In the nodule or on the nodule? The hidden Frankia biodiversity in Casuarina nodules across continents

Abstract

Abstract Background and Aims Actinorhizal root nodule symbioses are formed between a diverse group of mostly woody dicotyledonous plants and nitrogen-fixing soil Actinomycetota of the genus Frankia . Some of the most ecologically relevant actinorhizal plants are  Casuarina species, used widely in shelter belts and phytoremediation due to their high tolerance to abiotic stresses and ability to thrive on marginal soils. All sequenced Frankia strains isolated from Casuarina nodules using standard culture techniques show high sequence identity and belong to a single species, Frankia casuarinae . This lack of diversity in nodules is unusual in actinorhizal symbioses. We hypothesized that Casuarina nodules are colonized by Frankia strains that could not be cultivated and exhibit genome erosion. Methods To test this, we directly sequenced nodule metagenomes from four countries, followed by reconstruction of metagenome-assembled genomes (MAGs). Results Our findings show that the dominant Frankia genotypes in field samples were far more diverse than the isolated strains and included MAGs with substantial genome reduction – one having over 25% reduction compared to F. casuarinae . Notably, we observed erosion of two types of [NiFe] hydrogenases, a phenomenon linked to evolution toward obligate symbiosis in other Frankia groups. Conclusion These results indicate that potentially obligate symbionts may dominate nodules in nature but had gone undetected by conventional approaches. For applications such as reforestation or tsunami shelter belts, crushed, nodule-derived strains may offer superior ecological compatibility. We speculate that Frankia strains followed two different evolutionary trajectories; one, towards obligate symbiosis accompanied by strong genome erosion, and two, towards rhizosphere colonization involving limited genome erosion.