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. 2023 Dec 18;11(12):3001.
doi: 10.3390/microorganisms11123001.

Differences in Bacterial Co-Occurrence Networks and Ecological Niches at the Surface Sediments and Bottom Seawater in the Haima Cold Seep

Song Zhong  1   2 , Jingchun Feng  1   2   3 , Jie Kong  2   3 , Yongji Huang  2   3 , Xiao Chen  2   3 , Si Zhang  2   3
Affiliations

Differences in Bacterial Co-Occurrence Networks and Ecological Niches at the Surface Sediments and Bottom Seawater in the Haima Cold Seep

Song Zhong et al. Microorganisms. .

Abstract

Cold seeps are highly productive chemosynthetic ecosystems in the deep-sea environment. Although microbial communities affected by methane seepage have been extensively studied in sediments and seawater, there is a lack of investigation of prokaryotic communities at the surface sediments and bottom seawater. We revealed the effect of methane seepage on co-occurrence networks and ecological niches of prokaryotic communities at the surface sediments and bottom seawater in the Haima cold seep. The results showed that methane seepage could cause the migration of Mn and Ba from the surface sediments to the overlying seawater, altering the elemental distribution at seepage sites (IS) compared with non-seepage sites (NS). Principal component analysis (PCA) showed that methane seepage led to closer distances of bacterial communities between surface sediments and bottom seawater. Co-occurrence networks indicated that methane seepage led to more complex interconnections at the surface sediments and bottom seawater. In summary, methane seepage caused bacterial communities in the surface sediments and bottom seawater to become more abundant and structurally complex. This study provides a comprehensive comparison of microbial profiles at the surface sediments and bottom seawater of cold seeps in the South China Sea (SCS), illustrating the impact of seepage on bacterial community dynamics.

Keywords: bacterial communities; co-occurrence networks; community construction; methane seepage; spatial distribution; surface sediments.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Location and landscapes of the sampling sites. (a) Map of the sampling sites with water depth. The box on the right is a zoom-in of the “Haima” area with the locations of four sites. (b) Landscapes of the seepage sites (ROV1 and ROV2). (c) Landscapes of the non-seepage sites (ROV3 and ROV5).
Figure 2
Figure 2
The physicochemical characteristics of seawater and sediment at the surface sediments and bottom seawater. (a) CH4, TOC and SO42− concentration in seawater and sediment. (b) Metals ion and Cl− concentration in seawater and sediment. “ns” means no significant difference between groups; “*” means significant difference between groups (p < 0.05; multiple comparison with ANOVA tests).
Figure 3
Figure 3
Compositions of bacterial communities at the surface sediments and bottom seawater. (a) Microbial alpha diversity in vertical profile. (b) PCA of microorganisms at the surface sediments and bottom seawater. (c) Graph of differences in microbial composition at the phylum level. (d) Graph of differences in microbial composition at the family level. “ns” means no significant difference between groups; “*” means significant difference between groups (p < 0.05; multiple comparison with ANOVA tests).
Figure 4
Figure 4
Structures and functions of bacterial communities at the surface sediments and bottom seawater. (a) Graph of differences in microbial composition at the genera level. (b) Bacterial function predictions based on the FAPROTAX tool.
Figure 5
Figure 5
RDA of bacterial community structure and environmental factors.
Figure 6
Figure 6
Co-occurrence networks and stability of bacterial communities in the NS and IS groups. (a) The nodes are colored based on the phylum level of prokaryotic microorganisms. A connection indicates a strong (Spearman’s ρ > 0.9) and significant (p < 0.01) correlation. The size of each node is proportional to the degree of ASV. (b) The relationship between bacterial ASV richness and average variation degree (AVD) of assembled bacterial communities. “ns” means no significant difference between groups; “*” means the significant difference between groups (p < 0.05; multiple comparisons using ANOVA tests).
Figure 7
Figure 7
Mechanisms of bacterial assembly at the surface sediments and bottom seawater. (a) Niche breadth of bacterial communities at the surface sediments and bottom seawater. (b) Assessment of community structure based on the Raup–Crick index. (c) Assessment of the relative importance of deterministic and stochastic processes in community assembly based on the neutral community models. The solid blue line represents the best-fit value of the neutral community models, the dashed blue line represents the 95% confidence interval of the model, ASVs with a higher or lower frequency than predicted by the neutral community models are shown in different colours. “ns” means no significant difference between groups; “*” means significant difference between groups (p < 0.05; multiple comparison with ANOVA tests).
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