Drivers of Microbial Community Composition in Crops: A Focus on Lettuce

Abstract

Understanding interactions between crops and their associated microbiomes is important for improving plant resilience, productivity, and sustainability, particularly in the face of climate change in resource-limited agricultural systems. In this dissertation, I investigated the diversity, composition, and functional potential of microbial communities associated with lettuce (Lactuca sativa L.), with a specific focus on foliar and root-associated fungi and bacteria across diverse genotypes, among species of Lactuca, across various cultivation environments, and from the perspectives of amplicon sequencing (metabarcoding), metagenomics, and genome characterization. In the first study, I used metabarcoding to characterize the endophytic microbiomes of 12 lettuce genotypes grown under desert agriculture conditions. I found that microbial community composition differed among lettuce genotypes and was associated with root morphology and leaf nutrient profiles, particularly zinc. These findings suggest a potential link between host traits and microbial community structure, with implications for breeding programs aiming to enhance crop nutrition and resilience via microbiome selection. In the second study, I compared foliar fungal communities across 98 accessions of wild and cultivated Lactuca species grown under controlled greenhouse conditions. I accessed published genomes of the plants themselves, mining those datasets for fungal genomic signatures. This metagenomic-based approach revealed that wild relatives consistently hosted more diverse and compositionally distinct fungal communities relative to L. sativa. These differences were independent of geographic origin and were associated with reduced pest and disease susceptibility. My results thus support the broad hypothesis that domestication may have led to the loss of beneficial microbial associations, or the tools for establishing them, and underscore the potential of microbiome-informed breeding and rewilding strategies to enhance crop health.The third study focused on the isolation and genomic characterization of five fungal endophytes from a wild relative of cultivated lettuce: Lactuca serriola, which grows as a roadside- and field weed in southern Arizona. These isolates, which represented common fungi from L. serriola in dryland conditions, were selected based on successful culturing and representation of distinct morphotypes. I assembled and annotated draft genomes of endophytic strains of Alternaria postmessia, Alternaria alternata (two strains), Fusarium falciforme, and Aspergillus terreus. These data represent foundational genomic resources for future research into the functional roles and evolutionary relationships of endophytes in wild relatives of crops, which may be transferred to crop plants as biostimulants, bioprotectants, or biocontrol agents. In the fourth study, I sequenced and analyzed genomes of nine fungal isolates from field-grown lettuce to assess the biosynthetic potential of their secondary metabolite pathways and carbohydrate-active enzymes. These isolates were selected based on successful culturing, taxonomic diversity, and representation of both epiphytic and endophytic lifestyles. While initial hypotheses predicted reduced biosynthetic gene cluster (BGC) richness in lettuce-associated fungi due to selective pressures associated with lettuce breeding and cultivation, comparative analyses revealed variation across isolates and showed that species identity, rather than host type or lifestyle, was the primary predictor of BGC count. Several Alternaria isolates harbored conserved polyketide clusters, including those associated with alternariol and T4HN biosynthesis, which showed 100% similarity to experimentally validated entries in the MiBIG database. Although BiG-SCAPE identified gene cluster families (GCFs) across the dataset, these reference-matching clusters were not always grouped, reflecting methodological differences in how the tools assess similarity. These findings challenge assumptions about host-driven genome streamlining in crop-associated fungi and instead highlight the importance of species-level context in shaping biosynthetic and functional diversity. Together, these four studies provide an integrated view of how plant genotype, domestication status, and environmental conditions shape the structure and functional potential of the lettuce microbiome. This work advances understanding of plant-microbe interactions in arid agroecosystems and contributes to emerging frameworks for microbiome-assisted breeding, sustainable crop management, and functional trait discovery in plant-associated microbes.