Using multilocus sequence analysis to distinguish pathogenic from saprotrophic strains of Pseudomonas from stone fruit and kiwifruit

  • Sandra B. VisnovskyEmail author
  • Maria V. Marroni
  • Shamini Pushparajah
  • Kerry R. Everett
  • Robert K. Taylor
  • Boris A. Vinatzer
  • Andrew R. Pitman
Original Article


A variety of pseudomonads are associated with diseases of Actinidia and Prunus plants. A recently emerged virulent haplotype of Pseudomonas syringae pv. actinidiae (biovar 3) causes severe stem cankers on kiwifruit associated with dieback of canes. Pseudomonas syringae also causes one of the most important bacterial diseases affecting cherry orchards worldwide. Bacterial canker of cherry limits production in orchards in New Zealand. Less virulent and non-pathogenic pseudomonads also exist on both hosts, providing an opportunity to investigate the diversity of pseudomonads on these hosts, to find identifiers for new emerging highly pathogenic strains that could be used at the border to prevent incursions. In this study, genetic typing was used to explore the diversity of Pseudomonas on kiwifruit and a variety of Prunus plants. Multilocus sequence analysis (MLSA) of four house-keeping genes separated pseudomonads from kiwifruit and stone fruit plants into two major groups: one corresponding to P. syringae sensu lato and one corresponding to other Pseudomonas species. Within P. syringae sensu lato, strains were assigned to six of the nine previously described genomospecies or five of the seven previously described phylogroups. In the other major group, strains from both hosts clustered with a variety of well characterised non-pathogenic pseudomonads. The classification of strains into the two major groups is of practical diagnostic value since the most common pathogens of fruit trees belong to the P. syringae species complex. Furthermore, our analysis suggests that molecular diagnostics might be possible for the classification of strains into these two groups as a first tool to screen for exotic pathogenic pseudomonads on germplasm imports of both commodities.


Pseudomonas MLSA Kiwifruit Stone fruits 



This work was funded by the Better Border Biosecurity programme (B3) (

The authors thanks Drs Erik Rikkerink, Hayley Ridgway and Faulk Kalamorz from The New Zealand Institute for Plant and Food Research Ltd. for their valuable feedback to the manuscript.

Compliance with ethical standards

The manuscript complies with ethical rules of the European Journal of Plant Pathology, as reported in the “Ethical Responsibilities of Authors” in the “Instruction for Authors” section.

Conflict of interest and human or animal participants

There are no potential conflicts of interest, and the research does not involve human participants and / or animals.

Ethical approval

All authors have approved the manuscript and agreed with its submission to European Journal of Plant Pathology.

Supplementary material

10658_2019_1799_MOESM1_ESM.png (449 kb)
Figure S1 An unrooted Maximum Likelihood tree (Guindon et al. 2010) constructed using concatenated partial DNA sequences of gyrB and gapA from pseudomonads collected from kiwifruit plants, other hosts and the environment. The pseudomonads included P. viridiflava strains and other pseudomonads downloaded from the Plant Associated and Environmental Microbes Database (PAMDB). Twenty-seven isolates Group A from our collection from kiwifruit and from Prunus were also included. This analysis supported our multilocus sequence analysis (MLSA) data, confirming the identity of ABAC 43 and ICMP 11289 as P. viridiflava. ICMP 3272 and ICMP 13303, which were considered P. viridiflava, did not cluster with the P. viridiflava isolates, indicating that they are probably P. syringae phylogroup III. (PNG 449 kb)
10658_2019_1799_MOESM2_ESM.docx (21 kb)
Table S1 (DOCX 20 kb)
10658_2019_1799_MOESM3_ESM.docx (16 kb)
Table S2 (DOCX 15.9 kb)


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Copyright information

© Koninklijke Nederlandse Planteziektenkundige Vereniging 2019

Authors and Affiliations

  1. 1.The New Zealand Institute for Plant and Food Research LtdChristchurchNew Zealand
  2. 2.The New Zealand Institute for Plant and Food Research LtdAucklandNew Zealand
  3. 3.Better Border BiosecurityAucklandNew Zealand
  4. 4.Plant Health and Environment LaboratoryMinistry for Primary IndustriesAucklandNew Zealand
  5. 5.School of Plant and Environmental SciencesVirginia TechBlacksburgUSA

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