Isochrysis galbana is valuable in aquaculture due to its production of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). However, achieving high yields of polyunsaturated fatty acids (PUFAs) presents challenges, leading to exploration of innovative approaches. This study investigated the influence of Bacillus jeotgali on the growth of I. galbana and its fatty acid composition. Co-culturing I. galbana with B. jeotgali significantly increased chlorophyll a content and cell abundance, particularly at higher bacterial population densities (algae-to-bacteria ratio of 1:10). Physiological and biochemical analyses found elevated soluble protein content in microalgae co-cultured with B. jeotgali, accompanied by decreased superoxide dismutase (SOD) activity. Fatty acid composition analysis demonstrated a distinctive profile in co-cultured I. galbana, characterized by increased PUFAs, especially EPA and DHA. Gene expression analysis indicated an upregulation of desaturase genes (d4FAD, d5FAD, d6FAD, and d8FAD) associated with PUFA synthesis pathway in I. galbana during co-culturing with B. jeotgali. This study advances our understanding of bacteria-microalgae interactions and presents a promising strategy for enhancing the production of DHA and EPA.
伽蓝异核藻(Isochrysis galbana)可产生二十碳五烯酸(EPA)和二十二碳六烯酸(DHA),因此在水产养殖中很有价值。然而,实现多不饱和脂肪酸(PUFAs)的高产量是一项挑战,因此需要探索创新方法。本研究调查了枯草芽孢杆菌(Bacillus jeotgali)对加尔巴那藻类(I. galbana)生长及其脂肪酸组成的影响。将蚬贝与空肠芽孢杆菌共培养可显著提高叶绿素 a 含量和细胞丰度,尤其是在细菌种群密度较高的情况下(藻类与细菌的比例为 1:10)。生理和生化分析发现,与焦藻类共培养的微藻可溶性蛋白质含量增加,同时超氧化物歧化酶(SOD)活性降低。脂肪酸组成分析表明,与 I. galbana 共培养的微藻具有独特的特征,即增加了 PUFAs,尤其是 EPA 和 DHA。基因表达分析表明,在 I. galbana 与 B. jeotgali 的共培养过程中,与 PUFA 合成途径相关的去饱和酶基因(d4FAD、d5FAD、d6FAD 和 d8FAD)上调。这项研究加深了我们对细菌与微藻之间相互作用的了解,并为提高 DHA 和 EPA 的产量提供了一种前景广阔的策略。
{"title":"Enhancement of Docosahexaenoic Acid and Eicosapentaenoic Acid Biosynthesis in Isochrysis galbana by Bacillus jeotgali.","authors":"Yijun Xu, Minnan Wu, Jiayi Cao, Yingying Wang, Lin Zhang, Xiaojun Yan, Yanrong Li, Jilin Xu","doi":"10.1007/s10126-024-10337-5","DOIUrl":"https://doi.org/10.1007/s10126-024-10337-5","url":null,"abstract":"<p><p>Isochrysis galbana is valuable in aquaculture due to its production of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). However, achieving high yields of polyunsaturated fatty acids (PUFAs) presents challenges, leading to exploration of innovative approaches. This study investigated the influence of Bacillus jeotgali on the growth of I. galbana and its fatty acid composition. Co-culturing I. galbana with B. jeotgali significantly increased chlorophyll a content and cell abundance, particularly at higher bacterial population densities (algae-to-bacteria ratio of 1:10). Physiological and biochemical analyses found elevated soluble protein content in microalgae co-cultured with B. jeotgali, accompanied by decreased superoxide dismutase (SOD) activity. Fatty acid composition analysis demonstrated a distinctive profile in co-cultured I. galbana, characterized by increased PUFAs, especially EPA and DHA. Gene expression analysis indicated an upregulation of desaturase genes (d4FAD, d5FAD, d6FAD, and d8FAD) associated with PUFA synthesis pathway in I. galbana during co-culturing with B. jeotgali. This study advances our understanding of bacteria-microalgae interactions and presents a promising strategy for enhancing the production of DHA and EPA.</p>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141911311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-08DOI: 10.1007/s10126-024-10353-5
Yi Jiang, Xiaochen Liu, Yan Shang, Jitao Li, Baoquan Gao, Yichao Ren, Xianliang Meng
Nitrite is a common environmental pollutant in intensive aquaculture systems. In this study, physiological and transcriptomic analyses were performed to investigate nitrite stress responses in the swimming crab Portunus trituberculatus, an important aquaculture species in China. The results revealed that nitrite can affect neurotransmitter signaling via the expression of neurotransmitter receptors such as octopamine receptor (OAR) and 5-hydroxytryptamine receptor (5-HTR), and depress ecdysteroid signaling by downregulating ecdysteroid receptor (EcR) as well as its downstream transcription factors in hepatopancreas. In addition, nitrite suppressed the expression of hemocyanins, the oxygen-transporting protein, which at least partly contributed to tissue hypoxia, resulting in a switchover of energy metabolism from aerobic to anaerobic pathway. To meet the energy demand, glycogens and lipids were mobilized and transported to the hemolymph, and the catabolism of amino acids and fatty acids was enhanced to provide energy for hepatopancreas. β-oxidation of fatty acids, the major process by which fatty acids are oxidized to generate energy, seems to occur mainly not in mitochondria but in peroxisomes. Although the cellular protective mechanisms, including antioxidant defense, heat shock response (HSR), unfolded protein response (UPR), and autophagy, were activated, nitrite-induced cellular stress overwhelmed the repairing capacity and caused significant increase in the levels of apoptosis. These results indicated that nitrite stress influences neurotransmitter and endocrine signaling, disturbs energy metabolism, damages cellular components, and induces apoptosis in P. trituberculatus. The findings of this study provide new insights into nitrite stress response in the swimming crab and provide valuable information for aquaculture management of this species.
{"title":"Physiological and Transcriptomic Analyses Provide Insights into Nitrite Stress Responses of the Swimming Crab Portunus trituberculatus.","authors":"Yi Jiang, Xiaochen Liu, Yan Shang, Jitao Li, Baoquan Gao, Yichao Ren, Xianliang Meng","doi":"10.1007/s10126-024-10353-5","DOIUrl":"https://doi.org/10.1007/s10126-024-10353-5","url":null,"abstract":"<p><p>Nitrite is a common environmental pollutant in intensive aquaculture systems. In this study, physiological and transcriptomic analyses were performed to investigate nitrite stress responses in the swimming crab Portunus trituberculatus, an important aquaculture species in China. The results revealed that nitrite can affect neurotransmitter signaling via the expression of neurotransmitter receptors such as octopamine receptor (OAR) and 5-hydroxytryptamine receptor (5-HTR), and depress ecdysteroid signaling by downregulating ecdysteroid receptor (EcR) as well as its downstream transcription factors in hepatopancreas. In addition, nitrite suppressed the expression of hemocyanins, the oxygen-transporting protein, which at least partly contributed to tissue hypoxia, resulting in a switchover of energy metabolism from aerobic to anaerobic pathway. To meet the energy demand, glycogens and lipids were mobilized and transported to the hemolymph, and the catabolism of amino acids and fatty acids was enhanced to provide energy for hepatopancreas. β-oxidation of fatty acids, the major process by which fatty acids are oxidized to generate energy, seems to occur mainly not in mitochondria but in peroxisomes. Although the cellular protective mechanisms, including antioxidant defense, heat shock response (HSR), unfolded protein response (UPR), and autophagy, were activated, nitrite-induced cellular stress overwhelmed the repairing capacity and caused significant increase in the levels of apoptosis. These results indicated that nitrite stress influences neurotransmitter and endocrine signaling, disturbs energy metabolism, damages cellular components, and induces apoptosis in P. trituberculatus. The findings of this study provide new insights into nitrite stress response in the swimming crab and provide valuable information for aquaculture management of this species.</p>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141900551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-07DOI: 10.1007/s10126-024-10354-4
Najib Abdellaoui, Min Sun Kim
For Atlantic salmon development, the most critical phase is the early development stage from egg to fry through alevin. However, the studies investigating the early development of Atlantic salmon based on RNA-seq are scarce and focus only on one stage of development. Therefore, using the RNA-seq technology, the assessment of different gene expressions of various early development stages (egg, alevin, and fry) was performed on a global scale. Over 22 GB of clean data was generated from 9 libraries with three replicates for each stage with over 90% mapping efficiency. A total of 5534 genes were differentially expressed, among which 19, 606, and 826 genes were specifically expressed in each stage, respectively. The transcriptome analysis showed that the number of differentially expressed genes (DEGs) increased as the Atlantic salmon progressed in development from egg to fry stage. In addition, gene ontology enrichment demonstrated that egg and alevin stages are characterized by upregulation of genes involved in spinal cord development, neuron projection morphogenesis, axonogenesis, and cytoplasmic translation. At the fry stage, upregulated genes were enriched in the muscle development process (muscle cell development, striated muscle cell differentiation, and muscle tissue development), immune system (defense response and canonical NF-kappaB signal transduction), as well as epidermis development. These results suggest that the early development of Atlantic salmon is characterized by a dynamic shift in gene expression and DEGs between different stages, which provided a solid foundation for the investigation of Atlantic salmon development.
{"title":"Transcriptome Profiling of Gene Expression in Atlantic Salmon (Salmo salar) at Early Stage of Development.","authors":"Najib Abdellaoui, Min Sun Kim","doi":"10.1007/s10126-024-10354-4","DOIUrl":"https://doi.org/10.1007/s10126-024-10354-4","url":null,"abstract":"<p><p>For Atlantic salmon development, the most critical phase is the early development stage from egg to fry through alevin. However, the studies investigating the early development of Atlantic salmon based on RNA-seq are scarce and focus only on one stage of development. Therefore, using the RNA-seq technology, the assessment of different gene expressions of various early development stages (egg, alevin, and fry) was performed on a global scale. Over 22 GB of clean data was generated from 9 libraries with three replicates for each stage with over 90% mapping efficiency. A total of 5534 genes were differentially expressed, among which 19, 606, and 826 genes were specifically expressed in each stage, respectively. The transcriptome analysis showed that the number of differentially expressed genes (DEGs) increased as the Atlantic salmon progressed in development from egg to fry stage. In addition, gene ontology enrichment demonstrated that egg and alevin stages are characterized by upregulation of genes involved in spinal cord development, neuron projection morphogenesis, axonogenesis, and cytoplasmic translation. At the fry stage, upregulated genes were enriched in the muscle development process (muscle cell development, striated muscle cell differentiation, and muscle tissue development), immune system (defense response and canonical NF-kappaB signal transduction), as well as epidermis development. These results suggest that the early development of Atlantic salmon is characterized by a dynamic shift in gene expression and DEGs between different stages, which provided a solid foundation for the investigation of Atlantic salmon development.</p>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141896431","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Golden cuttlefish play a significant role in the food web of the East and Yellow Seas and are a valuable fishery resource in Chinese coastal waters. Samples of golden cuttlefish were obtained from the northern East China Sea between September 2021 and March 2022, and stable isotope methods were utilized in this study to examine the variations in the forage ecology of golden cuttlefish. Our findings reveal dynamic shifts in carbon and nitrogen stable isotopes (δ13C and δ15N), highlighting intricate foraging strategies tailored to growth and environmental changes. A notable trend emerges: an initial growth-linked rise in δ13C and δ15N enrichment, followed by seasonal fluctuations mirroring seasonal food availability. The ontogenetic niche evolution displays striking habitat shifts and trophic level escalation in small mantle length stages, transitioning to niche overlap and subtle trophic shifts later on. Sex-specific differences emerge, with females occupying higher trophic levels than males in most samples. This comprehensive study underscores the complexity and adaptability of golden cuttlefish feeding ecology, inviting further inquiry into their intricate relationships within the marine ecosystem.
{"title":"Ontogenetic, Sexual, and Monthly Niche Segregation of Sepia esculenta in the Northern East China Sea Revealed by Stable Carbon and Nitrogen Isotopes.","authors":"Zhenfang Zhao, Guanyu Hu, Long Chen, Yingcong Chen, Fang Guo, Zhou Fang","doi":"10.1007/s10126-024-10352-6","DOIUrl":"https://doi.org/10.1007/s10126-024-10352-6","url":null,"abstract":"<p><p>Golden cuttlefish play a significant role in the food web of the East and Yellow Seas and are a valuable fishery resource in Chinese coastal waters. Samples of golden cuttlefish were obtained from the northern East China Sea between September 2021 and March 2022, and stable isotope methods were utilized in this study to examine the variations in the forage ecology of golden cuttlefish. Our findings reveal dynamic shifts in carbon and nitrogen stable isotopes (δ<sup>13</sup>C and δ<sup>15</sup>N), highlighting intricate foraging strategies tailored to growth and environmental changes. A notable trend emerges: an initial growth-linked rise in δ<sup>13</sup>C and δ<sup>15</sup>N enrichment, followed by seasonal fluctuations mirroring seasonal food availability. The ontogenetic niche evolution displays striking habitat shifts and trophic level escalation in small mantle length stages, transitioning to niche overlap and subtle trophic shifts later on. Sex-specific differences emerge, with females occupying higher trophic levels than males in most samples. This comprehensive study underscores the complexity and adaptability of golden cuttlefish feeding ecology, inviting further inquiry into their intricate relationships within the marine ecosystem.</p>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141888166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Numerous biologically active natural products have been discovered from marine sponges, particularly from Theonella swinhoei, which is known to be a prolific source of natural products such as polyketides and peptides. Recent studies have revealed that many of these natural products are biosynthesized by Candidatus Entotheonella phylotypes, which are uncultivated symbionts within T. swinhoei. Consequently, Entotheonella is considered an untapped biochemical resource. In this study, we conducted metagenomic analyses to assess the diversity of Entotheonella in two T. swinhoei Y and two T. swinhoei W (Y and W referring to the yellow and white interior of the sponge, respectively), after separating filamentous bacteria using density gradient centrifugation. We obtained five Entotheonella metagenome-assembled genomes (MAGs) from filamentous bacteria-enriched fractions. Notably, one of these MAGs is significantly different from previously reported Entotheonella variants. Additionally, we identified closely related Entotheonella members present across different chemotypes of T. swinhoei. Thus, our metagenomic insights reveal that the diversity of Entotheonella within Theonella sponges is greater than previously recognized.
{"title":"Metagenomic Insights Reveal Unrecognized Diversity of Entotheonella in Japanese Theonella Sponges.","authors":"Sota Yamabe, Kazutoshi Yoshitake, Akihiro Ninomiya, Jörn Piel, Haruko Takeyama, Shigeki Matsunaga, Kentaro Takada","doi":"10.1007/s10126-024-10350-8","DOIUrl":"https://doi.org/10.1007/s10126-024-10350-8","url":null,"abstract":"<p><p>Numerous biologically active natural products have been discovered from marine sponges, particularly from Theonella swinhoei, which is known to be a prolific source of natural products such as polyketides and peptides. Recent studies have revealed that many of these natural products are biosynthesized by Candidatus Entotheonella phylotypes, which are uncultivated symbionts within T. swinhoei. Consequently, Entotheonella is considered an untapped biochemical resource. In this study, we conducted metagenomic analyses to assess the diversity of Entotheonella in two T. swinhoei Y and two T. swinhoei W (Y and W referring to the yellow and white interior of the sponge, respectively), after separating filamentous bacteria using density gradient centrifugation. We obtained five Entotheonella metagenome-assembled genomes (MAGs) from filamentous bacteria-enriched fractions. Notably, one of these MAGs is significantly different from previously reported Entotheonella variants. Additionally, we identified closely related Entotheonella members present across different chemotypes of T. swinhoei. Thus, our metagenomic insights reveal that the diversity of Entotheonella within Theonella sponges is greater than previously recognized.</p>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141892542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-01Epub Date: 2024-07-23DOI: 10.1007/s10126-024-10347-3
Fei Wang, Zi-Rou Zhong, Qing Xie, Jie Ou, Ning-Xia Xiong, Ming-Zhu Huang, Shi-Yun Li, Gang Hu, Zi-Le Qin, Sheng-Wei Luo
Aeromonas veronii is one of the predominant pathogenic species that can imperil the survival of farmed fish. However, the interactive networks of immune regulation and metabolic response in A. veronii-infected fish are still unclear. In this investigation, we aimed to explore immunometabolic interplay in white crucian carp (WCC) after the A. veronii challenge. Elevated levels of immune-related genes were observed in various tissues after A. veronii infection, along with the sharp alteration of disease-related enzymatic activities. Besides, decreased levels of antioxidant status were observed in the liver, but most metabolic gene expressions increased dramatically. Multiomics analyses revealed that metabolic products of amino acids, such as formiminoglutamic acid (FIGLU), L-glutamate (L-Glu), and 4-hydroxyhippuric acid, were considered the crucial liver biomarkers in A. veronii-infected WCC. In addition, A. veronii infection may dysregulate endoplasmic reticulum (ER) function to affect the metabolic process of lipids, carbohydrates, and amino acids in the liver of WCC. These results may have a comprehensive implication for understanding immunometabolic response in WCC upon A. veronii infection.
{"title":"Multiomics Analyses Explore the Immunometabolic Interplay in the Liver of White Crucian Carp (Carassius cuvieri) After Aeromonas veronii Challenge.","authors":"Fei Wang, Zi-Rou Zhong, Qing Xie, Jie Ou, Ning-Xia Xiong, Ming-Zhu Huang, Shi-Yun Li, Gang Hu, Zi-Le Qin, Sheng-Wei Luo","doi":"10.1007/s10126-024-10347-3","DOIUrl":"10.1007/s10126-024-10347-3","url":null,"abstract":"<p><p>Aeromonas veronii is one of the predominant pathogenic species that can imperil the survival of farmed fish. However, the interactive networks of immune regulation and metabolic response in A. veronii-infected fish are still unclear. In this investigation, we aimed to explore immunometabolic interplay in white crucian carp (WCC) after the A. veronii challenge. Elevated levels of immune-related genes were observed in various tissues after A. veronii infection, along with the sharp alteration of disease-related enzymatic activities. Besides, decreased levels of antioxidant status were observed in the liver, but most metabolic gene expressions increased dramatically. Multiomics analyses revealed that metabolic products of amino acids, such as formiminoglutamic acid (FIGLU), L-glutamate (L-Glu), and 4-hydroxyhippuric acid, were considered the crucial liver biomarkers in A. veronii-infected WCC. In addition, A. veronii infection may dysregulate endoplasmic reticulum (ER) function to affect the metabolic process of lipids, carbohydrates, and amino acids in the liver of WCC. These results may have a comprehensive implication for understanding immunometabolic response in WCC upon A. veronii infection.</p>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141747117","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-01Epub Date: 2024-07-22DOI: 10.1007/s10126-024-10346-4
K Shasti Risha, Kiran D Rasal, Dhalongsaih Reang, Mir Asif Iquebal, Arvind Sonwane, Manoj Brahmane, Aparna Chaudhari, Naresh Nagpure
DNA methylation is an epigenetic alteration that impacts gene expression without changing the DNA sequence affecting an organism's phenotype. This study utilized a reduced representation bisulfite sequencing (RRBS) approach to investigate the patterns of DNA methylation in genetically selected Clarias magur stocks. RRBS generated 249.22 million reads, with an average of 490,120 methylation sites detected in various parts of genes, including exons, introns, and intergenic regions. A total of 896 differentially methylated regions (DMRs) were identified; 356 and 540 were detected as hyper-methylated and hypo-methylated regions, respectively. The DMRs and their association with overlapping genes were explored using whole genome data of magur, which revealed 205 genes in exonic, 210 in intronic, and 480 in intergenic regions. The analysis identified the maximum number of genes enriched in biological processes such as RNA biosynthetic process, response to growth factors, nervous system development, neurogenesis, and anatomical structure morphogenesis. Differentially methylated genes (DMGs) such as myrip, mylk3, mafb, egr3, ndnf, meis2a, foxn3, bmp1a, plxna3, fgf6, sipa1l1, mcu, cnot8, trim55b, and myof were associated with growth and development. The selected DMGs were analyzed using real-time PCR, which showed altered mRNA expression levels. This work offers insights into the epigenetic mechanisms governing growth performance regulation in magur stocks. This work provides a valuable resource of epigenetic data that could be integrated into breeding programs to select high-performing individuals.
{"title":"DNA Methylation Profiling in Genetically Selected Clarias magur (Hamilton, 1822) Provides Insights into the Epigenetic Regulation of Growth and Development.","authors":"K Shasti Risha, Kiran D Rasal, Dhalongsaih Reang, Mir Asif Iquebal, Arvind Sonwane, Manoj Brahmane, Aparna Chaudhari, Naresh Nagpure","doi":"10.1007/s10126-024-10346-4","DOIUrl":"10.1007/s10126-024-10346-4","url":null,"abstract":"<p><p>DNA methylation is an epigenetic alteration that impacts gene expression without changing the DNA sequence affecting an organism's phenotype. This study utilized a reduced representation bisulfite sequencing (RRBS) approach to investigate the patterns of DNA methylation in genetically selected Clarias magur stocks. RRBS generated 249.22 million reads, with an average of 490,120 methylation sites detected in various parts of genes, including exons, introns, and intergenic regions. A total of 896 differentially methylated regions (DMRs) were identified; 356 and 540 were detected as hyper-methylated and hypo-methylated regions, respectively. The DMRs and their association with overlapping genes were explored using whole genome data of magur, which revealed 205 genes in exonic, 210 in intronic, and 480 in intergenic regions. The analysis identified the maximum number of genes enriched in biological processes such as RNA biosynthetic process, response to growth factors, nervous system development, neurogenesis, and anatomical structure morphogenesis. Differentially methylated genes (DMGs) such as myrip, mylk3, mafb, egr3, ndnf, meis2a, foxn3, bmp1a, plxna3, fgf6, sipa1l1, mcu, cnot8, trim55b, and myof were associated with growth and development. The selected DMGs were analyzed using real-time PCR, which showed altered mRNA expression levels. This work offers insights into the epigenetic mechanisms governing growth performance regulation in magur stocks. This work provides a valuable resource of epigenetic data that could be integrated into breeding programs to select high-performing individuals.</p>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141733158","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-01Epub Date: 2024-06-01DOI: 10.1007/s10126-024-10327-7
Xinchun Li, Yitian Bai, Chengxun Xu, Shikai Liu, Hong Yu, Lingfeng Kong, Shaojun Du, Qi Li
The molluscan family Ostreidae, commonly known as oysters, is an important molluscan group due to its economic and ecological importance. In recent years, an abundance of genomic data of Ostreidae species has been generated and available in public domain. However, there is still a lack of a high-efficiency database platform to store and distribute these data with comprehensive tools. In this study, we developed an oyster genome database (OysterDB) to consolidate oyster genomic data. This database includes eight oyster genomes and 208,923 protein-coding gene annotations. Bioinformatic tools, such as BLAST and JBrowse, are integrated into the database to provide a user-friendly platform for homologous sequence searching, visualization of genomes, and screen for candidate gene information. Moreover, OysterDB will be continuously updated with ever-growing oyster genomic resources and facilitate future studies for comparative and functional genomic analysis of oysters ( http://oysterdb.com.cn/ ).
{"title":"OysterDB: A Genome Database for Ostreidae.","authors":"Xinchun Li, Yitian Bai, Chengxun Xu, Shikai Liu, Hong Yu, Lingfeng Kong, Shaojun Du, Qi Li","doi":"10.1007/s10126-024-10327-7","DOIUrl":"10.1007/s10126-024-10327-7","url":null,"abstract":"<p><p>The molluscan family Ostreidae, commonly known as oysters, is an important molluscan group due to its economic and ecological importance. In recent years, an abundance of genomic data of Ostreidae species has been generated and available in public domain. However, there is still a lack of a high-efficiency database platform to store and distribute these data with comprehensive tools. In this study, we developed an oyster genome database (OysterDB) to consolidate oyster genomic data. This database includes eight oyster genomes and 208,923 protein-coding gene annotations. Bioinformatic tools, such as BLAST and JBrowse, are integrated into the database to provide a user-friendly platform for homologous sequence searching, visualization of genomes, and screen for candidate gene information. Moreover, OysterDB will be continuously updated with ever-growing oyster genomic resources and facilitate future studies for comparative and functional genomic analysis of oysters ( http://oysterdb.com.cn/ ).</p>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141183247","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-01Epub Date: 2024-06-12DOI: 10.1007/s10126-024-10330-y
Rose Chinly Mae H Ortega-Kindica, Chinee S Padasas-Adalla, Sharon Rose M Tabugo, Joey Genevieve T Martinez, Olive A Amparado, Carlo Stephen O Moneva, Rodelyn Dalayap, Carlos O Lomeli-Ortega, Jose Luis Balcazar
This study aimed to investigate the taxonomic and functional patterns of the microbiome associated with Barbour's seahorse (Hippocampus barbouri) using a combination of shotgun metagenomics and bioinformatics. The analyses revealed that Pseudomonadota and Bacillota were the dominant phyla in the seahorse skin microbiome, whereas Pseudomonadota and, to a lesser extent, Bacillota and Bacteroidota were the dominant phyla in the seahorse gut microbiome. Several metabolic pathway categories were found to be enriched in the skin microbiome, including amino acid metabolism, carbohydrate metabolism, cofactor and vitamin metabolism, energy metabolism, nucleotide metabolism, as well as membrane transport, signal transduction, and cellular community-prokaryotes. In contrast, the gut microbiome exhibited enrichment in metabolic pathways associated with the metabolism of terpenoids and polyketides, biosynthesis of other secondary metabolites, xenobiotics biodegradation and metabolism, and quorum sensing. Additionally, although the relative abundance of bacteriocins in the skin and gut was slightly similar, notable differences were observed at the class level. Specifically, class I bacteriocins were found to be more abundant in the skin microbiome, whereas class III bacteriocins were more abundant in the gut microbiome. To the best of our knowledge, this study represents the first comprehensive examination of the taxonomic and functional patterns of the skin and gut microbiome in Barbour's seahorse. These findings can greatly contribute to a deeper understanding of the seahorse-associated microbiome, which can play a pivotal role in predicting and controlling bacterial infections, thereby contributing to the success of aquaculture and health-promoting initiatives.
{"title":"Shotgun Metagenomics Reveals Taxonomic and Functional Patterns of the Microbiome Associated with Barbour's Seahorse (Hippocampus barbouri).","authors":"Rose Chinly Mae H Ortega-Kindica, Chinee S Padasas-Adalla, Sharon Rose M Tabugo, Joey Genevieve T Martinez, Olive A Amparado, Carlo Stephen O Moneva, Rodelyn Dalayap, Carlos O Lomeli-Ortega, Jose Luis Balcazar","doi":"10.1007/s10126-024-10330-y","DOIUrl":"10.1007/s10126-024-10330-y","url":null,"abstract":"<p><p>This study aimed to investigate the taxonomic and functional patterns of the microbiome associated with Barbour's seahorse (Hippocampus barbouri) using a combination of shotgun metagenomics and bioinformatics. The analyses revealed that Pseudomonadota and Bacillota were the dominant phyla in the seahorse skin microbiome, whereas Pseudomonadota and, to a lesser extent, Bacillota and Bacteroidota were the dominant phyla in the seahorse gut microbiome. Several metabolic pathway categories were found to be enriched in the skin microbiome, including amino acid metabolism, carbohydrate metabolism, cofactor and vitamin metabolism, energy metabolism, nucleotide metabolism, as well as membrane transport, signal transduction, and cellular community-prokaryotes. In contrast, the gut microbiome exhibited enrichment in metabolic pathways associated with the metabolism of terpenoids and polyketides, biosynthesis of other secondary metabolites, xenobiotics biodegradation and metabolism, and quorum sensing. Additionally, although the relative abundance of bacteriocins in the skin and gut was slightly similar, notable differences were observed at the class level. Specifically, class I bacteriocins were found to be more abundant in the skin microbiome, whereas class III bacteriocins were more abundant in the gut microbiome. To the best of our knowledge, this study represents the first comprehensive examination of the taxonomic and functional patterns of the skin and gut microbiome in Barbour's seahorse. These findings can greatly contribute to a deeper understanding of the seahorse-associated microbiome, which can play a pivotal role in predicting and controlling bacterial infections, thereby contributing to the success of aquaculture and health-promoting initiatives.</p>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141305060","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-01Epub Date: 2024-06-26DOI: 10.1007/s10126-024-10338-4
Athira P P, Anju M V, Anooja V V, Archana K, Neelima S, Muhammed Musthafa S, I S Bright Singh, Rosamma Philip
Antimicrobial peptides (AMPs), including beta-defensin from fish, are a crucial class of peptide medicines. The focus of the current study is the molecular and functional attributes of CmDef, a 63-amino acid beta-defensin AMP from Malabar trevally, Carangoides malabaricus. This peptide demonstrated typical characteristics of AMPs, including hydrophobicity, amphipathic nature, and +2.8 net charge. The CmDef was recombinantly expressed and the recombinant peptide, rCmDef displayed a strong antimicrobial activity against bacterial fish pathogens with an MIC of 8 µM for V. proteolyticus and 32 µM for A. hydrophila. The E. tarda and V. harveyi showed an inhibition of 94% and 54%, respectively, at 32 µM concentration. No activity was observed against V. fluvialis and V. alginolyticus. The rCmDef has a multimode of action that exerts an antibacterial effect by membrane depolarization followed by membrane permeabilization and ROS production. rCmDef also exhibited anti-cancer activities in silico without causing hemolysis. The peptide demonstrated stability under various conditions, including different pH levels, temperatures, salts, and metal ions (KCl and CaCl2), and remained stable in the presence of proteases such as trypsin and proteinase K at concentrations up to 0.2 µg/100 µl. The strong antibacterial efficacy and non-cytotoxic nature suggest that rCmDef is a single-edged sword that can contribute significantly to aquaculture disease management.
抗菌肽(AMPs),包括鱼类中的β-防御素,是一类重要的肽类药物。本研究的重点是马拉巴尔鲹(Carangoides malabaricus)的一种 63 氨基酸 beta-defensin AMP(CmDef)的分子和功能特性。该肽具有 AMP 的典型特征,包括疏水性、两性性质和 +2.8 净电荷。CmDef 经重组表达后,重组肽 rCmDef 对细菌性鱼类病原体具有很强的抗菌活性,对蛋白溶解弧菌的 MIC 值为 8 µM,对嗜水青鱼的 MIC 值为 32 µM。在 32 µM 浓度下,对 E. tarda 和 V. harveyi 的抑制率分别为 94% 和 54%。对 V. fluvialis 和 V. alginolyticus 没有活性。rCmDef 具有多种作用模式,通过膜去极化、膜渗透和产生 ROS 发挥抗菌作用。该多肽在各种条件下都表现出稳定性,包括不同的 pH 值、温度、盐分和金属离子(KCl 和 CaCl2),并且在蛋白酶(如胰蛋白酶和蛋白酶 K)存在下保持稳定,浓度最高可达 0.2 µg/100 µl。强大的抗菌功效和无细胞毒性表明,rCmDef 是一把单刃剑,可为水产养殖疾病管理做出重大贡献。
{"title":"A Novel Beta-Defensin Isoform from Malabar Trevally, Carangoides malabaricus (Bloch & Schneider, 1801), an Arsenal Against Fish Bacterial Pathogens: Molecular Characterization, Recombinant Production, and Mechanism of Action.","authors":"Athira P P, Anju M V, Anooja V V, Archana K, Neelima S, Muhammed Musthafa S, I S Bright Singh, Rosamma Philip","doi":"10.1007/s10126-024-10338-4","DOIUrl":"10.1007/s10126-024-10338-4","url":null,"abstract":"<p><p>Antimicrobial peptides (AMPs), including beta-defensin from fish, are a crucial class of peptide medicines. The focus of the current study is the molecular and functional attributes of CmDef, a 63-amino acid beta-defensin AMP from Malabar trevally, Carangoides malabaricus. This peptide demonstrated typical characteristics of AMPs, including hydrophobicity, amphipathic nature, and +2.8 net charge. The CmDef was recombinantly expressed and the recombinant peptide, rCmDef displayed a strong antimicrobial activity against bacterial fish pathogens with an MIC of 8 µM for V. proteolyticus and 32 µM for A. hydrophila. The E. tarda and V. harveyi showed an inhibition of 94% and 54%, respectively, at 32 µM concentration. No activity was observed against V. fluvialis and V. alginolyticus. The rCmDef has a multimode of action that exerts an antibacterial effect by membrane depolarization followed by membrane permeabilization and ROS production. rCmDef also exhibited anti-cancer activities in silico without causing hemolysis. The peptide demonstrated stability under various conditions, including different pH levels, temperatures, salts, and metal ions (KCl and CaCl<sub>2</sub>), and remained stable in the presence of proteases such as trypsin and proteinase K at concentrations up to 0.2 µg/100 µl. The strong antibacterial efficacy and non-cytotoxic nature suggest that rCmDef is a single-edged sword that can contribute significantly to aquaculture disease management.</p>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141449284","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}