Abstract Description

The rhizosphere of medicinal plants harbors complex microbial consortia that influence plant health, soil ecology, and biotic interactions. Syzygium cordatum (waterberry), a medicinal plant in Limpopo Province, South Africa, interacts with the plant-parasitic nematode Xiphinema, but little is known about its rhizosphere microbiome or its association with nematode symbionts. Therefore, the aim of the study was to study the microbiome associated with Xiphinema isolated from the rizosphere of waterberry in Limpopo Province. Surface-sterilized Xiphinema specimens were subjected to DNA extraction using the ZymoBIOMICS™ DNA Miniprep Kit, and the bacterial 16S rDNA (V3–V4) region was amplified with primers 341f/785r by Inqaba Biotec. Sequencing was performed on the Illumina MiSeq platform, and data were processed in QIIME2, with taxonomy assigned via the Greengenes database. Soil physicochemical properties were also analyzed spectrophotometrically. The nematode species was identified using 28S rDNA, namely X. elongatum. After removing noise and aligning the forward and reverse reads, a total of 967 sequences, representing 280 Amplicon Sequence Variants (ASVs), were compiled from four replicated nematode samples. The microbiome associated with Xiphinema was diverse and dominated by Proteobacteria, Verrucomicrobia, Actinobacteria, and Firmicutes, with variations across samples. Importantly, Xiphinematobacter—a rare endosymbiont typically restricted to Xiphinema nematodes—was detected for the first time in the rhizosphere of a medicinal plant and in association with a nematode. The result of the soil analysis also revealed soil texture with significant effect on the Xiphinematobacter distribution in the soil. This discovery reveals a unique tripartite interaction among plant, nematode, and bacterium, suggesting possible roles in nematode fitness, nutrient cycling, and plant–microbe–nematode dynamics. These findings underscore the importance of studying rhizosphere microbiomes of medicinal plants as reservoirs of novel bacterial symbionts, with implications for ecology, biotechnology, and nematode management.