| 1. |
- Anderson, Craig, 1976, et al.
(författare)
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In situ ecological development of a bacteriogenic iron oxide-producing microbial community from a subsurface granitic rock environment
- 2006
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Ingår i: Geobiology. - : Wiley. - 1472-4677 .- 1472-4669. ; 4:1, s. 29-42
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Tidskriftsartikel (refereegranskat)abstract
- The initial development and diversity of an in situ subsurface microbial community producing bacteriogenic iron oxides (BIOS) were investigated at the initiation of biofilm growth (2-month period) and after a 1-year period of undisturbed growth. Water chemistry data, samples of iron encrusted biofilm material and groundwater were collected from BRIC (BIOS reactor, in situ, continuous flow) apparatuses installed 297 m below sea level at the Äspö Hard Rock Laboratory (HRL) in south eastern Sweden. Comparisons between the BIOS BRIC system and an anaerobic control (AC) BRIC revealed that water mixing at the inflow leads to profuse development of BIOS related to a slightly elevated level of O2 (up to 0.3 mg L-1 at the transition zone between BIOS development and non-development) and elevated Eh (>120 mV) in the first 70 mm of water depth. Decreases in dissolved and particulate iron were connected to the visible appearance of BIOS biofilms. The basic phylogenetic diversity of this site was evaluated using amplified ribosomal DNA restriction enzyme analysis (ARDRA), denaturing gradient gel electrophoresis (DGGE) and partial sequencing of 16S rDNA. From 67 clones that were positive for 16S rDNA inserts, a total of 42 different ARDRA profiles were recognized, representing four bacterial phyla and 14 different metabolic lifestyles. DGGE profiles indicated that there are differences in the representative bacteria when considering either BIOS biofilms or groundwater. DGGE also indicated that the DNA extraction protocols and any polymerase chain reaction biases were consistent. Bacterial metabolic groups associated with indirect metal adsorption and reduction along with bacteria utilizing many alternative electron acceptors were strongly represented within the clones. This study indicates that the microbial diversity of BIOS is greater than previously thought.
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| 2. |
- Anderson, Craig, 1976, et al.
(författare)
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In situ growth of Gallionella biofilms and partitioning of lanthanides and actinides between biological material and ferric oxyhydroxides
- 2003
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Ingår i: Geobiology. - : Wiley. - 1472-4677 .- 1472-4669. ; 1:2, s. 169-178
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Tidskriftsartikel (refereegranskat)abstract
- Gallionella ferruginea is an iron-oxidizing chemolithotrophic micro-organism that lives in low-oxygen conditions (0.1–1.5 mg L-1 saturation). It produces a stalk structure from the concave side of the cell depending on population development, pH and redox conditions. After Gallionella oxidizes ferrous iron, bacteriogenic iron oxides (BIOS) precipitate on the stalk material and over time the stalks and/or the precipitated BIOS attenuate trace metals from surrounding groundwater. Gallionella ferruginea biofilms were cultured in situ in an artificial channel (2000 × 300 × 250 mm) using groundwater sourced from a borehole 297 m below sea level in the Äspö Hard Rock Laboratory in southern Sweden. The pH of the groundwater in the channels was always between 7.4 and 7.7 with oxygen saturation below 1.5 mg L-1 and Eh between 100 and 200 mV. Oxygen eventually declined to <0.3 mg L-1, terminating prolific biofilm growth. Biofilms formed within 2 weeks and were sampled every 2 weeks over 3 months. Cell number, stalk length and ferric iron concentration were measured for each sample and trace metal concentration was measured by inductively coupled plasma mass spectrometry. Results from well-developed in situ biofilms suggest that Gallionella could concentrate metals at levels up to 1 × 103-fold higher than found within the host rock and more than 1 × 106 times the levels found in the groundwater. These new experiments were used to support the results from the well-developed biofilms and to relate biofilm development and population characteristics to metal attenuation. After 3 months, rare earth element (REE) plots indicated that BIOS can accumulate metals at levels up to 1 × 104-fold higher than found in the groundwater and fractionate heavy rare earth elements over light rare earth elements. Generally the presence of the organic phase promotes the adsorption of all lanthanides and actinides that are not adsorbed by the inorganic phase. The iron oxides are directly correlated with stalk length (R = 0.96), indicating that rapid REE and actinide adsorption requires both iron oxides and a nucleating biological structure for the iron oxides.
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| 3. |
- Nielsen, M.E., et al.
(författare)
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Microbial nitrate respiration of lactate at in situ conditions in ground water from a granitic aquifer situated 450 m underground
- 2006
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Ingår i: Geobiology. - : Wiley. - 1472-4677 .- 1472-4669. ; 4:1, s. 43-52
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Tidskriftsartikel (refereegranskat)abstract
- There is widespread interest in developing methods to investigate in situ microbial activity in subsurface environments. Novel experiments based on single borehole push–pull methods were conducted to measure in situ microbial activity at the Äspö Hard Rock Laboratory (HRL). Microbial nitrate reduction and lactate consumption were measured at in situ conditions at a depth of 450 m in the HRL tunnel. A circulation system was used to circulate ground water from the aquifer through pressure-maintaining flow cells containing coupons for biofilm growth. The system allows microbial investigations at in situ pressure, temperature and chemistry. Four experiments were conducted in which a combination of a conservative tracer, nitrate and lactate was injected into the circulation system. Rate of nitrate utilization was 5 µm h-1 without lactate and 13 µm h-1 with lactate. Lactate consumption increased from 30 to 50 µm h-1 with the addition of an exogenous electron acceptor (nitrate). Attached and unattached cells were enumerated using epifluorescence microscopy to calculate cell-specific rates of activity. The biofilm had an average cell density of 1 × 106 cells cm-2 and there was an average of 6 × 105 unattached cells mL-1 in circulation. Cell-specific rates of lactate consumption were higher than previously reported using radiotracer methods in similar environments. The differences highlight the importance of conducting microbial investigations at in situ conditions. The results demonstrate that an indigenous community of microbes survives at a depth of 450 m in the Fennoscandian shield aquifer with the potential to oxidize simple organic molecules such as lactate.
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| 4. |
- Edberg, Frida, et al.
(författare)
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Mobilization of metals from uranium mine waste : the role of pyoverdines produced by Pseudomonas fluorescens
- 2010
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Ingår i: Geobiology. - : Wiley. - 1472-4677 .- 1472-4669. ; 8:4, s. 278-292
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Tidskriftsartikel (refereegranskat)abstract
- Microorganisms produce chelating agents, such as siderophores and other ligands, which allow them to mobilize and scavenge essential elements from the environment when bioavailability is low. To better understand the effects of biologically mediated leaching of metals from mine waste, Pseudomonas fluorescens was cultivated in the presence of processed ore from the former uranium mine in Ranstad, southern Sweden. Light conditions, the concentration of the mineral source and oxygen availability were varied. The presence of ore in the culture flasks enhanced bacterial growth and raised the pH of the culture medium. Increasing the amount of ore or enhancing aeration of the medium further encouraged cell growth and pH rise. Bacteria mobilized Fe, Ni and Co from the ore. Fe-siderophore complexes were detected and estimated to be present at approximately 9 μm. In the presence of bacteria and light, dissolved Fe and U concentrations were higher compared to dark conditions. Increasing the amount of ore resulted in higher dissolved Ni concentrations but lower dissolved Fe, most likely due to precipitate formation. Data from this study support siderophore production by bacteria that allowed mobilization of essential nutrients from the processed ore. However, the availability of potentially toxic metals like Ni and U may also be enhanced. Microbial-promoted mobilization could contribute to leaching of toxic metals in current and historic mining areas. This process should be considered during design and implementation of remediation projects where trace metals are of environmental concern.
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| 5. |
- Ernest, Chi Fru, 1972
(författare)
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Constraints in the colonization of natural and engineered subterranean igneous rock aquifers by aerobic methane-oxidizing bacteria inferred by culture analysis
- 2008
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Ingår i: Geobiology. - : Wiley. - 1472-4677 .- 1472-4669.
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Tidskriftsartikel (refereegranskat)abstract
- The aerobic methane-oxidizing bacteria (MOB) are suggested to be important for the removal of oxygen from subterranean aquifers that become oxygenated by natural and engineering processes. This is primarily because MOB are ubiquitous in the environment and in addition reduce oxygen efficiently. The biogeochemical factors that will control the success of the aerobic MOB in these kinds of underground aquifers remain unknown. In this study, viable and cultivable MOB occurring at natural and engineered deep granitic aquifers targeted for the disposal of spent nuclear fuel (SNF) in the Fennoscandian Shield (~3–1000 m) were enumerated. The numbers were correlated with in situ salinity, methane concentrations, conductivity, pH, and depth. A mixed population habiting freshwater aquifers (~3–20 m), a potential source for the inoculation of MOB into the deeper aquifers was tested for tolerance to NaCl, temperature, pH, and an ability to produce cysts and exospores. Extrapolations show that due to changing in situ parameters (salinity, conductivity, and pH), the numbers of MOB in the aquifers dropped quickly with depth. A positive correlation between the most probable numbers of MOB and methane concentrations was observed. Furthermore, the tolerance-based tests of cultured strains indicated that the MOB in the shallow aquifers thrived best in mesophilic and neutrophilic conditions as opposed to the hyperthermophilic and alkaliphilic conditions expected to develop in an engineered subterranean SNF repository. Overall, the survival of the MOB both quantitatively and physiologically in the granitic aquifers was under the strong influence of biogeochemical factors that are strongly depth-dependent.
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| 6. |
- Holm, Nils G.
(författare)
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The significance of Mg in prebiotic geochemistry
- 2012
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Ingår i: Geobiology. - : Wiley. - 1472-4677 .- 1472-4669. ; 10:4, s. 269-279
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Forskningsöversikt (refereegranskat)abstract
- Magnesium plays a special role in biochemistry because of its ability to coordinate six oxygen atoms efficiently in its first coordination shell. Such oxygen atoms may be part of one or two charged oxyanions, which means that Mg2+ can, for instance, tie together two different phosphate groups that are located at distance from each other in a macromolecule, and in this way be responsible for the folding of molecules like RNA. This property of Mg2+ also helps the stabilization of diphosphate and triphosphate groups of nucleotides, as well as promoting the condensation of orthophosphate to oligophosphates, like pyrophosphate and trimetaphosphate. Borates, on the other hand, are known to promote the formation of nucleobases and carbohydrates, ribose in particular, which is yet another constituent of nucleotides. The oldest borate minerals that we find on Earth today are magnesium borates. Dissolved borate stabilizes pentose sugars by forming complexes with cis-hydroxyl groups. In the furanose form of ribose, the preferential binding occurs to the 2 and 3 carbon, leaving the 5 carbon free for phosphorylation. The central role of Mg2+ in the function of ribozymes and its archaic position in ribosomes, and the fact that magnesium generally has coordination properties different from other cations, suggests that the inorganic chemistry of magnesium had a key position in the first chemical processes leading to the origin and early evolution of life.
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| 7. |
- Ivarsson, Magnus, et al.
(författare)
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Fossilized microorganisms associated with zeolite-carbonate interfaces in sub-seafloor hydrothermal environments
- 2008
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Ingår i: Geobiology. - : Wiley. - 1472-4677 .- 1472-4669. ; 6:2, s. 155-170
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Tidskriftsartikel (refereegranskat)abstract
- In this paper we describe carbon-rich filamentous structures observed in association with the zeolite mineral phillipsite from sub-seafloor samples drilled and collected during the Ocean Drilling Program (ODP) Leg 197 at the Emperor Seamounts. The filamentous structures are ~5 µm thick and ~100–200 µm in length. They are found attached to phillipsite surfaces in veins and entombed in vein-filling carbonates. The carbon content of the filaments ranges between ~10 wt% C and 55 wt% C. They further bind to propidium iodide (PI), which is a dye that binds to damaged cell membranes and remnants of DNA. Carbon-rich globular microstructures, 1–2 µm in diameter, are also found associated with the phillipsite surfaces as well as within wedge-shaped cavities in phillipsite assemblages. The globules have a carbon content that range between ~5 wt% C and 55 wt% C and they bind to PI. Ordinary globular iron oxides found throughout the samples differ in that they contain no carbon and do not bind to the dye PI. The carbon-rich globules are mostly concentrated to a film-like structure that is attached to the phillipsite surfaces. This film has a carbon content that ranges between ~25 wt% C and 75 wt% C and partially binds to PI. EDS analyses show that the carbon in all structures described are not associated with calcium and therefore not bound in carbonates. The carbon content and the binding to PI may indicate that the filamentous structures could represent fossilized filamentous microorganisms, the globules could represent fossilized microbial cells and the film-like structures could represent a microbially produced biofilm. Our results extend the knowledge of possible habitable niches for a deep biosphere in sub-seafloor environments and suggests, as phillipsite is one of the most common zeolite mineral in volcanic rocks of the oceanic crust, that it could be a common feature in the oceanic crust elsewhere.
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| 8. |
- Konn, C., et al.
(författare)
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New insight into the contributions of thermogenic processes and biogenic sources to the generation of organic compounds in hydrothermal fluids
- 2011
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Ingår i: Geobiology. - : Wiley. - 1472-4677 .- 1472-4669. ; 9:1, s. 79-93
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Tidskriftsartikel (refereegranskat)abstract
- Experiments on hydrothermal degradation of Pyrococcus abyssi biomass were conducted at elevated pressure (40 MPa) over a 200–450 °C temperature range in sapphire reaction cells. Few organic compounds could be detected in the 200 °C experiment. This lack was attributed to an incomplete degradation of P. abyssi cells. On the contrary, a wide range of soluble organic molecules were generated at temperatures ≥350 °C including toluene, styrene, C8–C16 alkyl-benzenes, naphthalene, C11–C16 alkyl-naphthalenes, even carbon number C12–C18 polycyclic aromatic hydrocarbons, C15–C18 alkyl-phenanthrenes and C8:0–C16:0 n-carboxylic acids. The effect of time on the final organic composition of the degraded P. abyssi solutions at 350 °C was also investigated. For that purpose the biomass was exposed for 10, 20, 60, 90, 270 and 720 min at 350 °C. We observed a similar effect of temperature and time on the chemical diversity obtained. In addition, temperature and time increased the degree of alkylation of alkyl-benzenes. This study offers additional evidence that a portion of the aliphatic hydrocarbons present in the fluids from the Rainbow ultramafic-hosted hydrothermal field may be abiogenic whereas a portion of the aromatic hydrocarbons and n-carboxylic acids may have a biogenic origin. We suggest that aromatic hydrocarbons and linear fatty acids at the Rainbow site may be derived directly from thermogenic alteration of material from the sub-seafloor biosphere. Yet we infer that the formation and dissolution of carboxylic acids in hydrothermal fluids may be controlled by other processes than in our experiments.
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| 9. |
- Rosling, A., et al.
(författare)
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Phosphorous availability influences the dissolution of apatite by soil fungi
- 2007
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Ingår i: Geobiology. - : Wiley. - 1472-4677 .- 1472-4669. ; 5:3, s. 265-280
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Tidskriftsartikel (refereegranskat)abstract
- Apatite (Ca-10(PO4)(6)(OH,F,Cl)(2)) is the primary inorganic source of phosphorus in the biosphere. Soil fungi are known to increase plant-available phosphorus by promoting dissolution of various phosphate minerals. Yet no apatite dissolution studies exist using fungi as weathering agents, and regulation of fungal weathering activity in response to different levels of phosphorus availability is largely unknown. Fungi were isolated from a grassland soil in northern California. Three pathways of tri-calcium phosphate (Ca-3(PO4)(2)) (TCP) dissolution in liquid culture were identified among biogeochemically active fungi: (1) acidification (pH 3.3 +/- 0.16), (2) moderate acidification (pH 4.9 +/- 0.11) and (3) no acidification. Isolates representing pathway 1 and 2 were Zygomycetes in the order of Mucorales. All non-acidifying isolates in pathway 3 were Ascomycetes and cleared the media by altering TCP into hydroxyapatite (Ca-10(PO4)(6)(OH)(2)) and sequestering it within mycelial spheres. One isolate representing each pathway was used in fluorapatite dissolution experiments either with the fungi present or under abiotic conditions using cell-free liquid media conditioned by fungal growth at different phosphorus and calcium availabilities. Both Mucorales isolates acidify their substrate when growing in the presence of phosphorus. Mucorales exudates were mainly oxalic acid, and conditioned cell-free media with phosphorus induced fluorapatite dissolution at a rate of 10(-0.9 +/- 0.14) and 10(-1.2 +/- 0.22) mu mol P m(-2) s(-1). The ascomycete isolate on the other hand, induced fluorapatite dissolution at a rate of 10(-1.1 +/- 0.05) mu mol P m(-2) s(-1) by lowering the pH of the media under phosphorus-limited conditions, without producing significant amounts of low molecular weight organic acids (LMWOAs). Oxalate strongly etches fluorapatite along channels parallel to [001], forming needle-like features, while exudates from the ascomycete-induced surface rounding. We conclude that while LMWOAs are well-studied weathering agents, these do not appear to be produced by fungi in response to phosphorus-limiting growth conditions.
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| 10. |
- Siljeström, Sandra, 1980-, et al.
(författare)
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Analysis of hopanes and steranes in single oil-bearing fluid inclusions using time-of-flight secondary ion mass spectrometry (ToF-SIMS)
- 2010
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Ingår i: Geobiology. - : Wiley. - 1472-4677 .- 1472-4669. ; 8:1, s. 37-44
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Tidskriftsartikel (refereegranskat)abstract
- Steranes and hopanes are organic biomarkers used as indicators for the first appearance of eukaryotes and cyanobacteria on Earth. Oil-bearing fluid inclusions may provide a contamination-free source of Precambrian biomarkers, as the oil has been secluded from the environment since the formation of the inclusion. However, analysis of biomarkers in single oil-bearing fluid inclusions, which is often necessary due to the presence of different generations of inclusions, has not been possible due to the small size of most inclusions. Here, we have used time-of-flight secondary ion mass spectrometry (ToF-SIMS) to monitor in real time the opening of individualinclusions trapped in hydrothermal veins of fluorite and calcite and containing oil from Ordovician source rocks. Opening of the inclusions was performed by using a focused C60+ ion beam and the in situ content was preciselyanalysed for C27–C29 steranes and C29–C32 hopanes using Bi3+ as primary ions. The capacity to unambiguouslydetect these biomarkers in the picoliter amount of crude oil from a single, normal-sized (15–30 µm in diameter)inclusion makes the approach promising in the search of organic biomarkers for life’s early evolution on Earth.
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