Nitrification-the microbial oxidation of ammonium (NH4+) to nitrate (NO3-) via nitrite (NO2-)-plays a critical role in coastal/estuarine systems, by consuming ammonia and oxygen, by producing the potent greenhouse gas, N2O, and by linking the decomposition of nitrogenous organic matter to N loss via denitrification. Despite the tremendous biogeochemical importance of nitrification, surprisingly little is known regarding the microbial communities responsible for this process, or how key environmental factors (e.g., ammonia, oxygen, salinity, etc.) and gradients influence the distribution, diversity, and activity of estuarine nitrifying microorganisms. In particular, although the first and rate-limiting step of nitrification, ammonia oxidation (catalyzed by the enzyme ammonia monooxygenase), has been long believed to be carried out exclusively by members of the domain Bacteria (ammonia-oxidizing bacteria, AOB), it has recently been discovered that some mesophilic Crenarchaeota (one of the most ubiquitous and abundant microbial groups on the planet) may also be significant ammonia-oxidizers. The discovery of ammonia-oxidizing archaea (AOA) represents a surprising new 'twist' within the global N cycle, and our understanding of the microbial ecology of nitrification therefore requires careful re-evaluation.  The overarching goal of this study is to compare the relative diversity, abundance, and activity of AOA and AOB communities in several estuarine systems along the California coast. In particular, we have used bacterial and archaeal amoA genes, putatively encoding the a-subunit of ammonia monooxygenase, as molecular markers to characterize these two apparently 'functionally-equivalent' groups at multiple sites along the estuarine gradient.  Overall, this approach has provided new insights into how the diversity and functioning of estuarine nitrifying communities may be influenced by complex physical/chemical gradients and environmental perturbations.