Ammonium induces differential expression of methane and nitrogen metabolism‐related genes in Methylocystis sp. strain SC2

Nitrogen source and concentration are major determinants of methanotrophic activity, but their effect on global gene expression is poorly studied. Methylocystis sp. strain SC2 produces two isozymes of particulate methane monooxygenase. These are encoded by pmoCAB1 (low‐affinity pMMO1) and pmoCAB2 (h...

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Bibliographic Details
Published in:Environmental microbiology 2014-10, Vol.16 (10), p.3115-3127
Main Authors: Dam, Bomba, Dam, Somasri, Kim, Yongkyu, Liesack, Werner
Format: Article
Language:English
Subjects:
Ammonium Compounds - pharmacology
ammonium fertilizers
Animal, plant and microbial ecology
Bacteriology
Biological and medical sciences
Fundamental and applied biological sciences. Psychology
Gene expression
gene expression regulation
Gene Expression Regulation, Bacterial
General aspects
genes
isozymes
Metabolism
Methane
Methane - metabolism
Methylocystaceae - drug effects
Methylocystaceae - enzymology
Methylocystaceae - genetics
Methylocystaceae - metabolism
Methylocystis
Microbial ecology
Microbiology
Miscellaneous
Nitrates
nitrogen
Nitrogen - metabolism
nitrogen content
oxidation
Oxidation-Reduction
Oxygenases - genetics
Oxygenases - metabolism
reverse transcriptase polymerase chain reaction
Transcriptome - drug effects
upland soils
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Summary:Nitrogen source and concentration are major determinants of methanotrophic activity, but their effect on global gene expression is poorly studied. Methylocystis sp. strain SC2 produces two isozymes of particulate methane monooxygenase. These are encoded by pmoCAB1 (low‐affinity pMMO1) and pmoCAB2 (high‐affinity pMMO2). We used RNA‐Seq to identify strain SC2 genes that respond to standard (10 mM) and high (30 mM) NH₄ ⁺ concentrations in the medium, compared with 10 mM NO₃ –. While the expression of pmoCAB1 was unaffected, pmoCAB2 was significantly downregulated (log₂ fold changes of −5.0 to −6.0). Among nitrogen metabolism‐related processes, genes involved in hydroxylamine detoxification (haoAB) were highly upregulated, while those for assimilatory nitrate/nitrite reduction, high‐affinity ammonium uptake and nitrogen regulatory protein PII were downregulated. Differential expression of pmoCAB2 and haoAB was independently validated by end‐point reverse transcription polymerase chain reaction. Methane oxidation by SC2 cells exposed to 30 mM NH₄ ⁺ was inhibited at ≤ 400 ppmv CH₄, where pMMO2 but not pMMO1 is functional. When transferred back to standard nitrogen concentration, methane oxidation capability and pmoCAB2 expression were restored. Given that Methylocystis contributes to atmospheric methane oxidation in upland soils, differential expression of pmoCAB2 explains, at least to some extent, the strong inhibitory effect of ammonium fertilizers on this activity.
ISSN:1462-2912
1462-2920
DOI:10.1111/1462-2920.12367