Little Hot Creek 4 terrestrial hot spring Genome sequencing and assembly
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ABSTRACT:
PROVIDER: PRJNA983228 | ENA |
REPOSITORIES: ENA
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Project description:Microbial mats are found in a variety of modern environments, with evidence for their presence as old as the Archean. There is much debate about the rates and conditions of processes that eventually lithify and preserve mats as microbialites. Here, we apply novel tracer experiments to quantify both mat biomass addition and the formation of CaCO3. Microbial mats from Little Hot Creek (LHC), California, contain calcium carbonate that formed within multiple mat layers, and thus constitute a good test case to investigate the relationship between the rate of microbial mat growth and carbonate precipitation. The laminated LHC mats were divided into four layers via color and fabric, and waters within and above the mat were collected to determine their carbonate saturation states. Samples of the microbial mat were also collected for 16S rRNA analysis of microbial communities in each layer. Rates of carbonate precipitation and carbon fixation were measured in the laboratory by incubating homogenized samples from each mat layer with δ13C-labeled HCO3- for 24 h. Comparing these rates with those from experimental controls, poisoned with NaN3 and HgCl2, allowed for differences in biogenic and abiogenic precipitation to be determined. Carbon fixation rates were highest in the top layer of the mat (0.17% new organic carbon/day), which also contained the most phototrophs. Isotope-labeled carbonate was precipitated in all four layers of living and poisoned mat samples. In the top layer, the precipitation rate in living mat samples was negligible although abiotic precipitation occurred. In contrast, the bottom three layers exhibited biologically enhanced carbonate precipitation. The lack of correlation between rates of carbon fixation and biogenic carbonate precipitation suggests that processes other than autotrophy may play more significant roles in the preservation of mats as microbialites.
| S-EPMC6053513 | biostudies-literature
Project description:Hot spring environments can create physical and chemical gradients favorable for unique microbial life. They can also include authigenic mineral precipitates that may preserve signs of biological activity on Earth and possibly other planets. The abiogenic or biogenic origins of such precipitates can be difficult to discern, therefore a better understanding of mineral formation processes is critical for the accurate interpretation of biosignatures from hot springs. Little Hot Creek (LHC) is a hot spring complex located in the Long Valley Caldera, California, that contains mineral precipitates composed of a carbonate base (largely submerged) topped by amorphous silica (largely emergent). The precipitates occur in close association with microbial mats and biofilms. Geological, geochemical, and microbiological data are consistent with mineral formation via degassing and evaporation rather than direct microbial involvement. However, the microfabric of the silica portion is stromatolitic in nature (i.e., wavy and finely laminated), suggesting that abiogenic mineralization has the potential to preserve textural biosignatures. Although geochemical and petrographic evidence suggests the calcite base was precipitated via abiogenic processes, endolithic microbial communities modified the structure of the calcite crystals, producing a textural biosignature. Our results reveal that even when mineral precipitation is largely abiogenic, the potential to preserve biosignatures in hot spring settings is high. The features found in the LHC structures may provide insight into the biogenicity of ancient Earth and extraterrestrial rocks.
| S-EPMC5981138 | biostudies-literature
Project description:Cone Pool (Little Hot Creek) Microbiological Characterization
| PRJNA386811 | ENA
Project description:The thermophilic Aquificales inhabit and play important biogeochemical roles in the geothermal environments globally. Although intensive studies on physiology, microbial ecology, biochemistry, metagenomics and metatranscriptomics of the Aquificales¬ species and Aquificales-containing environmental samples have been conducted, comprehensive understandings about their ecophysiology, especially in the natural niches have been limited. In the present study, an integrated suite of metagenomic, metatranscriptomic and metaproteomic analyses, for the first time, were conducted on a filamentous microbial community from the Apron and Channel Facies (ACF) of CaCO3 (travertine) deposition at Narrow Gauge, Mammoth Hot Springs, Yellowstone National Park.
2020-05-26 | PXD006506 | Pride
Project description:We used the mummichog (Fundulus heteroclitus) array we developed to test whether our arrays could be used to monitor the efficacy of remediation at an estuarine Superfund site. Shipyard Creek is a chromium-contaminated Superfund site in Charleston, SC undergoing remediation, therefore it provides a unique opportunity to study the efficacy of arrays as a molecular biomarker in of toxicant effects in mummichogs. Mummichogs were captured in Shipyard Creek in Charleston, SC prior to remediation (2000), after remediation began (2003), and as remediation further progressed (2005). Simultaneously, mummichogs were collected from a reference site at the Winyah-Bay National Estuarine Research Reserve (NERR). The hepatic gene expression pattern of fish captured at Shipyard Creek showed wide differences from the fish captured at NERR in 2000. As remediation progressed the gene expression pattern of fish captured at Shipyard Creek became increasingly similar to fish captured at NERR, and the number of genes differently expressed dropped from 22 to 4. The magnitude of differential gene expression of the individual genes also decreased during remediation. The recovering gene expression profile is associated with lower chromium bioavailability, demonstrated through significantly decreased body burden and sediment concentrations. For example, sediment concentrations at Shipyard Creek were 80-fold greater than NERR in 2000, 51-fold greater in 2003, and only 8-fold greater in 2005. However, hydraulic dredging in 2005 stirred up the sediments and increased body burden of chromium even though chromium sediment concentrations continued to drop. Therefore, the number of differentially expressed genes increased to 9. Overall, the data supports our hypothesis that arrays can be used to monitor site mitigation, as the number of genes differentially expressed mimics the body burden and also indicates when on-site remediation is increasing bioavailability. Keywords: Field site
2006-09-01 | GSE4212 | GEO
Project description:We used the mummichog (Fundulus heteroclitus) array we developed to test whether our arrays could be used to monitor the efficacy of remediation at an estuarine Superfund site. Shipyard Creek is a chromium-contaminated Superfund site in Charleston, SC undergoing remediation, therefore it provides a unique opportunity to study the efficacy of arrays as a molecular biomarker in of toxicant effects in mummichogs. Mummichogs were captured in Shipyard Creek in Charleston, SC prior to remediation (2000), after remediation began (2003), and as remediation further progressed (2005). Simultaneously, mummichogs were collected from a reference site at the Winyah-Bay National Estuarine Research Reserve (NERR). The hepatic gene expression pattern of fish captured at Shipyard Creek showed wide differences from the fish captured at NERR in 2000. As remediation progressed the gene expression pattern of fish captured at Shipyard Creek became increasingly similar to fish captured at NERR, and the number of genes differently expressed dropped from 22 to 4. The magnitude of differential gene expression of the individual genes also decreased during remediation. The recovering gene expression profile is associated with lower chromium bioavailability, demonstrated through significantly decreased body burden and sediment concentrations. For example, sediment concentrations at Shipyard Creek were 80-fold greater than NERR in 2000, 51-fold greater in 2003, and only 8-fold greater in 2005. However, hydraulic dredging in 2005 stirred up the sediments and increased body burden of chromium even though chromium sediment concentrations continued to drop. Therefore, the number of differentially expressed genes increased to 9. Overall, the data supports our hypothesis that arrays can be used to monitor site mitigation, as the number of genes differentially expressed mimics the body burden and also indicates when on-site remediation is increasing bioavailability. Keywords: Field site
2006-09-01 | GSE4211 | GEO
Project description:We used the mummichog (Fundulus heteroclitus) array we developed to test whether our arrays could be used to monitor the efficacy of remediation at an estuarine Superfund site. Shipyard Creek is a chromium-contaminated Superfund site in Charleston, SC undergoing remediation, therefore it provides a unique opportunity to study the efficacy of arrays as a molecular biomarker in of toxicant effects in mummichogs. Mummichogs were captured in Shipyard Creek in Charleston, SC prior to remediation (2000), after remediation began (2003), and as remediation further progressed (2005). Simultaneously, mummichogs were collected from a reference site at the Winyah-Bay National Estuarine Research Reserve (NERR). The hepatic gene expression pattern of fish captured at Shipyard Creek showed wide differences from the fish captured at NERR in 2000. As remediation progressed the gene expression pattern of fish captured at Shipyard Creek became increasingly similar to fish captured at NERR, and the number of genes differently expressed dropped from 22 to 4. The magnitude of differential gene expression of the individual genes also decreased during remediation. The recovering gene expression profile is associated with lower chromium bioavailability, demonstrated through significantly decreased body burden and sediment concentrations. For example, sediment concentrations at Shipyard Creek were 80-fold greater than NERR in 2000, 51-fold greater in 2003, and only 8-fold greater in 2005. However, hydraulic dredging in 2005 stirred up the sediments and increased body burden of chromium even though chromium sediment concentrations continued to drop. Therefore, the number of differentially expressed genes increased to 9. Overall, the data supports our hypothesis that arrays can be used to monitor site mitigation, as the number of genes differentially expressed mimics the body burden and also indicates when on-site remediation is increasing bioavailability. Keywords: Field site
2006-09-01 | GSE4210 | GEO
Project description:The thermophilic Aquificales inhabit and play important biogeochemical roles in the geothermal environments globally. Although intensive studies on physiology, microbial ecology, biochemistry, metagenomics and metatranscriptomics of the Aquificales¬ species and Aquificales-containing environmental samples have been conducted, comprehensive understandings about their ecophysiology, especially in the natural niches have been limited. In the present study, an integrated suite of metagenomic, metatranscriptomic and metaproteomic analyses, for the first time, were conducted on a filamentous microbial community from the Apron and Channel Facies (ACF) of CaCO3 (travertine) deposition at Narrow Gauge, Mammoth Hot Springs, Yellowstone National Park.
2020-05-26 | PXD006504 | Pride
Project description:The preeminent source of biological methane on Earth is methyl coenzyme M reductase (Mcr)-dependent archaeal methanogenesis. A growing body of evidence suggests a diversity of archaea possess Mcr, although experimental validation of hypothesized methane metabolisms has been missing. Here, we provide evidence of a functional Mcr-based methanogenesis pathway in a novel member of the family Archaeoglobaceae, designated Methanoglobus nevadensis, which we enriched from a terrestrial hot spring on the polysaccharide xyloglucan. Our incubation assays demonstrate methane production that is highly sensitive to the Mcr inhibitor bromoethanesulfonate, stimulated by xyloglucan and xyloglucan-derived sugars, concomitant with the consumption of molecular hydrogen, and causing a deuterium fractionation in methane characteristic of hydrogenotrophic and methylotrophic methanogens. Combined with the recovery and analysis of a high-quality M. nevadensis metagenome-assembled genome encoding a divergent Mcr and diverse potential electron and carbon transfer pathways, our observations suggest methanogenesis in M. nevadensis occurs via Mcr and is fueled by the consumption of cross-fed byproducts of xyloglucan fermentation mediated by other community members. Phylogenetic analysis shows close affiliation of the M. nevadensis Mcr with those from Korarchaeota, Nezhaarchaeota, Verstraetearchaeota, and other Archaeoglobales that are divergent from well-characterized Mcr. We propose these archaea likely also use functional Mcr complexes to generate methane on the basis of our experimental validation in M. nevadensis. Thus, divergent Mcr-encoding archaea may be underestimated sources of biological methane in terrestrial and marine hydrothermal environments.
| S-EPMC10504316 | biostudies-literature