Microorganisms 2025, 13(1), 214; https://doi.org/10.3390/microorganisms13010214 (registering DOI) - 20 Jan 2025
Abstract
As transitional ecosystems between land and sea, estuaries are characterized by a unique environment that supports complex and diverse microbial communities. A comprehensive analysis of microbial diversity and ecological processes at different trophic levels is crucial for understanding the ecological functions of estuarine
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As transitional ecosystems between land and sea, estuaries are characterized by a unique environment that supports complex and diverse microbial communities. A comprehensive analysis of microbial diversity and ecological processes at different trophic levels is crucial for understanding the ecological functions of estuarine ecosystems. In this study, we systematically analyzed the diversity patterns, community assembly, and environmental adaptability of bacterial and protist communities using high-throughput sequencing techniques. The results revealed a higher alpha diversity for the bacteria than for protists, and the beta diversity pattern was dominated by species turnover in both communities. In addition, the two community assemblages were shown to be dominated by deterministic and stochastic processes, respectively. Furthermore, our results emphasized the influence of the local species pool on microbial communities and the fact that, at larger scales, geographic factors played a more significant role than environmental factors in driving microbial community variation. The study also revealed differences in environmental adaptability among different microbial types. Bacteria exhibited strong adaptability to salinity, while protists demonstrated greater resilience to variations in dissolved oxygen, nitrate, and ammonium concentrations. These results suggested differences in environmental adaptation strategies among microorganisms at different trophic levels, with bacteria demonstrating a more pronounced environmental filtering effect.
Full article
(This article belongs to the Special Issue Microbial Nitrogen Cycling in Estuarine and Coastal Ecosystems)
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Figure 1
Figure 1
<p>(<b>a</b>) Alpha diversity indexes for the bacterial and protist communities. Significant differences between groups are indicated by different letters (a, b). (Wilcoxon rank-sum test, <span class="html-italic">p</span> < 0.05). (<b>b</b>) Relative abundances of bacteria and protists at the phylum level.</p> Full article ">Figure 2
<p>Beta diversity of bacterial and protist communities based on unweighted and weighted Unifrac distances (<b>a</b>) and differences in the turnover and nestedness of beta diversity patterns (<b>b</b>) (Wilcoxon rank-sum test, <span class="html-italic">p</span> < 0.05. Significant differences between groups are indicated by different letters “a” and “b”. “N.D.” indicates not detected).</p> Full article ">Figure 3
<p>(<b>a</b>) Linear regression analysis of the number of shared ASVs between different samples and their corresponding beta diversity distance based on unweighted and weighted Unifrac distances. (<b>b</b>) Differences in the beta nearest taxon index (betaNTI) between bacterial and protist communities. Each point represents a pair of samples, with the dotted lines indicating the thresholds of 2 and −2, which separate deterministic processes from random processes. Significant differences between groups are indicated by different letters a and b. The symbol *** represents a significant correlation. (<b>c</b>) Relative importance of ecological processes in structuring the aggregation of bacterial and protist communities.</p> Full article ">Figure 4
<p>Linear regression of environmental similarity based on Euclidean distance (<b>a</b>) and geographic distance (<b>b</b>) with the similarities of bacterial and protist communities based on weighted and unweighted Unifrac distances. The symbol *** represents a significant correlation. (<b>c</b>) VPA analysis of bacterial and protist communities based on environmental variables and spatial factors.</p> Full article ">Figure 5
<p>(<b>a</b>) Environmental drivers of alpha and beta diversity in bacterial and protist communities. The edge width and color correspond to the R value and statistical significance, respectively. The color gradient within the right-angle triangle indicates the Pearson’s correlation coefficient between environmental factors. Differences in environmental breadth (<b>b</b>) and phylogenetic signal (<b>c</b>) between bacterial and protist communities.</p> Full article ">
<p>(<b>a</b>) Alpha diversity indexes for the bacterial and protist communities. Significant differences between groups are indicated by different letters (a, b). (Wilcoxon rank-sum test, <span class="html-italic">p</span> < 0.05). (<b>b</b>) Relative abundances of bacteria and protists at the phylum level.</p> Full article ">Figure 2
<p>Beta diversity of bacterial and protist communities based on unweighted and weighted Unifrac distances (<b>a</b>) and differences in the turnover and nestedness of beta diversity patterns (<b>b</b>) (Wilcoxon rank-sum test, <span class="html-italic">p</span> < 0.05. Significant differences between groups are indicated by different letters “a” and “b”. “N.D.” indicates not detected).</p> Full article ">Figure 3
<p>(<b>a</b>) Linear regression analysis of the number of shared ASVs between different samples and their corresponding beta diversity distance based on unweighted and weighted Unifrac distances. (<b>b</b>) Differences in the beta nearest taxon index (betaNTI) between bacterial and protist communities. Each point represents a pair of samples, with the dotted lines indicating the thresholds of 2 and −2, which separate deterministic processes from random processes. Significant differences between groups are indicated by different letters a and b. The symbol *** represents a significant correlation. (<b>c</b>) Relative importance of ecological processes in structuring the aggregation of bacterial and protist communities.</p> Full article ">Figure 4
<p>Linear regression of environmental similarity based on Euclidean distance (<b>a</b>) and geographic distance (<b>b</b>) with the similarities of bacterial and protist communities based on weighted and unweighted Unifrac distances. The symbol *** represents a significant correlation. (<b>c</b>) VPA analysis of bacterial and protist communities based on environmental variables and spatial factors.</p> Full article ">Figure 5
<p>(<b>a</b>) Environmental drivers of alpha and beta diversity in bacterial and protist communities. The edge width and color correspond to the R value and statistical significance, respectively. The color gradient within the right-angle triangle indicates the Pearson’s correlation coefficient between environmental factors. Differences in environmental breadth (<b>b</b>) and phylogenetic signal (<b>c</b>) between bacterial and protist communities.</p> Full article ">
