New insight to niche partitioning and ecological function of ammonia oxidizing archaea in subtropical estuarine ecosystem

Abstract

Nitrification plays a central role in the estuarine nitrogen cycle. Previous studies in estuary mainly focused on the niche partition between ammonia-oxidizing archaea (AOA) and bacteria (AOB), while the diversity, activity, biogeography, and ecophysiology of different AOA groups remained unclear. Here, we for the first time report on niche partitioning and differentially distributed active populations among diverse AOA (inferred from amoA gene) in a typical subtropical estuary - Pearl River estuary (PRE). In the water column of the PRE, the AOA communities mainly consisted of water column A (WCA) and SCM1-like (Nitrosopumilus maritimus-like) sublineages. Surprisingly, we observed a strong disagreement in AOA communities at DNA and RNA levels. In DNA samples, WCA generally dominated the AOA community, and the distributional pattern indicated that WCA I and WCA II sublineages preferred oceanic and coastal conditions, respectively. In contrast, diverse SCM1-like sublineages were identified, and outnumbered WCA at RNA level, in which SCM1-like-III was limited to freshwater, while the rest of the sublineages were widely distributed in the estuary. The SCM1-like sublineages strongly correlated with nitrification rate, which indicated their important contribution to ammonia oxidation. Furthermore, intense nitrification contributed significantly to hypoxia conditions (nitrification contributed averaged 12.18% of oxygen consumption) in the estuary. These results revealed different ammonia-oxidizing activities and niche partitioning among different AOA sublineages in estuarine water, which was unexplored in previous DNA and clone library-based studies. The ecological significance and functioning of the diverse AOA should be further explored in the marine ecosystem.