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Title: Microbial rRNA Synthesis and Growth Compared through Quantitative Stable Isotope Probing with H 2 18O

Abstract

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 H 2 18O. 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 H 2 18O. The positive correlation between 18O content of DNA and rRNA of taxa, with a slope statistically indistinguishable from 1 (slope = 0.96; 95% confidence interval [CI], 0.90 to 1.02), 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 values 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 nondividing taxa do not dominate soil metabolic activity. IMPORTANCE: Utilizing quantitative stable isotopemore » probing of microbial RNA and DNA with H 2 18O, we show that most soil taxa are metabolically active and grow because their nucleic acids are significantly labeled with 18O. A majority of the populations that make new rRNA also grow, which argues against the common paradigm that most soil taxa are dormant. Moreover, 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.« less

Authors:
ORCiD logo [1]; ORCiD logo [2];  [2];  [2]
  1. Northern Arizona Univ., Flagstaff, AZ (United States); Univ. of Nevada, Las Vegas, NV (United States); Desert Research Inst. (DRI), Las Vegas, NV (United States)
  2. Northern Arizona Univ., Flagstaff, AZ (United States)
Publication Date:
Research Org.:
Northern Arizona Univ., Flagstaff, AZ (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23). Biological Systems Science Division
OSTI Identifier:
1503612
Grant/Contract Number:  
SC0010579
Resource Type:
Accepted Manuscript
Journal Name:
Applied and Environmental Microbiology
Additional Journal Information:
Journal Volume: 84; Journal Issue: 8; Journal ID: ISSN 0099-2240
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; rRNA; DNA; quantitative stable isotope probing; qSIP; atom percent excess 18O values of nucleic acids; APE 18O; density shift, rRNA-to-DNA ratio; relative sequence abundance; microbial activity; microbial growth; soil; atom percent excess; environmental microbiology; soil microbiology

Citation Formats

Papp, Katerina, Hungate, Bruce A., Schwartz, Egbert, and Stams, Alfons J. M. Microbial rRNA Synthesis and Growth Compared through Quantitative Stable Isotope Probing with H218O. United States: N. p., 2018. Web. doi:10.1128/aem.02441-17.
Papp, Katerina, Hungate, Bruce A., Schwartz, Egbert, & Stams, Alfons J. M. Microbial rRNA Synthesis and Growth Compared through Quantitative Stable Isotope Probing with H218O. United States. doi:10.1128/aem.02441-17.
Papp, Katerina, Hungate, Bruce A., Schwartz, Egbert, and Stams, Alfons J. M. Fri . "Microbial rRNA Synthesis and Growth Compared through Quantitative Stable Isotope Probing with H218O". United States. doi:10.1128/aem.02441-17. https://www.osti.gov/servlets/purl/1503612.
@article{osti_1503612,
title = {Microbial rRNA Synthesis and Growth Compared through Quantitative Stable Isotope Probing with H218O},
author = {Papp, Katerina and Hungate, Bruce A. and Schwartz, Egbert and Stams, Alfons J. M.},
abstractNote = {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% confidence interval [CI], 0.90 to 1.02), 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 values 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 nondividing taxa do not dominate soil metabolic activity. IMPORTANCE: Utilizing 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 with 18O. A majority of the populations that make new rRNA also grow, which argues against the common paradigm that most soil taxa are dormant. Moreover, 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.},
doi = {10.1128/aem.02441-17},
journal = {Applied and Environmental Microbiology},
number = 8,
volume = 84,
place = {United States},
year = {2018},
month = {2}
}

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Works referenced in this record:

Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
journal, July 2006

  • DeSantis, T. Z.; Hugenholtz, P.; Larsen, N.
  • Applied and Environmental Microbiology, Vol. 72, Issue 7, p. 5069-5072
  • DOI: 10.1128/AEM.03006-05