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

Xu X, Passey T, Wei F, Saville R, Harrison RJ - Hortic Res (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: East Malling Research , East Malling, West Malling, Kent, ME19 6BJ, UK.

ABSTRACT
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.

No MeSH data available.


Density plots of three statistics for 124 cases for which there were significant differences in fungal abundance between non-yield-decline and yield-decline samples: overall OTU abundance across all samples, log2-fold changes and BH-adjusted p-values.
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fig7: Density plots of three statistics for 124 cases for which there were significant differences in fungal abundance between non-yield-decline and yield-decline samples: overall OTU abundance across all samples, log2-fold changes and BH-adjusted p-values.

Mentions: A total of 452 bacterial and 485 fungal OTUs were omitted from differential abundance testing because of extreme low counts across all samples (total counts ≤ 3), leaving 1690 bacterial and 1537 fungal OTUs for statistical testing. Of all pairwise comparisons, 715 comparisons were statistically significant at the 5% level. Figures 6 and 7 show the density plots of three statistics for these significant comparisons: average abundance for the OTUs, log2-fold change (no-yield-decline samples over yield-decline samples) and BH-adjusted p-values. Overall, more bacterial OTUs appeared to be more abundant in the non-yield-decline soils than in the yield-decline soils; the opposite was true for fungal OTUs.


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

Xu X, Passey T, Wei F, Saville R, Harrison RJ - Hortic Res (2015)

Density plots of three statistics for 124 cases for which there were significant differences in fungal abundance between non-yield-decline and yield-decline samples: overall OTU abundance across all samples, log2-fold changes and BH-adjusted p-values.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4595980&req=5

fig7: Density plots of three statistics for 124 cases for which there were significant differences in fungal abundance between non-yield-decline and yield-decline samples: overall OTU abundance across all samples, log2-fold changes and BH-adjusted p-values.
Mentions: A total of 452 bacterial and 485 fungal OTUs were omitted from differential abundance testing because of extreme low counts across all samples (total counts ≤ 3), leaving 1690 bacterial and 1537 fungal OTUs for statistical testing. Of all pairwise comparisons, 715 comparisons were statistically significant at the 5% level. Figures 6 and 7 show the density plots of three statistics for these significant comparisons: average abundance for the OTUs, log2-fold change (no-yield-decline samples over yield-decline samples) and BH-adjusted p-values. Overall, more bacterial OTUs appeared to be more abundant in the non-yield-decline soils than in the yield-decline soils; the opposite was true for fungal OTUs.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: East Malling Research , East Malling, West Malling, Kent, ME19 6BJ, UK.

ABSTRACT
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.

No MeSH data available.