# Unlocking the microbiome of an extremophile plant: metagenomic insights into Calotropis procera’s endo-rhizosphere communities

## TL;DR

This study investigates the root-associated microbes of Calotropis procera, an invasive plant in Brazil, revealing how it shapes its microbiome in different environments.

## Contribution

The study provides new insights into host-driven microbiome regulation in an extremophile plant across contrasting ecosystems.

## Key findings

- Root endosphere was enriched with stress-tolerant bacteria and novel archaea.
- Host filtering was evident for bacteria and fungi but not archaea.
- Plant may selectively recruit or vertically transmit its microbiome.

## Abstract

This study explores the root-associated microbiome of Calotropis procera, a drought-adapted, invasive plant thriving in Brazil. We analyzed microbial communities from the root endosphere, rhizosphere, and adjacent soil in two contrasting ecosystems: Caatinga (semi-arid) and Restinga (coastal). Using 16S rDNA sequencing and shotgun metagenomics, we tested three hypotheses: (I) environmental specificity of the rhizospheric bacterial microbiome, (II) continuity of bacterial composition between bulk soil and rhizosphere, and (III) host-driven filtering of the endophytic microbiome. Despite differing soil conditions – more sodium in Restinga and higher organic carbon in Caatinga – microbial profiles in root compartments remained consistent. The root endosphere was enriched with stress-tolerant bacteria and novel archaea, while fungal genera included Fusarium and Puccinia. Results partially supported environmental specificity and showed moderate soil-rhizosphere continuity, with evidence of plant-mediated selection. Host filtering was evident for bacteria and fungi but not archaea. These data indicate a C. procera-mediated regulation of its root microbiome composition, whereby the plant may either selectively recruit specific taxa from prevalent soil microbial communities (e.g., through root exudates) or vertically transmit a conserved subset of its microbiome via seeds. Our study enhances understanding of the C. procera microbiome and its microbial interactions, identifying potential candidates for future biotechnological applications.

The online version contains supplementary material available at 10.1007/s11274-026-04902-4.