Microbial communities in terrestrial and aquatic ecosystems are incredibly diverse. Molecular techniques have revealed that the vast majority of microbial taxa have not been isolated and characterized in laboratory cultures. Determining the role of this uncharacterized microbial diversity in ecosystem functioning has therefore been a major research challenge. Based on a review of the literature, we will assess the strengths and weaknesses of recent approaches for linking microbial community structure to ecosystem functioning, with a focus on biogeochemical cycles. The goal of this review is to identify how molecular approaches can be most effectively used to determine underlying principles that govern the dynamic structure and functioning of natural microbial communities. 
Results/Conclusions

Integrating molecular and culture-based techniques has revealed novel microbial functions, such as anaerobic ammonium oxidation (anammox). Focusing on functional groups of bacteria, such as denitrifiers and nitrifiers, in observational and experimental field manipulations has lead to correlations between process rates and molecular data within these groups. “Meta-omic” approaches, such as genomic and proteomic approaches, and recent advances in spatially explicit techniques, such as reporter bacteria and nano-SIMS have the potential to reveal structure-functioning linkages. High throughput sequencing has provided insights into the rare biosphere and the assembly and maintenance of microbial communities.