Remarkably little information is available about the interaction between the gut microbiota and intestinal immunity in fish and crustaceans. In our study, we used Illumina MiSeq sequencing and real-time quantitative PCR to compare the microbial community and immunity genes expression in the foregut, midgut and hindgut of Chinese mitten crab (Eriocheir sinensis). Our results indicated that the community richness of the midgut is higher than in the foregut or the hindgut, although the bacterial diversity in the hindgut is higher. The predominant phyla were Tenericutes and Firmicutes in the foregut, Tenericutes and Proteobacteria in the midgut and Proteobacteria, Tenericutes and Bacteroidetes in the hindgut. When compared with the midgut, the expression of antimicrobial peptides (AMPs) were significantly elevated in the hindgut (P < 0.05), and the gene expression of EsRelish (IMD pathway) was higher than the Toll signaling pathway genes. Actinobacteria and Lactobacillus had negative correlationship with the expression of AMPs, although Acinetobacter, Bacteroides, Flavobacterium can up-regulate the expression of AMP genes. Collectively, our data indicate that microbiota are site-specific within the digestive tracts of crabs and the bacterial community and intestinal immunity have a close relationship in E. sinensis.

Background: The Chinese grass shrimp,Palaemonetes sinensis, is an economically important freshwater shrimp in China, and the study of genetic diversity and structure can positively contribute to the exploration of germplasm resources and assist in the understanding ofP. sinensisaquaculture. Microsatellite markers are widely used in research of genetic backgrounds since it is considered an important molecular marker for the analyses of genetic diversity and structure. Hence, the aim of this study was to evaluate the genetic diversity and structure of wildP. sinensispopulations in China using the polymorphic microsatellite makers from the transcriptome.Results: Sixteen polymorphic microsatellite markers were developed forP. sinensisfrom transcriptome, and analyzed for differences in genetic diversity and structure in multiple wildP. sinensispopulations in China. Totally of 319 individual shrimps from seven different populations were genotyped to find that allelic polymorphisms varied in two to thirteen alleles seen in the entire loci. Compared to other populations analyzed, the two populations including LD and SJ showed lower genetic diversity. Both the genetic distance (D) and Wrights fixation index (F_ST) comparing any two populations also indicated that LD and SJ populations differed from the other five populations. An UPGMA tree analysis showed three main clusters containing SJ, LD and other populations which were also confirmed using STRUCTURE analysis.Conclusion: This is the first study where polymorphic microsatellite markers from the transcriptome were used to analyze genetic diversity and structures of different wildP. sinensispopulations. All the polymorphic microsatellite makers are believed useful for evaluating the extent of the genetic diversity and population structure ofP. sinensis. Compared to the other five populations, the LD and SJ populations exhibited lower genetic diversity, and the genetic structure was differed from the other five populations. Therefore, they needed to be protected against further declines in genetic diversity. The other five populations, LP, LA, LSL, LSY and LSH, are all belonging to Liaohe River Drainage with a relatively high genetic diversity, and hence can be considered as hot spots for in-situ conservation ofP. sinensisas well as sources of desirable alleles for breeding values.

Introduction: To support the sustainable development of rice and aquaculture industries, various rice-animal coculture systems have been developed. One such system, the rice-crab coculture system (RCC), has been practiced for decades in northern China. However, studies on the crab physiological status in RCC remain limited. Microorganisms play a crucial role in aquaculture by influencing animal nutrition, health, nutrient cycling, water quality, and environmental impact. Research on the gut and environmental microbiota in RCC is scarce.Methods: This study compared the growth performance, immune and digestive enzyme activities of crabs between RCC and traditional pond farming system (PF). In addition, the microbiota in crab guts, water, and sediment from both systems was investigated using 16S rRNA gene sequencing.Results: Crabs in RCC exhibited superior growth performance and higher enzymatic activities, including acid phosphatase (ACP), alkaline phosphatase (AKP), lipase (LPS), and trypsin (TRY). Significant differences were observed in microbiota composition across crab gut, water, and sediment samples, respectively. RCC crabs had a lower abundance of Bacteroidota and a higher abundance of Firmicutes in their gut microbiota. The RCC environment was enriched with beneficial bacteria such as Rhizobiales, Methylococcales, KD4-96, C39, Xanthomonadales, and Nitrosomonadaceae. Microbial function predictions confirmed enhanced methanotrophy and nitrogen fixation in the RCC.Discussion: The RCC enhances the growth rate and immune capability of crabs. Crabs from RCC consume more animal-based nutrition, which results in distinct differences in gut microbiota composition and higher levels of LPS and TRY compared to those in PF. Additionally, RCC supports environmentally beneficial bacteria that contribute to greenhouse gas reduction, carbon and nitrogen fixation, organic matter decomposition, and ammonia oxidation, benefiting both the crabs and their ecosystem. These findings enhance our understanding of crab physiology and microbial communities in RCC and PF systems.

The aquaculture industry of red swamp crayfish (RSC), Procambarus clarkii, has grown significantly in recent decades due to increasing market demand. In China, low water temperatures, particularly during overwintering, pose a challenge, hindering the development of the RSC aquaculture industry in northern regions. Understanding the molecular mechanism of RSCs’ responses to cold stress could be beneficial for its aquaculture practices. In this study, we exposed RSCs to 4 °C (T4) and 22 °C (T22: control) for 96 h. Transcriptomic and metabolomic analyses of hepatopancreas tissues were performed to identify key genes and metabolites that participate in cold stress response. A total of 787 differentially expressed genes (DEGs) and 198 differentially expressed metabolites (DEMs) were identified between T4 and T22. DEGs were significantly enriched in KEGG pathways related to carbohydrate, lipid, amino acid, and nucleotide metabolism, immunity, and signaling, while DEMs were significantly enriched in pathways associated with lipid and amino acid metabolism and membrane transport. The results indicated that cold stress altered RSCs’ metabolism and their innate immune system. This study provides valuable information to increase our understanding of cold stress responses in RSCs.