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33 results for “extremophile”
Additional file 1 of Medium development and production of carotenoids and exopolysaccharides by the extremophile Rhodothermus marinus DSM16675 in glucose-based defined media
<p>The biodegradative capacity of bacteria in their natural habitats is affected by water availability. In this work, we have examined the activity and effector specificity of the transcriptional regulator XylR of the TOL plasmid pWW0 of Pseudomonas putida mt-2 for biodegradation of m-xylene when external water potential was manipulated with polyethylene glycol PEG8000. By using non-disruptive luxCDEAB reporter technology, we noticed that the promoter activated by XylR (Pu) restricted its activity and the regulator<br> became more effector-specific towards head TOL substrates when cells were grown under water subsaturation. Such a tight specificity brought about by water limitation was relaxed when intracellular osmotic stress was counteracted by the external addition of the compatible solute glycine betaine. With these facts in hand, XylR variants isolated earlier as effectorspecificity responders to the non-substrate 1,2,4-trichlorobenzene under high matric stress were re-examined and found to be unaffected by water potential in vivo. All these phenomena could be ultimately explained as the result of water potential-dependent conformational changes in the A domain of XylR and its effector-binding pocket, as suggested by AlphaFold prediction of protein structures. The consequences of this scenario for the evolution of specificities in regulators and the emergence of catabolic pathways are discussed.</p>
Data from: Nascent transcription reveals regulatory changes in extremophile fishes inhabiting hydrogen sulfide-rich environments
<p>Regulating transcription allows organisms to respond to their environment, both within a single generation (plasticity) and across generations (adaptation). We examined transcriptional differences in gill tissues of fishes in the Poecilia mexicana species complex (family Poeciliidae), which have colonized toxic springs rich in hydrogen sulfide (H2S) in southern Mexico. There are gene expression differences between sulfidic and non-sulfidic populations, yet regulatory mechanisms mediating this gene expression variation remain poorly studied. We combined capped-small RNA sequencing (csRNA-seq), which captures actively transcribed (i.e., nascent) transcripts, and traditional messenger RNA sequencing (mRNA-seq) to examine how variation in transcription, enhancer activity, and associated transcription factor binding sites may facilitate adaptation to extreme environments. csRNA-seq revealed thousands of differentially initiated transcripts between sulfidic and non-sulfidic populations, many of which are involved in H2S detoxification and response. Analyses of transcription factor binding sites in promoter and putative enhancer csRNA-seq peaks identify a suite of transcription factors likely involved in regulating H2S-specific shifts in gene expression, including several key transcription factors known to respond to hypoxia. Our findings uncover a complex interplay of regulatory processes that reflect the divergence of extremophile populations of P. mexicana from their non-sulfidic ancestors and suggest shared responses among evolutionarily independent lineages.</p>
Data from: Survival limits of yeasts and other extremophilic microorganisms with relevance for planetary protection of the icy moons
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Data from: Nascent transcription reveals regulatory changes in extremophile fishes inhabiting hydrogen sulfide-rich environments
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Supplementary videos of "Description of a novel extremophile green algae, Chlamydomonas pacifica, and its potential as a biotechnology host" Molino et al
<p><strong>Supplementary Video 1: </strong>Motility tracking of <em>C. pacifica</em> - (Raw_402_Video_1.mp4)</p> <p> </p> <p><strong>Supplementary Video 2: </strong>Motility tracking of <em>C. pacifica</em> - (Raw_402_Video_2.mp4)</p> <p> </p> <p><strong>Supplementary Video 3:</strong> Motility tracking of <em>C. pacifica</em> - (Raw_402_Video_3.mp4)</p> <p> </p> <p><strong>Supplementary Video 4:</strong> Motility tracking of <em>C. pacifica</em> - (TrackMate capture of Video_1_402.avi)</p> <p> </p> <p><strong>Supplementary Video 5: </strong>Motility tracking of <em>C. pacifica</em> - (TrackMate capture of Video_2_402.avi)</p> <p> </p> <p><strong>Supplementary Video 6:</strong> Motility tracking of <em>C. pacifica</em> - (TrackMate capture of Video_3_402.avi)</p> <p> </p> <p><strong>Supplementary Video 7:</strong> Mating video 1 - (Starting to aggregate 402 403.avi)</p> <p> </p> <p><strong>Supplementary Video 8:</strong> Mating video 2 - (Fusing_cell_wall_motility.avi)</p> <p> </p> <p> </p>
Functional consequences of phenotypic variation between locally adapted populations: swimming performance and ventilation in extremophile fish
<p>Natural selection drives the evolution of traits to optimize organismal performance, but optimization of one aspect of performance can often influence other aspects of performance. Here, we asked how phenotypic variation between locally adapted fish populations affects locomotion and ventilation, testing for functional trade-offs and trait-performance correlations. Specifically, we investigated two populations of livebearing fish (<em>Poecilia mexicana</em>) that inhabit distinct habitat types (hydrogen-sulfide-rich springs and adjacent nonsulfidic streams). For each individual, we quantified different metrics of burst swimming during simulated predator attacks, steady swimming, as well as gill ventilation. Coinciding with predictions, we documented significant population differences in all aspects of performance, with fish from sulfidic habitats exhibiting higher steady swimming performance and higher ventilation capacity, but slower burst swimming. There was a significant functional trade-off between steady and burst swimming, but not between different aspects of locomotion and ventilation. While our findings about population differences in locomotion performance largely parallel the results from previous studies, we provide novel insights about how morphological variation might impact ventilation and ultimately oxygen acquisition. Overall, our analyses provided insights into the functional consequences of previously documented phenotypic variation, which will help to disentangle the effects of different sources of selection that may coincide along complex environmental gradients.</p>
Data from: The many origins of extremophile fishes
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Functional consequences of phenotypic variation between locally adapted populations: swimming performance and ventilation in extremophile fish
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Data from: Integrative analyses of convergent adaptation in sympatric extremophile fishes
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Data from: Extremophile Poeciliidae: multivariate insights into the complexity of speciation along replicated ecological gradients
Background: Replicate population pairs that diverge in response to similar selective regimes allow for an investigation of (a) whether phenotypic traits diverge in a similar and predictable fashion, (b) whether there is gradual variation in phenotypic divergence reflecting variation in the strength of natural selection among populations, (c) whether the extent of this divergence is correlated between multiple character suites (i.e., concerted evolution), and (d) whether gradual variation in phenotypic divergence predicts the degree of reproductive isolation, pointing towards a role for adaptation as a driver of (ecological) speciation. Here, we use poeciliid fishes of the genera Gambusia and Poecilia that have repeatedly evolved extremophile lineages able to tolerate high and sustained levels of toxic hydrogen sulfide (H2S) to answer these questions. Results: We investigated evolutionary divergence in response to H2S in Gambusia spp. (and to a lesser extent Poecilia spp.) using a multivariate approach considering the interplay of life history, body shape, and population genetics (nuclear miscrosatellites to infer population genetic differentiation as a proxy for reproductive isolation). We uncovered both shared and unique patterns of evolution: most extremophile Gambusia predictably evolved larger heads and offspring size, matching a priori predictions for adaptation to sulfidic waters, while variation in adult life histories was idiosyncratic. When investigating patterns for both genera (Gambusia and Poecilia), we found that divergence in offspring-related life histories and body shape were positively correlated across populations, but evidence for individual-level associations between the two character suites was limited, suggesting that genetic linkage, developmental interdependencies, or pleiotropic effects do not explain patterns of concerted evolution. We further found that phenotypic divergence was positively correlated with both environmental H2S-concentration and neutral genetic differentiation (a proxy for gene flow). Conclusions: Our results suggest that higher toxicity exerts stronger selection, and that divergent selection appears to constrain gene flow, supporting a scenario of ecological speciation. Nonetheless, progress toward ecological speciation was variable, partially reflecting variation in the strength of divergent selection, highlighting the complexity of selective regimes even in natural systems that are seemingly governed by a single, strong selective agent.
Data from: Living on a volcano's edge: genetic isolation of an extremophile terrestrial metazoan
Communities of organisms inhabiting extreme terrestrial environments provide a unique opportunity to study evolutionary forces that drive population structure and genetic diversity under the combined challenges posed by multiple geogenic stressors. High abundance of an invasive pantropical earthworm (and the absence of indigenous lumbricid species) in the Furnas geothermal field (Sao Miguel Island, Azores) indicates its remarkable tolerance to high soil temperature, exceptionally high carbon dioxide and low oxygen levels, and elevated metal bioavailability, conditions which are lethal for the majority of terrestrial metazoans. Mitochondrial and nuclear markers were used to analyze the relationship between populations living inside and outside the geothermal field. Results showed that Pontoscolex corethrurus (Annelida, Oligochaeta, Glossoscolecidae) to be a genetically heterogeneous complex within the Sao Miguel landscape and is probably differentiated into cryptic species. The population exposed to the hostile soil conditions within the volcanic caldera possesses the lowest within-population mitochondrial diversity but an unexpectedly high degree of nuclear variability with several loci evidencing positive selection, parameters indicative of a genetically unique population only distantly related to conspecifics living outside the caldera. In conclusion, P. corethrurus inhabiting active volcanic soil is a discrete extremophile population that has evolved by tolerating a mixture of non-anthropogenic chemical and physical stressors.
Data from: Eco-morphological differentiation in Lake Magadi tilapia, an extremophile cichlid fish living in hot, alkaline and hypersaline lakes in East Africa
Ecological diversification through divergent selection is thought to be a major force during the process of adaptive radiations. However, the large sizes and complexity of most radiations such as those of the cichlids in the African Great Lakes make it impossible to infer the exact evolutionary history of any population divergence event. The genus Alcolapia, a small cichlid lineage endemic to Lakes Magadi and Natron in East Africa, exhibits phenotypes similar to some of those found in cichlids of the radiations of the African Great Lakes. The simplicity within Alcolapia makes it an excellent model system to investigate ecological diversification and speciation. We used an integrated approach including population genomics based on RAD-seq data, geometric morphometrics, and stable isotope analyses to investigate the eco-morphological diversification of tilapia in Lake Magadi and its satellite lake Little Magadi. Additionally, we reconstructed the demographic history of the species using coalescent simulations based on the joint site frequency spectrum. The population in Little Magadi has a characteristically upturned mouth - possibly an adaptation to feeding on prey from the water surface. Eco-morphological differences between populations within Lake Magadi are more subtle, but are consistent with known ecological differences between its lagoons such as high concentrations of nitrogen attributable to extensive guano deposits in Rest of Magadi relative to Fish Springs Lagoon. All populations diverged simultaneously only about 1,100 generations ago. Differences in levels of gene flow between populations and the effective population sizes have likely resulted in the inferred heterogeneous patterns of genome-wide differentiation.
Dataset from the paper "Viruses from geothermal springs have ancient origins reflecting long-term interactions with extremophilic red algal mats"
<p>Dataset of viral operational taxonomic units (vOTUs) and viral metagenome-assembled genomes (vMAGs) from the Lemonade Creek, Yellowstone National Park (YNP), USA, from the paper "Viruses from geothermal springs have ancient origins reflecting long-term interactions with extremophilic red algal mats".</p><p>L. Felipe Benites1*, Timothy G. Stephens1, Julia Van Etten1,2, Timeeka James1, William C. Christian4, Kerrie Barry5, Igor V. Grigoriev5,6, Timothy R. McDermott3 and Debashish Bhattacharya1</p><p>1Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, United States of America</p><p>2Graduate Program in Ecology and Evolution, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901 United States of America</p><p>3Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, United States of America</p><p>4Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America</p><p>5U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States of America</p><p>6Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, United States of America</p>
Data from: Extremophile Poeciliidae: multivariate insights into the complexity of speciation along replicated ecological gradients
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Data from: Living on a volcano's edge: genetic isolation of an extremophile terrestrial metazoan
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Data from: Eco-morphological differentiation in Lake Magadi tilapia, an extremophile cichlid fish living in hot, alkaline and hypersaline lakes in East Africa
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Dataset and Tables - DOCTORAL THESIS - EXTREMOPHILES IN ASTROBIOLOGY: CONTRIBUTIONS TO THE UNDERSTANDING OF BIOSIGNATURES PRODUCTION AND SURVIVAL MOLECULAR STRATEGIES
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Data from: Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote
Some microbial eukaryotes, such as the extremophilic red alga Galdieria sulphuraria, can live in hot, toxic metal-rich, acidic environments. To elucidate the underlying molecular mechanisms of adaptation, we sequenced the 13.7 Mb genome of G. sulphuraria. This alga shows an enormous metabolic flexibility, growing either photoautotrophically or heterotrophically on more than 50 carbon sources. Environmental adaptation seems to have been facilitated by horizontal gene transfer from various bacteria and archaea, often followed by gene family expansion. At least 5% of protein-coding genes of G. sulphuraria were probably acquired horizontally. These proteins are involved in ecologically important processes ranging from heavy metal detoxification to glycerol uptake and metabolism. Thus, our findings show that a pan-domain gene pool has facilitated environmental adaptation in this unicellular eukaryote.
Data from: Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote
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International Space Station flight project EXTREMOPHILES
The International Space Station (ISS) is a unique habitat for humans and microorganisms. Here, we report the results of the ISS experiment EXTREMOPHILES, including the analysis of microbial communities from several areas aboard at three time points. We assess microbial diversity, distribution, functional capacity and resistance profile using a combination of cultivation-independent analyses (amplicon and shot-gun sequencing) and cultivation-dependent analyses (physiological and genetic characterization of microbial isolates, antibiotic resistance tests, co-incubation experiments). We show that the ISS microbial communities are highly similar to those present in ground-based confined indoor environments and are subject to fluctuations, although a core microbiome persists over time and locations. The genomic and physiological features selected by ISS conditions do not appear to be directly relevant to human health, although adaptations towards biofilm formation and surface interactions were observed. Our results do not raise direct reason for concern with respect to crew health, but indicate a potential threat towards material integrity in moist areas.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.