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• W2899702958 abstract "Multi-omic techniques can offer a comprehensive overview of microbial communities at the gene, transcript and protein levels. However, to what extent these levels reflect in situ process rates is less clear, especially in highly complex habitats such as soils. Here we performed microcosm incubations using soil from a site with a history of agricultural management. Microcosms, amended with isotopically labelled 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 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 (AOB) Nitrosomonas and Nitrosospira . In contrast, ammonia-oxidizing archaea (AOA)and complete ammonia oxidizer (comammox) nitrifiers showed stable gene expression during incubations but were generally more abundant (DNA level) than their Betaproteobacteria AOB counterparts. A strong relationship between nitrification activity and (mostly) betaproteobacterial ammonia monooxygenase ( amoA ; NH 4 + →NH 2 OH) and nitrite oxidoreductase ( nxrA ; NO 2 - →NO 3 - ) transcript abundances revealed that mRNA levels quantitatively reflected measured activity and were generally more sensitive than the DNA level in the microcosm incubations. 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 complex microbial communities and provide the molecular means to assess nitrification processes in soils." @default.
• W2899702958 created "2018-11-16" @default.
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• W2899702958 date "2018-11-10" @default.
• W2899702958 modified "2023-09-23" @default.
• W2899702958 title "Comparing DNA, RNA and protein levels for measuring microbial activity in nitrogen-amended soils" @default.
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• W2899702958 doi "https://doi.org/10.1101/466680" @default.
• W2899702958 hasPublicationYear "2018" @default.
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