28 research outputs found
Samail Ophiolite 16S rRNA gene amplicon sequencing
No full textThis is a central repository for 16S rRNA gene amplicon sequencing data generated from samples of biomass from the Samail Ophiolite, Oman.
Further information on processing of this data is available on Github and is archived via Zenodo:
Nothaft, D. B., Rempfert, K. R. & Kraus, E. A. danote/Samail_16S_compilation: First release of Samail 16S data processing repository. Zenodo https://doi.org/10.5281/ZENODO.4768396 (2021
Parapatric speciation of Meiothermus in serpentinite-hosted aquifers in Oman
No full textThe factors that control the distribution and evolution of microbial life in subsurface environments remain enigmatic due to challenges associated with sampling fluids from discrete depth intervals via boreholes while avoiding mixing of fluids. Here, using an inflatable packer system, fracture waters were isolated and collected from three discrete depth intervals spanning >130 m in a borehole intersecting an ultramafic rock formation undergoing serpentinization in the Samail Ophiolite, Sultanate of Oman. Near surface aquifer waters were moderately reducing and had alkaline pH while deeper aquifer waters were reduced and had hyperalkaline pH, indicating extensive influence by serpentinization. Metagenomic sequencing and analysis of DNA from filtered biomass collected from discrete depth intervals revealed an abundance of aerobes in near surface waters and a greater proportion of anaerobes at depth. Yet the abundance of the putatively obligate aerobe, Meiothermus, increased with depth, providing an opportunity to evaluate the influence of chemical and spatial variation on its distribution and speciation. Two clades of Meiothermus metagenome assembled genomes (MAGs) were identified that correspond to surface and deep populations termed Types I (S) and II (D), respectively; both clades comprised an apparently Oman-specific lineage indicating a common ancestor. Type II (D) clade MAGs encoded fewer genes and were undergoing slower genome replication as inferred from read mapping. Further, single nucleotide variants (SNVs) and mobile genetic elements identified among MAGs revealed detectable, albeit limited, evidence for gene flow/recombination between spatially segregated Type I (S) and Type II (D) populations. Together, these observations indicate that chemical variation generated by serpentinization, combined with physical barriers that reduce/limit dispersal and gene flow, allowed for the parapatric speciation of Meiothermus in the Samail Ophiolite or a geologic precursor. Further, Meiothermus genomic data suggest that deep and shallow aquifer fluids in the Samail Ophiolite may mix over shorter time scales than has been previously estimated from geochemical data
Aqueous geochemical and microbial variation across discrete depth intervals in a peridotite aquifer assessed using a packer system in the Samail Ophiolite, Oman
No full textThe potential for molecular hydrogen ((Formula presented.)) generated via serpentinization to fuel subsurface microbial ecosystems independent from photosynthesis has prompted biogeochemical investigations of serpentinization-influenced fluids. However, investigations typically sample via surface seeps or open-borehole pumping, which can mix chemically distinct waters from different depths. Depth-indiscriminate sampling methods could thus hinder understanding of the spatial controls on nutrient availability for microbial life. To resolve distinct groundwaters in a low-temperature serpentinizing environment, we deployed packers (tools that seal against borehole walls during pumping) in two (Formula presented.) -deep, peridotite-hosted wells in the Samail Ophiolite, Oman. Isolation and pumping of discrete intervals as deep as (Formula presented.) to (Formula presented.) below ground level revealed multiple aquifers that ranged in pH from 8 to 11. Chemical analyses and 16S rRNA gene sequencing of deep, highly reacted (Formula presented.) groundwaters bearing up to (Formula presented.), (Formula presented.) methane ((Formula presented.)) and (Formula presented.) sulfate ((Formula presented.)) revealed an ecosystem dominated by Bacteria affiliated with the class Thermodesulfovibrionia, a group of chemolithoheterotrophs supported by (Formula presented.) oxidation coupled to (Formula presented.) reduction. In shallower, oxidized (Formula presented.) groundwaters, aerobic and denitrifying heterotrophs were relatively more abundant. High (Formula presented.) and (Formula presented.) of (Formula presented.) (up to (Formula presented.) and (Formula presented.), respectively) indicated microbial (Formula presented.) oxidation, particularly in (Formula presented.) waters with evidence of mixing with (Formula presented.) waters. This study demonstrates the power of spatially resolving groundwaters to probe their distinct geochemical conditions and chemosynthetic communities. Such information will help improve predictions of where microbial activity in fractured rock ecosystems might occur, including beyond Earth.</p
Geologic map of the Samail Ophiolite, Oman and United Arab Emirates
No full textA geologic map of the Samail Ophiolite in Oman and the United Arab Emirates has been georeferenced and digitized. The data are provided in GeoPackage (.gpkg) format that can be imported into GIS software such as QGIS and Arc. The GeoPackage contains vector layers for lithologies and faults. Five lithologies are represented: Dunite/Wehrlite, Harzburgite, Mafic, Metamorphic Sole, and Plagiogranite. Further, a QGIS project file is provided, which should allow for layer styles to be preserved if opened in QGIS. The map data (not georeferenced) were originally published as
Nicolas, A., Boudier, F., Ildefonse, B., Ball, E., 2000. Accretion of Oman and United Arab Emirates ophiolite - Discussion of a new structural map. Mar Geophys Res 21, 147–179. doi:10.1023/A:1026769727917
Please cite both works if you use the georeferenced data. A GeoTIFF of the original Nicolas et al. map subdivided into greater lithological detail is also provided in the GeoPackage.</div
Subsurface biogeochemical cycling of nitrogen in the actively serpentinizing Samail Ophiolite, Oman
No full textNitrogen (N) is an essential element for life. N compounds such as ammonium (NH+ 4 ) may act as electron donors, while nitrate (NO− 3 ) and nitrite (NO− 2 ) may serve as electron acceptors to support energy metabolism. However, little is known regarding the availability and forms of N in subsurface ecosystems, particularly in serpentinite-hosted settings where hydrogen (H2) generated through water–rock reactions promotes habitable conditions for microbial life. Here, we analyzed N and oxygen (O) isotope composition to investigate the source, abundance, and cycling of N species within the Samail Ophiolite of Oman. The dominant dissolved N species was dependent on the fluid type, with Mg2+-HCO− 3 type fluids comprised mostly of NO− 3 , and Ca2+-OH− fluids comprised primarily of ammonia (NH3). We infer that fixed N is introduced to the serpentinite aquifer as NO− 3 . High concentrations of NO− 3 (>100µM) with a relict meteoric oxygen isotopic composition (δ 18O ∼ 22‰, 117O ∼ 6‰) were observed in shallow aquifer fluids, indicative of NO− 3 sourced from atmospheric deposition (rainwater NO− 3 : δ 18O of 53.7‰, 117O of 16.8‰) mixed with NO− 3 produced in situ through nitrification (estimated endmember δ 18O and 117O of ∼0‰). Conversely, highly reacted hyperalkaline fluids had high concentrations of NH3 (>100µM) with little NO− 3 detectable. We interpret that NH3 in hyperalkaline fluids is a product of NO− 3 reduction. The proportionality of the O and N isotope fractionation (18ε / 15ε) measured in Samail Ophiolite NO− 3 was close to unity (18ε / 15ε ∼ 1), which is consistent with dissimilatory NO− 3 reduction with a membrane-bound reductase (NarG); however, abiotic reduction processes may also be occurring. The presence of genes commonly involved in N reduction processes (narG, napA, nrfA) in the metagenomes of biomass sourced from aquifer fluids supports potential biological involvement in the consumption of NO− 3 . Production of NH+ 4 as the end-product of NO− 3 reduction via dissimilatory nitrate reduction to ammonium (DNRA) could retain N in the subsurface and fuel nitrification in the oxygenated near surface. Elevated bioavailable N in all sampled fluids indicates that N is not likely limiting as a nutrient in serpentinites of the Samail Ophiolite
Geologic map of the Samail Ophiolite, Oman and United Arab Emirates
No full textA geologic map of the Samail Ophiolite in Oman and the United Arab Emirates has been georeferenced and digitized. The data are provided in GeoPackage (.gpkg) format that can be imported into GIS software such as QGIS and Arc. The GeoPackage contains vector layers for lithologies and faults. Five lithologies are represented: Dunite/Wehrlite, Harzburgite, Mafic, Metamorphic Sole, and Plagiogranite. Further, a QGIS project file is provided, which should allow for layer styles to be preserved if opened in QGIS. The map data (not georeferenced) were originally published as
Nicolas, A., Boudier, F., Ildefonse, B., Ball, E., 2000. Accretion of Oman and United Arab Emirates ophiolite - Discussion of a new structural map. Mar Geophys Res 21, 147–179. doi:10.1023/A:1026769727917
Please cite both works if you use the georeferenced data. A GeoTIFF of the original Nicolas et al. map subdivided into greater lithological detail is also provided in the GeoPackage.</div
Accessing the Subsurface Biosphere Within Rocks Undergoing Active Low‐Temperature Serpentinization in the Samail Ophiolite (Oman Drilling Project)
No full textThe Oman Drilling Project established an “Active Alteration” multi-borehole observatory in peridotites undergoing low-temperature serpentinization in the Samail Ophiolite. The highly serpentinized rocks are in contact with strongly reducing fluids. Distinct hydrological regimes, governed by differences in rock porosity and fracture density, give rise to steep redox (Eh +200 to −750 mV) and pH (pH range 8.5–11.2) gradients within the 300–400 m deep boreholes. The serpentinites and fluids host an active subsurface ecosystem. Microbial cell abundances in serpentinite vary at least six orders of magnitude, from ≤3.5 × 101 to 2.9 × 107 cells/g. Low levels of biological sulfate reduction (2–1,000 fmol/cm3/day) can be detected in rock cores, particularly in rocks in contact with reduced groundwaters with pH \u3c 10.5. Thermodesulfovibrio is the predominant sulfate reducer identified via metagenomic sequencing of adjacent groundwater communities. We infer that transport and reaction of microbially generated sulfide with the serpentine and brucite assemblages gives rise to optical darkening and sulfide overprinting, including the formation of tochilinite-vallerite group minerals, potentially serving as an indicator that this system is inhabited by microbial life. Olivine mesh-cores replaced with ferroan brucite and minor awaruite, abundant veins containing hydroandradite garnet and polyhedral serpentine, and late-stage carbonate veins are suggested as targets for future spatially resolved life-detection investigations. The high-quality whole-round core samples that have been preserved can be further probed to define how life distributes itself and functions within a system where chemical disequilibria are sustained by low-temperature water/rock interaction, and how biosignatures of in situ microbial activity are generated
Initial results from the Oman drilling project multi‐borehole observatory: petrogenesis and ongoing alteration of mantle peridotite in the weathering horizon
No full textThe Oman Drilling Project “Multi-Borehole Observatory” (MBO) samples an area of active weathering of tectonically exposed peridotite. This article reviews the geology of the MBO region, summarizes recent research, and provides new data constraining ongoing alteration. Host rocks are partially to completely serpentinized, residual mantle harzburgites, and replacive. Dunites show evidence for “reactive fractionation,” in which cooling, crystallizing magmas reacted with older residues of melting. Harzburgites and dunites are 65%–100% hydrated. Ferric to total iron ratios vary from 50% to 90%. In Hole BA1B, alteration extent decreases with depth. Gradients in water and core composition are correlated. Serpentine veins are intergrown with, and cut, carbonate veins with measurable 14C. Ongoing hydration is accompanied by SiO2 addition. Sulfur enrichment in Hole BA1B may result from oxidative leaching of sulfur from the upper 30 m, coupled with sulfate reduction and sulfide precipitation at 30–150 m. Oxygen fugacity deep in Holes BA3A, NSHQ14, and BA2A is fixed by the reaction 2H2O = 2H2 + O2 combined with oxidation of ferrous iron in serpentine, brucite, and olivine. fO2 deep in Holes BA1A, BA1D, and BA4A is 3–4 log units above the H2O-H2 limit, controlled by equilibria involving serpentine and brucite. Variations in alteration are correlated with texture, with reduced, low SiO2 assemblages in mesh cores recording very low water/rock ratios, juxtaposed with adjacent veins recording much higher ratios. The proportion of reduced mesh cores versus oxidized veins increases with depth, and the difference in fO2 recorded in cores and veins decreases with depth
danote/Samail_16S_compilation: First release of Samail 16S data processing repository
No full textThis is the first release
For the sake of learning: essays in honor of Anthony Grafton
No full textScope and content: "In this tribute to Anthony Grafton, a preeminent historian of early modern European intellectual and textual culture and of classical scholarship, fifty-eight contributors present new research across the many areas in which Grafton has been active. The articles span topics from late antiquity to the 20th century, from Europe to North American, and a full spectrum of fields of learning, including art history, the history of science, classics, Jewish and oriental studies, church history and theology, English and German literature, political, social, and book history. Major themes include the communities and dynamics of the Republic of Letters, the reception of classical texts, libraries and book culture, the tools, genres and methods of learning. Contributors are: James S. Amelang, Ann Blair, Christopher S. Celenza, Stuart Clark, Thomas Dandelet, Lorraine Daston, Mordechai Feingold, Paula Findlen, Anja-Silvia Goeing, Robert Goulding, Alastair Hamilton, James Hankins, Nicholas Hardy, Kristine Louise Haugen, Bruce Janacek, Lisa Jardine, Henk Jan de Jonge, Diane Greco Josefowicz, Roland Kany, Thomas DaCosta Kaufmann, Arthur Kiron, Jill Kraye, Urs B. Leu, Scott Mandelbrote, Suzanne Marchand, Margaret Meserve, Paul Michel, Peter N. Miller, Glenn W. Most, Martin Mulsow, Paul Nelles, William R. Newman, C. Philipp E. Nothaft, Laurie Nussdorfer, Jürgen Oelkers, Brian W. Ogilvie, Nicholas Popper, Virginia Reinburg, Daniel Rosenberg, Sarah Gwyneth Ross, Ingrid D. Rowland, David Ruderman, Hester Schadee, Wilhelm Schmidt-Biggemann, Richard Serjeantson, Salvatore Settis, Jonathan Sheehan, William H. Sherman, Nancy Siraisi, Jacob Soll, Peter Stallybrass, Daniel Stolzenberg, N.M. Swerdlow, Dirk van Miert, Kasper van Ommen, Arnoud Visser, Joanna Weinberg and Helmut Zedelmaier"--Provided by publisher
