Distinct Assembly Processes Structure Planktonic Bacterial Communities Among Near- and Offshore Ecosystems in the Yangtze River Estuary

Abstract

The estuarine system functions as natural filters due to its ability to facilitate material transformation, planktonic bacteria play a crucial role in the cycling of complex nutrients and pollutants within estuaries, and understanding the community composition and assembly therein is crucial for comprehending bacterial ecology within estuaries. Despite extensive investigations into the composition and community assembly of two bacterial fractions (free-living, FLB; particle-attached, PAB), the process by which bacterioplankton communities in these two habitats assemble in the nearshore and offshore zones of estuarine ecosystems remains poorly understood. In this study, we conducted sampling in the Yangtze River Estuary (YRE) to investigate potential variations in the composition and community assembly of FLB and PAB in nearshore and offshore regions. We collected 90 samples of surface, middle, and bottom water from 16 sampling stations and performed 16S rRNA gene amplicon analysis along with environmental factor measurements. The results unveiled that the nearshore communities demonstrated significantly greater species richness and Chao1 indices compared to the offshore communities. In contrast, the nearshore communities had lower values of Shannon and Simpson indices. When compared to the FLB, the PAB exhibit a higher level of biodiversity and abundance. However, no distinct alpha and beta diversity differences were observed between the bottom, middle, and surface water layers. The community assembly analysis indicated that nearshore communities are predominantly shaped by deterministic processes, particularly due to heterogeneous selection of PAB; In contrast, offshore communities are governed more by stochastic processes, largely due to homogenizing dispersal of FLB. Consequently, the findings of this study demonstrate that nearshore and PAB communities exhibit higher levels of species diversity, while stochastic and deterministic processes exert distinct influences on communities among near- and offshore regions. This study further sheds new light on our understanding of the mechanisms governing bacterial communities in estuarine ecosystems.

Keywords: Community assembly; Free-living; Nearshore; Offshore; Particle-attached; Yangtze River Estuary.

Fig. 1

An overview of geographical location in the Yangtze River Estuary (dark circles). A total of 90 samples were collected from 16 sites in October 2020. The map was generated with the Ocean Data View (http://odv.awi.de); water depths are indicated with colored column on the right side. Stations belong to near- or offshore region were shown in light green and light red boxes, respectively

Fig. 2

Dominant bacterioplankton composition and alpha diversity between FL and PA bacterial communities among near- and offshore zones. A ASVs with Relative abundance of sequences ≥ 2% was calculated, the top ten phyla for each sample were used, others represent the phyla not unassigned at the phylum level. B Richness, Chao1, Shannon, and Simpson index. p values of Tukey’s HSD (honestly significant difference) test between groups are indicated on the top of bar plots. ***p < 0.001

Fig. 3

Principal coordinate analysis (PCoA) of bacterioplankton communities based on Bray–Curtis dissimilarity. Communities within ellipses are associated with 95% confidence intervals. The red, green, pink, light green, and dark blue circles represent FLB (free-living bacterial communities), PAB (particle-attached bacterial communities), bottom, middle, and surface water, respectively. Samples within green and red boxes are bacterial communities of near- and offshore, respectively. R² indicates the variance can be explained by geographical distance, the p value indicates the significance of the variance

Fig. 4

Specificity-occupancy plots showing ASVs that different between the PA and FL in the nearshore and offshore water from the Yangtze River Estuary. A, B The x-axis represents occupancy, i.e., how well an ASV is distributed in each habitat across all sites; the y-axis represents specificity, i.e., whether ASVs are also found in other habitats. C Venn diagrams showing the numbers of unique and shared ASVs among the four bacterial communities. D Detailed bacterial phyla of unique and shared ASVs. Dotted box on the top right are ASVs having a spec-occ > 0.7

Fig. 5

Relative importance of different ecological processes between near- and offshore communities. A, B Nearshore. C, D Offshore. Values on the ring indicate the fraction of ecological processes (deterministic: homogeneous and heterogeneous selection; stochastic: dispersal limitations and homogenizing dispersal; drift and others).

Fig. 6

Fit of the neutral community model (NCM) of community assembly. The predicted occurrence frequencies for nearshore, offshore, and all represent bacterial communities from nearshore (green colored), offshore (pink colored), and both region (white colored), respectively. The solid blue lines indicate the best fit to the NCM as in Sloan et al., and the dashed blue lines represent 95% confidence intervals around the model prediction. ASVs that occur more or less frequently than predicted by the NCM are shown in green or red colors. Nm represents the metacommunity size multiplied by immigration, and R² represents the fit to the model