| 1. |
- Ahmed, Engy, et al.
(författare)
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Mineral Type Structures Soil Microbial Communities
- 2017
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Ingår i: Geomicrobiology Journal. - : Taylor & Francis. - 0149-0451 .- 1521-0529. ; 34:6, s. 538-545
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Tidskriftsartikel (refereegranskat)abstract
- Soil microorganisms living in close contact with minerals play key roles in the biogeochemical cycling of elements, soil formation, and plant nutrition. Yet, the composition of microbial communities inhabiting the mineralosphere (i.e., the soil surrounding minerals) is poorly understood. Here, we explored the composition of soil microbial communities associated with different types of minerals in various soil horizons. To this effect, a field experiment was set up in which mineral specimens of apatite, biotite, and oligoclase were buried in the organic, eluvial, and upper illuvial horizons of a podzol soil. After an incubation period of two years, the soil attached to the mineral surfaces was collected, and microbial communities were analyzed by means of Illumina MiSeq sequencing of the 16S (prokaryotic) and 18S (eukaryotic) ribosomal RNA genes. We found that both composition and diversity of bacterial, archaeal, and fungal communities varied across the different mineral surfaces, and that mineral type had a greater influence on structuring microbial assemblages than soil horizon. Thus, our findings emphasize the importance of mineral surfaces as ecological niches in soils.
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| 2. |
- Ahmed, Engy, et al.
(författare)
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Siderophore Production by Microorganisms Isolated From a Podzol Soil Profile
- 2015
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Ingår i: Geomicrobiology Journal. - : Informa UK Limited. - 0149-0451 .- 1521-0529. ; 32:5, s. 397-411
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Tidskriftsartikel (refereegranskat)abstract
- Siderophore-producing bacteria/actinobacteria and fungi were isolated from O- (organic), E- (eluvial), B- (upper illuvial), and C- (parent material) horizons of podzol soil. Siderophores were isolated and hydroxamate type siderophores were detected and quantitated by high-performance liquid chromatography coupled to electrospray ionization mass spectrometry. The molecular identification of siderophore-producing isolates showed that there was a high diversity of fungal and bacterial/actinobacterial species throughout the soil profile. The isolated bacteria/actinobacteria showed different abilities in the production of ferrioxamines (E, B, G and D). Moreover, the isolated fungal species showed great variety in the production of ferrichromes, coprogens and fusarinines.
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| 3. |
- Alsanius, Beatrix
(författare)
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Patterns of Fungal and Bacterial Carbon Mineralization Across Northern European Peatlands
- 2015
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Ingår i: Geomicrobiology Journal. - : Informa UK Limited. - 0149-0451 .- 1521-0529. ; 32, s. 914-923
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Tidskriftsartikel (refereegranskat)abstract
- The fungal and bacterial activity was determined in 20 northern European peatlands ranging from ombrotrophic bogs to eutrophic fens with key differences in degree of humification, pH, dry bulk density, carbon (C) content and vegetation communities using the selective inhibition (SI) technique. These peatlands were partly disturbed and the respective water tables lowered below the surface layer. Basal respiration ranged from 24 to 128 mu g CO2-C g(-1) dry peat d(-1). Bacterial contributions to CO2 production were high in most peatlands and showed the following pattern: eutrophic >> transitional mesotrophic >> ombrotrophic peatland types. The fungal-to-bacterial (F:B) ratios varied substantially within peatland type, and this was mainly attributed to differences in peat botanical compositions and chemistry. The computed mean Inhibitor Additivity Ratio (IAR) was quite close to 1 to suggest that the SI techniques can be used to partition eukaryotic and prokaryotic activity in wide range of peatlands. Overall, basal respiration, microbial biomass-C, fungal and bacterial activities varied across the studied peatland types, and such differences could have consequences for C- and nutrient-cycling as well as how bogs and fens will respond to environmental changes.
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| 4. |
- Anderson, Craig, 1976, et al.
(författare)
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Autoradiographic comparisons of radionuclide adsorption between subsurface anaerobic biofilms and granitic host rocks
- 2006
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Ingår i: Geomicrobiology Journal. - : Informa UK Limited. - 0149-0451 .- 1521-0529. ; 23:1, s. 15-29
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Tidskriftsartikel (refereegranskat)abstract
- In high level nuclear waste repositories, the host rock is considered to be an important barrier to radionuclide migration by adsorbing metals at fluid rock interfaces. In granitic rock environments the surfaces of hydraulically conductive fractures are covered with mixed community biofilms. Biofilms were grown in situ on glass and rock surfaces in high pressure flow cells using groundwater sourced from a borehole 450 meters below sea level in the Aspo hard rock laboratory, Sweden. Scanning electron microscopy (SEM), epifluorescence microscopy and energy dispersive X-Ray spectroscopy (EDS) revealed monolayer biofilms consisting of up to 2 x 10(4) bacteria/mm(2) surrounded by an extensive extracellular matrix and carbonate precipitates that covered
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| 5. |
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| 6. |
- Barragan, Carlos Eduardo, et al.
(författare)
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Isolation of Arsenic Resistant and Arsenopyrite Oxidizing Acidithiobacillus Species from pH Neutral Colombian Mine Effluents
- 2020
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Ingår i: Geomicrobiology Journal. - : Taylor & Francis Group. - 0149-0451 .- 1521-0529. ; 37:7, s. 682-689
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Tidskriftsartikel (refereegranskat)abstract
- Inactive mines provide a great source of bacterial diversity for studying acidophilic communities and their biotechnological applications, but prospecting of these anthropogenic environments in Colombia has been limited. Conventional microbiological methods were used to isolate acidophilic bacterial strains from effluents emanating from the Colombian gold mine 'El Zancudo' (Titiribi, Antioquia). Despite the drainage waters having circumneutral pH, all of the isolated strains were phylogenetically related to the extreme acidophile Acidithiobacillus genus. However, based upon 16S rRNA gene sequences the mesophilic sulfur-oxidizing indigenous strains could not be assigned to a species. Pure cultures were selected by screening in medium with soluble inorganic arsenic (III) and their mineral-oxidative activity was evaluated at 30 degrees C in Erlenmeyer flasks with arsenopyrite ore under rotary shaking conditions. The indigenous strains were able to catalyze arsenopyrite oxidation in a mixed culture with a pulp density of 10%, maintaining their growth in the presence of >80 mM leached arsenic. This research provides information regarding the isolation of arsenic resistant bacterial communities from neutral effluents from El Zancudo mine and the possibility of the isolated strains to be useful in the biooxidation pretreatment of refractory gold-bearing arsenopyrite ores and concentrates.
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| 7. |
- Baskar, Sushmitha, et al.
(författare)
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Biogenic evidences of moonmilk deposition in the Mawmluh cave, Meghalaya, India
- 2011
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Ingår i: Geomicrobiology Journal. - : Taylor & Francis. - 0149-0451 .- 1521-0529. ; 28:3, s. 252-265
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Tidskriftsartikel (refereegranskat)abstract
- Moonmilk, a microcrystalline secondary cave deposit, actively forms on the floor of Krem Mawmluh - a limestone cave in Meghalaya, Northeastern India. Due to the abundance of micrite and calcified microbial filaments, we hypothesize that these deposits form as a result of ongoing microbial interactions. Consistent with this idea, we report electron microscopic and microbiological evidences for the biological origin of moonmilk in Krem Mawmluh. Scanning electron microscopy indicated abundant calcified microbial filaments, needle calcite, fibre calcites (micro-fibre and nano-fibre calcite crystals), biofilm and microbial filaments in the moonmilk. The total viable culturable microbes showed high population densities for microbes in the moonmilk and moonmilk pool waters. In vitro culture experiments, confirmed the capability of many of the isolated strains to precipitate calcite and some of the identified isolates belonged to the Bacillus sp. and Actinomycetes. These results clearly support the biogenic nature of the deposits.
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| 8. |
- Baskar, Sushmitha, et al.
(författare)
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Evidences for Microbial Precipitation of Calcite in Speleothems from Krem Syndai in Jaintia Hills, Meghalaya, India
- 2016
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Ingår i: Geomicrobiology Journal. - : TAYLOR & FRANCIS INC. - 0149-0451 .- 1521-0529. ; 33:10, s. 906-933
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Forskningsöversikt (refereegranskat)abstract
- Speleothems from Krem Syndai, Meghalaya in Northeast India were studied for their microbial diversity using 16S rDNA-based phylogenetic approach and conventional microbiological techniques along with geochemistry, mineralogy and in vitro experiments to understand participation of microorganisms in CaCO3 precipitation. Speleothems imaged by scanning electron microscopy showed round coccoid-like, sporangia-like and spinose calcified structures, numerous broken cocci shells with spotted interiors inside a calcite crystal, honeycomb long reticulate, smooth, flat, twisted, ribbon-like, tubular, beaded, microbe-mineralized filaments and extracellular polymeric substances (EPS). Fourier spectroscopy indicated the presence of various organic compounds. C-13 and O-18 isotopic ratios of speleothems ranged from -4.65 to -7.34 parts per thousand and -3.06 to -6.80 parts per thousand, respectively. Total number of microbial cells using SYBR Gold was high. Fluorescence in situ hybridization (FISH) indicated approximately 3x 10(5) to 5x 10(5) cells g sed(-1) in the speleothems out of which the number of microbes belonging to Eubacteria ranged from 1.8x 10(5) to 3.6x 10(5) cells, g sed(-1). FISH showed approximate to 45% active microbial cells of the total cell number in samples. DNA-based high-throughput amplicon sequencing revealed 19 bacterial phyla in the speleothem. Approximately 42% of the sequences were similar to Proteobacteria (Alphaproteobacteria: 22.4%, Betaproteobacteria: 8.9%, Gammaproteobacteria: 8.6%). Sequences similar to Nitrospiraceae (22.8%) had the highest proportion of sequences belonging to a single family. Bacterial strains isolated from the speleothems raised alkalinity and precipitated calcite in the laboratory cultures which was confirmed by X-ray diffraction (XRD) analyses. These isolates belonged to Bacillus spp., Actinomycetes spp., Streptomyces spp., Pseudomonas spp., Micrococcus spp., Staphylococcus spp., Xanthobacter spp. and Arthrobacter spp. Overall, the results showed unequivocal evidence of bacterial fingerprints during CaCO3 precipitation in the cave.
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| 9. |
- Baskar, Sushmitha, et al.
(författare)
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Speleothems from Sahastradhara Caves in Siwalik Himalaya, India: Possible Biogenic Inputs
- 2014
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Ingår i: Geomicrobiology Journal. - : Taylor andamp; Francis: STM, Behavioural Science and Public Health Titles. - 0149-0451 .- 1521-0529. ; 31:8, s. 664-681
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Tidskriftsartikel (refereegranskat)abstract
- Stalactites and moonmilk from Sahastradhara caves in Siwalik Himalayas were studied to understand the role of microbes in their genesis. Fourier spectroscopy in the moonmilk indicates a complex milieu of organic compounds that is unusual for inorganic formations. Stable C and O isotopes show trends in the moonmilk and stalactite, which suggest biogenic input; the geochemical inference is consistent with evidence from microscopy and laboratory-based microbial cultures. Light microscopy of moonmilk samples show the presence of a number of microbial forms similar to Cyanobacteria, and scanning electron microscope (SEM) images show microbial structures similar to Spirulina. The total number of microbial cells using SYBR Gold is 6.5 x 10(5) cells, g sed(-1) in moonmilk and 3.2 x 10(5) cells, g sed(-1) in stalactites. FISH indicates approximately 3.5 x 10(5) cells, g sed(-1) in moonmilk and 2 x 10(5) cells, g sed(-1) in stalactites. SEM images of the moonmilk indicate a large network of microbial filaments along with minerals, which are identified as calcite based on their x-ray diffraction pattern. In vitro laboratory cultures with pure monogenic strains isolated from the moonmilk and stalactites raise pH in the medium, which facilitate calcite precipitation. The mineral precipitating isolates were identified as: Bacillus pumilis, B. cereus, B. anthracis, B. lentus, B. sphaericus, B. circulans and Actinomycetes. The Sahastradhara moonmilk and statactites are colonized by a diverse microbial community and the isolated bacterial strains induce biomineralization on different nutrient media, supporting their biogenic origin.
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| 10. |
- Belle, Simon
(författare)
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Reconstruction of Past Dynamics of Methane-Oxidizing Bacteria in Lake Sediments Using a Quantitative PCR Method: Connecting Past Environmental Changes and Microbial Community
- 2019
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Ingår i: Geomicrobiology Journal. - : Informa UK Limited. - 0149-0451 .- 1521-0529. ; 36, s. 570-579
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Tidskriftsartikel (refereegranskat)abstract
- In this study, a quantitative PCR (qPCR) method was applied to amplify ancient DNA (aDNA) of different methane-oxidizing bacteria (MOB) types in lake sediments and to reconstruct microbial community dynamics over the last 1200 years. We also used reconstructions of in-lake nutrients concentrations, air temperature fluctuations, and sedimentary organic matter dynamics to study impacts of past environmental and climatic changes on MOB community composition. DNA preservation in lake sediments is sufficient, and qPCR amplification was successfully applied to the analysis of MOB aDNA. Temporal changes in MOB community showed different patterns between lakes, and drivers of past MOB dynamics slightly differed between lakes and among MOB groups. Overall, MOB developments were generally correlated to proxies of organic matter quality/quantity and climate data. Moreover, our results could emphasize the importance of nutrients availability in structuring MOB community, and the higher ability of MOB type 2 to access nutrients under nitrogen/nutrients limited conditions. Therefore, our study provides an operational and time-effective method to reconstruct past CH4 oxidation in lakes and could help to identify the driving factors of past temporal dynamics of MOB community.
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| 11. |
- Eriksson, Sara, 1974, et al.
(författare)
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Indicators of petroleum hydrocarbon biodegradation in anaerobic granitic groundwater
- 2006
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Ingår i: Geomicrobiology Journal. - : Informa UK Limited. - 0149-0451 .- 1521-0529. ; 23:1, s. 45-58
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Tidskriftsartikel (refereegranskat)abstract
- The aim of this study was to find indicators of petroleum biodegradation in granitic groundwater. Both pristine and contaminated groundwaters from boreholes around petroleum storage vaults located approximately 40 m below the surface in granite and with storage capacities of up to 120,000 m(3) were sampled. Total numbers of microorganisms, "most probable numbers" (MPN) of anaerobic bacteria, and chemical indications of microbial activity were determined in the groundwater. Hydrocarbon contaminants and metabolites were detected using gas chromatographymass spectrometry (GC-MS). In contaminated groundwater, the total number of microorganisms was 2-4 x 10(6) ml(-1), which was significantly higher than the 6 x 10(4) ml(-1) found in pristine groundwater. This microbial abundance was also reflected in the MPN analysis. Up to 7 x 10(4) nitrate-, 2 x 10(3) iron-, and 3 x 10(4) sulfate-reducing bacteria were detected in contaminated groundwaters. In such groundwaters, depletion of anaerobic electron acceptors and detection of reduced species could be established. We also proposed using a high alkalinity/hardness of water quota (A/H quota) as an indicator of microbial activity. In contaminated groundwaters the A/H quota averaged 2.8, while in pristine groundwater the same was only 1.3. Moreover, the presence of 20 oxidized petroleum hydrocarbons, i.e., putative metabolites of which 9 were strictly intracellular, was detected in the contaminated groundwaters. Phylogenetic neighbor-joining analysis of 16S rRNA genes provided information about the bacterial communities. The bacteria in contaminated groundwater were found to be strikingly similar to bacteria in other hydrocarbon-contaminated environments.
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| 12. |
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| 13. |
- Ferris, F. G., et al.
(författare)
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Fragmentation of Bacteriogenic Iron Oxides in Response to Hydrodynamic Shear Stress
- 2015
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Ingår i: Geomicrobiology Journal. - : Informa UK Limited. - 0149-0451 .- 1521-0529. ; 32:7, s. 564-569
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Tidskriftsartikel (refereegranskat)abstract
- A viscous shear stress of 1.97 Nm2 was applied to suspensions of freshwater, brackish and marine bacteriogenic iron oxides (BIOS) in shake flasks. Samples were taken at intervals over 480 minutes for scanning electron microscopy. The remains of three Fe2+-oxidizing bacteria (FeOB) genera were conspicuous biomass constituents in the BIOS samples; these included the filamentous extracellular sheaths of Leptothrix, as well as helical fibrous stalks of Gallionella and Mariprofundus. The applied hydrodynamic shear stress resulted in an exponential decrease in Leptothrix sheath and Gallionella-Mariprofundus stalk lengths; first-order breakage rate constants derived from the experimental measurements ranged from 0.009 to 0.023 min−1 and 0.014 to 0.021 min��1, respectively. Breakage half-times extended from 30 to 70 min. Shear strength values calculated from the time course data ranged from 27.8 to 29.6 Nm−2 for Leptothrix sheaths, and from 28.0 to 28.8 Nm−2 for Gallionella-Mariprofundus stalks. Computational analyses showed that breakage half-times decreased rapidly with increasing shear stress, implying that the accumulation of BIOS is constrained hydrodynamically to quiescent aqueous environments. These results imply that there is considerable potential for natural hydrodynamic fluctuations in basal shear stress levels to bring about resuspension and advective dispersal of BIOS. Immediate consequences anticipated from such events include enhanced particulate transport of BIOS-associated chemical species through aquatic systems, as well as reduced preservation potential and underrepresentation of BIOS bacteria structures as microfossils in the geological record.
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| 14. |
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| 15. |
- Hallberg, Rolf, et al.
(författare)
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Multiwall Carbon Nanotubes and Nanofibers in Gallionella
- 2014
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Ingår i: Geomicrobiology Journal. - : Informa UK Limited. - 0149-0451 .- 1521-0529. ; 31:9, s. 764-768
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Tidskriftsartikel (refereegranskat)abstract
- This is a report of microbial formation of multiwall carbon nanotubes (MWCNT) and nanofibers at normal pressure and temperature. Our results demonstrate a single cell organism's ability to form complicated material of high industrial interest. The microorganism, Gallionella, is classified as autotrophic and dysoxic. It uses CO2 for its carbon source and grows in environments with low concentrations of free oxygen. The organisms were taken from a deep bedrock tunnel where water leaking from cracks in the rock formed a precipitate of iron as a bacterial slime on the rock wall. Detailed investigations of the samples by transmission electron microscopy (TEM) revealed several types of MWCNT. The stalk single MWCNT was observed with a diameter of about 10nm and with an inner diameter of 1.35nm. The wall of the nanotube is built by graphite layers. The 10 to 20 sheets are used to form the tubes. The measured spacing between the lines is 0.34nm, which is an average value of interlayer spacing, close to the graphitic distance (0.335nm). HRTEM images reveal a two-dimensional lattice with a spacing of 0.24nm, indicating the presence of graphene.
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| 16. |
- Hallberg, Rolf O., et al.
(författare)
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Microbial Fossils in the 2.63 Ga Jeerinah Formation, Western Australia-Evidence of Microbial Oxidation
- 2018
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Ingår i: Geomicrobiology Journal. - : Informa UK Limited. - 0149-0451 .- 1521-0529. ; 35:4, s. 255-260
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Tidskriftsartikel (refereegranskat)abstract
- A diamond drill core from the upper part of the Jeerinah Formation (similar to 2.63 Ga), underlying the Hamersley Group, deposited at a time when the oxygen concentrations in the marine environment were extremely low, was examined for microbial fossils. The paper presents organo-mineral structures in the form of twisted stalks produced by bacteria being present in the laminated black carbonaceous shale sediments. These twisted stalks are organo-mineral structures produced by microaerophilic Fe(II)-oxidizing-type bacteria such as Gallionella and/or Mariprofundus that are active at very low-oxygen concentrations, thus providing evidence for oxygen being present in the marine environment at 2.63 Ga.
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| 17. |
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| 18. |
- Hillier, Stephen
(författare)
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A New Lead Hydroxycarbonate Produced During Transformation of Lead Metal by the Soil Fungus Paecilomyces javanicus
- 2016
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Ingår i: Geomicrobiology Journal. - : Informa UK Limited. - 0149-0451 .- 1521-0529. ; 33, s. 250-260
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Tidskriftsartikel (refereegranskat)abstract
- Previous research has demonstrated the transformation of metallic lead into pyromorphite in solid and liquid medium by several species of fungi. In this work, the soil fungus Paecilomyces javanicus was found to mediate formation of an unknown lead mineral phase after incubation in liquid media with lead shot. After 2 weeks' incubation, precipitated mineral phase particles were collected and X-ray powder diffraction (XRPD) revealed the presence of plumbonacrite (Pb-10(CO3)(6)O(OH)(6)). After 4 weeks' incubation, the lead particles that accumulated inside the fungal pellets were transformed into a white lead-containing secondary mineral phase. Energy dispersive X-ray analysis (EDXA) and XRPD were used to attempt to identify the lead-containing secondary minerals produced. XRPD showed that lead oxalate (PbC2O4) and cerussite (PbCO3) were present as lead mineral species. However, another mineral phase was present that was not identifiable by XRPD. Fourier transform infrared spectroscopy (FTIR) identified hydroxyl (-OH) and carbonate (-CO32-) groups as the main functional groups within this unidentified secondary mineral phase. It was therefore concluded that this mineral phase is a new species of lead hydroxycarbonate. This is the first discovery of fungal-mediated formation of plumbonacrite and a new lead hydroxycarbonate, and therefore reveals a novel step in lead carbonation by fungi.
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| 19. |
- Hillier, Stephen
(författare)
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Chemical and Physical Mechanisms of Fungal Bioweathering of Rock Phosphate
- 2021
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Ingår i: Geomicrobiology Journal. - : Informa UK Limited. - 0149-0451 .- 1521-0529. ; 38, s. 384-394
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Tidskriftsartikel (refereegranskat)abstract
- This research has investigated fungal transformations of rock phosphate (RP) by geoactive fungi, with particular emphasis on Aspergillus niger. Direct hyphal interaction with RP particles induced morphological and mineralogical changes, as revealed by scanning electron microscopy (SEM) and X-ray diffraction (XRD) analysis. The formation of the oxalate mineral calcium oxalate monohydrate (whewellite, CaC2O4 center dot H2O) on RP surfaces showed that mycogenic oxalic acid was driving the chemical dissolution of apatite, with consequent phosphate release and secondary mineral formation. This was supported by abiotic testing of common fungal excreted organic acids which confirmed that oxalic acid was the only effective RP transforming agent and therefore responsible for the morphological and mineralogical changes observed in RP when exposed to fungal colonization. Cryogenic SEM provided evidence of fungal penetration and tunneling through RP particles demonstrating that physical interactions are also important for RP bioweathering, as well as biochemical mechanisms. These findings emphasize the important role of fungi in P cycling, with active participation in the transformation of mineral phosphates through physicochemical mechanisms and secondary oxalate biomineral formation.
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| 20. |
- Ivarsson, M., et al.
(författare)
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Fossilized Life in Subseafloor Ultramafic Rocks
- 2018
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Ingår i: Geomicrobiology Journal. - : Informa UK Limited. - 0149-0451 .- 1521-0529. ; 35:6, s. 460-467
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Tidskriftsartikel (refereegranskat)abstract
- Ultramafic rocks are hypothesized to support a subseafloor hydrogen-driven biosphere because of extensive production of bioavailable energy sources like H-2 or CH4 from fluid-rock interactions. Hence, the apparent lack of microbial remains in subseafloor ultramafic rocks, in contrast to their frequent observation in subseafloor basalts, is somewhat of a paradox. Here we report fossilized microbial remains in aragonite veins in ultramafic rocks from the 15 degrees 20N Fracture Zone area on the Mid-Atlantic Ridge (MAR), collected during Ocean Drilling Program (ODP) Leg 209. The microbial remains consist of filamentous structures associated with biofilms. The young age (<1 Myr) and absence of diagenesis result in fossilized microbial communities with a pristine composition characterized by carbonaceous matter (CM) and the enrichment in trace elements such as Ni, Co, Mo and Mn. Our study confirms the presence of the hypothesized deep subseafloor biosphere hosted in ultramafic rocks. We further show that host rock composition may influence the microbial elemental composition, which is recorded during the fossilization.
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| 21. |
- Johnsson, Anna, 1975, et al.
(författare)
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Solid-aqueous phase partitioning of radionuclides by complexing compounds excreted by subsurface bacteria
- 2006
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Ingår i: Geomicrobiology Journal. - : Informa UK Limited. - 0149-0451 .- 1521-0529. ; 23(8), s. 621-630
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Tidskriftsartikel (refereegranskat)abstract
- Radionuclides are present in numerous aerobic and anaerobic subsurface environments due to nuclear weapons testing, leakage from process and storage facilities, and discharge of radioactive waste. The partitioning of radionuclides between liquid and solid phases by complexing compounds excreted by subsurface bacteria was studied. The solid-aqueous phase partitioning of pico- to submicromolar amounts of 59 Fe, 147 Pm, 234 Th, and 241 Am was analyzed in the presence of quartz sand and exudates from three species of subsurface bacteria: Pseudomonas fluorescens, Pseudomonas stutzeri, and Shewanella putrefaciens. All were grown under aerobic conditions, and P. stutzeri and S. putrefaciens were grown under anaerobic conditions as well. The supernatants of the aerobic and anaerobic cultures were collected and radionuclide was added. Quartz sand, with a Brunauer, Emmett, and Teller (BET) surface area of 0.1 m 2 g -1 , was added to the supernatant radionuclide mix, and the pH was adjusted to approximately 8. After centrifuging, the amount of radionuclide in the liquid phase of the samples and controls was analyzed using scintillation. Relative to the control, aerobic supernatants maintained more than 50% of the added 59 Fe, 234 Th, and 241 Am. The highest amount of metal present in the liquid phase of the anaerobic supernatants was found in the case of 241 Am, with 40% more 241 Am in samples than in controls. Both aerobic and anaerobic supernatants tested positive for complexing compounds when analyzed using the Chrome Azurol S assay. The great amounts of radionuclides in the liquid phases of samples were likely due to complexation with such compounds. Bacterially excreted complexing compounds hence seem able to influence the solid-aqueous phase partitioning of radionuclides. This could influence the mobility of radionuclides in contaminated subsurface environments.
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| 22. |
- Julies, Elsabe M., et al.
(författare)
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Organic Carbon Degradation in Anoxic Organic-Rich Shelf Sediments : Biogeochemical Rates and Microbial Abundance
- 2010
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Ingår i: Geomicrobiology Journal. - : Informa UK Limited. - 0149-0451 .- 1521-0529. ; 27:4, s. 303-314
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Tidskriftsartikel (refereegranskat)abstract
- Identifying and explaining bottlenecks in organic carbon mineralization and the persistence of organic matter in marine sediments remain challenging. This study aims to illuminate the process of carbon flow between microorganisms involved in the sedimentary microbial food chain in anoxic, organic-rich sediments of the central Namibian upwelling system, using biogeochemical rate measurements and abundances of Bacteroidetes, Gammaproteobacteria, and sulfate-reducing bacteria at two sampling stations. Sulfate reduction rates decreased by three orders of magnitude in the top 20 cm at one sampling station (280 nmol cm-3 d-1 - 0.1 nmol cm-3 d-1) and by a factor of 7 at the second station (65 nmol cm-3 d-1 - 9.6 nmol cm-3 d-1). However, rates of enzymatic hydrolysis decreased by less than a factor of three at both sampling stations for the polysaccharides laminarin (23 nmol cm-3 d-1- 8 nmol cm-3 d-1 and 22 nmol cm-3 d-1- 10 nmol cm-3 d-1) and pullulan (11 nmol cm-3 d-1- 4 nmol cm-3 d-1 and 8 nmol cm-3 d-1- 6 nmol cm-3 d-1). Increasing imbalance between carbon turnover by hydrolysis and terminal oxidation with depth, the steep decrease in cell specific activity of sulfate reducing bacteria with depth, low concentrations of volatile fatty acids (less than 15 M), and persistence of dissolved organic carbon, suggest decreasing bioavailability and substrate limitation with depth.
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| 23. |
- Kalinowski, Birgitta E., et al.
(författare)
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Microbial mobilization of uranium from shale mine waste
- 2006
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Ingår i: Geomicrobiology Journal. - : Informa UK Limited. - 0149-0451 .- 1521-0529. ; 23:3-4, s. 157-164
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Tidskriftsartikel (refereegranskat)abstract
- The alum shale in the Billingen area in southern Sweden was mined in Ranstad for 5 years during the 1960s. The crushed tailings (processed and unprocessed) were left behind when the Ranstad mine was closed that has caused leaching of metals to the surroundings. The siderophore producing bacterium Pseudomonas fluorescens (sp, SE Sweden) was grown in batch cultures for 5 to 8 days with naturally weathered (unprocessed) uranium ore (0.0029% U by weight), kolm (0.52% U by weight) and acid-leached ore (0.0099% U by weight) in chemically defined media (unbuffered and buffered). Pseudomonas fluorescens grown with ore and unbuffered medium changed the pH from 4.7 to 9.3 and leached out 0.016 to 0.9% (normalized to surface area) of the total amount of U from the different ores. Incubation of the acid-leached ore with bacteria in buffered medium leached out 0.04% of the total U. Uranium was leached out selectively at all conditions, but this could be a pH effect, as pH increased at the same time as the U concentrations did. The observed release of Fe was most likely attributed to the production of microbial siderophores (Fe3+ specific chelators) since Fe3+ has a low solubility at pH > 4. As siderophores contain a number of chelating groups they may still function as complexators even in partly degraded form also for other metals than Fe. Thus, the production of microbial chelators could contribute to the elevated metal concentrations in the drainage water from the closed Ranstad mine, as abiotic processes cannot fully explain these high metal concentrations. In the extension: ligand promoted leaching of toxic elements could also be the key to bioremediation as there is a need for nontoxic cleanup methods for metal contaminated sites.
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| 24. |
- Karnachuk, Olia V, et al.
(författare)
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Sulfate reduction potential in sediments in the Norilsk mining area, northern Siberia
- 2005
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Ingår i: Geomicrobiology Journal. - Philadelphia : Taylor & Francis. - 0149-0451 .- 1521-0529. ; 22:1-2, s. 11-25
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Tidskriftsartikel (refereegranskat)abstract
- The purpose of this study was to characterize the distribution and activity of sulfate-reducing bacteria in tailings and sediments impacted by effluents from mining and smelting operations in the Norilsk area in northern Siberia. The Norilsk mining complex involves three smelter operations, a hydrometallurgical plant, and extensive tailings areas located in the permafrost zone. Sulfate reduction rates measured with a (35)SO(4)(2-) tracer technique under various in-situ conditions ranged from 0.05 to 30 nmol S cm(-3) day(-1). Acetate and glucose addition greatly stimulated sulfate reduction, whereas lactate had less effect. The most pronounced stimulation of sulfate reduction (6.5-fold) was observed with phosphate amendment. Most-probable-number (MPN) counts of sulfate-reducing bacteria in media with glucose, ethanol, lactate, and acetate as electron donors were generally highest at around 10(7) cells ml(-1). The actual MPN counts varied with the sample, electron donor, and incubation conditions (pH 7.2 vs. pH 3.5; 28 degrees C vs. 4 degrees C). Enrichment cultures of sulfate-reducing bacteria were established from a sample that showed the highest rate of sulfate reduction. After multiple serial transfers, the dominant sulfate-reducers were identified by fluorescence in situ hybridization using genus and group-specific 16S rRNA-targeted oligonucleotide probes. Desulfobulbus spp. prevailed in ethanol and lactate enrichments and the Desulfosarcina-Desulfococcus group dominated in acetate and benzoate enrichments. Psychrophilic Desulfotalea-Desulfofustis and moderately psychrophilic Desulforhopalus spp. were identified in enrichments incubated at 4 degrees C, but they were also found in mesophilic enrichments.
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| 25. |
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| 26. |
- Leefman, Tim, et al.
(författare)
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An Imaging Mass Spectrometry Study on the Formation of Conditioning Films and Biofilms in the Subsurface (Äspö Hard Rock Laboratory, SE Sweden)
- 2015
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Ingår i: Geomicrobiology Journal. - : Informa UK Limited. - 0149-0451 .- 1521-0529. ; 32:3-4, s. 197-206
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Tidskriftsartikel (refereegranskat)abstract
- Conditioning films and biofilms forming on surfaces of solid materials exposed to aqueous media play a key role in in the interaction between the geo- and biospheres. In this study, time-of-flight secondary ion mass spectrometry and scanning electron microscopy were used to investigate the time scale, mode of formation, and chemistry of conditioning films and biofilms that formed on Si substrates exposed to aquifer water in the subsurface Äspö Hard Rock Laboratory, SE-Sweden. The detection of fragment ions of amino acids, carbohydrates, and carboxylic acids revealed that different types of organic compounds had adhered to the Si surface already after 10 min of exposure to the aquifer fluids, whereas the attachment of microbial cells was first observed after 1000 min. The organic compounds first formed isolated μm-sized accumulations and subsequently started to distribute on the wafer surface more homogenously. Simultaneously further microorganisms attached to the surface and formed biofilm-like cell accumulations after 3 months of exposure to aquifer water.
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| 27. |
- Lindsay, Matthew B. J., et al.
(författare)
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Microbiology and geochemistry of mine tailings amended with organic carbon for passive treatment of pore water
- 2011
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Ingår i: Geomicrobiology Journal. - : Informa UK Limited. - 0149-0451 .- 1521-0529. ; 28:3, s. 229-241
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Tidskriftsartikel (refereegranskat)abstract
- A field-scale experiment was conducted to evaluate organic carbon amendment of mine tailings as a technique for pore water and drainage treatment. Six test cells were constructed by amending sulfide- and carbonate- rich tailings with varied mixtures of peat, spent-brewing grain and municipal biosolids. Samples were collected for microbial, geochemical and mineralogical analysis approximately three years after commencing this experiment. Test cells amended with spent-brewing grain promoted sulfate reduction and effective removal of sulfate and metal(loid)s. The addition of municipal biosolids did not sustain enhanced sulfidogenesis after three years, and peat was an ineffective source of organic carbon. Terminal-restriction fragment length polymorphism revealed that test cells which supported sulfidogenesis exhibited the greatest microbial diversity. Indigenous bacteria identified using molecular and cultivation analyses were found to be related to Cellulomonas, Thiobacillus, Bacteroides, Paludibacter and Desulfovibrio, which was the only sulfate-reducing bacterial (SRB) isolated. The results demonstrate that mixtures of solid organic materials which supported complex anaerobic microbial communities, including sulfate- reducing bacteria, were most effective in promoting pore-water treatment.
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| 28. |
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| 29. |
- Pedersen, Karsten, 1952, et al.
(författare)
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Sulphate-controlled Diversity of Subterranean Microbial Communities over Depth in Deep Groundwater with Opposing Gradients of Sulphate and Methane
- 2014
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Ingår i: Geomicrobiology Journal. - : Informa UK Limited. - 0149-0451 .- 1521-0529. ; 31:7, s. 617-631
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Tidskriftsartikel (refereegranskat)abstract
- The groundwater system in Olkiluoto, Finland, is stratified with a mixing layer at a depth of approximately 300m between sulphate-rich, methane-poor and sulphate-poor, methane-rich groundwaters. New sequence library data obtained by 454 pyrotag sequencing of the v4v6 16S rDNA region indicated that sulphate-reducing bacteria (SRB) dominated the mixing layer while SRB could not be detected in the deep sulphate-poor groundwater samples. With the indispensable support of the sequence data, it could be demonstrated that sulphate was the only component needed to trigger a very large community transition in deep sulphate-poor, methane-rich groundwater from a non-sulphate-reducing community comprising Hydrogenophaga, Pseudomonas, Thiobacillus, Fusibacter, and Lutibacter to a sulphate-reducing community with Desulfobacula, Desulfovibrio, Desufobulbaceae, Desulfobacterium, Desulfosporosinus, and Desulfotignum. Experiments with biofilms and planktonic microorganisms in flow cells under in situ conditions confirmed that adding sulphate to the sulphate-poor groundwater generated growth of cultivable SRB and detectable SRB-related sequences. It was also found that the 16S rDNA diversity of the biofilms was conserved over 103 d and that there was great similarity in diversity between the microorganisms in the biofilms and in the flowing groundwater. This work demonstrates that the presence/absence of only one geochemical parameter, i.e., sulphate, in the groundwater significantly influenced the diversity of the investigated subterranean microbial community.
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| 30. |
- Plymale, Andrew E., et al.
(författare)
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Niche Partitioning of Microbial Communities at an Ancient Vitrified Hillfort : Implications for Vitrified Radioactive Waste Disposal
- 2021
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Ingår i: Geomicrobiology Journal. - : Taylor & Francis. - 0149-0451 .- 1521-0529. ; 38:1, s. 36-56
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Tidskriftsartikel (refereegranskat)abstract
- Because microbes cannot be eliminated from radioactive waste disposal facilities, the consequences of bio-colonization must be understood. At a pre-Viking era vitrified hillfort, Broborg, Sweden, anthropogenic glass has been subjected to bio-colonization for over 1,500 years. Broborg is used as a habitat analogue for disposed radioactive waste glass to inform how microbial processes might influence long-term glass durability. Electron microscopy and DNA sequencing of surficial material from the Broborg vitrified wall, adjacent soil, and general topsoil show that the ancient glass supports a niche microbial community of bacteria, fungi, and protists potentially involved in glass alteration. Communities associated with the vitrified wall are distinct and less diverse than soil communities. The vitrified niche of the wall and adjacent soil are dominated by lichens, lichen-associated microbes, and other epilithic, endolithic, and epigeic organisms. These organisms exhibit potential bio-corrosive properties, including silicate dissolution, extraction of essential elements, and secretion of geochemically reactive organic acids, that could be detrimental to glass durability. However, long-term biofilms can also possess a homeostatic function that could limit glass alteration. This study documents potential impacts that microbial colonization and niche partitioning can have on glass alteration, and subsequent release of radionuclides from a disposal facility for vitrified radioactive waste.
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| 31. |
- Polymanakou, Paraskevi, et al.
(författare)
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Organic Matter Preservation and Microbial Community Accumulations in Deep-Hypersaline Anoxic Basins
- 2007
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Ingår i: Geomicrobiology Journal. - : Informa UK Limited. - 0149-0451 .- 1521-0529. ; 24:1, s. 19-29
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Tidskriftsartikel (refereegranskat)abstract
- The Eastern Mediterranean Sea hosts several deep hypersaline anoxic basins (DHABs) such as the Bannock, L'Atalante, Discovery, and Urania which, due to strong salinity gradients, have a limited exchange with the overlying seawater. In the present study, a series of environmental variables associated with the origin and quality of organic matter were thoroughly investigated in an attempt to understand the function of these unique ecosystems. The redox potential of sediments collected from the brines as well as from reference sites varied from -136 to 543 mV and salinity varied from 38 to 380 psu. Principal component analysis of chemical characteristics, including salinity, redox potential, organic carbon and nitrogen content, and C/N ratio grouped the sediments into two major clusters according to their redox state. Aliphatic hydrocarbon analysis revealed that the organic matter in the DHABs was predominantly of terrestrial origin but there was also evidence for petroleum inputs and for organic matter of phototrophic origin. Phospholipid linked fatty acids (PLFA) which were employed to assess the composition of microbial communities were found in greater abundance in stations situated inside the anoxic basins providing also strong evidence for the presence of methanotrophs and sulfate reducers. These results may represent an enhanced preservation of organic matter and an accumulation of microorganisms in these extreme environments. Heterogeneity in microbial community fatty acid profiles was documented between the anoxic sediments and the oxic and suboxic stations. However there were no significant correlations between PLFA and organic matter parameters. Redox conditions appear to influence microbial community composition, highlighting the role of the redox state as a regulator of organic matter preservation and microbial community accumulations in these ancient hypersaline anoxic lakes.
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| 32. |
- Purvis, William O., et al.
(författare)
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Mineralization in Rust-coloured Acarospora
- 2008
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Ingår i: Geomicrobiology Journal. - : Informa UK Limited. - 0149-0451 .- 1521-0529. ; 25:3-4, s. 142-148
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Tidskriftsartikel (refereegranskat)abstract
- The upper cortex and extracellular hyphal wall matrix are mineralized in both rust-coloured Acarospora sinopica and the paler A. smaragdula 'f. subochracea' in the form of microgranular or microbotryoidal phases. Analysis confirmed the distinctive colours are not simply due to hydrated iron oxides, as previously believed, and suggests mixed sulphide and oxide phases with little crystallinity, as well as other elements arising from clay minerals are present. These aspects highlight the need for a more detailed study employing a range of micro-analytical techniques, including analytical TEM, which will allow mineral characterisation and localisation down to the nanometre scale.
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| 33. |
- Rosling, Anna
(författare)
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Trees, Mycorrhiza and Minerals -Field Relevance of in vitro Experiments
- 2009
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Ingår i: Geomicrobiology Journal. - : Informa UK Limited. - 0149-0451 .- 1521-0529. ; 26, s. 389-401
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Tidskriftsartikel (refereegranskat)abstract
- Ectomycorrhizal fungi are mutualistic symbionts of boreal forest trees and may mediate mineral weathering through their direct access to photosyntentically derived carbon. In soil, fungal mycelia (i) provide a large surface for nutrient uptake; (ii) induce intense colonization of nutrient rich substrates; (iii) cause local acidification and (iv) produce organic acids. Mechanisms of ectomyorrhizal fungi induced weathering in response to nutrient limiting growth conditions remains largely unresolved. This review summarizes how current knowledge on fungal weathering is affected by experimental setup and conditions, i.e., pure or symbiotic growth, nitrogen source, the mean of detecting weathering activity and species examined.
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| 34. |
- Sjöberg, Susanne, et al.
(författare)
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Microbial Communities Inhabiting a Rare Earth Element Enriched Birnessite-Type Manganese Deposit in the Ytterby Mine, Sweden
- 2018
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Ingår i: Geomicrobiology Journal. - : Informa UK Limited. - 0149-0451 .- 1521-0529. ; 35:8, s. 657-674
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Tidskriftsartikel (refereegranskat)abstract
- The dominant initial phase formed during microbially mediated manganese oxidation is a poorly crystalline birnessite-type phyllomanganate. The occurrence of manganese deposits containing this mineral is of interest for increased understanding of microbial involvement in the manganese cycle. A culture independent molecular approach is used as a first step to investigate the role of microorganisms in forming rare earth element enriched birnessite-type manganese oxides, associated with water bearing rock fractures in a tunnel of the Ytterby mine, Sweden. 16S rRNA gene results show that the chemotrophic bacterial communities are diverse and include a high percentage of uncultured unclassified bacteria while archaeal diversity is low with Thaumarchaeota almost exclusively dominating the population. Ytterby clones are frequently most similar to clones isolated from subsurface environments, low temperature milieus and/or settings rich in metals. Overall, bacteria are dominant compared to archaea. Both bacterial and archaeal abundances are up to four orders of magnitude higher in manganese samples than in fracture water. Potential players in the manganese cycling are mainly found within the ferromanganese genera Hyphomicrobium and Pedomicrobium, and a group of Bacteroidetes sequences that cluster within an uncultured novel genus most closely related to the Terrimonas. This study strongly suggest that the production of the YBS deposit is microbially mediated.
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| 35. |
- Vilinska, Annamaria, et al.
(författare)
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Surface characterization of Acidithiobacillus ferrooxidans adapted to high copper and zinc ions concentration
- 2011
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Ingår i: Geomicrobiology Journal. - : Informa UK Limited. - 0149-0451 .- 1521-0529. ; 28:3, s. 221-228
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Tidskriftsartikel (refereegranskat)abstract
- Changes in surface chemical properties of Acidithiobacillus ferrooxidans after adaptation to high copper and zinc ion concentration were studied by surface sensitive techniques such as zeta-potential, XPS and FT-IR measurements. The adapted bacteria were also characterized by their surface energies and adhesion capacities on different sulphide minerals. Their surface negative charge was decreased due to changes in the structure of bacterial surface layers. The metal ions adapted cells secreted more extracellular polymeric substances with a modified composition compared to unadapted ferrous ions grown cells. Bacterial cells hydrophilic property increased after adaptation and altered their adhesion behavior to sulphide mineral.
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| 36. |
- Öquist, Mats, et al.
(författare)
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Effects of a transient oxic period on mineralization of organic matter to CH4 and CO2 in anoxic peat incubations
- 1998
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Ingår i: Geomicrobiology Journal. - : Informa UK Limited. - 0149-0451 .- 1521-0529. ; 15:4, s. 325-333
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Tidskriftsartikel (refereegranskat)abstract
- Rates of organic matter mineralization in peatlands, and hence production of the greenhouse gases CH4 and CO2, are highly dependent on the distribution of oxygen in the peat. Using laboratory incubations of peat, we investigated the sensitivity of the anoxic production of CH4 and CO2 to a transient oxic period of a few weeks’ duration. Production rates during 3 successive anoxic periods were compared with rates in samples incubated in the presence of oxygen during the second period. In surface peat (5–10‐cm depth), with an initially high level of CH4 production, oxic conditions during period 2 did not result in a lower potential CH4 production rate during period 3, although production was delayed 1 week. In permanently anoxic, deep peat (50–55‐cm depth) with a comparatively low initial production of CH4, oxic conditions during period 2 resulted in zero production of CH4 during period 3. Thus, the methanogens in surface peal—but not in deep peat—remained viable after several weeks of oxic conditions. In contrast to CH4 production, the oxic period had a negligible effect on anoxic CO2 production during period 3, in surface as well as deep peat. In both surface and deep peat, CO2 production was several times higher under oxic than under anoxic conditions. However, for the first 2 weeks of oxic conditions, CO2 production in the deep peat was very low. Still, deep peat obviously contained facultative microorganisms that, after a relatively short period, were able to maintain a considerably higher rate of organic matter mineralization under oxic than under anoxic conditions.
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| 37. |
- Toupalas, Georgios, et al.
(författare)
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Tuning Photoinduced Electron Transfer in POM-Bodipy Hybrids by Controlling the Environment : Experiment and Theory
- 2021
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Ingår i: Angewandte Chemie - International Edition. - : Wiley. - 1433-7851 .- 1521-3773. ; 60:12, s. 6518-6525
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Tidskriftsartikel (refereegranskat)abstract
- The optical and electrochemical properties of a series of polyoxometalate (POM) oxoclusters decorated with two bodipy (boron-dipyrromethene) light-harvesting units were examined. Evaluated here in this polyanionic donor-acceptor system is the effect of the solvent and associated counterions on the intramolecular photoinduced electron transfer. The results show that both solvents and counterions have a major impact upon the energy of the charge-transfer state by modifying the solvation shell around the POMs. This modification leads to a significantly shorter charge separation time in the case of smaller counterion and slower charge recombination in a less polar solvent. These results were rationalized in terms of Marcus theory and show that solvent and counterion both affect the driving force for photoinduced electron transfer and the reorganization energy. This was corroborated with theoretical investigations combining DFT and molecular dynamics simulations.
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