Seasonal Dynamics of Root-Associated Fungal Microbiomes in Annual and Perennial Halophytes

Abstract Halophytes host diverse fungal communities that can influence plant fitness and whole ecosystem functioning. Despite their importance, general knowledge on the root-associated endophytic fungal microbiomes of halophytes is limited to few species. In our study, we investigated fungal microbiomes associated with roots of two annual ( Salicornia procumbens and Suaeda maritima , both Amaranthaceae) and two perennial ( Atriplex portulacoides , Amaranthaceae, and Puccinellia maritima , Poaceae) halophytes using amplicon sequencing of nuclear ribosomal DNA. We investigated the fungal communities with respect to host life history strategy, host identity and seasonality. Moreover, we investigated species-specific root anatomical traits, which could potentially influence microbiome assembly. Overall, our results revealed a strong effect of host identity on fungal microbiomes. Furthermore, variation in microbiome composition throughout seasons seems to be a species-specific process which does not depend on plant life history strategy. We observed higher richness, diversity and evenness in samples of the grass P. maritima compared to the three Amaranthaceae, particularly those collected in autumn. Species-specific root anatomical traits, such as larger roots cells in P. maritima go along with the higher diversity. The fungal orders Pleosporales and Xylariales were, in general, the most common endophytes in all species, but Glomeromycota was also detected in roots of P. maritima in summer. Overall, our study provides a better understanding on the dynamics of fungal microbiome assembly in roots of halophytes throughout seasons emphasizing the importance of host identity on fungal microbiome assembly.