Nitrification is microbe-mediated sequential oxidation of ammonia to nitrate, which interconnects the biological nitrogen fixation and nitrogen loss processes in the nitrogen cycle. Ammonia oxidation is the first and rate-limiting step of nitrification. Ammonia-oxidizing archaea (AOA) have been recognized as the major ammonia oxidizer in the ocean, and they are distributed ubiquitously in the marine water columns, estuaries, and sediments. The diversification and ecophysiology of marine AOA are critically important to understand the marine nitrogen cycle. The current study offers a comprehensive understanding of the diversity, abundance, niche partitioning, environmental determinants, and ecophysiology of the marine AOA. Our first study used high-throughput 454 pyrosequencing of amoA ge...[ Read more ]

Nitrification is microbe-mediated sequential oxidation of ammonia to nitrate, which interconnects the biological nitrogen fixation and nitrogen loss processes in the nitrogen cycle. Ammonia oxidation is the first and rate-limiting step of nitrification. Ammonia-oxidizing archaea (AOA) have been recognized as the major ammonia oxidizer in the ocean, and they are distributed ubiquitously in the marine water columns, estuaries, and sediments. The diversification and ecophysiology of marine AOA are critically important to understand the marine nitrogen cycle. The current study offers a comprehensive understanding of the diversity, abundance, niche partitioning, environmental determinants, and ecophysiology of the marine AOA. Our first study used high-throughput 454 pyrosequencing of amoA genes to unravel the highly diverse AOA community in the oxygen minimum zone (OMZ) off the Costa Rica Dome (CRD) located within the largest OMZ in Eastern tropical North Pacific. Based on our results, a distinct community was selected in the oxygen depleted waters, showing significant differences in the oxygenated layers. Furthermore, phylotypes enriched in the core-OMZs were also retrieved from the geographic distant OMZs, indicating that low-oxygen tolerating phylotypes are widely distributed in marine OMZs that are geographically far apart. In addition, our result provided the first insight into environmental determinants of WCB sub-clade (“Deep” water ecotype) at a finer resolution, which has been found widely distributed but not yet have culturable representatives. Next, we conducted a comprehensive investigation of the AOA community at DNA and RNA levels along with nitrification rates in a typical subtropical estuary – the Pearl River estuary. We unraveled highly diverse AOA sublineages that showed differential distribution along the river-sea environmental gradient, which provided new insights for the niche partitioning of different AOA sublineages. More importantly, sharp disagreement was observed between the AOA community composition at DNA and RNA levels. In particular, the SCM1-like sublineages predominated the AOA community at the RNA level. Moreover, considerable evidence in this study supported that SCM1-like sublineages were the key ammonia oxidizer, and they contributed significantly to the bottom water hypoxia in the Pearl River estuary. Moreover, we further observed highly diverse and active bacterial communities, bacterial and AOA biomass accumulation, and high oxygen consumption rates (respiration and nitrification) in the hypoxic zone. Recurring degradation-nitrification microbial assemblages were further revealed by their co-occurrence pattern at DNA and RNA levels. In addition, we examined the effect of mesozooplankton vertical migration on nitrifying communities and their activities in the South China Sea. Our results showed that mesozooplankton excretion products could generally facilitate nitrification activities. Altogether, our studies provide new insights into the ecological role, niche partition, diversification, and key environmental determinants of marine AOA, and offer comprehensive references for further studies to better understand the ecological role of marine AOA.