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

Abstract

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.

Draft Genome Sequence of Bacillus pumilus SCAL1, an Endophytic Heat-Tolerant Plant Growth-Promoting Bacterium

“… Bacillus pumilus forms endospores and naturally occurs in roots, leaves, seeds, stems, needles, twigs, and bark of various plant species ( 1 – 4 ). In this context, plant growth-promoting bacteria improve plant growth either (i) directly, through production of phytohormones, ammonia, siderophores, or enzymes (ACC deaminase and catalase), or by providing nitrogen, phosphate, or iron, or (ii) indirectly, by antagonistic mechanisms which protect plants from pathogens and insects.…”

“…After sample collection, surface sterilization was done ( 1 ). Strain taxonomy was based on 16S rRNA gene sequencing ( 2 , 7 , 9 ).…”

The first Taxus rhizosphere microbiome revealed by shotgun metagenomic sequencing

“…A paclitaxel‐producing fungal endophyte, Paraconiothyrium SSM001 , can migrate to pathogen entry points including branch cracks. Extensive overlap of rainforest bacterial endophytes between rhizosphere soil, plant parts, and plant species was also revealed . Environmental stress and elicitors enhance paclitaxel production of endophytic strains .…”

Draft genome sequence of an endophytic bacterium, Paenibacillus tyrfis strain SUK123, isolated from Santiria apiculata stem

“…The endophytic Paenibacillus tyrfis , strain SUK123, was isolated from the Santiria apiculata stem located at the Universiti Kebangsaan Malaysia forest reserve, whilst screening for endophytes with antimicrobial potential against ESKAPE ( Enterococcus faecium , Staphylococcus aureus , Klebsiella pneumoniae , Acinetobacter baumannii , Pseudomonas aeruginosa , and Enterobacter species ) pathogens. After sample collection, the stem surface was sterilized to avoid surface-bound epiphytes as described previously [11] . The sterilized stem was cut into a 2 cm section and plated on water agar plate medium from where SUK123 (an antibiotic producing bacterium) was isolated.…”