Vega-Avila A D, Gumiere T, Andrade P A M, Lima-Perim J E, Durrer A, Baigori M, Vazquez F, Andreote F D
Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo (ESALQ/USP), Av. Padua Dias, 11, Piracicaba, Brazil,
Antonie Van Leeuwenhoek. 2015 Feb;107(2):575-88. doi: 10.1007/s10482-014-0353-7. Epub 2014 Dec 20.
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.
植物与根际中无数的微生物细胞相互作用，根际环境被认为对植物生长发育至关重要。然而，对于大多数植物物种而言，不同农业实践下植物栽培导致的根际微生物群落结构差异仍有待描述。在此，我们结合多种非培养方法，描述了常规栽培和有机栽培条件下葡萄的根际微生物组。通过定量PCR（qPCR）对细菌16S rRNA和nifH基因进行定量分析，结果显示两个葡萄园根际中这些基因的含量相似。利用PCR-DGGE检测细菌群落结构的差异，包括整个群落以及特定分类群，如α-变形菌纲、β-变形菌纲、放线菌纲以及携带固氮相关基因nifH的细菌。通过多变量分析方法（冗余分析）进行分析时，根际物理和化学特性的变化对细菌群落中观察到的变化解释力较弱。这些方法通过基于16S rRNA基因V6区域的高通量测序（67,830条序列）得到补充，确定了葡萄根际中存在的主要细菌类群：变形菌门、放线菌门、厚壁菌门、拟杆菌门、酸杆菌门、绿弯菌门、疣微菌门和浮霉菌门，它们在每个葡萄园根际中的比例各不相同。这些差异可能与每个葡萄园不同微生物细胞库对植物代谢的选择有关。研究结果填补了葡萄根际知识方面的空白，同时也表明了农业实践导致这些细菌群落存在差异。
