Proteomics as a tool to understand the distribution and activity of ammonia-oxidizing archaea

Nitrification plays a central role in the marine nitrogen cycle and ammonia-oxidizing archaea (AOA) are now known to be the principle microorganisms involved in catalyzing the first step of nitrification in the ocean. Typical AO rate profiles show lower rates in surface waters and increasing rates with depth, reaching a maximum just below the photic zone. Despite numerous observations of this ubiquitous and abundant group, the interactions between environment and AOA genetic capability that shape their natural distribution and activity are largely unknown. Here we use proteomics to study the response of an AOA isolate (Nitrosopulimus maritimus) to environmental stress (e.g., sunlight and low nutrient conditions) in order to understand factors determining AOA distributions. We hypothesize that the activity of marine AOA may be impacted by sunlight and/or competition for nutrients. For instance, harmful ultraviolet radiation can exert stress on cellular machinery by both direct damage and indirect damage caused by photochemically produced reactive oxygen species. Our aim is to elucidate N. maritimus response to varying conditions of environmental stress by surveying protein damage and regulation using shotgun proteomic approaches. Ultimately we will use these tools to assess the status of natural AOA communities to provide a more complete understanding of the environmental factors that influence AOA physiology, activity and biogeography across marine ecosystems.