《Nature》: 土壤根部的微生物群落 (封面故事)

Nature 488 (7409) | doi:10.1038/nature11237
发表日期：12年8月2日

一种陆地植物与其根部微生物组中的土壤微生物之间的关系，对这种植物的生长状态很重要。更深入了解这些微生物群落，将为控制植物生长和对病原体的易感性提供机会，尤其是在可持续性农业生产体系中。两个单独工作、但并行探索最佳实践的研究小组，对模型植物拟南芥的根部微生物群落进行了定性。这两个小组分别在两个大洲、用五种不同土壤类型进行研究，但却得出了相似的总体结论。每个“根腔”（根周围紧挨着根的“根围”及存在于“根内”的内生腔）中的菌落受土壤类型影响最大，受宿主基因型的影响较小。在自然土壤中，拟南芥植物优先被放线菌、变形菌、拟杆菌和绿弯菌建立菌落。而且对于未来研究工作来说重要的一点是，拟南芥的根在受控环境条件下对土壤细菌的选择性，会模仿那些在某种自然环境中生长的植物（对土壤细菌的选择性）。
封面：Tim Robberts/Getty Images。

Defining the core Arabidopsis thaliana root microbiome

Land plants associate with a root microbiota distinct from the complex microbial community present in surrounding soil. The microbiota colonizing the rhizosphere (immediately surrounding the root) and the endophytic compartment (within the root) contribute to plant growth, productivity, carbon sequestration and phytoremediation1, 2, 3. Colonization of the root occurs despite a sophisticated plant immune system4, 5, suggesting finely tuned discrimination of mutualists and commensals from pathogens. Genetic principles governing the derivation of host-specific endophyte communities from soil communities are poorly understood. Here we report the pyrosequencing of the bacterial 16S ribosomal RNA gene of more than 600 Arabidopsis thaliana plants to test the hypotheses that the root rhizosphere and endophytic compartment microbiota of plants grown under controlled conditions in natural soils are sufficiently dependent on the host to remain consistent across different soil types and developmental stages, and sufficiently dependent on host genotype to vary between inbred Arabidopsis accessions. We describe different bacterial communities in two geochemically distinct bulk soils and in rhizosphere and endophytic compartments prepared from roots grown in these soils. The communities in each compartment are strongly influenced by soil type. Endophytic compartments from both soils feature overlapping, low-complexity communities that are markedly enriched in Actinobacteria and specific families from other phyla, notably Proteobacteria. Some bacteria vary quantitatively between plants of different developmental stage and genotype. Our rigorous definition of an endophytic compartment microbiome should facilitate controlled dissection of plant–microbe interactions derived from complex soil communities.

http://www.nature.com/nature/journal/v488/n7409/full/nature11237.html

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