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Journal of Integrative Agriculture  2016, Vol. 15 Issue (9): 2049-2058    DOI: 10.1016/S2095-3119(16)61354-0
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Identification of candidate soil microbes responsible for small-scale heterogeneity in strawberry plant vigour
WEI Feng1, 2*, FAN Rong1, 2*, Thomas Passey2, HU Xiao-ping1, Xiangming Xu2
1 State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, P.R.China
2 NIAB East Malling Research, East Malling, Kent, ME19 6BJ, UK
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Abstract      Studies were conducted to identify candidate soil microbes responsible for observed differences in strawberry vigour at a small spatial scale, which was not associated with visual disease symptoms. Samples were obtained from the soils close to the rhizosphere of ‘big’ and ‘small’ plants from small plots which exhibited large local heterogeneity in plant vigour. A metabarcoding approach was used to profile bacterial and fungal compositions, using two primer pairs for 16S ribosomal RNA genes (16S rDNA) and one for the fungal internal transcribed spacer (ITS) region. Of the two 16S rDNA primer sets, the 341F/805R resulted in sequences of better quality. A total 28 operational taxonomic units (OTUs) had differential relative abundance between samples from ‘big’ and ‘small’ plants. However, plausible biological explanation was only possible for three fungal OTUs. Two were possible phytopathogens: Verticillium spp. and Alternaria alternata although the latter has never been considered as a main pathogen of strawberry in the UK. For samples from ‘small’ plants, the abundance of these OTUs was much greater than from ‘big’ plants. The opposite was true for a mycorrhizal OTU. These results suggest that soil microbes related to crop production can be identified using metabarcoding technique. Further research is needed to assess whether A. alternata and Verticillium spp. could affect strawberry growth in the field.
Keywords:  soil microbes        plant health       soilborne pathogens        mycorrhizal fungi        metabarcoding  
Received: 18 December 2015   Accepted:

This research is funded by Innovate UK (100867) with matching funding from several commercial companies. Wei Feng and Fan Rong gratefully acknowledge the financial assistance of the China Scholarship Council (201306300133 and 201506300012).

Corresponding Authors:  HU Xiao-ping, Tel/Fax: +86-29-87091095, E-mail:; Xiangming Xu, Tel: +44-1732-523753, Fax: +44-1732-849067, E-mail:    
About author:  WEI Feng, E-mail:;

Cite this article: 

WEI Feng, FAN Rong, Thomas Passey, HU Xiao-ping, Xiangming Xu. 2016. Identification of candidate soil microbes responsible for small-scale heterogeneity in strawberry plant vigour. Journal of Integrative Agriculture, 15(9): 2049-2058.

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