Rhizosphere microbiome co-occurrence network analysis across a tomato domestication gradient

Authors: DIXON, MARY - Colorado State University; AFKAIRIN, ANTISAR - Colorado State University; Manter, Daniel; VIVANCO, JORGE - Colorado State University

Submitted to: Microorganisms
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/22/2024
Publication Date: 8/24/2024
Citation: Dixon, M.M., Afkairin, A.S., Manter, D.K., Vivanco, J.M. 2024. Rhizosphere microbiome co-occurrence network analysis across a tomato domestication gradient. Microorganisms. 12(9). Article e1756. https://doi.org/10.3390/microorganisms12091756.
DOI: https://doi.org/10.3390/microorganisms12091756

Interpretive Summary: Plant-microbial interactions are critical for P solubility and plant acquisition, and plant domestication can influence the microbial species involved in these interactions and their success. This study used co-occurrence networks to identify the microbial associations with tomato accessions across a domestication gradient under high and low P fertilization. Each tomato accession rhizosphere contained a unique complex of microbes which differed in their ability to solubilize P in the soil. This work is a key step in furthering our understanding of how plant domestication and breeding influences plant-microbe interactions and nutrient acquisition.

Technical Abstract: When plant available phosphorus (P) is lost from soil solution, it often accumulates in the soil as a pool of unavailable legacy P. To acquire legacy P, plants employ recovery strategies, such as forming associations with soil microbes. However, the degree to which plants rely on microbial associations for this purpose varies with crop domestication and subsequent breeding. Here, by generating microbial co-occurrence networks, we sought to explore rhizosphere bacterial interactions in low-P conditions and how they change with tomato domestication and breeding. We grew wild tomato, traditional tomato (developed circa 1900), and modern tomato (developed circa 2020) in high-P and low-P soil throughout their vegetative developmental stage. Co-occurrence network analysis revealed that as tomato progressed along stages of domestication, the rhizosphere microbiome complexity changed, wherein there was a decline in complexity with traditional tomato and subsequent increase in network complexity with modern tomato. Further, traditional tomato showcased a unique rhizosphere by harboring keystone taxa (Peribacillus muralis) capable of performing many beneficial soil functions. By illustrating these changing patterns of network complexity in the tomato rhizosphere microbiome, we can further understand how plant domestication and breeding has shaped plant-microbe interactions.