INTERACTIONS OF SOIL- AND RHIZOSPHERE MICROBIOMES, PLANT NUTRITION,NITRIFICATION, AND NITROUS OXIDE PRODUCTION IN AGRICULTURAL CROPPING SYSTEMS

The planned research for this project encompasses three main objectives:1) Enrich representatives of globally-predominant soil AOA lineages in laboratory culture and determine genome sequences and gene expression patterns. We will use a new chemostat enrichment strategy developed in the Martens-Habbena lab to enrich 36-72 representative strains of globally predominant soil archaeal lineages, obtain high-quality genome sequences from metagenomes, and study their gene expression patterns under different growth conditions. These analyses will be conducted to address major knowledge gaps on the genomic inventory, environmental adaptation of AOA, and their potential for interactions with plant hosts.2) Identify and characterize associations of AOA with the rhizosphere and mycorrhizal fungi of a diverse range of agricultural crops and other land plants. We will sample a broad range of monocot and dicot crops and wild plants across south Florida, and determine abundance and composition of AOA, and fungi in bulk soil and rhizosphere samples by combination of quantitative PCR, amplicon sequencing of marker genes (amoA, 16SrRNA, fungal ITS), as well as microscopic analysis by fluorescence in situ hybridization (FISH). These experiments will yield a comprehensive inventory of the potential physical interactions of AOA, AMF, and plant roots across monocot and dicot plants.3) Characterize physical and chemical interactions between AOA, NOB, AMF, and plants in laboratory model systems. We will use FISH and scanning electron microscopy (SEM) to characterize conditions of development of physical associations AOA, NOB, AMF, and plant roots in agricultural crops, and determine N fluxes through the multi-domain network using stable isotope tracing techniques. These studies will reveal fundamental mechanistic insights into the chemistry of these multi-domain interactions.