Direct and simultaneous extraction of DNA and RNA from soil

Selenska‐Pobell, Sonja

doi:10.1007/978-94-011-0351-0_11

Cited by 8 publications

(9 citation statements)

References 42 publications

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“…In this sample no acidobacterial sequences were retrieved whereas in the sample JG35‐K1 only a few sequences of this phylum were found. Due to the fact that only high molecular DNA, extracted from intact bacterial cells according to (Selenska‐Pobell, 1995; Selenska‐Pobell et al ., 2001), was subjected to amplifications we conclude that the failure to detect acidobacterial sequences in the sample JG35+U1 indicates that a large part of these bacteria was killed by the treatment with uranium and that their number went below the limit of detection of the used method. We suggest that these dead bacterial populations release to the environment significant quantities of biopolymers such as siderophores, polypeptides, polysaccharides, phosphorilated peptides, alginates, nucleic acids, orthophosphate, aminoacids, etc.…”

Section: Discussionmentioning

confidence: 99%

Addition of U(VI) to a uranium mining waste sample and resulting changes in the indigenous bacterial community

Geissler

Selenska‐Pobell

2005

Geobiology

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Based on 16S rRNA gene sequence retrieval, changes in natural bacterial community structure induced by addition of uranyl or sodium nitrate to soil samples from a uranium mining waste pile were investigated. Our results demonstrate that both treatments cause drastic changes in the bacterial composition of the studied samples, resulting in strongly reducing the originally predominant Acidobacteria and Alphaproteobacteria. The addition of sodium nitrate induced a strong propagation of particular denitrifying and nitrate‐reducing populations belonging to Actinobacteria and Bacteroidetes. The treatment of the samples with uranyl nitrate demonstrated that most part of the mentioned Bacteroidetes and some of the actinobacterial populations do not tolerate high U(VI) concentrations. Instead, a strong propagation of Pseudomonas spp. from the Gammaproteobacteria occurred. At the initial stages of incubation (4 weeks after the addition of uranyl nitrate) U(VI)‐reducing Geobacter spp. appeared. However, at the later stages of incubation (14 weeks after the beginning of supplementation) no Geobacter populations were detected anymore. Interestingly, different U‐sensitive Bacteroidetes and alphaproteobacterial populations propagated in the U(VI)‐treated samples at these late stages of incubation. That indicated that the added U(VI) was no longer bioavailable. The drastic changes in bacterial community structure of the soil samples from the depleted uranium mining waste caused by the addition of uranyl nitrate indicate that most of the established indigenous bacterial populations do not tolerate U(VI). By the treatment with uranyl nitrate they are replaced by particular uranium resistant nitrate‐reducing and denitrifying populations that potentially interact with the added radionuclide. On the other hand, the large number of dead uranium‐sensitive bacteria likely liberates phosphate‐rich and other biopolymers capable of binding U(VI). On the basis of our results, we propose that bacteria along with the abiotic soil components such as minerals and humic acids may influence the behaviour of U(VI) in nature.

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Section: Discussionmentioning

confidence: 99%

Addition of U(VI) to a uranium mining waste sample and resulting changes in the indigenous bacterial community

Geissler

Selenska‐Pobell

2005

Geobiology

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“…DNA was extracted from BIOS using a protocol based on that used by Selenska Pobell (1995) amended with a cartridge DNA purification step instead of a CsCl gradient centrifugation. Briefly, 10 mL of BIOS biofilm material was added to 20 mL of extraction buffer (0.12 m Na 2 HPO4 solution at pH 8 and 5 mL of a 5% SDS solution) in a sterile Erlenmeyer flask.…”

Section: Field Measurements and Samplingmentioning

confidence: 96%

In situ ecological development of a bacteriogenic iron oxide‐producing microbial community from a subsurface granitic rock environment

et al. 2006

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The initial development and diversity of an in situ subsurface microbial community producing bacteriogenic iron oxides (BIOS) were investigated at the initiation of biofilm growth (2‐month period) and after a 1‐year period of undisturbed growth. Water chemistry data, samples of iron encrusted biofilm material and groundwater were collected from BRIC (BIOS reactor, in situ, continuous flow) apparatuses installed 297 m below sea level at the Äspö Hard Rock Laboratory (HRL) in south eastern Sweden. Comparisons between the BIOS BRIC system and an anaerobic control (AC) BRIC revealed that water mixing at the inflow leads to profuse development of BIOS related to a slightly elevated level of O2 (up to 0.3 mg L−1 at the transition zone between BIOS development and non‐development) and elevated Eh (>120 mV) in the first 70 mm of water depth. Decreases in dissolved and particulate iron were connected to the visible appearance of BIOS biofilms. The basic phylogenetic diversity of this site was evaluated using amplified ribosomal DNA restriction enzyme analysis (ARDRA), denaturing gradient gel electrophoresis (DGGE) and partial sequencing of 16S rDNA. From 67 clones that were positive for 16S rDNA inserts, a total of 42 different ARDRA profiles were recognized, representing four bacterial phyla and 14 different metabolic lifestyles. DGGE profiles indicated that there are differences in the representative bacteria when considering either BIOS biofilms or groundwater. DGGE also indicated that the DNA extraction protocols and any polymerase chain reaction biases were consistent. Bacterial metabolic groups associated with indirect metal adsorption and reduction along with bacteria utilizing many alternative electron acceptors were strongly represented within the clones. This study indicates that the microbial diversity of BIOS is greater than previously thought.

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“…Using a technique modi¢ed from [28], 4 g of sediment (wet weight) was placed in a 0.5-ml microcentrifuge tube and suspended in 8 ml of extraction bu¡er (0.2 M sodium phosphate bu¡er pH 8.0 and 0.1 M EDTA). To this sediment slurry, 4 g of 0.1 mm zirconia/silica beads (Biospec, Bartlesville, OK), 200 mg of polyvinylpolypyrrolidone (PVPP) and 1.5 ml 10% SDS were added, the mixture vortexed at maximum velocity for 3 min, and then placed in a 70³C water bath for 15 min.…”

Section: Dna Extraction and Puri¢cationmentioning

confidence: 99%

Molecular analysis of microbial communities in mobile deltaic muds of Southeastern Papua New Guinea

Todorov

2000

FEMS Microbiology Ecology

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A culture-independent examination of microbial diversity in mobile deltaic sediments from the Gulf of Papua, Papua New Guinea, was conducted by sequence analysis of 16S rDNA clone library. Universal small subunit primers were used to amplify DNA extracted from the sediment. Of 91 clones randomly selected from the library, 33 contained unique non-chimeric sequences. Analysis of these unique sequences showed that the majority of them belonged to bacteria (94.5%), with proteobacteria being the dominant division (74

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Direct and simultaneous extraction of DNA and RNA from soil

Cited by 8 publications

References 42 publications

Addition of U(VI) to a uranium mining waste sample and resulting changes in the indigenous bacterial community

Addition of U(VI) to a uranium mining waste sample and resulting changes in the indigenous bacterial community

In situ ecological development of a bacteriogenic iron oxide‐producing microbial community from a subsurface granitic rock environment

Molecular analysis of microbial communities in mobile deltaic muds of Southeastern Papua New Guinea

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