Academic literature on the topic 'Soil DNA'
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Journal articles on the topic "Soil DNA"
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Zanella, A. "Vegetation, soil, DNA and natural evolution." Forest@ - Rivista di Selvicoltura ed Ecologia Forestale 20, no. 1 (February 28, 2023): 10–12. http://dx.doi.org/10.3832/efor4285-019.
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Mahmoudi, Nagissa, Greg F. Slater, and Roberta R. Fulthorpe. "Comparison of commercial DNA extraction kits for isolation and purification of bacterial and eukaryotic DNA from PAH-contaminated soils." Canadian Journal of Microbiology 57, no. 8 (August 2011): 623–28. http://dx.doi.org/10.1139/w11-049.
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Molecular characterization of the microbial populations of soils and sediments contaminated with polycyclic aromatic hydrocarbons (PAHs) is often a first step in assessing intrinsic biodegradation potential. However, soils are problematic for molecular analysis owing to the presence of organic matter, such as humic acids. Furthermore, the presence of contaminants, such as PAHs, can cause further challenges to DNA extraction, quantification, and amplification. The goal of our study was to compare the effectiveness of four commercial soil DNA extraction kits (UltraClean Soil DNA Isolation kit, PowerSoil DNA Isolation kit, PowerMax Soil DNA Isolation kit, and FastDNA SPIN kit) to extract pure, high-quality bacterial and eukaryotic DNA from PAH-contaminated soils. Six different contaminated soils were used to determine if there were any biases among the kits due to soil properties or level of contamination. Extracted DNA was used as a template for bacterial 16S rDNA and eukaryotic 18S rDNA amplifications, and PCR products were subsequently analyzed using denaturing gel gradient electrophoresis (DGGE). We found that the FastDNA SPIN kit provided significantly higher DNA yields for all soils; however, it also resulted in the highest levels of humic acid contamination. Soil texture and organic carbon content of the soil did not affect the DNA yield of any kit. Moreover, a liquid–liquid extraction of the DNA extracts found no residual PAHs, indicating that all kits were effective at removing contaminants in the extraction process. Although the PowerSoil DNA Isolation kit gave relatively low DNA yields, it provided the highest quality DNA based on successful amplification of both bacterial and eukaryotic DNA for all six soils. DGGE fingerprints among the kits were dramatically different for both bacterial and eukaryotic DNA. The PowerSoil DNA Isolation kit revealed multiple bands for each soil and provided the most consistent DGGE profiles among replicates for both bacterial and eukaryotic DNA.
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Rosa, Márcia Maria, Sâmia Maria Tauk-Tornisielo, and Sandra Regina Ceccato-Antonini. "EVALUATION OF DIFFERENT TECHNIQUES FOR DNA DIRECT EXTRACTION FROM BRAZILIAN AGRICULTURAL SOIL." Holos Environment 10, no. 1 (October 5, 2010): 12. http://dx.doi.org/10.14295/holos.v10i1.1842.
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Soil is an ecosystem characterized by a great complexity and hard to study due to its heterogeneity, especially the soil microorganism’s community. Currently, molecular biology tools have been used to study the soil biodiversity mainly through microbial genes. DNA Direct Extraction from soil is an important step in this kind of study, however the majority of techniques were developed for soils from temperate climate and just a few can be applied efficiently to Brazilian soils. This work aimed to evaluate nine different techniques for soil DNA direct extraction from sugarcane crop areas under organic and conventional managements and also to propose modifications which might result in higher DNA yield and low cost. DNA bands were observed only for three techniques (Selbach´s, Direito´s and commercial kit), two of them already tested for tropical climate soils. The best results for DNA yield (µg.g-1 soil) were obtained through Selbach´s and commercial kit techniques, however not differing statistically from those results through a protocol here proposed. This modified protocol showed the best results for DNA yield whatever soil was used. The best DNA yields were found in soil under organic management probably due to higher microbial biomass. This protocol showed better results in yield of DNA regardless of the soil used and was easier to perform and less costly.
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Singh, Hina, KyungHwa Won, Hien T. T. Ngo, Juan Du, MooChang Kook, and Tae-Hoo Yi. "Phycicoccus soli sp. nov., isolated from soil." International Journal of Systematic and Evolutionary Microbiology 65, Pt_8 (August 1, 2015): 2351–56. http://dx.doi.org/10.1099/ijs.0.000265.
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A Gram-stain-positive, non-motile, coccus-shaped bacterium, strain THG-a14T, was isolated from soil of Gyeyang mountain in Incheon, Republic of Korea. The isolate grew optimally at 28 °C, at pH 6.5–7.5 and with 0–3 % (w/v) NaCl. Based on 16S rRNA gene sequence comparisons, strain THG-a14T was closely related to Phycicoccus aerophilus 5516T-20T (97.7 %), P. ginsenosidimutans BXN5-13T (97.6 %), ‘P. ochangensis’ L1b-b9 (97.4 %) and P. bigeumensis MSL-03 (97.2 %). The DNA G+C content of strain THG-a14T was 71.6 mol%. In DNA–DNA hybridization, the DNA–DNA relatedness between strain THG-a14T and its closest phylogenetically neighbours was below 50.0 %. Strain THG-a14T was characterized chemotaxonomically as having meso-diaminopimelic acid in the cell-wall peptidoglycan. Strain THG-a14T contained glucose and ribose as whole-cell-wall sugars and menaquinone MK-8(H4) as the major isoprenoid quinone. Polar lipids in strain THG-a14T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphoaminoglycolipids, unidentified phospholipids and unidentified lipids. The major fatty acids were iso-C16: 0, iso-C15: 0 and C17: 1ω8c. On the basis of our polyphasic taxonomy study, strain THG-a14T represents a novel species within the genus Phycicoccus, for which the name Phycicoccus soli sp. nov. is proposed. The type strain is THG-a14T ( = KACC 17892T = JCM 19837T).
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Huang, Danqiong, Guiping Yan, Neil C. Gudmestad, and Jonathan Whitworth. "Assessment of Factors Associated with Molecular Quantification of Stubby Root Nematode Paratrichodorus allius from Field Soil DNA." Plant Disease 103, no. 12 (December 2019): 3265–73. http://dx.doi.org/10.1094/pdis-12-18-2240-re.
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Factors relating to SYBR Green-based quantitative real-time PCR (qPCR) quantification of stubby root nematode Paratrichodorus allius using soil DNA were evaluated in this study. Soils used were loamy sand from potato fields in North Dakota and Idaho. Results showed that the largest nematode individuals (body length >720 µm) produced significant lower Cq values than the smallest individuals (<359 µm), indicating more total DNA amount in the largest nematodes. Soil pre-treatments showed that autoclaved field soil had significantly reduced DNA amount and quality. The air- or oven-dried soil yielded a lower amount of DNA with similar purity, compared with natural field soil. PCR inhibitors were detected in soil DNA substrates targeting pBluescript II SK(+)-plasmid DNA. Al(NH4)(SO4)2 treatment during DNA preparation significantly reduced the inhibitors compared with post-treatment of soil DNA with polyvinylpolypyrrolidone column. The effect of PCR inhibitors on qPCR was suppressed by bovine serum albumin. Quantification results did not significantly change when increasing the number of DNA extractions from three to six per soil sample when soil grinding and grid sampling strategies were used. Two standard curves, generated from serial dilutions of plasmid DNA containing P. allius ITS1 rDNA and soil DNA containing known nematode numbers, produced similar correlations between Cq values and amount of targets. The targets in soil DNA quantified by qPCR using either standard curve correlated well with microscopic observations using both artificially and naturally infested field soils. This is the first study for assessing various factors that may affect qPCR quantification of stubby root nematodes. Results will be useful during the setup or optimization of qPCR-based quantification of plant-parasitic nematodes from soil DNA.
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kheyrodin, Hamid. "Soil DNA Purification and Isolation." Global Journal of Agricultural Innovation, Research & Development 2, no. 2 (July 21, 2016): 43–48. http://dx.doi.org/10.15377/2409-9813.2015.02.02.2.
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Robe, Patrick, Renaud Nalin, Carmela Capellano, Timothy M. Vogel, and Pascal Simonet. "Extraction of DNA from soil." European Journal of Soil Biology 39, no. 4 (October 2003): 183–90. http://dx.doi.org/10.1016/s1164-5563(03)00033-5.
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Woods, Angela, Maribeth Watwood, and Egbert Schwartz. "Identification of a Toluene-Degrading Bacterium from a Soil Sample through H218O DNA Stable Isotope Probing." Applied and Environmental Microbiology 77, no. 17 (July 8, 2011): 5995–99. http://dx.doi.org/10.1128/aem.05689-11.
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ABSTRACTDNA stable isotope probing (DNA-SIP) with H218O was used to identify a toluene-degrading bacterium in soil amended with 48 ppm toluene. After quantification of toluene degradation rates in soil, DNA was extracted from soil incubated with H218O, H216O, H216O and 48 ppm toluene, or H218O and 48 ppm toluene. A single DNA band formed along a cesium chloride gradient after isopycnic centrifugation of extracts from soils incubated with H216O. With extracts from soils to which only H218O was added, two distinct DNA bands formed, while three bands formed when DNA extracted from soil incubated with both H218O and toluene was analyzed. We suggest that this third band formed because toluene does not contain any oxygen atoms and toluene-degrading organisms had to transfer oxygen atoms from H218O into metabolic intermediates to form nucleic acidsde novo. We extracted the third DNA band and amplified a large fraction of the bacterial 16S rRNA gene. Direct sequencing of the PCR product obtained from the labeled DNA, as well as cloned 16S rRNA amplicons, identified a known toluene degrader,Rhodococcus jostiiRHA1. A toluene-degrading bacterial strain was subsequently isolated from soil and shown to beRhodococcus jostiiRHA1. Finally, quantitative real-time PCR analysis showed that the abundance of the 16S rRNA gene ofRhodococcus jostiiRHA1 increased in soil after toluene exposure but not in soils from which toluene was withheld. This study indicates that H218O DNA-SIP can be a useful method for identifying pollutant-degrading bacteria in soil.
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Reavy, Brian, Maud M. Swanson, Peter J. A. Cock, Lorna Dawson, Thomas E. Freitag, Brajesh K. Singh, Lesley Torrance, Arcady R. Mushegian, and Michael Taliansky. "Distinct Circular Single-Stranded DNA Viruses Exist in Different Soil Types." Applied and Environmental Microbiology 81, no. 12 (April 3, 2015): 3934–45. http://dx.doi.org/10.1128/aem.03878-14.
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ABSTRACTThe potential dependence of virus populations on soil types was examined by electron microscopy, and the total abundance of virus particles in four soil types was similar to that previously observed in soil samples. The four soil types examined differed in the relative abundances of four morphological groups of viruses. Machair, a unique type of coastal soil in western Scotland and Ireland, differed from the others tested in having a higher proportion of tailed bacteriophages. The other soils examined contained predominantly spherical and thin filamentous virus particles, but the Machair soil had a more even distribution of the virus types. As the first step in looking at differences in populations in detail, virus sequences from Machair and brown earth (agricultural pasture) soils were examined by metagenomic sequencing after enriching for circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) virus genomes. Sequences from the familyMicroviridae(icosahedral viruses mainly infecting bacteria) of CRESS-DNA viruses were predominant in both soils. Phylogenetic analysis ofMicroviridaemajor coat protein sequences from the Machair viruses showed that they spanned most of the diversity of the subfamilyGokushovirinae, whose members mainly infect obligate intracellular parasites. The brown earth soil had a higher proportion of sequences that matched the morphologically similar familyCircoviridaein BLAST searches. However, analysis of putative replicase proteins that were similar to those of viruses in theCircoviridaeshowed that they are a novel clade ofCircoviridae-related CRESS-DNA viruses distinct from knownCircoviridaegenera. Different soils have substantially different taxonomic biodiversities even within ssDNA viruses, which may be driven by physicochemical factors.
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Wnuk, Ewa, Adam Waśko, Anna Walkiewicz, Piotr Bartmiński, Romualda Bejger, Lilla Mielnik, and Andrzej Bieganowski. "The effects of humic substances on DNA isolation from soils." PeerJ 8 (July 24, 2020): e9378. http://dx.doi.org/10.7717/peerj.9378.
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Background Humic substances (HS) are compounds with a complicated structure, present in the humus soil layer, water, lake sediments, peat, brown coal and shales. Due to their similar physicochemical properties to DNA, they may have an adverse effect on the subsequent use of the isolated material. The main aim of this research was to examine the effect of HS on DNA isolation depending on the soil type and land use, taking into account the spectroscopic full characteristics of HS fractions. Methods The research was conducted on eight types of soil sample. Soils represented the most important Soil Reference Groups for temperate climates: Fluvisols, Regosols, Cambisols, Arenosols, Histosols and Luvisols. Soil samples were also collected from areas diversified in terms of use: arable land, grassland and forest. The extraction of HS fractions was performed using the procedure recommended by the International HS Society. The fractional composition of HS was characterized by UV–Vis and fluorescence methods. Soil DNA is extracted by direct cell lysis in the using a CTAB-based method with a commonly-used commercial soil DNA isolation kit. The basis for assessing the quantity and quality of extracted DNA was the Polymerase chain reaction (PCR) reaction since the analysis of soil DNA often relies on the use of PCR to study soil microorganisms. Results Based on the results, it can be concluded that in the presence of a high concentration of HS, the isolated DNA was low quality and the additional purification procedure was necessary. Despite the differentiation of the internal structure of HS fractions, the decisive factor in the efficiency of DNA isolation from soil samples was the total carbon content in HS. Reduced DNA yields can significantly constrain PCR detection limits to levels inadequate for metagenomic analysis, especially from humus-rich soils.
Dissertations / Theses on the topic "Soil DNA"
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Mueller, Sabrina R. "Chromium, DNA, and Soil Microbial Communities." Cincinnati, Ohio : University of Cincinnati, 2006. http://rave.ohiolink.edu/etdc/view.cgi?acc_num=ucin1141334651.
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Thesis (Ph. D.)--University of Cincinnati, 2008.Advisor: Brian K. Kinkle. Title from electronic thesis title page (viewed Apr. 23, 2009). Keywords: SEC-ICP-MS; Fungal community; bacterial community; DGGE. Includes abstract. Includes bibliographical references.
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Kapadia, Jaimin Maheshbhai. "DNA transfer in the soil bacterium Rhodococcus." Digital Commons @ East Tennessee State University, 2020. https://dc.etsu.edu/honors/565.
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Gene transfer plays an important role in bacterial evolution. Especially in an under explored species like Rhodococcus, a type of bacteria found in the soil. Rhodococcus has several applications in the pharmaceutical industry and in the production of antibiotics. Rhodococcus possess several unique sets of properties which makes it beneficial to have a reliable method of producing mutants of Rhodococcus. The goal of the experiment was to find an efficient way of forming Rhodococcus colonies with kanamycin resistant genes. The project began from an unexpected observation from an earlier experiment with Rhodococcus strain MTM3W5.2. where I attempted to transform this strain with a transposon via electro-transformation. The colonies that grew/ appeared transformants were screened to confirm the presence of kanamycin gene, however there was no amplified DNA seen on the PCR gel (i.e. absence of the kanamycin gene). The electro-transformant colonies were selected on LB plates containing different higher concentrations of kanamycin. Then the appeared transformants were again screened via disk diffusion assay and were classified into 3 different kanamycin resistant phenotypes. Majority of the “C” phenotypic colonies (i.e., high level resistance to kanamycin) appear to contain the kanamycin gene, but these colonies were less in numbers. This led us to try another method of gene transfer which is conjugation. Conjugation was carried on a double selection antibiotic plate containing both chloramphenicol (30 µg) and kanamycin (100 µg). The transconjugate colonies that appeared on the double selection plates were also screened by PCR, but none of the colonies had amplified DNA suggesting absence of the kanamycin gene. The colonies seen on the double selection plate were possibly due to spontaneous mutation or some type of unknown phenotypic variation. However, in the future, double selection plates with higher concentrations of antibiotics can possibly give us transconjugants with kanamycin genes.
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au, N. Williams@murdoch edu, and Nari Michelle Anderson. "DNA methods for the detection of Phytophthora cinnamomi from soil." Murdoch University, 2006. http://wwwlib.murdoch.edu.au/adt/browse/view/adt-MU20070820.130155.
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This project assesses two aspects of DNA detection of Phytophthora species from soil samples. Firstly, a nested PCR protocol was established with both primary and nested PCR specific for P. cinnamomi detection. PCR amplification of P. cinnamomi DNA isolated from soil was optimised with the addition of bovine serum albumin and formamide. This was found to improve both the specificity and sensitivity of PCR amplification of DNA in the presence of inhibitors co-extracted along with the target DNA from soil samples. The application of diagnostic nested PCR with the addition of BSA and formamide was verified by comparison with routine culture based detection methods. In all cases, nested PCR detection incorporating BSA and formamide was found to be considerably more sensitive than the culture based detection methods.
The second component of this thesis investigates the simultaneous detection of multiple species of Phytophthora using microarray analysis. Microarray based detection has been previously limited by variable and inconsistent hybridisation intensities across the diversity of probes used in each array. In this study a novel concept for the differentiation of detection targets using duplex melting kinetics is introduced. A microarray assay was developed on a PamChip ¥ microarray enabling the differentiation of target Phytophthora species using the melting kinetics of probe-target duplexes. In the majority of cases the hybridization kinetics of target and non-target duplexes differed significantly. Analysis of the melting kinetics of duplexes formed by probes with target and non-target DNA was found to be an effective method for determining specific hybridization and was independent of fluctuations in hybridization signal intensity. This form of analysis was more robust than the traditional approach based on hybridisation intensity, and allowed the detection of individual Phytophthora species and mixtures there of.
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Anderson, Nari Michelle. "DNA methods for the detection of Phytophthora cinnamomi from soil." Thesis, Anderson, Nari Michelle (2006) DNA methods for the detection of Phytophthora cinnamomi from soil. PhD thesis, Murdoch University, 2006. https://researchrepository.murdoch.edu.au/id/eprint/42/.
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This project assesses two aspects of DNA detection of Phytophthora species from soil samples. Firstly, a nested PCR protocol was established with both primary and nested PCR specific for P. cinnamomi detection. PCR amplification of P. cinnamomi DNA isolated from soil was optimised with the addition of bovine serum albumin and formamide. This was found to improve both the specificity and sensitivity of PCR amplification of DNA in the presence of inhibitors co-extracted along with the target DNA from soil samples. The application of diagnostic nested PCR with the addition of BSA and formamide was verified by comparison with routine culture based detection methods. In all cases, nested PCR detection incorporating BSA and formamide was found to be considerably more sensitive than the culture based detection methods.
The second component of this thesis investigates the simultaneous detection of multiple species of Phytophthora using microarray analysis. Microarray based detection has been previously limited by variable and inconsistent hybridisation intensities across the diversity of probes used in each array. In this study a novel concept for the differentiation of detection targets using duplex melting kinetics is introduced. A microarray assay was developed on a PamChip microarray enabling the differentiation of target Phytophthora species using the melting kinetics of probe-target duplexes. In the majority of cases the hybridization kinetics of target and non-target duplexes differed significantly. Analysis of the melting kinetics of duplexes formed by probes with target and non-target DNA was found to be an effective method for determining specific hybridization and was independent of fluctuations in hybridization signal intensity. This form of analysis was more robust than the traditional approach based on hybridisation intensity, and allowed the detection of individual Phytophthora species and mixtures there of.
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Anderson, Nari Michelle. "DNA methods for the detection of Phytophthora cinnamomi from soil." Anderson, Nari Michelle (2006) DNA methods for the detection of Phytophthora cinnamomi from soil. PhD thesis, Murdoch University, 2006. http://researchrepository.murdoch.edu.au/42/.
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This project assesses two aspects of DNA detection of Phytophthora species from soil samples. Firstly, a nested PCR protocol was established with both primary and nested PCR specific for P. cinnamomi detection. PCR amplification of P. cinnamomi DNA isolated from soil was optimised with the addition of bovine serum albumin and formamide. This was found to improve both the specificity and sensitivity of PCR amplification of DNA in the presence of inhibitors co-extracted along with the target DNA from soil samples. The application of diagnostic nested PCR with the addition of BSA and formamide was verified by comparison with routine culture based detection methods. In all cases, nested PCR detection incorporating BSA and formamide was found to be considerably more sensitive than the culture based detection methods.
The second component of this thesis investigates the simultaneous detection of multiple species of Phytophthora using microarray analysis. Microarray based detection has been previously limited by variable and inconsistent hybridisation intensities across the diversity of probes used in each array. In this study a novel concept for the differentiation of detection targets using duplex melting kinetics is introduced. A microarray assay was developed on a PamChip microarray enabling the differentiation of target Phytophthora species using the melting kinetics of probe-target duplexes. In the majority of cases the hybridization kinetics of target and non-target duplexes differed significantly. Analysis of the melting kinetics of duplexes formed by probes with target and non-target DNA was found to be an effective method for determining specific hybridization and was independent of fluctuations in hybridization signal intensity. This form of analysis was more robust than the traditional approach based on hybridisation intensity, and allowed the detection of individual Phytophthora species and mixtures there of.
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Kasu, Mohaimin. "The validation of forensic DNA extraction systems to utilize soil contaminated biological evidence." Master's thesis, University of Cape Town, 2013. http://hdl.handle.net/11427/5921.
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Smart, Trevor Blake. "Microbial Community Response to Fumigation in Potato Soils." BYU ScholarsArchive, 2018. https://scholarsarchive.byu.edu/etd/7355.
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Soil microorganisms have a variety of beneficial and deleterious effects on plants, impacting such processes as plant growth, soil nutrient cycling, crop yield, disease resistance and tolerance to an array of biotic and abiotic stressors. The disruption of soil microbial community structures, particularly when beneficial soil biota are altered, has been shown to reduce crop yield and leave plants susceptible to disease. Long-term disruption of microbial communities may occur with repeated fumigation, being the application of gaseous pesticides, in agricultural soils. For this reason, we characterized bacterial, fungal, oomycete and nematode populations in paired fumigated and nonfumigated potato fields located in Idaho, Oregon, Washington and Minnesota. Samples were taken at three distinct timepoints: one before a fall fumigation event and two others at important stages in potato production, row closure and vine death. Soil biota populations were assessed by targeting the 16S, 18S and ITS1 gene regions. FunGuild, a database capable of guild and trophic assignment of fungal lineages, was used to sort fungal OTUs in different trophic modes. Fungal analyses indicated an increase in relative abundances of saprotrophic fungal populations and a decrease in pathotrophic fungal populations, both during row closure. Principally, the fungal genera of Humicola and Mortierella were responsible for the increase of saprotrophs while Alternaria decreased the most for pathotrophs. Other fungi occupying multiple trophic modes, such as Fusarium, also decreased during row closure. We found that fumigation treatments, in combination with various pesticide and fertilizer applications, alter both alpha- and beta- bacterial soil diversity although certain treatments, i.e. chloropicrin, may alter bacterial populations more than other treatment types such as metam-sodium. Nematode populations were likewise distinct at each location with soils from Boardman, OR, Minidoka, ID and Pine Point, MN with these having higher levels of nematodes associated with better soil health, i.e. Dorylaimidae. Conversely, nematodes associated with plant pathogenesis were found in higher relative abundances at Minidoka, ID and Quincy, WA. In this study, we characterize the populations of bacteria, fungi, oomycetes and nematodes with an emphasis on fungal taxa. We found that relative abundances of fungal trophic modes vary temporally. Additionally, we catalogue several other high abundance taxa with seasonal differential abundances whose functional capacity in potatoes remain uncharacterized.
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He, Jizheng, and n/a. "Molecular Biological Studies of Soil Microbial Communities Under Different Management Practices in Forest Ecosystems of Queensland." Griffith University. Australian School of Environmental Studies, 2005. http://www4.gu.edu.au:8080/adt-root/public/adt-QGU20060309.095702.
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Soil microorganisms play important roles in maintaining soil quality and ecosystem health. Development of effective methods for studying the composition, diversity, and behavior of microorganisms in soil habitats is essential for a broader understanding of soil quality. Forest management strategies and practices are of vital significance for sustainable forest production. How the different forest management measures will influence soil microbial communities is a widespread concern of forest industry and scientific communities. Only a small proportion (~0.1%) of the bacteria from natural habitats can be cultured on laboratory growth media. Direct extraction of whole-community DNA from soil, followed by polymerase chain reaction (PCR) and other analysis circumvents the problems of the culture-dependent methods and may shed light on a broader range of microbial communities in the soil. DNA-based molecular methods rely on high quality soil microbial DNA as template, and thus extraction of good quality DNA from soil samples has been a challenge because of the complex and heterogeneous nature of the soil matrix. The objectives of this research were to establish a set of DNA-based molecular methods and to apply them to investigate forest soil microbial composition and diversity. Soil samples were collected from different forest ecosystems, i.e., the natural forest (YNF) and the first rotation (~ 50 years) (Y1R) and the second rotation (~ 1 year) (Y2R) of hoop pine plantations at Yarraman, and from different forest residue management practices (the experiments had established 6.4 years before the samples were collected) at Gympie, two long-term experimental sites of the Queensland Department of Primary Industry-Forestry in subtropical Queensland, Australia. Some DNA-based molecular techniques, including DNA extraction and purification, PCR amplification, DNA screening, cloning, sequencing and phylogenetic analyses, were explored using Yarraman soil samples, which were high in organic matter, clay and iron oxide contents. A set of methods was assembled based on the recommendations of the method development experiments and applied to the investigations of the microbial composition and diversity of the Yarraman and Gympie soil samples. Four soil DNA extraction methods, including the Zhou method (Zhou et al., 1996), the Holben method (Holben, 1994), the UltraClean (Mo Bio) and FastDNA (Bio 101) soil DNA extraction kits, were explored. It was necessary to modify these methods for Yarraman soil. I designed and introduced a pre-lysis buffer washing step, to partially remove soil humic substances and promote soil dispersion. This modification greatly improved the quality of the extracted DNA, decreasing co-extracted humic substances by 31% and increasing DNA yield by 24%. The improved Holben method was recommended for fungal community studies, and the improved Zhou method for bacterial community studies. The extracted DNA was good in quality, with a consistent size of ~20 kb and a yield of 48-87 g g-1 soil, and could be successfully used for 16S (Zhou method) and 18S (Holben method) rDNA amplifications. For less difficult environmental samples, UltraClean kits could be a good option, because they are simple and fast and the extracted DNA are also of good quality. Screening of the DNA PCR products using TGGE, Heteroduplex-TGGE and SSCP was also explored. These methods were not so effective for the screening of the soil DNA PCR products, owing to the difficulty in interpretation of the results. Cloning was a necessary step to obtain a single sequence at species level in soil microbial community studies. The screening of the clone library by TGGE, Heteroduplex-TGGE and SSCP could only separate the clones into several major bands, although SSCP gave better separation. Sequencing of selected clones directly from the clone library obtained ultimate results of microbial taxonomic composition and diversity through well-established sequence analysis software packages and the databases. It was recommended that, in this project with the target of microbial community composition and diversity, soil DNA PCR products were directly cloned to construct clone libraries and a sample of clones were sequenced to achieve an estimate of the taxonomic composition of the soil. Fungal communities of the Yarraman soil samples under the natural forest (YNF) and the hoop pine plantations (YHP) were investigated using 18S rDNA based cloning and sequencing approaches. Twenty-eight clone sequences were obtained and analysed. Three fungal orders, i.e., Zygomycota, Ascomycota and Basidiomycota were detected from the YNF and YHP samples. By contrast, culture-based analyses of fungi in the literature were mostly Ascomycetes. YNF appeared to have more Ascomycota but less Zygomycota than YHP, and within the Zygomycota order, YHP had more unidentified species than YNF. Bacterial communities of Yarraman soil samples of YNF, Y1R and Y2R were investigated using 16S rDNA-based cloning and sequencing approaches. 305 16S rDNA clone sequences were analysed and showed an overall bacterial community composition of Unclassified bacteria (34.4%), Proteobacteria (22.0%), Verrucomicrobia (15.7%), Acidobacteria (10.2%), Chloroflexi (6.9%), Gemmatimonadetes (5.6%), and Actinobacteria (5.2%). There was a significant difference among YNF, Y1R and Y2R in the taxonomic group composition. YNF had a greater proportion of Acidobacteria (18.0%), Verrucomicrobia (23.0%) and Chloroflexi (9.0%) than Y1R and Y2R (corresponding to 6.3%, 12.1% and 5.9%, respectively), while Y1R and Y2R had a higher percentage of the Unclassified group (38.5% for Y1R and 46.5% for Y2R) than YNF (18.0%). For the Proteobacteria group, YNF had more Alpha-subdivision but Y1R and Y2R had more Delta-subdivision. From YNF to Y1R to Y2R, the clone sequence variable site ratios, 5% and 10% OTU numbers and Shannon's diversity index H' values tended to decrease, indicating the soil bacterial diversity decreased from the natural forest to the first and the second rotation hoop pine plantations. The large amount of unclassified clone sequences could imply a novel group of bacteria in the soil, particularly in the hoop pine soil samples. Alternatively they may result from artefacts during the PCR process. Bacterial communities of the Gympie soil under different residue management practices, i.e., residue (litter plus logging residue) removed (G0R), residue retained (G1R), and residue doubled (G2R), were also investigated using the 16S rDNA-based cloning and sequencing approaches. Acidobacteria (37.6%) and Proteobacteria (35.6%, including Alpha-subdivision of 29.9% and Gamma-subdivision of 5.7%) were dominant components of the communities, followed by Actinobacteria (14.7%), Verrucomicrobia (7.3%) and Unclassified bacteria. There was no significant difference among G0R, G1R and G2R in the bacterial community compositions and diversity. These findings provided an in-depth vision of the soil microbial communities under different forest management practices. Their combination with other soil analysis results, such as physical and chemical properties, and forest production data, could provide an improved understanding of sustainable forest management strategies.
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He, Jizheng. "Molecular Biological Studies of Soil Microbial Communities Under Different Management Practices in Forest Ecosystems of Queensland." Thesis, Griffith University, 2005. http://hdl.handle.net/10072/367075.
Full textAbstract:
Soil microorganisms play important roles in maintaining soil quality and ecosystem health. Development of effective methods for studying the composition, diversity, and behavior of microorganisms in soil habitats is essential for a broader understanding of soil quality. Forest management strategies and practices are of vital significance for sustainable forest production. How the different forest management measures will influence soil microbial communities is a widespread concern of forest industry and scientific communities. Only a small proportion (~0.1%) of the bacteria from natural habitats can be cultured on laboratory growth media. Direct extraction of whole-community DNA from soil, followed by polymerase chain reaction (PCR) and other analysis circumvents the problems of the culture-dependent methods and may shed light on a broader range of microbial communities in the soil. DNA-based molecular methods rely on high quality soil microbial DNA as template, and thus extraction of good quality DNA from soil samples has been a challenge because of the complex and heterogeneous nature of the soil matrix. The objectives of this research were to establish a set of DNA-based molecular methods and to apply them to investigate forest soil microbial composition and diversity. Soil samples were collected from different forest ecosystems, i.e., the natural forest (YNF) and the first rotation (~ 50 years) (Y1R) and the second rotation (~ 1 year) (Y2R) of hoop pine plantations at Yarraman, and from different forest residue management practices (the experiments had established 6.4 years before the samples were collected) at Gympie, two long-term experimental sites of the Queensland Department of Primary Industry-Forestry in subtropical Queensland, Australia. Some DNA-based molecular techniques, including DNA extraction and purification, PCR amplification, DNA screening, cloning, sequencing and phylogenetic analyses, were explored using Yarraman soil samples, which were high in organic matter, clay and iron oxide contents. A set of methods was assembled based on the recommendations of the method development experiments and applied to the investigations of the microbial composition and diversity of the Yarraman and Gympie soil samples. Four soil DNA extraction methods, including the Zhou method (Zhou et al., 1996), the Holben method (Holben, 1994), the UltraClean (Mo Bio) and FastDNA (Bio 101) soil DNA extraction kits, were explored. It was necessary to modify these methods for Yarraman soil. I designed and introduced a pre-lysis buffer washing step, to partially remove soil humic substances and promote soil dispersion. This modification greatly improved the quality of the extracted DNA, decreasing co-extracted humic substances by 31% and increasing DNA yield by 24%. The improved Holben method was recommended for fungal community studies, and the improved Zhou method for bacterial community studies. The extracted DNA was good in quality, with a consistent size of ~20 kb and a yield of 48-87 g g-1 soil, and could be successfully used for 16S (Zhou method) and 18S (Holben method) rDNA amplifications. For less difficult environmental samples, UltraClean kits could be a good option, because they are simple and fast and the extracted DNA are also of good quality. Screening of the DNA PCR products using TGGE, Heteroduplex-TGGE and SSCP was also explored. These methods were not so effective for the screening of the soil DNA PCR products, owing to the difficulty in interpretation of the results. Cloning was a necessary step to obtain a single sequence at species level in soil microbial community studies. The screening of the clone library by TGGE, Heteroduplex-TGGE and SSCP could only separate the clones into several major bands, although SSCP gave better separation. Sequencing of selected clones directly from the clone library obtained ultimate results of microbial taxonomic composition and diversity through well-established sequence analysis software packages and the databases. It was recommended that, in this project with the target of microbial community composition and diversity, soil DNA PCR products were directly cloned to construct clone libraries and a sample of clones were sequenced to achieve an estimate of the taxonomic composition of the soil. Fungal communities of the Yarraman soil samples under the natural forest (YNF) and the hoop pine plantations (YHP) were investigated using 18S rDNA based cloning and sequencing approaches. Twenty-eight clone sequences were obtained and analysed. Three fungal orders, i.e., Zygomycota, Ascomycota and Basidiomycota were detected from the YNF and YHP samples. By contrast, culture-based analyses of fungi in the literature were mostly Ascomycetes. YNF appeared to have more Ascomycota but less Zygomycota than YHP, and within the Zygomycota order, YHP had more unidentified species than YNF. Bacterial communities of Yarraman soil samples of YNF, Y1R and Y2R were investigated using 16S rDNA-based cloning and sequencing approaches. 305 16S rDNA clone sequences were analysed and showed an overall bacterial community composition of Unclassified bacteria (34.4%), Proteobacteria (22.0%), Verrucomicrobia (15.7%), Acidobacteria (10.2%), Chloroflexi (6.9%), Gemmatimonadetes (5.6%), and Actinobacteria (5.2%). There was a significant difference among YNF, Y1R and Y2R in the taxonomic group composition. YNF had a greater proportion of Acidobacteria (18.0%), Verrucomicrobia (23.0%) and Chloroflexi (9.0%) than Y1R and Y2R (corresponding to 6.3%, 12.1% and 5.9%, respectively), while Y1R and Y2R had a higher percentage of the Unclassified group (38.5% for Y1R and 46.5% for Y2R) than YNF (18.0%). For the Proteobacteria group, YNF had more Alpha-subdivision but Y1R and Y2R had more Delta-subdivision. From YNF to Y1R to Y2R, the clone sequence variable site ratios, 5% and 10% OTU numbers and Shannon's diversity index H' values tended to decrease, indicating the soil bacterial diversity decreased from the natural forest to the first and the second rotation hoop pine plantations. The large amount of unclassified clone sequences could imply a novel group of bacteria in the soil, particularly in the hoop pine soil samples. Alternatively they may result from artefacts during the PCR process. Bacterial communities of the Gympie soil under different residue management practices, i.e., residue (litter plus logging residue) removed (G0R), residue retained (G1R), and residue doubled (G2R), were also investigated using the 16S rDNA-based cloning and sequencing approaches. Acidobacteria (37.6%) and Proteobacteria (35.6%, including Alpha-subdivision of 29.9% and Gamma-subdivision of 5.7%) were dominant components of the communities, followed by Actinobacteria (14.7%), Verrucomicrobia (7.3%) and Unclassified bacteria. There was no significant difference among G0R, G1R and G2R in the bacterial community compositions and diversity. These findings provided an in-depth vision of the soil microbial communities under different forest management practices. Their combination with other soil analysis results, such as physical and chemical properties, and forest production data, could provide an improved understanding of sustainable forest management strategies.Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Australian School of Environmental Studies
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Spiegelman, Dan. "Exploring the fusion of metagenomic library and DNA microarray technologies." Thesis, McGill University, 2006. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=98805.
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We explored the combination of metagenomic library and DNA microarray technologies into a single platform as a novel way to rapidly screen metagenomic libraries for genetic targets. In the "metagenomic microarray" system, metagenomic library clone DNA is printed on a microarray surface, and clones of interest are detected by hybridization to single-gene probes. This study represents the initial steps in the development of this technology. We constructed two 5,000-clone large-insert metagenomic libraries from two diesel-contaminated Arctic soil samples. We developed and optimized an automated fosmid purification protocol to rapidly-extract clone DNA in a high-throughput 96-well format. We then created a series of small prototype arrays to optimize various parameters of microarray printing and hybridization, to identify and resolve technical challenges, and to provide proof-of-principle of this novel application. Our results suggest that this method shows promise, but more experimentation must be done to establish the feasibility of this approach.
Books on the topic "Soil DNA"
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Sawicki, Andrzej. Mechanika gruntów dla obciążeń cyklicznych. Gdańsk: Wydawn. IBW PAN, 1991.
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Utomo, Wani Hadi. Konservasi tanah di Indonesia: Suatu rekaman dan analisa. Jakarta: Rajawali Pers, 1989.
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A, Crossley D., and Hendrix Paul F, eds. Fundamentals of soil ecology / David C. Coleman, D.A. Crossley, Jr., Paul F. Hendrix. 2nd ed. Amsterdam: Elsevier Academic Press, 2004.
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Sekilas soal sastra dan budaya. Jakarta: Balai Pustaka, 1992.
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Chatamarrasjid. Penerobosan cadar perseroan dan soal-soal aktual hukum perusahaan. Bandung: Citra Aditya Bakti, 2004.
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Bilski, Jerzy. Zakwaszenie i zasolenie podłoża jako czynniki stresowe dla roślin. Warszawa: Państwowe Wydawn. Nauk., 1990.
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Cori, Patricia. The starseed dialogues: Soul searching the universe. Berkeley, Calif: North Atlantic Books, 2008.
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Jun, Tsuji. The soul of DNA: The true story of a Catholic sister and her role in the greatest scientific discovery of the twentieth century. Coral Springs, FL: Llumina Press, 2004.
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al-Hafiz, Abu Hassan Din. Soal jawab seks, perkahwinan dan keluarga Islam. 3rd ed. Kuala Lumpur: Pustaka al-Mizan, 1988.
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Bahrul, Hayat. Penggunaan bentuk soal pilihan ganda dan uraian. Jakarta: Departemen Pendidikan dan Kebudayaan, Badan Penelitian dan Pengembangan Pendidikan dan Kebudayaan, Pusat Penelitian dan Pengembangan Sistem Pengujian, 1997.
Find full textBook chapters on the topic "Soil DNA"
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Huang, Yu-Tuan, David J. Lowe, G. Jock Churchman, Louis A. Schipper, Nicolas J. Rawlence, and Alan Cooper. "Carbon Storage and DNA Adsorption in Allophanic Soils and Paleosols." In Soil Carbon, 163–72. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-04084-4_17.
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Myrold, David D., Kendall J. Martin, and Nancy J. Ritchie. "Gel purification of soil DNA extracts." In Molecular Microbial Ecology Manual, 79–87. Dordrecht: Springer Netherlands, 1995. http://dx.doi.org/10.1007/978-94-011-0351-0_8.
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Nazar, Ross N., E. Jane Robb, and Tatiana Volossiouk. "Direct extraction of fungal DNA from soil." In Molecular Microbial Ecology Manual, 1–8. Dordrecht: Springer Netherlands, 1996. http://dx.doi.org/10.1007/978-94-009-0215-2_1.
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Amorim, Jaime Henrque, João Carlos Teixeira Dias, and Rachel Rezende. "DNA Extraction Methods, RAPD Profiling, Landfarm Soil." In Encyclopedia of Metagenomics, 1–3. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-6418-1_727-2.
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Subbotin, Sergei A. "Phylogenetic analysis of DNA sequence data." In Techniques for work with plant and soil nematodes, 265–82. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781786391759.0265.
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Abstract The goal of phylogenetics is to construct relationships that are true representations of the evolutionary history of a group of organisms or genes. The history inferred from phylogenetic analysis is usually depicted as branching in tree-like diagrams or networks. In nematology, phylogenetic studies have been applied to resolve a wide range of questions dealing with improving classifications and testing evolution processes, such as co-evolution, biogeography and many others. There are several main steps involved in a phylogenetic study: (i) selection of ingroup and outgroup taxa for a study; (ii) selection of one or several gene fragments for a study; (iii) sample collection, obtaining PCR products and sequencing of gene fragments; (iv) visualization, editing raw sequence data and sequence assembling; (v) search for sequence similarity in a public database; (vi) making and editing multiple alignment of sequences; (vii) selecting appropriate DNA model for a dataset; (viii) phylogenetic reconstruction using minimum evolution, maximum parsimony, maximum likelihood and Bayesian inference; (ix) visualization of tree files and preparation of tree for a publication; and (x) sequence submission to a public database. Molecular phylogenetic study requires particularly careful planning because it is usually relatively expensive in terms of the cost in reagents and time.
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Subbotin, Sergei A. "Phylogenetic analysis of DNA sequence data." In Techniques for work with plant and soil nematodes, 265–82. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781786391759.0015.
Full textAbstract:
Abstract The goal of phylogenetics is to construct relationships that are true representations of the evolutionary history of a group of organisms or genes. The history inferred from phylogenetic analysis is usually depicted as branching in tree-like diagrams or networks. In nematology, phylogenetic studies have been applied to resolve a wide range of questions dealing with improving classifications and testing evolution processes, such as co-evolution, biogeography and many others. There are several main steps involved in a phylogenetic study: (i) selection of ingroup and outgroup taxa for a study; (ii) selection of one or several gene fragments for a study; (iii) sample collection, obtaining PCR products and sequencing of gene fragments; (iv) visualization, editing raw sequence data and sequence assembling; (v) search for sequence similarity in a public database; (vi) making and editing multiple alignment of sequences; (vii) selecting appropriate DNA model for a dataset; (viii) phylogenetic reconstruction using minimum evolution, maximum parsimony, maximum likelihood and Bayesian inference; (ix) visualization of tree files and preparation of tree for a publication; and (x) sequence submission to a public database. Molecular phylogenetic study requires particularly careful planning because it is usually relatively expensive in terms of the cost in reagents and time.
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Subbotin, Sergei A. "Molecular identification of nematodes using polymerase chain reaction (PCR)." In Techniques for work with plant and soil nematodes, 218–39. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781786391759.0218.
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Abstract Molecular diagnostics are a vital component of the management of economically important pests, including plant-parasitic nematodes. Various molecular techniques for diagnostics have been introduced to nematology during last decades, but the most popular is Polymerase Chain Reaction (PCR) based. This chapter presents procedures for DNA extraction, PCR techniques, cloning and DNA sequencing of nematodes.
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Subbotin, Sergei A. "Molecular identification of nematodes using polymerase chain reaction (PCR)." In Techniques for work with plant and soil nematodes, 218–39. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781786391759.0012a.
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Abstract Molecular diagnostics are a vital component of the management of economically important pests, including plant-parasitic nematodes. Various molecular techniques for diagnostics have been introduced to nematology during last decades, but the most popular is Polymerase Chain Reaction (PCR) based. This chapter presents procedures for DNA extraction, PCR techniques, cloning and DNA sequencing of nematodes.
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Selenska, Sonja, and Walter Klingmüller. "Direct Detection of E.Agglomerans DNA Sequences in Soil." In The Release of Genetically Modified Microorganisms—REGEM 2, 157–59. Boston, MA: Springer US, 1992. http://dx.doi.org/10.1007/978-1-4613-0493-7_22.
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Selenska, S., S. Schentzinger, and W. Klingmüller. "Direct Detection of Particular DNA Sequences in Soil." In Gene Transfers and Environment, 3–7. Berlin, Heidelberg: Springer Berlin Heidelberg, 1992. http://dx.doi.org/10.1007/978-3-642-77450-8_1.
Full textConference papers on the topic "Soil DNA"
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Chengyou Cao, Min Yang, Xiaojiao Xu, and Ying Zhang. "Technologies of extraction and purification of microbial total DNA from a meadow soil." In 2011 International Conference on Remote Sensing, Environment and Transportation Engineering (RSETE). IEEE, 2011. http://dx.doi.org/10.1109/rsete.2011.5966032.
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Sidarenka, A. V., H. A. Bareika, L. N. Valentovich, D. S. Paturemski, V. N. Kuptsou, M. A. Titok, and E. I. Kalamiyets. "Molecular diagnostics of bacterial and fungal plant diseases." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.229.
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Taxon-specific primers were developed and PCR conditions were optimized for diagnostics of bacterial and fungal plant pathogens. Methods for phytopathogens DNA isolation from plant material, soil and water were selected.
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"Time series regression uncovers significant correlation between soil microbial DNA concentration and enzymatic glucose neo-generation." In 22nd International Congress on Modelling and Simulation. Modelling and Simulation Society of Australia and New Zealand (MSSANZ), Inc., 2017. http://dx.doi.org/10.36334/modsim.2017.a5.ives.
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Ali, Muhammad Asad, Khushi Muhammad, Aftab Ahmad Anjum, Mansur-ud-Din Ahmad, Masood Rabbani, Muhammad Zubair Shabbir, Arfan Ahmad, et al. "Association of soil chemistry and other factors with spatially distributed Burkholderia mallei DNA in Punjab province, Pakistan." In 2017 14th International Bhurban Conference on Applied Sciences and Technology (IBCAST). IEEE, 2017. http://dx.doi.org/10.1109/ibcast.2017.7868058.
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Huang, Doreen Yu-Tuan, Saúl Rodriguez, Jonatan Klaminder, Andy Dugmore, and Nick Cutler. "Using soil ancient DNA for the reconstruction of past environments: insights in the new applications of paleosols on well-dated tephras." In Goldschmidt2021. France: European Association of Geochemistry, 2021. http://dx.doi.org/10.7185/gold2021.6320.
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Taura, Usman, Sara Al-Araimi, Saif Al-Bahry, Yahya Al-Wahaibi, and Lujain Al-Rashdi. "Isolation of Autochthonous Consortium for the Bioremediation of Oil Contaminated Produced Water." In SPE Nigeria Annual International Conference and Exhibition. SPE, 2022. http://dx.doi.org/10.2118/212024-ms.
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Abstract In this research, we isolated indigenous bacteria capable of remediating oil-contaminated produced water in an efficient, cost-effective and environmentally friendly manner. Nine different produced water samples were collected from Omani oil fields and analysed for their physicochemical properties and microbial communities present. Different technologies were performed to extract the DNA of the microbial community cultured in different media. Metagenomic classification of the microbial community showed that the abundant genera are the Acidithiobacillus, Proteinphilum and Marinobacter. The isolated microbes that showed the highest efficiency in oil degradation were further evaluated for liquid-based biodegradation as well as in naturally occurring and artificially contaminated soil. Fourteen bacteria samples were found to be efficient in bioremediating the three environments tested. In the liquid-based media, the isolates were able to degrade the heavy oil carbon chains (C14-C20) by at least 50% after 1 week period, while some of the most potent isolates have achieved more than 95% or completely degraded all the hydrocarbon chains. Similarly, in the naturally contaminated soil, the isolates demonstrated a complete degradation of the lighter carbon molecules from C10-C16 and also achieved a higher than 90% degradation for the heavier components. Likewise, the isolates have exhibited similar biodegradation ability when exposed to an induced contaminated soil where all the lower carbon chains (C12-C17) were mostly degraded by the microbes in the samples.
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Wakeham, A., G. Keane, M. Proctor, and R. Kennedy. "Monitoring infection risk for air and soil borne fungal plant pathogens using antibody and DNA techniques and mathematical models describing environmental parameters." In MICROBES IN APPLIED RESEARCH - Current Advances and Challenges. WORLD SCIENTIFIC, 2012. http://dx.doi.org/10.1142/9789814405041_0030.
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Agusta, Arifian, Guomin Ji, and Svein Sævik. "Non-Linear Clay Soil Model for Lateral Pipe-Soil Interaction." In ASME 2016 35th International Conference on Ocean, Offshore and Arctic Engineering. American Society of Mechanical Engineers, 2016. http://dx.doi.org/10.1115/omae2016-54658.
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This paper describes implementation and application of nonlinear lateral soil models for pipeline lateral buckling analysis. Several lateral soil models have been developed in the past and the model developed by Verley is often referenced in pipeline on-bottom hydrodynamic stability analyses (see [11], [13]). The Verley’s model includes the build up of soil passive resistance as a function of small cyclic lateral motions and it is implemented in the PONDUS software (developed by MARINTEK) for on-bottom stability analysis as well as the DNV-RP-F109. However, the Verley model does not include the build up of additional soil berm resistance due to large cyclic in-place lateral motions applicable for lateral thermal buckling behaviors. The effect of additional soil berm resistance from large cyclic motions has been investigated by other research projects, such as the SAFEBUCK JIP [5]. In this paper, a complete non-linear lateral soil models with inherent soil berm resistance including both effects are formulated. The soil model combines the Verley model, the models described in DNV-RP-F109, and the berm model from SAFEBUCK’s results. The DNV and Verley’s model are used to model soil resistance in small amplitude cycle continued by the berm model after breakout achieved during large amplitude cycle. The new model is compared with PONDUS to validate the results of Verley and DNV model. The soil model is implemented inside SIMLA software [15] to enable finite element analysis. An example application of the model to pipeline global buckling analysis is then presented.
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"The Bunch Moth of the Tirathaba Species As A Hidden Pest on The Peat Soil of Oil Palm Plantations: Implications of Biological Life Cycles, The DNA Barcoding Approach, and Infestation Pattern Detection." In 3rd International Conference on Chemical, Agricultural and Medical Sciences. International Institute of Chemical, Biological & Environmental Engineering, 2015. http://dx.doi.org/10.15242/iicbe.c1215036.
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Muntyan, Victoria S., Alla S. Saksaganskaia, Alexey N. Muntyan, Mariia E. Vladimirova, and Marina L. Roumiantseva. "STRESS AND IMMUNITY OF NODULE BACTERIA SINORHIZOBIUM MELILOTI: LOCALIZATION, POLYMORPHISM AND PHYLOGENY OF GENETIC DETERMINANTS." In 22nd SGEM International Multidisciplinary Scientific GeoConference 2022. STEF92 Technology, 2022. http://dx.doi.org/10.5593/sgem2022/6.1/s25.15.
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Sinorhizobium meliloti are agriculturally valuable species of soil bacteria that form nitrogen-fixing symbiosis with alfalfa plants. Global climate changes lead to an increase of agricultural areas subjected to salinity. Current knowledge about about high-salt stress impact on soil saprophitic root nodulated microsymbionts of legumes is weakly studied and rhizobia gene pool responsible for salt tolerance are fragment and far from clear. An increase of bacteria nonspecific resistance (immune status) to unfavorable stress factors can occur through the induction of defense mechanisms like restrictionmodification systems and CRISPR/cas systems which are aimed to protect bacteria cells from bacteriophages widespread in soil microbiome. The aim of this research was to evaluate the role of the megaplasmid pSymA in the formation of ecological genome of S. meliloti, which is related to stress tolerance and to determine the location of elements of adaptive immune systems protecting root nodule bacteria against external foreign DNA. The analysis was done on 11 genes, products of which involved in response to ion stress and synthesis of osmoprotectors. It was found that 6 out of 11 genes were found in the genomes of all analyzed S. meliloti strains, while it was not a case for other 5 genes. It was found that, unlike chromosome, megaplasmid I of S. meliloti accumulated copies of 4 from 5 genes, except kdpA gene, which is represented by a single copy and localized on megaplasmid I in all so far studied strains. It was predicted that closest phylogenetic relatives of genes whose products are involved in response to ion stress as well in synthesis of osmoprotectors are homologous genes of closely related S. medicae species. The exception was for betI2, for which the closest phylogenetic relative was homologous gene of Klebsiella pneumonia, and another exception is kdpA gene introduced onto megaplasmid-I from actinobacteria. Regarding elements of immune systems it was revealed that nonsymbiotic plasmids of S. meliloti harbored incomplete elements of RMS-I, -II, and - III systems, while the 4 complete RMS-IV systems were detected on a single plasmid. It was found out that corresponding methylases had similarities with similar enzymes detected in nitrogen-fixing strains of Agrobacterium tumefaciens, Mezorhizobium sp., Bradyrhizobium sp. CRISPR sequences were not detected on megaplasmid-I, while they were on chromosome, megaplasmid-II and on cryptic plasmids. So, it was concluded that megaplasmid-I of S. meliloti are enriched in copies of genes related to osmotic stress tolerance, but it role in immune status of rhizobia is requested further elucidation.
Reports on the topic "Soil DNA"
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Kistler, Harold Corby, and Talma Katan. Identification of DNA Unique to the Tomato Fusarium Wilt and Crown Rot Pathogens. United States Department of Agriculture, September 1995. http://dx.doi.org/10.32747/1995.7571359.bard.
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Wilt and crown rot are two important diseases of tomato caused by different strains ("formae speciales") of the fungus, Fusarium oxysporum. While both pathogens are members of the same fungal species, each differs genetically and resistance to the diseases is controlled by different genes in the plant. Additionally, the formae speciales differ in their ecology (e.g. optimal temperature of disease development) and epidemiology. Nevertheless, the distinction between these diseases based on symptoms alone may be unclear due to overlapping symptomatology. We have found in our research that the ambiguity of the pathogens is further confounded because strains causing tomato wilt or crown rot each may belong to several genetically and phylogenetically distinct lineages of F. oxysporum. Furthermore, individual lineages of the pathogen causing wilt or crown rot may themselves be very closely related. The diseases share the characteristic that the pathogen's inoculum may be aerially dispersed. This work has revealed a complex evolutionary relationship among lineages of the pathogens that makes development of molecular diagnostic methods more difficult than originally anticipated. However, the degree of diversity found in these soil-borne pathogens has allowed study of their population genetics and patterns of dispersal in agricultural settings.
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Minz, Dror, Stefan J. Green, Noa Sela, Yitzhak Hadar, Janet Jansson, and Steven Lindow. Soil and rhizosphere microbiome response to treated waste water irrigation. United States Department of Agriculture, January 2013. http://dx.doi.org/10.32747/2013.7598153.bard.
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Research objectives : Identify genetic potential and community structure of soil and rhizosphere microbial community structure as affected by treated wastewater (TWW) irrigation. This objective was achieved through the examination soil and rhizosphere microbial communities of plants irrigated with fresh water (FW) and TWW. Genomic DNA extracted from soil and rhizosphere samples (Minz laboratory) was processed for DNA-based shotgun metagenome sequencing (Green laboratory). High-throughput bioinformatics was performed to compare both taxonomic and functional gene (and pathway) differences between sample types (treatment and location). Identify metabolic pathways induced or repressed by TWW irrigation. To accomplish this objective, shotgun metatranscriptome (RNA-based) sequencing was performed. Expressed genes and pathways were compared to identify significantly differentially expressed features between rhizosphere communities of plants irrigated with FW and TWW. Identify microbial gene functions and pathways affected by TWW irrigation*. To accomplish this objective, we will perform a metaproteome comparison between rhizosphere communities of plants irrigated with FW and TWW and selected soil microbial activities. Integration and evaluation of microbial community function in relation to its structure and genetic potential, and to infer the in situ physiology and function of microbial communities in soil and rhizospere under FW and TWW irrigation regimes. This objective is ongoing due to the need for extensive bioinformatics analysis. As a result of the capabilities of the new PI, we have also been characterizing the transcriptome of the plant roots as affected by the TWW irrigation and comparing the function of the plants to that of the microbiome. *This original objective was not achieved in the course of this study due to technical issues, especially the need to replace the American PIs during the project. However, the fact we were able to analyze more than one plant system as a result of the abilities of the new American PI strengthened the power of the conclusions derived from studies for the 1ˢᵗ and 2ⁿᵈ objectives. Background: As the world population grows, more urban waste is discharged to the environment, and fresh water sources are being polluted. Developing and industrial countries are increasing the use of wastewater and treated wastewater (TWW) for agriculture practice, thus turning the waste product into a valuable resource. Wastewater supplies a year- round reliable source of nutrient-rich water. Despite continuing enhancements in TWW quality, TWW irrigation can still result in unexplained and undesirable effects on crops. In part, these undesirable effects may be attributed to, among other factors, to the effects of TWW on the plant microbiome. Previous studies, including our own, have presented the TWW effect on soil microbial activity and community composition. To the best of our knowledge, however, no comprehensive study yet has been conducted on the microbial population associated BARD Report - Project 4662 Page 2 of 16 BARD Report - Project 4662 Page 3 of 16 with plant roots irrigated with TWW – a critical information gap. In this work, we characterize the effect of TWW irrigation on root-associated microbial community structure and function by using the most innovative tools available in analyzing bacterial community- a combination of microbial marker gene amplicon sequencing, microbial shotunmetagenomics (DNA-based total community and gene content characterization), microbial metatranscriptomics (RNA-based total community and gene content characterization), and plant host transcriptome response. At the core of this research, a mesocosm experiment was conducted to study and characterize the effect of TWW irrigation on tomato and lettuce plants. A focus of this study was on the plant roots, their associated microbial communities, and on the functional activities of plant root-associated microbial communities. We have found that TWW irrigation changes both the soil and root microbial community composition, and that the shift in the plant root microbiome associated with different irrigation was as significant as the changes caused by the plant host or soil type. The change in microbial community structure was accompanied by changes in the microbial community-wide functional potential (i.e., gene content of the entire microbial community, as determined through shotgun metagenome sequencing). The relative abundance of many genes was significantly different in TWW irrigated root microbiome relative to FW-irrigated root microbial communities. For example, the relative abundance of genes encoding for transporters increased in TWW-irrigated roots increased relative to FW-irrigated roots. Similarly, the relative abundance of genes linked to potassium efflux, respiratory systems and nitrogen metabolism were elevated in TWW irrigated roots when compared to FW-irrigated roots. The increased relative abundance of denitrifying genes in TWW systems relative FW systems, suggests that TWW-irrigated roots are more anaerobic compare to FW irrigated root. These gene functional data are consistent with geochemical measurements made from these systems. Specifically, the TWW irrigated soils had higher pH, total organic compound (TOC), sodium, potassium and electric conductivity values in comparison to FW soils. Thus, the root microbiome genetic functional potential can be correlated with pH, TOC and EC values and these factors must take part in the shaping the root microbiome. The expressed functions, as found by the metatranscriptome analysis, revealed many genes that increase in TWW-irrigated plant root microbial population relative to those in the FW-irrigated plants. The most substantial (and significant) were sodium-proton antiporters and Na(+)-translocatingNADH-quinoneoxidoreductase (NQR). The latter protein uses the cell respiratory machinery to harness redox force and convert the energy for efflux of sodium. As the roots and their microbiomes are exposed to the same environmental conditions, it was previously hypothesized that understanding the soil and rhizospheremicrobiome response will shed light on natural processes in these niches. This study demonstrate how newly available tools can better define complex processes and their downstream consequences, such as irrigation with water from different qualities, and to identify primary cues sensed by the plant host irrigated with TWW. From an agricultural perspective, many common practices are complicated processes with many ‘moving parts’, and are hard to characterize and predict. Multiple edaphic and microbial factors are involved, and these can react to many environmental cues. These complex systems are in turn affected by plant growth and exudation, and associated features such as irrigation, fertilization and use of pesticides. However, the combination of shotgun metagenomics, microbial shotgun metatranscriptomics, plant transcriptomics, and physical measurement of soil characteristics provides a mechanism for integrating data from highly complex agricultural systems to eventually provide for plant physiological response prediction and monitoring. BARD Report
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Crowley, David E., Dror Minz, and Yitzhak Hadar. Shaping Plant Beneficial Rhizosphere Communities. United States Department of Agriculture, July 2013. http://dx.doi.org/10.32747/2013.7594387.bard.
Full textAbstract:
PGPR bacteria include taxonomically diverse bacterial species that function for improving plant mineral nutrition, stress tolerance, and disease suppression. A number of PGPR are being developed and commercialized as soil and seed inoculants, but to date, their interactions with resident bacterial populations are still poorly understood, and-almost nothing is known about the effects of soil management practices on their population size and activities. To this end, the original objectives of this research project were: 1) To examine microbial community interactions with plant-growth-promoting rhizobacteria (PGPR) and their plant hosts. 2) To explore the factors that affect PGPR population size and activity on plant root surfaces. In our original proposal, we initially prqposed the use oflow-resolution methods mainly involving the use of PCR-DGGE and PLFA profiles of community structure. However, early in the project we recognized that the methods for studying soil microbial communities were undergoing an exponential leap forward to much more high resolution methods using high-throughput sequencing. The application of these methods for studies on rhizosphere ecology thus became a central theme in these research project. Other related research by the US team focused on identifying PGPR bacterial strains and examining their effective population si~es that are required to enhance plant growth and on developing a simulation model that examines the process of root colonization. As summarized in the following report, we characterized the rhizosphere microbiome of four host plant species to determine the impact of the host (host signature effect) on resident versus active communities. Results of our studies showed a distinct plant host specific signature among wheat, maize, tomato and cucumber, based on the following three parameters: (I) each plant promoted the activity of a unique suite of soil bacterial populations; (2) significant variations were observed in the number and the degree of dominance of active populations; and (3)the level of contribution of active (rRNA-based) populations to the resident (DNA-based) community profiles. In the rhizoplane of all four plants a significant reduction of diversity was observed, relative to the bulk soil. Moreover, an increase in DNA-RNA correspondence indicated higher representation of active bacterial populations in the residing rhizoplane community. This research demonstrates that the host plant determines the bacterial community composition in its immediate vicinity, especially with respect to the active populations. Based on the studies from the US team, we suggest that the effective population size PGPR should be maintained at approximately 105 cells per gram of rhizosphere soil in the zone of elongation to obtain plant growth promotion effects, but emphasize that it is critical to also consider differences in the activity based on DNA-RNA correspondence. The results ofthis research provide fundamental new insight into the composition ofthe bacterial communities associated with plant roots, and the factors that affect their abundance and activity on root surfaces. Virtually all PGPR are multifunctional and may be expected to have diverse levels of activity with respect to production of plant growth hormones (regulation of root growth and architecture), suppression of stress ethylene (increased tolerance to drought and salinity), production of siderophores and antibiotics (disease suppression), and solubilization of phosphorus. The application of transcriptome methods pioneered in our research will ultimately lead to better understanding of how management practices such as use of compost and soil inoculants can be used to improve plant yields, stress tolerance, and disease resistance. As we look to the future, the use of metagenomic techniques combined with quantitative methods including microarrays, and quantitative peR methods that target specific genes should allow us to better classify, monitor, and manage the plant rhizosphere to improve crop yields in agricultural ecosystems. In addition, expression of several genes in rhizospheres of both cucumber and whet roots were identified, including mostly housekeeping genes. Denitrification, chemotaxis and motility genes were preferentially expressed in wheat while in cucumber roots bacterial genes involved in catalase, a large set of polysaccharide degradation and assimilatory sulfate reduction genes were preferentially expressed.
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Freeman, Stanley, and Daniel Legard. Epidemiology and Etiology of Colletotrichum Species Causing Strawberry Diseases. United States Department of Agriculture, September 2001. http://dx.doi.org/10.32747/2001.7695845.bard.
Full textAbstract:
Diseases caused by Colletotrichum spp. are one of the most important limitations on international strawberry production, affecting all vegetative and fruiting parts of the plant. From 1995 to 1997, C. acutatum infections reached epidemic levels in Israeli strawberry nurseries, causing extensive loss of transplants in fruit-bearing fields and additional reductions in yield. Although C. acutatum also occurs on strawberry in Florida, recent crown rot epidemics have been primarily caused by C. gloeosporioides. Little is known about the basic epidemiology of these important diseases on strawberry. The source of initial inoculum for epidemics in Israel, Florida (other US states including California) and the rest of the world is not well understood. Subspecies relationships between Colletotrichum isolates that cause the different diseases on strawberry (i.e. attack different tissues) are also not well understood. Objectives of this proposal were to detennine the potential of infested soil, strawberry debris and other hosts as sources of primary inoculum for strawberry diseases caused by Colletotrichum spp. in Israel and Florida. In addition, traditional (ie. morphological characteristics, benomyl sensitivity, vegetative compatibility grouping) and DNA based methods were used to investigate the etiology of these diseases in order to resolve epidemiologically important subspecies variation. In Israel it was found that C. gloeosporioides and C. acutatum infecting strawberry could remain viable in sterilized soil for up to one year and in methyl-bromide fumigated soil for up to 4 months; inoculum in mummified fruit remained viable for at least 5 months under field conditions whereas that in infected crowns was not recovered. Therefore, the contribution of these inocula to disease epidemics should be considered. The host range and specificity of C. acutatum from strawberry was examined on pepper, eggplant, tomato, bean and strawberry under greenhouse conditions. The fungus was recovered from all plant species over a three-month period but caused disease symptoms only on strawberry. C. acutatum was also isolated from healthy looking, asymptomatic plants of the weed species, Vicia and Conyza, growing in infected strawberry fruiting fields. Isolates of C. acutatum originating from strawberry and anemone infected both plant species in artificial inoculations. The habitation of a large number of plant species including weeds by C. acutatum suggests that although it causes disease only on strawberry and anemone in Israel, these plants may serve as a potential inoculum source for strawberry infection and pennit survival of the pathogen between seasons. In Florida, isolates of Colletotrichum spp. from diseased strawberry fruit and crowns were evaluated to detennine their etiology and the genetic diversity of the pathogens. Only C. acutatum was recovered from fruit and C. gloeosporioides were the main species recovered from crowns. These isolates were evaluated at 40 putative genetic loci using random amplified polymorphic DNA (RAPD). Genetic analysis of RAPD markers revealed that the level of linkage disequilibrium among polymorphic loci in C. gloeosporioides suggested that they were a sexually reproducing population. Under field conditions in Florida, it was detennined that C. gloeosporioides in buried crowns survived
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PHELAN, JAMES M., and JAMES L. BARNETT. Phase Partitioning of TNT and DNT in Soils. Office of Scientific and Technical Information (OSTI), February 2001. http://dx.doi.org/10.2172/780293.
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Clausen, Jay, Richard Hark, Russ Harmon, John Plumer, Samuel Beal, and Meghan Bishop. A comparison of handheld field chemical sensors for soil characterization with a focus on LIBS. Engineer Research and Development Center (U.S.), February 2022. http://dx.doi.org/10.21079/11681/43282.
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Commercially available handheld chemical analyzers for forensic applications have been available for over a decade. Portable systems from multiple vendors can perform X-ray fluorescence (XRF) spectroscopy, Raman spectroscopy, Fourier transform infrared(FTIR) spectroscopy, and recently laser-induced breakdown spectroscopy (LIBS). Together, we have been exploring the development and potential applications of a multisensor system consisting of XRF, Raman, and LIBS for environmental characterization with a focus on soils from military ranges. Handheld sensors offer the potential to substantially increase sample throughput through the elimination of transport of samples back to the laboratory and labor-intensive sample preparation procedures. Further, these technologies have the capability for extremely rapid analysis, on the order of tens of seconds or less. We have compared and evaluated results from the analysis of several hundred soil samples using conventional laboratory bench top inductively coupled plasma atomic emission spectroscopy (ICP-AES) for metals evaluation and high-performance liquid chromatography (HPLC) and Raman spectroscopy for detection and characterization of energetic materials against handheld XRF, LIBS, and Raman analyzers. The soil samples contained antimony, copper, lead, tungsten, and zinc as well as energetic compounds such as 2,4,6-trinitrotoluene(TNT), hexahydro-1,3,5-triazine (RDX), nitroglycerine (NG), and dinitrotoluene isomers (DNT). Precision, accuracy, and sensitivity of the handheld field sensor technologies were compared against conventional laboratory instrumentation to determine their suitability for field characterization leading to decisional outcomes.
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Schutt, Timothy C., and Manoj K. Shukla. Computational Investigation on Interactions Between Some Munitions Compounds and Humic Substances. Engineer Research and Development Center (U.S.), February 2021. http://dx.doi.org/10.21079/11681/39703.
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Humic acid substances (HAs) in natural soil and sediment environments effect the retention and degradation of insensitive munitions compounds and legacy high explosives (MCs): DNAN, DNi- NH4+, nMNA, NQ, NTO (neutral and anionic forms), TNT, and RDX.A humic acid model compound has been considered using molecular dynamics, thermodynamic integration, and density functional theory to characterize the munition binding ability, ionization potential, and electron affinity compared to that in the water solution. Humic acids bind most compounds and act as both a sink and source for electrons. Ionization potentials suggest HAs are more susceptible to oxidation than the MCs studied. The electron affinity of HAs are very conformation-dependent and spans the same range as the munition compounds. When HAs and MCs are complexed the HAs tend to radicalize first thus buffering MCs against reductive as well as oxidative attacks.
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Jung, Carina, Karl Indest, Matthew Carr, Richard Lance, Lyndsay Carrigee, and Kayla Clark. Properties and detectability of rogue synthetic biology (SynBio) products in complex matrices. Engineer Research and Development Center (U.S.), September 2022. http://dx.doi.org/10.21079/11681/45345.
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Synthetic biology (SynBio) aims to rationally engineer or modify traits of an organism or integrate the behaviors of multiple organisms into a singular functional organism through advanced genetic engineering techniques. One objective of this research was to determine the environmental persistence of engineered DNA in the environment. To accomplish this goal, the environmental persistence of legacy engineered DNA building blocks were targeted that laid the foundation for SynBio product development and application giving rise to “post-use products.” These building blocks include genetic constructs such as cloning and expression vectors, promoter/terminator elements, selectable markers, reporter genes, and multi-cloning sites. Shotgun sequencing of total DNA from water samples of pristine sites was performed and resultant sequence data mined for frequency of legacy recombinant DNA signatures. Another objective was to understand the fate of a standardized contemporary synthetic genetic construct (SC) in the context of various chassis systems/genetic configurations representing different degrees of “genetic bioavailability” to the environmental landscape. These studies were carried out using microcosms representing different environmental matrices (soils, waters, wastewater treatment plant (WWTP) liquor) and employed a novel genetic reporter system based on volatile organic compounds (VOC) detection to assess proliferation and persistence of the SC in the matrix over time.
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Dontsova, Katerina, Susan Taylor, Rose Pesce-Rodriguez, Mark Brusseau, Jennifer Arthur, Noah Mark, Marianne Walsh, James Lever, and Jiri Simunek. Dissolution of NTO, DNAN, and Insensitive Munitions Formulations and Their Fates in Soils. Fort Belvoir, VA: Defense Technical Information Center, September 2014. http://dx.doi.org/10.21236/ada609594.
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Dontsova, Katerina, Susan Taylor, Jennifer Arthur, Julie Becher, Mark Brusseau, Edward Hunt, Noah Mark, Dave Ringelberg, Jirí Šimunek, and Marianne Walsh. Dissolution of NTO, DNAN, and insensitive munitions formulations and their fates in soils : SERDP ER-2220. Engineer Research and Development Center (U.S.), November 2022. http://dx.doi.org/10.21079/11681/45920.
Full textAbstract:
The US military is interested in replacing TNT (2,4,6-trinitrotoluene) and RDX (1,3,5-hexahydro-1,3,5-trinitro-1,3,5-triazine) with DNAN (2,4-di-nitroanisole) and NTO (3-nitro-1,2,4-triazol-5-one), which have similar explosive characteristics but are less likely to detonate unintentionally. Although these replacements are good explosives, basic information about their fate and transport was needed to evaluate their environmental impact and life-cycle management. This project measured their dissolution, photodegradation, and how aqueous solutions interact with soils, data critical to determining exposure potential and, consequently, risk.