Skip to content
1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 75, Issue 11

sp. nov., a Gram-negative bacterium isolated from sweet corn ( L.) in the USA Open Access

Abstract

In 2024, bacterial strains KXB24, KXB25 and KXB45 were isolated from sweet corn ( L.) plants exhibiting foliar chlorosis and streaking, typical symptoms of bacterial infection, in the Everglades Agricultural Area in Florida, USA. A polyphasic taxonomic study was conducted on these strains. Phylogenetic analysis of 16S rRNA gene sequences, whole-genome comparisons and biochemical characterization confirmed that the isolates belong to the genus. The Biolog Gen III MicroPlate system identified substrate utilization profiles that were unique to these strains, distinguishing them from closely related species. The strain KXB24 showed positive utilization of -serine, γ-amino-butyric acid, citric acid and other compounds. On nutrient agar, KXB24, colonies are circular, smooth, convex and yellow and do not produce fluorescent pigment on King’s medium B. The DNA G+C content of KXB24 was determined to be 57.0 mol%. Based on phenotypic distinctions, phylogenomics evidence, average nucleotide identity values below 94.26% and digital DNA–DNA hybridization values below 57.9% when compared to type strains of recognized species, we propose sp. nov., with KXB24 (=NCPPB 4802=LMG 33887) as the type strain. This discovery enriches the current understanding of species and calls for further research into the potential role of in sweet corn disease aetiology and its broader agricultural impacts.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Everglades Agricultural Area , Florida , maize and phytopathology
Funding
This study was supported by the:
  • Hatch Project (Award FLA-ERC-006271)
    • Principal Award Recipient: KatiaV. Xavier
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006952
2025-11-03
2025-11-08

Metrics

Loading full text...

Full text loading...

/deliver/fulltext/ijsem/75/11/ijsem006952.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.006952&mimeType=html&fmt=ahah

References

  1. Leng G, Peng J, Huang S. Recent changes in county-level maize production in the United States: spatial-temporal patterns, climatic drivers and the implications for crop modelling. Sci Total Environ 2019; 686:819–827 [View Article] [PubMed]
     [Google Scholar]
  2. USDA NASS 2022 census of agriculture - Florida State and County Data; 2024 https://www.nass.usda.gov/Publications/AgCensus/2022/Full_Report/Volume_1,_Chapter_1_State_Level/Florida/ accessed 9 July 2024
  3. Bayabil H, Li Y, Olczyk T, Liu G. Sweet corn production in Miami-Dade County, Florida. EDIS; 2022 https://edis.ifas.ufl.edu/publication/TR013 accessed 7 March 2025
  4. Bhadha JH, Trotta L, Cavazos D, VanWeelden M. Trends in Florida rice production and varieties: SL439/SS653, rev. 8/2024. EDIS 2024; 2024: [View Article]
     [Google Scholar]
  5. Bai X, Li Y, Manirakiza N, Coffin C, Bhadha JH. Histosols of South Florida: past, present, and future: SL527/SS741, 2/2025. EDIS 2025; 2025: [View Article]
     [Google Scholar]
  6. Ferreira L, Moura V, Xavier K. Identification of Pantoea spp. causing epidemics on sweet corn in Southern Florida. Phytopathology 2024; 114:S1 [PubMed]
     [Google Scholar]
  7. Adeolu M, Alnajar S, Naushad S, Gupta RS. Genome-based phylogeny and taxonomy of the ‘Enterobacteriales’: proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. Int J Syst Evol Microbiol 2016; 66:5575–5599
     [Google Scholar]
  8. Coutinho TA, Venter SN. Pantoea ananatis: an unconventional plant pathogen. Mol Plant Pathol 2009; 10:325–335 [View Article] [PubMed]
     [Google Scholar]
  9. Gutierrez-Castillo MrDE, Barrett MsE, Yasuhara-Bell DrJ, Roberts DrR. First report of two pantoea species causing bacterial leaf blight on wheat in the United States. Plant Dis 2024 [View Article]
     [Google Scholar]
  10. Wdowiak-Wróbel S, Kalita M, Palusińska-Szysz M, Marek-Kozaczuk M, Sokołowski W et al. Pantoea trifolii sp. nov., a novel bacterium isolated from Trifolium rubens root nodules. Sci Rep 2024; 14:2698 [View Article] [PubMed]
     [Google Scholar]
  11. Crosby KC, Rojas M, Sharma P, Johnson MA, Mazloom R et al. Genomic delineation and description of species and within-species lineages in the genus Pantoea. Front Microbiol 2023; 14:1254999 [View Article] [PubMed]
     [Google Scholar]
  12. Olson RD, Assaf R, Brettin T, Conrad N, Cucinell C et al. Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR. Nucleic Acids Res 2023; 51:D678–D689 [View Article] [PubMed]
     [Google Scholar]
  13. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
     [Google Scholar]
  14. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
     [Google Scholar]
  15. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article] [PubMed]
     [Google Scholar]
  16. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 2014; 9:e112963 [View Article] [PubMed]
     [Google Scholar]
  17. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article] [PubMed]
     [Google Scholar]
  18. Trifinopoulos J, Nguyen L-T, von Haeseler A, Minh BQ. W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res 2016; 44:W232–5 [View Article] [PubMed]
     [Google Scholar]
  19. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res 2021; 49:W293–W296 [View Article] [PubMed]
     [Google Scholar]
  20. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article] [PubMed]
     [Google Scholar]
  21. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:1–14 [View Article] [PubMed]
     [Google Scholar]
  22. Kirzinger MWB, Butz CJ, Stavrinides J. Inheritance of Pantoea type III secretion systems through both vertical and horizontal transfer. Mol Genet Genomics 2015; 290:2075–2088 [View Article] [PubMed]
     [Google Scholar]
  23. Frederick RD, Ahmad M, Majerczak DR, Arroyo-Rodriguez AS, Manulis S et al. Genetic organization of the Pantoea stewartii subsp. stewartii hrp gene cluster and sequence analysis of the hrpA, hrpC, hrpN, and wtsE operons. Mol Plant Microbe Interact 2007; 14:1213–1222 [View Article]
     [Google Scholar]
  24. Wang J, Chen T, Xue L, Wei X, White JF et al. A new bacterial leaf blight disease of oat (Avena sativa) caused by Pantoea agglomerans in china. Plant Pathol 2022; 71:470–478 [View Article]
     [Google Scholar]
  25. Brady CL, Venter SN, Cleenwerck I, Engelbeen K, Vancanneyt M et al. Pantoea vagans sp. nov., Pantoea eucalypti sp. nov., Pantoea deleyi sp. nov. and Pantoea anthophila sp. nov. Int J Syst Evol Microbiol 2009; 59:2339–2345 [View Article] [PubMed]
     [Google Scholar]
  26. Ma Q, He S, Wang X, Rengel Z, Chen L et al. Isolation and characterization of phosphate-solubilizing bacterium Pantoea rhizosphaerae sp. nov. from Acer truncatum rhizosphere soil and its effect on Acer truncatum growth. Front Plant Sci 2023; 14:1218445 [View Article] [PubMed]
     [Google Scholar]
  27. Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics 2022; 38:5315–5316 [View Article] [PubMed]
     [Google Scholar]
  28. Parks DH, Chuvochina M, Rinke C, Mussig AJ, Chaumeil P-A et al. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res 2022; 50:D785–D794 [View Article] [PubMed]
     [Google Scholar]
  29. Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Krichevsky MI et al. Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
     [Google Scholar]
  30. Brenner DJ. Deoxyribonucleic acid reassociation in the taxonomy of enteric bacteria. Int J Syst Bacteriol 1973; 23:298–307 [View Article]
     [Google Scholar]
  31. Rossellö -Mora R, Amann R. The species concept for prokaryotes. FEMS Microbiol Rev 2001; 25:39–67 [View Article]
     [Google Scholar]
  32. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
     [Google Scholar]
  33. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  34. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A 2005; 102:2567–2572 [View Article] [PubMed]
     [Google Scholar]
  35. Shin GY, Asselin JA, Smith A, Aegerter B, Coutinho T et al. Plasmids encode and can mobilize onion pathogenicity in Pantoea agglomerans. ISME J 2025; 19:wraf019 [View Article] [PubMed]
     [Google Scholar]
  36. Zhao M, Shin GY, Stice S, Bown JL, Coutinho T et al. A novel biosynthetic gene cluster across the Pantoea species complex is important for pathogenicity in onion. Mol Plant Microbe Interact 2023; 36:176–188 [View Article] [PubMed]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006952
Loading
Pantoea graminicola sp. nov., a Gram-negative bacterium isolated from sweet corn (Zea mays L.) in the USA
Int J Syst Evol Microbiol 75, 006952 (2025); https://doi.org/10.1099/ijsem.0.006952
/content/journal/ijsem/10.1099/ijsem.0.006952
/content/journal/ijsem/10.1099/ijsem.0.006952
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

EXCEL

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An error occurred
Approval was partially successful, following selected items could not be processed due to error