DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

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.
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
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.
@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}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1038/s41598-019-53679-0

Citation Metrics:
Cited by: 9 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data
journal, September 2010

  • Cox, Murray P.; Peterson, Daniel A.; Biggs, Patrick J.
  • BMC Bioinformatics, Vol. 11, Issue 1
  • DOI: 10.1186/1471-2105-11-485

Nitrifier denitrification as a distinct and significant source of nitrous oxide from soil
journal, January 2011


Higher diversity and abundance of denitrifying microorganisms in environments than considered previously
journal, March 2015

  • Wei, Wei; Isobe, Kazuo; Nishizawa, Tomoyasu
  • The ISME Journal, Vol. 9, Issue 9
  • DOI: 10.1038/ismej.2015.9

Nitrous Oxide (N2O): The Dominant Ozone-Depleting Substance Emitted in the 21st Century
journal, August 2009


Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil
journal, July 2009


Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses
journal, July 2013

  • Blazewicz, Steven J.; Barnard, Romain L.; Daly, Rebecca A.
  • The ISME Journal, Vol. 7, Issue 11
  • DOI: 10.1038/ismej.2013.102

Archaea rather than bacteria control nitrification in two agricultural acidic soils: Archaeal nitrification in acidic soils
journal, October 2010


Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
journal, June 2007

  • Wang, Q.; Garrity, G. M.; Tiedje, J. M.
  • Applied and Environmental Microbiology, Vol. 73, Issue 16
  • DOI: 10.1128/AEM.00062-07

Microbial metatranscriptomics in a permanent marine oxygen minimum zone: OMZ community gene expression
journal, January 2011


Absolute quantification of Dehalococcoides proteins: enzyme bioindicators of chlorinated ethene dehalorespiration
journal, October 2009


Metatranscriptomic analysis of ammonia-oxidizing organisms in an estuarine bacterioplankton assemblage
journal, November 2010

  • Hollibaugh, James T.; Gifford, Scott; Sharma, Shalabh
  • The ISME Journal, Vol. 5, Issue 5
  • DOI: 10.1038/ismej.2010.172

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
journal, August 2006


The consequences of niche and physiological differentiation of archaeal and bacterial ammonia oxidisers for nitrous oxide emissions
journal, January 2018


Functional analysis of natural microbial consortia using community proteomics
journal, March 2009

  • VerBerkmoes, Nathan C.; Denef, Vincent J.; Hettich, Robert L.
  • Nature Reviews Microbiology, Vol. 7, Issue 3
  • DOI: 10.1038/nrmicro2080

Coupling a Detergent Lysis/Cleanup Methodology with Intact Protein Fractionation for Enhanced Proteome Characterization
journal, October 2012

  • Sharma, Ritin; Dill, Brian D.; Chourey, Karuna
  • Journal of Proteome Research, Vol. 11, Issue 12
  • DOI: 10.1021/pr300709k

Evaluation of metatranscriptomic protocols and application to the study of freshwater microbial communities: Metatranscriptomics of freshwater communities
journal, June 2014

  • Tsementzi, Despina; Poretsky, Rachel; Rodriguez-R, Luis M.
  • Environmental Microbiology Reports, Vol. 6, Issue 6
  • DOI: 10.1111/1758-2229.12180

Impact of elevated N input on soil N cycling and losses in old-growth lowland and montane forests in Panama
journal, June 2010

  • Corre, Marife D.; Veldkamp, Edzo; Arnold, Julia
  • Ecology, Vol. 91, Issue 6
  • DOI: 10.1890/09-0274.1

Ammonia oxidation pathways and nitrifier denitrification are significant sources of N2O and NO under low oxygen availability
journal, April 2013

  • Zhu, X.; Burger, M.; Doane, T. A.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 16
  • DOI: 10.1073/pnas.1219993110

Dosage-Dependent Proteome Response of Shewanella oneidensis MR-1 to Acute Chromate Challenge
journal, May 2007

  • Thompson, Melissa R.; VerBerkmoes, Nathan C.; Chourey, Karuna
  • Journal of Proteome Research, Vol. 6, Issue 5
  • DOI: 10.1021/pr060502x

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
journal, April 2012


Microbial metaproteomics: identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities
journal, June 2012

  • Hettich, Robert L.; Sharma, Ritin; Chourey, Karuna
  • Current Opinion in Microbiology, Vol. 15, Issue 3
  • DOI: 10.1016/j.mib.2012.04.008

pH regulates key players of nitrification in paddy soils
journal, February 2015


Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets
journal, October 2013


Evaluation of methods for nitrogen‐15 analysis of inorganic nitrogen in soil extracts. II. Diffusion methods
journal, June 1995

  • Herman, D. J.; Brooks, P. D.; Ashraf, M.
  • Communications in Soil Science and Plant Analysis, Vol. 26, Issue 11-12
  • DOI: 10.1080/00103629509369400

Complete nitrification by Nitrospira bacteria
journal, November 2015

  • Daims, Holger; Lebedeva, Elena V.; Pjevac, Petra
  • Nature, Vol. 528, Issue 7583
  • DOI: 10.1038/nature16461

Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes
journal, March 2015

  • Hultman, Jenni; Waldrop, Mark P.; Mackelprang, Rachel
  • Nature, Vol. 521, Issue 7551
  • DOI: 10.1038/nature14238

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data
journal, October 2012


Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage
journal, December 2014


Accelerated Profile HMM Searches
journal, October 2011


FunGene: the functional gene pipeline and repository
journal, January 2013


Microbially mediated nitrogen retention and loss in a salt marsh soil
journal, January 2015

  • Yang, Wendy H.; Traut, Bibit H.; Silver, Whendee L.
  • Ecosphere, Vol. 6, Issue 1
  • DOI: 10.1890/ES14-00179.1

The soil N cycle: new insights and key challenges
journal, January 2015


Complete nitrification by a single microorganism
journal, November 2015

  • van Kessel, Maartje A. H. J.; Speth, Daan R.; Albertsen, Mads
  • Nature, Vol. 528, Issue 7583
  • DOI: 10.1038/nature16459

The activity level of a microbial community function can be predicted from its metatranscriptome
journal, November 2011

  • Helbling, Damian E.; Ackermann, Martin; Fenner, Kathrin
  • The ISME Journal, Vol. 6, Issue 4
  • DOI: 10.1038/ismej.2011.158

Detecting Nitrous Oxide Reductase (nosZ) Genes in Soil Metagenomes: Method Development and Implications for the Nitrogen Cycle
journal, June 2014


BLAST+: architecture and applications
journal, January 2009

  • Camacho, Christiam; Coulouris, George; Avagyan, Vahram
  • BMC Bioinformatics, Vol. 10, Issue 1
  • DOI: 10.1186/1471-2105-10-421

PEAR: a fast and accurate Illumina Paired-End reAd mergeR
journal, October 2013


Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
journal, January 2011

  • Sievers, Fabian; Wilm, Andreas; Dineen, David
  • Molecular Systems Biology, Vol. 7, Issue 1
  • DOI: 10.1038/msb.2011.75

New and improved proteomics technologies for understanding complex biological systems: Addressing a grand challenge in the life sciences
journal, September 2012

  • Hood, Leroy E.; Omenn, Gilbert S.; Moritz, Robert L.
  • PROTEOMICS, Vol. 12, Issue 18
  • DOI: 10.1002/pmic.201270086

Molecular Dynamics of the Shewanella oneidensis Response to Chromate Stress
journal, March 2006

  • Brown, Steven D.; Thompson, Melissa R.; VerBerkmoes, Nathan C.
  • Molecular & Cellular Proteomics, Vol. 5, Issue 6
  • DOI: 10.1074/mcp.M500394-MCP200

Year-Round Shotgun Metagenomes Reveal Stable Microbial Communities in Agricultural Soils and Novel Ammonia Oxidizers Responding to Fertilization
journal, November 2017

  • Orellana, Luis H.; Chee-Sanford, Joanne C.; Sanford, Robert A.
  • Applied and Environmental Microbiology, Vol. 84, Issue 2
  • DOI: 10.1128/AEM.01646-17

Measuring gross nitrogen mineralization, and nitrification by 15 N isotopic pool dilution in intact soil cores
journal, September 1991


Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient
journal, November 2018

  • Meziti, Alexandra; Tsementzi, Despina; Rodriguez-R, Luis M.
  • The ISME Journal, Vol. 13, Issue 3
  • DOI: 10.1038/s41396-018-0307-6

The microbial nitrogen-cycling network
journal, February 2018

  • Kuypers, Marcel M. M.; Marchant, Hannah K.; Kartal, Boran
  • Nature Reviews Microbiology, Vol. 16, Issue 5
  • DOI: 10.1038/nrmicro.2018.9

Pathways and key intermediates required for obligate aerobic ammonia-dependent chemolithotrophy in bacteria and Thaumarchaeota
journal, February 2016

  • Kozlowski, Jessica A.; Stieglmeier, Michaela; Schleper, Christa
  • The ISME Journal, Vol. 10, Issue 8
  • DOI: 10.1038/ismej.2016.2

Plant and Microbial Controls on Nitrogen Retention and loss in a Humid Tropical Forest
journal, November 2008

  • Templer, Pamela H.; Silver, Whendee L.; Pett-Ridge, Jennifer
  • Ecology, Vol. 89, Issue 11
  • DOI: 10.1890/07-1631.1

Refined NrfA Phylogeny Improves PCR-Based nrfA Gene Detection
journal, January 2014

  • Welsh, Allana; Chee-Sanford, Joanne C.; Connor, Lynn M.
  • Applied and Environmental Microbiology, Vol. 80, Issue 7
  • DOI: 10.1128/AEM.03443-13

Physiology and Diversity of Ammonia-Oxidizing Archaea
journal, October 2012


Comammox—a newly discovered nitrification process in the terrestrial nitrogen cycle
journal, October 2017