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

Xiangming Xu,Feng Wei,Richard J Harrison,Thomas Passey,Robert Saville

doi:10.1038/hortres.2015.22

Xiangming Xu, Feng Wei + Show 3 more

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https://doi.org/10.1038/hortres.2015.22

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Journal: Horticulture research	Publication Date: Jun 3, 2015
Citations: 38	License type: CC BY 4.0

Affiliation: East Malling Research (United Kingdom)

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.

Highlights

Verticillium dahliae Kleb. is a soil-borne fungal pathogen, which penetrates the roots of a wide range of host plant species causing the disease Verticillium wilt[1]
The amplicon-based metagenomic analysis of soil samples utilised in this study identified several groups of microbial organisms that may be involved in causing strawberry yield decline
Many operational taxonomy units (OTUs) differ in their abundance between samples from the yield decline and non-decline soils

Summary

Introduction

Verticillium dahliae Kleb. is a soil-borne fungal pathogen, which penetrates the roots of a wide range of host plant species causing the disease Verticillium wilt[1]. Wilt incidence tends to be higher in soils infested with the root lesion nematode, Pratylenchus penetrans, which feed on the roots causing wounds, increasing entry sites for the pathogen and affecting fungal infection/ colonisation of vascular tissue[2,3], the magnitude of this interaction may vary greatly with individual fungal strains[4] Chemical treatments, such as methyl bromide and chloropicrin, have been an indispensable tool for the past 40 years because of their excellent efficacy, effectively managing Verticillium wilt in strawberry; several of these treatments are already banned (e.g. methyl bromide) or face an uncertain future due to legislation (e.g. chloropicrin)[5]. Control efficacy depends on many factors, including soil characteristics, types of organic material, temperature, dosage and exposure time

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