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Microbial expression profiles in the rhizosphere of two maize lines differing in N use efficiency

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Abstract

Aims

Study of the microbial expression profile in the rhizosphere of two contrasting maize lines, differing in the Nitrogen Use efficiency (NUE).

Methods

The Lo5 and T250 inbred maize characterized by high and low NUE, respectively, were grown in rhizoboxes allowing precise sampling of rhizosphere and bulk soils. We conducted metatranscriptomic of rhizosphere and bulk soil by m-RNA sequencing.

Results

High activity of bacteria was observed compared to archaea and fungi in both rhizosphere and bulk soils of both maize lines. Proteobacteria and Actinobacteria were involved in all processes, while significant shifts occurred in the expression of Bacteroidetes, Chloroflexi, Firmicutes, Acidobacteria, Cyanobacteria, archaea and fungi, indicating their possible role in specific processes occurring in rhizosphere of two maize lines. Maize plants with different NUE induced changes in microbial processes, especially in N cycling, with high NUE maize favouring ammonification and nitrification processes and low NUE maize inducing expression of genes encoding for denitrifying process, likely favoured by longer N residence time in the rhizosphere.

Conclusions

Overall our results showed that maize lines with different NUE shaped not only microbial communities but also conditioned the microbial functions and the N cycle in their rhizosphere. While the plant NUE is genetically determined and an inherent plant physiological trait, it also stimulates changes in the microbial community composition and gene expression in the rhizosphere, favouring microbial processes that mineralize and oxidize N in the high NUE maize. These results can improve our understanding on plant-microbe interaction in the rhizosphere of crop plants with potential applications for improving the management practices of the agro-ecosystems.

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Acknowledgments

This research was supported by the Ministry for Education and Research project “PRIN 2009MWY5F9”. Shamina Imran Pathan was supported by the Marie Curie ITN action “TRAINBIODIVERSE”, grant no. 289949. The Department of Agrifood Production and Environmental Sciences thanks to the Ente Cassa di Risparmio di Firenze for the financial support for the acquisition of new instruments. Moreover, we would like to thank Editor and anonymous Reviewer for their valuable suggestions.

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Authors and Affiliations

  1. Department of Agrifood Production and Environmental Sciences, University of Florence, Piazzale delle Cascine 28, 50144, Florence, Italy

    Shamina Imran Pathan, Laura Giagnoni, Paolo Nannipieri & Giancarlo Renella

  2. Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, 14220, Praha 4, Czech Republic

    Tomáš Větrovský & Petr Baldrian

  3. Department of Geology and Pedology, Mendel University, 613 00, Brno, Czech Republic

    Rahul Datta

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  1. Shamina Imran Pathan
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  2. Tomáš Větrovský
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  3. Laura Giagnoni
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  4. Rahul Datta
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  5. Petr Baldrian
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Correspondence to Shamina Imran Pathan.

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Pathan, S.I., Větrovský, T., Giagnoni, L. et al. Microbial expression profiles in the rhizosphere of two maize lines differing in N use efficiency. Plant Soil 433, 401–413 (2018). https://doi.org/10.1007/s11104-018-3852-x

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