Microbial Ecology

, Volume 72, Issue 2, pp 428–442 | Cite as

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

  • L. C. Kelly
  • Y. Colin
  • M-P. Turpault
  • S. Uroz
Soil Microbiology


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.


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



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).

Supplementary material

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Fig. S1 (PDF 117 kb)
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Fig. S2 (PDF 60 kb)
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Fig. S3 (PDF 121 kb)
248_2016_774_MOESM4_ESM.xlsx (49 kb)
Table S1 (XLSX 48 kb)
248_2016_774_MOESM5_ESM.xlsx (68 kb)
Table S2 (XLSX 67 kb)


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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • L. C. Kelly
    • 1
    • 2
    • 4
  • Y. Colin
    • 1
    • 2
    • 3
  • M-P. Turpault
    • 3
  • S. Uroz
    • 1
    • 2
    • 3
  1. 1.INRA, UMR1136 “Interactions Arbres-Microorganismes”, Centre INRA de NancyChampenouxFrance
  2. 2.Université de Lorraine, UMR1136 “Interactions Arbres-Microorganismes”Vandoeuvre-lès-NancyFrance
  3. 3.INRA UR1138 “Biogéochimie des Ecosystèmes Forestiers”, Centre INRA de NancyChampenouxFrance
  4. 4.School of Science and the Environment, Division of Biology and Conservation EcologyManchester Metropolitan UniversityManchesterUK

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