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

Abstract

Abstract 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-NO 3 − g −1 dry soil d −1 ) and accumulation of N 2 O after 192 hours of incubation. Nitrification activity (NH 4 +  → NH 2 OH → NO → NO 2 -  → NO 3 − ) 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 formore » assessing diverse microbial communities in soils and provide new insights into nitrification.« less

Authors:
; ; ORCiD logo; ; ; ; ORCiD logo; ; ; ORCiD logo;
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1619597
Alternate Identifier(s):
OSTI ID: 1606042
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Published Article
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Name: Scientific Reports Journal Volume: 9 Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

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., and Konstantinidis, Konstantinos T. Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer. United Kingdom: N. p., 2019. Web. doi:10.1038/s41598-019-53679-0.
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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. Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer. United Kingdom. https://doi.org/10.1038/s41598-019-53679-0
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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., and Konstantinidis, Konstantinos T. Tue . "Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer". United Kingdom. https://doi.org/10.1038/s41598-019-53679-0.
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@article{osti_1619597,
title = {Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer},
author = {Orellana, Luis H. and Hatt, Janet K. and Iyer, Ramsunder and Chourey, Karuna and Hettich, Robert L. and Spain, Jim C. and Yang, Wendy H. and Chee-Sanford, Joanne C. and Sanford, Robert A. and Löffler, Frank E. and Konstantinidis, Konstantinos T.},
abstractNote = {Abstract 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-NO 3 − g −1 dry soil d −1 ) and accumulation of N 2 O after 192 hours of incubation. Nitrification activity (NH 4 +  → NH 2 OH → NO → NO 2 -  → NO 3 − ) 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.},
doi = {10.1038/s41598-019-53679-0},
journal = {Scientific Reports},
number = 1,
volume = 9,
place = {United Kingdom},
year = {2019},
month = {11}
}
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