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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.


Relative abundance of the 16 (12 bacterial and 4 fungal OTUs – Table 7) organisms per sample that may have played a role in affecting strawberry yield decline observed at HB12 and PV12; counts data were proportionally adjusted to the total reads of 300 000 per sample. Samples from chloropicrin-treated plots at HB12 and PV12 were excluded.
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fig8: Relative abundance of the 16 (12 bacterial and 4 fungal OTUs – Table 7) organisms per sample that may have played a role in affecting strawberry yield decline observed at HB12 and PV12; counts data were proportionally adjusted to the total reads of 300 000 per sample. Samples from chloropicrin-treated plots at HB12 and PV12 were excluded.

Mentions: Figure 8 shows the relative abundance of these 16 candidate OTUs at the four sites. HB13 and EM13 had much higher levels of Bacillus and Pseudomonas OTUs than HB12 and PV12. The level of wet-loving bacterial OTUs was higher at PV12 than at the other sites; the opposite was true for the level of bacterial OTUs related to nitrogen cycling. For fungal OTUs, the level of two Ilyonectria species was the highest and lowest at PV12 and HB13, respectively. There was a higher level of wet-loving fungi at HB12 than at the other three sites. Nematode-parasitic fungi were nearly exclusively found at HB13.


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)

Relative abundance of the 16 (12 bacterial and 4 fungal OTUs – Table 7) organisms per sample that may have played a role in affecting strawberry yield decline observed at HB12 and PV12; counts data were proportionally adjusted to the total reads of 300 000 per sample. Samples from chloropicrin-treated plots at HB12 and PV12 were excluded.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig8: Relative abundance of the 16 (12 bacterial and 4 fungal OTUs – Table 7) organisms per sample that may have played a role in affecting strawberry yield decline observed at HB12 and PV12; counts data were proportionally adjusted to the total reads of 300 000 per sample. Samples from chloropicrin-treated plots at HB12 and PV12 were excluded.
Mentions: Figure 8 shows the relative abundance of these 16 candidate OTUs at the four sites. HB13 and EM13 had much higher levels of Bacillus and Pseudomonas OTUs than HB12 and PV12. The level of wet-loving bacterial OTUs was higher at PV12 than at the other sites; the opposite was true for the level of bacterial OTUs related to nitrogen cycling. For fungal OTUs, the level of two Ilyonectria species was the highest and lowest at PV12 and HB13, respectively. There was a higher level of wet-loving fungi at HB12 than at the other three sites. Nematode-parasitic fungi were nearly exclusively found at HB13.

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.