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Influence of Sugarcane Variety on Rhizosphere Microbiota Under Irrigated and Water-Limiting Conditions

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Abstract

Drought is one of the main problems linked to climate change that is faced by agriculture, affecting various globally important crops, including sugarcane. Environmentally sustainable strategies have been sought to mitigate the effects of climate change on crops. Among them, the use of beneficial microorganisms offers a promising approach. However, it is still necessary to understand the mechanisms that regulate plant-microorganism interactions, in normal situations and under stress. In this work, the rhizosphere metagenomes of two sugarcane varieties, one resistant and the other susceptible to drought, were compared under normal conditions and under water-limiting conditions. The results showed that for the drought-resistant sugarcane variety, bacteria belonging to the order Sphingomonadales and the family Xanthomonadaceae presented increased activities in terms of mobility, colonization, and cell growth. In contrast, the rhizosphere associated with the drought-sensitive variety exhibited increases of bacteria belonging to the family Polyangiaceae, and the genus Streptomyces, with modifications in DNA metabolism and ribosome binding proteins. The results pointed to variation in the rhizosphere microbiota that was modulated by the host plant genotype, revealing potential bacterial candidates that could be recruited to assist plants during water-limiting conditions.

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Data Availability

The datasets generated during the current study are available in the NCBI Sequence Read Archive (SRA), under accession numbers SRX10956439 to SRX10956441. The rhizosphere microbiome associated with the drought-resistant sugarcane has been previously deposited by Pereira et al. [12], under accession numbers SRR10617562 to SRR10617570.

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Acknowledgements

The authors thank the Centre for Sugar Technology for supplying the plant material, Dr Alexandra Sawaya for assistance in the chromatographic analyses, and the Irish Centre for High-End Computing (ICHEC) for supporting the bioinformatic analyses. We are also grateful to the São Paulo State Research Foundation (FAPESP), Coordination for the Improvement of Higher Education Personnel (CAPES), and the National Council for Scientific and Technological Development (CNPq).

Funding

This work was supported by the São Paulo State Research Foundation (FAPESP, Grant Numbers 2015/00408–5 and 2016/08994–3), FAPESP/CAPES (Grant Number 2014/05929–0), and the National Council for Scientific and Technological Development (CNPq, Grant Number 140547/2014–2).

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Authors and Affiliations

  1. Laboratory of Environmental Molecular Biology, Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas (UNICAMP), Campinas, SP, Brazil

    Leticia B. Pereira & Laura M. M. Ottoboni

  2. Systems Biology Laboratory, Department of Genetics, Evolution, Microbiology and Immunology, State University of Campinas (UNICAMP), Campinas, SP, Brazil

    Victor Marques de Oliveira Gambarini & Renato Vicentini

  3. Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland

    Alexandre Barretto de Menezes

Authors
  1. Leticia B. Pereira
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  2. Victor Marques de Oliveira Gambarini
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  3. Alexandre Barretto de Menezes
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  4. Laura M. M. Ottoboni
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  5. Renato Vicentini
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Contributions

LBP: carried out the experiments. LBP, VMOG, ABM, and RV: analyzed the data. LBP: wrote the manuscript, with support from VMOG, ABM, RV, and LMMO. LMMO and RV: supervised the project.

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Correspondence to Leticia B. Pereira.

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Pereira, L.B., Gambarini, V.M.d., de Menezes, A.B. et al. Influence of Sugarcane Variety on Rhizosphere Microbiota Under Irrigated and Water-Limiting Conditions. Curr Microbiol 79, 246 (2022). https://doi.org/10.1007/s00284-022-02946-x

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