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Phylogenetic and multivariate analyses to determine the effect of agricultural land-use intensification and soil physico-chemical properties on N-cycling microbial communities in drained Mediterranean peaty soils

Abstract

This study aims to provide first insights on the impact of land-use intensification and soil properties in shaping the composition of N-cycling microbial communities in Mediterranean peaty soils drained for agricultural purposes. An intensively cultivated peaty soil represented by an intensive maize cropping system was compared with an extensive grassland and an agricultural soil left abandoned for 15 years. Clone-library sequencing based on partial amoA and nirK functional genes was used to characterize the composition of ammonia-oxidizer microorganisms and nirK-type bacterial denitrifiers, respectively. The relative roles of land-use intensification and soil physico-chemical properties in community composition shaping were quantified by multivariate analyses. Phylogenetic and multivariate analyses showed that (i) the majority of sequences of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) grouped within the Nitrosotalea and Nitrosospira clusters, respectively; (ii) uncultured denitrifying bacteria were unique to our soil; (iii) land-use intensification shaped the composition of N-cycling communities; (iv) ammonia-oxidizing communities were driven by clay (AOA), bulk density (AOB), and exchangeable calcium (both AOA and AOB); and (v) nirK-type denitrifier bacteria were shaped by silt, ammonium, and exchangeable potassium. Based on the variation partitioning, soil properties were the primary determinants of the AOA and nirK-type denitrifier community composition, while land-use intensification was the major factor shaping the community composition of AOB. These findings improve the knowledge on such vulnerable agrosystems aiming to optimize the management of soil microbes in order to enhance the sustainability of N fertilization.

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Acknowledgments

This work represents a part of VC’s Ph.D. thesis, which was funded by the Scuola Superiore Sant’Anna, Pisa, Italy. The work was also supported by the “Consorzio di Bonifica Versilia-Massaciuccoli” and the “Regione Toscana” (“Restoration of a Mediterranean Drained Peatland”—https://sites.google.com/site/restomedpeatland/home).

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Ciccolini, V., Bonari, E., Ercoli, L. et al. Phylogenetic and multivariate analyses to determine the effect of agricultural land-use intensification and soil physico-chemical properties on N-cycling microbial communities in drained Mediterranean peaty soils. Biol Fertil Soils 52, 811–824 (2016). https://doi.org/10.1007/s00374-016-1121-9

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Keywords

  • Land-use change
  • Ammonia-oxidizing archaea (AOA)
  • Ammonia-oxidizing bacteria (AOB)
  • nirK
  • Nitrogen cycle
  • Microbial diversity