ORIGINAL RESEARCH article

Front. Microbiol.

Sec. Microbial Symbioses

Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1583797

This article is part of the Research TopicUnveiling Microbiome Interactions and Functions in Soil HotspotsView all 7 articles

Avocado Rhizosphere Community Profiling: White Root Rot and its Impact on Microbial Composition

Provisionally accepted
Phinda MagagulaPhinda Magagula1*Velushka SwartVelushka Swart1*Arista FourieArista Fourie2Alicia VermeulenAlicia Vermeulen1Johannes Harold NelsonJohannes Harold Nelson1Zelda van RooyenZelda van Rooyen3Noelani Van Den BergNoelani Van Den Berg1*
  • 1University of Pretoria, Pretoria, South Africa
  • 2Utrecht University, Utrecht, Netherlands, Netherlands
  • 3Westfalia Fruit, Westfalia iTeam, Polokwane, South Africa

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The avocado rhizosphere supports diverse microbial communities essential for plant health and defence against pathogens. This study aimed to investigate the impact of Dematophora necatrix, the causal agent of white root rot (WRR), on the microbial composition and soil physicochemical properties of infected and non-infected avocado trees in two South African orchards. Using ITS and 16S metabarcoding, we found that D. necatrix did not significantly alter overall microbial diversity but influenced relative abundance of specific taxa. In Orchard A, dominant bacterial genera included Sphingomonas, Rokubacteriales and Lysobacter, while Orchard B featured Sphingomonas and Acidothermus while beneficial microbes such as Streptomyces and Bacillus were enriched in WRR non-infected (WRR-N) soils. The fungal profiles revealed Trichoderma and Penicillium as potential biocontrol agents enriched in WRR-N soils. Furthermore, dual-culture assays demonstrated that Bacillus, Pseudomonas, Penicillium and Trichoderma isolates inhibited D. necatrix, highlighting their biocontrol potential. Key parameters, such as soil pH and iron (Fe), correlated strongly with microbial composition, suggesting they play an important role in pathogen resilience. These findings underscore the complexity of the avocado rhizosphere and its role in managing WRR, offering a foundation for developing integrated disease management strategies to enhance avocado productivity.

Keywords: Dematophora necatrix, metabarcoding, microbiome, soil physicochemical properties, Persea americana

Received: 26 Feb 2025; Accepted: 25 Apr 2025.

Copyright: © 2025 Magagula, Swart, Fourie, Vermeulen, Nelson, van Rooyen and Van Den Berg. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
Phinda Magagula, University of Pretoria, Pretoria, South Africa
Velushka Swart, University of Pretoria, Pretoria, South Africa
Noelani Van Den Berg, University of Pretoria, Pretoria, South Africa

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Supplementary Material