Proteomic Response of Three Marine Ammonia-Oxidizing Archaea to Hydrogen Peroxide and Their Metabolic Interactions with a Heterotrophic Alphaproteobacterium

Ammonia-oxidizing archaea (AOA) play an important role in the nitrogen cycle and account for a considerable fraction of the prokaryotic plankton in the ocean. Most AOA lack the hydrogen peroxide (H(2)O(2))-detoxifying enzyme catalase, and some AOA have been shown to grow poorly under conditions of exposure to H(2)O(2). However, differences in the degrees of H(2)O(2) sensitivity of different AOA strains, the physiological status of AOA cells exposed to H(2)O(2), and their molecular response to H(2)O(2) remain poorly characterized. Further, AOA might rely on heterotrophic bacteria to detoxify H(2)O(2), and yet the extent and variety of costs and benefits involved in these interactions remain unclear. Here, we used a proteomics approach to compare the protein profiles of three Nitrosopumilus strains grown in the presence and absence of catalase and in coculture with the heterotrophic alphaproteobacterium Oceanicaulis alexandrii. We observed that most proteins detected at a higher relative abundance in H(2)O(2)-exposed Nitrosopumilus cells had no known function in oxidative stress defense. Instead, these proteins were putatively involved in the remodeling of the extracellular matrix, which we hypothesize to be a strategy limiting the influx of H(2)O(2) into the cells. Using RNA-stable isotope probing, we confirmed that O. alexandrii cells growing in coculture with the Nitrosopumilus strains assimilated Nitrosopumilus-derived organic carbon, suggesting that AOA could recruit H(2)O(2)-detoxifying bacteria through the release of labile organic matter. Our results contribute new insights into the response of AOA to H(2)O(2) and highlight the potential ecological importance of their interactions with heterotrophic free-living bacteria in marine environments. IMPORTANCE Ammonia-oxidizing archaea (AOA) are the most abundant chemolithoautotrophic microorganisms in the oxygenated water column of the global ocean. Although H(2)O(2) appears to be a universal by-product of aerobic metabolism, genes encoding the hydrogen peroxide (H(2)O(2))-detoxifying enzyme catalase are largely absent in genomes of marine AOA. Here, we provide evidence that closely related marine AOA have different degrees of sensitivity to H(2)O(2), which may contribute to niche differentiation between these organisms. Furthermore, our results suggest that marine AOA rely on H(2)O(2) detoxification during periods of high metabolic activity and release organic compounds, thereby potentially attracting heterotrophic prokaryotes that provide this missing function. In summary, this report provides insights into the metabolic interactions between AOA and heterotrophic bacteria in marine environments and suggests that AOA play an important role in the biogeochemical carbon cycle by making organic carbon available for heterotrophic microorganisms.