Improvements in Extraction Methods of High-molecular-weight DNA from Soils by Modifying Cell Lysis Conditions and Reducing Adsorption of DNA onto Soil Particles.
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ABSTRACT:
SUBMITTER: Sakai Y
PROVIDER: S-EPMC8446751 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:This SuperSeries is composed of the SubSeries listed below.
2016-02-01 | GSE71470 | GEO
Project description:Polymer/graphene oxide (GO) nanocomposite particles were prepared via heteroflocculation between 140-220 nm cationic latex nanoparticles and anionic GO nanosheets in either acidic or basic conditions. It is demonstrated that nanocomposite particles can be formed using either poly(2-vinylpyridine)-b-poly(benzyl methacrylate) (P2VP-PBzMA) block copolymer nanoparticles prepared by reversible-addition chain-transfer (RAFT)-mediated polymerization-induced self-assembly (PISA), or poly(ethylene glycol)methacrylate (PEGMA)-stabilized P2VP latexes prepared by traditional emulsion polymerization. These two latexes are different morphologically as the P2VP-PBzMA block copolymer latexes have P2VP steric stabilizer chains in their corona, whereas the PEGMA-stabilized P2VP particles have a P2VP core and a nonionic steric stabilizer. Nevertheless, both the P2VP-PBzMA and PEGMA-stabilized P2VP latexes are cationic at low pH. Thus, the addition of GO to these latexes causes flocculation to occur immediately due to the opposite charges between the anionic GO nanosheets and cationic latexes. Control heteroflocculation experiments were conducted using anionic sterically stabilized poly(potassium 3-sulfopropyl methacrylate)-b-poly(benzyl methacrylate) (PKSPMA-PBzMA) and nonionic poly(benzyl methacrylate) (PBzMA) nanoparticles to demonstrate that polymer/GO nanocomposite particles were not formed. The degree of flocculation and the strength of electrostatic interaction between the cationic polymer latexes and GO were assessed using disc centrifuge photosedimentometry (DCP), transmission electron microscopy (TEM), and UV-visible spectrophotometry. These studies suggest that the optimal conditions for the formation of polymer/GO nanocomposite particles were GO contents between 10% and 20% w/w relative to latex, with the latexes containing P2VP in their corona having a stronger electrostatic attraction to the GO sheets.
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Project description:As our understanding of soil biology deepens, there is a growing demand for investigations addressing microbial processes in the earth beneath the topsoil layer, called subsoil. High clay content in subsoils often hinders the recovery of sufficient quantities of DNA as clay particles bind nucleic acids. Here, an efficient and reproducible DNA extraction method for 200 mg dried soil based on sodium dodecyl sulfate (SDS) lysis in the presence of phosphate buffer has been developed. The extraction protocol was optimized by quantifying bacterial 16S and fungal 18S rRNA genes amplified from extracts obtained by different combinations of lysis methods and phosphate buffer washes. The combination of one minute of bead beating, followed by ten min incubation at 65°C in the presence of 1 M phosphate buffer with 0.5% SDS, was found to produce the best results. The optimized protocol was compared with a commonly used cetyltrimethylammonium bromide (CTAB) method, using Phaeozem soil collected from 60 cm depth at a conventional agricultural field and validated on five subsoils. The reproducibility and robustness of the protocol was corroborated by an interlaboratory comparison. The DNA extraction protocol offers a reproducible and cost-effective tool for DNA-based studies of subsoil biology.
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Project description:Antibiotics used in agriculture may reach the environment and stimulate the development and dissemination of antibiotic resistance in the soil microbiome. However, the scope of this phenomenon and the link to soil properties needs to be elucidated. This study compared the short-term effects of a range of gentamicin concentrations on the microbiome and resistome of bacterial enrichments and microcosms of an agricultural soil using a metagenomic approach. Gentamicin impact on bacterial biomass was roughly estimated by the number of 16SrRNA gene copies. In addition, the soil microbiome and resistome response to gentamicin pollution was evaluated by 16SrRNA gene and metagenomic sequencing, respectively. Finally, gentamicin bioavailability in soil was determined. While gentamicin pollution at the scale of µg/g strongly influenced the bacterial communities in soil enrichments, concentrations up to 1 mg/g were strongly adsorbed onto soil particles and did not cause significant changes in the microbiome and resistome of soil microcosms. This study demonstrates the differences between the response of bacterial communities to antibiotic pollution in enriched media and in their environmental matrix, and exposes the limitations of culture-based studies in antibiotic-resistance surveillance. Furthermore, establishing links between the effects of antibiotic pollution and soil properties is needed.
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Project description:The adsorption of thallium (Tl) onto phyllosilicate minerals plays a critical role in the retention of Tl in soils and sediments and the potential transfer of Tl into plants and groundwater. Especially micaceous minerals are thought to strongly bind monovalent Tl(I), in analogy to their strong binding of Cs. To advance the understanding of Tl(I) adsorption onto phyllosilicate minerals, we studied the adsorption of Tl(I) onto Na- and K-saturated illite and Na-saturated smectite, two muscovites, two vermiculites and a naturally Tl-enriched soil clay mineral fraction. Macroscopic adsorption isotherms were combined with the characterization of the adsorbed Tl by X-ray absorption spectroscopy (XAS). In combination, the results suggest that the adsorption of Tl(I) onto phyllosilicate minerals can be interpreted in terms of three major uptake paths: (i) highest-affinity inner-sphere adsorption of dehydrated Tl+ on a very low number of adsorption sites at the wedge of frayed particle edges of illite and around collapsed zones in vermiculite interlayers through complexation between two siloxane cavities, (ii) intermediate-affinity inner-sphere adsorption of partially dehydrated Tl+ on the planar surfaces of illite and muscovite through complexation onto siloxane cavities, (iii) low-affinity adsorption of hydrated Tl+, especially in the hydrated interlayers of smectite and expanded vermiculite. At the frayed edges of illite particles and in the vermiculite interlayer, Tl uptake can lead to the formation of new wedge sites that enable further adsorption of dehydrated Tl+. On the soil clay fraction, a shift in Tl(I) uptake from frayed edge sites (on illite) to planar sites (on illite and muscovite) was observed with increasing Tl(I) loading. The results from this study show that the adsorption of Tl(I) onto phyllosilicate minerals follows the same trends as reported for Cs and Rb and thus suggests that concepts to describe the retention of (radio)cesium by different types of phyllosilicate minerals in soils, sediments and rocks are also applicable to Tl(I).
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Project description:Complexity and heterogeneity of soil samples have often implied the inclusion of purification steps in conventional DNA extraction for polymerase chain reaction (PCR) assays. Unfortunately the purification steps are also time and labor intensive. Therefore the necessity of DNA purification was re-visited and investigated for a variety of environmental soil samples that contained various amounts of PCR inhibitors. Bead beating and centrifugation was used as the baseline (without purification) method for DNA extraction. Its performance was compared with that of conventional DNA extraction kit (with purification). The necessity criteria for DNA purification were established with environmental soil samples. Using lysis conditions at 3000 rpm for 3 minutes with 0.1 mm glass beads, centrifugation time of 10 minutes and 1:10 dilution ratio, the baseline method outperformed conventional DNA extraction on cell seeded sand samples. Further investigation with PCR inhibitors (i.e., humic acids, clay, and magnesium [Mg]) showed that sand samples containing less than 10 ?g/g humic acids and 70% clay may not require purifications. Interestingly, the inhibition pattern of Mg ion was different from other inhibitors due to the complexation interaction of Mg ion with DNA fragments. It was concluded that DNA extraction method without purification is suitable for soil samples that have less than 10 ?g/g of humic acids, less than 70% clay content and less than 0.01% Mg ion content.
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Project description:The Onto-Tools suite is composed of an annotation database and six seamlessly integrated, web-accessible data mining tools: Onto-Express, Onto-Compare, Onto-Design, Onto-Translate, Onto-Miner and Pathway-Express. The Onto-Tools database has been expanded to include various types of data from 12 new databases. Our database now integrates different types of genomic data from 19 sequence, gene, protein and annotation databases. Additionally, our database is also expanded to include complete Gene Ontology (GO) annotations. Using the enhanced database and GO annotations, Onto-Express now allows functional profiling for 24 organisms and supports 17 different types of input IDs. Onto-Translate is also enhanced to fully utilize the capabilities of the new Onto-Tools database with an ultimate goal of providing the users with a non-redundant and complete mapping from any type of identification system to any other type. Currently, Onto-Translate allows arbitrary mappings between 29 types of IDs. Pathway-Express is a new tool that helps the users find the most interesting pathways for their input list of genes. Onto-Tools are freely available at http://vortex.cs.wayne.edu/Projects.html.
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Project description:Soils interact in many ways with metal ions thereby modifying their mobility, phase distribution, plant availability, speciation, and so on. The most prominent of such interactions is sorption. In this study, we investigated the sorption of Pb, Cd, and Cu in five natural soils of Nigerian origin. A relatively sparsely used method of modelling soil-metal ion adsorption, i.e. adaptive neuro-fuzzy inference system (ANFIS), was applied comparatively with multiple linear regression (MLR) models. The isotherms were well described by Freundlich and Langmuir equations (R2 ≥ 0.95) and the kinetics by nonlinear two-stage kinetic model, TSKM (R2 ≥ 0.81). Based on the values delivered by the Langmuir equation, the maximum adsorption capacities (Qm*) were found to be in the ranges 10,000-20,000, 12,500-50,000, and 4929-35,037 µmol kg-1 for Cd, Cu, and Pb, respectively. The study revealed significant correlations between Qm* and routinely determined soil parameters such as soil organic carbon (Corg), cation exchange capacity (CEC), amorphous Fe and Mn oxides, and percentage clay content. These soil parameters, combined with operational variables (i.e. solution/soil pH, initial metal concentration (Co), and temperature), were used as input vectors in ANFIS and MLR models to predict the adsorption capacities (Qe) of the soil-metal ion systems. A total of 255 different ANFIS and 255 different MLR architectures/models were developed and compared based on three performance metrics: MAE (mean absolute error), RMSE (root mean square errors), and R2 (coefficient of determination). The best ANFIS returned MAEtest 0.134, RMSEtest 0.164, and R2test 0.76, while the best MLR returned MAEtest 0.158, RMSEtest 0.199, and R2test 0.66, indicating the predictive advantage of ANFIS over MLR. Thus, ANFIS can fairly accurately predict the adsorption capacity and/or distribution coefficient of a soil-metal ion system a priori. Nevertheless, more investigation is required to further confirm the robustness/generalisation of the proposed ANFIS.
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