Community-level analysis: genes encoding methanopterin-dependent enzymes

This chapter describes a set of novel tools for the environmental detection of C1 transfer functions linked to the cofactor methanopterin. These tools include degenerate environmental primers targeting four of the most conserved genes in the methanopterin-linked C1 transfer pathway in bacteria, fae, mtdB, mch, and fhcD, and extensive databases of the respective genes. The tools described are suitable for detecting methanopterin-linked formaldehyde-oxidizing capacity in natural microbial communities and for determining the phylogenetic affiliations of major phyla involved in single-carbon cycling in the environment. The range of detection includes a variety of methano- and methylotrophic groups, other proteobacterial species capable of methanopterin-mediated reactions, and a variety of planctomycetes, as well as groups of microbes with currently unknown phylogenetic affiliations.