the β-nearest taxon index (βNTI) analysis revealed dominance of stochastic processes in community assembly, suggesting that bacterial endophyte operational taxonomic units (OTUs) were randomly distributed among plant species and organs and rhizosphere soil. Percentage turnover of OTUs within pairs of samples was similar both for plant individuals of the same species and of different species at around 80–90%. Our results suggest that sampling extra individuals, extra plant organs, extra species, or use of rhizosphere soil, might be about equally effective for obtaining new OTUs for culture. These observations suggest that the plant endophyte community may be much more diverse, but less predictable, than would be expected from culturing efforts alone.

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We are grateful to the University Kebangsaan University Forest Reserve and Herbarium staff. We thank Muhanna Al-Shabanni, Aishah Ismail, Radhiah Binti Khairon, and Nur Faizah Abu Bakar, for their assistance during sampling. We thank Dr. Binu Tripathi for his contribution on the beta-NTI analysis. This work was funded by the Universiti Kebangsaan Malaysia Research Grant (GUP 2015-042).

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Correspondence to Noraziah M. Zin or Jonathan M. Adams.

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Haruna, E., Zin, N.M., Kerfahi, D. et al. Extensive Overlap of Tropical Rainforest Bacterial Endophytes between Soil, Plant Parts, and Plant Species. Microb Ecol 75, 88–103 (2018). https://doi.org/10.1007/s00248-017-1002-2

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  • Endophytes
  • Metagenetics
  • Rhizospheric bacteria
  • Stochastic assembly
  • Tropical rainforest plants