Transcriptome sequencing of a keystone aquatic herbivore yields insights on the temperature-dependent metabolism of essential lipids
Ontology highlight
ABSTRACT:
ORGANISM(S): Daphnia magna
PROVIDER: GSE130674 | GEO | 2019/05/04
REPOSITORIES: GEO
Similar Datasets
Project description:BACKGROUND:Nutritional quality of phytoplankton is a major determinant of the trophic transfer efficiency at the plant-herbivore interface in freshwater food webs. In particular, the phytoplankton's content of the essential polyunsaturated omega-3 fatty acid eicosapentaenoic acid (EPA) has been repeatedly shown to limit secondary production in the major zooplankton herbivore genus Daphnia. Despite extensive research efforts on the biological model organism Daphnia, and the availability of several Daphnia genomes, little is known regarding the molecular mechanisms underlying the limitations in Daphnia related to dietary EPA availability. RESULTS:We used RNA-seq to analyse the transcriptomic response of Daphnia magna which were fed with two different diets - each with or without supplementation of EPA - at two different temperature levels (15 and 20 °C). The transcripts were mapped to the D. magna genome assembly version 2.4, containing 26,646 translations. When D. magna fed on green alga, changing the temperature provoked a differential expression of 2001 transcripts, and in cyanobacteria-fed daphnia, 3385 transcripts were affected. The supplementation of EPA affected 1635 (on the green algal diet), or 175 transcripts (on the cyanobacterial diet), respectively. Combined effects for diet and temperature were also observed (669 for the green algal and 128 transcripts for the cyanobacterial diet). Searching for orthologous genes (COG-analysis) yielded a functional overview of the altered transcriptomes. Cross-matched transcript sets from both feed types were compiled to illuminate core responses to the factors temperature and EPA-supplementation. CONCLUSIONS:Our highly controlled eco-physiological experiments revealed an orchestrated response of genes involved in the transformation and signalling of essential fatty acids, including eicosanoid-signalling pathways with potential immune functions. We provide an overview of downstream-regulated genes, which contribute to enhance growth and reproductive output. We also identified numerous EPA-responsive candidate genes of yet unknown function, which constitute new targets for future studies on the molecular basis of EPA-dependent effects at the freshwater plant-herbivore interface.
| S-EPMC6873670 | biostudies-literature
Project description:The availability of polyunsaturated fatty acids (PUFAs) in food items influences the fitness of organisms at higher trophic levels. Omega 3 and omega 6 fatty acids are essential compounds that cannot be synthesised de novo in these animals. Especially the omega 3 PUFA eicosapentaenoic acid (EPA) is an important molecule, as it is a limiting nutritional component for growth and reproduction in numerous marine and freshwater zooplankton species. With our transcriptomic study in Daphnia magna we address the transcriptomic network behind the metabolism and conversion that is connected to physiological EPA-limitation under temperature stress (20°C vs. 15°C).
2019-05-04 | GSE130673 | GEO
Project description:Transcriptome sequencing of a keystone aquatic herbivore yields insights on the temperature-dependent metabolism of essential lipids
| PRJNA540965 | ENA
Project description:Spring phenologies are advancing in many ecosystems associated with climate warming causing unpredictable changes in ecosystem functioning. Here we establish a phenological model for Daphnia, an aquatic keystone herbivore based on decadal data on water temperatures and the timing of Daphnia population maxima from Lake Constance, a large European lake. We tested this model with long-term time-series data from two lakes (Müggelsee, Germany; Lake Washington, USA), and with observations from a diverse set of 49 lakes/sites distributed widely across the Northern Hemisphere (NH). The model successfully captured the observed temporal variation of Daphnia phenology in the two case study sites (r(2) = 0.25 and 0.39 for Müggelsee and Lake Washington, respectively) and large-scale spatial variation in the NH (R(2) = 0.57). These results suggest that Daphnia phenology follows a uniform temperature dependency in NH lakes. Our approach--based on temperature phenologies--has large potential to study and predict phenologies of animal and plant populations across large latitudinal gradients in other ecosystems.
| S-EPMC3465311 | biostudies-literature
Project description:The sea urchin Diadema antillarum was the most important herbivore on Caribbean reefs until 1983, when mass mortality reduced its populations by more than 97%. Knowledge of its past demography is essential to reconstruct reef ecology as it was before human impact, which has been implicated as having caused high pre-mortality Diadema abundance. To determine the history of its population size, we sequenced the ATPase 6 and 8 region of mitochondrial DNA from populations in the Caribbean and in the eastern Atlantic (which was not affected by the mass mortality), as well as from the eastern Pacific D. mexicanum. The Caribbean population harbours an order of magnitude more molecular diversity than those of the eastern Pacific or the eastern Atlantic and, despite the recent mass mortality, its DNA sequences bear the genetic signature of a previous population expansion. By estimating mutation rates from divergence between D. antillarum and D. mexicanum, that were separated at a known time by the Isthmus of Panama, and by using estimates of effective population size derived from mismatch distributions and a maximum likelihood coalescence algorithm, we date the expansion as having occurred no more recently than 100 000 years before the present. Thus, Diadema was abundant in the Caribbean long before humans could have affected ecological processes; the genetic data contain no evidence of a recent, anthropogenically caused, population increase.
| S-EPMC1088886 | biostudies-other
Project description:The regulation of aquatic carbon cycles by temperature is a significant uncertainty in our understanding of how watersheds will respond to climate change. Aquatic ecosystems transport substantial quantities of carbon to the atmosphere and ocean, yet we have limited understanding of how temperature modifies aquatic ecosystem metabolic processes and contributions to carbon cycles at watershed to global scales. We propose that geomorphology controls the distribution and quality of organic material that forms the metabolic base of aquatic ecosystems, thereby controlling the response of aquatic ecosystem metabolism to temperature across landscapes. Across 23 streams and four years during summer baseflow, we estimated variation in the temperature sensitivity of ecosystem respiration (R) among streams draining watersheds with different geomorphic characteristics across a boreal river basin. We found that geomorphic features imposed strong controls on temperature sensitivity; R in streams draining flat watersheds was up to six times more temperature sensitive than streams draining steeper watersheds. Further, our results show that this association between watershed geomorphology and temperature sensitivity of R was linked to the carbon quality of substrates that changed systematically across the geomorphic gradient. This suggests that geomorphology will control how carbon is transported, stored, and incorporated into river food webs as the climate warms.
| S-EPMC6879538 | biostudies-literature
Project description:Transient receptor potential vanilloid 1 (TRPV1), a non-selective ligand-gated cation channel with high permeability for Ca2+, has received considerable attention as potential therapeutic target for the treatment of several disorders including pain, inflammation, and hyperlipidemia. In particular, TRPV1 regulates lipid metabolism by mechanisms that are not completely understood. Interestingly, TRPV1 and lipids regulate each other in a reciprocal and complex manner. This review surveyed the recent literature dealing with the role of TRPV1 in the hyperlipidemia-associated metabolic syndrome. Besides TRPV1 structure, molecular mechanisms underlying the regulatory effect of TRPV1 on lipid metabolism such as the involvement of uncoupling proteins (UCPs), ATP-binding cassette (ABC) transporters, peroxisome proliferation-activated receptors (PPAR), sterol responsive element binding protein (SREBP), and hypoxia have been discussed. Additionally, this review extends our understanding of the lipid-dependent modulation of TRPV1 activity through affecting both the gating and the expression of TRPV1. The regulatory role of different classes of lipids such as phosphatidylinositol (PI), cholesterol, estrogen, and oleoylethanolamide (OEA), on TRPV1 has also been addressed.
| S-EPMC9797668 | biostudies-literature
Project description:Both oxygen and temperature are fundamental factors determining metabolic performance, fitness, ecological niches, and responses of many aquatic organisms to climate change. Despite the importance of physical and physiological constraints on oxygen supply affecting aerobic metabolism of aquatic ectotherms, ecological theories such as the metabolic theory of ecology have focused on the effects of temperature rather than oxygen. This gap currently impedes mechanistic models from accurately predicting metabolic rates (i.e., oxygen consumption rates) of aquatic organisms and restricts predictions to resting metabolism, which is less affected by oxygen limitation. Here, we expand on models of metabolic scaling by accounting for the role of oxygen availability and temperature on both resting and active metabolic rates. Our model predicts that oxygen limitation is more likely to constrain metabolism in larger, warmer, and active fish. Consequently, active metabolic rates are less responsive to temperature than are resting metabolic rates, and metabolism scales to body size with a smaller exponent whenever temperatures or activity levels are higher. Results from a metaanalysis of fish metabolic rates are consistent with our model predictions. The observed interactive effects of temperature, oxygen availability, and body size predict that global warming will limit the aerobic scope of aquatic ectotherms and may place a greater metabolic burden on larger individuals, impairing their physiological performance in the future. Our model reconciles the metabolic theory with empirical observations of oxygen limitation and provides a formal, quantitative framework for predicting both resting and active metabolic rate and hence aerobic scope of aquatic ectotherms.
| S-EPMC7749359 | biostudies-literature
Project description:Transgenerational inheritance of environmentally induced epigenetic marks can have significant impacts on eco-evolutionary dynamics, but the phenomenon remains controversial in ecological model systems. We used whole-genome bisulfite sequencing of individual water fleas (Daphnia magna) to assess whether environmentally induced DNA methylation is transgenerationally inherited. Genetically identical females were exposed to one of three natural stressors, or a de-methylating drug, and their offspring were propagated clonally for four generations under control conditions. We identified between 70 and 225 differentially methylated CpG positions (DMPs) in F1 individuals whose mothers were exposed to a natural stressor. Roughly half of these environmentally induced DMPs persisted until generation F4. In contrast, treatment with the drug demonstrated that pervasive hypomethylation upon exposure is reset almost completely after one generation. These results suggest that environmentally induced DNA methylation is non-random and stably inherited across generations in Daphnia, making epigenetic inheritance a putative factor in the eco-evolutionary dynamics of freshwater communities.
| S-EPMC9097707 | biostudies-literature
Project description:Diabetes adversely affects multiple organs, including the kidney, eye and nerve, leading to diabetic kidney disease, diabetic retinopathy and diabetic neuropathy, respectively. In both type 1 and type 2 diabetes, tissue damage is organ specific and is secondary to a combination of multiple metabolic insults. Hyperglycaemia, dyslipidaemia and hypertension combine with the duration and type of diabetes to define the distinct pathophysiology underlying diabetic kidney disease, diabetic retinopathy and diabetic neuropathy. Only recently have the commonalities and differences in the metabolic basis of these tissue-specific complications, particularly those involving local and systemic lipids, been systematically examined. This review focuses on recent progress made using preclinical models and human-based approaches towards understanding how bioenergetics and metabolomic profiles contribute to diabetic kidney disease, diabetic retinopathy and diabetic neuropathy. This new understanding of the biology of complication-prone tissues highlights the need for organ-specific interventions in the treatment of diabetic complications.
| S-EPMC6679814 | biostudies-literature