1. Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence
- Author
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Yannick Colin, M.-P. Turpault, Jizhong Zhou, Stéphane Uroz, J. D. Van Nostrand, O. Nicolitch, Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), University of Oklahoma (OU), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Tsinghua University [Beijing] (THU), Unité de recherche Biogéochimie des Ecosystèmes Forestiers (BEF), Institut National de la Recherche Agronomique (INRA), ANR (ANR-11-LABX-0002-01, ANR-11-JSV7-0001, ANR-11-LABX-0002-01), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), and Tsinghua University [Beijing]
- Subjects
0301 basic medicine ,Secondary Metabolism ,lcsh:Medicine ,microbiome ,facteur édaphique ,RNA, Ribosomal, 16S ,relation plante-microorganisme ,species richness ,arbre forestier feuillu ,lcsh:Science ,Soil Microbiology ,2. Zero hunger ,Rhizosphere ,Multidisciplinary ,biology ,Ecology ,Microbiota ,Soil classification ,Soil type ,Other Physical Sciences ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,diversité spécifique ,rhizosphère ,richesse spécifique ,16S ,030106 microbiology ,[SDU.STU]Sciences of the Universe [physics]/Earth Sciences ,Context (language use) ,plant - microorganism relationship ,fagus sylvatica ,Article ,03 medical and health sciences ,Fagus sylvatica ,european beech ,Botany ,Microbiome ,Beech ,Ribosomal ,lcsh:R ,toposéquence ,15. Life on land ,biology.organism_classification ,Carbon ,030104 developmental biology ,élément nutritif du sol ,Soil water ,séquence d'arn ,RNA ,Metagenome ,Microbial Interactions ,lcsh:Q ,Metagenomics ,Biochemistry and Cell Biology - Abstract
It has been rarely questioned as to whether the enrichment of specific bacterial taxa found in the rhizosphere of a given plant species changes with different soil types under field conditions and under similar climatic conditions. Understanding tree microbiome interactions is essential because, in contrast to annual plants, tree species require decades to grow and strongly depend on the nutritive resources of the soil. In this context, we tested using a natural toposequence the hypothesis that beech trees select specific taxa and functions in their rhizosphere based on the soil conditions and their nutritive requirements. Our 16S rRNA gene pyrosequencing analyses revealed that the soil type determines the taxa colonizing the beech rhizosphere. A rhizosphere effect was observed in each soil type, but a stronger effect was observed in the nutrient-poor soils. Although the communities varied significantly across the toposequence, we identified a core beech rhizosphere microbiome. Functionally, GeoChip analyses showed a functional redundancy across the toposequence, with genes related to nutrient cycling and to the bacterial immune system being significantly enriched in the rhizosphere. Altogether, the data suggest that, regardless of the soil conditions, trees enrich variable bacterial communities to maintain the functions necessary for their nutrition.
- Published
- 2017