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Mineral Type and Solution Chemistry Affect the Structure and Composition of Actively Growing Bacterial Communities as Revealed by Bromodeoxyuridine Immunocapture and 16S rRNA Pyrosequencing

Abstract

Understanding how minerals affect bacterial communities and their in situ activities in relation to environmental conditions are central issues in soil microbial ecology, as minerals represent essential reservoirs of inorganic nutrients for the biosphere. To determine the impact of mineral type and solution chemistry on soil bacterial communities, we compared the diversity, composition, and functional abilities of a soil bacterial community incubated in presence/absence of different mineral types (apatite, biotite, obsidian). Microcosms were prepared containing different liquid culture media devoid of particular essential nutrients, the nutrients provided only in the introduced minerals and therefore only available to the microbial community through mineral dissolution by biotic and/or abiotic processes. By combining functional screening of bacterial isolates and community analysis by bromodeoxyuridine DNA immunocapture and 16S rRNA gene pyrosequencing, we demonstrated that bacterial communities were mainly impacted by the solution chemistry at the taxonomic level and by the mineral type at the functional level. Metabolically active bacterial communities varied with solution chemistry and mineral type. Burkholderia were significantly enriched in the obsidian treatment compared to the biotite treatment and were the most effective isolates at solubilizing phosphorous or mobilizing iron, in all the treatments. A detailed analysis revealed that the 16S rRNA gene sequences of the OTUs or isolated strains assigned as Burkholderia in our study showed high homology with effective mineral-weathering bacteria previously recovered from the same experimental site.

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Acknowledgments

This work was funded by an ANR grant (ANRJCJC SVSE7, project “BACTOWEATHER”). The authors thank Dr. S. McMahon for helpful discussions concerning BrdU immunocapture, Dr. J. Ranger and A. Legout for giving access to the Breuil-Chenue experimental site, and C. Bach for technical assistance. The UMR1136 is supported by the French Agency through the Laboratory of Excellence Arbre (ANR-11-LABX-0002-01).

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Kelly, L.C., Colin, Y., Turpault, MP. et al. Mineral Type and Solution Chemistry Affect the Structure and Composition of Actively Growing Bacterial Communities as Revealed by Bromodeoxyuridine Immunocapture and 16S rRNA Pyrosequencing. Microb Ecol 72, 428–442 (2016). https://doi.org/10.1007/s00248-016-0774-0

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Keywords

  • Forest soil
  • Minerals
  • BrdU immunocapture
  • 16S rDNA-based pyrosequencing
  • Culture-dependent approach