Genotypic and phenotypic analyses reveal distinct population structures and ecotypes for sugar beet-associated Pseudomonas in Oxford and Auckland

Zhang, Xue-Xian; Ritchie, Stephen R.; Chang, Hao; Arnold, Dawn L.; Jackson, Robert W.; Rainey, Paul B.

Abstract

Fluorescent pseudomonads represent one of the largest groups of bacteria inhabiting the surfaces of plants, but their genetic composition in planta is poorly understood. Here, we examined the population structure and diversity of fluorescent pseudomonads isolated from sugar beet grown at two geographic locations (Oxford, United Kingdom and Auckland, New Zealand). To seek evidence for niche adaptation, bacteria were sampled from three types of leaves (immature, mature, and senescent) and then characterized using a combination of genotypic and phenotypic analysis. We first performed multilocus sequence analysis (MLSA) of three housekeeping genes (gapA, gltA, and acnB) in a total of 152 isolates (96 from Oxford, 56 from Auckland). The concatenated sequences were grouped into 81 sequence types and 22 distinct operational taxonomic units (OTUs). Significant levels of recombination were detected, particularly for the Oxford isolates (rate of recombination to mutation (r/m) = 5.23 for the whole population). Subsequent ancestral analysis performed in STRUCTURE found evidence of six ancestral populations, and their distributions significantly differed between Oxford and Auckland. Next, their ability to grow on 95 carbon sources was assessed using the Biolog™ GN2 microtiter plates. A distance matrix was generated from the raw growth data (A660) and subjected to multidimensional scaling (MDS) analysis. There was a significant correlation between substrate utilization profiles and MLSA genotypes. Both phenotypic and genotypic analyses indicated presence of a geographic structure for strains from Oxford and Auckland. Significant differences were also detected for MLSA genotypes between strains isolated from immature versus mature/senescent leaves. The fluorescent pseudomonads thus showed an ecotypic population structure, suggestive of adaptation to both geographic conditions and local plant niches.

Citation

Zhang, X., Ritchie, S. R., Chang, H., Arnold, D. L., Jackson, R. W., & Rainey, P. B. (2020). Genotypic and phenotypic analyses reveal distinct population structures and ecotypes for sugar beet-associated Pseudomonas in Oxford and Auckland. Ecology and Evolution, 10(12), 5963-5975. https://doi.org/10.1002/ece3.6334

• Journal Article Type: Article
• Acceptance Date: Apr 14, 2020
• Online Publication Date: May 11, 2020
• Publication Date: Jun 1, 2020
• Deposit Date: Apr 20, 2020
• Publicly Available Date: May 15, 2020
• Journal: Ecology and Evolution
• Electronic ISSN: 2045-7758
• Publisher: Wiley Open Access
• Peer Reviewed: Peer Reviewed
• Volume: 10
• Issue: 12
• Pages: 5963-5975
• DOI: https://doi.org/10.1002/ece3.6334
• Keywords: multilocus sequence analysis; mutation; population structure; Pseudomonas; recombination; sugar beet; urocanate
• Public URL: https://uwe-repository.worktribe.com/output/5883487