, Volume 132, Issue 1–2, pp 185–201 | Cite as

Successional patterns of key genes and processes involved in the microbial nitrogen cycle in a salt marsh chronosequence

  • Joana Falcão Salles
  • Michele C. Pereira e SilvaEmail author
  • Francisco Dini-Andreote
  • Armando C. F. Dias
  • Nadine Guillaumaud
  • Franck Poly
  • Jan Dirk van Elsas


Here, we investigated the patterns of microbial nitrogen cycling communities along a chronosequence of soil development in a salt marsh. The focus was on the abundance and structure of genes involved in N fixation (nifH), bacterial and archaeal ammonium oxidation (amoA; AOB and AOA), and the abundances of genes involved in denitrification (nirS, nirK, nosZ). Potential nitrification and denitrification activities were also measured, and increases in nitrification were found in soils towards the end of succession, whereas denitrification became maximal in soils at the intermediate stages. The nifH, nirK and nirS gene markers revealed increases in the sizes of the respective functional groups towards the intermediate stage (35 years), remaining either constant (for nifH) or slightly declining towards the latest stage of succession (for nirK and nirS). Moreover, whereas the AOB abundance peaked in soils at the intermediate stage, that of AOA increased linearly along the chronosequence. The abundance of nosZ was roughly constant, with no significant regression. The drivers of changes in abundance and structure were identified using path analysis; whereas the ammonia oxidizers (AOA and AOB) showed patterns that followed mainly N availability, those of the nitrogen fixers followed plant diversity and soil structure. The patterns of denitrifiers were group-dependent, following the patterns of plant diversity (nirK and nirS) and belowground shifts (nosZ). The variation observed for the microbial groups associated with the same function highlights their differential contribution at different stages of soil development, revealing an interplay of changes in terms of niche complementarity and adaptation to the local environment.


Nitrogen cycling Microbial ecology Functional genes Ecological niches Environmental microbiology 



This work was supported by the NWO-ERGO Programme and by an NWO-RUG fellowship to FD-A, and it was part of a collaborative project with Prof. dr. Han Olff, Community and Conservation Ecology (COCON), Groningen University, The Netherlands. We thank Maarten Schrama for help in the sampling expeditions. Nitrification and denitrification measurements were performed at the AME platform (UMR5557-USC1364, FR41, University of Lyon).

Supplementary material

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Copyright information

© Springer International Publishing Switzerland 2017

Authors and Affiliations

  • Joana Falcão Salles
    • 1
  • Michele C. Pereira e Silva
    • 1
    • 2
    Email author
  • Francisco Dini-Andreote
    • 1
  • Armando C. F. Dias
    • 2
  • Nadine Guillaumaud
    • 3
  • Franck Poly
    • 3
  • Jan Dirk van Elsas
    • 1
  1. 1.Department of Microbial Ecology, GELIFESUniversity of GroningenGroningenThe Netherlands
  2. 2.Department of Soil Science, “Luiz de Queiroz” College of AgricultureUniversity of São PauloPiracicabaBrazil
  3. 3.Microbial Ecology CentreCNRS-Université Lyon 1VilleurbanneFrance

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