Application of ‘omics technologies, including high-throughput nucleic acid sequencing and advanced mass spectrometry, show huge potential to increase our understanding of bioprocesses occurring in both natural and engineering microbial ecosystems. Field studies of such systems are inherently complicated, while laboratory reactor models involve extensive community modifications following inoculation and may not accurately reflect the biology of the source community. Here we develop a complementary approach to dissecting structure-function relationships of complex microbial communities, by applying experimental perturbations to freshly sourced, intact communities in a controlled fashion. In an investigation examining nitrogen transformation in wastewater treatment, we use metatranscriptomics in a time series design (n=20 samples) to study changes associated with onset of oxygenation. This stimulus switches the community between de-nitrification and nitrification phases of the nitrogen cycle, thus modeling a key aspect of wastewater process control. This model permits identification of functional genes, in both known and previously unknown taxa, and represents a readily adaptable model studying structure-function relationships in microbial communities. If time permits, I will discuss how this perturbation metatranscriptomics approach has implications for improving our ability to perform metagenome assembly.