Rice flowering improves the muscle nutrient, intestinal microbiota diversity, and liver metabolism profiles of tilapia (Oreochromis niloticus) in rice-fish symbiosis

Weak salinization alleviates the harmful impact of cyanobacteria on water fleas

Climate change and anthropogenic activities are driving dramatic changes in aquatic ecosystems. In this context, cyanobacterial blooms and freshwater salinization have recently received much attention, however, the comprehensive effects of these stressors on aquatic organisms are complex and have yet to be accurately clarified. This study tested the harmful effects of cyanobacteria and increasing salinity on zooplankton by characterizing the life-history traits and gut microbiota composition in the large-bodied Daphnia pulex and small-bodied Simocephalus vetulus. In 0 g L-1 salinity, the intrinsic growth rates of both species decreased when fed a diet containing cyanobacteria. Without cyanobacteria, the intrinsic growth rate of D. pulex was highest at 1 g L-1 salinity and lowest at 2 g L-1, whereas that of S. vetulus declined as salinity levels rose. Salinity alleviated the negative effects of cyanobacteria on water fleas. D. pulex performed worse than S. vetulus under high salinity (2 g L-1), cyanobacteria or their combined effects. Salinity changed the dominant gut microbiota in the water fleas when fed cyanobacteria. Bacteroides sp. and Cetobacterium sp. in D. pulex and Cetobacterium sp. in S. vetulus were most abundant when the water fleas were reared at low salinity (1 g L-1). The consistent changes in the dominant bacterial groups and the life-history traits indicate that the gut microbiota might adjust their tolerance to cyanobacteria.

Morphological and Histological Analysis of the Gastrointestinal Systems in Triplophysa strauchii and Triplophysa tenuis: Insights into Digestive Adaptations

Fish are vital for material cycling and energy flow in aquatic ecosystems. The genus Triplophysa, with over 100 known species, is significant in the Central Asian highlands' freshwater ecosystems. T. strauchii and T. tenuis, as representatives, occupy distinct ecological niches and face challenges from climate change and human activities. There is a lack of research on Triplophysa fishes' digestive systems, especially comparative studies, so this research aims to fill this gap. In September 2024, 40 samples of T. strauchii were collected from Sayram Lake and 40 samples of T. tenuis were collected from the Muzat River in Xinjiang. After acclimation, morphological observations (measuring fish and digestive tract parameters) and histological analyses (paraffin sectioning, HE staining, and microscopy) were carried out. The data were sorted in Excel and analyzed with an independent samples t-test in SPSS 27.0. Morphologically, T. strauchii has an obtuse snout, terminal mouth, specific upper lip papillae, and an S-shaped intestine about (1.45 ± 0.11) times its body length, while T. tenuis has an arc-shaped subterminal mouth, fringed papillae, and a spiral-shaped intestine around (0.82 ± 0.09) times its body length. Both possess a digestive tract, glands, and a hepatopancreas attached to the mesentery. Histologically, a large number of club cells were found in the oropharyngeal cavities of both species; their secretions have an adhesive effect on food, aiding food selection. Their digestive systems vary in structure and cell composition: the oropharyngeal cavity has three layers; the esophagus has four layers with more goblet cells in T. strauchii; the stomach has three regions without goblet cells and a thicker muscular layer in T. strauchii; the intestinal wall has four layers with different villi and goblet cell distributions; the hepatopancreas has lobules; and T. strauchii has a typical portal area. In conclusion, this study systematically compared the gastrointestinal systems of T. strauchii and T. tenuis for the first time, revealing significant structural differences related to their niches and feeding patterns as adaptations to specific environments. It fills the research gap, provides a basis for exploring fish ecological adaptation and environmental impacts on digestion, offers new ideas for Triplophysa protection strategies, and guides fish evolutionary biology research and Triplophysa resource protection and utilization.

Rice-Fish Farming Improved Antioxidant Defences, Glucose Metabolism, and Muscle Nutrient of Carassius auratus in Sichuan Province

Rice-fish farming is an ancient and enduring aquaculture model in China. This study aimed to assess the variations in digestive enzymes, antioxidant properties, glucose metabolism, and nutritional content between Carassius auratus reared in paddy fields and ponds. Notably, the levels of amylase and trypsin in C. auratus from rice paddies were considerably higher compared to those from ponds. Additionally, the hepatic catalase (CAT) activity in fish from paddy (2.45 ± 0.16 U/mg) exceeded that of their pond counterparts (2.27 ± 0.25 U/mg). Regarding glucose metabolism, the activities of key enzymes such as Na+/K+-ATPase (NKA) (paddy: 82.45 ± 6.11 U/g; pond: 78.53 ± 7.18 U/g), hexokinase (HK) (paddy: 9.55 ± 0.58 U/g; pond: 8.83 ± 0.72 U/g), glucokinase (GK) (paddy: 4.09 ± 0.21 IU/g; pond: 3.44 ± 0.33 IU/g), glucose-6-phosphatase (G6Pase) (paddy: 85.71 ± 4.49 IU/g; pond: 79.12 ± 9.34 IU/g), and glucose-6-phosphate dehydrogenase (G6PDH) (paddy: 47.23 ± 3.22 U/g; pond: 42.31 ± 4.93 U/g) were significantly elevated in rice paddy-cultured fish compared to those in ponds. Conversely, phosphor-pyruvate kinase (PK) (paddy: 418.15 ± 31.89 U/g; pond: 570.16 ± 56.06 U/g) activity was markedly reduced in the paddy group. Hepatic glycogen content (paddy: 15.70 ± 0.98 ng/g; pond: 14.91 ± 1.24 ng/g) was also substantially higher in fish from paddy, although no significant differences in muscle glycogen content (paddy: 7.14 ± 0.59 ng/g; pond: 6.70 ± 0.52 ng/g) were observed between the two environments. In terms of nutritional composition, fish raised in paddy exhibited higher crude protein (paddy: 18.46 ± 0.47 g/100 g muscle; pond: 15.57 ± 0.25 g/100 g muscle) and crude ash (paddy: 1.19 ± 0.02 g/100 g muscle; pond: 0.97 ± 0.02 g/100 g muscle) than those in ponds, whereas the crude fat (paddy: 0.87 ± 0.04 g/100 g muscle; pond: 1.66 ± 0.04 g/100 g muscle) was notably lower in paddy fish. Furthermore, fish from rice paddies had a greater total content of monounsaturated fatty acids (MUFA) (paddy: 4.25 ± 0.24 g/100 g muscle; pond: 6.73 ± 0.27 g/100 g muscle), non-essential amino acids (NEAA) (paddy: 9.04 ± 0.3 g/100 g muscle; pond: 7.19 ± 0.21 g/100 g muscle), and delicious amino acids (DAA) (paddy: 7.11 ± 0.2 g/100 g muscle; pond: 5.45 ± 0.19 g/100 g muscle) compared to those from pond cultures. These findings suggest that rice-fish co-culture systems can yield healthier and more environmentally sustainable aquatic products by improving feed digestion and optimizing nutrient metabolism.

Metagenomic and Metabolomic Analyses Reveal the Role of Gut Microbiome-Associated Metabolites in the Muscle Elasticity of the Large Yellow Croaker (Larimichthys crocea)

The large yellow croaker (LYC, Larimichthys crocea) is highly regarded for its delicious taste and unique flavor. The gut microbiota has the ability to affect the host muscle performance and elasticity by regulating nutrient metabolism. The purpose of this study is to establish the relationship between muscle quality and intestinal flora in order to provide reference for the improvement of the muscle elasticity of LYC. In this study, the intestinal contents of high muscle elasticity males (IEHM), females (IEHF), and low muscle elasticity males (IELM) and females (IELF) were collected and subjected to metagenomic and metabolomic analyses. Metagenomic sequencing results showed that the intestinal flora structures of LYCs with different muscle elasticities were significantly different. The abundance of Streptophyta in the IELM (24.63%) and IELF (29.68%) groups was significantly higher than that in the IEHM and IEHF groups. The abundance of Vibrio scophthalmi (66.66%) in the IEHF group was the highest. Based on metabolomic analysis by liquid chromatograph-mass spectrometry, 107 differentially abundant metabolites were identified between the IEHM and IELM groups, and 100 differentially abundant metabolites were identified between the IEHF and IELF groups. Based on these metabolites, a large number of enriched metabolic pathways related to muscle elasticity were identified. Significant differences in the intestinal metabolism between groups with different muscle elasticities were identified. Moreover, the model of the relationship between the intestinal flora and metabolites was constructed, and the molecular mechanism of intestinal flora regulation of the nutrient metabolism was further revealed. The results help to understand the molecular mechanism of different muscle elasticities of LYC and provide an important reference for the study of the mechanism of the effects of LYC intestinal symbiotic bacteria on muscle development, and the development and application of probiotics in LYC.

Integration of Gut Microbiota with Transcriptomic and Metabolomic Profiling Reveals Growth Differences in Male Giant River Prawns (Macrobrachium rosenbergii)

The giant freshwater prawn (GFP; Macrobrachium rosenbergii), a tropical species cultured worldwide, has high market demand and economic value. Male GFP growth varies considerably; however, the mechanisms underlying these growth differences remain unclear. In this study, we collected gut and hemolymphatic samples of large (ML), medium (MM), and small (MS) male GFPs and used the 16S rRNA sequencing and liquid chromatography-mass spectrometry-based metabolomic methods to explore gut microbiota and metabolites associated with GFP growth. The dominant bacteria were Firmicutes and Proteobacteria; higher growth rates correlated with a higher Firmicutes/Bacteroides ratio. Serum metabolite levels significantly differed between the ML and MS groups. We also combined transcriptomics with integrative multiomic techniques to further elucidate systematic molecular mechanisms in the GFPs. The results revealed that Faecalibacterium and Roseburia may improve gut health in GFP through butyrate release, affecting physiological homeostasis and leading to metabolic variations related to GFP growth differences. Notably, our results provide novel, fundamental insights into the molecular networks connecting various genes, metabolites, microbes, and phenotypes in GFPs, facilitating the elucidation of differential growth mechanisms in GFPs.

Integrated rice-yellow catfish farming resulting in variations in the agricultural environment, rice growth performance, and soil bacterial communities

Different rice production patterns exert varying comprehensive impacts on the agricultural environment. Integrated rice-fish farming, an advanced and rapidly developing agricultural production pattern, aims to improve resource utilization efficiency and enhance food productivity. To unravel the responses and internal interactions of the agricultural ecological environment to integrated rice-fish farming, we assessed and compared environmental factor, rice growth performance, and soil microbiome in both integrated rice-yellow catfish farming (IRYF) and rice monoculture (RM) systems. Our results revealed significant increases in the total nitrogen and ammonia concentrations in the paddy water and soil induced by the IRYF. Rice growth performance in the IRYF group surpassed that in the RM group. IRYF obviously impacted almost all dominant bacterial phyla, genera, and functional groups (top ten most abundant), enhancing the ability of bacteria to degrade and utilize organic matter. Additionally, IRYF led to noticeable reductions in the Shannon, Simpson, Chao 1, and Pielou_J indices. IRYF strengthened the interconnections between various taxonomic units in bacterial co-occurrence network, resulting in increased complexity, stability, and disturbance resistance in the soil bacterial community. IRYF notably facilitated the transition from a community assembly dominated by stochastic processes to one dominated by deterministic processes for the soil bacterial community. The deterministic process driving this transition was variable selection. All the environmental factors, except for soil nitrate, demonstrated relatively high contributions to alterations in soil bacterial communities, with environmental variables significantly positively correlated with the soil bacterial community in the IRYF group. Alterations in functionality, composition, and diversity of the soil bacterial community were clearly associated with most environmental variables and rice growth performance indices. Our research contributed to understanding the comprehensive impacts of integrated rice-fish farming on agricultural ecosystems and provide theoretical support for achieving the sustainable agricultural production and optimizing the rice production patterns.

Mechanism of sturgeon intestinal inflammation induced by Yersinia ruckeri and the effect of florfenicol intervention

The mechanism by which Y. ruckeri infection induces enteritis in Chinese sturgeon remains unclear, and the efficacy of drug prevention and control measures is not only poor but also plagued with numerous issues. We conducted transcriptomic and 16 S rRNA sequencing analyses to examine the differences in the intestinal tract of hybrid sturgeon before and after Y. ruckeri infection and florfenicol intervention. Our findings revealed that Y. ruckeri induced the expression of multiple inflammatory factors, including il1β, il6, and various chemokines, as well as casp3, casp8, and multiple tumor necrosis factor family members, resulting in pathological injury to the body. Additionally, at the phylum level, the relative abundance of Firmicutes and Bacteroidota increased, while the abundance of Plesiomonas and Cetobacterium decreased at the genus level, altering the composition of the intestinal flora. Following florfenicol intervention, the expression of multiple apoptosis and inflammation-related genes was down-regulated, promoting tissue repair. However, the flora became further dysregulated, increasing the risk of infection. In conclusion, our analysis of the transcriptome and intestinal microbial composition demonstrated that Y. ruckeri induces intestinal pathological damage by triggering apoptosis and altering the composition of the intestinal microbiota. Florfenicol intervention can repair pathological damage, but it also exacerbates flora imbalance, leading to a higher risk of infection. These findings help elucidate the molecular mechanism of Y. ruckeri-induced enteritis in sturgeon and evaluate the therapeutic effect of drugs on intestinal inflammation in sturgeon.

Heat-Killed Saccharomyces boulardii Alleviates Dextran Sulfate Sodium-Induced Ulcerative Colitis by Restoring the Intestinal Barrier, Reducing Inflammation, and Modulating the Gut Microbiota

Ulcerative colitis (UC) is a global intestinal disease, and conventional therapeutic drugs often fail to meet the needs of patients. There is an urgent need to find efficient and affordable novel biological therapies. Saccharomyces boulardii has been widely used in food and pharmaceutical research due to its anti-inflammatory properties and gut health benefits. However, there is still a relatively limited comparison and evaluation of different forms of S. boulardii treatment for UC. This study aimed to compare the therapeutic effects of S. boulardii, heat-killed S. boulardii, and S. boulardii β-glucan on UC, to explore the potential of heat-killed S. boulardii as a new biological therapy. The results demonstrate that all three treatments were able to restore body weight, reduce the disease activity index (DAI), inhibit splenomegaly, shorten colon length, and alleviate histopathological damage to colonic epithelial tissues in DSS-induced colitis mice. The oral administration of S. boulardii, heat-killed S. boulardii, and S. boulardii β-glucan also increased the levels of tight junction proteins (Occludin and ZO-1), decreased the levels of pro-inflammatory cytokines (TNF-α, IL-1β, and IL-6) in the serum, and suppressed the expressions of TNF-α, IL-1β, and IL-6 mRNA in the colon. In particular, in terms of gut microbiota, S. boulardii, heat-killed S. boulardii, and S. boulardii β-glucan exhibited varying degrees of modulation on DSS-induced dysbiosis. Among them, heat-killed S. boulardii maximally restored the composition, structure, and functionality of the intestinal microbiota to normal levels. In conclusion, heat-killed S. boulardii showed greater advantages over S. boulardii and S. boulardii β-glucan in the treatment of intestinal diseases, and it holds promise as an effective novel biological therapy for UC. This study is of great importance in improving the quality of life for UC patients and reducing the burden of the disease.

Inhibiting release of phenanthrene from rice-crab coculture sediments to overlying water with rice stalk biochar: Performance and mechanisms

Rice crab coculture is a new ecological agriculture model combining rice cultivation and crab farming. Current research related to rice crab coculture only focuses on production theory and technical system establishment, while ignoring the potential ecological risk of Polycyclic aromatic hydrocarbon(PAHs) in rice crab coculture sediment. In this study, rice straw was used to make rice straw biochar to explore the performance and mechanism of inhibiting release of phenanthrene(PHE) from rice-crab coculture sediments to overlying water with rice stalk biochar. The kinetic and isotherm adsorption data were best represented by the Langmuir model and pseudo-second-order model with a maximum adsorption capacity of 53.35 mg/g at 12 h contact time. The results showed that PHE was released from the rice-crab substrate to the overlying water in dissolved and particle forms as a result of bioturbation, and the PHE concentrations in dissolved and particle forms were 20.9 μg/L and 14.22 μg/L, respectively. This leads to secondary ecological risks in rice-crab co-culture systems. This is related to dissolved organic carbon(DOC) carrying the dissolved PHE and total suspended solids(TSS) carrying the particle PHE in the overlying water. Due to its large specific surface area, rice straw biochar is rich in functional groups, providing multiple hydrophobic adsorption sites. After adding rice straw biochar at 0.5 % w/w (dry weight) dose, the removal efficiency of dissolved and particulate PHE in the overlying water were 78.99 % and 42.11 %, respectively. Rice straw biochar is more competitively adsorbed PHE in the overlying water than TSS and DOC. The removal efficiency of PHE from the sediment was 52.75 %. This study confirmed that rice stalk biochar could effectively inhibit PHE migration and release in paddy sediment. It provides an environment- friendly in situ remediation method for the management of PAHs pollution from crab crops in rice fields.

Multi-Omics Analysis to Understand the Effects of Dietary Proanthocyanidins on Antioxidant Capacity, Muscle Nutrients, Lipid Metabolism, and Intestinal Microbiota in Cyprinus carpio

Proanthocyanidins (Pros), a natural polyphenolic compound found in grape seed and other plants, have received significant attention as additives in animal feed. However, the specific mechanism by which Pros affect fish health remains unclear. Therefore, the aim of this study was to investigate the potential effects of dietary Pro on common carp by evaluating biochemical parameters and multi-omics analysis. The results showed that Pro supplementation improved antioxidant capacity and the contents of polyunsaturated fatty acids (n-3 and n-6) and several bioactive compounds. Transcriptomic analysis demonstrated that dietary Pro caused an upregulation of the sphingolipid catabolic process and the lysosome pathway, while simultaneously downregulating intestinal cholesterol absorption and the PPAR signaling pathway in the intestines. Compared to the normal control (NC) group, the Pro group exhibited higher diversity in intestinal microbiota and an increased relative abundance of Cetobacterium and Pirellula. Furthermore, the Pro group had a lower Firmicutes/Bacteroidetes ratio and a decreased relative abundance of potentially pathogenic bacteria. Collectively, dietary Pro improved antioxidant ability, muscle nutrients, and the diversity and composition of intestinal microbiota. The regulation of lipid metabolism and improvement in muscle nutrients were linked with changes in the intestinal microbiota.

Effects of dietary chito-oligosaccharide and β-glucan on the water quality and gut microbiota, intestinal morphology, immune response, and meat quality of Chinese soft-shell turtle (Pelodiscus sinensis)

Chito-oligosaccharides (COS) and β-glucan are gradually being applied in aquaculture as antioxidants and immunomodulators. However, this study examined the effects of dietary supplementation of COS and β-glucan on the water quality, gut microbiota, intestinal morphology, non-specific immunity, and meat quality of Chinese soft-shell turtle. To investigate the possible mechanisms, 3-year-old turtles were fed basal diet (CK group) and 0.1%, 0.5%, and 1% COS or β-glucan supplemented diet for 4 weeks. Colon, liver, blood and muscle tissues, colon contents, water and sediment of paddy field samples were collected and analyzed after feeding 2 and 4 weeks. The results indicated that COS and β-glucan altered microbial community composition and diversity in Chinese soft-shell turtles. The relative abundance of Cellulosilyticum, Helicobacter and Solibacillus were increased after feeding COS, while Romboutsia, Akkermansia and Paraclostridium were increased after feeding β-glucan, whereas Cetobacterium, Vibrio and Edwardsiella were enriched in the control group. Furthermore, colon morphology analysis revealed that COS and β-glucan improved the length and number of intestinal villi, and the effect of 0.5% β-glucan was more obvious. Both β-glucan and COS significantly improved liver and serum lysozyme activity and antibacterial capacity. COS significantly increased the total antioxidant capacity in the liver. Further, 0.1% β-glucan significantly increased the activity of hepatic alkaline phosphatase, which closely related to the bacteria involved in lipid metabolism. Moreover, dietary supplementation with 1% COS and 1% β-glucan significantly enhanced the content of total amino acids, especially umami amino acids, in muscle tissue, with β-glucan exerting a stronger effect than COS. Additionally, these two prebiotics promoted the quality of culture water in paddy fields and reshaped the bacterial community composition of aquaculture environment. All these phenotypic changes were closely associated with the gut microbes regulated by these two prebiotics. In summary, the findings suggest that dietary supplementation with COS and β-glucan in Pelodiscus sinensis could modulate the gut microbiota, improve intestinal morphology, enhance non-specific immunity and antioxidant capacity of liver and serum, increase meat quality, and improve the culture water environment. This study provides new insights and a comprehensive understanding of the positive effects of COS and β-glucan on Pelodiscus sinensis.

Effects of hypoxia and reoxygenation on apoptosis, oxidative stress, immune response and gut microbiota of Chinese mitten crab, Eriocheir sinensis

Hypoxia causes irreversible damage to aquatic animals. However, few reports have explored the effect of hypoxia stress and reoxygenation on intestinal homeostatic imbalance and consequent hepatopancreas-intestine axis health in crustacean. Herein, 180 Chinese mitten crabs (Eriocheir sinensis) were equally divided into control (DO 7.0 ± 0.2 mg/L) and treatment groups. The treatment group was exposed with continuous hypoxic stress (DO 3.0 ± 0.1 mg/L) for 96 h and then reoxygenated (DO 6.9 ± 0.1 mg/L) for 96 h. The effects on intestines and hepatopancreas of Chinese mitten crab were investigated, and the role of gut microbiota in hypoxia induced damages was explored. Hypoxia impaired intestinal tissue structure, and decreased swelling and the number of goblet cells, which are features that did not significantly improve after reoxygenation. With prolonged hypoxic stress, the activities of antioxidant enzymes (LDH, SOD and CAT) and MDA content in intestine were significantly elevated. Moreover, the level of oxidative stress increased, which led to upregulated apoptosis rate and expression of apoptosis-related genes (Caspase 3, Caspase 8 and BAX). In addition, the expression of immune related genes (MyD88, ALF1, Relish and Crustin) in hepatopancreas and intestine was both significantly induced under hypoxia, which activated the immune defense mechanism of Chinese mitten crab to adapt to the hypoxic environment. Furthermore, diversity and relative abundance of gut microbiota decreased noticeably during hypoxic stress; the number of beneficial bacteria downregulated. Finally, KEGG pathway analysis revealed that nine pathways were significantly enriched in intestinal microorganisms, including autoimmune disease and environmental adaptation. Collectively, these results suggested that hypoxia negatively affected E. sinensis health by triggering oxidative stress, altering the composition of the gut microbiota and inhibiting the immune response.