Stable isotope probing of nucleic acids in methanotrophs and methylotrophs: A review

Stable isotope probing (SIP) is a method which attempts to link an organism’s identity with its biological function under conditions approaching those in situ. Addition of 13C labelled substrate to an environmental sample results in 13C labelling of actively dividing bacteria when the 13C labelled substrate is used as a carbon source. The microorganism’s DNA therefore becomes heavier and can be separated by CsCl density gradient centrifugation from 12C DNA of bacteria which have not assimilated labelled substrate. SIP has been applied to study the functionally active methanotroph population in peat soil, acidic forest soil, cave water and soda lake sediments. Studies have analysed both phylogenetic (16S rRNA) and functional (pmoA, mmoX and mxaF) genes to determine methanotroph diversity. These studies are reviewed here and the advantages and limitations of the SIP technique are discussed.