Forest soil microbial communities: Using metagenomic approaches to survey permanent plots

Forest soil ecosystems include some of the most complex microbial communities on Earth (Fierer et al. 2012). These assemblages of archaea, bacteria, fungi, and protists play essential roles in biogeochemical cycles (van der Heijden et al. 2008) and account for considerable terrestrial biomass (Nielsen et al. 2011). Yet, determining the microbial composition of forest soils remains a great challenge due in part to their overwhelming diversity and variability. Until recently, studies of microbial diversity in natural systems have relied on clonal cultures. Early environmental gene sequencing, which cloned specific genes to produce a profile of diversity in a natural sample, revealed that the vast majority of microbial diversity had been overlooked using these direct cultivation methods.