Plant and Soil

, Volume 433, Issue 1–2, pp 401–413 | Cite as

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

  • Shamina Imran PathanEmail author
  • Tomáš Větrovský
  • Laura Giagnoni
  • Rahul Datta
  • Petr Baldrian
  • Paolo Nannipieri
  • Giancarlo Renella
Regular Article



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


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.


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.


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.


Metatranscriptomic mRNA Gene expression Functional diversity Rhizosphere Nitrogen use efficiency 



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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Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  • Shamina Imran Pathan
    • 1
    Email author
  • Tomáš Větrovský
    • 2
  • Laura Giagnoni
    • 1
  • Rahul Datta
    • 3
  • Petr Baldrian
    • 2
  • Paolo Nannipieri
    • 1
  • Giancarlo Renella
    • 1
  1. 1.Department of Agrifood Production and Environmental SciencesUniversity of FlorenceFlorenceItaly
  2. 2.Laboratory of Environmental MicrobiologyInstitute of Microbiology of the CASPraha 4Czech Republic
  3. 3.Department of Geology and PedologyMendel UniversityBrnoCzech Republic

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