Mycorrhizal control of microbial gene transcription and taxonomic composition in the rhizosphere and bulk soil

Sep 29, 2026

Interactions between arbuscular mycorrhizal fungi and soil microbial communities that support plant nutrient acquisition are still poorly characterized. This study tests how Rhizophagus irregularis regulates microbial mRNA transcription and microbial taxonomic composition in Zea mays mesocosms, comparing rhizosphere and bulk soil. Metatranscriptomics with 16S rRNA and ITS amplicon sequencing shows AMF change bacterial gene expression without shifting composition, while increasing fungal richness and evenness.

LanguageEnglish

CategoryResearch & Report

FormatPDF

Pages13

Reading Time33 min

AccessFree to download

Abstract

Introduction

The ISME Journal, 2025, 19(1), wraf282 [https://doi.org/10.1093/ismejo/wraf282](https://doi.org/10.1093/ismejo/wraf282) Advance access publication: 19 December 2025 Original Article Mycorrhizal control of microbial gene transcription and taxonomic composition in the rhizosphere and bulk soil Fergus Wright 1 , Stéphanie Grand 2 , Ian Sanders 1 ,‡, Ricardo Arraiano-Castilho 1 ,‡, * 1 Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Vaud, Switzerland 2 Institute of Earth Surface Dynamics, University of Lausanne, 1015, Vaud, Switzerland *Corresponding author. Department of Ecology and Evolution, University of Lausanne-Biophore, Lausanne 1015, Vaud, Switzerland. E-mail: [ricardo.m.castilho@gmail.com](ricardo.m.castilho@gmail.com) ‡Ian Sanders and Ricardo Arraiano Castilho contributed equally as senior authors of this work. Abstract Interactions between arbuscular mycorrhizal fungi (AMF) and soil microbial communities that support plant nutrient acquisition remain poorly understood. Here, we investigate how the model AMF species Rhizophagus irregularis influences microbial mRNA transcription and microbial taxonomic composition in rhizosphere and bulk soil compartments of Zea mays mesocosms. Using metatranscriptomic profiling alongside 16S rRNA and ITS amplicon sequencing, we show that AMF alter bacterial gene expression without shifting community composition and significantly increase fungal richness and evenness. We identify genotype-specific effects of AMF on microbial diversity and function and find that AMF colonisation stimulates microbial B-vitamin biosynthesis. We also link elevated plant leaf phosphorus levels under AMF colonisation with changes in root gene expression and increased abundance of AMF-stimulated rhizosphere bacterial taxa. These findings highlight the importance of feedback loops between plant, AMF and soil microorganisms and show how these interactions can contribute to increases in plant nutrient uptake. It is hoped these results will be useful for sustainable crop production and ecosystem regeneration through microbiome-informed management strategies. Keywords: soil microbiome; microbial interactions; AMF; bacteria; zea mays; rhizophagus irregularis; metatranscriptomics Introduction The relationships between plant roots and the soil microbiome play an important role in global nutrient cycling, plant health, and ecosystem stability [1] . A deeper understanding of these interactions is urgently needed to advance sustainable agricultural practices and restoration ecology in the face of anthropogenic damage. Arbuscular mycorrhizal fungi (AMF) are a group of obligate symbionts, ubiquitous in terrestrial ecosystems, that form mutualistic associations with the roots of over 70% of all known plant species [2] . These fungi provide plants with essential nutrients and water in exchange for an estimated 4%–20% of photosynthesised plant carbon [3] . Their hyphae extend out from the rhizosphere (i.e. soil in the direct vicinity of plant roots) into the bulk soil (i.e. the soil compartment inaccessible to plant roots) . In the rhizosphere, plant root exudates support a diverse community of microbes [4] . Whereas the bulk soil, without a direct supply of plant carbon, has lower rates of microbial activity and nutrient turnover [5], there is evidence to suggest that bulk soil microbial activity is enhanced in the presence of AMF hyphae [6–8] . This zone of interaction surrounding AMF hyphae and spores, referred to as the mycorrhizosphere, is increasingly recognised as a distinct ecological niche. It harbours mycorrhizal helper bacteria, plant growth promoting bacteria, facilitates microbial mobility along fungal hyphae, and receives organic inputs through exudates and decaying hyphal material [9 , 10] . Specific microbial communities are often found strictly associated with AMF mycelia, and recently it has been shown bacteria from these communities can colonise the r

FAQs

What is the main research question of this study?

How Rhizophagus irregularis influences microbial mRNA transcription and microbial taxonomic composition in rhizosphere and bulk soil compartments of Zea mays mesocosms.

Which experimental approaches are used to assess microbial activity and community structure?

Metatranscriptomic profiling is used alongside 16S rRNA and ITS amplicon sequencing to measure gene transcription and taxonomic composition.

What key effect does AMF have on microbes?

AMF alters bacterial gene expression without shifting community composition and increases fungal richness and evenness.

Sep 29, 2026

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