摘要: Environmental selection and neutral processes drive diversification and evolution, thereby influencing the biodiversity and biogeography of the microbiome. The deep sea, with its vast and complex geological structures, is ideal for studying microbial biogeography; however, it remains underexplored due to technical limitations. Based on the Anna Karenina principle, we hypothesize that environmental selection induced by complex topography increases community heterogeneity, which further leads to instability of deep-sea microbial communities. To test this, near-bottom water samples were collected from the trench ridge cross-linked zone with complex topography and from the abyssal plain in the western Pacific Ocean. Utilizing next-generation and third-generation sequencing technologies, we analyzed population expansion, ecological niches, and community structure and dynamics, including beta diversity, stability and assembly process, of the deep-sea ciliates. The results indicated that both environmental selection and neutral processes were important factors driving the ciliate communities, while their relative importance varied across different topographies in the deep sea. In the topographically complex region, environmental selection promoted the population expansion of specific ciliate species, indicated by higher haplotype diversity and increased distinct amplicon sequence variants aligning to the same species. This specific population expansion resulted in higher alpha diversity but lower beta diversity. Higher niche breadth and niche overlap values, and more positive interactions, were observed in the co-occurrence network of ciliates in the topographically complex region, leading to higher community stability. In the abyssal plain, however, neutral processes dominated the ciliate community assembly, with limited population expansion, lower alpha diversity but higher community heterogeneity. These findings contradict our hypothesis based on the Anna Karenina principle. Our study challenges the Anna Karenina principle and provides novel insights into the diversity and dynamics of deep-sea ciliate communities under varying topographic complexities from individual species to community-wide scales.

摘要: This study examined the effects of Picria fel-terrae Lour. (PFL) on soybean meal-induced enteritis in zebrafish (Danio rerio) and evaluated whether its increased resistance to Aeromonas hydrophila using both in vivo and in vitro approaches. Compared to plain soybean meal, the addition of 0.05 ​%, 0.1 ​%, or 0.2 ​% PFL to zebrafish larval diet reduced intestinal neutrophil (0.1 ​% and 0.2 ​% PFL), macrophage (0.05 ​% and 0.1 ​% PFL), and T cell aggregation (0.01 ​%, 0.05 ​% and 0.1 ​% PFL). Following a six-week feeding trial with 0.1 ​% PFL, the hindgut of 3-month-old zebrafish showed a higher length/width ratio of intestinal ridges and the regulation of macrophages and CD4⁺ cells compared to fish fed soybean meal. Immune cell infiltration analysis also demonstrated immune modulatory effects of PFL, such as decreased activated memory CD4 T cells and increased M2 macrophages, and we observed a reduction in nuclear density in the liver, accompanied by an increase in PAS-stained glycogen and p-STAT3 signals. Enrichment analyses revealed that PFL may mitigate intestinal inflammation by upregulating genes involved in DNA replication and downregulating inflammatory processes, such as leukocyte chemotaxis, lysosomes, and phagosomes. The enriched hepatic terms and pathways indicated that PFL facilitated the metabolism of fatty acids and monocarboxylic acids while inhibiting the alteration of tight junctions and the generation of reactive oxygen species by NADPH oxidases. Hexanorcucurbitacin F and its target genes were revealed by network pharmacological analysis and molecular docking, and its target proteins Src and Ptk2ab were related to macrophage function. PFL increased Bifidobacterium longum and species of Faecalitalea, which may contribute to gut homeostasis. During the Aeromonas hydrophila challenge, PFL resulted in a higher survival rate and reduced swelling of the intrabronchial lymphoid tissue compared to soybean meal. PFL water extract also inhibited the growth of A. hydrophila in vitro. In conclusion, PFL dietary inclusion restored intestinal immune homeostasis by modulating the function and aggregation of immune cells, stimulating cell regeneration, rebalancing gut flora, and controlling hepatic metaflammation. These findings demonstrate that PFL enhances immune responses across the gut–liver axis and improves mucosal antibacterial defenses in fish, and is a potential functional feed additive.

摘要: Qiandao Lake, a key drinking water reservoir and a national model for Stocking-based Ecological Fisheries (SEF) in China, has been intensively managed to balance fishery productivity with ecological health. We investigated the spatiotemporal dynamics of its fish assemblage and its interactions with water quality, phytoplankton, zooplankton, and macrobenthos. Non-Metric Multidimensional Scaling (NMDS) and Analysis of Similarities (ANOSIM) highlighted seasonal and spatial disparities in fish assemblage structure. Machine learning models demonstrated that water quality variables were strong predictors of fish and assemblage composition than biotic indicators. Phytoplankton and zooplankton density and biomass predominantly influenced fish abundance. Non-native species have steadily increased in abundance and biomass, coupled with a decline in native piscivorous fish, indicating the need to change fishing bans and enhance protected areas.

摘要: The absence of knowledge about carcass dynamics in fish mortality events hampers their detection, the quantification of biomass or number of dead fish, and accountability of the responsible agent. This study aimed to investigate factors influencing carcass recapture in fish mortality events. Over 12 months, we simulated 36 mortality events in a major river of the São Francisco basin. We released varying numbers of Nile tilapia (Oreochromis niloticus) of different sizes. A team patrolled a 45 ​km stretch downstream from the release site daily to recapture the released carcasses. Only 4.28 ​% of the 3643 released carcasses were recaptured. The number of recaptured carcasses increased with the number of carcasses released and was higher for larger individuals. River flow influenced the distance traveled by the carcasses, while water temperature and rainfall affected the number of recaptures. We observed that small-scale events are challenging to identify. The information from our study, unprecedented for the tropics, provides a basis for better understanding and quantifying future fish mortality events.

摘要: Genomic selection (GS) is a powerful breeding tool that utilizes statistical models to predict breeding values for candidate populations by leveraging genotype–phenotype relationships. In contrast to marker-assisted selection, GS eliminates the need for the mapping of genes associated with traits, making it especially suitable for complex quantitative traits controlled by numerous small-effect genes. By facilitating faster breeding cycles and reducing costs, GS is poised to revolutionize aquaculture breeding programs. This paper provides a comprehensive review of the latest statistical models for GS, focusing on their application in aquaculture species. It also highlights the most widely used computational tools for implementing these models. Furthermore, it compares the genomic prediction accuracy of different models across multiple aquaculture species and provides practical guidance on model selection based on model assumptions, strengths, and suitable application scenarios. Additionally, it discusses the challenges faced by GS models and offers insights into their future prospects. The paper provides strategies and ideas for future research to advance GS in aquaculture breeding.

摘要: Multiple stressors present a significant challenge to global freshwater ecosystems, particularly affecting microbial dynamics. The response of microbial communities at the water and sediment interface varies depending on the specific stressors and habitat conditions. Previous studies have shown that biodiversity and community structure change predictably along single stress gradients. However, the interactions among multiple stressors and their combined effects on microbial communities, especially in water and sediment remain poorly understood. To investigate these interactions, 48 mesocosms were constructed to simulate shallow freshwater lake ecosystems, exposing them to the individual or combined effects of temperature (continuous warming (W), multiple heatwaves (H)), glyphosate herbicide (G), and eutrophication (E) induced by nitrogen and phosphorus addition. Results indicated that eutrophication significantly enhanced the congruence of microbial species richness at the water and sediment interface, and functional richness (p ​< ​0.05). Changes in beta-diversity in both water and sediment were primarily driven by temperature and eutrophication, with effects varying according to microbial habitat. The combined effects of temperature and eutrophication on beta-diversity were either antagonistic interactions (less than) or additive interactions (approximating the cumulative impact of each factor individually). Glyphosate herbicide had no significant influence on microbial congruence or diversity at the water and sediment interface, nor did it interact with warming or eutrophication. This research provides insights into the changes and adaptations of freshwater ecosystems under multiple stressors from a microbial community perspective. These findings have important implications for developing cost-effective ecological monitoring strategies for freshwater systems.

摘要: Cyanobacteria, as essential photosynthetic microorganisms, play a pivotal role in aquatic ecosystems by contributing to primary production and nitrogen fixation. However, they can also lead to harmful cyanobacterial blooms, threatening water quality and ecosystem stability. Cyanophages, viruses that specifically infect cyanobacteria, are key regulators of cyanobacterial populations and drivers of microbial ecosystem dynamics. While marine cyanophage biology has been extensive studied, the mechanisms underlying freshwater cyanophage infections remain poorly understood. In this study, we investigate the infection dynamics of cyanophage A-4(L) in Nostoc sp. PCC 7120, a model species known for nitrogen fixation and cellular differentiation. Through integrated transcriptomic and proteomic analysis, we revealed that A-4(L) infection is characterized by phased gene expression, with host transcription factors playing key regulatory roles. Notably, the infection induces downregulation of photosynthesis-related genes, likely reflecting a strategy to redirect host metabolic resources toward viral replication. Additionally, we examined how environmental factors, such as nitrogen sources and light conditions, influence these interactions. Our findings offer novel insights into phage-host dynamics in freshwater ecosystems, enhancing our understanding of phage-mediated ecological processes and paving the way for biotechnological and environmental applications.

摘要: Teleosts, the most diverse vertebrate group comprising over 30,000 species, exhibit the most complex sex determination systems and mechanisms among vertebrates. With the increasing availability of sequenced and assembled fish genomes, numerous sex-determining genes (SDGs) have been successfully identified. Despite the diversity of SDGs discovered in teleosts, members of the TGF-β superfamily are frequently and independently recruited as SDGs across divergent fish lineages. Of over 150 teleost species with identified SDGs, approximately 60 ​% have recruited TGF-β superfamily members as their SDGs. Within the species utilizing TGF-β members as SDGs, 85 ​% use homologs of anti-Müllerian hormone (amh) and its dedicated type II receptor (amhr2) as SDGs. To date, 34 teleost species have been documented to utilize amh and 43 utilize amhr2 homologs as SDGs respectively. This selection bias underscores amh/amhr2 as the current 'star players' among identified teleost SDGs. However, the reasons behind the recurrent recruitment of amh/amhr2 as SDGs, along with their downstream signaling pathways and molecular mechanisms governing teleost sex determination, remain unclear. Here, we systematically summarize recent advances in understanding the recruitment of amh/amhr2 as SDGs in teleosts. We propose that this preference may stem from functional redundancy, single-copy genomic architecture, ligand-receptor binding specificity and high affinity regulatory capacity in germ cell proliferation, as well as differentiation and extensive crosstalk with downstream male and female sex determination pathways. Future research should focus on the following aspects: elucidating the specificity and conservation of components in the Amh/Amhr2 signaling pathway, systematically identifying its downstream target genes and regulatory networks, and thoroughly investigating the evolutionary driving mechanisms behind its frequent recruitment as SDG. This review enhances mechanistic insights into the repeated co-option of amh/amhr2 as SDGs and advances the exploration of their signaling cascades and molecular networks in teleost sex determination.

摘要: Largemouth bass ranavirus (LMBV) is a double-stranded DNA virus that poses a serious threat to the bass farming industry. Given the significant economic losses caused by LMBV outbreaks, the development of safe and efficacious vaccines has become a crucial strategy for the sustainable prevention and control of aquatic viral infections. Here, we engineered self-assembled nanoparticles by integrating low molecular weight protamine, MCP-2 protein and ferritin into a vaccine construct. Characterization experiments demonstrated that the resulting nanoparticles (LPM-DFH and LPM-MFH) exhibited uniform dispersion and an average particle size of approximately 24 ​nm, confirming their structural stability and suitability for further immunological evaluation. Furthermore, we assessed the immune efficacy of the ferritin-based nanovaccine in largemouth bass (Micropterus salmoides). The results showed that both LPM-DFH and LPM-MFH nanovaccines elicited sustained and robust production of specific antibodies following immersion immunization, with antibody levels significantly higher than those observed in the LPM group. Notably, LPM-DFH and LPM-MFH demonstrated significant immune protection against LMBV infection in largemouth bass, achieving relative immune protection rates of 61.6 ​% and 69.2 ​% respectively. This demonstrates their potential as effective vaccine candidates for combating LMBV. These findings highlight the promising application of nanoparticle-based vaccines in the prevention and control of LMBV, offering a viable solution to mitigate the impact of this viral threat on the bass farming industry.

摘要: Nutrient enrichment, predominantly due to human activities, significantly compromises the ecological integrity of aquatic ecosystems, particularly in freshwater systems. As an essential component of the trophic pyramid, zooplankton play a key role in energy transfer from primary producers (e.g., phytoplankton) to apex predators (e.g., fish communities). Therefore, our study aimed to explore potential similarities in the structure of zooplankton communities in aquatic ecosystems (lakes, wetlands, and rivers) in a highly urbanized city in China, and their functional responses to various eutrophic conditions. This study examined the negative effects of eutrophication on the miniaturization, functional diversity, and resource use efficiency of zooplankton communities (RUEzp) based on a five-year field survey conducted across these diverse urban aquatic ecosystems. Findings indicated that total phosphorous enrichment intensified zooplankton miniaturization and reduced the functional diversity of their communities. Moreover, a significant decrease in RUEzp was observed with diminished functional dispersion (FDis). Miniaturization characterized the response of zooplankton to nutrient enrichment at the community and ecosystem functional levels, suggesting it can serve as a useful indicator for future ecological studies in aquatic environments.