Identification of candidate soil microbes responsible for small-scale heterogeneity in strawberry plant vigour
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 p...
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| Format: | Article |
| Language: | English |
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KeAi Communications Co., Ltd.
2016-09-01
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| Series: | Journal of Integrative Agriculture |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2095311916613540 |
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| author | Feng WEI Rong FAN Thomas Passey Xiao-ping HU Xiangming Xu |
| author_facet | Feng WEI Rong FAN Thomas Passey Xiao-ping HU Xiangming Xu |
| author_sort | Feng WEI |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-feb50db1f80944d8a19dbdde890fcad5 |
| institution | Kabale University |
| issn | 2095-3119 |
| language | English |
| publishDate | 2016-09-01 |
| publisher | KeAi Communications Co., Ltd. |
| record_format | Article |
| series | Journal of Integrative Agriculture |
| spelling | doaj-art-feb50db1f80944d8a19dbdde890fcad52025-08-20T03:42:10ZengKeAi Communications Co., Ltd.Journal of Integrative Agriculture2095-31192016-09-011592049205810.1016/S2095-3119(16)61354-0Identification of candidate soil microbes responsible for small-scale heterogeneity in strawberry plant vigourFeng WEI0Rong FAN1Thomas Passey2Xiao-ping HU3Xiangming Xu4State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, P.R.China; NIAB East Malling Research, East Malling, Kent, ME19 6BJ, UK; WEI FengState Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, P.R.China; NIAB East Malling Research, East Malling, Kent, ME19 6BJ, UKNIAB East Malling Research, East Malling, Kent, ME19 6BJ, UKState Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, P.R.China; WEI FengNIAB East Malling Research, East Malling, Kent, ME19 6BJ, UK; Correspondence HU Xiao-ping, Tel/Fax: +86-29-87091095; Xiangming Xu, Tel: +44-1732-523753, Fax: +44-1732-849067Studies 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.http://www.sciencedirect.com/science/article/pii/S2095311916613540soil microbesplant healthsoilborne pathogensmycorrhizal fungimetabarcoding |
| spellingShingle | Feng WEI Rong FAN Thomas Passey Xiao-ping HU Xiangming Xu Identification of candidate soil microbes responsible for small-scale heterogeneity in strawberry plant vigour Journal of Integrative Agriculture soil microbes plant health soilborne pathogens mycorrhizal fungi metabarcoding |
| title | Identification of candidate soil microbes responsible for small-scale heterogeneity in strawberry plant vigour |
| title_full | Identification of candidate soil microbes responsible for small-scale heterogeneity in strawberry plant vigour |
| title_fullStr | Identification of candidate soil microbes responsible for small-scale heterogeneity in strawberry plant vigour |
| title_full_unstemmed | Identification of candidate soil microbes responsible for small-scale heterogeneity in strawberry plant vigour |
| title_short | Identification of candidate soil microbes responsible for small-scale heterogeneity in strawberry plant vigour |
| title_sort | identification of candidate soil microbes responsible for small scale heterogeneity in strawberry plant vigour |
| topic | soil microbes plant health soilborne pathogens mycorrhizal fungi metabarcoding |
| url | http://www.sciencedirect.com/science/article/pii/S2095311916613540 |
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