Applied and Environmental Microbiology
Applied and Environmental Microbiology
5 years ago

Comparison of Microbial Ribosomal RNA Synthesis and Growth through Quantitative Stable Isotope Probing with H218O.

Bruce A Hungate, Katerina Papp, Egbert Schwartz
Growing bacteria have a high concentration of ribosomes to ensure sufficient protein synthesis, which is necessary for genome replication and cellular division. To elucidate whether metabolic activity of soil microorganisms is coupled with growth, we investigated the relationship between rRNA and DNA synthesis in a soil bacterial community using quantitative stable isotope probing (qSIP) with H218O. Most soil bacterial taxa were metabolically active and grew, and there was no significant difference between the isotopic composition of DNA and RNA extracted from soil incubated with H218O. The positive correlation between18O content of DNA and rRNA of taxa, with a slope statistically indistinguishable from 1 (slope = 0.96, 95% CI [lsqb]0.90 - 1.02[rsqb]), indicated that few taxa made new rRNA without synthesizing new DNA. There was no correlation between rRNA to DNA ratios obtained from sequencing libraries and the atom percent excess (APE)18O of DNA or rRNA, suggesting that the ratio of rRNA to DNA is a poor indicator of microbial growth or rRNA synthesis. Our results support the notion that metabolic activity is strongly coupled to cellular division, and suggest that non-dividing taxa do not dominate soil metabolic activity.IMPORTANCEUsing quantitative stable isotope probing of microbial RNA and DNA with H218O, we show that most soil taxa are metabolically active and grow because their nucleic acids are significantly labeled with18O. A majority of the populations that make new rRNA also grow, which argues against the common paradigm that most soil taxa are dormant. Additionally, our results indicate that relative sequence abundance-based RNA to DNA ratios, which are frequently used for identifying active microbial populations in the environment, underestimate the number of metabolically active taxa within soil microbial communities.

Publisher URL: http://doi.org/10.1128/AEM.02441-17

DOI: 10.1128/AEM.02441-17

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