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• The contribution of oyster reefs characteristics to the omnivorous fish intestinal microbiota was distinct. • Microbial communities in the oyster reefs and fish intestines showed various predictive functions and unique core indicators. • The microbial diversity in sediments were significantly higher than that in intestines. The habitats of oyster reefs had played various ecological services functions, as an important means of marine ecological restoration and fishery resources conservation, which had been widely used worldwide. And the characteristics of microbial communities would be inevitably affected by habitat of oyster reefs. The aim of this study was to reveal the relationship between oyster reefs and the intestinal microbiota of fish (Takifugu ocellatus , Acanthopagrus latus , Clupanodon thrissa , and Mugil cephalus). Here, based on 16S rRNA sequencing, this research analyzed the microbial communities of fishes gut in the oyster reefs from the most crucial estuary economic zone in Southern China. It was significantly lower that the bacterial alpha-diversity in the fish intestines than in the sediments of oyster reefs. The non-metric multidimensional scaling (NMDS) and analysis of similarities (ANOSIM) results showed that intestines microbiota of T. ocellatus and A. latus were more homologous to sediments microbiota, but intestines microbiota of C. thrissa and M. cephalus were more similar to the water microbiota. There were obvious differences in the contribution of oyster reefs habitat to intestinal microorganisms of four fishes. Source tracking analysis as well reached the similar conclusion. For instance, contribution of water to T. ocellatus and A. latus was lesser than sediments, which was related to their benthic habits. Based on the differences in microbial community compositions, the functional prediction analysis had demonstrated that special functional pathways and independent core indicators had been formed separately from oyster reefs and fish intestines. Overall, these findings highlighted the characteristics of microbial diversity and functions from the omnivorous fish living in oyster reefs habitats. This research proposed new insights into the function of oyster reefs habitats, which have enriched the ecological service value of oyster reefs from microbial ecology and provided a reference for the application of oyster reefs habitats in other estuaries. [ABSTRACT FROM AUTHOR]

• A multi-dimensional functional space was built to visualize the functional structure. • The functional structure and trait composition of fish in the PRE vary seasonally. • The CWM traits were mainly affected by temperature, DO, chlorophyll-a, and depth. Estuaries are one of the most important ecosystems with high biological productivity. They connect freshwater and marine ecosystems, and the fish community assemblages face intense environmental changes, so estuarine fish communities have unique ecological characteristics. With the increase of human activities and the discharge of pollutants, the pressure on the ecosystem of the Pearl River Estuary (PRE) is intensifying, and its ecosystem functions and services are inevitably affected. To better understand the functional structure of the fish community in the PRE and its response to environmental changes, we analyzed the trait composition of the community and its relationships to environmental factors based on 10 functional traits of 130 fish species collected in the PRE during the summer and winter of 2020–2021. In addition, we built a multi-dimensional functional space to visualize the overall functional structure of the PRE and explore the seasonal variation of the selected traits in the functional space. Our findings suggest that the functional traits of the fish communities in the PRE were mainly affected by temperature, dissolved oxygen, chlorophyll-a, and depth. Among them, the effects of dissolved oxygen, temperature, and chlorophyll-a on CWM traits were reflected in seasonal differences, while the effects of depth were reflected in spatial differences. We also found the main trait categories that occupied the most functional space and contributed the most to the seasonal differences in functional space. The results of this study are significant for understanding the seasonal variation of the functional structure in the PRE and how environmental gradients drive the functional traits of fish communities, and also provide insights for effective ecosystem-based management in the PRE. [ABSTRACT FROM AUTHOR]