| 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. |
- 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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| 5. |
- 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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| 6. |
- 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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| 7. |
- 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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| 8. |
- 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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| 9. |
- 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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| 10. |
- 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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| 11. |
- 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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