Although increasing attention has been attracted to the study and application of biofloc technology (BFT) in aquaculture, few details have been reported about the bacterial community of biofloc and its manipulation strategy for commercial shrimp production. An 8-week trial was conducted to investigate the effects of three input C/N ratios (8:1, 12:1 and 16:1) on the bacterial community of water biofloc and shrimp gut in a commercial BFT tank system with intensive aquaculture of P. vannamei. Each C/N ratio group had three randomly assigned replicate tanks (culture water volume of 30 m³), and each tank was stocked with juvenile shrimp at a density of 300 shrimp m⁻³. The tank systems were operated with zero-water exchange, pH maintenance and biofloc control. During the trial, the microbial biomass and bacterial density of water biofloc showed similar variation trends, with no significant difference under respective biofloc control measures for the three C/N ratio groups. Significant changes were found in the alpha diversity, composition and relative abundance of bacterial communities across the stages of the trial, and they showed differences in water biofloc and shrimp gut among the three C/N ratio groups. Meanwhile, high similarity could be found in the composition of the bacterial community between water biofloc and shrimp gut. Additionally, nitrogen dynamics in culture water showed some differences while shrimp performance showed no significant difference among the three C/N ratio groups. Together, these results confirm that the manipulation of input C/N ratio could affect the bacterial community of both water biofloc and shrimp gut in the environment of a commercial BFT system with intensive production of P. vannamei. Moreover, there should be different operations for the nitrogen dynamics and biofloc management during shrimp production process under different C/N ratios.

Ammonia is the main pollution factor of the aquatic environment in marine shrimp culture systems. In order to demonstrate the feasibility of the combination of biofloc technology and nitrifying biofilter for the ammonia removal, a 70-day production trial was conducted in a simplified pilot-scale hybrid biofloc-based recirculating aquaculture system (biofloc-RAS) with the intensive culture of Litopenaeus vannamei. Nitrogen dynamics and nitrifying microbial communities were investigated in three replicated systems simultaneously under the conditions of high feed loading and zero water exchange. Along with biofloc development in the culture tank and biofilm formation in the nitrifying biofilter during the trial, nitrification could be fastly and effectively established in the system, which was indicated by the dynamics of total ammonia nitrogen (TAN), NO₂^–-N, NO₃^–-N, and total nitrogen (TN) concentrations. Meanwhile, similar nitrifying microorganisms could be found between biofloc and biofilm, despite some differences in abundance, diversity, and composition of ammonia-oxidizing archaea and bacteria and nitrite-oxidizing bacteria. High TAN removal rate could be achieved and was significantly and positively correlated with abundances of these nitrifying microbial communities in both biofloc and biofilm, further indicating that both biofloc and biofilm could contribute highly to nitrification performance of the biofloc-RAS. The results of this study indicate a potential application of the biofloc-RAS in coastal intensive aquaculture.

Salinity is a crucial environmental factor influencing the survival, growth, development, and reproduction of aquatic animals. However, the underlying molecular mechanisms of the shrimp’s response to salinity stress are not yet fully understood. Therefore, we used the Illumina NovaSeq 6000 platform to perform transcriptome sequencing of the hepatopancreas of Litopenaeus vannamei under high-salinity (30 PSU), medium-salinity (10 PSU), and low-salinity (0.5 PSU) conditions. We obtained 63.23 Gb of high-quality data and identified 3589 differentially expressed genes (DEGs), including 1638 upregulated and 1951 downregulated genes. Notably, a comparison between the control group (30 PSU) and the low-salinity group (0.5 PSU) revealed that the BBOX1 and CHE1 genes were significantly upregulated, while the ACOX1, MPV, CYP2L1, GCH, MVK, TREt1, and XDH genes were significantly downregulated. These genes are primarily involved in key metabolic pathways, such as fatty acid oxidation, cholesterol metabolism, and hormone synthesis and metabolism. The key genes involved in fatty acid β-oxidation, such as ACOX1, ACAD, HADH, HSD17B4, PECR, CROT, PIPOX, and CG5009, all showed a downward trend, suggesting that L. vannamei may respond to salt stress by regulating fatty acid oxidative metabolism, optimizing energy utilization, and maintaining cell homeostasis under low-salinity conditions. Functional annotation of gene ontology (GO) and KEGG pathway enrichment analysis highlighted the roles of these significant DEGs in the adaptation of L. vannamei to environments of varying salinity, underscoring the importance of metabolic pathways in their adaptive physiological responses. This study provides a crucial molecular biological basis for understanding the molecular mechanisms and physiological protection strategies of L. vannamei under salinity stress.

Given the widespread use of commercial probiotics in aquaculture, it is important to evaluate the quality and environmental effects of these additives. Here, the effects of a Bacillus probiotic compound, BG4, on Penaeus vannamei survival rate, water quality factors, and microbial communities were assessed. An analysis of the BG4 powder confirmed the content of probiotic bacteria: 50.2% Bacillus licheniformis, 48.4% Bacillus subtilis, and 1.4% Bacillus amyloliquefaciens, consistent with the information on the product packaging. The effective bacterial quantity (1.1 × 10⁹ CFU/g) was higher than that indicated on the product label (2 × 10⁸ CFU/g). BG4 was added to a sterilized aquaculture water system, according to the indicated bacterial quantity; after 7 days, the maximum ammonia nitrogen, phosphate, and chemical oxygen demand degradation rates were 36.3%, 28.9%, and 15.2%, respectively. In the shrimp culture experiment, the survival rate of P. vannamei and water quality did not differ significantly between the BG4 and control groups. The bacterial quantity and high-throughput sequencing results indicated that Bacillus content in BG4 group decreased continuously from 3.5 × 10⁴ CFU/mL to 6.9 × 10² CFU/mL. To ensure the desired effect of probiotics in commercial aquaculture applications, additional quality evaluations and scientific assessments are needed.

Sthenoteuthis oualaniensis is an important biological resource in the South China Sea. However, the microbiological characteristics of this squid, especially those of the dwarf-form, are poorly understood. This study was conducted to analyze the microbial community structure and metabolic characteristics of the intestinal and gill tissues of dwarf-form populations of S. oualaniensis. The dwarf-form squids of different sexes and gonadal maturities were collected from South China Sea in spring 2020. Results showed that Mycoplasma was the most dominant group of bacteria in the intestinal samples of the females with immature gonads (FN), females at sexual maturity (FY), and males at sexual maturity (MY) and the second-highest relative abundance group in males with immature gonads (MN). The microbial community structure in squid gills differed from that of intestinal flora. The BD1-7 clade was the dominant genus in gill samples of all groups. Furthermore, the microbial community activities in gills were higher than in intestinal groups, especially FYG. The larger dwarf-form populations had microbial communities with more robust utilization of carbon sources, assessed via average well color development (AWCD). Correlation and redundancy analysis determined that AWCD significantly positively correlated with the relative abundance of BD1-7 clade (p < 0.05). The results indicated that the dominant group of bacteria and microbial community structure were different between the intestinal and gill microbial communities in the dwarf-form S. oualaniensis populations of different sexes and maturities. Moreover, the metabolic potential of the gill microbial community was higher than that of the intestinal microbial community in the dwarf-form populations.

The tiger shrimp Penaeus monodon is a commercially important species; however, the intensification of the farming of this species has led to the production and release of significant amounts of organic waste. Traditional aquaculture uses water exchange for waste removal, which may cause pollution and infection of reared species with external pathogens. This study aimed to evaluate the effects of two different aquaculture modes on the antioxidant status, nonspecific immune response, and growth performance of P. monodon, and reveal differences in their microbial communities. The experiment was divided into two groups: one using bioflocs and zero water exchange (Group ZC), and the other using a clear water system (Group C). The results showed that, compared with those in Group C, P. monodon in Group ZC exhibited a higher final body weight, lower feed conversion ratio, higher survival rate, and higher unit yield. Additionally, P. monodon in Group ZC showed higher antioxidant and digestive enzyme activities, as well as upregulated expression of immune-related genes (such as lysozyme, anti-lipopolysaccharide factor, and Toll-like receptors). Therefore, biofloc technology can improve the growth performance, immunity, and antioxidant capacity of P. monodon, offering an environmentally friendly and efficient aquaculture model for P. monodon farming.