Microbial community development and unseen diversity recovery in inoculated sterile soil

Abstract

Soil is considered as one of the most biodiverse environments on Earth; yet, the taxonomy, occurrence, and role of its different microbial populations are largely unknown. Here, two sterilized soils (from England and Italy) were inoculated with a subsample of their initial microbial communities and/or those from the other soil to study their microbial community evolution. This approach compared two driving factors (original community and soil physico-chemical characteristics) for microbial community definition. After 2 months of incubation and based on metagenomic datasets, the two inoculated communities (from an English grassland and an Italian forest) possessed similar functional and taxonomical structures when inoculated in the same sterile soil. For example, the newly colonized Italian soil was dominated by Actinobacteria related organisms (>66 % of the detected community) with a functional distribution independent of the inoculated soil origin. In addition, some of the organisms that dominated the different inoculated communities after 2 months were similar for a given sterile soil whether they came from the English grassland or the Italian forest, and they had not been detected in the original microbial community from either soil. Thus, similar microorganisms with low representation from the two distinct communities emerged in each sterilized soil, thus increasing the microbial diversity recovered from the microbial community of the donor soil. So far, these observations support the idea that different temperate soil microbial communities have different evenness due to environmental physico-chemical variations, yet have similar community composition (richness), and thus develop similarly when colonizing the same habitat.

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Acknowledgment

We would like to thank Penny Hirsch and Ian Clark for providing the soil from Rothamsted, as well as Denis Le Paslier and Eric Pelletier for their involvement in generating metagenomic datasets at the Genoscope. This research was supported by the French National Research Agency (Agence National de Recherche) project Metasoil (Projet ANR-08-GENM-025). TOD was funded by the Rhone-Alpes Région.

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Correspondence to Timothy M. Vogel.

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Fig. S1
figure7

Box plots of variance based on the relative number of sequenced reads annotated into the specific subsystem for each of the nine experiments (see material and method section) in replicates after 8 weeks in microcosms and clustered by group. (GIF 3588 kb)

Fig. S2
figure8

Box plots of variance based on the relative number of sequenced reads annotated into the specific subsystem for each of the nine experiments (see material and method section) in replicates after 8 weeks in microcosms and clustered by group. (GIF 4296 kb)

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High resolution image (TIFF 799 kb)

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Delmont, T.O., Francioli, D., Jacquesson, S. et al. Microbial community development and unseen diversity recovery in inoculated sterile soil. Biol Fertil Soils 50, 1069–1076 (2014). https://doi.org/10.1007/s00374-014-0925-8

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Keywords

  • Metagenomic
  • Biodiversity
  • Richness
  • Evenness
  • Microbial colonization