Bacterial diversity and composition on the rinds of specific melon cultivars and hybrids from across different growing regions in the United States

Authors: GOFORTH, MADISON - UNIVERSITY OF ARIZONA; OBERGH, VICTORIA - UNIVERSITY OF ARIZONA; PARK, RICHARD - UNIVERSITY OF ARIZONA; PORCHAS, MARTIN - UNIVERSITY OF ARIZONA; CROSBY, KEVIN - TEXAS A&M UNIVERSITY; JIFON, JOHN - TEXAS A&M UNIVERSITY; RAVISHANKAR, SADHANA - UNIVERSITY OF ARIZONA; BRIERLEY, PAUL - UNIVERSITY OF ARIZONA; LESKOVAR, DANIEL - TEXAS A&M UNIVERSITY; TURINI, THOMAS - UNIVERSITY OF CALIFORNIA AGRICULTURE AND NATURAL RESOURCES (UCANR); SCHULTHEIS, JONATHAN - NORTH CAROLINA STATE UNIVERSITY; COOLONG, TIMOTHY - UNIVERSITY OF GEORGIA; MILLER, RHONDA - TEXAS A&M UNIVERSITY; KOIWA, HISASHI - TEXAS A&M UNIVERSITY; PATIL, BHIMANAGOUDA - TEXAS A&M UNIVERSITY; COOPER, MARGARETHE - UNIVERSITY OF ARIZONA; Huynh, Steven; Parker, Craig; GUAN, WENJING - TEXAS A&M UNIVERSITY; COOPER, KERRY - UNIVERSITY OF ARIZONA

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/3/2024
Publication Date: 4/11/2024
Citation: Goforth, M., Obergh, V., Park, R., Porchas, M., Crosby, K.M., Jifon, J.L., Ravishankar, S., Brierley, P., Leskovar, D.L., Turini, T.A., Schultheis, J., Coolong, T., Miller, R., Koiwa, H., Patil, B.S., Cooper, M.A., Huynh, S., Parker, C.T., Guan, W., Cooper, K.K. 2024. Bacterial diversity and composition on the rinds of specific melon cultivars and hybrids from across different growing regions in the United States. PLOS ONE. 19(4). Article e0293861. https://doi.org/10.1371/journal.pone.0293861.
DOI: https://doi.org/10.1371/journal.pone.0293861

Interpretive Summary: Commercial melon production has risen in popularity as a commodity crop that provides essential nutrients like carbohydrates, water and vitamins. Production has risen to more complex varieties of melons that include hybrids and specialty melons that are modified to be low maintenance and suitable for warmer climates. The aim of this study was to characterize the bacterial diversity on different melon varieties grown in different regions of the United States, and determine the influence that region, rind netting, and variety of melon has on the composition of the melon microbiome. Assessing the bacterial diversity of the microbiome on the melon rind can identify antagonistic and protagonistic bacteria for foodborne pathogens and spoilage organisms to improve melon safety, prolong shelf-life, and/or improve overall plant health. Bacterial community composition was determined using 16S rRNA gene amplicon sequencing of melons (n = 603) grown in seven locations over a four-year period. These sequences were analyzed to identify bacterial diversity and constituents. Statistically significant differences in relative abundances of those taxa based on the rind netting and growing region (p < 0.01) were found among the melon samples. The melon bacterial communities were more similar by region rather than melon variety (R2 value: 0.09 & R2 value: 0.02 respectively). Taxonomic profiling among the growing regions found Enterobacteriaceae, Bacillaceae, Microbacteriaceae, and Pseudomonadaceae present on the different melon rinds at an abundance of = 0.1%, but no specific group of bacteria was found on netted melons. However, Pseudomonadaceae, Bacillaceae, and Exiguobacteraceae (a core microbiome) were found for non-netted melons. The results of this study indicate that bacterial diversity is driven more by the region that the melons were grown in compared to rind netting or melon type. Establishing the foundation for regional differences in microbiomes could improve melon safety, shelf-life, and quality as well as the consumers’ health.

Technical Abstract: The goal of this study was to characterize the bacterial diversity on different melon varieties grown in different regions of the US, and determine the influence that region, rind netting, and variety of melon has on the composition of the melon microbiome. Assessing the bacterial diversity of the microbiome on the melon rind can identify antagonistic and protagonistic bacteria for foodborne pathogens and spoilage organisms to improve melon safety, prolong shelf-life, and/or improve overall plant health. Bacterial community composition of melons (n = 603) grown in seven locations over a four-year period were used for 16S rRNA gene amplicon sequencing and analysis to identify bacterial diversity and constituents. Statistically significant differences in alpha diversity based on the rind netting and growing region (p < 0.01) were found among the melon samples. Principal Coordinate Analysis based on the Bray-Curtis dissimilarity distance matrix found that the melon bacterial communities clustered more by region rather than melon variety (R2 value: 0.09 & R2 value: 0.02 respectively). Taxonomic profiling among the growing regions found Enterobacteriaceae, Bacillaceae, Microbacteriaceae, and Pseudomonadaceae present on the different melon rinds at an abundance of = 0.1%, but no specific core microbiome was found for netted melons. However, a core of Pseudomonadaceae, Bacillaceae, and Exiguobacteraceae were found for non-netted melons. The results of this study indicate that bacterial diversity is driven more by the region that the melons were grown in compared to rind netting or melon type. Establishing the foundation for regional differences could improve melon safety, shelf-life, and quality as well as the consumers’ health.