| 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. |
- 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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| 3. |
- 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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| 4. |
- 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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| 5. |
- 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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| 6. |
- Willman, Sebastian, Docent
(författare)
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Morphology and wall ultrastructure of leiosphaeric and acanthomorphic acritarchs from the Ediacaran of Australia
- 2009
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Ingår i: Geobiology. - : Wiley. - 1472-4677 .- 1472-4669. ; 7:1, s. 8-20
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Tidskriftsartikel (refereegranskat)abstract
- Acritarchs are a group of organic-walled microfossils with unknown biological affinities. The wall ultrastructure of the unornamented, smooth Leiosphaeridia sp. and the acanthomorphic Gyalosphaeridium pulchrum from the Ediacaran Dey Dey Mudstone in the Officer Basin, South Australia, was studied by use of transmission and scanning electron microscopy, and transmitted light microscopy. The study of the ultrastructure reveals a complexity in the cell wall not seen in prokaryotes. Wall ultrastructures range from single-layered to three- or four-layered and from homogeneous to porous. Acritarchs with different wall ultrastructures may be different organisms, but may also reflect different stages in a life cycle. In this paper I review previous ultrastructure studies and discuss possible algal and metazoan affinities for the specimens studied herein.
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| 7. |
- Thiel, V, et al.
(författare)
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Analysis of archaeal core ether lipids using Time of Flight-Secondary Ion Mass Spectrometry (ToF-SIMS): Exploring a new prospect for the study of biomarkers in geobiology
- 2007
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Ingår i: Geobiology. - 1472-4677 .- 1472-4669. ; 5:1, s. 75-83
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Tidskriftsartikel (refereegranskat)abstract
- The capability of Time of Flight-Secondary Ion Mass Spectrometry (ToF-SIMS) of analysing molecular archaeal biomarkers in geobiological samples was tested and demonstrated. Using a bismuth cluster primary ion source, isopranyl glycerol di- and tetraether core lipids were detected in small amounts of total organic extracts from methanotrophic microbial mats, simultaneously and without further chemical treatment and chromatographic separation. ToF-SIMS was also employed to track the distribution of fossilized ether lipids in a massive carbonate (aragonite) microbialite that precipitated as a result of the microbial anaerobic oxidation of methane. An unambiguous signal was obtained when analysing a freshly broken rock surface (base of a microdrill core). Though some limitation occurred due to μm-topographical effects (sample roughness), it was possible to display the abundance of high molecular weight (C86) of tetraethers exposed in particular regions of the rock surface. 'Molecular mapping' revealed that a part of these molecules was encased within the rock fabric in a cluster-like distribution that might trace the arrangement of the calcifying microbial colonies in the once active mat system. The results reveal promising perspectives of ToF-SIMS for (i) the quasi-nondestructive analysis of lipids in extremely small geobiological samples at low concentrations; (ii) resolving the spatial distribution of these compounds on a μm2- to cm2-scale; and (iii) the more exact assignment of lipid biomarkers to their biological source. © 2006 The Authors.
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| 8. |
- Thiel, V, et al.
(författare)
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Biomarkers at the microscopic range: ToF-SIMS molecular imaging of Archaea-derived lipids in a microbial mat
- 2007
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Ingår i: Geobiology. - 1472-4677 .- 1472-4669. ; 5:4, s. 413-421
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Tidskriftsartikel (refereegranskat)abstract
- Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) with a bismuth cluster primary ion source was used for analysing microbial lipid biomarkers in 10-μm-thick microscopic cryosections of methanotrophic microbial mats from the Black Sea. Without further sample preparation, archaeal isopranyl glycerol di- and tetraether core lipids, together with their intact diglycoside (gentiobiosyl-) derivatives, were simultaneously identified by exact mass determination. Utilizing the imaging capability of ToF-SIMS, the spatial distributions of these biomarkers were mapped at a lateral resolution of < 5 μm in 500 × 500 μm 2 areas on the mat sections. Using cluster projectiles in the burst alignment mode, it was possible to reach a lateral resolution of 1 μm on an area of 233 × 233 μm, thus approaching the typical size of microbial cells. The mappings showed different 'provenances' within the sections that are distinguished by individual lipid fingerprints, namely (A) the diethers archaeol and hydroxyarchaeol co-occurring with glycerol dialkyl glycerol tetraethers (GDGT), (B) hydroxyarchaeol and dihydroxyarchaeol, and (C) GDGT and gentiobiosyl-GDGT. Because ToF-SIMS is a virtually nondestructive technique affecting only the outermost layers of the sample surface (typically 10-100 nm), it was possible to further examine the studied areas using conventional microscopy, and associate the individual lipid patterns with specific morphological traits. This showed that provenance (B) was frequently associated with irregular, methane-derived CaCO 3 crystallites, whereas provenance (C) revealed a population of fluorescent, filamentous microorganisms showing the morphology of known methanotrophic ANME-1 archaea. The direct coupling of imaging mass spectrometry with microscopic techniques reveals interesting perspectives for the in-situ study of lipids in geobiology, microbial ecology, and organic geochemistry. After further developing protocols for handling different kinds of environmental samples, ToF-SIMS could be used as a tool to attack many challenging problems in these fields, such as the attribution of biological source(s) to particular biomarkers in question, or the high-resolution tracking of biogeochemical processes in modern and ancient natural environments. © 2007 The Authors.
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