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Goforth M, Cooper MA, Oliver AS, Pinzon J, Skots M, Obergh V, Suslow TV, Flores GE, Huynh S, Parker CT, Mackelprang R, Cooper KK. Bacterial community shifts of commercial apples, oranges, and peaches at different harvest points across multiple growing seasons. PLoS One 2024; 19:e0297453. [PMID: 38625898 PMCID: PMC11020611 DOI: 10.1371/journal.pone.0297453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/04/2024] [Indexed: 04/18/2024] Open
Abstract
Assessing the microbes present on tree fruit carpospheres as the fruit enters postharvest processing could have useful applications, as these microbes could have a major influence on spoilage, food safety, verification of packing process controls, or other aspects of processing. The goal of this study was to establish a baseline profile of bacterial communities associated with apple (pome fruit), peach (stone fruit), and Navel orange (citrus fruit) at harvest. We found that commercial peaches had the greatest bacterial richness followed by oranges then apples. Time of harvest significantly changed bacterial diversity in oranges and peaches, but not apples. Shifts in diversity varied by fruit type, where 70% of the variability in beta diversity on the apple carposphere was driven by the gain and loss of species (i.e., nestedness). The peach and orange carposphere bacterial community shifts were driven by nearly an even split between turnover (species replacement) and nestedness. We identified a small core microbiome for apples across and between growing seasons that included only Methylobacteriaceae and Sphingomonadaceae among the samples, while peaches had a larger core microbiome composed of five bacterial families: Bacillaceae, Geodermtophilaceae, Nocardioidaceae, Micrococcaeceae, and Trueperaceae. There was a relatively diverse core microbiome for oranges that shared all the families present on apples and peaches, except for Trueperaceae, but also included an additional nine bacterial families not shared including Oxalobacteraceae, Cytophagaceae, and Comamonadaceae. Overall, our findings illustrate the important temporal dynamics of bacterial communities found on major commercial tree fruit, but also the core bacterial families that constantly remain with both implications being important entering postharvest packing and processing.
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Affiliation(s)
- Madison Goforth
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, United States of America
| | - Margarethe A. Cooper
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, United States of America
| | - Andrew S. Oliver
- USDA-ARS Western Human Nutrition Research Center, Davis, California, United States of America
| | - Janneth Pinzon
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
| | - Mariya Skots
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
| | - Victoria Obergh
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, United States of America
| | - Trevor V. Suslow
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
| | - Gilberto E. Flores
- Department of Biology, California State University, Northridge, Northridge, California, United States of America
| | - Steven Huynh
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, USDA, Albany, California, United States of America
| | - Craig T. Parker
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, USDA, Albany, California, United States of America
| | - Rachel Mackelprang
- Department of Biology, California State University, Northridge, Northridge, California, United States of America
| | - Kerry K. Cooper
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, United States of America
- BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
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Goforth M, Obergh V, Park R, Porchas M, Crosby KM, Jifon JL, Ravishankar S, Brierley P, Leskovar DL, Turini TA, Schultheis J, Coolong T, Miller R, Koiwa H, Patil BS, Cooper MA, Huynh S, Parker CT, Guan W, Cooper KK. Bacterial diversity and composition on the rinds of specific melon cultivars and hybrids from across different growing regions in the United States. PLoS One 2024; 19:e0293861. [PMID: 38603714 PMCID: PMC11008840 DOI: 10.1371/journal.pone.0293861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 02/03/2024] [Indexed: 04/13/2024] Open
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.
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Affiliation(s)
- Madison Goforth
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, United States of America
- USDA National Center of Excellence for Melon at the Vegetable and Fruit Improvement Center of Texas A&M University, College Station, TX, United States of America
| | - Victoria Obergh
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, United States of America
- USDA National Center of Excellence for Melon at the Vegetable and Fruit Improvement Center of Texas A&M University, College Station, TX, United States of America
| | - Richard Park
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, United States of America
- USDA National Center of Excellence for Melon at the Vegetable and Fruit Improvement Center of Texas A&M University, College Station, TX, United States of America
| | - Martin Porchas
- USDA National Center of Excellence for Melon at the Vegetable and Fruit Improvement Center of Texas A&M University, College Station, TX, United States of America
- Yuma Center of Excellence for Desert Agriculture, University of Arizona, Yuma, AZ, United States of America
| | - Kevin M. Crosby
- USDA National Center of Excellence for Melon at the Vegetable and Fruit Improvement Center of Texas A&M University, College Station, TX, United States of America
- Vegetable & Fruit Improvement Center, Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States of America
| | - John L. Jifon
- USDA National Center of Excellence for Melon at the Vegetable and Fruit Improvement Center of Texas A&M University, College Station, TX, United States of America
- Vegetable & Fruit Improvement Center, Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States of America
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States of America
| | - Sadhana Ravishankar
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, United States of America
- USDA National Center of Excellence for Melon at the Vegetable and Fruit Improvement Center of Texas A&M University, College Station, TX, United States of America
| | - Paul Brierley
- USDA National Center of Excellence for Melon at the Vegetable and Fruit Improvement Center of Texas A&M University, College Station, TX, United States of America
- Yuma Center of Excellence for Desert Agriculture, University of Arizona, Yuma, AZ, United States of America
| | - Daniel L. Leskovar
- USDA National Center of Excellence for Melon at the Vegetable and Fruit Improvement Center of Texas A&M University, College Station, TX, United States of America
- Vegetable & Fruit Improvement Center, Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States of America
- Texas A&M AgriLife Research and Extension Center, Texas A&M System, Uvalde, TX, United States of America
| | - Thomas A. Turini
- USDA National Center of Excellence for Melon at the Vegetable and Fruit Improvement Center of Texas A&M University, College Station, TX, United States of America
- University of California Cooperative Extension, Fresno, CA, United States of America
| | - Jonathan Schultheis
- USDA National Center of Excellence for Melon at the Vegetable and Fruit Improvement Center of Texas A&M University, College Station, TX, United States of America
- Department of Horticultural Sciences, North Carolina State University, Raleigh, NC, United States of America
| | - Timothy Coolong
- USDA National Center of Excellence for Melon at the Vegetable and Fruit Improvement Center of Texas A&M University, College Station, TX, United States of America
- Department of Horticulture, University of Georgia, Athens, GA, United States of America
| | - Rhonda Miller
- USDA National Center of Excellence for Melon at the Vegetable and Fruit Improvement Center of Texas A&M University, College Station, TX, United States of America
- Department of Animal Science, Texas A&M University, College Station, TX, United States of America
| | - Hisashi Koiwa
- USDA National Center of Excellence for Melon at the Vegetable and Fruit Improvement Center of Texas A&M University, College Station, TX, United States of America
- Vegetable & Fruit Improvement Center, Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States of America
| | - Bhimanagouda S. Patil
- USDA National Center of Excellence for Melon at the Vegetable and Fruit Improvement Center of Texas A&M University, College Station, TX, United States of America
- Vegetable & Fruit Improvement Center, Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States of America
| | - Margarethe A. Cooper
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, United States of America
| | - Steven Huynh
- Produce Safety and Microbiology, Agricultural Research Service, USDA, Albany, CA, United States of America
| | - Craig T. Parker
- Produce Safety and Microbiology, Agricultural Research Service, USDA, Albany, CA, United States of America
| | - Wenjing Guan
- USDA National Center of Excellence for Melon at the Vegetable and Fruit Improvement Center of Texas A&M University, College Station, TX, United States of America
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States of America
- Southwest Purdue Agricultural Center, Vincennes, IN, United States of America
| | - Kerry K. Cooper
- USDA National Center of Excellence for Melon at the Vegetable and Fruit Improvement Center of Texas A&M University, College Station, TX, United States of America
- Yuma Center of Excellence for Desert Agriculture, University of Arizona, Yuma, AZ, United States of America
- BIO5 Institute, University of Arizona, Tucson, AZ, United States of America
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