Title: Microbial rRNA Synthesis and Growth Compared through Quantitative Stable Isotope Probing with H₂¹⁸O

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 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 andmore » 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.« less

Authors:

Papp, Katerina  ^[1];

• Search DOE PAGES for author "Papp, Katerina"
• Search DOE PAGES for ORCID "0000-0001-8126-4822"

Hungate, Bruce A.  ^[2];

• Search DOE PAGES for author "Hungate, Bruce A."
• Search DOE PAGES for ORCID "0000-0002-7337-1887"

Schwartz, Egbert ^[2]; Stams, Alfons J. M. ^[2]

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+ Show Author Affiliations

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:

Fri Feb 09 00:00:00 EST 2018

Research Org.:

Northern Arizona Univ., Flagstaff, AZ (United States)

Sponsoring Org.:

USDOE Office of Science (SC), Biological and Environmental Research (BER). 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