Antonie van Leeuwenhoek

, Volume 107, Issue 3, pp 785–797 | Cite as

Exploring the dynamics of bacterial community composition in soil: the pan-bacteriome approach

  • Giovanni Bacci
  • Maria Teresa Ceccherini
  • Alessia Bani
  • Marco Bazzicalupo
  • Maurizio Castaldini
  • Marco Galardini
  • Luciana Giovannetti
  • Stefano Mocali
  • Roberta Pastorelli
  • Ottorino Luca Pantani
  • Paola Arfaioli
  • Giacomo Pietramellara
  • Carlo Viti
  • Paolo Nannipieri
  • Alessio Mengoni
Original Paper

Abstract

We performed a longitudinal study (repeated observations of the same sample over time) to investigate both the composition and structure of temporal changes of bacterial community composition in soil mesocosms, subjected to three different treatments (water and 5 or 25 mg kg−1 of dried soil Cd2+). By analogy with the pan genome concept, we identified a core bacteriome and an accessory bacteriome. Resident taxa were assigned to the core bacteriome, while occasional taxa were assigned to the accessory bacteriome. Core and accessory bacteriome represented roughly 35 and 50 % of the taxa detected, respectively, and were characterized by different taxonomic signatures from phylum to genus level while 15 % of the taxa were found to be unique to a particular sample. In particular, the core bacteriome was characterized by higher abundance of members of Planctomycetes, Actinobacteria, Verrucomicrobia and Acidobacteria, while the accessory bacteriome included more members of Firmicutes, Clamydiae and Proteobacteria, suggesting potentially different responses to environmental changes of members from these phyla. We conclude that the pan-bacteriome model may be a useful approach to gain insight for modeling bacterial community structure and inferring different abilities of bacteria taxa.

Keywords

Core and accessory bacteriome Bacterial communities 16S rRNA metabarcoding Soil Cd 

Supplementary material

10482_2014_372_MOESM1_ESM.rar (975 kb)
Supplementary material 1 (RAR 974 kb)
10482_2014_372_MOESM2_ESM.docx (12 kb)
Supplementary material 2 (DOCX 12 kb)

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Giovanni Bacci
    • 1
    • 2
  • Maria Teresa Ceccherini
    • 3
  • Alessia Bani
    • 1
  • Marco Bazzicalupo
    • 1
  • Maurizio Castaldini
    • 4
  • Marco Galardini
    • 5
  • Luciana Giovannetti
    • 3
  • Stefano Mocali
    • 4
  • Roberta Pastorelli
    • 4
  • Ottorino Luca Pantani
    • 3
  • Paola Arfaioli
    • 3
  • Giacomo Pietramellara
    • 3
  • Carlo Viti
    • 3
  • Paolo Nannipieri
    • 3
  • Alessio Mengoni
    • 1
  1. 1.Department of BiologyUniversity of FlorenceSesto FiorentinoItaly
  2. 2.Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per lo Studio delle Relazioni tra Pianta e Suolo (CRA-RPS)RomeItaly
  3. 3.Department of Agrifood Production and Environmental ScienceUniversity of FlorenceFlorenceItaly
  4. 4.Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per l’Agrobiologia e la Pedologia (CRA-ABP)FlorenceItaly
  5. 5.EMBL-EBI––European Bioinformatics Institute Wellcome Trust Genome Campus HinxtonCambridgeUK

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