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Alterations in the Endophyte-Enriched Root-Associated Microbiome of Rice Receiving Growth-Promoting Treatments of Urea Fertilizer and Rhizobium Biofertilizer

  • Plant Microbe Interactions
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Abstract

We examined the bacterial endophyte–enriched root-associated microbiome within rice (Oryza sativa) 55 days after growth in soil with and without urea fertilizer and/or biofertilization with a growth-promotive bacterial strain (Rhizobium leguminosarum bv. trifolii E11). After treatment to deplete rhizosphere/rhizoplane communities, washed roots were macerated and their endophyte-enriched communities were analyzed by 16S ribosomal DNA 454 amplicon pyrosequencing. This analysis clustered 99,990 valid sequence reads into 1105 operational taxonomic units (OTUs) with 97% sequence identity, 133 of which represented a consolidated core assemblage representing 12.04% of the fully detected OTU richness. Taxonomic affiliations indicated Proteobacteria as the most abundant phylum (especially α- and γ-Proteobacteria classes), followed by Firmicutes, Bacteroidetes, Verrucomicrobia, Actinobacteria, and several other phyla. Dominant genera included Rheinheimera, unclassified Rhodospirillaceae, Pseudomonas, Asticcacaulis, Sphingomonas, and Rhizobium. Several OTUs had close taxonomic affiliation to genera of diazotrophic rhizobacteria, including Rhizobium, unclassified Rhizobiales, Azospirillum, Azoarcus, unclassified Rhizobiaceae, Bradyrhizobium, Azonexus, Mesorhizobium, Devosia, Azovibrio, Azospira, Azomonas, and Azotobacter. The endophyte-enriched microbiome was restructured within roots receiving growth-promoting treatments. Compared to the untreated control, endophyte-enriched communities receiving urea and/or biofertilizer treatments were significantly reduced in OTU richness and relative read abundances. Several unique OTUs were enriched in each of the treatment communities. These alterations in structure of root-associated communities suggest dynamic interactions in the host plant microbiome, some of which may influence the well-documented positive synergistic impact of rhizobial biofertilizer inoculation plus low doses of urea-N fertilizer on growth promotion of rice, considered as one of the world’s most important food crops.

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Acknowledgments

We thank Terrance Marsh for the helpful revisions to the manuscript.

Funding

This work was supported by the National Science Foundation grant INT 0211267, US-Egypt Science & Technology Fund BIO10-001-011 Contract/Agreement No. 303, US-Egypt Science & Technology Joint Fund 3852 (58-3148-1-140), US Department of Energy Office of Biological and Environmental Research grant DE-FG02-99ER62848, the Michigan AgBioResearch program, and University Grant Commission No. F-5 20/2013[IC], India.

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Authors and Affiliations

  1. Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA

    Prabhat N. Jha, Benli Chai & Frank B. Dazzo

  2. Department of Civil & Environmental Engineering, Michigan State University, East Lansing, MI, 48824, USA

    Abu-Bakr Gomaa, Tiffany M. Stedtfeld, Robert D. Stedtfeld & Syed A. Hashsham

  3. Department of Microbiology, Sakha Agricultural Research Station, Kafr El-Sheikh, 33717, Egypt

    Youssef G. Yanni & Abd-Elgawad Y. El-Saadany

  4. Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA

    Stephan Gantner, James Cole & Frank B. Dazzo

  5. Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, 333031, India

    Prabhat N. Jha

  6. Department of Biochemistry, Faculty of Science, King Abdul-Aziz University, Jeddah, Saudi Arabia

    Abu-Bakr Gomaa

  7. Department of Agricultural Microbiology, National Research Centre, Cairo, Egypt

    Abu-Bakr Gomaa

  8. Swift Biosciences, Inc., Ann Arbor, MI, USA

    Tiffany M. Stedtfeld, Robert D. Stedtfeld & Benli Chai

  9. Department of Medicine, Economics and Health, University of Applied Sciences, Cologne, Germany

    Stephan Gantner

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The sequence data discussed in this publication have been disposed in NCBI’s Sequence Read Archive (SRA) and are accessible through BioProject accession PRJNA526033.

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Jha, P.N., Gomaa, AB., Yanni, Y.G. et al. Alterations in the Endophyte-Enriched Root-Associated Microbiome of Rice Receiving Growth-Promoting Treatments of Urea Fertilizer and Rhizobium Biofertilizer. Microb Ecol 79, 367–382 (2020). https://doi.org/10.1007/s00248-019-01406-7

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