Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer

Orellana, Luis H.; Hatt, Janet K.; Iyer, Ramsunder; Chourey, Karuna; Hettich, Robert L.; Spain, Jim C.; Yang, Wendy H.; Chee-Sanford, Joanne C.; Sanford, Robert A.; Löffler, Frank E.; Konstantinidis, Konstantinos T.

doi:10.1038/s41598-019-53679-0

Title: Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer

Journal Article · 26 November 2019 · Scientific Reports

DOI: https://doi.org/10.1038/s41598-019-53679-0 · OSTI ID:1619597

Orellana, Luis H. ^[1]; Hatt, Janet K. ^[1];

^[2]; Chourey, Karuna ^[3]; Hettich, Robert L. ^[3]; Spain, Jim C. ^[4];

^[5]; Chee-Sanford, Joanne C. ^[6]; Sanford, Robert A. ^[5];

^[7]; Konstantinidis, Konstantinos T. ^[1]

Georgia Inst. of Technology, Atlanta, GA (United States)
Univ. of Tennessee, Knoxville, TN (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Chemical Sciences Division
Univ. of West Florida, Pensacola, FL (United States)
Univ. of Illinois at Urbana-Champaign, IL (United States)
U.S. Dept. of Agriculture, Urbana, IL (United States)
Univ. of Tennessee, Knoxville, TN (United States). Center for Environmental Biotechnology, Dept. of Microbiology, Dept. of Civil and Environmental Engineering, and Dept. of Biosystems Engineering and Soil Science

To what extent multi-omic techniques could reflect in situ microbial process rates remains unclear, especially for highly diverse habitats like soils. Here, we performed microcosm incubations using sandy soil from an agricultural site in Midwest USA. Microcosms amended with isotopically labeled ammonium and urea to simulate a fertilization event showed nitrification (up to 4.1 ± 0.87 µg N-NO3- g-1 dry soil d-1) and accumulation of N₂O after 192 hours of incubation. Nitrification activity (NH₄⁺ → NH₂OH → NO → NO₂- → NO₃^-) was accompanied by a 6-fold increase in relative expression of the 16S rRNA gene (RNA/DNA) between 10 and 192 hours of incubation for ammonia-oxidizing bacteria Nitrosomonas and Nitrosospira, unlike archaea and comammox bacteria, which showed stable gene expression. A strong relationship between nitrification activity and betaproteobacterial ammonia monooxygenase and nitrite oxidoreductase transcript abundances revealed that mRNA quantitatively reflected measured activity and was generally more sensitive than DNA under these conditions. Although peptides related to housekeeping proteins from nitrite-oxidizing microorganisms were detected, their abundance was not significantly correlated with activity, revealing that meta-proteomics provided only a qualitative assessment of activity. Altogether, these findings underscore the strengths and limitations of multi-omic approaches for assessing diverse microbial communities in soils and provide new insights into nitrification.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1619597

Alternate ID(s):: OSTI ID: 1606042

Journal Information:: Scientific Reports, Vol. 9, Issue 1; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Higher diversity and abundance of denitrifying microorganisms in environments than considered previously Wei, Wei; Isobe, Kazuo; Nishizawa, Tomoyasu The ISME Journal, Vol. 9, Issue 9 https://doi.org/10.1038/ismej.2015.9	journal	March 2015
Physiology and Diversity of Ammonia-Oxidizing Archaea Stahl, David A.; de la Torre, José R. Annual Review of Microbiology, Vol. 66, Issue 1 https://doi.org/10.1146/annurev-micro-092611-150128	journal	October 2012
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Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes Hultman, Jenni; Waldrop, Mark P.; Mackelprang, Rachel Nature, Vol. 521, Issue 7551 https://doi.org/10.1038/nature14238	journal	March 2015
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Impact of elevated N input on soil N cycling and losses in old-growth lowland and montane forests in Panama Corre, Marife D.; Veldkamp, Edzo; Arnold, Julia Figshare https://doi.org/10.6084/m9.figshare.c.3302985.v1	collection	January 2016

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