Molecular Identification of Fungal Communities in a Soil Cultivated with Vegetables and Soil Suppressiveness toRhizoctonia solani

Silvana Pompéia Val-Moraes,Eliana Gertrudes Macedo Lemos,Eliamar Aparecida Nascimbem Pedrinho,Lucia Maria Carareto-Alves

doi:10.1155/2013/268768

Silvana Pompéia Val-Moraes, Eliana Gertrudes Macedo Lemos + Show 2 more

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https://doi.org/10.1155/2013/268768

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Abstract

Fungi constitute an important part of the soil ecosystem, playing key roles in decomposition, cycling processes, and biotic interactions. Molecular methods have been used to assess fungal communities giving a more realistic view of their diversity. For this purpose, total DNA was extracted from bulk soils cultivated with tomato (STC), vegetables (SHC), and native forest (SMS) from three sites of the Taquara Branca river basin in Sumaré County, São Paulo State, Brazil. This metagenomic DNA was used as a template to amplify fungal 18S rDNA sequences, and libraries were constructed inEscherichia coliby cloning PCR products. The plasmid inserts were sequenced and compared to known rDNA sequences in the GenBank database. Of the sequenced clones, 22 were obtained from the SMS sample, 18 from the SHC sample, and 6 from the STC sample. Although most of the clone sequences did not match the sequences present in the database, individual amplified sequences matched with Glomeromycota (SMS), Fungi incertae sedis (SMS), and Neocallimastigomycota (SHC). Most of the sequences from the amplified taxa represent uncultured fungi. The molecular analysis of variance (AMOVA) indicated that fluctuations observed of haplotypes in the composition may be related to herbicide application.

Highlights

Despite the importance of soil microbial communities in regulating soil ecosystem-level processes, such as the nutrient cycle and organic matter decomposition, little is known about the structure of these microbial communities and the factors that influence it in soils
Comparative studies have reported that microbial communities can change in response to soil disturbances, and differences have been observed between microbial communities in fields with different histories of soil amendment, irrigation, tillage, and plant community structure [4]
The organic matter was lowest in soil cultivated with tomatoes

Summary

Introduction

Despite the importance of soil microbial communities in regulating soil ecosystem-level processes, such as the nutrient cycle and organic matter decomposition, little is known about the structure of these microbial communities and the factors that influence it in soils This lack of knowledge arises, in part, from the enormous complexity of soil microbial communities, which are estimated to contain more than 4,000 different genomic equivalents in a single gram of soil [1]. Concerning rDNA genes, the small subunit 16S has been successfully used to Applied and Environmental Soil Science assess bacterial diversity in natural ecosystems, offering the possibility to discover new species [6,7,8,9] This method has been successful for the evaluation of bacterial communities in soil [8] of the region studied in the present paper

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