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Title: Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence

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.

Authors:
 [1]; ORCiD logo [1]; ORCiD logo [2];  [3];  [1];  [1]
  1. Univ. de Lorraine, Champenoux (France)
  2. Univ. of Oklahoma, Norman, OK (United States)
  3. Univ. of Oklahoma, Norman, OK (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth Sciences Division; Tsinghua Univ., Beijing (China)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1567096
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 7; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Colin, Y., Nicolitch, O., Van Nostrand, J. D., Zhou, J. Z., Turpault, M. -P., and Uroz, S. Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence. United States: N. p., 2017. Web. doi:10.1038/s41598-017-07639-1.
Colin, Y., Nicolitch, O., Van Nostrand, J. D., Zhou, J. Z., Turpault, M. -P., & Uroz, S. Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence. United States. doi:10.1038/s41598-017-07639-1.
Colin, Y., Nicolitch, O., Van Nostrand, J. D., Zhou, J. Z., Turpault, M. -P., and Uroz, S. Tue . "Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence". United States. doi:10.1038/s41598-017-07639-1. https://www.osti.gov/servlets/purl/1567096.
@article{osti_1567096,
title = {Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence},
author = {Colin, Y. and Nicolitch, O. and Van Nostrand, J. D. and Zhou, J. Z. and Turpault, M. -P. and Uroz, S.},
abstractNote = {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.},
doi = {10.1038/s41598-017-07639-1},
journal = {Scientific Reports},
number = 1,
volume = 7,
place = {United States},
year = {2017},
month = {8}
}

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