Alternate states dominate the bacterial endophyte community of a tropical tree

Little is known about how bacterial endophyte communities may vary from one tree to another of the same species. We sampled nine standardized replicates from the green stems of an ethnomedicinal tropical tree, Santiria apiculata, in a Malaysian rainforest, to investigate endophyte variation from one plant to another. DNA was extracted axenically from the inner stem, and PCR-amplified for the 16s rRNA gene, followed by Illumina HiSeq sequencing. For comparison, the rhizosphere soil of the same trees was also sampled, and the 16s rRNA genes sequenced. Santiria stems contained a diverse community of more than 1100 Operational Taxonomic Units (OTUs), which partitioned clearly into two community types. One community (here dubbed ‘rhizosphere-like’) resembled the rhizosphere soil in its major OTUs, while the other (‘rhizosphere-unlike’) was more distinct and dominated by the genus Bacillus. Nestedness analysis confirmed that both the rhizosphere-like and the rhizosphere-unlike stem communities tended to be a subset of the rhizosphere community. The β-nearest taxon index (βNTI) analysis revealed that the stem communities were dominated by stochastic processes, whereas deterministic processes with homogenizing selection dominated the rhizosphere soil. It appears that the endophyte community in Santiria may be dominated by colonization and priority effects, and it may derive from the rhizosphere community. The potential for alternate steady states within the endophyte community should be considered as a possible influence on plant growth and ecology.