Selective stimulation in a natural community of methane oxidizing bacteria: Effects of copper on pmoA transcription and activity

Copper is an essential element, but often not readily available to microorganisms potentially causing copper limitation in situ. In most methane oxidizing bacteria (methanotrophs), the copper-containing membrane bound methane monooxygenase (pMMO) catalyzes the first step in methane oxidation. We focused on the response of methanotrophic activity to a copper amendment in a rice paddy soil, measuring methane oxidation rates and following changes of pmoA diversity (a gene encoding for a subunit of the pMMO) both at DNA and mRNA level with a diagnostic microarray. Using transcripts (mRNA) as a proxy for taxon-specific activity, we found a clear separation between overall (DNA) and active (mRNA) community, the latter being dominated by type Ia methanotrophs. Copper addition transiently stimulated methane uptake. This stimulation correlated to a change within Methylosarcina-related transcripts shifting from Methylosarcina quisquiliarum to a yet uncultivated Methylosarcina sp. Overall, we demonstrate copper limitation in a soil, but to an extent that still allowed pmoA expression. The taxon-specific response suggests a fine-scale niche differentiation between methanotrophs, with Methylobacter and Methylosarcina reacting immediately to a copper amendment.