The phyllosphere of Nigerian medicinal plants, Euphorbia lateriflora and Ficus thonningii is inhabited by a specific microbiota

Abstract

The microbiota of medicinal plants is known to be highly specific and can contribute to medicinal activity. However, the majority of plant species have not yet been studied. Here, we investigated the phyllosphere composition of two common Nigerian medicinal plants, Euphorbia lateriflora and Ficus thonningii, by a polyphasic approach combining analyses of metagenomic DNA and isolates. Microbial abundance estimated via qPCR using specific marker gene primers showed that all leaf samples were densely colonized, with up to 10⁸ per gram of leaf, with higher bacterial and fungal abundance than Archaea. While no statistically significant differences between both plant species were found for abundance, amplicon sequencing of 16S rRNA and ITS genes revealed distinct microbiota compositions. Only seven of the 27 genera isolated were represented on both plants, e.g. dominant Sphingomonas spp., and numerous members of Xanthomonadaceae and Enterobacteriaceae. The most dominant fungal families on both plants were Cladosporiaceae, Mycosphaerellaceae and Trichosphaeriaceae. In addition, 225 plant-specific isolates were identified, with Pseudomonadota and Enterobacteriaceae being dominant. Interestingly, 29 isolates are likely species previously unknown, and 14 of these belong to Burkholderiales. However, a high proportion, 56% and 40% of the isolates from E. lateriflora and F. thonningii, respectively, were characterized as various Escherichia coli. The growth of most of the bacterial isolates was not influenced by extractable secondary metabolites of plants. Our results suggest that a specific and diverse microbial community inhabits the leaves of both E. lateriflora and F. thonningii, including potentially new species and producers of antimicrobials.

Keywords: Euphorbia lateriflora; Ficus thonningii; Antimicrobials; Medicinal plants; Phyllosphere.

Figure 1

qPCR estimation of the abundance of archaeal 16S rRNA, bacterial 16S rRNA and fungal ITS genes in the community DNA of E. lateriflora and F. thonningii. Gene copies were normalized to the weight of DNA extraction starting plant material.

Figure 2

16S rRNA- and ITS-based bacterial and fungal diversity, composition and abundance in the phyllosphere of E. lateriflora and F. thonningii. Sample labels EL1 and EL2 represent technical replicates of E. lateriflora, while FT1 and FT2 represent technical replicates of F. thonningii.

Figure 3

16S rRNA gene sequence-based phylogeny of cultured isolates from E. lateriflora and F. thonningiiI. Metadata bars represent host plant and phyla, order and family classification.

Figure 4

Distribution of type 1 and type 2 Escherichia spp. on E. lateriflora and F. thonningii.

Figure 5

16S rRNA gene sequence-based phylogeny of selected cultured strains representing the different OTUs showing susceptibility to ethyl acetate extracts of E. lateriflora and F. thonningii. The letters preceding organism names in the tree represents the plant origin of isolate; EL and FT for E. lateriflora and F. thonningii respectively, while the numerals represent isolate numbers. Associated metadata are source plant, phyla and order taxonomy, minimum inhibitory concentrations of E. lateriflora and F. thonningii extracts and chlorocresol.