# Physiological, Transcriptomic, and Metabolomic Responses of Brachiaria decumbens Roots During Symbiosis Establishment with Piriformospora indica

## TL;DR

This study explores how the fungus Piriformospora indica interacts with Brachiaria decumbens roots, revealing how it boosts plant growth and stress resistance through complex biological changes.

## Contribution

The first comprehensive multi-omics analysis of the P. indica–B. decumbens symbiosis, revealing key pathways and regulatory mechanisms.

## Key findings

- Colonized roots showed reduced stress markers and increased growth-related compounds like IAA.
- Transcriptomic and metabolomic data revealed extensive reprogramming of root processes, including secondary metabolism and lipid biosynthesis.
- Phenylpropanoid biosynthesis and α-linolenic acid metabolism were consistently co-enriched across colonization stages.

## Abstract

Brachiaria decumbens is an economically important forage grass widely cultivated in tropical regions. Although the root endophytic fungus Piriformospora indica is well known for enhancing plant growth and stress tolerance in many species, its effects on B. decumbens have not been well characterized. This study investigated the potential benefits of P. indica for B. decumbens and the underlying mechanisms involved. Colonized roots exhibited reduced stress signatures and altered levels of endogenous growth-related compounds. By integrating transcriptomic and metabolomic profiling across multiple colonization stages, we found that P. indica triggers extensive reprogramming of root biological processes. Several candidate regulatory proteins and metabolites also appeared to coordinate these responses. This study provides the first comprehensive, system-level view of the P. indica–B. decumbens interaction, offering a valuable foundation for improving the growth and stress resistance of this important forage to enhance feed quality and promote more sustainable livestock production.

Brachiaria decumbens is a high-yielding forage grass of major economic value in tropical regions. The root endophytic fungus Piriformospora indica is widely recognized for promoting plant growth and stress tolerance, yet its effects on B. decumbens remain poorly characterized. Here, we profiled root responses to P. indica colonization at 10 days after inoculation (dais; early stage) and 20 dais (late stage) during symbiosis establishment. Colonization was confirmed by phenotypic and physiological assessments, with inoculated plants showing enhanced root growth; colonized roots exhibited higher activities of catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD), along with increased indole-3-acetic acid (IAA) levels, whereas malondialdehyde (MDA), jasmonic acid (JA), and the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) were reduced. Transcriptome and metabolomic profiling identified 1884 and 1077 differentially expressed genes (DEGs) and 2098 and 1509 differentially accumulated metabolites (DAMs) at 10 dais (Pi10d vs. CK10d) and 20 dais (Pi20d vs. CK20d), respectively, and 3355 DEGs and 2314 DAMs between stages (Pi20d vs. Pi10d). Functional enrichment highlighted key pathways related to secondary metabolism, carbohydrate metabolism, and lipid biosynthesis. Differentially expressed transcription factors spanned multiple families, including MYB, AP2/ERF, MADS-box, and bZIP, consistent with broad transcriptional reprogramming during symbiosis establishment. Integrative multi-omics analysis further highlighted phenylpropanoid biosynthesis and α-linolenic acid metabolism as consistently co-enriched pathways, suggesting coordinated shifts in gene expression and metabolite accumulation across colonization stages. Collectively, these results provide a multi-layered resource and a framework for mechanistic dissection of the P. indica–B. decumbens interaction.