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Front. Plant Sci. | doi: 10.3389/fpls.2018.00345

Long-term irrigation affects the dynamics and activity of the wheat rhizosphere microbiome

  • 1Biological Sciences, University of Southern Mississippi, United States
  • 2Chemistry and Biomolecular Sciences, Macquarie University, Australia
  • 3Plant Pathology, Washington State University, United States
  • 4Biochemistry and Molecular Biology, Gustavus Adolphus College, United States
  • 5State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agriculture, Northwest A&F University, China
  • 6Wheat Health, Genetics, and Quality Research (USDA-ARS), United States

The Inland Pacific Northwest (IPNW) encompasses 1.6 million cropland hectares and is a major wheat-producing area in the western United States. The climate throughout the region is semi-arid, making the availability of water a significant challenge for IPNW agriculture. Much attention has been given to uncovering the effects of water stress on the physiology of wheat and the dynamics of its soilborne diseases. In contrast, the impact of soil moisture on the establishment and activity of microbial communities in the rhizosphere of dryland wheat remains poorly understood. We addressed this gap by conducting a three-year field study involving wheat grown in adjacent irrigated and dryland (rainfed) plots established in Lind, Washington State. We used deep amplicon sequencing of the V4 region of the 16S rRNA to characterize the responses of the wheat rhizosphere microbiome to overhead irrigation. We also characterized the population dynamics and activity of indigenous Phz+ rhizobacteria that produce the antibiotic phenazine-1-carboxylic acid (PCA) and contribute to the natural suppression of soilborne pathogens of wheat. Results of the study revealed that irrigation affected the Phz+ rhizobacteria adversely, which was evident from the significantly reduced plant colonization frequency, population size and levels of PCA in the field. The observed differences between irrigated and dryland plots were reproducible and amplified over the course of the study, thus identifying soil moisture as a critical abiotic factor that influences the dynamics and activity of indigenous Phz+ communities. The three seasons of irrigation had a slight effect on the overall diversity within the rhizosphere microbiome but led to significant differences in the relative abundances of specific OTUs. In particular, irrigation differentially affected multiple groups of Bacteroidetes and Proteobacteria, including taxa with known plant growth-promoting activity. Analysis of environmental variables revealed that the separation between irrigated and dryland treatments was due to changes in the water potential (Ψm) and pH. In contrast, the temporal changes in the composition of the rhizosphere microbiome correlated with temperature and precipitation. In summary, our long-term study provides insights into how the availability of water in a semi-arid agroecosystem shapes the belowground wheat microbiome.

Keywords: microbiome, rhizosphere, wheat, soil moisture, Pseudomonas, phenazine

Received: 15 Dec 2017; Accepted: 28 Feb 2018.

Edited by:

Corné M. Pieterse, Utrecht University, Netherlands

Reviewed by:

Leo Van Overbeek, Wageningen University & Research, Netherlands
Stéphane Compant, Austrian Institute of Technology, Austria  

Copyright: © 2018 Mavrodi, Mavrodi, Elbourne, Tetu, Bonsall, Parejko, Yang, Paulsen, Weller and Thomashow. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
Dr. David M. Weller, Wheat Health, Genetics, and Quality Research (USDA-ARS), 365 Johnson Hall, WSU, Pullman, 99164, Washington, United States,
Dr. Linda Thomashow, Wheat Health, Genetics, and Quality Research (USDA-ARS), 365 Johnson Hall, WSU, Pullman, 99164, Washington, United States,