Rice-shrimp culture: a better intestinal microbiota, immune enzymatic activities, and muscle relish of crayfish (Procambarus clarkii) in Sichuan Province

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.

Analysis of Gut Microbiota Associated with WSSV Resistance in Litopenaeus vannamei

Microorganisms in the digestive tract regulate the metabolism of host cells as well as stimulate the immune system of the host. If the microbiota is in good balance, it will promote the good health of the host. In this study, using 16S rRNA sequencing, we analyzed the microbiota of three groups of shrimp: a group of normal shrimp (control group), shrimp that were killed by infection with the white spot syndrome virus (WSSV) (susceptible group), and shrimp that survived WSSV infection (resistant group). The results showed that although the alpha diversity of the microbiota was barely affected by the WSSV, the bacterial communities in the three groups had different prevalences. The resistant group harbored significantly more bacteria than both the other groups. Remarkably, the resistant group had the greatest prevalence of the phylum Bacterioidetes, the families Rhodobacteraceae and Flavobacteriaceae, and the genus Nautella, suggesting their potential as biomarkers for shrimp resistance to WSSV infection. In addition, analysis of functional diversity in bacterial communities showed that the abundance of bacterial metagenomes in two groups infected with WSSV was mostly linked to metabolism and cellular processes. The susceptible WSSV group exhibited a significant reduction in amino acid metabolism. This result suggested that metabolism was the principal factor affecting the alteration in the microbiota after WSSV infection. This overview of the gut microbiota of shrimp infected with the WSSV offers crucial insights for aquaculture management and simplifies the use of control strategies in the future.

Red Swamp Crayfish (Procambarus clarkii) as a Growing Food Source: Opportunities and Challenges in Comprehensive Research and Utilization

The red swamp crayfish (Procambarus clarkii) was introduced from Japan to China in the 1920s. Crayfish are now widely distributed in almost all types of freshwater wetlands, including rice fields, ditches, swamps, lakes, and ponds in most provinces of China, owing to their multi-directional movement, rapid growth, adaptability to the environment, and relatively high fecundity. The delectable taste and high nutritional value of crayfish have made them popular among consumers, leading to the significant development of red swamp crayfish farming in the last two decades. Currently, it represents the largest proportion of commercially farmed freshwater crustaceans in China and has become an integral component of China's aquatic economy. Crayfish are highly valued for their edibility and for their by-products, which have various important uses. This review discusses nutrient composition, active ingredients, safety evaluation, processing and preservation, and comprehensive utilization of crayfish by-products to explore and organize the existing knowledge about crayfish and to promote the growth of the crayfish industry. This comprehensive review aims to provide a basis for the optimal utilization and sustainable development of crayfish resources worldwide.

Insights into chlorantraniliprole exposure via activating cytochrome P450-mediated xenobiotic metabolism pathway in the Procambarus clarkii: Identification of P450 genes involved in detoxification

To investigate the impact of chlorantraniliprole on Procambarus clarkii, acute toxicity tests were performed. Results indicated that 96 h post-exposure to chlorantraniliprole (60 mg/L) led to the separation of the hepatopancreas basement membrane, causing cell swelling, rupture, and vacuolation. Moreover, acid phosphatase (ACP) and alkaline phosphatase (AKP) activities exhibited divergent trends across four concentrations of chlorantraniliprole (0, 30, 60, and 90 mg/L). Hydrogen peroxide (H2O2) and catalase (CAT) levels significantly increased, while total superoxide dismutase (T-SOD) and malonaldehyde (MDA) activities decreased, indicating oxidative stress in the hepatopancreas. A total of 276 differentially expressed genes (DEGs) were identified, with 204 up-regulated and 72 down-regulated. Out of these, 114 DEGs were successfully annotated and classified into 99 pathways, with a primary focus on the cytochrome P450-mediated xenobiotic metabolism pathway. The DEGs enriched in this pathway, along with transcriptome data, were validated using quantitative-polymerase chain reaction. This study enhances the transcriptome database of P. clarkii and provides fundamental insights into its immune defense and antioxidant mechanisms. Additionally, it lays a theoretical foundation for future research on disease prevention in P. clarkii within rice-shrimp culture systems.

Effects of Dietary Bio-Fermented Selenium Supplementation on Growth, Immune Performance, and Intestinal Microflora of Chinese Mitten Crabs, Eriocheir sinensis

Selenium is a vital trace mineral that is crucial for maintaining regular biological processes in aquatic animals. In this study, a four-week dietary trial was carried out to assess the impact of bio-fermented selenium (Bio-Se) on the growth and immune response of Chinese mitten crabs, Eriocheir sinensis. The crabs were randomly allocated to five dietary treatment groups, each receiving a different dose of Bio-Se. The doses included 0, 0.3, 0.6, 1.5, and 3.0 mg/kg and were accurately measured in basal diet formulations. The results showed the weight gain rate (WGR), specific growth rate (SGR), and survival rate (SR) in the 1.5 mg/kg Bio-Se group were the highest, and 3.0 mg/kg of Bio-Se has an inhibitory effect on the WGR, SGR, and SR. The activities of the immune enzymes, including glutathione peroxidase (GPX), superoxide dismutase (SOD), and acid phosphatase (ACP), of the hepatopancreas were significantly (p < 0.05) increased in the 1.5 mg/kg Bio-Se group, while they decreased (p < 0.05) in the 3.0 mg/kg feeding group compared to the 0 mg/kg feeding group. The concentration of maleic dialdehyde (MDA) exhibited the opposite pattern. Similarly, the mRNA expression levels of antimicrobial peptides (ALF-1, Crus-1, and LYS), ERK, and Relish genes were also observed to be the highest in the 1.5 mg/kg Bio-Se group compared with the other groups. Furthermore, the administration of 1.5 mg/kg of Bio-Se resulted in an increase in the thickness of the intestinal plica and mucosal layer, as well as in alterations in the intestinal microbial profile and bacterial diversity compared to the dose of 0 mg/kg of Bio-Se. Notably, the population of the beneficial bacterial phylum Fusobacteria was increased after crabs were fed the 1.5 mg/kg Bio-Se diet. In conclusion, the oral administration of 1.5 mg/kg of Bio-Se improved the growth efficiency, antioxidant capabilities, immunity, and intestinal health of E. sinensis. Through a broken-line analysis of the WGR against dietary Bio-Se levels, optimal dietary Bio-Se levels were determined to be 1.1 mg/kg. These findings contribute valuable insights to the understanding of crab cultivation and nutrition.

Integrated microbiome and metabolome analyses reveal the effects of low pH on intestinal health and homeostasis of crayfish (Procambarus clarkii)

Low pH (LpH) poses a significant challenge to the health, immune response, and growth of aquatic animals worldwide. Crayfish (Procambarus clarkii) is a globally farmed freshwater species with a remarkable adaptability to various environmental stressors. However, the effects of LpH stress on the microbiota and host metabolism in crayfish intestines remain poorly understood. In this study, integrated analyses of antioxidant enzyme activity, histopathological damage, 16S rRNA gene sequencing, and liquid chromatography-mass spectrometry (LC-MS) were performed to investigate the physiology, histopathology, microbiota, and metabolite changes in crayfish intestines exposed to LpH treatment. The results showed that LpH stress induced obvious changes in superoxide dismutase and catalase activities and histopathological alterations in crayfish intestines. Furthermore, 16S rRNA gene sequencing analysis revealed that exposure to LpH caused significant alterations in the diversity and composition of the crayfish intestinal microbiota at the phylum and genus levels. At the genus level, 14 genera including Bacilloplasma, Citrobacter, Shewanella, Vibrio, RsaHf231, Erysipelatoclostridium, Anaerorhabdus, Dysgonomonas, Flavobacterium, Tyzzerella, Brachymonas, Muribaculaceae, Propionivibrio, and Comamonas, exhibited significant differences in their relative abundances. The LC-MS analysis revealed 859 differentially expressed metabolites in crayfish intestines in response to LpH, including 363 and 496 upregulated and downregulated metabolites, respectively. These identified metabolites exhibited significant enrichment in 24 Kyoto Encyclopedia of Genes and Genomes pathways (p < 0.05), including seven and 17 upregulated and downregulated pathways, respectively. These pathways are mainly associated with energy and amino acid metabolism. Correlation analysis revealed a strong correlation between the metabolites and intestinal microbiota of crayfish during LpH treatment. These findings suggest that LpH may induce significant oxidative stress, intestinal tissue damage, disruption of intestinal microbiota homeostasis, and alterations in the metabolism in crayfish. These findings provide valuable insights into how the microbial and metabolic processes of crayfish intestines respond to LpH stress.

Effects of antimicrobial peptides from dietary Hermetia illucens larvae on the growth, immunity, gene expression, intestinal microbiota and resistance to Aeromonas hydrophila of juvenile red claw crayfish (Cherax quadricarinatus)

Antimicrobial peptides (AMPs), which are widely present in animals and plants, have a broad distribution, strong broad-spectrum antibacterial activity, low likelihood of developing drug resistance, high thermal stability and antiviral properties. The present study investigated the effects of adding AMPs from Hermetia illucens larvae on the growth performance, muscle composition, antioxidant capacity, immune response, gene expression, antibacterial ability and intestinal microbiota of Cherax quadricarinatus (red claw crayfish). Five experimental diets were prepared by adding 50 (M1), 100 (M2), 150 (M3) and 200 (M4) mg/kg of crude AMP extract from H. illucens larvae to the basal diet feed, which was also used as the control (M0). After an eight-week feeding experiment, it was discovered that the addition of 100-150 mg/kg of H. illucens larvae AMPs to the feed significantly improved the weight gain rate and specific growth rate of C. quadricarinatus. Furthermore, the addition of H. illucens larvae AMPs to the feed had no significant effect on the moisture content, crude protein, crude fat and ash content of the C. quadricarinatus muscle. The addition of 100-150 mg/kg of H. illucens larvae AMPs in the feed also increased the antioxidant capacity, nonspecific immune enzyme activity and related gene expression levels in C. quadricarinatus, thereby enhancing their antioxidant capacity and immune function. The H. illucens larvae AMPs improved the structure and composition of the intestinal microbiota of C. quadricarinatus, increasing the microbial community diversity of the crayfish gut. Finally, the addition of 100-150 mg/kg of H. illucens larvae AMPs in the feed enhanced the resistance of C. quadricarinatus against Aeromonas hydrophila, improving the survival rate of the crayfish. Based on the aforementioned findings, it is recommended that H. illucens larvae AMPs be incorporated into the C. quadricarinatus feed at a concentration of 100-150 mg/kg.

Ecological Toxicity of Cyantraniliprole against Procambarus clarkii: Histopathology, Oxidative Stress, and Intestinal Microbiota

Cyantraniliprole is a novel insecticide recently introduced for rice pest control that may cause potential threats to the red swamp crayfish (Procambarus clarkii) in rice-crayfish coculture systems. In this study, we investigated the acute toxicity of cyantraniliprole against P. clarkii with a LC50 value of 149.77 mg/L (96 h), first. Some abnormal behaviors of P. clarkii treated with 125 mg/L cyantraniliprole, including incunabular hyperexcitability, imbalance, inactivity, and increased excretion were observed. Moreover, it was observed that exposure to 5 mg/L cyantraniliprole for 14 days resulted in histopathological alterations in abdominal muscle, gills, hepatopancreas, and intestines. Furthermore, exposure to 0.05 and 5 mg/L cyantraniliprole induced increased activities of several oxidative stress-related enzymes, which was verified by the upregulation of related genes. Additionally, dysregulation of the intestinal microbiota was determined via 16S rRNA sequencing. These results will provide the basis for the utilization of cyantraniliprole in the fields of rice-crayfish integrated system.

Effects of hydroxy methionine zinc on growth performance, immune response, antioxidant capacity, and intestinal microbiota of red claw crayfish (Procambarus clarkii)

This study aimed to evaluate the effects of varying zinc (Zn) levels on the growth performance, non-specific immune response, antioxidant capacity, and intestinal microbiota of red claw crayfish (Procambarus clarkii (P. clarkii)). Adopting hydroxy methionine zinc (Zn-MHA) as the Zn source, 180 healthy crayfish with an initial body mass of 6.50 ± 0.05 g were randomly divided into the following five groups: X1 (control group) and groups X2, X3, X4, and X5, which were fed the basal feed supplemented with Zn-MHA with 0, 15, 30, 60, and 90 mg kg-1, respectively. The results indicated that following the addition of various concentrations of Zn-MHA to the diet, the following was observed: Specific growth rate (SGR), weight gain rate (WGR), total protein (TP), total cholesterol (TC), the activities of alkaline phosphatase (AKP), phenoloxidase (PO), total antioxidant capacity (T-AOC), total superoxide dismutase (T-SOD) and catalase (CAT), the expression of CTL, GPX, and CuZn-SOD genes demonstrated a trend of rising and then declining-with a maximum value in group X4-which was significantly higher than that in group X1 (P < 0.05). Zn deposition in the intestine and hepatopancreas, the activity of GSH-PX, and the expression of GSH-PX were increased, exhibiting the highest value in group X5. The malonaldehyde (MDA) content was significantly reduced, with the lowest value in group X4, and the MDA content of the Zn-MHA addition groups were significantly lower than the control group (P < 0.05). In the analysis of the intestinal microbiota of P. clarkii, the number of operational taxonomic units in group X4 was the highest, and the richness and diversity indexes of groups X3 and X4 were significantly higher than those in group X1 (P < 0.05). Meanwhile, the dietary addition of Zn-MHA decreased and increased the relative abundance of Proteobacteria and Tenericutes, respectively. These findings indicate that supplementation of dietary Zn-MHA at an optimum dose of 60 mg kg-1 may effectively improve growth performance, immune response, antioxidant capacity, and intestinal microbiota richness and species diversity in crayfish.

Comparison of the gut microbiota and metabolism in different regions of Red Swamp Crayfish (Procambarus clarkii)

Background

The gut microbiota is very important for maintaining the homeostasis and health of crustaceans. Many factors affect the gut microbiota of crustaceans, one of which is temperature. However, it is currently unclear how temperature affects the gut microbiota and metabolites of Procambarus clarkii.

Methods

Using metagenomic sequencing and gas chromatography-mass spectrometry (GC-MS) techniques, the gut microbiota and metabolites of P. clarkii from Hubei (HB), Jiangsu (JS), Shandong (SD), and Zhejiang (ZJ) in China were investigated.

Results

Under the impact of temperature, the gut microbiota and metabolites of P. clarkii exhibit a specific trend of change. The primary pathogenic bacteria affecting P. clarkii are Citrobacter, Enterobacterium, and Aeromonas, which are affected by temperature. Two metabolites, namely, sugars and amino acids, are regulated by temperature.

Implication

This study demonstrated that the gut microbiota and gut metabolites of P. clarkii were considerably affected by temperature. It provides a theoretical basis for the systematic study of P. clarkii and provides a basis for a healthy culture of P. clarkii.

Sub-acute toxicity of the herbicide glufosinate-ammonium exposure in adult red swamp crayfish (Procambarus clarkii)

Glufosinateammonium (GLA) is one of the most widely used agricultural herbicides. It is frequently detected in surface waters near farmland and may pose a risk to non-target aquatic species. This study aimed to explore the toxicity of subacute GLA exposure in crayfish. Adult red swamp crayfish were exposed to GLA (0, 1, 10, and 100 mg/L) for 21 days. Bioaccumulation, oxidative stress, nonspecific immunity, and the expression of genes encoding xenobiotic detoxification-related enzymes were examined. The results showed GLA accumulation and hepatopancreatic histopathological changes (dilation of hepatic tubules and vacuolation of hepatocytes) in the exposed crayfish. GLA exposure induced ROS production, inhibited glutathione expression, and catalase activity in the crayfish hepatopancreas, as well as inhibited immunoenzyme expression (acid phosphatase, alkaline phosphatase, and lysozyme) in the hemolymph. In addition, the total hemocyte number decreased, and the proportion of hemocyte subsets changed significantly. Superoxide dismutase first increased and then decreased with increasing GLA dosage. GLA promoted the expression of biotransformation enzymes (cypb5, gst) in the hepatopancreas. Our results suggest that subacute GLA exposure caused structural damage to the hepatopancreatic tissue and decreased antioxidant capacity and non-specific immunity in crayfish. These findings provide insight into the toxicity of herbicides on non-target organisms.

Effect of different rice transplanting patterns on microbial community in water, sediment, and Procambarus clarkii intestine in rice-crayfish system

Although the microbial ecology of integrated rice-crayfish farming systems is receiving increasing attention with the expanding application area in China, the effects of rice transplanting patterns on the microbial community of water, sediment and Procambarus clarkii intestine in rice-crayfish system has yet to be determined. This study explored the microbial community present in water, sediment and intestine samples from three transplant patterns (rice crayfish with wide-narrow row transplanting, rice-crayfish with normal transplanting and pond-crayfish, abbreviated as RC-W, RC, and PC, respectively) using high-throughput sequencing. The results showed that the dominant microbial taxa from sediment, surrounding water, and intestine at phylum level were Proteobacteria, Chloroflexi, Cyanobacteria, Actinobacteria, Bacteroidetes. The patterns of rice transplanting had significant effects on microbial biodiversity and species composition in surrounding water. The OTUs community richness of water under RC group was significantly higher than that of PC group and RC-W group. The OTU relative abundance of top 10 operational taxonomic units had significantly different (p < 0.05) in the water samples from the three groups. The intestinal OTU community richness of Procambarus clarkii in the three groups was positively correlated with the community richness of water. The proximity between intestinal and water samples in PCA diagram indicated that their species composition was more similar. The results also showed that rice transplanting patterns can affect intestinal microbial biodiversity of Procambarus clarkii and the intestinal microbial biodiversity correlated with water bodies. Although the intestinal microbial diversity of crayfish in RC-W group was lower than that in RC group, the relative abundance of potential pathogenic bacteria, such as Vibrio, Aeromonas, in intestine of the crayfish in the RC-W group was significantly decreased under rice wide-narrow row transplanting model. Redundancy analysis revealed that environmental parameters, such as pH, DO, nitrate, which regulate the composition of microbial community structures. This study provides an understanding for microbial response to different rice transplanting pattern in rice-crayfish farming system.

Probiotics, Prebiotics, and Synbiotics Utilization in Crayfish Aquaculture and Factors Affecting Gut Microbiota

Aquaculture is affected by numerous factors that may cause various health threats that have to be controlled by the most environmentally friendly approaches. In this context, prebiotics, probiotics, and synbiotics are frequently incorporated into organisms' feeding rations to ameliorate the health status of the host's intestine, enhancing its functionality and physiological performance, and to confront increasing antimicrobial resistance. The first step in this direction is the understanding of the complex microbiome system of the organism in order to administer the optimal supplement, in the best concentration, and in the correct way. In the present review, pre-, pro-, and synbiotics as aquaculture additives, together with the factors affecting gut microbiome in crayfish, are discussed, combined with their future prospective outcomes. Probiotics constitute non-pathogenic bacteria, mainly focused on organisms' energy production and efficient immune response; prebiotics constitute fiber indigestible by the host organism, which promote the preferred gastrointestinal tract microorganisms' growth and activity towards the optimum balance between the gastrointestinal and immune system's microbiota; whereas synbiotics constitute their combination as a blend. Among pro-, pre-, and synbiotics' multiple benefits are boosted immunity, increased resistance towards pathogens, and overall welfare promotion. Furthermore, we reviewed the intestinal microbiota abundance and composition, which are found to be influenced by a plethora of factors, including the organism's developmental stage, infection by pathogens, diet, environmental conditions, culture methods, and exposure to toxins. Intestinal microbial communities in crayfish exhibit high plasticity, with infections leading to reduced diversity and abundance. The addition of synbiotic supplementation seems to provide better results than probiotics and prebiotics separately; however, there are still conflicting results regarding the optimal concentration.

Intestinal microbiome in crayfish: Its role upon growth and disease presentation

The intestine-associated microbiota in crustaceans are considered a key element for maintaining homeostasis and health within the organisms. Recently, efforts have been made to characterize bacterial communities of freshwater crustaceans, including crayfish, and their interplay with the host's physiology and the aquatic environments. As a result, it has become evident that crayfish intestinal microbial communities display high plasticity, which is strongly influenced by both the diet, especially in aquaculture, and the environment. Moreover, studies regarding the characterization and distribution of the microbiota along the gut portions led to the discovery of bacteria with probiotic potential. The addition of these microorganisms to their food has shown a limited positive correlation with the growth and development of crayfish freshwater species. Finally, there is evidence that infections, particularly those from viral etiology, lead to low diversity and abundance of the intestinal microbial communities. In the present article, we have reviewed data on the crayfish' intestinal microbiota, highlighting the most frequently observed taxa and emphasizing the dominance of phylum within this community. In addition, we have also searched for evidence of microbiome manipulation and its potential impact on productive parameters, and discussed the role of the microbiome in the regulation of diseases presentation, and environmental perturbations.

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

BACKGROUND

Rice-fish symbiosis, as an ecological and green aquaculture model, is an effective measure to relieve the environmental stress from intensive aquaculture. Compared with traditional aquaculture, the altered rearing pattern and environment will make differences in muscle nutrient and quality, intestinal microbiota, body metabolism, and even disease resistance in fish.

RESULTS

To investigate this, we explored the differences between rice-tilapia (aRT and bRT) and tank-tilapia (aTT and bTT) models at the periods before and after rice flowering using 16S rRNA sequencing and untargeted metabolomics. The results showed that compared with tilapia reared in the tank model, the fish body length and weight, the muscle total umami amino acid, and monounsaturated fatty acid content were obviously higher in the rice-fish model, especially after rice flowering. Compared with other groups, the intestinal microbiota diversity of fish in the bRT group was significantly higher; the dominant microbiota was Bacteroidetes and Firmicutes at the phylum level, Bacteroides and Turicibacter at the genus level, and the relative abundances of Gram-negative, potentially pathogenic, and stress-tolerant bacteria were the highest, lowest, and highest, respectively. Besides, the differential metabolite analysis indicated that rice-fish symbiosis improved the metabolic profiles and modulated the metabolic pathways in tilapia. Moreover, the correlation analysis of 16S sequencing and metabolomics showed that Bacteroides showed a positive correlation with many metabolites related to amino acid, fatty acid, and lipid metabolism. Video Abstract CONCLUSIONS: In summary, rice flowering improves the tilapia muscle nutrient, intestinal microbiota diversity, and disease resistance and modulates the host metabolism to acclimatize the comprehensive environment in rice-fish symbiosis. Specifically, rice flowering alters the microbiota abundance involved in amino acid, fatty acid, and lipid metabolism, resulting in improving the muscle nutrient and quality through the crosstalk of gut microbial and host metabolism. Our study will provide not only new insight into the gut microbiota-metabolism-phenotype axis, but also strong support for the promotion and application of rice-fish symbiosis in aquaculture.

Infection with white spot syndrome virus affects the microbiota in the stomachs and intestines of kuruma shrimp

Maintaining eubiosis of the gastrointestinal (GI) microbiota is essential for animal health. White spot syndrome virus (WSSV) is the most lethal viral pathogen because it causes extremely high mortality in shrimp farming. However, it remains poorly understood how WSSV infection affects the microbiota in different regions of the GI tract of shrimp. In the present study, we established an experimental model of kuruma shrimp (Marsupenaeus japonicus) infection with WSSV and then investigated the effects of WSSV infection on the microbiota in the cardiac stomach, pyloric stomach, and intestines using metataxonomics. We identified 34 phyla and 576 genera of bacteria collectively. At the phylum level, Proteobacteria and Firmicutes were the most abundant in all the three GI segments. The WSSV infection decreased microbial diversity to a different extent in the stomachs and in a time-dependent manner. The infection with WSSV affected the microbiota composition in the two stomachs, but not the intestines. Firmicutes increased significantly, while Actinobacteria, Bacteroidetes, and Cyanobacteria decreased in the two stomachs of the WSSV-infected shrimp. At the genus level, Trichococcus and Vibrio increased, but Bradyrhizobium and Roseburia decreased in the cardiac stomach of the WSSV-infected shrimp. Trichococcus and Photobacterium increased in the pyloric stomach. Although Vibrio showed a slight downward trend, Aliivibrio (formerly Vibrio) increased in the pyloric stomach. Thiothrix, Fusibacter, and Shewanella decreased in the pyloric stomach, but no significant differences in these genera were detected in the cardiac stomach. Analysis of the predicted functions of the GI microbiota indicated that the WSSV infection resulted in losses of some microbiota functions. The new information from this study may help better understand the bacteria-virus interaction in the GI tract of shrimp and other crustacean species, and inform pathogen prevention/control and sustainable aquaculture production.

Effects of Pelleted and Extruded Feed on Growth Performance, Intestinal Histology and Microbiota of Juvenile Red Swamp Crayfish (Procambarus clarkii)

The study was conducted to evaluate the extruded and pelleting feed production on growth performance, intestinal histology and microbiome analysis of juvenile red swamp crayfish, Procambarus clarkii. Crayfish were fed either pelleted or extruded feeds that were made using the same formula. Crayfish fed extruded feed had a lower feed conversion ratio, as well as significantly higher levels of trypsin and amylase (p < 0.05) than those fed pelleted feed. However, other growth indices and the activity of lipase were not significantly influenced by the feed processing technique (p > 0.05). In comparison with the pelleted feed group, the lamina propria thickness of crayfish fed extruded feed was significantly lower (p < 0.05). Additionally, the abundance of intestinal microbiota in the extruded feed group was higher than that in the pelleted feed group. The dominant phyla in the intestine of both groups were Proteobacteria, Tenericutes, and Firmicutes, and the relative abundance of Proteobacteria in the extruded feed group was significantly higher than that in the pelleted feed group (p < 0.05). These results revealed that P. clarkii fed extruded feed had higher feed utilization and better intestinal health.

Sustainability of the rice-crayfish co-culture aquaculture model: microbiome profiles based on multi-kingdom analyses

While the rice-crayfish culture (RCFP) model, an important aquaculture model in Asia, is generally considered a sustainable model, its sustainability in terms of microbial community profiles has not been evaluated. In this study, multi-kingdom analyses of microbiome profiles (i.e., bacteria, archaea, viruses, and eukaryotes) were performed using environmental (i.e., water and sediment) and animal gut (i.e., crayfish and crab gut) microbial samples from the RCFP and other aquaculture models, including the crab-crayfish co-culture, crayfish culture, and crab culture models, to evaluate the sustainability of the RCFP systematically. Results showed that RCFP samples are enriched with a distinct set of microbes, including Shewanella, Ferroplasma, Leishmania, and Siphoviridae, when compared with other aquaculture models. Additionally, most microbes in the RCFP samples, especially microbes from different kingdoms, were densely and positively connected, which indicates their robustness against environmental stress. Whereas microbes in different aquaculture models demonstrated moderate levels of horizontal gene transfer (HGT) across kingdoms, the RCFP showed relatively lower frequencies of HGT events, especially those involving antibiotic resistance genes. Finally, environmental factors, including pH, oxidation-reduction potential, temperature, and total nitrogen, contributed profoundly to shaping the microbial communities in these aquaculture models. Interestingly, compared with other models, the microbial communities of the RCFP model were less influenced by these environmental factors, which suggests that microbes in the latter have stronger ability to resist environmental stress. The findings collectively reflect the unique multi-kingdom microbial patterns of the RCFP model and suggest that this model is a sustainable model from the perspective of microbiome profiles.

The Microbiome Structure of a Rice-Crayfish Integrated Breeding Model and Its Association with Crayfish Growth and Water Quality

The rice-crayfish (RC) integrated breeding model is an important and special agricultural ecosystem that provides a unique ecological environment for exploring the microbial diversity, composition, and functional capacity. To date, little is known about the effect of the breeding model on microbiome assembly and breeding model-specific microbiome composition and the association of the microbiome with water quality and crayfish growth. In the present study, we assessed the taxonomic shifts in gut and water microbiomes and their associations with water quality and crayfish growth in the RC and crayfish monoculture (CM) breeding models across six time points of rice growth, including seedling (a), tillering and jointing (b), blooming (c), filling (d), fruiting (e), and rotting of rice residues (f). Dominant bacterial phyla, such as Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes, were detected in both gut and water microbiomes across breeding models. Notably, the diversity and structure of the gut and water microbiomes significantly (P < 0.001) differed between the RC and CM models, with higher microbial diversity being noted in the RC model than in the CM model. The taxa enriched in the RC model included Bacillus sp., Streptomyces sp., Lactobacillus sp., Prevotella sp., Rhodobacter sp., Bifidobacterium sp., Akkermansia sp., and Lactococcus sp., some of which are potentially beneficial to animals. However, opportunistic pathogens, such as Citrobacter sp. and Aeromonas sp., were depleted in the RC model. Furthermore, in the RC model, the enriched taxa that formed complex cooccurrence networks showed a significant positive correlation with water quality and crayfish growth, whereas the depleted taxa showed a significant negative correlation with water quality and crayfish growth. These results suggest that the RC model has a better microbiome composition and that RC model-specific microbes could play important roles in improving crayfish growth and water quality.

IMPORTANCE The present study comprehensively compared two different breeding models in terms of their microbiome composition and the associations of the microbiomes with crayfish growth and water quality. RC model-specific microbiome composition was identified; these microbes were found to have a positive association with water quality and crayfish growth. These results provide valuable information for guiding microbial isolation and culture and for potentially harnessing the power of the microbiome to improve crayfish production and health and water quality.

Development of a rational framework for the therapeutic efficacy of fecal microbiota transplantation for calf diarrhea treatment

BACKGROUND

Establishing fecal microbiota transplantation (FMT) to prevent multifactorial diarrhea in calves is challenging because of the differences in farm management practices, the lack of optimal donors, and recipient selection. In this study, the underlying factors of successful and unsuccessful FMT treatment cases are elucidated, and the potential markers for predicting successful FMT are identified using fecal metagenomics via 16S rRNA gene sequencing, fecal metabolomics via capillary electrophoresis time-of-flight mass spectrometry, and machine learning approaches.

RESULTS

Specifically, 20 FMT treatment cases, in which feces from healthy donors were intrarectally transferred into recipient diarrheal calves, were conducted with a success rate of 70%. Selenomonas was identified as a microorganism genus that showed significant donor-recipient compatibility in successful FMT treatments. A strong positive correlation between the microbiome and metabolome data, which is a prerequisite factor for FMT success, was confirmed by Procrustes analysis in successful FMT (r = 0.7439, P = 0.0001). Additionally, weighted gene correlation network analysis confirmed the positively or negatively correlated pairs of bacterial taxa (family Veillonellaceae) and metabolomic features (i.e., amino acids and short-chain fatty acids) responsible for FMT success. Further analysis aimed at establishing criteria for donor selection identified the genus Sporobacter as a potential biomarker in successful donor selection. Low levels of metabolites, such as glycerol 3-phosphate, dihydroxyacetone phosphate, and isoamylamine, in the donor or recipients prior to FMT, are predicted to facilitate FMT.

CONCLUSIONS

Overall, we provide the first substantial evidence of the factors related to FMT success or failure; these findings could improve the design of future microbial therapeutics for treating diarrhea in calves. Video abstract.

Herbicide atrazine exposure induce oxidative stress, immune dysfunction and WSSV proliferation in red swamp crayfish Procambarus clarkii

Atrazine is considered as a potential environmental endocrine disruptors and exhibits various toxic effects on animals. It has a great impact in the aquatic ecosystems, but there are few studies on its immunotoxicity in crustaceans. In the present study, the Procambarus clarkii were utilized to assess the immune toxicity after 0.5 mg/L and 5 mg/L atrazine exposure. A significant decrease in total hemocytes count (THC) was observed at 5 mg/L atrazine exposure throughout the experiment. The activities of antioxidant enzymes including superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) were significantly inhibited, but the content of reactive oxygen species (ROS) and malondialdehyde (MDA) were up-regulated, indicating the potential oxidative stress. The analysis of the integrated biomarker response (IBR) showed the induction of oxidative stress biomarkers and the inhibition of antioxidants. After 5 mg/L atrazine exposure for 144 h, the integrity of crayfish hepatopancreas was destroyed with disappeared connections between tubules and increased liver tubules vacuoles. The relative expression levels of different immune genes in hepatopancreas after atrazine exposure were measured. Most of these genes were suppressed and exhibited a certain dose-dependent effect. The results of crayfish white spot syndrome virus (WSSV) replication shown the amount of virus in muscle was significantly higher and exhibited a higher mortality rate at 5 mg/L group than other groups. The present study determined the impact of atrazine exposure on WSSV outbreaks, and also provide an important basis for further assessing the occurrence of pesticides on diseases of P. clarkii.

Maternal and environmental microbes dominate offspring microbial colonization in the giant freshwater prawn Macrobrachium rosenbergii

Microbial colonization is vital for physiological equilibrium in animals. However, the impact of maternal and environmental microbes on microbial succession in the early developmental stages of Macrobrachium rosenbergii remains elusive. In this study, the effects of maternal and environmental microbes on the embryonic and larval microbiota of M. rosenbergii were evaluated by high-throughput sequencing. The results showed that Proteobacteria and Firmicutes were the dominant phyla in the intestine, gonads, and hepatopancreases of maternal prawn. In addition, Actinobacteria was dominant in the intestine while Actinobacteria, Bacteroidetes, and Acidobacteria were dominant in gonads of maternal prawn. During the embryonic stages, Proteobacteria, Actinobacteria, and Bacteroidetes became the dominant phyla. In post-larval stages, Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes tended to dominate. In the water, Proteobacteria, Actinobacteria, and Bacteroidetes were the dominant phyla at 7, 14, and 21 dph water. Maternal microbes prominently impacted the microbial composition during the embryonic stages. Specifically, microbial colonization during embryonic stages was directly related to the maternal hepatopancreas according to source-tracking models. When the post-larvae developed to 7 days, the high contribution to the larval microbiota mimicked the environment. These results indicated that microbial colonization in embryonic and post-larval stages was attributed to the maternal and environmental microbe community, respectively. This study provides a theoretical basis for microbial community manipulation to promote prawn growth and physiological health in aquaculture.

Integrative analysis identifies the quality advantage and corresponding regulatory mechanism of paddy field-cultured crayfish (Procambarus clarkii)

Procambarus clarkii is the dominant economic variety of crayfish in China, and paddy field shrimp cultivation is an organic mode of traditional rice-fish cultivation, with paddy field shrimp being the country's prevailing aquatic product. However, little has been reported on the differences in meat quality and digestive ability between paddy field and pond fish. In this study, the muscle composition and digestive function regulation of P. clarkii in ponds and paddies were studied to explore the influence of paddy field culture on P. clarkii quality. The results showed that the muscle composition of paddy field shrimp was significantly changed, with increased protein and decreased lipid levels. Through the study of the hepatopancreas and intestinal microbial diversity of P. clarkii, we hypothesized that rice farming may cause changes in its bacterial spectrum, stimulate the digestive functions of its intestines and hepatopancreas, cause differential expression of multi-substance metabolic pathways, and ultimately result in the substances' deposition in its muscles. This study revealed the impact of rice cultivation on P. clarkii from the perspective of meta-metabolism, and it demonstrated the advantages of paddy field shrimp cultivation.Key points• We explored the influence of paddy field culture on P. clarkii quality.• Muscle composition of paddy field shrimp was significantly changed, with increased protein and decreased lipid levels in paddy field.• Rice farming caused changes in its bacterial spectrum and stimulated the digestive functions of hepatopancreas.

Imidacloprid induces locomotion impairment of the freshwater crayfish, Procambarus clarkii via neurotoxicity and oxidative stress in digestive system

Imidacloprid (IMI) is used in integrated farming like the rice-crayfish co-culture system to prevent water weevil. However, the toxic effect of IMI on the freshwater crayfish Procambarus clarkii is unknown. In the current study, the effects of IMI on the locomotion, antioxidative status, digestion and intestinal microbiota of P. clarkii were investigated. The results showed that IMI caused locomotion impairment with reduced crawl velocity, and attenuated their dark preference, aggressiveness and reversal ability. Inhibited AChE in muscle and hepatopancreas indicates the neurotoxicity of IMI which may directly lead their locomotion dysfunction. The increase of antioxidative enzymes activity and MDA level were found after 25 μg/L and 250 μg/L exposure. Significant up-regulation of several antioxidative and immune-related genes, including CZ-SOD, CAT, GPx, GST, AFL, proPO, HSP27 and HSP70 confirmed that oxidative stress was induced in all treatments when exposed to IMI. In addition, there was significant increase of LDH, indicating the different energy allocation during the exposure. Meanwhile, results from DNA damage analysis showed elevated OTM value and 8-OHdG level in hepatopancretic cells. On the other hand, decreases of alpha-amylase, lipase and increase of trypsin in hepatopancreas was observed at 25 and 250 μg/L. In addition, significant changes of composition of intestinal microbiota at both phylum and genus levels were observed according to the 16S rRNA sequencing results. Increase of pathogenic genera and decrease of beneficial bacterial communities revealed the disequilibrium of intestinal flora of crayfish. In summary, results in the present study suggest that IMI at environmentally realistic concentration could induce AChE inhibition and oxidative stress, conjointly leading the locomotion impairment in crayfish. IMI also affected the digestive functions by enzymes inhibition and gut microbiota dysbiosis.

Effects of Dietary Saccharomyces cerevisiae YFI-SC2 on the Growth Performance, Intestinal Morphology, Immune Parameters, Intestinal Microbiota, and Disease Resistance of Crayfish (Procambarus clarkia)

The present study aimed to evaluate the effect of the dietary supplementation of Saccharomyces cerevisiae YFI-SC2 on the growth performance, intestinal morphology, immune parameters, intestinal microbiota, and disease resistance of crayfish (Procambarus clarkia). Crayfish were randomly assigned to six different boxes and two different groups in triplicate. The control group received a basal diet and the treatment group received a diet containing S. cerevisiae at 10⁷ CFU/g. After feeding for 28 days, crayfish of the treatment group exhibited a significantly better weight gain ratio (WGR) and a specific growth rate (SGR) (p < 0.05) than crayfish of the control group. Compared to the treatment group, the control group intestines showed an oedema connective tissue layer and a weak muscle layer. For immune-related genes, Crustin2 expression was similar between the groups, whereas Lysozyme and prophenoloxidase from treatment group expression levels were upregulated significantly (p < 0.05) after 14 and 28 days of feeding. Prophenoloxidase showed the highest expression, with 10.5- and 8.2-fold higher expression than in the control group at 14 and 28 days, respectively. The intestinal microbiota community structure was markedly different between the two groups. After 14 and 28 days of feeding, the relative abundance of Cetobacterium and Lactobacillus increased, whereas Citrobacter and Bacteroides decreased in the treatment group compared with that of the control group. The challenge test showed that crayfish of the treatment group had a significantly enhanced resistance against Citrobacter freundii (p < 0.05). Our results suggest that a S. cerevisiae-containing diet positively influenced the health status, immune parameters, intestinal microbiota composition, and disease resistance of crayfish.