Characterization of bacterial communities in freshwater and seawater of the Yellow River estuary by 16S rRNA gene high-throughput absolute abundance quantification

Abstract:

[Objective] The Yellow River estuary located at the confluence of the Yellow River, land, and ocean is an area with mixed freshwater and seawater and a diverse and productive estuary ecosystem. This study aims to characterize the bacterial communities in freshwater and seawater of the Yellow River estuary. [Methods] High-throughput absolute abundance quantification was adopted to measure the absolute abundance of bacterial communities. The dominant taxa, α and β diversity, co-occurrence network, assembly mechanisms, and potential functions were compared between the bacterial communities in freshwater and seawater. The correlations between dominant taxa and environmental factors were explored. [Results] The absolute abundance of bacteria in freshwater was 2.61×10⁶ copies/mL, which was 1.8 times of that in seawater. The common dominant phyla in freshwater and seawater were Actinomycetota, Pseudomonadota, Cyanobacteriota, and Bacteroidota, with significant differences in absolute abundance. The abundance of Actinomycetota ranked first in freshwater, which was approximately equal to the sum of all dominant phyla in seawater. The abundance of Pseudomonadota was the highest in seawater. The alpha diversity of bacteria in freshwater was higher than that in seawater. There were significant differences in the bacterial community structure between freshwater and seawater, mainly due to the differences in the abundance of the dominant taxa. The bacterial co-occurrence network in freshwater was more complex and stable than that in seawater, and stochastic processes dominated the bacterial community assembly in both freshwater and seawater. The bacterial communities in freshwater and seawater presented different functions, while they shared some common functions. Metabolism was the most abundant function, with higher relative abundance in freshwater than in seawater. Five environmental factors ((pH, oxidation-reduction potential (ORP), electrical conductivity (EC), total organic carbon (TOC), and total nitrogen (TN)) correlated with the dominant bacterial taxa to different extent. There were collinear relationships among the four environmental factors except EC. The dominant genera showing positive correlations with pH, TOC and TN were all negatively correlated with ORP, and vice versa. Actinomycetota and Pseudomonadota were positively and negatively correlated with pH, respectively. [Conclusion] The bacterial communities showed great differences between freshwater and seawater in the Yellow River estuary. The differences were mainly reflected in the abundance, diversity, functional structure, and co-occurrence network. The bacterial communities in freshwater and seawater had similar dominant taxa and assembly mechanisms. The results provide data support for studying the microbial ecology and exploiting microbial resources in the Yellow River estuary.