Bacterial communities in the rhizosphere of Vitis vinifera L. cultivated under distinct agricultural practices in Argentina

Plants interact with a myriad of microbial cells in the rhizosphere, an environment that is considered to be important for plant development. However, the differential structuring of rhizosphere microbial communities due to plant cultivation under differential agricultural practices remains to be de...

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Bibliographic Details
Published in:	Antonie van Leeuwenhoek Vol. 107; no. 2; pp. 575 - 588
Main Authors:	Vega-Avila, A. D, Gumiere, T, Andrade, P. A. M, Lima-Perim, J. E, Durrer, A, Baigori, M, Vazquez, F, Andreote, F. D
Format:	Journal Article
Language:	English
Published:	Cham Springer-Verlag 01-02-2015 Springer International Publishing Springer Nature B.V
Subjects:	Acidobacteria Actinobacteria Agricultural practices Agriculture - methods alpha-Proteobacteria Argentina Bacteria bacterial communities Bacteriodetes beta-Proteobacteria Biomedical and Life Sciences Biota Cultivation Denaturing Gradient Gel Electrophoresis DNA, Bacterial - chemistry DNA, Bacterial - genetics DNA, Ribosomal - chemistry DNA, Ribosomal - genetics Firmicutes Fruit cultivation genes high-throughput nucleotide sequencing Life Sciences Medical Microbiology metabolism Microbial activity Microbiology microbiome Nitrogen fixation Original Paper Oxidoreductases - genetics Phylogenetics Planctomycetes plant development Plant metabolism Plant Sciences Plant species Proteobacteria quantitative polymerase chain reaction Real-Time Polymerase Chain Reaction Rhizosphere ribosomal RNA RNA, Ribosomal, 16S - genetics Sequence Analysis, DNA Soil Microbiology Soil microorganisms Soil Science & Conservation Taxonomy Verrucomicrobia Verrucomicrobium Vineyards Vitaceae Vitis - growth & development Vitis vinifera Argentina Cultivation-independent analysis Bacterial communities Plant–microbe interactions Rhizosphere microbiome Organic management
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Summary:	Plants interact with a myriad of microbial cells in the rhizosphere, an environment that is considered to be important for plant development. However, the differential structuring of rhizosphere microbial communities due to plant cultivation under differential agricultural practices remains to be described for most plant species. Here we describe the rhizosphere microbiome of grapevine cultivated under conventional and organic practices, using a combination of cultivation-independent approaches. The quantification of bacterial 16S rRNA and nifH genes, by quantitative PCR (qPCR), revealed similar amounts of these genes in the rhizosphere in both vineyards. PCR-DGGE was used to detect differences in the structure of bacterial communities, including both the complete whole communities and specific fractions, such as Alphaproteobacteria, Betaproteobacteria, Actinobacteria, and those harboring the nitrogen-fixing related gene nifH. When analyzed by a multivariate approach (redundancy analysis), the shifts observed in the bacterial communities were poorly explained by variations in the physical and chemical characteristics of the rhizosphere. These approaches were complemented by high-throughput sequencing (67,830 sequences) based on the V6 region of the 16S rRNA gene, identifying the major bacterial groups present in the rhizosphere of grapevines: Proteobacteria, Actinobacteria, Firmicutes, Bacteriodetes, Acidobacteria, Cloroflexi, Verrucomicrobia and Planctomycetes, which occur in distinct proportions in the rhizosphere from each vineyard. The differences might be related to the selection of plant metabolism upon distinct reservoirs of microbial cells found in each vineyard. The results fill a gap in the knowledge of the rhizosphere of grapevines and also show distinctions in these bacterial communities due to agricultural practices.
Bibliography:	http://dx.doi.org/10.1007/s10482-014-0353-7 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	0003-6072 1572-9699
DOI:	10.1007/s10482-014-0353-7