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

Yanhong Lu,Ling Chen,Jianping Gan,Xiaomin Xia,Minhan Dai,Hongbin Liu,Shuh-Ji Kao,Shunyan Cheung

doi:10.5194/bg-17-6017-2020

Abstract

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.

Highlights

Nitrification is a microbial mediated oxidation process of ammonia to nitrate, interconnects the source (N fixation) and sink (N loss), and plays a central role in the marine nitrogen cycling (Ward, 1996)
Our results suggest that nitrification could contribute a large proportion of oxygen consumption in the hypoxia zone (Table S3)
Downstream of the Pearl River, nitrification could contribute to onethird of the total oxygen consumption (Dai et al, 2008)

Summary

Introduction

Nitrification is a microbial mediated oxidation process of ammonia to nitrate, interconnects the source (N fixation) and sink (N loss), and plays a central role in the marine nitrogen cycling (Ward, 1996). Regarding the biogeochemical significance of ammonia oxidation (i.e., the first and rate-determining step of nitrification) in the estuarine ecosystem, the physiology and ecological function of ammonia oxidizers (i.e., ammoniaoxidizing archaea, AOA, and bacteria, AOB) have been of major interest for understanding the estuarine N transformation (Bernhard and Bollmann, 2010). Y. Lu et al.: New insight to niche partitioning and ecological function mostly conducted in the sediment of estuarine ecosystems (summarized in Table S1; Damashek et al, 2016). Lu et al.: New insight to niche partitioning and ecological function mostly conducted in the sediment of estuarine ecosystems (summarized in Table S1; Damashek et al, 2016) These studies mainly focused on the niche partition between AOA and AOB, inferred from amoA gene abundance, and collectively showed that AOA outnumbered AOB in the estuarine ecosystem (Caffrey et al, 2007; Abell et al, 2010; Bernhard et al, 2010). The biogeography, niche partition, and ecological function of different AOA groups were analyzed very little (Table S1)

Objectives

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Results

Conclusion