| 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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