Background: The red swamp crayfish Procambarus clarkii is a freshwater species that possesses high adaptability, environmental tolerance, and fecundity. P. clarkii is artificially farmed on a large scale in China. However, the molecular mechanisms of ovarian development in P. clarkii remain largely unknown. In this study, we identified four stages of P. clarkii ovary development, the previtellogenic stage (stage I), early vitellogenic stage (stage II), middle vitellogenic stage (stage III), and mature stage (stage IV) and compared the transcriptomics among these four stages through next-generation sequencing (NGS). Results: The total numbers of clean reads of the four stages ranged from 42,013,648 to 62,220,956. A total of 216,444 unigenes were obtained, and the GC content of most unigenes was slightly less than the AT content. Principal Component Analysis (PCA) and Anosim analysis demonstrated that the grouping of these four stages was feasible, and each stage could be distinguished from the others. In the expression pattern analysis, 2301 genes were continuously increase from stage I to stage IV, and 2660 genes were sharply decrease at stage IV compared to stages I-III. By comparing each of the stages at the same time, four clusters of differentially expressed genes (DEGs) were found to be uniquely highly expressed in stage I (136 genes), stage II (43 genes), stage III-IV (49 genes), and stage IV (22 genes), thus exhibiting developmental stage specificity. Moreover, in comparisons between adjacent stages, the number of DEGs between stage III and IV was the highest. GO enrichment analysis demonstrated that nutrient reservoir activity was highest at stage II and that this played a foreshadowing role in ovarian development, and the GO terms of cell, intracellular and organelle participated in the ovary maturation during later stages. In addition, KEGG pathway analysis revealed that the early development of the ovary was mainly associated with the PI3K-Akt signaling pathway and focal adhesion; the middle developmental period was related to apoptosis, lysine biosynthesis, and the NF-kappa B signaling pathway; the late developmental period was involved with the cell cycle and the p53 signaling pathway. Conclusion: These transcriptomic data provide insights into the molecular mechanisms of ovarian development in P. clarkii. The results will be helpful for improving the reproduction and development of this aquatic species.

The red swamp crayfish (Procambarus clarkii) is a famous invasive species. However, it has become one of the most important freshwater aquaculture resources in China. Herein, we focus on five artificial cultured populations of P. clarkii in Guangxi, southern China to investigate the genetic diversity based on mitochondrial DNA and microsatellites. The results revealed that the genetic diversity of P. clarkii populations in southern Guangxi (NN and DT) was lower than in central (LZ and LB) and northern (RS) Guangxi. A total of 17 haplotypes were captured from 100 individuals and haplotype 2 mainly existed, and the number of haplotype in NN and DT was less than other populations. The AMOVA showed that genetic variation was determined by within populations. The observed mismatch distribution of overall populations fit the expected distributions, indicating that no obvious demographic expansion, but unimodal was observed in RS, LZ and LB. Fst among most of groups exhibited moderate differentiation. Nevertheless, the gene flow demonstrated there had extensive gene exchanges between different populations, particularly between LZ and LB. UPGMA tree revealed that NN and DT belonged to the same clade, whereas the remaining populations were in the other clade. According to the genetic diversity, there is a need to improve the germplasm resources of P. clarkii in southern Guangxi.

The rice flower carp (Cyprinus carpio) is an important fish in integrated rice-fishery farming. Here, we performed the first genome-wide association study (GWAS) for seven growth traits (including body mass, total length, body length, body height, body width, caudal-peduncle depth, and eye spacing) in 200 rice flower carp samples using 369,688 high-quality SNPs and 42,225 indels obtained by double-digest genotyping-by-sequencing (ddGBS). The morphometrics of these traits were highly correlated (Pearson’s correlation coefficients = 0.74–0.99, p < 0.001). GWAS detected 15, 5, 4, 26, 7, 16, and 17 loci significant associated (-log10P ≥ 5) with body mass, total length, body length, body width, body height, caudal-peduncle depth, and eye spacing, respectively. Subsequently, within the 50 kb upstream and downstream regions surrounding these significant loci, 38, 19, 18, 20, 52, 27, and 37 candidate genes for the seven growth traits were detected, respectively. Importantly, B6_4352672 and A8_4978825 were significantly associated with more than five growth traits. These results showed loci significantly associated with more than five growth traits will be helpful for future marker-assisted selection (MAS). Interestingly, chromosomes A8 and B25 had many loci significantly associated with growth traits, most of which were shared among multiple growth-related traits. These results indicated that chromosome A8 and B25 may be closely related to growth traits. Our findings not only help understand the genetic architecture of growth traits in fish but facilitate the identification of candidate genes for marker-assisted selection towards breeding faster-growing rice flower carp in the future.

In aquaculture, the use of probiotics to improve growth, immunity, and stress resistance in crustaceans has gained increasing attention. This study examined the effects of incorporating different levels of Rhodotorula mucilaginosa (0.0, 0.1, 1.0, and 10.0 g/kg) into the diet on growth performance, antioxidant capacity (AOC), immune function, Toll/Imd, and JAK‐STAT signaling pathways in red claw crayfish ( Cherax quadricanatus ). The investigation was conducted through a 56‐day feeding trial. The main results are as follows: Compared with the control group (0.0 g/kg), different R. mucilaginosa levels significantly increased ( p < 0.05) the specific growth rate (SGR) and weight gain rate (WGR) of red claw crayfish, significantly increased ( p < 0.05) the activities of superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPX), glutathione S‐transferase (GST), total AOC (T‐AOC), and acid phosphatase (ACP) in hepatopancreas of red claw crayfish, and significantly upregulated ( p < 0.05) the relative expression levels of tumor necrosis factor receptor‐associated protein 6, akirin, immunodeficiency homolog, interferon regulatory factor 4, Toll‐like receptor (TLR) 6, TLR 2, Janus kinase, signal transducer activator of transcription, tumor necrosis factor α, interleukin‐1β, transforming growth factor‐β1 genes in the hepatopancreas of red claw crayfish. In conclusion, R. mucilaginosa significantly enhanced red claw crayfish’s growth, AOC, and immune function, and activated the Toll/Imd and JAK‐STAT signaling pathways. In this experimental context, the ideal addition level of R. mucilaginosa is 1.0 g/kg.

Bacterioplankton play an important role in estuarine ecosystem functions and services; however, potentially pathogenic bacteria may exhibit infectivity and pose a serious threat to environmental and human health. In this study, geographic patterns and assembly processes of bacterioplankton communities in 30 subtropical estuaries were explored, and potential pathogenic bacteria in the estuaries were detected and profiled.

The growth environment significantly influences the intestinal microbiota of aquatic organisms. We investigated the composition and functional differences in the intestinal microbiota of red claw crayfish (Cherax quadricarinatus) in rice fields (RB) and ponds (PB) by 16S rDNA high-throughput sequencing technology. The results indicate that the Shannon, Simpson, Sobs, Chao1, and ACE indices of PB are all higher than those of RB, demonstrating greater diversity and richness of intestinal microbiota. The dominant phyla in the intestinal microbiota of the Cherax quadricarinatus were Proteobacteria, Tenericutes, and Firmicutes. Tenericutes and Proteobacteria were significantly more abundant in the RB than in the PB, while Planctomycetes and Firmicutes were significantly more abundant in the PB than in the RB. The results of network correlation analysis indicate that Proteobacteria and Firmicutes exhibit strong connectivity with other microbial groups in the gut microbiota of Cherax quadricarinatus, showing significant centrality. They play an important role in the interactions within the gut microbiota community. The dominant bacterial genera in the Cherax quadricarinatus’s gut were Citrobacter, Candidatus_Bacilloplasma, and Clostridium_sensu_stricto_1. The abundance of the genus Clostridium was significantly higher in the PB than in the RB, whereas the abundance of Candidatus_Hepatoplasma and Vibrio was significantly lower in the PB than in the RB. The prediction function of KEGG enrichment showed that the abundance of Amino acid metabolism, Biosynthesis of Other Secondary Metabolites, Transport and Catabolism, Cancers, and Nervous System, Substance Dependence were significantly higher in the PB, while the infectious diseases pathway was enriched in the RB. In summary, our results revealed significant differences in the composition and diversity of intestinal microbiota in the Cherax quadricarinatus between rice paddy and pond farming environments. The intestinal microbiota of the Cherax quadricarinatus grown in pond environments exhibit higher diversity and stability, manifested by an increase in beneficial bacteria abundance and a decrease in opportunistic pathogens. These findings significantly improve understanding of the complex relationship among Cherax quadricarinatus, intestinal microbiota, and the environment.