Moenne-Loccoz, Y. | 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

A multidisciplinary on-farm survey of maize-bean intercropping shows that revival of traditionalagricultural systems requires careful consideration of partner varieties and agronomic practices.

O_LICereal-legume intercropping is a promising strategy for sustainable agroecosystems. The traditional intercropping of maize and bean is experiencing a revival in some modern agricultural settings, such as in southwestern France, where maize hybrids are intercropped with the commercialized Tarbais bean. We conducted on-farm surveys and a field assay to address the following questions: How does the cropping system impact yield, nutrient uptake, and rhizosphere bacterial assemblages? Do positive or negative interactions between maize and beans dominate in intercropping? What is the effect of intercropping on plant transcriptomics? C_LIO_LIWe recorded farming practices, conducted yield and nutrient measurements, and characterized soil bacterial assemblages to compare sole-cropped maize and beans with intercropped plants. A controlled field assay was also established to extend this comparison to plant gene expression differences. C_LIO_LIIntercropping was associated with a trend towards increased bacterial diversity. The cropping system significantly influenced agronomic traits, with frequent farm-by-cropping system interactions underscoring the critical role of farming practices. Competition dominated maize-bean intercropping, with 34 negative correlations among the 47 significant ones between maize and bean traits. This competition affected yield and nutrition, but primarily impacted beans, which produced fewer but bigger/heavier seeds. Transcriptomic results concurred with these findings, revealing no differentially expressed genes in maize but 5,070 in beans under competition. C_LIO_LIOverall, our findings suggest that beneficial interactions between the two crops are hindered under current field conditions, underscoring the importance of carefully considering partner varieties and farming practices to revive traditional agricultural systems. C_LI Societal Impact StatementCereal-legume intercropping is a promising strategy for sustainable agroecosystems that leverages the biological complementarities between plant species, reducing the need for chemical inputs while enhancing field biodiversity. Here, we focused on maize-bean intercropping, which is experiencing a revival in modern conventional agricultural settings. We found a trend towards an increased soil bacterial diversity in intercropping. However, competition between the two crops dominated and primarily impacted yield and gene expression in beans. Despite lower yield, bean seeds exhibited greater size. Our study indicates that implementing variety selection of both species and adapting farming practices is essential to fully harness the potential of intercropping.

plant biology↗