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  • Liermann, Laura J.
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  • 1
    Language: English
    In: Geochimica et Cosmochimica Acta, Dec 15, 2012, Vol.99, p.18(21)
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.gca.2012.09.029 Byline: Tiffany Yesavage (a), Matthew S. Fantle (a), Jeffrey Vervoort (b), Ryan Mathur (c), Lixin Jin (d), Laura J. Liermann (a), Susan L. Brantley (a) Abstract: During weathering, Fe in primary minerals is solubilized by ligands and/or reduced by bacteria and released into soil porewaters. Such Fe is then removed or reprecipitated in soils. To understand these processes, we analyzed Fe chemistry and isotopic composition in regolith of the Shale Hills watershed, a Critical Zone Observatory in central Pennsylvania overlying iron-rich shale of the Rose Hill Formation. Elemental concentrations were measured in soil from a well-drained catena on a planar hillslope on the south side of the catchment. Based upon X-ray diffraction and bulk elemental data, loss of Fe commences as clay begins to weather [approximately equal to]15cm below the depth of auger-refusal. More Fe(III) was present than Fe(II) in all soil samples from the ridge top to the valley floor. Both total and ferrous iron are depleted from the land surface of catena soils relative to the bedrock. Loss of ferrous Fe is attributed mostly to abiotic or biotic oxidation. Loss of Fe is most likely due to transport of micron-sized particles that are not sampled by porous-cup lysimeters, but which are sampled in stream and ground waters. The isotopic compositions ([delta].sup.56Fe, relative to IRMM-014) of bulk Fe and 0.5N HCl-extracted Fe (operationally designed to remove amorphous Fe (oxyhydr)oxides) range between -0.3a[degrees] and +0.3a[degrees], with [DELTA].sup.56Fe.sub.bulk-extractable values between [approximately equal to]0.2a[degrees] and 0.4a[degrees]. Throughout the soils along the catena, [delta].sup.56Fe signatures of both bulk Fe and HCl-extracted Fe become isotopically lighter as the extent of weathering proceeds. The isotopic trends are attributed to one of two proposed mechanisms. One mechanism involves Fe fractionation during mobilization of Fe from the parent material due to either Fe reduction or ligand-promoted dissolution. The other mechanism involves fractionation during immobilization of Fe (oxyhydr)oxides. If the latter mechanism is true, then shale - which comprises one quarter of continental rocks - could be an important source of isotopically heavy Fe for rivers. Author Affiliation: (a) Department of Geosciences, The Pennsylvania State University, University Park, PA 16802, USA (b) School of Earth and Environmental Sciences, Washington State University, Pullman, WA 99164, USA (c) Department of Geology, Juniata College, Huntington, PA 16652, USA (d) Department of Geological Sciences, University of Texas at El Paso, TX 79968, USA Article History: Received 11 January 2012; Accepted 17 September 2012 Article Note: (miscellaneous) Associate editor: Jerome Gaillardet
    Keywords: Shales -- Analysis
    ISSN: 0016-7037
    Source: Cengage Learning, Inc.
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  • 2
    Language: English
    In: Geochimica et Cosmochimica Acta, 15 December 2012, Vol.99, pp.18-38
    Description: During weathering, Fe in primary minerals is solubilized by ligands and/or reduced by bacteria and released into soil porewaters. Such Fe is then removed or reprecipitated in soils. To understand these processes, we analyzed Fe chemistry and isotopic composition in regolith of the Shale Hills watershed, a Critical Zone Observatory in central Pennsylvania overlying iron-rich shale of the Rose Hill Formation. Elemental concentrations were measured in soil from a well-drained catena on a planar hillslope on the south side of the catchment. Based upon X-ray diffraction and bulk elemental data, loss of Fe commences as clay begins to weather ∼15 cm below the depth of auger-refusal. More Fe(III) was present than Fe(II) in all soil samples from the ridge top to the valley floor. Both total and ferrous iron are depleted from the land surface of catena soils relative to the bedrock. Loss of ferrous Fe is attributed mostly to abiotic or biotic oxidation. Loss of Fe is most likely due to transport of micron-sized particles that are not sampled by porous-cup lysimeters, but which are sampled in stream and ground waters. The isotopic compositions (δ Fe, relative to IRMM-014) of bulk Fe and 0.5 N HCl-extracted Fe (operationally designed to remove amorphous Fe (oxyhydr)oxides) range between −0.3‰ and +0.3‰, with Δ Fe values between ∼0.2‰ and 0.4‰. Throughout the soils along the catena, δ Fe signatures of both bulk Fe and HCl-extracted Fe become isotopically lighter as the extent of weathering proceeds. The isotopic trends are attributed to one of two proposed mechanisms. One mechanism involves Fe fractionation during mobilization of Fe from the parent material due to either Fe reduction or ligand-promoted dissolution. The other mechanism involves fractionation during immobilization of Fe (oxyhydr)oxides. If the latter mechanism is true, then shale – which comprises one quarter of continental rocks – could be an important source of isotopically heavy Fe for rivers.
    Keywords: Geology
    ISSN: 0016-7037
    E-ISSN: 1872-9533
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  • 3
    Language: English
    In: Soil Science Society of America journal, 2011, Vol.75(2), pp.348-356
    Description: Quartz diorite bedrock underlying the Luquillo Mountains of eastern Puerto Rico undergoes weathering at one of the fastest documented rates for granitic rocks in the world. Although tropical temperatures and precipitation promote rapid weathering in this location, increased bacterial densities in the regolith immediately above the bedrock suggest that microorganisms contribute to mineral weathering as well. Deep saprolite and saprock samples were obtained at the bedrock interface in an upland location (Guaba Ridge) in the Rio Icacos watershed for examination by environmental scanning electron microscopy (ESEM). In ESEM images, mineral nanotubes were observed to occur frequently in association with coccus- and rod-shaped structures resembling bacteria. These nanotubes (50–140-nm width and 150–2700-nm length) were identified as halloysite using transmission electron microscopy. Observations of multiple nanotubes on the surfaces of an individual cell are consistent with the cell's exterior functional groups interacting with Si in pore water to facilitate halloysite nucleation. We propose that one mechanism by which bacteria contribute to the rapid weathering of quartz diorite minerals in this regolith is by lowering the free energy for secondary mineral formation. The presence of bacterial surfaces may result in more rapid removal of Si from solution, thereby increasing the dissolution rates of primary minerals. ; p. 348-356.
    Keywords: Transmission Electron Microscopy ; Bedrock ; Diorite ; Watersheds ; Silicon ; Weathering ; Temperature ; Saprolite ; Mountains ; Bacteria ; Nanotubes ; Quartz ; Halloysite ; Scanning Electron Microscopy ; Regolith ; Energy
    ISSN: 0361-5995
    E-ISSN: 14350661
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  • 4
    In: FEMS Microbiology Ecology, 2012, Vol. 79(1), pp.218-228
    Description: G eobacter sulfurreducens exists in the subsurface and has been identified in sites contaminated with radioactive metals, consistent with its ability to reduce metals under anaerobic conditions. The natural state of organisms in the environment is one that lacks access to high concentrations of nutrients, namely electron donors and terminal electron acceptors (TEAs). Most studies have investigated G . sulfurreducens under high-nutrient conditions or have enriched for it in environmental systems via acetate amendments. We replicated the starvation state through long-term batch culture of G . sulfurreducens , where both electron donor and TEA were scarce. The growth curve revealed lag, log, stationary, death, and survival phases using acetate as electron donor and either fumarate or iron(III) citrate as TEA. In survival phase, G . sulfurreducens persisted at a constant cell count for as long as 23 months without replenishment of growth medium. G eobacter sulfurreducens demonstrated an ability to acquire a growth advantage in stationary-phase phenotype (GASP), with strains derived from subpopulations from death- or survival phase being able to out-compete mid-log-phase populations when co-cultured. The molecular basis for GASP was not because of any detectable mutation in the rpoS gene (GSU1525) nor because of a mutation in a putative homolog to E scherichia coli lrp , GSU3370.
    Keywords: Dissimilatory Iron Reduction ; Starvation ; Stationary Phase
    ISSN: 01686496
    E-ISSN: 1574-6941
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  • 5
    Language: English
    In: Geomicrobiology Journal, 03 July 2015, Vol.32(6), pp.494-510
    Description: Fe oxidation is often the first chemical reaction that initiates weathering and disaggregation of intact bedrock into regolith. Here we explore the use of pyrosequencing tools to test for evidence that bacteria participate in these reactions in deep regolith. We analyze regolith developed on...
    Keywords: Biogeochemical Cycling ; Community Structure ; Iron-Oxidizing Bacteria ; Subsurface Microbiology ; Biology ; Chemistry
    ISSN: 0149-0451
    E-ISSN: 1521-0529
    Source: Taylor & Francis (Taylor & Francis Group)
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  • 6
    Language: English
    In: Chemical Geology, 2011, Vol.281(3), pp.167-180
    Description: Isotopic fractionation of Fe and Mo during weathering could contribute toward the isotopic signatures of river and ocean waters. To investigate weathering processes, batch experiments were carried out at pH 6 under oxygenated conditions to investigate the influence of a nitrogen-fixing soil bacterium and organic ligands on the extent and isotopic signature of Fe and Mo release from two Pennsylvania shales with different mineralogies: an olive to grey shale (Rose Hill) and a black shale (Marcellus). Results of these studies showed that Fe and Mo were mainly released from illite, chlorite/vermiculite, and Fe oxides in the RHS and from pyrite in the MS. Dissolution rates of the clays estimated from our batch experiments are broadly consistent with published estimates. Release of Fe from both shales was only enhanced by the hydroxamate siderophore desferrioxamine B (DFAM). In contrast, none of the treatments enhanced release of Mo. Furthermore, release of this metal was measurable only for the black shale. For both shales, Fe that was released in the presence of DFAM was depleted in Fe as compared to the bulk rock. In contrast, leachate solutions were enriched in the heavier Mo isotope as compared to the bulk Marcellus in all experiments with and without organic ligands and the bacterium. The isotopic fractionations in Fe and Mo are broadly consistent with previously reported fractionation effects during sorption onto precipitating Fe,Mn oxides. The observed Mo isotope fractionation is also consistent with all published studies of rivers, i.e., riverine Mo is enriched in heavy Mo isotopes. The observed Fe isotope fractionation is likewise consistent with published studies for some rivers, i.e., riverine Fe is sometimes depleted in Fe. Our experimental results are consistent with sorption of Fe and Mo onto Fe (oxyhydr)oxides during weathering as a possible explanation for the isotopic signatures of these metals in many rivers. ► Batch dissolution experiments conducted using two distinct end-member shales. ► Fe released from clay minerals and Fe oxides in Rose Hill (brown) shale. ► Fe and Mo released from pyrite in Marcellus (black) shale. ► Fe release enhanced by siderophore, isotopically depleted compared to bulk rock. ► Mo released from Marcellus shale isotopically enriched under all conditions.
    Keywords: Shale Weathering ; Iron Isotopes ; Molybdenum Isotopes ; Organic Ligands ; Bacteria ; Geology
    ISSN: 0009-2541
    E-ISSN: 1872-6836
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  • 7
    Language: English
    In: Geomicrobiology Journal, 11/03/2015, pp.00-00
    Description: The natural environment of Geobacter sulfurreducens is oligotrophic and described as limiting in both electron donors and terminal electron acceptors (TEA). In previous studies we examined the effects of long-term TEA (fumarate) limitation, and in this study we examine long-term batch cultures under limiting electron donor. The microorganism survived under long-term electron donor (acetate) starvation, maintaining a stable population of ∼1–2× 10 8 cells mL −1 for 〉650 days. Proteins that varied in abundance with a high level of statistical significance ( p 〈 0.05) for stages between mid-log to survival phase (acetate starved) were identified using iTRAQ based mass spectroscopy. The most highly represented proteins that significantly increased in level in the survival phase cells are generally membrane-associated and are involved in energy metabolism and protein fate. These results document that changes in the outer and cytoplasmic membranes may help G. sulfurreducens survive during starvation through detection and transport of nutrients into the cell. A sizeable portion of the identified proteins with unknown or hypothetical function further suggest that much of the biological process involved in survival have yet to be fully understood. G. sulfurreducens was also able to survive under long-term TEA-starvation conditions with ferric citrate as TEA and maintained a stable population of 1.5–3 × 10 7 cells mL −1 for 〉650 days. We also found that survival phase cells from fumarate-limiting conditions were able to quickly resuscitate and reduce metal such as ferric iron as compared to the mid-log phase cells. Article just-accepted.
    Keywords: Article ; Starvation Phase ; Survival Strategy ; Electron Donor Limitation ; Acetate Starvation ; Itraq ; Lc-Ms/Ms ; Proteomics ; Uranium Bioremediation ; Iron Reduction ; Resuscitation ; Revival ; Ferric Citrate Starvation ; Electron Acceptor Starvation;
    ISSN: 0149-0451
    E-ISSN: 1521-0529
    Source: Informa - Taylor & Francis (via CrossRef)
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  • 8
    Language: English
    In: Geomicrobiology Journal, 01 November 2012, Vol.29(9), pp.792-803
    Description: Microbe-mineral associations in regolith overlying granodiorite bedrock (4.6-4.9 m depth) from the Luquillo Experimental Forest, Puerto Rico, were imaged with confocal scanning laser microscopy at a novel scale of 400X magnification. After adding BacLight™ stain, proportionally more surface...
    Keywords: Regolith, Confocal Microscopy, Iron Oxidation, Saprolite, 16s Rrna ; Biology ; Chemistry
    ISSN: 0149-0451
    E-ISSN: 1521-0529
    Source: Taylor & Francis (Taylor & Francis Group)
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  • 9
    Language: English
    In: Journal of Proteome Research, 04 October 2013, Vol.12(10)
    Description: The bioavailability of terminal electron acceptors (TEAs) and other substrates affects the efficiency of subsurface bioremediation. While it is often argued that microorganisms exist under "feast or famine", in the laboratory most organisms are studied under "feast" conditions, whereas they typically encounter "famine" in nature. The work described here aims to understand the survival strategies of the anaerobe Geobacter sulfurreduces under TEA-starvation conditions. Cultures were starved for TEA and at various times sampled to perform global comparative proteomic analysis using iTRAQ to obtain insight into the dynamics of change in proteins/enzymes expression associated with change in nutrient availability/environmental stress. Proteins varying in abundance with a high level of statistical significance (p 〈 0.05) were identified to understand how cells change from midlog to (i) stationary phase and (ii) conditions of prolonged starvation (survival phase). The most highly represented and significantly up-regulated proteins in the survival phase cells are involved in energy metabolism, cell envelope, and transport and binding functional categories. The majority of the proteins were predicted to be localized in the cell membranes. These results document that changes in the outer and cytoplasmic membranes are needed for survival of Geobacter under starvation conditions. The cell shuts down anabolic processes and becomes poised, through changes in its membrane proteins, to sense nutrients in the environment, to transport nutrients into the cell, and to detect or utilize TEAs that are encountered. Under TEA-limiting conditions, the cells turned from translucent white to red in color, indicating higher heme content. The increase in heme content supported proteomics results showing an increase in the number of cytochromes involved in membrane electron transport during the survival phase. The cell is also highly reduced with minimal change in energy charge (ATP to total adenine nucleotide ratio). Nonetheless, these proteomic and biochemical results indicate that even under TEA starvation cells remain poised for bioremediation.
    Keywords: Chemistry
    ISSN: 1535-3893
    E-ISSN: 1535-3907
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  • 10
    Language: English
    In: Geochimica et Cosmochimica Acta, 2004, Vol.68(15), pp.3189-3204
    Description: Fe released into solution is isotopically lighter (enriched in the lighter isotope) than hornblende starting material when dissolution occurs in the presence of the siderophore desferrioxamine mesylate (DFAM). In contrast, Fe released from goethite dissolving in the presence of DFAM is isotopically unchanged. Furthermore, Delta (super 56) Fe (sub solution-hornblende) for Fe released to solution in the presence of ligands varies with the affinity of the ligand for Fe. The extent of isotopic fractionation of Fe released from hornblende also increases when experiments are agitated continuously. The Fe isotope fractionation observed during hornblende dissolution with organic ligands is attributed predominantly to retention of (super 56) Fe in an altered surface layer, while the lack of isotopic fractionation during goethite dissolution in DFAM is consistent with the lack of an altered layer. When a siderophore-producing soil bacterium is added to the system (without added organic ligands), Fe released to solution from both hornblende and goethite differs isotopically from Fe in the bulk mineral: Delta (super 56) Fe (sub solution-starting material) = -0.56+ or -0.19 (hornblende) and -1.44+ or -0.16 (goethite). Increased isotopic fractionation is attributed in this case to the fact that as bacterial respiration depletes the system in oxygen and aqueous Fe is reduced, equilibration between aqueous ferrous and ferric iron creates a pool of isotopically heavy ferric iron that is assimilated by bacterial cells. Adsorption of isotopically heavy ferrous iron (Fe(II) enriched in the heavier isotope) or precipitation of isotopically heavy Fe minerals may also contribute to observed fractionations. To test whether these Fe isotope signatures are recorded in natural systems, we also investigated extractions of samples of soils from which the bacteria were isolated. These extractions show variability in the isotopic signatures of exchangeable Fe and Fe oxyhydroxide fractions from one soil sample to another, but exchangeable Fe is observed to be lighter than Fe in soil Fe oxyhydroxides and hornblende. This observation is consistent with isotopically light Fe-organic complexes in soil pore water derived from the Fe-silicate starting materials in the presence of growing microorganisms, as documented in experiments reported here. The contributions from phenomena including organic ligand-promoted nonstoichiometric dissolution of Fe silicates, uptake of ferric iron by organisms, adsorption of isotopically heavy ferrous iron, and precipitation of iron minerals should create complex isotopic signatures in soils. Better understanding of these processes and the timescales over which they contribute to fractionation is needed.
    Keywords: Geology
    ISSN: 0016-7037
    E-ISSN: 1872-9533
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