The Good, the Bad, and the Ugly: Describing and Evaluating the Pathobiome of Solanum lycopersicum

Traditional pathology models disease as the intersection of a pathogen, a favorable environment, and a host, neglecting the influence of a plant’s microbiome in its response to infection. During the summer of 2024, the Restrepo lab isolated fungi and bacteria from diseased tomato and pigweed plants at the Homer C. Thompson Vegetable Research Farm in Freeville, NY. This project complements the lab’s effort to describe the pigweed pathobiome, or “sick” microbiome, by characterizing the pathobiome of nearby tomatoes. To do this, tomato fungal and bacterial isolates were fully identified, and their pathogenicity was evaluated. The isolates were characterized by morphology–shape, color, texture, and form–and by PCR amplification of the 16S ribosomal RNA gene (bacteria) and the nuclear internal transcribed spacer region (fungi). Following Sanger sequencing, BLAST searches were performed to determine the genus of each strain. Bacterial isolates from the genus Pseudomonas and fungal isolates from Alternaria, Epicoccum, and Fusarium were identified. Based on similarities between the identified genera in tomato and pigweed, as well as literature on their potential pathogenicity, selected isolates were characterized to the species level. Additionally, detached leaf inoculations were performed to assess the pathogenicity of the isolates in tomato. Ultimately, investigating the tomato pathobiome offers insight into a complex model of disease resilience that mandates both collaboration and competition among a dynamic collection of microorganisms.

The summer of 2025, through the Plant Genome REU hosted by the Boyce Thompson Institute, I was extremely lucky to work in Dr. Silvia Restrepo’s lab under the mentorship of postdoctoral associate Dr. Juliana Gonzalez-Tobon. Under Juliana’s guidance, I developed key skills in microbiology, such as culturing bacterial and fungal isolates, as well as the vocabulary to describe the isolates. To classify the isolates on a molecular as well as a morphological basis, Juliana and Silvia extended my understanding of PCR amplification and Sanger sequencing. With research technician Ivan Delgado, I learned to construct and analyze high-resolution phylogenies, which allowed me to draw species-level inferences. The Restrepo lab allowed me to grow not only as a microbiologist and as a molecular biologist, but also as a member of a team. I am grateful to have worked closely with each lab member, whether isolating fungi and bacteria from leaves, making microcultures for fungi, or weeding and sampling in the field. In a non-lab setting, too, Silvia and Juliana challenged their team of researchers to collaborate, facilitating a planning session for a grant proposal at Mann Library and discussing ideas for an upcoming epigenetics project with me and Ivan. I learned that an environment most conducive to critical thinking includes even the least experienced of voices–and so I was never afraid to ask questions. The broader community at BTI also welcomed my voice, whether during weekly seminars, the bioinformatics course taught by Adrian Powell, or the postgraduate mingling session organized by REU coordinators Delanie Sickler and Megan Truesdail. As I begin my junior year at Colby College and prepare to apply to PhD programs in either molecular biology or biochemistry, I hope to pursue research environments much like the Restrepo lab that are at once caring, collaborative, and challenging.