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Identification of candidate soil microbes responsible for small-scale heterogeneity in strawberry plant vigour

Journal of Integrative Agriculture 2016年第9期15卷 2049-2058页

作者： WEI Feng FAN Rong thomas passey HU Xiao-ping Xiangming Xu State 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 Mailing Kent ME19 6B J UK

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 16 S ribosomal RNA genes（16S r DNA） and one for the fungal internal transcribed spacer（ITS） region. Of the two 16 S r DNA primer sets, the 341F/805 R 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.

关键词： soil microbes plant health soilborne pathogens mycorrhizal fungi metabarcoding

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Amplicon-based metagenomics identified candidate organisms in soils that caused yield decline in strawberry

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Horticulture Research 2015年第1期2卷 201-213页

作者： Xiangming Xu thomas passey Feng Wei Robert Saville Richard J.Harrison East Malling Research East MallingWest MallingKentME196BJUK

A phenomenon of yield decline due to weak plant growth in strawberry was recently observed in non-chemo-fumigated soils,which was not associated with the soil fungal pathogen Verticillium dahliae,the main target of ***-based metagenomics was used to profile soil microbiota in order to identify microbial organisms that may have caused the yield decline.A total of 36 soil samples were obtained in 2013 and 2014 from four sites for metagenomic studies;two of the four sites had a yield-decline problem,the other two did *** than 2000 fungal or bacterial operational taxonomy units(OTUs)were found in these *** abundance of individual OTUs was statistically compared for differences between samples from sites with or without yield decline.A total of 721 individual comparisons were statistically significant–involving 366 unique bacterial and 44 unique fungal *** on further selection criteria,we focused on 34 bacterial and 17 fungal OTUs and found that yield decline resulted probably from one or more of the following four factors:(1)low abundance of Bacillus and Pseudomonas populations,which are well known for their ability of supressing pathogen development and/or promoting plant growth;(2)lack of the nematophagous fungus(Paecilomyces species);(3)a high level of two non-specific fungal root rot pathogens;and(4)wet soil *** study demonstrated the usefulness of an amplicon-based metagenomics approach to profile soil microbiota and to detect differential abundance in microbes.

关键词： soil straw soils

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