Life outside of the roots: using RNA-seq and proteomics to investigate the mechanisms underlying AMF growth in soil and their promotion of soil quality
Plant Cultivation, Plant Nutrition, Agricultural Technology
Final Report Abstract
Arbuscular mycorrhizal fungi (AMF) are important symbionts of plants, supplying mineral nutrients and providing various environmental services. However, the metabolic growth of their hyphae outside host plant roots is still largely unknown. This project aimed to elucidate the metabolism of Rhizophagus irregularis and Acaulospora longula in artificial soil environments. Significant methodological challenges, such as low fungal biomass, hindered comprehensive molecular analyses. In our first (originally proposed) experiment, we observed AMF hyphae in the samples but obtained low RNA and protein quantities, likely due to binding to the artificial soil clays and cellulose. To address these challenges, we optimized our methods and designed new experiments, including in vitro cultures, to enhance fungal biomass and improve analytical conditions. Initially, we planned a single experiment using artificial soils, but due to unforeseen challenges, we expanded to nine experiments. While soil system experiments yielded limited transcript and protein data, in vitro cultures revealed a significant number of expressed proteins. The soil experiments showed proteome changes influenced by iron oxides, indicating increased expression of genes related to lipid and carbohydrate metabolism. The in vitro culture experiment identified over 917 proteins associated with hyphal growth, making it the most extensive AMF proteome to date. The presence of the clay kaolinite also changed the expression of proteins, including many proteins with unknown functions. We are currently expressing and characterizing some of these proteins to better understand their structure and potential roles. Despite the project difficulties, our research made significant contributions by testing various growth systems, optimizing analytical techniques, and presenting the most extensive AMF proteome to date. Our findings highlighted the complexity of accessing AMF transcripts and proteomes, emphasizing the need for advancements in methodological tools. At the same time, this project has advanced our understanding of AMF metabolism and provided valuable insights into the proteomic profile of these fungi in response to soil components.
