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Influence of soil type, cultivar and Verticillium dahliae on the structure of the root and rhizosphere soil fungal microbiome of strawberry.

Nallanchakravarthula S, Mahmood S, Alström S, Finlay RD - PLoS ONE (2014)

Bottom Line: Inoculation with the pathogen V. dahliae had a significant influence on community structure, generally decreasing the number of rhizosphere soil- and root-inhabiting fungi.Leptodontidium sp.The results suggest that 1) plant roots select microorganisms from the wider rhizosphere pool, 2) that both rhizosphere soil and root inhabiting fungal communities are influenced by V. dahliae and 3) that soil type has a stronger influence on both of these communities than cultivar.

View Article: PubMed Central - PubMed

Affiliation: Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.

ABSTRACT
Sustainable management of crop productivity and health necessitates improved understanding of the ways in which rhizosphere microbial populations interact with each other, with plant roots and their abiotic environment. In this study we examined the effects of different soils and cultivars, and the presence of a soil-borne fungal pathogen, Verticillium dahliae, on the fungal microbiome of the rhizosphere soil and roots of strawberry plants, using high-throughput pyrosequencing. Fungal communities of the roots of two cultivars, Honeoye and Florence, were statistically distinct from those in the rhizosphere soil of the same plants, with little overlap. Roots of plants growing in two contrasting field soils had high relative abundance of Leptodontidium sp. C2 BESC 319 g whereas rhizosphere soil was characterised by high relative abundance of Trichosporon dulcitum or Cryptococcus terreus, depending upon the soil type. Differences between different cultivars were not as clear. Inoculation with the pathogen V. dahliae had a significant influence on community structure, generally decreasing the number of rhizosphere soil- and root-inhabiting fungi. Leptodontidium sp. C2 BESC 319 g was the dominant fungus responding positively to inoculation with V. dahliae. The results suggest that 1) plant roots select microorganisms from the wider rhizosphere pool, 2) that both rhizosphere soil and root inhabiting fungal communities are influenced by V. dahliae and 3) that soil type has a stronger influence on both of these communities than cultivar.

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Ranked abundance of the 30 most abundant fungal operational taxonomic units (OTUs) present in the rhizosphere and roots of two strawberry cultivars, Honeoye and Florence, grown in conventionally (A and B) and organically (C and D) managed field soils.Only OTUs with ≥95% identity are included.
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pone-0111455-g002: Ranked abundance of the 30 most abundant fungal operational taxonomic units (OTUs) present in the rhizosphere and roots of two strawberry cultivars, Honeoye and Florence, grown in conventionally (A and B) and organically (C and D) managed field soils.Only OTUs with ≥95% identity are included.

Mentions: Rank abundance plots of the 30 most abundant fungal taxa in each of the rhizosphere and root compartments in the absence of Verticillium (Figure 2) revealed that the structure of the fungal microbiome in these two compartments is markedly different, with little overlap. The dominant OTUs from the roots were found at low frequencies in the rhizosphere, while OTUs that were dominant in the rhizosphere were absent or occurred at very low frequencies in the roots, in both field soils (Figure 2a–d). These results are in agreement with other recent studies of bacterial microbiomes of Arabidopsis thaliana and the fungal microbiome of Pisum sativum[6], [7], [58] that also show distinct communities in the rhizosphere and root endophyte compartments. Within each soil this pattern was the same for both Honeoye and Florence, however there were large differences between the rank abundance distributions of taxa between the two soils. The same lack of overlap between root and rhizosphere soil fungal communities was found in the presence of Verticillium (data not shown).


Influence of soil type, cultivar and Verticillium dahliae on the structure of the root and rhizosphere soil fungal microbiome of strawberry.

Nallanchakravarthula S, Mahmood S, Alström S, Finlay RD - PLoS ONE (2014)

Ranked abundance of the 30 most abundant fungal operational taxonomic units (OTUs) present in the rhizosphere and roots of two strawberry cultivars, Honeoye and Florence, grown in conventionally (A and B) and organically (C and D) managed field soils.Only OTUs with ≥95% identity are included.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4210224&req=5

pone-0111455-g002: Ranked abundance of the 30 most abundant fungal operational taxonomic units (OTUs) present in the rhizosphere and roots of two strawberry cultivars, Honeoye and Florence, grown in conventionally (A and B) and organically (C and D) managed field soils.Only OTUs with ≥95% identity are included.
Mentions: Rank abundance plots of the 30 most abundant fungal taxa in each of the rhizosphere and root compartments in the absence of Verticillium (Figure 2) revealed that the structure of the fungal microbiome in these two compartments is markedly different, with little overlap. The dominant OTUs from the roots were found at low frequencies in the rhizosphere, while OTUs that were dominant in the rhizosphere were absent or occurred at very low frequencies in the roots, in both field soils (Figure 2a–d). These results are in agreement with other recent studies of bacterial microbiomes of Arabidopsis thaliana and the fungal microbiome of Pisum sativum[6], [7], [58] that also show distinct communities in the rhizosphere and root endophyte compartments. Within each soil this pattern was the same for both Honeoye and Florence, however there were large differences between the rank abundance distributions of taxa between the two soils. The same lack of overlap between root and rhizosphere soil fungal communities was found in the presence of Verticillium (data not shown).

Bottom Line: Inoculation with the pathogen V. dahliae had a significant influence on community structure, generally decreasing the number of rhizosphere soil- and root-inhabiting fungi.Leptodontidium sp.The results suggest that 1) plant roots select microorganisms from the wider rhizosphere pool, 2) that both rhizosphere soil and root inhabiting fungal communities are influenced by V. dahliae and 3) that soil type has a stronger influence on both of these communities than cultivar.

View Article: PubMed Central - PubMed

Affiliation: Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.

ABSTRACT
Sustainable management of crop productivity and health necessitates improved understanding of the ways in which rhizosphere microbial populations interact with each other, with plant roots and their abiotic environment. In this study we examined the effects of different soils and cultivars, and the presence of a soil-borne fungal pathogen, Verticillium dahliae, on the fungal microbiome of the rhizosphere soil and roots of strawberry plants, using high-throughput pyrosequencing. Fungal communities of the roots of two cultivars, Honeoye and Florence, were statistically distinct from those in the rhizosphere soil of the same plants, with little overlap. Roots of plants growing in two contrasting field soils had high relative abundance of Leptodontidium sp. C2 BESC 319 g whereas rhizosphere soil was characterised by high relative abundance of Trichosporon dulcitum or Cryptococcus terreus, depending upon the soil type. Differences between different cultivars were not as clear. Inoculation with the pathogen V. dahliae had a significant influence on community structure, generally decreasing the number of rhizosphere soil- and root-inhabiting fungi. Leptodontidium sp. C2 BESC 319 g was the dominant fungus responding positively to inoculation with V. dahliae. The results suggest that 1) plant roots select microorganisms from the wider rhizosphere pool, 2) that both rhizosphere soil and root inhabiting fungal communities are influenced by V. dahliae and 3) that soil type has a stronger influence on both of these communities than cultivar.

Show MeSH