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Quantitative stable isotope probing with H218O reveals that most bacterial taxa in soil synthesize new ribosomal RNA

The ISME Journal (2018) | Download Citation

Abstract

Most soil bacterial taxa are thought to be dormant, or inactive, yet the extent to which they synthetize new rRNA is poorly understood. We analyzed 18O composition of RNA extracted from soil incubated with H218O and used quantitative stable isotope probing to characterize rRNA synthesis among microbial taxa. RNA was not fully labeled with 18O, peaking at a mean of 23.6 ± 6.8 atom percent excess (APE) 18O after eight days of incubation, suggesting some ribonucleotides in soil were more than eight days old. Microbial taxa varied in the degree they incorporated 18O into their rRNA over time and there was no correlation between the APE 18O of bacterial rRNA and their rRNA to DNA ratios, suggesting that the ratios were not appropriate to measure ribonucleotide synthesis. Our study indicates that, on average, 94% of soil taxa produced new rRNA and therefore were metabolically active.

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Subject Categories: Microbial population and community ecology, Microbial ecology and functional diversity of natural habitats

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Acknowledgements

This research was supported by award 1142096 from the National Science Foundation, division of solar programs, NSF DEB-1241094, the Department of Energy’s Biological Systems Science Division, Program in Genomic Science (DE-SC0010579, and DE-SC0016207), and by the IGERT Fellowship. Additionally, the authors would like to thank Dr. Paul Dijkstra, Dr. Matthew Bowker and Lela Andrews from Northern Arizona University.

Author information

Author notes

    • Katerina Papp

    Present address: Department of Civil and Environmental Engineering and Construction, University of Las Vegas, Las Vegas, NV, USA

Affiliations

  1. Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA

    • Katerina Papp
    • , Rebecca L. Mau
    • , Michaela Hayer
    • , Benjamin J. Koch
    • , Bruce A. Hungate
    •  & Egbert Schwartz
  2. Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA

    • Katerina Papp
    • , Rebecca L. Mau
    • , Michaela Hayer
    • , Benjamin J. Koch
    • , Bruce A. Hungate
    •  & Egbert Schwartz
  3. Division of Hydrological Sciences, Desert Research Institute, Las Vegas, NV, USA

    • Katerina Papp

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Conflict of interest

The authors declare that they have no conflict of interest.

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Correspondence to Katerina Papp.

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DOI

https://doi.org/10.1038/s41396-018-0233-7