This study explored the variations in the characteristics of the trophic structure of Daya Bay island waters over the last four decades based on the survey findings and research data on biogenic elements (dissolved inorganic nitrogen (DIN), NO₂⁻, NO₃⁻, NH₄⁺, PO₄³⁻, and SiO₃²⁻) in Daya Bay during 1985–2021. At this time, the DIN concentration increased from 21.14 µg·L⁻¹ to 558.42 µg·L⁻¹ (26.41-fold increase), whereas the SiO₃²⁻ concentration increased by only 3.6-fold. The PO₄³⁻ concentrations attained a peak in 2004 and experienced a steady decline over the rest of the survey period. The fractions of NH₄⁺, NO₃⁻, and NO₂⁻ in DIN changed from 0.45, 0.40, and 0.15 in 1986 to 0.26, 0.74, and 0.003 in 2021, respectively. Overall, the mean values of NH₄⁺, NO₃⁻, and NO₂⁻ accounted for 45.2%, 42.5%, and 12.3%, respectively. The N/P(DIN/PO₄³⁻) ratio in Daya Bay increased from 28.08 in the 1980s to 51.63 in the 2010s. Meanwhile, the nutrient limitation conditions showed a gradual shift from N-limited to P-limited conditions. According to the nutrient quality index (NQI) analysis, the trophic state level of Daya Bay waters fell into the oligotrophic category 30 years ago (1985–2002, NQI < 2), whereas it increased from the mesotrophic level in 2005 (NQI = 2.03) to the eutrophic level in 2019 (NQI = 3.33) over the last 20 years. The results based on the eutrophication index (EI) of Daya Bay waters were generally consistent with those based on the NQI, displaying that the trophic level of Daya Bay waters indicated an increasing trend from 2005 to 2019. Moreover, the assessment data in 2021 indicated a decrease in the NQI to 0.90, thereby attaining the oligotrophic level again. This may be related to the decrease in aquacultural area in the bay over the last two years. The correlation analysis among the DIN, PO₄³⁻, and nutrient levels of Daya Bay waters indicated that the input of nitrogen and phosphorus was the primary reason for the higher nutrient levels in the water bodies; among them, municipal sewage discharge, aquaculture, and atmospheric deposition from industry are the main factors for the over importation. This indicates that the changes in the biogenic element concentrations led to variations in the trophic structure and level of Daya Bay and may be attributed to population growth and the development of the seaside industry and agriculture in the region.

Herbivorous fishes play an important role in preventing the overabundance of macroalgae on coral reefs. Understanding the feeding selectivity and consumption of macroalgae by herbivorous fishes can be challenging in studies of their ecological role in the preservation and recovery of coral reefs. Coral reef decline, macroalgal overgrowth and overfishing are clearly visible in the Xisha Islands, China. However, there are seldom studies on the feeding behaviors of herbivorous fishes in this area. We used microscopy, 18S rRNA high-throughput sequencing, and stable isotope analyses to comprehensively examine the diet of eight herbivorous reef fish species common in the Xisha Islands, including one parrotfish, two chub, two unicorn fish, and three rabbitfish. Based on microscopic examination,Siganus argenteusfed on the highest number of macroalgae species (five species), followed byNaso unicornis(four species).Kyphosus cinerascens,K. vaigiensis,N. unicornisandS. punctatissimusfed on the entire macroalgal thallus, indicating their greater ecological importance compared with species that only consume algal fronds. According to the 18S rRNA high-throughput sequencing of fish intestinal contents, cluster analysis revealed that consumed macroalgae composition from the eight fishes always grouped together based on the fish species, but with low similarity.K. vaigiensisremoved the highest diversity of macroalgae species as well as the greatest quantity of macroalgae.Calotomus carolinuscan consume the red algaPneophyllum conicum, which is widely distributed on Indo-Pacific coral reefs and can overgrow and kill live corals.N. unicorniswas found to occupy the lowest trophic position based on stable isotope analysis. Multi-technique analyses revealed thatK. vaigiensis,N. unicornisandS. argenteusshowed a high consumption potential of macroalgae, suggesting that they are the key browsers that should receive priority protection in the Xisha Islands. A diverse herbivorous fish fauna is also very important in the Xisha coral reefs. These results not only demonstrated the various functions of different herbivorous fish species in macroalgal removal, but also provided insights into the management of herbivorous fishes on the coral reefs of the South China Sea.

Coral reefs are known as “tropical rain forests” in the ocean. Fish diversity is extremely high, accounting for one-third of marine fishes. To better protect and manage coral reef fishes, this study systematically compiled documents and databases published in China. We counted 2855 species of coral reef fishes in China, which belong to 3 classes, 41 orders, 252 families, and 1017 genera. Among these, Perciformes was the dominant order, accounting for 57.31% of the total species. Gobiidae (7.43%), Labridae (5.36%), Pomacentridae (4.52%), and Serranidae (4.38%) were the main families, while other families accounted for less than 4%. Furthermore, 5.56% of coral reef fish species have entered the IUCN Red List. The present study found that coral reef fishes can be divided into nearshore and offshore. This was mainly because the nearshore coral reef fishes were more affected by human disturbance and runoff from the mainland, whereas offshore coral reef fishes were in areas with high salinity and temperature far from the mainland, where human disturbance was less. Coral reef fish species’ diversity had a significant positive correlation with coral species diversity (p < 0.05), mainly because corals provide habitat and shelter. This study is the first systematic compilation and analysis of coral reef fishes in China and provides a basic reference for global protection management and biological geographical analysis.

Mangroves are among the most productive marine and coastal ecosystems and play an important role in maintaining the stability and diversity of fish communities. To explore the structure of mangrove fish communities in China, we compiled previous studies, monographs, and two databases on 54 mangrove areas published in the past 30 years. Mangrove fish communities in China comprised Osteichthys (597 species) and Chondrichthyes (14 species), representing 611 species in 344 genera, 117 families, and 28 orders. Perciformes were the predominant taxon, with 350 species in 52 families, accounting for 57% of the total species richness. Reef fish accounted for 29.62%. With regard to feeding groups, there were 328 carnivorous species (53.68%), 214 omnivorous species (35.02%), 41 herbivorous species (6.71%), and 28 detritivores species (4.58%). Classified by body size, 57.61% were small-sized, 24.22% medium-sized, and 18.17% were large-sized fishes. A total of 5.23% (32 species) of these mangrove fish are currently on IUCN red lists, i.e., 2 species are critically endangered, 4 are endangered, 12 are vulnerable, and 14 are near threatened. Cluster analyses shows that Chinese mangroves fish were divided into two categories, i.e., coastal mangrove and island mangrove type. This is closely related to the distribution of reef fish. Moreover, the number of fish species showed a strong positive correlation with mangrove area, but not with latitude. The main reasons may be the subtropical and tropical geographic locations, as well as the characteristics of the South China Sea and the Taiwan Warm Current. The size and integrity of mangrove area are crucial to the local ecosystems; thus, protecting and restoring mangroves is of great significance to large-scale ecosystem-stability and local biodiversity.

To understand the molecular mechanisms and adaptive strategies of holocentrid fish, we sequenced the mitogenome of eight species within the family Holocentridae and compared them with six other holocentrid species. The mitogenomes were found to be 16,507–16,639 bp in length and to encode 37 typical mitochondrial genes, including 13 PCGs, two ribosomal RNAs, and 22 transfer RNA genes. Structurally, the gene arrangement, base composition, codon usage, tRNA size, and putative secondary structures were comparable between species. Of the 13 PCGs, nad6 was the most specific gene that exhibited negative AT-skews and positive GC-skews. Most of the genes begin with the standard codon ATG, except cox1, which begins with the codon GTG. By examining their phylogeny, Sargocentron and Neoniphon were verified to be closely related and to belong to the same subfamily Holocentrinae, while Myripristis and Ostichthys belong to the other subfamily Myripristinae. The subfamilies were clearly distinguished by high-confidence-supported clades, which provide evidence to explain the differences in morphology and feeding habits between the two subfamilies. Selection pressure analysis indicated that all PCGs were subject to purifying selection. Overall, our study provides valuable insight into the habiting behavior, evolution, and ecological roles of these important marine fish.