Nitrification, the oxidation of ammonia to nitrite and nitrate, has long been considered a central biological process in the global nitrogen cycle, with its first description dated 133 years ago. Until 2005, bacteria were considered the only organisms capable of nitrification. However, the recent discovery of a chemoautotrophic ammonia-oxidizing archaeon, Nitrosopumilus maritimus, changed our concept of the range of organisms involved in nitrification, highlighting the importance of ammonia-oxidizing archaea (AOA) as potential players in global biogeochemical nitrogen transformations. The uniqueness of these archaea justified the creation of a novel archaeal phylum, Thaumarchaeota. These recent discoveries increased the global scientific interest within the microbial ecology society and have triggered an analysis of the importance of bacterial vs archaeal ammonia oxidation in a wide range of natural ecosystems. In this mini review we provide a chronological perspective of the current knowledge on the ammonia oxidation pathway of nitrification, based on the main physiological, ecological and genomic discoveries.

The space-for-time substitution approach provides a valuable empirical assessment to infer temporal effects of disturbance from spatial gradients. Applied to predict the response of different ecosystems under current climate change scenarios, it remains poorly tested in microbial ecology studies, partly due to the trophic complexity of the ecosystems typically studied. The McMurdo Dry Valleys (MDV) of Antarctica represent a trophically simple polar desert projected to experience drastic changes in water availability under current climate change scenarios. We used this ideal model system to develop and validate a microbial space-for-time sampling approach, using the variation of geochemical profiles that follow alterations in water availability and reflect past changes in the system. Our framework measured soil electrical conductivity, pH, and water activity in situ to geochemically define 17 space-for-time transects from the shores of four dynamic and two static Dry Valley lakes. We identified microbial taxa that are consistently responsive to changes in wetness in the soils and reliably associated with long-term dry or wet edaphic conditions. Comparisons between transects defined at static (open-basin) and dynamic (closed-basin) lakes highlighted the capacity for geochemically defined space-for-time gradients to identify lasting deterministic impacts of historical changes in water presence on the structure and diversity of extant microbial communities. We highlight the potential for geochemically defined space-for-time transects to resolve legacy impacts of environmental change when used in conjunction with static and dynamic scenarios, and to inform future environmental scenarios through changes in the microbial community structure, composition, and diversity.

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