The chemical landscape of leaves as a driver for microbial community structure and metabolic interactions

The intercellular space of leaves (e.g., the apoplast) is critical for plants, functioning in nutrient, water and photosynthate transport as well as cell homeostasis. It is also where important microbiota colonize, presumably by utilizing host resources. This environment is truly dynamic; the fluctuation of nutrients and a large array of defense molecules suggests it is a challenging niche for microbial colonization, where microbe-microbe interactions may play an important role. Thus, linking leaf resources to assembly of the leaf microbial community would have major impacts on understanding plant-microbe interactions. In the frame of this thesis, an infiltration-centrifugation method was optimized to recover apoplastic fluid wash (AFW) from leaves of diverse plant species. Closely related Flaveria species could be differentiated based on the AFW metabolomic profile, specifically on the quantities of valuable amino acids that are costly for microorganisms to synthesize. The AFW could also be used to assess bacterial diversity in the leaf apoplast. Amplicon sequencing analyses revealed that more alpha diversity could be recovered from AFW samples than from crushed leaves (the conventional method to assess leaf microbial diversity) and that beta diversity differences were clearer when using AFW. The optimized method was then used to track diurnal oscillations of metabolites and microbial communities in leaves of three Flaveria species with different carbon fixing strategies. Although additional work is needed to overcome low bacterial reads at some time points, the results suggested that enrichment of taxa over the day corresponded with increasing metabolite complexity of the AFW in a species-dependent manner. Considering the differences found in levels of amino acids between F. robusta and F. trinervia, an in vitro assay was established. Leaf bacteria from these two species were enriched with either sucrose as a sole carbon source or with addition of amino acids.