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Genotypic and phenotypic analyses reveal distinct population structures and ecotypes for sugar beet-associated Pseudomonas in Oxford and Auckland
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  • Xue-Xian Zhang,
  • Stephen Ritchie,
  • Hao Chang,
  • Dawn Arnold,
  • Robert Jackson,
  • Paul Rainey
Xue-Xian Zhang
Massey University, Auckland
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Stephen Ritchie
The University of Auckland Faculty of Medical and Health Sciences
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Hao Chang
Massey University Auckland
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Dawn Arnold
University of the West of England - City Campus
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Robert Jackson
University of Birmingham
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Paul Rainey
Massey University - Albany Campus
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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, UK 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, 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 strains. Next, the ability to grow on 95 carbon sources was assessed using the BiologTM 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 the 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 genotypically detected between strains isolated from immature versus mature/senescent leaves. The fluorescent pseudomonads thus showed an ecotypic population structure, suggestive of adaptation to both geographical and local plant environments.

Peer review status:ACCEPTED

18 Feb 2020Submitted to Ecology and Evolution
19 Feb 2020Submission Checks Completed
19 Feb 2020Assigned to Editor
20 Feb 2020Reviewer(s) Assigned
02 Mar 2020Review(s) Completed, Editorial Evaluation Pending
26 Mar 2020Editorial Decision: Revise Minor
10 Apr 20201st Revision Received
10 Apr 2020Review(s) Completed, Editorial Evaluation Pending
10 Apr 2020Submission Checks Completed
10 Apr 2020Assigned to Editor
14 Apr 2020Editorial Decision: Accept