Detection of mtoX homologs in metagenomic data sets

Metagenomic data sets were obtained from the CAMERA (Sun et al., 2011) project website and searched for mtoX homologs using tblastn and the amino acid sequences of MtoX of Hyphomicrobium sp. VS, M. thiooxydans (locus tags MDMS009_211 and MDMS009_768) and R. pomeroyi DSS-3 (SPOA0269) as queries with a cutoff in e-value of 1e⁻²⁰. In case of libraries that represented short read data (that is, <125 bp), a cutoff value of 1e⁻⁰⁵ was used. Similarly, the metagenomic data sets were searched for homologs of the DMSP demethylase dmdA (R. pomeroyi locus SPO1913) and the bacterial housekeeping gene recA from E. coli at a cutoff of 1e⁻²⁰ to estimate the fractional abundance of mtoX-containing cells in the bacterial community and compare it to that of the DMSP demethylase gene dmdA.