Helotiales fungi as potential nutritional partners for non-mycorrhizal plants: a machine learning and experimental approach
4 affiliations
- 1Université Lyon 1, CNRS, INRAE, LEM, UMR 5557, UMR 1418, Villeurbanne, France.
- 2Université Bourgogne Europe, Institut Agro Dijon, INRAE, UMR Agroécologie, Dijon, France.
- 3Institut Universitaire de France, Paris, France.
- 4Université Lyon 1, CNRS, INRAE, LEM, UMR 5557, UMR 1418, Villeurbanne, France. [email protected].
Abstract
Background: Most land plants benefit from the ancestral arbuscular mycorrhizal (AM) symbiosis for phosphorus (P) acquisition. However, several plant lineages have independently lost this symbiosis, raising fundamental questions about how these ‘non-mycorrhizal’ plants meet their nutritional requirements without this crucial partnership. Results: Comparative genomic analyses confirmed that Cyperaceae, Caryophyllaceae, and Brassicaceae lack genes essential for AM symbiosis, indicating that these lineages independently abandoned this association 90–122 million years ago. Field surveys of 42 wild populations across seven sites revealed that non-mycorrhizal plants generally maintain shoot P levels comparable to those in AM neighbors. To identify fungal taxa potentially associated with P nutrition in non-mycorrhizal plants, we applied a machine-learning approach to predict plant P-accumulation from root microbiome composition. The model explained substantial variance in plant P-accumulation (57–69%), and identified 85 fungal taxa as key predictors of shoot P-accumulation, predominantly belonging to the Helotiales (28%) and Pleosporales (23%) orders. Experimental validation of two phylogenetically distant Helotiales lineages (Tetracladium maxilliforme OTU29 and Helotiales sp. OTU7), using isotopic tracing, demonstrated their capacity to enhance plant growth and transfer P (and N) to their native non-mycorrhizal hosts under P-limiting conditions. Conclusions: Our findings suggest that non-mycorrhizal plants engage in nutritional partnerships with diverse Helotiales lineages that could collectively contribute to their mineral nutrition. However, given the widespread distribution of these Helotiales fungi, including in roots of AM plants, they may play a broader role in plant nutrition, i.e. also in mycorrhizal hosts. This study provides proof of concept for a novel framework integrating machine-learning predictions with experimental validation to identify functionally important microbial partnerships in natural plant communities.
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BibTeX
@article{bruyant2026helotiales,
title = {{Helotiales fungi as potential nutritional partners for non-mycorrhizal plants: a machine learning and experimental approach}},
author = {Pauline Bruyant and Lauren M Gillespie and Jeanne Doré and Pierre Emmanuel Courty and Yvan Moënne-Loccoz and Juliana Almario},
journal = {Microbiome},
year = {2026},
month = aug,
doi = {10.1186/s40168-026-02484-9},
url = {https://hal.science/hal-05828860v1},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Helotiales fungi as potential nutritional partners for non-mycorrhizal plants: a machine learning and experimental approach
AU - Pauline Bruyant
AU - Lauren M Gillespie
AU - Jeanne Doré
AU - Pierre Emmanuel Courty
AU - Yvan Moënne-Loccoz
AU - Juliana Almario
PY - 2026
DA - 2026/08/04
JO - Microbiome
DO - 10.1186/s40168-026-02484-9
UR - https://hal.science/hal-05828860v1
AB - Background: Most land plants benefit from the ancestral arbuscular mycorrhizal (AM) symbiosis for phosphorus (P) acquisition. However, several plant lineages have independently lost this symbiosis, raising fundamental questions about how these ‘non-mycorrhizal’ plants meet their nutritional requirements without this crucial partnership. Results: Comparative genomic analyses confirmed that Cyperaceae, Caryophyllaceae, and Brassicaceae lack genes essential for AM symbiosis, indicating that these lineages independently abandoned this association 90–122 million years ago. Field surveys of 42 wild populations across seven sites revealed that non-mycorrhizal plants generally maintain shoot P levels comparable to those in AM neighbors. To identify fungal taxa potentially associated with P nutrition in non-mycorrhizal plants, we applied a machine-learning approach to predict plant P-accumulation from root microbiome composition. The model explained substantial variance in plant P-accumulation (57–69%), and identified 85 fungal taxa as key predictors of shoot P-accumulation, predominantly belonging to the Helotiales (28%) and Pleosporales (23%) orders. Experimental validation of two phylogenetically distant Helotiales lineages (Tetracladium maxilliforme OTU29 and Helotiales sp. OTU7), using isotopic tracing, demonstrated their capacity to enhance plant growth and transfer P (and N) to their native non-mycorrhizal hosts under P-limiting conditions. Conclusions: Our findings suggest that non-mycorrhizal plants engage in nutritional partnerships with diverse Helotiales lineages that could collectively contribute to their mineral nutrition. However, given the widespread distribution of these Helotiales fungi, including in roots of AM plants, they may play a broader role in plant nutrition, i.e. also in mycorrhizal hosts. This study provides proof of concept for a novel framework integrating machine-learning predictions with experimental validation to identify functionally important microbial partnerships in natural plant communities.
SN - 2049-2618
ER -