Microbial communities associated with fish mucosal tissues play important roles in host health and environmental adaptation. However, the effects of contrasting aquaculture conditions on the microorganisms of the large yellow croaker (Larimichthys crocea, L. crocea) remain poorly understood. In this study, 16S rRNA gene sequencing was used to compare the gut and gill microbiota of L. crocea cultured in a marine system and a saline–alkaline system, together with the corresponding surrounding water samples. The results showed that both host tissue type and rearing environment significantly influenced microbial community structure. Water samples generally exhibited higher alpha diversity than host-associated samples, whereas the gut and gill communities were clearly separated from the surrounding water microbial community. The intestine showed stronger culture system differentiation than the gill, suggesting greater niche selectivity, while the gill retained a closer association with the rearing water. Across multiple taxonomic levels, microbial composition differed markedly among water, gut, and gill samples, and the divergence between the marine culture and saline–alkaline culture system became more pronounced at finer taxonomic resolution. Differentially enriched taxa further revealed clear tissue- and habitat-associated microbial patterns. In addition, several dominant taxa were significantly correlated with environmental variables, especially salinity and nutrient-related factors, indicating that physicochemical heterogeneity contributed substantially to microbial community assembly. Overall, this study shows that host mucosal niche and rearing environment are associated with distinct gut and gill microbiota patterns in L. crocea and provides preliminary ecological information for future microbiome-informed aquaculture management, functional validation of candidate taxa, and the development of land-based culture systems for marine fish.

Sea urchins harbor diverse microbial communities that may contribute to host-associated ecological interactions, microbial competition, and chemical defense. However, the compartment-specific organization of sea urchin-associated microbiota and their predicted chemical-defense-related functional potential remain poorly understood under aquaculture conditions. In this study, 16S rRNA gene amplicon sequencing was used to characterize microbial communities in rearing water, coelomic fluid, intestine, stomach contents, and surface mucus of Hemicentrotus pulcherrimus (H. pulcherrimus). KEGG Orthology (KO)-based functional prediction was further performed to evaluate predicted chemical-defense-related functional potential, including predicted chemical-defense-related pathways, siderophore-related functions, quorum sensing-related functions, and bacterial competition- and secretion system-related functions. Rarefaction curves and Coverage values indicated sufficient sequencing depth. Alpha diversity and Nonmetric multidimensional scaling (NMDS) analyses revealed clear microbial differentiation among the five sample types, with rearing water showing higher microbial richness. Taxonomic analysis identified Pseudomonadota, Bacteroidota, Campylobacterota, Bacillota, Planctomycetota, and Spirochaetota as dominant phyla, with several discriminative taxa across compartments. KO prediction showed that total predicted abundance of predicted chemical-defense-related KOs differed significantly among sample types. Among host-associated compartments, surface mucus showed relatively higher predicted siderophore-related KO potential, whereas stomach contents showed higher predicted quorum sensing-related KO potential among host-associated compartments. These findings suggest compartment-specific microbial communities and predicted chemical-defense-related functional potential in cultured H. pulcherrimus under aquaculture conditions. Because these functions were inferred from 16S-based KO prediction, they should be interpreted as preliminary hypotheses for future metagenomic, metabolomic, and culture-dependent validation.

External mucosal microbiota form important interfaces between fish and the aquatic environment, yet their variation during host growth remains poorly understood. We characterized the gill and skin-mucus microbiota of cultured Decapterus maruadsi across three successive body-size stages (4.98–6.81 g, 16.67–19.63 g, and 27.30–28.66 g) using 16S rRNA gene amplicon sequencing. Fish were sampled from the same cohort maintained in the same culture system, and two supplied-seawater samples were included as environmental references. Factorial multivariate analysis indicated significant effects of mucosal tissue, sampling stage, and their interaction on community composition. Broad taxonomic structure remained dominated by Pseudomonadota, whereas extensive differentiation occurred at finer taxonomic resolutions. Skin-mucus richness decreased across successive sampling stages, whereas no corresponding alpha-diversity difference was detected in the gill. Host-wide prevalence analysis revealed contrasting changes in the abundance contribution of recurrent ASVs between the two mucosal compartments; however, tissue-specific sensitivity analyses showed that occurrence categories depended partly on the sample set used to define prevalence. The same dominant Limimaricola ASV occurred at high abundance in one supplied-seawater sample and in middle-stage skin mucus, indicating environmental microbial input as a plausible contributor to the observed composition. Overall, this study provides a descriptive baseline for stage-associated variation in the external mucosal microbiota of one cultured D. maruadsi cohort and highlights distinct responses of gill and skin-mucus communities without attributing these changes solely to host growth.

Gut microbial communities undergo continuous reorganization during fish development, but changes in microbial persistence and ecological niche strategies across post-juvenile growth remain insufficiently understood. Here, we characterized the gut bacterial communities of cultured Larimichthys crocea across three successive body-size classes: EGC (5–8 g), MGC (39–46 g), and LGC (160–162 g). The three stages were successively sampled from the same cultured population maintained in the same culture pond. At each stage, 15 fish were sampled, and intestinal samples from three individuals were pooled to generate one pooled intestinal sample, yielding five pooled samples per stage. Fish received the same feed formulation throughout cultivation, while feeding quantity was adjusted according to growth. Rarefaction analysis indicated adequate sequencing coverage, and ASV-level community structure differed significantly among growth stages (ANOSIM, R = 0.4698, p = 0.001). Pseudomonadota remained the dominant phylum throughout growth, whereas pronounced restructuring emerged at finer taxonomic resolutions. EGC communities showed a comparatively consistent composition dominated by Methylobacterium, while MGC and particularly LGC exhibited substantial redistribution among dominant bacterial lineages. Stage-specific membership also changed with growth: unique genera increased from 36 in EGC to 48 in MGC and 50 in LGC, whereas stage-specific ASVs showed a nonlinear pattern and peaked in MGC (118, 173, and 124 unique ASVs in EGC, MGC, and LGC, respectively); 88 ASVs were shared across all three stages. Persistent taxa remained numerically important, accounting for 36.34%, 31.59%, and 36.95% of detected taxa in EGC, MGC, and LGC, respectively, but their contribution to total community abundance declined from 90.30% to 75.29% and 68.06%. Conversely, intermittent taxa increased in abundance contribution from 6.80% to 14.85% and 29.17%. Niche-breadth analysis further showed that specialists represented 74.38% of classified taxa and generalists 19.26%. Although generalists remained quantitatively dominant, their contribution declined from EGC to LGC, whereas specialist contribution increased. Growth-associated taxa further showed contrasting trajectories, particularly a progressive decline in Methylobacterium and increase in Aquabacterium. Collectively, these findings reveal pronounced ecological reorganization of the gut microbiota across successive size- and age-associated sampling stages of L. crocea. Because body size and age covaried with chronological sampling time in a single culture pond, these patterns should be interpreted as growth-associated temporal restructuring rather than as effects attributable solely to host growth.

External mucosal surfaces form major interfaces between fish and the aquatic environment, yet their microbial succession during host growth remains incompletely resolved. We characterized the gill and skin mucus microbiota of cultured Larimichthys crocea at three successive body-size stages (5–8 g, 39–46 g, and 160–162 g) using 16S rRNA gene amplicon sequencing. At each stage, 15 fish were sampled, and material from three fish was pooled to generate one pooled sample, yielding five pooled samples for each host-associated group. Four samples of truck-delivered seawater supplied by the same provider used throughout cultivation were included as an environmental reference. Rarefaction curves approached saturation, and amplicon sequence variant (ASV)-level community structure differed significantly among the seven groups (ANOSIM, R = 0.7521, p = 0.001). Early-stage gill and skin mucus communities occupied clearly separated regions of ordination space and showed distinct dominant taxa, whereas large-stage gill and skin mucus communities showed reduced separation and greater similarity in dominant taxonomic composition. At the genus level, 2013Ark19i characterized early-stage gills, Vibrio and Photobacterium were prominent in early-stage skin mucus, and Methylobacterium increased markedly in both large-stage mucosal communities. Although 17 phyla, 67 families, and 69 genera were shared across all groups, only 30 ASVs were universally shared, indicating extensive fine-scale turnover. Dataset-wide prevalence classification further showed that persistent ASVs contributed an increasing fraction of community abundance during growth, rising from 21.93% to 75.48% in gills and from 12.77% to 67.61% in skin mucus. Middle-stage skin mucus contained 1387 group-specific ASVs and the highest transient-ASV contribution among host-associated groups, indicating particularly extensive turnover. Overall, external mucosal microbiota exhibited tissue-specific and non-linear growth-associated reorganization, with pronounced intermediate-stage turnover and increasing abundance dominance of persistent ASVs during later growth.

Gut microbiome development during fish growth involves not only taxonomic turnover but also changes in the persistence and ecological dominance of microbial members. Here, we characterized the gut microbiota of D. maruadsi across three successive growth-associated body-size groups: the early-growth group (BLEGC; 4.98–6.81 g), middle-growth group (BLMG; 16.67–19.63 g), and late-growth group (BLLGC; 27.30–28.66 g). The three groups were successively sampled from the same cohort continuously reared in the same culture system. Fish received the same diet formulation throughout cultivation, with feeding quantity adjusted according to growth stage. At each stage, 15 fish were sampled, and rinsed intestinal tissues from five individuals were pooled to generate one composite sample, yielding three pooled intestinal samples per growth stage. Gut bacterial communities differed significantly among growth stages (ANOSIM: R = 0.2593, p = 0.005), while Pseudomonadota remained the dominant phylum across all groups. Complementary PERMANOVA supported an overall stage-associated difference, although PERMDISP also indicated heterogeneous multivariate dispersion among stages. Growth-associated restructuring became more evident at finer taxonomic levels and was accompanied by a pronounced contraction of stage-specific microbial membership. The number of unique ASVs declined from 361 in BLEGC to 286 in BLMG and 69 in BLLGC, whereas 84 ASVs were shared across all three stages. Forty ASVs met the global persistent criterion of detection in at least eight of the nine pooled samples, and their abundance contribution increased from 58.43 ± 15.08% in BLEGC to 79.54 ± 6.38% in BLMG and 90.14 ± 2.14% in BLLGC. When mean abundance was calculated only among samples in which each ASV was detected, prevalence remained positively associated with conditional mean abundance. Collectively, these results indicate that growth-associated gut microbiome succession in D. maruadsi involves not only taxonomic turnover but also progressive redistribution of community abundance toward highly prevalent and persistent bacterial members.