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

• Published in: Ecology and evolution Vol. 10; no. 12; pp. 5963 - 5975
• Main Authors: Zhang, Xue‐Xian, Ritchie, Stephen R., Chang, Hao, Arnold, Dawn L., Jackson, Robert W., Rainey, Paul B.
• Format: Journal Article
• Language: English
• Published: England John Wiley & Sons, Inc 01.06.2020; John Wiley and Sons Inc; Wiley
• Subjects: Adaptation; Bacteria; Carbon sources; Correlation analysis; Ecotypes; Fluorescence; Genomes; Genotypes; Geographical locations; Glycerol; Leaves; Multidimensional scaling; multilocus sequence analysis; Mutation; Niches; Original Research; Pathogens; Plant diseases; Population; Population structure; Pseudomonas; Recombination; Sequence analysis; Strains (organisms); Substrates; sugar beet; Sugar beets; urocanate; New Zealand; United Kingdom > UK; multilocus sequence analysis; mutation; recombination; population structure; Pseudomonas; urocanate; sugar beet
• ISSN: 2045-7758; 2045-7758
• DOI: 10.1002/ece3.6334

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. Fluorescent pseudomonads are the largest group of bacteria inhabiting the phyllosphere of sugar beet, but our understanding of their population structure is limited. Here, we performed multilocus sequence analysis and Biolog phenotypic assay of 152 isolates from sugar beet grown in Oxford and Auckland. Results indicate that the sugar beet‐associated pseudomonads have an ecotypic population structure, suggestive of adaptation to both geographical and local plant environments.