农林科学最新文献

{"title":"Using a comprehensive donor and host dataset to decipher the heritability and genetic architecture of pearl traits in the black-lipped oyster (Pinctada margaritifera)","authors":"L. Benestan ,&nbsp;C. Massault ,&nbsp;E. Vigouroux ,&nbsp;O. Chevalier ,&nbsp;D.B. Jones ,&nbsp;D.R. Jerry ,&nbsp;J. Le Luyer","doi":"10.1016/j.aquaculture.2025.742837","DOIUrl":"10.1016/j.aquaculture.2025.742837","url":null,"abstract":"<div><div>Since ancient times, natural pearls have captivated mankind for their rarity, value and beauty. Today, commercial pearl culture is based on implanting a seed nucleus along with mantle tissue from a donor oyster into the gonad of a recipient or host oyster. Due to the complexity of the biological system involved (e.g. pearls are the potential product of two genomes from both donor and host oysters), the genetic determinants underlying pearl quality traits remain poorly understood. Our study is the first to combine experimental grafting with genome-wide SNP genotyping to investigate how genetic and environmental factors influence pearl quality in donor and host black-lipped pearl oysters (<em>Pinctada margaritifera</em>). Pearl quality traits such as quality score, lustre, size, nacre thickness, weight and roundness were evaluated on 1821 pearls originating from 214 hatchery-produced donors and 1033 unrelated host oysters, reared at two distinct pearl farms. Using a custom 65 K SNP array, we successfully assigned the 214 donor oysters to 15 half and full-sib families and estimated genetic parameters. In donor oysters, the heritability for quality score and roundness was low, while lustre and nacre deposition traits were moderately heritable (h² &gt; 0.20); gene-environment interactions significantly influenced lustre (σ_GxE = 0.194) but had a negligible impact on other traits. Genome-wide association study on the donor and host genomes revealed six candidate genes associated with pearl quality traits, characterized by patterns of pleiotropy and unique trait-specific variants. Although no interaction between donor and host oysters (σ_GxH &lt; 0.001) was detected, chitin synthase, a candidate gene known to be involved in nacre formation in mollusks, contains SNPs in association with multiple pearl quality traits in both donor and host oysters. Prediction accuracy was improved using an in silico analysis involving the top-ranked 1 K SNPs based on GWAS rather than using all SNPs for the most heritable trait (lustre), uncovering that a lower density SNP panel can be used for genomic selection. Overall, these findings advance our understanding of the heritability and genetic architecture of pearl quality traits in <em>Pinctada margaritifera</em>, providing valuable insights that can inform and guide future breeding programs.</div></div>","PeriodicalId":8375,"journal":{"name":"Aquaculture","volume":"610 ","pages":"Article 742837"},"PeriodicalIF":3.9,"publicationDate":"2026-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144694293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effect of environmental factors on the control of milky disease in Chinese mitten crab (Eriocheir sinensis)","authors":"Rui Zhang ,&nbsp;Zhigang Zhao ,&nbsp;Kun Guo ,&nbsp;Xu Zhao ,&nbsp;Xiangyi Deng ,&nbsp;Shihui Wang ,&nbsp;Liang Luo","doi":"10.1016/j.aquaculture.2025.742942","DOIUrl":"10.1016/j.aquaculture.2025.742942","url":null,"abstract":"<div><div>“Milk disease”, a relatively serious disease with a high infection and mortality rate, frequently threatens the aquaculture of the Chinese mitten crab area, especially in northern China in recent years. To explore effective measures on the “milky disease” control, gradient temperature and pH were designed for the aquaculture of the infected crabs according to the reproductive characteristics of the pathogens. Then, the tissue slice and the immune capacity were detected to analyze the treatment resulting response on the organism immune system; and the bacterial and fungal flora distribution of the hepatopancreas was analyzed to judge the trend of disease development. The results found that low temperature (16 °C) significantly increased the survival percentage of the infected crabs (<em>p</em> &lt; 0.05), which weakened the damage of the immune system and enhanced immunoenzyme activities (<em>p</em> &lt; 0.05), but without any significant change in the microbial flora structure, indicating low temperature delayed the onset of disease and can effectively gain time for further treatment and cure measures. High temperature decreased the survival percentage (<em>p</em> &lt; 0.05), but the only survived crabs showed a much higher immunocompetence and a reduced percent of community abundance of the pathogen in vivo (<em>p</em> &lt; 0.05). These crabs prompted the characteristics of the “cured” crabs and suggested immunity promotion and the competition/inhibition of the pathogen in vivo would be significant for the prophylaxis and treatment of the milky disease. The survival percentage and fluctuant enzyme activities of alkali-pH groups manifested that alkali pH brought a positive response in the preliminary stage but damaged the immune system of the infected crabs, indicating it is essential to reappraise the adaptability to environmental factors in the infected crabs for disease control. This study is of crucial meaning for establishing new strategies for prevention and control of the “milky disease”.</div></div>","PeriodicalId":8375,"journal":{"name":"Aquaculture","volume":"610 ","pages":"Article 742942"},"PeriodicalIF":3.9,"publicationDate":"2026-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144657015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impacts of present heat waves in freshwater environments during out-growth phase in rainbow trout, Oncorhynchus mykiss, underscores the need of new wisely designed mitigation strategies: climatological, physiological and molecular analyses","authors":"Marta F. Riesco ,&nbsp;Laura Calvo-Rodríguez ,&nbsp;Maria Ángeles Esteban ,&nbsp;Paulino de Paz ,&nbsp;Ignacio Fernández","doi":"10.1016/j.aquaculture.2025.742879","DOIUrl":"10.1016/j.aquaculture.2025.742879","url":null,"abstract":"<div><div>Extreme temperature events are urgent concerns for fish farming sustainability. Only scarce studies have focused on the potential effects of heat waves (HW). Here, the incidence of HW in a freshwater basin and the related abiotic conditions (dissolved oxygen content, water flow rate and water level) in 17 different locations of the major rainbow trout (<em>Oncorhynchus mykiss</em>) production region in Spain (Castilla y León), have been explored during the last 4 years. Results showed that, HW duration progressively increased (up to 71 days), mean intensities (I_mean) ranged 0.56–5.47 °C, and maximum intensities (I_max) reached up to 8.94 °C. Based on this, the growth performance and the biochemical and molecular responses at systemic and local levels in rainbow trout specimens during the out-growth phase (approx. 29 cm and 350 g) have been assessed when exposed to a conservative model of single HW lasting 19 days, with an I_mean of 4.18, and an I_max of 6.9 and (HW group), or maintained at 14.5 °C (Control group). Specimens exposed to this HW event in the freshwater showed different responses depending on the parameter and level considered. In exposed specimens, body weight tended to decrease, while malondialdehyde (MDA) content in skin mucus increased. Blood plasma activities of superoxide dismutase and glutathione peroxidase were also increased in HW specimens. Finally, although HW exposure didn't affect the expression of redox balance genes at gills and liver, the expression of particular heat shock related genes was up-regulated. Considering current and future climate change scenarios, higher environmental monitoring effort should be done for wise decision-making on operational activities (e.g., better selection of locations, improved rearing system designs and further adapted husbandry practices, preference for resistant fish strains, and/or implementing better systems for monitoring and weather forecasting) by fish farm managers to cope with HW events. Specifically, climatology data on incidence, intensity and duration of HW in southern Europe should be considered for strategic spatial planning for long-term continental aquaculture sustainability.</div></div>","PeriodicalId":8375,"journal":{"name":"Aquaculture","volume":"610 ","pages":"Article 742879"},"PeriodicalIF":3.9,"publicationDate":"2026-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144480215","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of salinity, temperature and photoperiod on egg production of Pseudodiaptomus annandalei (Copepoda: Calanoida) used as live feed in Mariculture","authors":"Neethu Kuriakose ,&nbsp;Imelda Joseph","doi":"10.1016/j.aquaculture.2025.742921","DOIUrl":"10.1016/j.aquaculture.2025.742921","url":null,"abstract":"<div><div>Copepods are essential for maintaining marine ecosystems, and nauplii of <em>Pseudodiaptomus annandalei</em> serves as a crucial food source for fish larvae. This study investigated how salinity, temperature, and photoperiod (Light: Dark cycle) affect the reproductive traits of this copepod in a controlled environment. Clutch size was highest at 15 ppt salinity, with an average of 18.00 ± 0.58 eggs, while it dropped significantly to 9.33 ± 0.33 at 30 ppt. The dimensions of egg sacs and the total length of adult females were also smallest at 30 ppt. Among different salinities, the shortest times to first and total maturity were recorded at 10 ppt, whereas the longest times occurred at 30 ppt. Temperature also played a critical role; clutch size peaked at 28 °C and was lowest at 25 °C, with an average of 11.00 ± 0.41. Photoperiod had a limited impact on reproductive output, but the highest clutch size was observed in a 0 hL:24 hD light cycle. The findings suggest that optimal conditions for maximizing nauplii production in <em>P. annandalei</em> are a salinity of 15 ppt, a temperature of 28 °C, and a continuous dark photoperiod (0 hL:24 hD). Under these conditions, the highest hatching percentage was achieved, highlighting the importance of these factors for effective breeding in this copepod species. This research provides valuable insights for marine ecology and aquaculture, emphasizing the significance of environmental conditions in copepod reproduction.</div></div>","PeriodicalId":8375,"journal":{"name":"Aquaculture","volume":"610 ","pages":"Article 742921"},"PeriodicalIF":3.9,"publicationDate":"2026-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144579907","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Letter to the editor: Comment on development of a TGC-based growth model for the olive flounder, Paralichthys olivaceus, and its application in developing a fish growth simulator architecture","authors":"Jianpeng Yu,&nbsp;Baochao Liao","doi":"10.1016/j.aquaculture.2025.742924","DOIUrl":"10.1016/j.aquaculture.2025.742924","url":null,"abstract":"","PeriodicalId":8375,"journal":{"name":"Aquaculture","volume":"610 ","pages":"Article 742924"},"PeriodicalIF":3.9,"publicationDate":"2026-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144579905","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide analysis of carotenoid accumulation related genes reveals key genes underlying ovarian color divergence in bivalves: Insights from Chlamys nobilis and Crassostrea gigas","authors":"Huiqi Li ,&nbsp;Changping Xu ,&nbsp;Yifan Li ,&nbsp;Xuanbing Wu ,&nbsp;Meizhen Chen ,&nbsp;Beiyu Yan ,&nbsp;Yaoting Liu ,&nbsp;Taixin Chen ,&nbsp;Caixuan Wang ,&nbsp;Hongkuan Zhang ,&nbsp;Huaiping Zheng","doi":"10.1016/j.aquaculture.2025.742929","DOIUrl":"10.1016/j.aquaculture.2025.742929","url":null,"abstract":"<div><div>Gonadal color polymorphism is a widespread phenomenon in marine species. It has critical implications for health assessment, reproductive signaling, and environmental adaptation. Carotenoids, lipid-soluble pigments with antioxidant and immunomodulatory functions, play central roles in gonadal pigmentation. However, the genetic mechanisms underlying interspecific divergence in gonadal coloration remain poorly understood, particularly in bivalves. In this study, we conducted a comprehensive genomic and transcriptomic analysis of five carotenoid-related gene families—scavenger receptor class B (<em>SR-B</em>), vitellogenin (<em>Vg</em>), glutathione S-transferase P (<em>GSTP</em>), steroidogenic acute regulatory protein (<em>STARD3</em>), and carotenoid cleavage dioxygenase (<em>CCD</em>)-across 18 bivalve species, comprising 3 <em>Mytilidae</em>, 7 <em>Ostreidae</em>, and 8 <em>Pectinidae</em>. Phylogenetic and gene family contraction/expansion analyses revealed significant expansion of <em>CCD</em> genes in scallops and conservation of <em>Vg</em> and <em>SR-B</em> genes across bivalves. Tissue expression analysis showed that <em>Vg</em> and <em>GSTP</em> were predominantly expressed in the ovaries of scallops (<em>Chlamys nobilis</em>), with <em>CnVG2</em> and <em>CnGSTP1</em> exhibiting striking female-biased expression. In contrast to scallops, oysters (<em>Crassostrea gigas</em>) showed limited sexual dimorphism in these genes. Expression analysis of ovarian developmental stage revealed that <em>Vg</em> and <em>GSTP</em> were significantly upregulated during ovarian maturation in scallops, and no significant changes in <em>CCD</em> expression, suggesting a “high uptake, low degradation” model driving carotenoid accumulation in scallops. Collectively, these findings highlight the divergent roles of carotenoid-related genes in scallops and oysters, with scallops utilizing these genes for vivid ovarian pigmentation and oysters repurposing them for stress resilience. This study provides new insights into the genetic basis of gonadal color divergence in bivalves and potential molecular targets for optimizing reproductive strategy in aquaculture.</div></div>","PeriodicalId":8375,"journal":{"name":"Aquaculture","volume":"610 ","pages":"Article 742929"},"PeriodicalIF":3.9,"publicationDate":"2026-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144633021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-cell RNA sequencing reveals the immune cell landscape of head kidney in the Perciform fish (Micropterus salmoides)","authors":"Zheng-Yang Zhou ,&nbsp;Chen-Wang Lu ,&nbsp;Zheng-Ran Jian ,&nbsp;Shang-Jie Bai ,&nbsp;Lin-Feng Kuang ,&nbsp;Jin-Lai Gu ,&nbsp;Ming-Zhu Liu ,&nbsp;Peng-Fei Li ,&nbsp;Gao-Xue Wang ,&nbsp;Qing Yu ,&nbsp;Fei Ling ,&nbsp;Jorge Galindo-Villegas ,&nbsp;Tao Liu","doi":"10.1016/j.aquaculture.2025.742918","DOIUrl":"10.1016/j.aquaculture.2025.742918","url":null,"abstract":"<div><div>Teleost fish, a key transitional group in vertebrate evolution, possess immune systems that diverge substantially from those of mammals in structure, composition, and function. Within this group, the order Perciformes stands out for its ecological breadth, evolutionary significance, and value as a model for immunological research. However, the cellular complexity and developmental dynamics of their immune system remain insufficiently characterized. In this study, we employed single-cell RNA sequencing (scRNA-seq) to construct a comprehensive transcriptomic atlas of the head kidney in largemouth bass (<em>Micropterus salmoides</em>), a representative perciform species. We identified and annotated eight major hematopoietic and stromal cell populations, including hematopoietic stem/progenitor cells (HSPCs), erythrocytes (Eryt), granulocytes (Gran), macrophages (Mac), dendritic cells (DC), T and B cells, and mesenchymal stromal cells (MSCs). Subsequent analyses revealed extensive subpopulation heterogeneity across these lineages. We delineated early progenitor subsets, mapped B cell developmental trajectories, and characterized functionally distinct Mac and T cell subtypes. Notably, we identified Eryt cells exhibiting high MHC class II expression, supporting immunological roles beyond oxygen transport. A dot plot of core erythrocyte genes revealed largely lineage-restricted expression. However, several hemoglobin paralogs were also expressed in non-erythroid cells, suggesting functional divergence. Additionally, we identified a putative Gran-erythroid progenitor population and Mac subsets with distinct transcriptional profiles, underscoring the complexity, potential functionality, and wide diversity of specialized immune cell dynamics in Perciformes. Together, these findings significantly advance our understanding of teleost immune cell diversity and lineage specialization. The generated cell atlas provides a valuable resource and novel perspectives for deciphering fish immunity and hematopoiesis, advancing comparative immunology, and informing aquaculture health management.</div></div>","PeriodicalId":8375,"journal":{"name":"Aquaculture","volume":"610 ","pages":"Article 742918"},"PeriodicalIF":3.9,"publicationDate":"2026-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144633022","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Market dynamics and E-commerce satisfaction in China's aquatic food sector: Machine learning and data insights","authors":"Mausam Budhathoki ,&nbsp;Lincen Li ,&nbsp;Hao Xu ,&nbsp;Wenbo Zhang ,&nbsp;Xuzhou Ma ,&nbsp;Sujita Pandey ,&nbsp;Marianne Thomsen","doi":"10.1016/j.aquaculture.2025.742904","DOIUrl":"10.1016/j.aquaculture.2025.742904","url":null,"abstract":"<div><div>China's growing demand for aquatic foods, driven by the rapid expansion of e-commerce, is reshaping global seafood markets and influencing the broader sustainable food system. This transformation is altering domestic market dynamics and creating new challenges and opportunities in international trade, sustainable supply chains, and market competitiveness. This study investigates production trends, import reliance, and consumer e-commerce satisfaction in the aquatic food market, with a focus on implications for sustainable supply chain policy and management. By employing supervised machine learning technique, Support Vector Machines (SVM), along with Latent Dirichlet Allocation (LDA), Mann-Whitney <em>U</em> test, and logistic regression, the study uncovers critical insights into consumer preferences, including the factors driving e-commerce satisfaction, and supply chain dynamics, such as the impact of product freshness and delivery efficiency.</div><div>The study highlights the growing reliance on imports in China's aquatic food market, despite expanding domestic production. Fresh and frozen products, particularly crustaceans and finfish, consistently receive higher consumer satisfaction on e-commerce platforms, primarily due to their quality and freshness. Domestic producers face increasing pressure to meet these high standards, particularly in freshness, quality control, and delivery efficiency. The findings point to challenges in meeting consumer expectations and suggest opportunities for policy interventions to enhance the competitiveness of domestic aquatic food products. The research highlights the transformative role of e-commerce platforms in shaping China's aquatic food market, providing actionable insights for policymakers, producers, and e-commerce stakeholders to navigate emerging trends, improve supply chain efficiency, and meet evolving consumer demands.</div></div>","PeriodicalId":8375,"journal":{"name":"Aquaculture","volume":"610 ","pages":"Article 742904"},"PeriodicalIF":3.9,"publicationDate":"2026-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144534692","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcription of immune genes in ranched southern bluefin tuna show correlations to Cardicola spp. (Digenea: Aporocotylidae) infection","authors":"Maree Widdicombe ,&nbsp;Sarah Eastwood ,&nbsp;Bronwyn E. Campbell ,&nbsp;Cecilia Power ,&nbsp;Barbara F. Nowak ,&nbsp;Paul A. Ramsland ,&nbsp;Nathan J. Bott","doi":"10.1016/j.aquaculture.2025.742877","DOIUrl":"10.1016/j.aquaculture.2025.742877","url":null,"abstract":"<div><div><em>Cardicola forsteri</em> and <em>C. orientalis</em> (Digenea: Aporocotylidae) are significant pathogens affecting the Southern bluefin tuna (SBT), <em>Thunnus maccoyii</em>, aquaculture industry. The aims of this research were to identify a relationship between immune gene expression of SBT and <em>C. forsteri</em> and <em>C. orientalis</em> infection burdens; and to understand how immune gene expression changes over time during commercial ranching. SBT were collected during commercial operations in 2022 after 4, 8 and 10 weeks of ranching and the transcription of <em>interleukin 1 beta (il1b), interleukin 8 (il8), tumour necrosis factor 2 (tnf2), immunoglobulin m (igm), major histocompatibility complex 2 (mhc2)</em> and <em>t cell receptor beta (tcrb)</em> were measured from the anterior kidney and gills using reverse transcription quantitative polymerase chain reaction (RT-qPCR). <em>Cardicola forsteri</em> and <em>C. orientalis</em> infection was quantified as number of eggs/mm of SBT gill filament, number of adult flukes in SBT heart and <em>C. forsteri</em> and <em>C. orientalis</em> ITS-2 rDNA copy number/mg in SBT gills. Expression of <em>il8</em> and <em>igm</em> in anterior kidney was positively correlated to <em>C. forsteri</em> and <em>C. orientalis</em> eggs/mm of SBT gill filament and to the copy number of <em>C. forsteri</em> ITS-2 rDNA in SBT gills. Expression of <em>igm</em> and <em>mhc2</em> was higher in SBT positive for adult flukes and the expression of <em>igm, mhc2</em> and <em>tcrb</em> in the anterior kidney was positively correlated to the number of adult flukes in SBT heart. Expression of <em>tcrb</em> in gills was negatively correlated to the number of adult flukes in SBT heart and negatively correlated to the copy number of <em>C. orientalis</em> ITS-2 rDNA. Expression of the adaptive immune genes <em>igm</em>, <em>mhc2</em> and <em>tcrb</em> increased over the ranching duration in the kidney of SBT and the innate immune genes <em>il1b</em> and <em>il8</em> decreased over the ranching duration in SBT gills. Despite evidence of an immune response to <em>C. forsteri</em> and <em>C. orientalis,</em> SBT were not able to clear infections during the standard industry ranching timeline.</div></div>","PeriodicalId":8375,"journal":{"name":"Aquaculture","volume":"610 ","pages":"Article 742877"},"PeriodicalIF":3.9,"publicationDate":"2026-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144502624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Achievement of prosperous nitrification cycle fosters diversity in freshwater microbiome within recirculating aquaculture systems after adjustment period","authors":"Jiho Yang ,&nbsp;Junhyuk Seo ,&nbsp;Jimin Choi ,&nbsp;Yehyeon Cha ,&nbsp;Yunhyeok Jang ,&nbsp;Ju-Ae Hwang ,&nbsp;Seung-Yoon Oh","doi":"10.1016/j.aquaculture.2025.742941","DOIUrl":"10.1016/j.aquaculture.2025.742941","url":null,"abstract":"<div><div>In recirculating aquaculture systems (RAS), a significant challenge involves managing the biological cycling of nitrogenous waste. As a result, there is worldwide focus on the diversity of biological groups involved in nitrogen cycling and their impacts. However, there is still a lack of information concerning the microbial diversity, particularly in relation to biological nitrogen cycling. We hypothesized that biological nitrification in RAS becomes fully established only after a distinct microbial adjustment period following microbial inoculant (MI) treatment, and that this phase features distinct shifts in microbiome composition and nitrogen compound dynamics. To test this, we monitored water chemistry and microbial community structure over an 8-week pre-treatment maturation phase in freshwater RAS for Japanese eel (<em>Anguilla japonica</em>) cultivation. Using 16S rRNA gene amplicon sequencing and qPCR targeting ammonia- and nitrite-oxidizing bacteria, we found that nitrifier abundance increased sharply from week 3 post-treatment. Random forest analysis and structural equation modeling revealed that nitrate levels—serving as a proxy for complete nitrification—had the strongest direct influence on microbiome diversity. Diversity indices and beta-dispersion analyses confirmed that microbial communities during the adjustment period (weeks 0–3) were significantly different from those in the stabilization phase (weeks 4–8). These findings demonstrate the existence of a critical, temporally defined adjustment phase in RAS maturation, during which microbiome structure and nitrification processes co-develop. Our study provides mechanistic insights into microbiome assembly in RAS and highlights the importance of temporal monitoring in optimizing MI-based water treatment strategies.</div></div>","PeriodicalId":8375,"journal":{"name":"Aquaculture","volume":"610 ","pages":"Article 742941"},"PeriodicalIF":3.9,"publicationDate":"2026-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144588174","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}