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 unclear, and has implications for bioprospecting efforts. Using V3 region of bacterial 16S rRNA gene, we investigated the diversity patterns in total, uncultured bacterial endophyte communities of three rainforest plant species, comparing leaf, stem, and root endophytes, plus rhizosphere soil community employing MiSeq. 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. Both the lack of clustering in an NMDS ordination and an NMTD analysis suggested that bacterial endophyte OTUs were stochastically distributed amongst plant species and organs, and rhizosphere soil. Percentage turnover of OTUs samples was similar for plant individuals of the same species and of different species, at around 80-90%. Our results suggest that sampling of extra individuals, extra plant organs, extra species, or use of rhizosphere soil, might be about equally effective for obtaining new OTUs for culture. Our observations suggest that the plant endophyte community may be much more diverse, but less predictable, than would be expected from culturing efforts alone.