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Microbiome
2024 Feb 14;121:27. doi: 10.1186/s40168-024-01759-3.
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Novel insights into the rhizosphere and seawater microbiome of Zostera marina in diverse mariculture zones.
Sun H, Wang T, Liu S, Tang X, Sun J, Liu X, Zhao Y, Shen P, Zhang Y.
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BACKGROUND: Seagrasses offer various ecosystem services and possess high levels of primary productivity. However, the development of mariculture has affected the homeostasis of seagrass meadow ecosystems. Plant-microbiome associations are essential for seagrasses health, but little is known about the role of environmental microbiomes and how they affect seagrass in a mariculture environment. In this study, we investigated the influence of mariculture on the rhizosphere and seawater microbiome surrounding Zostera marina and focused on the bacterial, eukaryotic, and fungal components in the composition, diversity, metabolism, and responses to mariculture-related environmental factors.
RESULTS: Significant differences in the composition, richness, diversity, and internal relations of the bacterial community between the seawater and rhizosphere sediment surrounding Z. marina were observed, while differences in the eukaryotic and fungal communities were less significant. More complex bacterial and fungal co-occurrence networks were found in the seawater and rhizosphere sediment of the Saccharina japonica (SJ) and sea cucumber (SC) culture zones. The seawater in the SJ zone had higher levels of dissimilatory and assimilatory nitrate reduction, denitrification, and nitrogen fixation processes than the other three zones. The assimilatory sulfate reduction enzymes were higher in the rhizosphere sediments of the SJ zone than in the other three zones. Tetracycline, sulfonamide, and diaminopyrimidine resistance genes were enriched in the mariculture SJ and SC zones.
CONCLUSIONS: Our findings might contribute to a better understanding of the effects of mariculture on the seagrass and the meadow ecosystems and thus revealing their potential operating mechanisms. These insights may serve to raise awareness of the effects of human activities on natural ecosystems, regulation of antibiotic usage, and environmental restoration. Video Abstract.
Fig. 1. The bacterial (A), eukaryotic (B), and fungal (C) community composition in seawater and rhizosphere sediment samples from the N, SJ, SC, and SR zones at class level. The top 20 classes are shown
Fig. 2. The LEfSe analysis for the bacterial, eukaryotic, and fungal communities in the seawater (A, B, and C) and rhizosphere sediment (D, E, and F) samples from the N, SJ, SC, and SR zones. Taxa that significantly higher in all of these four zones are set as the enriched taxa, and the taxa with LDA > 4 are shown
Fig. 3. Co-occurrence network diagram of bacterial communities at ASV level in seawater (A, B, C, and D) and rhizosphere sediment (E, F, G, and H) samples from the N, SJ, SC, and SR zones. ASVs of the top 100 abundance in each sample are selected. The colors of spots indicate different bacterial phyla, and lines between spots indicate correlations between ASVs. Red lines, positive correlations. Blue lines, negative correlations
Fig. 4. The Mantel test of bacterial, eukaryotic, and fungal communities in seawater (A, B, and C) and rhizosphere sediment (D, E, and F) samples from the N, SJ, SC, and SR zones. ASVs of the top 50 abundance in each sample are selected. Families (bacteria) or phyla (eukaryota and fungi) of top three abundance are merged respectively as Spec01, Spec02, and Spec03. Line colors and thickness represent the P and R values of the Mantel test
Fig. 5. The KEGG functions in bacterial, eukaryotic, archaeal, and viral communities in seawater and rhizosphere sediment samples from the N, SJ, SC, and SR zones. The top 10 KEGG functions are shown
Fig. 6. The LDA analysis of the KEGG functions in seawater (A) and rhizosphere sediment (B) samples from the N, SJ, SC, and SR zones. Functions that significantly higher in all of these four zones are set as enriched functions, and KEGG functions with LDA > 2 are shown
Fig. 7. The nitrogen metabolism in seawater (A) and rhizosphere sediment (B) samples from the N, SJ, SC, and SR zones. Wilcoxon rank-sum test is used to analyze the difference in nitrogen metabolic genes in the seawater and rhizosphere sediment samples between the N, SJ, SC, and SR zones. P < 0.05 is marked with “*”
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