Development and application of polymerase chain reaction primers based on fhcD for environmental detection of methanopterin-linked C sub(1)-metabolism in bacteria

• Published in: Environmental microbiology Vol. 7; no. 8; pp. 1269 - 1274
• Main Authors: Kalyuzhnaya, Marina G, Nercessian, Olivier, Lidstrom, Mary E, Chistoserdova, Ludmila
• Format: Journal Article
• Language: English
• Published: 01.08.2005
• ISSN: 1462-2912; 1462-2920
• DOI: 10.1111/j.1462-2920.2004.00831.x

In this work we describe development and testing of a novel pair of environmental primers targeting fhcD, a conserved gene in the H sub(4)MTP-linked C sub(1)-transfer pathway, and demonstrate that these primers enable confident detection of a broad variety of fhcD genes originating from phylogenetically diverse bacteria. The new primer pair was employed to analyse fhcD diversity in Lake Washington sediment, uncovering the presence of 40 fhcD phylotypes. Based on phylogenetic analyses, the phylotypes identified were affiliated with alpha -, beta - and gamma -proteobacteria, and Planctomycetes, while a number of sequences formed deep branches suggesting the presence of unknown groups of microorganisms. To assess the physiological potential and the possible substrate repertoire of the fhcD-containing species in Lake Washington, we conducted enrichments of natural populations on a variety of C sub(1) substrates, and observed specific shifts in community structure in response to different C sub(1) substrates. A specific shift in community structure was also observed in the presence of humic acids suggesting that C sub(1) transfer metabolism linked to H sub(4)MPT may be part of the degradation pathway for this natural polymer, possibly involving formaldehyde production. Overall, our data suggest that C sub(1) oxidation reactions linked to H sub(4)MPT are much more widespread in natural environments than previously thought.