Engineering Papers⌕ Search

Engineering topics

Fakra, Sirine C.

Publications and source records attributed to Fakra, Sirine C..

8 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism

Abstract Background Biofilms in sulfide-rich springs present intricate microbial communities that play pivotal roles in biogeochemical cycling. We studied chemoautotrophically based biofilms that host diverse CPR bacteria and grow in sulfide-rich springs to investigate microbial controls on biogeochemical cycling. Results Sulfide springs biofilms were investigated using bulk geochemical analysis, genome-resolved metagenomics, and scanning transmission X-ray microscopy (STXM) at room temperature and 87 K. Chemolithotrophic sulfur-oxidizing bacteria, including Thiothrix and Beggiatoa , dominate the biofilms, which also contain CPR Gracilibacteria, Absconditabacteria, Saccharibacteria, Peregrinibacteria, Berkelbacteria, Microgenomates, and Parcubacteria. STXM imaging revealed ultra-small cells near the surfaces of filamentous bacteria that may be CPR bacterial episymbionts. STXM and NEXAFS spectroscopy at carbon K and sulfur L 2,3 edges show that filamentous bacteria contain protein-encapsulated spherical elemental sulfur granules, indicating that they are sulfur oxidizers, likely Thiothrix . Berkelbacteria and Moranbacteria in the same biofilm sample are predicted to have a novel electron bifurcating group 3b [NiFe]-hydrogenase, putatively a sulfhydrogenase, potentially linked to sulfur metabolism via redox cofactors. This complex could potentially contribute to symbioses, for example, with sulfur-oxidizing bacteria such as Thiothrix that is based on cryptic sulfur cycling. One Doudnabacteria genome encodes adjacent sulfur dioxygenase and rhodanese genes that may convert thiosulfate to sulfite. We find similar conserved genomic architecture associated with CPR bacteria from other sulfur-rich subsurface ecosystems. Conclusions Our combined metagenomic, geochemical, spectromicroscopic, and structural bioinformatics analyses of biofilms growing in sulfide-rich springs revealed consortia that contain CPR bacteria and sulfur-oxidizing Proteobacteria, including Thiothrix , and bacteria from a new family within Beggiatoales. We infer roles for CPR bacteria in sulfur and hydrogen cycling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Mineralogical, magnetic and geochemical data constrain the pathways and extent of weathering of mineralized sedimentary rocks

The oxidative weathering of sulfidic rock can profoundly impact watersheds through the resulting export of acidity and metals. Weathering leaves a record of mineral transformation, particularly involving minor redox-sensitive phases, that can inform the development of conceptual and quantitative models. In sulfidic sedimentary rocks, however, variations in depositional history, diagenesis and mineralization can change or overprint the distributions of these trace minerals, complicating the interpretation of weathering signatures. Here we show that a combination of bulk mineralogical and geochemical techniques, micrometer-resolution X-ray fluorescence microprobe analysis and rock magnetic measurements, applied to drill core samples and single weathered fractures, can provide data that enable the development of a geochemically consistent weathering model. This work focused on one watershed in the Upper Colorado River Basin sitting within the Mesaverde Formation, a sedimentary sandstone bedrock with disseminated sulfide minerals, including pyrite and sphalerite, that were introduced during diagenesis and subsequent magmatic-hydrothermal mineralization. Combined analytical methods revealed the pathways of iron (Fe), carbonate and silicate mineral weathering and showed how pH controls element retention or release from the actively weathering fractured sandstone. Drill core logging, whole rock X-ray diffraction, and geochemical measurements document the progression from unweathered rock at depth to weathered rock at the surface. X-ray microprobe analyses of a 1-cm size weathering profile along a fracture surface are consistent with the mobilization of Fe(II) and Fe(III) into acidic pore water from the dissolution of primary pyrite, Fe-sphalerite, chlorite, and minor siderite and pyrrhotite. These reactions are followed by the precipitation of secondary minerals such as of goethite and jarosite, a Fe-(oxyhydr)oxide and hydrous Fe(III) sulfate, respectively. Microscale analyses also helped explain the weathering reactions responsible for the mineralogical transformations observed in the top and most weathered section of the drill core. For example, dissolution of feldspar and chlorite neutralizes the acidity generated by Fe and sulfide mineral oxidation, oversaturating the solution in both Fe-oxides. The combination of X-ray spectromicroscopy and magnetic measurements show that the Fe(III) product is goethite, mainly present either as a coating on fracture surfaces in the actively weathering region of the core or more homogeneously contained within the unconsolidated regolith at the top of the core. Low-temperature magnetic data reveal the presence of ferromagnetic Fe-sulfide pyrrhotite that, although it occurs at trace concentrations, could provide a qualitative proxy for unweathered sulfide minerals because the loss of pyrrhotite is associated with the onset of oxidative weathering. Pyrrhotite loss and goethite formation are detectable through room-temperature magnetic coercivity changes, suggesting that rock magnetic measurements can determine weathering intensity in rock samples at many scales. In conclusion, this work contributes evidence that the weathering of sulfidic sedimentary rocks follows a geochemical pattern in which the abundance of sulfide minerals controls the generation of acidity and dissolved elements, and the pH-dependent mobility of these elements controls their export to the ground- and surface-water.

58 GEOSCIENCES↗
DOE OSTI2022

The transformation of U(VI) and V(V) in carnotite group minerals during dissimilatory respiration by a metal reducing bacterium

Recent results from laboratory and field studies support that dissimilatory metal reducing (DMR) bacteria influence the fate and transport of uranium in anaerobic subsurface environments. To date, most research efforts have focused on the reduction of soluble U(VI) by DMR bacteria to form insoluble uraninite (UO 2 ). Subsurface environments harbor, however, large reservoirs of U(VI) in solid or mineral form. Uranium that is structure-bound in minerals is expected to be more refractory to microbial reduction than soluble U, based on analogy with Fe respiration. The reducibility of U(VI) could impact the fate of U(IV) by controlling mineral precipitation reactions, which has implications for the long-term immobilization of U in subsurface environments. Here, we studied anoxic cultures of Shewanella putrefaciens CN32 incubated with natural carnotite-group minerals by X-ray diffraction, electron microscopy, scanning transmission X-ray microscopy (STXM). Near-edge X-ray absorption fine structure (NEXAFS) spectroscopy measurements at U-N 4,5 , V-L 2,3 , and O-K edges on cultures incubated up to 10 months show that V(V) was reduced to V(IV), whereas U was not reduced. In contrast, V(V) and U(VI) in solution were both completely reduced to lower oxidation states by CN32, as precipitates within the exopolymer surrounding the bacteria. Assays for the toxicity of U and V to CN32 showed that biofilm formation was stimulated at 0.001 M U(VI), and growth was inhibited at concentrations of U(VI) greater than 0.001 M. Vanadium did not inhibit growth or stimulate biofilm formation at any concentration tested. Investigations of the bacteria-mineral and bacteria-metal interface at the nanometer and molecular scales provide new insights into the co-respiration of V and U that help explain their biogeochemical cycling and have implications for subsurface bioremediation of these elements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Nanoparticle cellular internalization is not required for RNA delivery to mature plant leaves

Rapidly growing interest in the nanoparticle-mediated delivery of DNA and RNA to plants requires a better understanding of how nanoparticles and their cargoes translocate in plant tissues and into plant cells. However, little is known about how the size and shape of nanoparticles influence transport in plants and the delivery efficiency of their cargoes, limiting the development of nanotechnology in plant systems. In this study we employed non-biolistically delivered DNA-modified gold nanoparticles (AuNPs) of various sizes (5-20 nm) and shapes (spheres and rods) to systematically investigate their transport following infiltration into Nicotiana benthamiana leaves. Generally, smaller AuNPs demonstrated more rapid, higher and longer-lasting levels of association with plant cell walls compared with larger AuNPs. We observed internalization of rod-shaped but not spherical AuNPs into plant cells, yet, surprisingly, 10 nm spherical AuNPs functionalized with small-interfering RNA (siRNA) were the most efficient at siRNA delivery and inducing gene silencing in mature plant leaves. These results indicate the importance of nanoparticle size in efficient biomolecule delivery and, counterintuitively, demonstrate that efficient cargo delivery is possible and potentially optimal in the absence of nanoparticle cellular internalization. Additionally, our results highlight nanoparticle features of importance for transport within plant tissues, providing a mechanistic overview of how nanoparticles can be designed to achieve efficacious biocargo delivery for future developments in plant nanobiotechnology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Ligand-Free Processable Perovskite Semiconductor Ink

We report traditional covalent semiconductors require complex processing methods for device fabrication due to their high cohesive energies. Here, we develop a stable, ligand-free perovskite semiconductor ink that can be used to make patterned semiconductor-based optoelectronics in one step. The perovskite ink is formed via the dissolution of crystals of vacancy-ordered double perovskite Cs 2 TeX 6 (X = Cl - , Br - , I - ) in polar aprotic solvents, leading to the stabilization of isolated [TeX 6 ] 2- octahedral anions and free Cs + cations without the presence of ligands. The stabilization of the fundamental perovskite ionic octahedral building blocks in solution creates multifunctional inks with the ability to reversibly transform between the liquid ink and the solid-state perovskite crystalline system in air within minutes. These easily processable inks can be patterned onto various materials via dropcasting, spraying or painting, and stamping, highlighting the crucial role of solvated octahedral complexes toward the rapid formation of phase-pure perovskite structures in ambient conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Origin of enhanced water oxidation activity in an iridium single atom anchored on NiFe oxyhydroxide catalyst

The efficiency of the synthesis of renewable fuels and feedstocks from electrical sources is limited, at present, by the sluggish water oxidation reaction. Single-atom catalysts (SACs) with a controllable coordination environment and exceptional atom utilization efficiency open new paradigms toward designing high-performance water oxidation catalysts. Here, using operando X-ray absorption spectroscopy measurements with calculations of spectra and electrochemical activity, we demonstrate that the origin of water oxidation activity of IrNiFe SACs is the presence of highly oxidized Ir single atom (Ir 5.3+ ) in the NiFe oxyhydroxide under operating conditions. We show that the optimal water oxidation catalyst could be achieved by systematically increasing the oxidation state and modulating the coordination environment of the Ir active sites anchored atop the NiFe oxyhydroxide layers. Based on the proposed mechanism, we have successfully anchored Ir single-atom sites on NiFe oxyhydroxides (Ir 0.1 /Ni 9 Fe SAC) via a unique in situ cryogenic–photochemical reduction method that delivers an overpotential of 183 mV at 10 mA · cm – 2 and retains its performance following 100 h of operation in 1 M KOH electrolyte, outperforming the reported catalysts and the commercial IrO 2 catalysts. These findings open the avenue toward an atomic-level understanding of the oxygen evolution of catalytic centers under in operando conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗