Amplicon-based metagenomics identified candidate organisms in soils that caused yield decline in strawberry
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 fumigation. Amplicon-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 not. More than 2000 fungal or bacterial operational taxonomy units (OTUs) were found in these samples. Relative 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 OTUs. Based 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 conditions. This study demonstrated the usefulness of an amplicon-based metagenomics approach to profile soil microbiota and to detect differential abundance in microbes.
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dig-wur-nl-wurpubs-6049782024-03-07 Xu, Xiangming Passey, Thomas Wei, Feng Saville, Robert Harrison, Richard J. Article/Letter to editor Horticulture Research 2 (2015) ISSN: 2052-7276 Amplicon-based metagenomics identified candidate organisms in soils that caused yield decline in strawberry 2015 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 fumigation. Amplicon-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 not. More than 2000 fungal or bacterial operational taxonomy units (OTUs) were found in these samples. Relative 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 OTUs. Based 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 conditions. This study demonstrated the usefulness of an amplicon-based metagenomics approach to profile soil microbiota and to detect differential abundance in microbes. en text/html https://research.wur.nl/en/publications/amplicon-based-metagenomics-identified-candidate-organisms-in-soi 10.1038/hortres.2015.22 https://edepot.wur.nl/581517 Life Science https://creativecommons.org/licenses/by/4.0/ Wageningen University & Research |
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Life Science Life Science Xu, Xiangming Passey, Thomas Wei, Feng Saville, Robert Harrison, Richard J. Amplicon-based metagenomics identified candidate organisms in soils that caused yield decline in strawberry |
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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 fumigation. Amplicon-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 not. More than 2000 fungal or bacterial operational taxonomy units (OTUs) were found in these samples. Relative 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 OTUs. Based 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 conditions. This study demonstrated the usefulness of an amplicon-based metagenomics approach to profile soil microbiota and to detect differential abundance in microbes. |
| format |
Article/Letter to editor |
| topic_facet |
Life Science |
| author |
Xu, Xiangming Passey, Thomas Wei, Feng Saville, Robert Harrison, Richard J. |
| author_facet |
Xu, Xiangming Passey, Thomas Wei, Feng Saville, Robert Harrison, Richard J. |
| author_sort |
Xu, Xiangming |
| title |
Amplicon-based metagenomics identified candidate organisms in soils that caused yield decline in strawberry |
| title_short |
Amplicon-based metagenomics identified candidate organisms in soils that caused yield decline in strawberry |
| title_full |
Amplicon-based metagenomics identified candidate organisms in soils that caused yield decline in strawberry |
| title_fullStr |
Amplicon-based metagenomics identified candidate organisms in soils that caused yield decline in strawberry |
| title_full_unstemmed |
Amplicon-based metagenomics identified candidate organisms in soils that caused yield decline in strawberry |
| title_sort |
amplicon-based metagenomics identified candidate organisms in soils that caused yield decline in strawberry |
| url |
https://research.wur.nl/en/publications/amplicon-based-metagenomics-identified-candidate-organisms-in-soi |
| work_keys_str_mv |
AT xuxiangming ampliconbasedmetagenomicsidentifiedcandidateorganismsinsoilsthatcausedyielddeclineinstrawberry AT passeythomas ampliconbasedmetagenomicsidentifiedcandidateorganismsinsoilsthatcausedyielddeclineinstrawberry AT weifeng ampliconbasedmetagenomicsidentifiedcandidateorganismsinsoilsthatcausedyielddeclineinstrawberry AT savillerobert ampliconbasedmetagenomicsidentifiedcandidateorganismsinsoilsthatcausedyielddeclineinstrawberry AT harrisonrichardj ampliconbasedmetagenomicsidentifiedcandidateorganismsinsoilsthatcausedyielddeclineinstrawberry |
| _version_ |
1813200533676097536 |