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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-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.
Highlights
To what extent multi-omic techniques could reflect in situ microbial process rates remains unclear, especially for highly diverse habitats like soils
The results revealed that metatranscriptomic data best reflected the measured nitrification rates under the tested experimental conditions and provided novel insights about nitrifier gene expression dynamics after a simulated nitrogen fertilization event
Patterns in nitrification rates were consistent with NO3− formation and NH4+ disappearance during an eight-day period following the amendment of soil microcosms with an equimolar nitrogen mixture of NH4+ and urea, representative of fertilizer application in the field
Summary
To what extent multi-omic techniques could reflect in situ microbial process rates remains unclear, especially for highly diverse habitats like soils. Peptides related to housekeeping proteins from nitrite-oxidizing microorganisms were detected, their abundance was not significantly correlated with activity, revealing that metaproteomics provided only a qualitative assessment of activity These findings underscore the strengths and limitations of multi-omic approaches for assessing diverse microbial communities in soils and provide new insights into nitrification. Our goal was to assess the strengths and limitations of multi-omics in detecting microbial activity by correlating measurements of DNA, RNA, and protein abundances with measured rates of nitrate formation and N2O production in soils incubated under controlled conditions in the laboratory. The results revealed that metatranscriptomic data best reflected the measured nitrification rates under the tested experimental conditions and provided novel insights about nitrifier gene expression dynamics after a simulated nitrogen fertilization event
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