The bacterial community in sediment is sensitive to artificial disturbance, and they respond differently to human disturbance, such as changing the nutrient cycling and energy flow in marine ecosystems. However, little is known about the dynamics and distribution of bacterial community structures in marine sediments and potential biogeochemical functions during the long-time succession in marine ranching. In the present study, we compared the dynamics of the bacterial composition and potential biogeochemical functions of sediment to ten years (TR) and one-year new artificial reef (NR) areas using metagenomic next-generation sequencing technology. Results revealed that NR reduces the Pielou’s evenness and Shannon index. Similarly, nonmetric multidimensional scaling showed that the beta diversity of sediment bacterial communities in NR significantly differed between TR and non-artificial reef areas. Previously, TR biomarkers were frequently associated with organic matter decomposing and assimilating in the organically enriched sediments (i.e., Acinetobacter). The soluble reactive phosphate (SRP) and total phosphorus (TP) concentrations were thought to be the primary driving forces in shaping the microbial community in sediment. Pseudomonas, Lactobacillus, and Ralstonia have a significant positive correlation with SRP, TP, nitrate, and TN, but a negative association with pH, Salinity, Hg, and depth. NR was found to have more negative correlation nodes, indicating that taxa face more competition or predation press. Vibrio served as the module-hubs in the network in all areas. In addition, chemoheterotrophy, aerobic chemoheterotrophy, and fermentation were the three most prominent functions of the three areas, accounting for 59.96% of the relative abundance of the functional annotation. Different bacteria in sediments may change the amount of biogeochemical cycle in the marine ranching ecosystem. These findings can increase our understanding of the succession of the microecosystem for the marine ranching sedimentary environment by revealing how artificial reefs affect the indigenous sediment bacterial community and their responses to environmental variation.

This paper aims to explore the impact of marine ranching construction on water quality and fishery resources in the surrounding marine areas. Utilizing in situ water quality and fishery resource data collected before and after the establishment of marine ranching, the study analyzes changes in water quality parameters from both temporal and spatial perspectives. A quantitative evaluation of the water quality data is conducted using several models to assess the accuracy of different evaluation methods. By integrating the SHAP algorithm with physical significance, the study examines the differences between optically sensitive and non-optically sensitive water quality parameters during the machine learning evaluation process. Finally, based on the inverted water quality data, the potential impact range and resource output following the deployment of artificial reefs are investigated. The results indicate that in the marine area near Wailingding Island, Zhuhai, the deployment of artificial reefs with a volume of 38,048 cubic meters led to an increase in fishery resources by 318 kg/km² in spring and 660 kg/km² in autumn. Additionally, deployment had varying degrees of impact on the concentrations of chlorophyll a (Chla), dissolved oxygen (DO), chemical oxygen demand (COD), and phosphate (PO4-P) in the surface water within an approximate range of 10 km. This study provides a valuable reference for calculating input–output ratios, as well as for the management and evaluation of marine ranching.

In the present study, we determined the complete mitogenome sequence of scleractinia, Favia favus using the Illumina HiSeq platform. The assembled mitogenome was 17,054 bp in length, comprising unique 13 protein-coding genes (PCGs), 2 ribosomal RNAs, and 2 transfer RNAs genes of each, showing a typical scleractinian pattern. New phylogenetic analysis upon complete mitogenomics revealed that F. favus is most closely related to Favites abdita, with high bootstrap values.

Dissolved inorganic nutrients are pivotal in maintaining the material and energy balance of marine ecosystems, impacting the survival and dynamic succession of marine organisms. To gain a deeper understanding of the source and sink characteristics of dissolved inorganic nutrients in bays affected by human activities and to elucidate the processes involving filter-feeding shellfish in relation to these nutrients, this study investigated the source and sink dynamics of dissolved inorganic nutrients in the Dapeng Cove sea area of Shenzhen. Over the past decade, a significant change in the N/P ratio within the survey area has been observed, suggesting a shift in nutrient limitation from nitrogen to phosphorus or phosphorus–silicon limitation. This induced change in the N/P ratio, along with Si/N and Si/P ratios, may facilitate the growth of cyanobacteria and, subsequently, alter the proportions of diatoms, dinoflagellates, and cyanobacteria. Seasonal fluctuations in human disturbance intensity and precipitation determine the seasonal and spatial distribution of nutrients in the bay, thereby influencing the bay ecosystem metabolism. The Land–Ocean Interactions in the Coastal Zone (LOICZ) model analysis revealed that the bay represents a major source of inorganic nitrogen and a source of phosphate in spring, summer, and autumn, while acting as a sink for phosphate in winter. Furthermore, rivers and groundwater represent the primary sources of phosphate and inorganic nitrogen in the bay. The bay exhibits an annual net ecosystem metabolic rate of 7.06 mmol C/m²/d, with denitrification dominating the nitrogen cycle at 12.65 mmol C/m²/d. Overall, the Dapeng Cove ecosystem displays net production exceeding respiration, classifying it as an autotrophic system. Additionally, the nitrogen cycle in the sea area is predominantly driven by denitrification. The analysis also revealed that the impact of oyster proliferation on the physical and chemical factors in the surveyed area is relatively weaker than that of surface runoff and groundwater inputs.

Environmental physicochemical factors and microorganisms play critical roles in the health of oysters. However, the impact of high-density oyster farming—a highly efficient filter-feeding bivalve system—on environmental conditions and microbial community structure and function remains poorly understood. This study conducted four-season monitoring of the water and sediment parameters in a semi-enclosed bay commercial oyster aquaculture (OA) system and a control area (CT), coupled with 16S rRNA amplicon sequencing of the environmental microbiota. Oyster aquaculture caused negligible disruption to water column parameters but significantly increased the concentrations of total organic carbon (TOC, annual mean OA vs. CT:1.15% vs. 0.56%), sulfides (annual mean OA vs. CT:67.72 vs. 24.99 mg·kg⁻¹), and heavy metals (Cd, Pb, Cu, Zn, and Cr) in the sediment. α-diversity (Shannon and Chao indices) exhibited minimal overall perturbation, with significant inter-regional differences observed only in winter for both water and sediment. The bacterial community structure of the water column was significantly altered only in winter, whereas sediment communities showed structural shifts in spring, summer, and autumn. Water microbiota were primarily influenced by turbidity, dissolved oxygen, salinity, the Si/N ratio, and silicates. Sediment microbiota were correlated with Pb, Cu, Zn, TOC, Cr, and sediment particle size. Water bacterial functions displayed only four significantly divergent biogeochemical processes annually (sulfur compound respiration; OA vs. CT). In contrast, sediment bacteria exhibited 29 significantly disrupted functions annually, with the greatest seasonal divergence in winter (11/67 functions). Spring, summer, and autumn sediment functions showed distinct patterns. Understanding these environmental–microbial interactions is essential for sustainable oyster aquaculture and ecological optimization.