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Spontaneous Mutations in the Nitrate Reductase Gene napC Drive the Emergence of Eco-friendly Low-N2O-Emitting Alfalfa Rhizobia in Regions with Different Climates

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Abstract

We have recently shown that commercial alfalfa inoculants (e.g., Sinorhizobium meliloti B399), which are closely related to the denitrifier model strain Sinorhizobium meliloti 1021, have conserved nitrate, nitrite, and nitric oxide reductases associated with the production of the greenhouse gas nitrous oxide (N2O) from nitrate but lost the N2O reductase related to the degradation of N2O to gas nitrogen. Here, we screened a library of nitrogen-fixing alfalfa symbionts originating from different ecoregions and containing N2O reductase genes and identified novel rhizobia (Sinorhizobium meliloti INTA1–6) exhibiting exceptionally low N2O emissions. To understand the genetic basis of this novel eco-friendly phenotype, we sequenced and analyzed the genomes of these strains, focusing on their denitrification genes, and found mutations only in the nitrate reductase structural gene napC. The evolutionary analysis supported that, in these natural strains, the denitrification genes were inherited by vertical transfer and that their defective nitrate reductase napC alleles emerged by independent spontaneous mutations. In silico analyses showed that mutations in this gene occurred in ssDNA loop structures with high negative free energy (−ΔG) and that the resulting mutated stem-loop structures exhibited increased stability, suggesting the occurrence of transcription-associated mutation events. In vivo assays supported that at least one of these ssDNA sites is a mutational hot spot under denitrification conditions. Similar benefits from nitrogen fixation were observed when plants were inoculated with the commercial inoculant B399 and strains INTA4–6, suggesting that the low-N2O-emitting rhizobia can be an ecological alternative to the current inoculants without resigning economic profitability.

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Acknowledgments

We thank Andrea Puebla and Pablo Vera (IABIMO) for their technical support in genomic sequencing.

Funding

This work was supported by Grants PICT-2017-0674 and FVT-39 provided to Nicolás Ayub.

Author information

Authors and Affiliations

  1. Instituto de Agrobiotecnología y Biología Molecular (IABIMO-CONICET), Buenos Aires, Argentina

    Silvina Brambilla, Gabriela Soto, Cintia Jozefkowicz & Nicolás Ayub

  2. Instituto de Genética (IGEAF-INTA), Buenos Aires, Argentina

    Silvina Brambilla, Gabriela Soto, Cintia Jozefkowicz & Nicolás Ayub

  3. Estación Experimental Agropecuaria Manfredi (INTA), Córdoba, Argentina

    Ariel Odorizzi & Valeria Arolfo

  4. Ottawa Research and Development Centre (AAFC), Ottawa, ON, Canada

    Wayne McCormick

  5. Departamento de Biología Molecular (UNRC), Córdoba, Argentina

    Emiliano Primo & Walter Giordano

Authors
  1. Silvina Brambilla
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  2. Gabriela Soto
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  3. Ariel Odorizzi
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  4. Valeria Arolfo
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  5. Wayne McCormick
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  6. Emiliano Primo
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  7. Walter Giordano
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  8. Cintia Jozefkowicz
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  9. Nicolás Ayub
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Corresponding author

Correspondence to Nicolás Ayub.

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Brambilla, S., Soto, G., Odorizzi, A. et al. Spontaneous Mutations in the Nitrate Reductase Gene napC Drive the Emergence of Eco-friendly Low-N2O-Emitting Alfalfa Rhizobia in Regions with Different Climates. Microb Ecol 79, 1044–1053 (2020). https://doi.org/10.1007/s00248-019-01473-w

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