Bruyant, P. | bioRxiv Science

bioRxiv2026

Helotiales fungi as potential nutritional partners for non-mycorrhizal plants: a machine learning and experimental approach

BackgroundMost land plants depend on 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. ResultsComparative 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 while non-mycorrhizal plants generally maintain shoot P levels comparable to those in AM neighbors, lower shoot P levels can be observed in low P soils. 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. ConclusionsOur 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.

microbiology↗

bioRxiv2024

Needle in a haystack: culturing plant-beneficial Helotiales lineages from plant roots

Root-associated Helotiales fungi are increasingly recognized as beneficial fungal partners promoting plant growth under nutrient-limited conditions, particularly in non-mycorrhizal hosts, lacking the ancestral arbuscular mycorrhizal symbiosis. However, the ecology of these fungi is still cryptic as relatively few lineages have been successfully cultivated from roots for further study. Here, we attempted the mass isolation of root endophytic fungi to evaluate the recovery of known plant-beneficial Helotiales lineages using a tailored culture-based approach. We sampled six wild non-mycorrhizal species from the Brassicaceae, Caryophyllaceae, and Cyperaceae, growing in nutrient-limited alpine soils. We isolated 602 root endophytes and compared this culturable diversity with the one observed via fungal ITS2 metabarcoding. Metabarcoding revealed that Helotiales taxa dominated the fungal communities, with 43% of these detected taxa also represented in our collection. Accordingly, most root endophytes in our collection (53%) were Helotiales. These isolates, some with P solubilisation potential, belonged primarily to three Helotialean clades and were phylogenetically related to plant growth-promoting or mycorrhizal-like strains. This analysis highlights that roots of alpine non-mycorrhizal plants are reservoirs of plant-beneficial root-endophytic Helotiales, and the isolates obtained are a promising resource to explore the plant-beneficial mechanisms and ecological traits of these fungi.

microbiology↗