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PROVIDER: PRJNA776842 | ENA |
REPOSITORIES: ENA
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Project description:Introduction: A major economic impediment to the aquaculture of marine finfish in land-based recirculating systems is maintaining the system salinity at a range for optimal growth. Florida Pompano (Trachinotus carolinus) are warm water, euryhaline, marine finfish shown to be a suitable candidate for low-salinity culture. Due to its popularity among sport and commercial fishers, high market value, and ability to readily consume pelleted feeds, the Florida Pompano has become a renewed target for commercialized aquaculture. Although the Florida Pompano has been successfully grown at various salinities, its optimal growth salinity has not yet been established. Studies have shown culturing at different salinities has an effect on digestion rates, feed utilization, and lipid biosynthesis. Identifying the optimal salinity for growth would result in decreased energy expenditure on maintaining homeostasis, since osmoregulation is a highly demanding process. This would allow for energy to be spent on the efficient use of nutrients. Methods: Our study was designed to determine how Florida Pompano larviculture at various salinities affects fish health with transcriptomics (RNA-seq) and fatty acid analysis. RNA-seq was used to identify genes actively transcribed and expressed at the time of sampling. After hatching in a salinity of ~ 30 ppt, larvae were reared in 345 L tanks at one of three salinities (10, 20, 30 ppt) in triplicate. Larvae samples for RNA-seq and fatty acid analysis were collected every three days until weaning. Samples for fatty acid composition were analyzed using a gas chromatography-mass spectrometry (GC/MS). RNA was extracted from homogenized whole-body samples using the Qiagen RNeasy Mini kit. Total RNA was sequenced on the Illumina HiSeq 4000 System. Raw sequences were filtered for low-quality sequences, aligned to the S. dumerili reference genome (NCBI Genome: 12614), and quantified. Each sampling day was compared across salinities to establish the differentially expressed genes (DEGs) between salinities. Results & Discussion: The numbers of DEGS in pooled samples was minimal (less than 15 total in each comparison) and the number of DEGS at each dph was variable. There were no significant differences between pooled samples or at each dph according to PERMANOVA analysis, but each dph was statistically different on pairwise analysis. Gene set enrichment analysis revealed that there was a downregulation of immune related genes in lower salinities versus higher salinities suggesting larvae may be dealing with less stress at lower salinities. Most osmoregulation, fatty acid, and immune related genes tested were not significantly different across salinities. This is likely be cause the Florida pompano is euryhaline and has a tolerance to the salinities selected. There was an increase in the expression levels of several immune related genes that may indicate an increase exposure to pathogens at later days post hatch likely related to feeding schedule. There was also an increase in fatty acid biosynthesis genes that corresponded with levels of fatty acids indicating a possible synthesis of essential fatty acids from precursors. Conclusions: From a transcriptomics perspective, the larvae did not show a negative response to lower salinities in comparison to higher salinities, which in fact showed upregulation of immune related genes. Further exploration of Florida pompano’s ability to biosynthesize essential fatty acids is necessary. This study will help enable the optimization of Florida Pompano larviculture using information on the optimal salinity and fatty acid content for growth and facilitate more cost-effective rearing methods.
2022-12-01 | GSE190968 | GEO
Project description:Stakeholder Florida Pompano Larviculture Across Different Salinities Whole Body Transcriptomes
| PRJNA789196 | ENA
Project description:Numerous studies have demonstrated that golden pompano (Trachinotus blochii) is sensititive to hypoxia, which causes a devastating blow to the golden pompano industry. And different methods of reoxygenation after hypoxia could bring differnt effects on metabolism for golden pompano.
2023-11-05 | GSE188265 | GEO
Project description:Analysis of microbial gene expression in response to physical and chemical gradients forming in the Columbia River, estuary, plume and coastal ocean was done in the context of the environmental data base. Gene expression was analyzed for 2,234 individual genes that were selected from fully sequenced genomes of 246 prokaryotic species (bacteria and archaea) as related to the nitrogen metabolism and carbon fixation. Seasonal molecular portraits of differential gene expression in prokaryotic communities during river-to-ocean transition were created using freshwater baseline samples (268, 270, 347, 002, 006, 207, 212).
2010-09-10 | GSE18303 | GEO
Project description:Fungia granulosa microbiome under different salinities
| PRJNA282461 | ENA
Project description:Numerous studies have demonstrated that the C. irritans can be efficiently propagated in the animal model golden pompano (Trachinotus blochii), especially in the process of intensive high-density culture, which causes large-scale infection and triggers bacterial invasion is a devastating blow to the golden pompano industry. This is in sharp contrast to the low sensitivity of S. oramin to C. irritans.
2022-10-23 | GSE186569 | GEO
Project description:The experiment compared flounder from the North Sea and the Baltic sea and their reactions on being exposed to water of different salinities
2006-12-20 | E-MAXD-22 | biostudies-arrayexpress
Project description:Bacteriophage – host dynamics and interactions are important for microbial community composition and ecosystem function. Nonetheless, empirical evidence in engineered environment is scarce. Here, we examined phage and prokaryotic community composition of four anaerobic digestors in full-scale wastewater treatment plants (WWTPs) across China. Despite relatively stable process performance in biogas production, both phage and prokaryotic groups fluctuated monthly over a year of study period. Nonetheless, there were significant correlations in their α- and β-diversities between phage and prokaryotes. Phages explained 40.6% of total prokaryotic community composition, much higher than the explainable power by abiotic factors (14.5%). Consequently, phages were significantly (P<0.010) linked to parameters related to process performance including biogas production and volatile solid concentrations. Association network analyses showed that phage-prokaryote pairs were deeply rooted, and two network modules were exclusively comprised of phages, suggesting a possibility of co-infection. Those results collectively demonstrate phages as a major biotic factor in controlling bacterial composition. Therefore, phages may play a larger role in shaping prokaryotic dynamics and process performance of WWTPs than currently appreciated, enabling reliable prediction of microbial communities across time and space.
2016-12-29 | GSE92978 | GEO
Project description:The alkaliphilic halotolerant bacterium Bacillus sp. N16-5 often faces salt stress in its natural habitats. One-color microarrays was used to investigate transcriptome expression profiles of Bacillus sp. N16-5 adaptation reactions to prolonged grown at different salinities (0%, 2%, 8% and 15% NaCl) and the initial reaction to suddenly alter salinity from 0% to 8% NaCl. Salt induced gene expression was measured when culture was grown on different salinities (0%, 2%, 8% and 15% NaCl) to mid-logarithmic phase. And salt induced gene expression was also measured at 0 min, 10 min, 30 min, 60min, 120min after a sudden change salinity from 0% to 8% NaCl.
2015-01-03 | E-GEOD-64621 | biostudies-arrayexpress