Artykuły w czasopismach: „Soil DNA”

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Zanella, A. "Vegetation, soil, DNA and natural evolution". Forest@ - Rivista di Selvicoltura ed Ecologia Forestale 20, nr 1 (28.02.2023): 10–12. http://dx.doi.org/10.3832/efor4285-019.

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Mahmoudi, Nagissa, Greg F. Slater i 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, nr 8 (sierpień 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 i Sandra Regina Ceccato-Antonini. "EVALUATION OF DIFFERENT TECHNIQUES FOR DNA DIRECT EXTRACTION FROM BRAZILIAN AGRICULTURAL SOIL". Holos Environment 10, nr 1 (5.10.2010): 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 i Tae-Hoo Yi. "Phycicoccus soli sp. nov., isolated from soil". International Journal of Systematic and Evolutionary Microbiology 65, Pt_8 (1.08.2015): 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 i Jonathan Whitworth. "Assessment of Factors Associated with Molecular Quantification of Stubby Root Nematode Paratrichodorus allius from Field Soil DNA". Plant Disease 103, nr 12 (grudzień 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, nr 2 (21.07.2016): 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 i Pascal Simonet. "Extraction of DNA from soil". European Journal of Soil Biology 39, nr 4 (październik 2003): 183–90. http://dx.doi.org/10.1016/s1164-5563(03)00033-5.

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Woods, Angela, Maribeth Watwood i Egbert Schwartz. "Identification of a Toluene-Degrading Bacterium from a Soil Sample through H218O DNA Stable Isotope Probing". Applied and Environmental Microbiology 77, nr 17 (8.07.2011): 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 i Michael Taliansky. "Distinct Circular Single-Stranded DNA Viruses Exist in Different Soil Types". Applied and Environmental Microbiology 81, nr 12 (3.04.2015): 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 i Andrzej Bieganowski. "The effects of humic substances on DNA isolation from soils". PeerJ 8 (24.07.2020): 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.

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Taylor-Cornejo, Elias. "Empowering Undergraduates to Fight Climate Change with Soil Microbes". DNA and Cell Biology 41, nr 1 (1.01.2022): 58–63. http://dx.doi.org/10.1089/dna.2021.0551.

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Sagova-Mareckova, Marketa, Ladislav Cermak, Jitka Novotna, Kamila Plhackova, Jana Forstova i Jan Kopecky. "Innovative Methods for Soil DNA Purification Tested in Soils with Widely Differing Characteristics". Applied and Environmental Microbiology 74, nr 9 (14.03.2008): 2902–7. http://dx.doi.org/10.1128/aem.02161-07.

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ABSTRACT Seven methods of soil DNA extraction and purification were tested in a set of 14 soils differing in bedrock, texture, pH, salinity, moisture, organic matter content, and vegetation cover. The methods introduced in this study included pretreatment of soil with CaCO3 or purification of extracted DNA by CaCl2. The performance of innovated methods was compared to that of the commercial kit Mo Bio PowerSoil and the phenol-chloroform-based method of D. N. Miller, J. E. Bryant, E. L. Madsen, and W. C. Ghiorse (Appl. Environ. Microbiol. 65:4715-4724, 1999). This study demonstrated significant differences between the tested methods in terms of DNA yield, PCR performance, and recovered bacterial diversity. The differences in DNA yields were correlated to vegetation cover, soil pH, and clay content. The differences in PCR performances were correlated to vegetation cover and soil pH. The innovative methods improved PCR performance in our set of soils, in particular for forest acidic soils. PCR was successful in 95% of cases by the method using CaCl2 purification and in 93% of cases by the method based on CaCO3 pretreatment, but only in 79% by Mo Bio PowerSoil, for our range of soils. Also, the innovative methods recovered a higher percentage of actinomycete diversity from a subset of three soils. Recommendations include the assessment of soil characteristics prior to selecting the optimal protocol for soil DNA extraction and purification.

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Wu, Lin Hui, Jian Li Liu, Jing Zeng i Ji Zhao. "Comparison of DNA Extraction and Purification Methods from Different Soils for Metagenomic Sequencing". Advanced Materials Research 955-959 (czerwiec 2014): 306–9. http://dx.doi.org/10.4028/www.scientific.net/amr.955-959.306.

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There is an increased interest in the extraction of nucleic acids from various environmental samples, since only a minority of naturally occurring microbes can be cultured using standard techniques. Nucleic acids extraction and purification from soils are extremely challenging due to the low biomass, high organic contents and high variability of soil types. This has been regarded as one of the major difficulties that hamper the development of soil microbial ecology study. No commercial nucleic acids kits currently available are capable of preparing the DNAs without modifications. The cost can be very high for DNA extraction from extreme environmental soil samples, such as soils that have extreme high or low pHs. In this work, we developed and optimized soil DNA extraction and purification methods on different soils and compared the impact of three different DNA extraction protocols on DNA yield and purity. For the three different types of soil we used, direct extraction obtained the highest DNA recover rate, but required more cleanup steps. MoBio PowerSoil® DNA Isolation Kit yields less but do not require as many downstream cleaning steps. Both of the two methods obtained a more abundant microbial community than Meta-G-NomeTMDNA Isolation Kit.

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Dimitrov, Mauricio R., Annelies J. Veraart, Mattias de Hollander, Hauke Smidt, Johannes A. van Veen i Eiko E. Kuramae. "Successive DNA extractions improve characterization of soil microbial communities". PeerJ 5 (1.02.2017): e2915. http://dx.doi.org/10.7717/peerj.2915.

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Currently, characterization of soil microbial communities relies heavily on the use of molecular approaches. Independently of the approach used, soil DNA extraction is a crucial step, and success of downstream procedures will depend on how well DNA extraction was performed. Often, studies describing and comparing soil microbial communities are based on a single DNA extraction, which may not lead to a representative recovery of DNA from all organisms present in the soil. The use of successive DNA extractions might improve soil microbial characterization, but the benefit of this approach has only been limitedly studied. To determine whether successive DNA extractions of the same soil sample would lead to different observations in terms of microbial abundance and community composition, we performed three successive extractions, with two widely used commercial kits, on a range of clay and sandy soils. Successive extractions increased DNA yield considerably (1–374%), as well as total bacterial and fungal abundances in most of the soil samples. Analysis of the 16S and 18S ribosomal RNA genes using 454-pyrosequencing, revealed that microbial community composition (taxonomic groups) observed in the successive DNA extractions were similar. However, successive DNA extractions did reveal several additional microbial groups. For some soil samples, shifts in microbial community composition were observed, mainly due to shifts in relative abundance of a number of microbial groups. Our results highlight that performing successive DNA extractions optimize DNA yield, and can lead to a better picture of overall community composition.

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Moon, Ji-Young, Soo-Jin Kim, Moriyuki Hamada, Jae-Hyung Ahn, Hang-Yeon Weon, Ken-ichiro Suzuki, Jung-Hoon Yoon i Soon-Wo Kwon. "Gryllotalpicola soli sp. nov., isolated from soil". International Journal of Systematic and Evolutionary Microbiology 64, Pt_12 (1.12.2014): 4079–83. http://dx.doi.org/10.1099/ijs.0.067710-0.

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A novel Gram-stain-positive, short rod-shaped, non-flagellated and mesophilic strain, KIS12-7T, isolated from a soil sample collected from Daecheong-Island in Ongjin County, Republic of Korea, was studied using a polyphasic approach. Phylogenetic trees based on the 16S rRNA gene sequence revealed that the novel strain was a member of the genus Gryllotalpicola , showing more than 97.0 % sequence similarity with Gryllotalpicola daejeonensis RU-04T (98.0 %), Gryllotalpicola koreensis RU-16T (97.7 %) and Gryllotalpicola kribbensis PU-02T (97.3 %). However, DNA–DNA relatedness values demonstrated that strain KIS12-7T could be clearly distinguished from closely related species of the genus Gryllotalpicola . The cell-wall peptidoglycan of strain KIS12-7T was of the type B2 and the acyl type was acetyl. The predominant menaquinones were MK-11 and MK-10. Polar lipids were diphosphatidylglycerol, phosphatidylglycerol, one unknown phosphoglycolipid, one unknown glycolipid, one unknown phospholipid and one unknown lipid. The G+C content of the genomic DNA was 72.1 mol%. On the basis of the evidence presented, strain KIS12-7T is a representative of a novel species of the genus Gryllotalpicola , and the name Gryllotalpicola soli sp. nov. is proposed; the type strain is KIS12-7T ( = DSM 27182T = KACC 17302T = NBRC 109659T).

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Schloss, Patrick D., Heather K. Allen, Amy K. Klimowicz, Christine Mlot, Jessica A. Gross, Sarah Savengsuksa, Jennifer McEllin, Jon Clardy, Roger W. Ruess i Jo Handelsman. "Psychrotrophic Strain ofJanthinobacterium lividumfrom a Cold Alaskan Soil Produces Prodigiosin". DNA and Cell Biology 29, nr 9 (wrzesień 2010): 533–41. http://dx.doi.org/10.1089/dna.2010.1020.

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Frostegård, Åsa, Sophie Courtois, Vincent Ramisse, Sylvie Clerc, Dominique Bernillon, Francoise Le Gall, Pascale Jeannin, Xavier Nesme i Pascal Simonet. "Quantification of Bias Related to the Extraction of DNA Directly from Soils". Applied and Environmental Microbiology 65, nr 12 (1.12.1999): 5409–20. http://dx.doi.org/10.1128/aem.65.12.5409-5420.1999.

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ABSTRACT In recent years, several protocols based on the extraction of nucleic acids directly from the soil matrix after lysis treatment have been developed for the detection of microorganisms in soil. Extraction efficiency has often been evaluated based on the recovery of a specific gene sequence from an organism inoculated into the soil. The aim of the present investigation was to improve the extraction, purification, and quantification of DNA derived from as large a portion of the soil microbial community as possible, with special emphasis placed on obtaining DNA from gram-positive bacteria, which form structures that are difficult to disrupt. Furthermore, we wanted to identify and minimize the biases related to each step in the procedure. Six soils, covering a range of pHs, clay contents, and organic matter contents, were studied. Lysis was carried out by soil grinding, sonication, thermal shocks, and chemical treatments. DNA was extracted from the indigenous microflora as well as from inoculated bacterial cells, spores, and hyphae, and the quality and quantity of the DNA were determined by gel electrophoresis and dot blot hybridization. Lysis efficiency was also estimated by microscopy and viable cell counts. Grinding increased the extracellular DNA yield compared with the yield obtained without any lysis treatment, but none of the subsequent treatments clearly increased the DNA yield. Phage λ DNA was inoculated into the soils to mimic the fate of extracellular DNA. No more than 6% of this DNA could be recovered from the different soils. The clay content strongly influenced the recovery of DNA. The adsorption of DNA to clay particles decreased when the soil was pretreated with RNA in order to saturate the adsorption sites. We also investigated different purification techniques and optimized the PCR methods in order to develop a protocol based on hybridization of the PCR products and quantification by phosphorimaging.

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Srinivasiah, Sharath, Jacqueline Lovett, Shawn Polson, Jaysheel Bhavsar, Dhritiman Ghosh, Krishnakali Roy, Jeffry J. Fuhrmann, Mark Radosevich i K. Eric Wommack. "Direct Assessment of Viral Diversity in Soils by Random PCR Amplification of Polymorphic DNA". Applied and Environmental Microbiology 79, nr 18 (21.06.2013): 5450–57. http://dx.doi.org/10.1128/aem.00268-13.

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ABSTRACTViruses are the most abundant and diverse biological entities within soils, yet their ecological impact is largely unknown. Defining how soil viral communities change with perturbation or across environments will contribute to understanding the larger ecological significance of soil viruses. A new approach to examining the composition of soil viral communities based on random PCR amplification of polymorphic DNA (RAPD-PCR) was developed. A key methodological improvement was the use of viral metagenomic sequence data for the design of RAPD-PCR primers. This metagenomically informed approach to primer design enabled the optimization of RAPD-PCR sensitivity for examining changes in soil viral communities. Initial application of RAPD-PCR viral fingerprinting to soil viral communities demonstrated that the composition of autochthonous soil viral assemblages noticeably changed over a distance of meters along a transect of Antarctic soils and across soils subjected to different land uses. For Antarctic soils, viral assemblages segregated upslope from the edge of dry valley lakes. In the case of temperate soils at the Kellogg Biological Station, viral communities clustered according to land use treatment. In both environments, soil viral communities changed along with environmental factors known to shape the composition of bacterial host communities. Overall, this work demonstrates that RAPD-PCR fingerprinting is an inexpensive, high-throughput means for addressing first-order questions of viral community dynamics within environmental samples and thus fills a methodological gap between narrow single-gene approaches and comprehensive shotgun metagenomic sequencing for the analysis of viral community diversity.

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Omer, Zahra Saad, Ann-Charlotte Wallenhammar i Maria Viketoft. "Development of Loop-Mediated Isothermal Amplification Assay for Rapid Detection and Analysis of the Root-Knot Nematode Meloidogyne hapla in Soil". Horticulturae 8, nr 2 (19.01.2022): 87. http://dx.doi.org/10.3390/horticulturae8020087.

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Soil analysis is crucial for estimating the risk of crop damage by the root-knot nematode Meloidogyne hapla. Here, we developed an analysis assay based on Loop-mediated Isothermal Amplification (LAMP). The LAMP primers were verified for specificity against 10 different nematode species. A manual soil DNA extraction, referred to as SKMM, was developed and compared with a FastDNA kit followed by DNA purification. DNA was extracted with both methods from artificially inoculated soils as well as from naturally infested soil collected from farm fields. The primers exclusively amplified DNA from M. hapla with both colorimetric and real-time LAMP. The detection limit was 193 gene copies and 0.0016 juveniles (12 pg µL−1) per reaction. DNA concentrations and purity (A260/A230) were significantly higher using the SKMM procedure compared with the kit. From the field samples collected in 2019, DNA was amplified from 16% of samples extracted with SKMM and from 11% of samples using the kit. Occurrence of M. hapla DNA was confirmed in soil samples from two out of six field soils in 2020 using both real-time LAMP and qPCR. In conclusion, the developed real-time LAMP is a fast and specific assay for detection and quantification of M. hapla DNA in soil.

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Yoon, Jung-Hoon, So-Jung Kang, Hwe-Su Yi, Tae-Kwang Oh i Choong-Min Ryu. "Rhizobium soli sp. nov., isolated from soil". International Journal of Systematic and Evolutionary Microbiology 60, nr 6 (1.06.2010): 1387–93. http://dx.doi.org/10.1099/ijs.0.013094-0.

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A Gram-negative, non-motile, pale-yellow, rod-shaped bacterial strain, DS-42T, was isolated from a soil in Korea and its taxonomic position was investigated by a polyphasic study. Strain DS-42T grew optimally at 25 °C and pH 7.0–8.0. Strain DS-42T did not form nodules on three different legumes, and the nodD and nifH genes were also not detected by PCR. Strain DS-42T contained Q-10 as the predominant ubiquinone. The major cellular fatty acid was C18 : 1 ω7c. The DNA G+C content was 60.8 mol%. Phylogenetic analyses based on 16S rRNA, atpD and recA gene sequences showed that strain DS-42T belonged to the genus Rhizobium. Strain DS-42T showed 16S rRNA gene sequence similarity of 94.1–97.7 % to the type strains of recognized Rhizobium species. DNA–DNA relatedness between strain DS-42T and the type strains of Rhizobium huautlense, R. galegae, R. loessense and R. cellulosilyticum was 13–19 %, indicating that strain DS-42T was distinct from them genetically. Strain DS-42T can also be differentiated from these four phylogenetically related Rhizobium species by various phenotypic properties. On the basis of phenotypic properties, phylogenetic distinctiveness and genetic data, strain DS-42T is considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium soli sp. nov. is proposed. The type strain is DS-42T (=KCTC 12873T =JCM 14591T).

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Choi, Jung-Hye, Min-Soo Kim, Seong Woon Roh i Jin-Woo Bae. "Acidovorax soli sp. nov., isolated from landfill soil". International Journal of Systematic and Evolutionary Microbiology 60, nr 12 (1.12.2010): 2715–18. http://dx.doi.org/10.1099/ijs.0.019661-0.

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A Gram-negative, aerobic, rod-shaped, non-motile strain, BL21T, was isolated from landfill soil in Pohang, Korea. Strain BL21T grew optimally at pH 7.0, 30 °C and 0 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain BL21T belonged to the class Betaproteobacteria and was related to the genus Acidovorax. The 16S rRNA gene sequence of strain BL21T was less than 98.30 % similar to those of other species in the genus Acidovorax. DNA–DNA hybridization values with phylogenetically related species of the genus Acidovorax were only 11.7–28.4 %. The major fatty acid components included summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c), C16 : 0, C18 : 1 ω7c and C10 : 0 3-OH. The DNA G+C content was 60.9 mol%. For these reasons, strain BL21T (=KCTC 22399T =JCM 15909T) is proposed as a novel species in the genus Acidovorax, with the name Acidovorax soli sp. nov.

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Philippot, Laurent, Cristina Abbate, Antonio Bispo, Thierry Chesnot, Sara Hallin, Philippe Lemanceau, Kristina Lindström i in. "Soil microbial diversity: an ISO standard for soil DNA extraction". Journal of Soils and Sediments 10, nr 7 (6.07.2010): 1344–45. http://dx.doi.org/10.1007/s11368-010-0265-8.

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Liles, Mark R., Lynn L. Williamson, Jitsupang Rodbumrer, Vigdis Torsvik, Robert M. Goodman i Jo Handelsman. "Recovery, Purification, and Cloning of High-Molecular-Weight DNA from Soil Microorganisms". Applied and Environmental Microbiology 74, nr 10 (21.03.2008): 3302–5. http://dx.doi.org/10.1128/aem.02630-07.

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ABSTRACT We describe here an improved method for isolating, purifying, and cloning DNA from diverse soil microbiota. Soil microorganisms were extracted from soils and embedded and lysed within an agarose plug. Nucleases that copurified with the metagenomic DNA were removed by incubating plugs with a high-salt and -formamide solution. This method was used to construct large-insert soil metagenomic libraries.

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24

Wolinska, Agnieszka, Zofia Stępniewska i Anna Pytlak. "The effect of environmental factors on total soil DNA content and dehydrogenase activity". Archives of Biological Sciences 67, nr 2 (2015): 493–501. http://dx.doi.org/10.2298/abs140120013w.

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The aim of the study was a statistical evaluation of the impact of selected soil factors ? water potential (pF), total organic carbon content (TOC) and land use ? on the total DNA content and dehydrogenase activity (DHA) in Mollic Gleysol. Additionally, we wanted to establish the interrelations between two of the most important biological parameters in soli: activity of intracellular dehydrogenases and total DNA content. Soil originating from the surface layer of the control site displayed higher DHA (c.a. by 57%) and DNA content (c.a. by 25%) as compared to an cultiavted meadow. Our results also indicate a significant (p <0.05) positive relationship between the soil DNA content and DHA. Importantly, intensive and systematical agricultural soil usage resulted in the reduction of its DHA and DNA content.

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25

Zwolinski, Michele D. "DNA Sequencing: Strategies for Soil Microbiology". Soil Science Society of America Journal 71, nr 2 (marzec 2007): 592–600. http://dx.doi.org/10.2136/sssaj2006.0125.

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BIENERT, FRIEDERIKE, SÉBASTIEN DE DANIELI, CHRISTIAN MIQUEL, ERIC COISSAC, CAROLE POILLOT, JEAN-JACQUES BRUN i PIERRE TABERLET. "Tracking earthworm communities from soil DNA". Molecular Ecology 21, nr 8 (17.01.2012): 2017–30. http://dx.doi.org/10.1111/j.1365-294x.2011.05407.x.

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Rougerie, Rodolphe, Thibaud Decaëns, Louis Deharveng, David Porco, Sam W. James, Chih-Han Chang, Benoit Richard, Mikhail Potapov, Yayuk Suhardjono i Paul D. N. Hebert. "DNA barcodes for soil animal taxonomy". Pesquisa Agropecuária Brasileira 44, nr 8 (sierpień 2009): 789–802. http://dx.doi.org/10.1590/s0100-204x2009000800002.

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The biodiversity of soil communities remains very poorly known and understood. Soil biological sciences are strongly affected by the taxonomic crisis, and most groups of animals in that biota suffer from a strong taxonomic impediment. The objective of this work was to investigate how DNA barcoding - a novel method using a microgenomic tag for species identification and discrimination - permits better evaluation of the taxonomy of soil biota. A total of 1,152 barcode sequences were analyzed for two major groups of animals, collembolans and earthworms, which presented broad taxonomic and geographic sampling. Besides strongly reflecting the taxonomic impediment for both groups, with a large number of species-level divergent lineages remaining unnamed so far, the results also highlight a high level (15%) of cryptic diversity within known species of both earthworms and collembolans. These results are supportive of recent local studies using a similar approach. Within an impeded taxonomic system for soil animals, DNA-assisted identification tools can facilitate and improve biodiversity exploration and description. DNA-barcoding campaigns are rapidly developing in soil animals and the community of soil biologists is urged to embrace these methods.

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Brierley, Jennie L., Jennifer A. Stewart i Alison K. Lees. "Quantifying potato pathogen DNA in soil". Applied Soil Ecology 41, nr 2 (luty 2009): 234–38. http://dx.doi.org/10.1016/j.apsoil.2008.11.004.

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Luo, Xiaonan, Jianli Zhang, Dai Li, Yuhua Xin, Di Xin i Lei Fan. "Planomicrobium soli sp. nov., isolated from soil". International Journal of Systematic and Evolutionary Microbiology 64, Pt_8 (1.08.2014): 2700–2705. http://dx.doi.org/10.1099/ijs.0.055426-0.

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A Gram-staining-positive bacterium, designated strain XN13T, was isolated from a soil sample collected from ALaShan National Geological Park in Inner Mongolia Autonomous Region, China and subjected to a taxonomic study using a polyphasic approach. Strain XN13T was found to have a range of chemical and morphological properties consistent with its classification in the genus Planomicrobium . Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain XN13T was related to members of the genus Planomicrobium . The closest phylogenetic relatives were Planomicrobium okeanokoites NBRC 12536T, Planomicrobium koreense JG07T, Planomicrobium mcmeekinii S23F2T and Planomicrobium flavidum ISL-41T with 98.2 %, 97.8 %, 97.8 % and 97.7 % 16S rRNA gene sequence similarity, respectively. The major cellular fatty acids were anteiso-C15 : 0, C16 : 1ω7c alcohol, iso-C14 : 0 and C16 : 1ω11c. The predominant menaquinones were MK-8 and MK-7. The DNA G+C content was 40.3 mol%. The DNA–DNA relatedness values between strain XN13T and Planomicrobium okeanokoites KCTC 3672T, Planomicrobium koreense KCTC 3684T, P. mcmeekinii CGMCC 1.2724T, Planomicrobium flavidum KCTC 13261T, Planomicrobium chinense CGMCC 1.3454T and Planomicrobium glaciei CGMCC 1.6846T were 36 %, 30 %, 34 %, 29 %, 30 % and 31 %, respectively. The organism is different from recognized species of the genus Planomicrobium in several phenotypic characteristics. On the basis of phenotypic and genotypic properties, strain XN13T represents a novel species of the genus Planomicrobium , for which the name Planomicrobium soli sp. nov. is proposed. The type strain is XN13T ( = CGMCC 1.12259T = KCTC 33047T).

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Kuske, Cheryl R., Kaysie L. Banton, Dante L. Adorada, Peter C. Stark, Karen K. Hill i Paul J. Jackson. "Small-Scale DNA Sample Preparation Method for Field PCR Detection of Microbial Cells and Spores in Soil". Applied and Environmental Microbiology 64, nr 7 (1.07.1998): 2463–72. http://dx.doi.org/10.1128/aem.64.7.2463-2472.1998.

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ABSTRACT Efficient, nonselective methods to obtain DNA from the environment are needed for rapid and thorough analysis of introduced microorganisms in environmental samples and for analysis of microbial community diversity in soil. A small-scale procedure to rapidly extract and purify DNA from soils was developed for in-the-field use. Amounts of DNA released from bacterial vegetative cells, bacterial endospores, and fungal conidia were compared by using hot-detergent treatment, freeze-thaw cycles, and bead mill homogenization. Combining a hot-detergent treatment with bead mill homogenization gave the highest DNA yields from all three microbial cell types and provided DNA from the broadest range of microbial groups in a natural soil community. Only the bead mill homogenization step was effective for DNA extraction from Bacillus globigii (B. subtilis subsp.niger) endospores or Fusarium moniliformeconidia. The hot-detergent–bead mill procedure was simplified and miniaturized. By using this procedure and small-scale, field-adapted purification and quantification procedures, DNA was prepared from four different soils seeded with Pseudomonas putida cells orB. globigii spores. In a New Mexico soil, seeded bacterial targets were detected with the same sensitivity as when assaying pure bacterial DNA (2 to 20 target gene copies in a PCR mixture). The detection limit of P. putida cells and B. globigii spores in different soils was affected by the amount of background DNA in the soil samples, the physical condition of the DNA, and the amount of DNA template used in the PCR.

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31

Kim, Byung-Yong, Hang-Yeon Weon, Seung-Hee Yoo, Seon-Young Lee, Soon-Wo Kwon, Seung-Joo Go i Erko Stackebrandt. "Variovorax soli sp. nov., isolated from greenhouse soil". International Journal of Systematic and Evolutionary Microbiology 56, nr 12 (1.12.2006): 2899–901. http://dx.doi.org/10.1099/ijs.0.64390-0.

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A Gram-negative, rod-shaped, non-spore-forming bacterium, strain GH9-3T, isolated from greenhouse soil, was investigated in a polyphasic study. The novel organism grew at 10–35 °C, 0–3 % NaCl and pH 5–9. It had ubiquinone 8 (Q-8) as the predominant isoprenoid quinone and possessed C16 : 0, summed feature 3, C17 : 0 cyclo and C18 : 1 ω7c as the major fatty acids (together representing 87.4 % of the total). The DNA G+C content was 67.1 mol%. 16S rRNA gene sequence analysis of strain GH9-3T showed that it grouped within the Variovorax cluster, with highest sequence similarities to Variovorax paradoxus IAM 12373T (98.3 %) and Variovorax dokdonensis DS-43T (98.0 %). DNA–DNA hybridization values between strain GH9-3T and V. paradoxus DSM 30034T and V. dokdonensis DS-43T were 38 and 29 %, respectively. Based on phenotypic, chemotaxonomic and phylogenetic features, it is proposed that strain GH9-3T represents a novel species of the genus Variovorax with the name Variovorax soli sp. nov. The type strain is GH9-3T (=KACC 11579T=DSM 18216T).

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32

Park, Min-Ju, Ho-Bin Kim, Dong-Shan An, Hee-Chan Yang, Seok-Tae Oh, Hae-Jung Chung i Deok-Chun Yang. "Paenibacillus soli sp. nov., a xylanolytic bacterium isolated from soil". International Journal of Systematic and Evolutionary Microbiology 57, nr 1 (1.01.2007): 146–50. http://dx.doi.org/10.1099/ijs.0.64533-0.

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Two novel polysaccharide-degrading bacteria (strains DCY03T and DCY04) were isolated from a soil sample of a ginseng field in the Republic of Korea and were identified as representing members of the genus Paenibacillus on the basis of phenotypic characteristics and phylogenetic inference based on 16S rRNA gene sequences. Cells of the two isolates were Gram-positive, spore-forming, non-motile, straight rods. Based on DNA–DNA relatedness data, the strains were considered to belong to the same species. The DNA G+C content ranged from 56.6 to 57.0 mol%. The predominant cellular fatty acid was anteiso-C15 : 0 (63.8–62.8 %). Levels of 16S rRNA gene sequence similarity between the two novel isolates and the type strains of recognized Paenibacillus species were 91.4–96.5 %. Strains DCY03T and DCY04 could clearly be distinguished from phylogenetically closely related Paenibacillus species on the basis of DNA–DNA relatedness data and phenotypic characteristics. Therefore, on the basis of these data, the two isolates are considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus soli sp. nov. is proposed. The type strain is DCY03T (=KCTC 13010T=LMG 23604T).

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Choi, Jung-Hye, Min-Soo Kim, Mi-Ja Jung, Seong Woon Roh, Kee-Sun Shin i Jin-Woo Bae. "Sphingopyxis soli sp. nov., isolated from landfill soil". International Journal of Systematic and Evolutionary Microbiology 60, nr 7 (1.07.2010): 1682–86. http://dx.doi.org/10.1099/ijs.0.013128-0.

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A Gram-negative, aerobic, rod-shaped, motile, oxidase-positive, catalase-negative bacterium, designated strain BL03T, was isolated from landfill soil in Pohang, Republic of Korea. Colonies on Luria–Bertani agar plates were yellow. The strain grew in the presence of 0–3 % (w/v) NaCl, at 15–42 °C and at pH 5.0–9.5. The predominant ubiquinone was Q-10, and the major cellular fatty acids were C17 : 1 ω6c, C15 : 0 2-OH and C18 : 1 ω7c. Polar lipids detected were phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid and an unknown glycolipid. Spermidine was identified as the major polyamine component. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BL03T belongs to the genus Sphingopyxis with high sequence similarity to Sphingopyxis taejonensis JSS54T (97.8 %), Sphingopyxis alaskensis RB2256T (97.4 %) and Sphingopyxis chilensis S37T (96.9 %). Levels of DNA–DNA relatedness between strain BL03T and the above three type strains were only 10.3–40.3 %. The DNA G+C content of strain BL03T was 65.9 mol%. Based on the data presented, strain BL03T is considered to represent a novel species of the genus Sphingopyxis, for which the name Sphingopyxis soli sp. nov. is proposed. The type strain is BL03T (=KCTC 22405T =JCM 15910T).

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34

Wang, Xiang, Hong-Xing Yang, Ying-Kun Zhang, Shi-Jun Zhu, Xiao-Wei Liu, Hao Zhang, Chen-Fei Zhang, Chao-Ran Zhao, Gang Hu i Qing Hong. "Luteimonas soli sp. nov., isolated from farmland soil". International Journal of Systematic and Evolutionary Microbiology 65, Pt_12 (1.12.2015): 4809–15. http://dx.doi.org/10.1099/ijsem.0.000652.

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A yellow-pigmented bacterial strain, designated Y2T, was isolated from farmland soil in Bengbu, Anhui province, China. Cells of strain Y2T were Gram-stain-negative, strictly aerobic, non-motile and rod-shaped. Strain Y2T grew optimally at pH 7.0, 30 °C and in the presence of 2 % (w/v) NaCl. The DNA G+C content was 68.9 mol%. The major fatty acids (>5 %) were iso-C15 : 0, iso-C17 : 0, summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1ω9c), iso-C11 : 0 3-OH and iso-C11 : 0. The major respiratory quinone was ubiquinone-8 (Q-8), and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Phylogenetic analysis of the 16S rRNA gene sequences showed that strain Y2T was most closely related to Luteimonas mephitis B1953/27.1T (99.1 % 16S rRNA gene sequence similarity), followed by Luteimonas lutimaris G3T (98.6 %), Luteimonas abyssi XH031T (96.2 %) and Luteimonas aquatica RIB1-20T (96.0 %). Strain Y2T exhibited low DNA–DNA relatedness with Luteimonas mephitis B1953/27.1T (43.6 ± 0.5 %) and Luteimonas lutimaris G3T (43.9 ± 2.1 %). On the basis of phenotypic, genotypic and phylogenetic evidence, strain Y2T represents a novel species of the genus Luteimonas, for which the name Luteimonas soli sp. nov. is proposed. The type strain is Y2T ( = ACCC 19799T = KCTC 42441T).

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35

Young, Monica R., i Paul D. N. Hebert. "Unearthing soil arthropod diversity through DNA metabarcoding". PeerJ 10 (1.02.2022): e12845. http://dx.doi.org/10.7717/peerj.12845.

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DNA metabarcoding has the potential to greatly advance understanding of soil biodiversity, but this approach has seen limited application for the most abundant and species-rich group of soil fauna–the arthropods. This study begins to address this gap by comparing information on species composition recovered from metabarcoding two types of bulk samples (specimens, soil) from a temperate zone site and from bulk soil samples collected at eight sites in the Arctic. Analysis of 22 samples (3 specimen, 19 soil) revealed 410 arthropod OTUs belonging to 112 families, 25 orders, and nine classes. Studies at the temperate zone site revealed little overlap in species composition between soil and specimen samples, but more overlap at higher taxonomic levels (families, orders) and congruent patterns of α- and β-diversity. Expansion of soil analyses to the Arctic revealed locally rich, highly dissimilar, and spatially structured assemblages compatible with dispersal limited and environmentally driven assembly. The current study demonstrates that DNA metabarcoding of bulk soil enables rapid, large-scale assessments of soil arthropod diversity. However, deep sequence coverage is required to adequately capture the species present in these samples, and expansion of the DNA barcode reference library is necessary to improve taxonomic resolution of the sequences recovered through this approach.

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36

Jiang, Wan-Kui, Qin-Qin Gao, Lu Zhang, Gao-Jie Sun, Ming-Liang Zhang, Xiao-An Liu, Hui Wang, Yi-Dong Zhou, Zhi-Jian Ke i Qing Hong. "Ornithinicoccus soli sp. nov., isolated from farmland soil". International Journal of Systematic and Evolutionary Microbiology 70, nr 3 (1.03.2020): 1793–99. http://dx.doi.org/10.1099/ijsem.0.003972.

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A Gram-stain-positive, aerobic, non-motile and coccoid-shaped bacterium, designated XNB-1T, was isolated from farmland soil in Taian, Shandong province, China. Strain XNB-1T contained iso-C15 : 0 and iso-C16 : 0 as the predominant fatty acids. The diagnostic diamino acid of the peptidoglycan was ornithine, and the interpeptide bridge was l-Orn←Gly(1, 2)←d-Glu. The polar lipid profile of strain XNB-1T consisted of diphosphatidylglycerol, phosphatidylglycerol, an unidentified phosphoglycolipid and three unidentified phospholipids. The predominant menaquinone of strain XNB-1T was MK-8(H4) and the DNA G+C content was 70.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain XNB-1T belonged to the genus Ornithinicoccus , and shared the highest similarity with Ornithinicoccus hortensis HKI 0125T (96.0 %), followed by Ornithinicoccus halotolerans EGI 80423T (95.5 %). Genome-based analysis of average nucleotide identity of strain XNB-1T with O. hortensis HKI 0125T and O. halotolerans EGI 80423T yielded values of 73.1 and 73.3 %, respectively, while the digital DNA–DNA hybridization values were 19.5 and 19.9 %, respectively. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain XNB-1T is considered to represent a novel species of the genus Ornithinicoccus , for which the name Ornithinicoccus soli sp. nov. is proposed. The type strain is XNB-1T (=CCTCC AB 2019099T=KCTC 49259T).

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Johnsen, Anders R., Anne Winding, Ulrich Karlson i Peter Roslev. "Linking of Microorganisms to Phenanthrene Metabolism in Soil by Analysis of 13C-Labeled Cell Lipids". Applied and Environmental Microbiology 68, nr 12 (grudzień 2002): 6106–13. http://dx.doi.org/10.1128/aem.68.12.6106-6113.2002.

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ABSTRACT Phenanthrene-metabolizing soil microbial communities were characterized by examining mineralization of [14C]phenanthrene, by most-probable-number (MPN) counting, by 16S-23S spacer DNA analysis of the numerically dominant, culturable phenanthrene-degrading isolates, and by examining incorporation of [13C]phenanthrene-derived carbon into sterols and polar lipid fatty acids (PLFAs). An unpolluted agricultural soil, a roadside soil diffusely polluted with polycyclic aromatic hydrocarbons (PAHs), and two highly PAH-polluted soils from industrial sites were analyzed. Microbial phenanthrene degraders were not detected by MPN counting in the agricultural soil and the roadside soil. In the industrial soils, phenanthrene degraders constituted 0.04 and 3.6% of the total number of CFU. 16S-23S spacer DNA analysis followed by partial 16S DNA sequencing of representative isolates from one of the industrial soils showed that one-half of the isolates belonged to the genus Sphingomonas and the other half were closely related to an unclassified beta-proteobacterium. The 13C-PLFA profiles of the two industrial soils were relatively similar and resembled the profiles of phenanthrene-degrading Sphingomonas reference strains and unclassified beta-proteobacterium isolates but did not match the profiles of Pseudomonas, Mycobacterium, or Nocardia reference strains. The 13C-PLFA profiles of phenanthrene degraders in the agricultural soil and the roadside soil were different from each other and different from the profiles of the highly polluted industrial soils. Only in the roadside soil were 10me/12me18:0 PLFAs enriched in 13C, suggesting that actinomycetes metabolized phenanthrene in this soil. The 13C-PLFA profiles of the unpolluted agricultural soil did not resemble the profiles of any of the reference strains. In all of the soils investigated, no excess 13C was recovered in the 18:2ω6,9 PLFA, suggesting that fungi did not contribute significantly to assimilation of [13C]phenanthrene.

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Lee, Myungjin, Sung-Geun Woo, Myoungsoo Chae i Leonid N. Ten. "Pusillimonas soli sp. nov., isolated from farm soil". International Journal of Systematic and Evolutionary Microbiology 60, nr 10 (1.10.2010): 2326–30. http://dx.doi.org/10.1099/ijs.0.020404-0.

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A Gram-negative, motile, non-spore-forming bacterial strain, designated MJ07T, was isolated from a farm soil and was characterized to determine its taxonomic position by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain MJ07T belongs to the family Alcaligenaceae, class Betaproteobacteria, and is related most closely to Pusillimonas ginsengisoli KCTC 22046T (98.6 % sequence similarity) and Pusillimonas noertemannii BN9T (96.9 %). The levels of 16S rRNA gene sequence similarity between strain MJ07T and members of all other recognized species of the family Alcaligenaceae were below 95.2 %. The G+C content of the genomic DNA of strain MJ07T was 59.4 mol%. The detection of a quinone system with ubiquinone Q-8 as the major respiratory lipoquinone, putrescine as the predominant polyamine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unknown aminolipids as major polar lipids and a fatty acid profile with C16 : 0 (32.0 %), C17 : 0 cyclo (24.7 %) and C19 : 0 cyclo ω8c (11.5 %) as the major components supported the affiliation of strain MJ07T to the genus Pusillimonas. Strain MJ07T exhibited relatively low levels of DNA–DNA relatedness with respect to P. ginsengisoli KCTC 22046T (50±8 %) and P. noertemannii KACC 13183T (18±7 %). On the basis of its phenotypic and genotypic properties together with its phylogenetic distinctiveness, strain MJ07T (=KCTC 22455T =JCM 16386T) should be classified in the genus Pusillimonas as the type strain of a novel species, for which the name Pusillimonas soli sp. nov. is proposed.

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39

Aliche, Ernest B., Warner Talsma, Teun Munnik i Harro J. Bouwmeester. "Characterization of maize root microbiome in two different soils by minimizing plant DNA contamination in metabarcoding analysis". Biology and Fertility of Soils 57, nr 5 (9.04.2021): 731–37. http://dx.doi.org/10.1007/s00374-021-01555-3.

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AbstractA micropore-filtration method was used to reduce the proportion of plant DNA in microbial DNA samples isolated from roots prior to sequencing. We tested the impact of this pre-sequencing filtration methodology and used it to characterize the root microbiome of maize grown on two soils with different fertility levels. The micropore filtration reduced plant DNA contamination and unveiled potential in the N-poor soil for N fixation in roots and phosphate uptake by roots in the phosphate-poor soil. Our methodology and findings allude to the potential capability of plants to initiate plant-microbe interactions under sub-optimal soil fertility.

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40

Hirano, Takeshi, i Kazuyoshi Tamae. "Heavy Metal-Induced Oxidative DNA Damage in Earthworms: A Review". Applied and Environmental Soil Science 2010 (2010): 1–7. http://dx.doi.org/10.1155/2010/726946.

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Earthworms can be used as a bio-indicator of metal contamination in soil, Earlier reports claimed the bioaccumulation of heavy metals in earthworm tissues, while the metal-induced mutagenicity reared in contaminated soils for long duration. But we examined the metal-induced mutagenicity in earthworms reared in metal containing culture beddings. In this experiment we observed the generation of 8-oxoguanine (8-oxo-Gua) in earthworms exposed to cadmium and nickel in soil. 8-oxo-Gua is a major premutagenic form of oxidative DNA damage that induces GC-to-TA point mutations, leading to carcinogenesis.

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41

Jauhani, Muhammad Afiful, i Sheilla Rachmania. "DNA Quality and Quantity on Blood Spot Post Soil and Ultraviolet-C Exposure". Journal of Agromedicine and Medical Sciences 6, nr 3 (12.10.2020): 181. http://dx.doi.org/10.19184/ams.v6i3.19937.

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Bercak darah dapat ditemukan di tempat kejadian perkara (TKP) pada banyak kasus tindak kekerasan. Asam deoksiribonukleat (DNA) pada darah dapat digunakan sebagai data primer untuk proses identifikasi akan tetapi bercak darah di TKP berisiko rusak akibat pajanan tanah dan ultraviolet. Tujuan utama dari penelitian ini adalah untuk mempelajari efek kombinasi dari pajanan sinar ultraviolet-C dan tanah terhadap kualitas dan kuantitas DNA pada bercak darah. Sebanyak 20 gelas berisi 200 gram tanah ditetesi 900µl darah dan diberikan pajanan sinar ultraviolet-C dalam tiga kelompok berdasarkan durasi pajanan yakni satu hari, tiga hari, dan lima hari. Satu kelompok digunakan sebagai kontrol. Ekstraksi DNA dilakukan menggunakan DNAZol dilanjutkan dengan pengukuran spektrofotometri untuk mengetahui kualitas dan kuantitas DNA. Peningkatan konsentrasi DNA dapat diamati yaitu 681,1 pada hari pertama menjadi 1274,7 pada hari ketiga dan mulai menurun menjadi 1090,6 pada hari kelima, sedangkan kemurnian DNA terus menurun secara konstan seiring dengan meningkatnya durasi pajanan. Penelitian ini menunjukkan bahwa pajanan sinar ultraviolet-C dan tanah menyebabkan degradasi molekul DNA menjadi fragmen-fragmen molekul yang lebih kecil sehingga terjadi peningkatan kuantitas DNA yang disertai penurunan kualitas DNA. Penurunan kualitas DNA dapat mempersulit proses identifikasi sehingga isolasi DNA sampel pada tanah terbuka yang terpajan matahari harus dilakukan sesegera mungkin. Kata Kunci: DNA, darah, tanah, ultraviolet C, patologi forensik

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42

Lee, Myungjin, Leonid N. Ten, Sung-Geun Woo i Joonhong Park. "Agromyces soli sp. nov., isolated from farm soil". International Journal of Systematic and Evolutionary Microbiology 61, nr 6 (1.06.2011): 1286–92. http://dx.doi.org/10.1099/ijs.0.021568-0.

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A Gram-positive, aerobic to microaerophilic, non-motile bacterial strain, designated MJ21T, was isolated from farm soil and was characterized to determine its taxonomic position by using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain MJ21T was placed within the genus Agromyces, and exhibited relatively high levels of similarity to Agromyces ulmi XIL01T (97.8 %), Agromyces aurantiacus YIM 21741T (97.1 %), Agromyces mediolanus JCM 3346T (96.7 %), A. mediolanus JCM 1376 (99.1 %), A. mediolanus JCM 9632 (99.1 %), A. mediolanus JCM 9633 (98.9 %) and A. mediolanus JCM 9631 (96.5 %). Chemotaxonomic data also supported the classification of strain MJ21T within the genus Agromyces. The new isolate contained MK-12 as the predominant menaquinone and rhamnose, galactose and xylose as cell-wall sugars. The major cellular fatty acids (>10 % of the total) were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. Cell-wall amino acids were 2,4-diaminobutyric acid, glutamic acid, glycine and alanine. Diphosphatidylglycerol, phosphatidylglycerol, two unknown glycolipids and one unidentified phospholipid were detected as polar lipids. The DNA G+C content of strain MJ21T was 73.4 mol%. However, levels of DNA–DNA relatedness between strain MJ21T and the seven phylogenetically closest Agromyces strains ranged from 14 to 56 %, showing clearly that the new isolate represents a novel genomic species. Strain MJ21T could be differentiated clearly from its phylogenetic neighbours on the basis of phenotypic, genotypic and chemotaxonomic features. Therefore, strain MJ21T is considered to represent a novel species of the genus Agromyces, for which the name Agromyces soli sp. nov. is proposed. The type strain is MJ21T ( = KCTC 19549T = JCM 16247T).

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Boggs, Laura M., Melissa K. R. Scheible, Gustavo Machado i Kelly A. Meiklejohn. "Single Fragment or Bulk Soil DNA Metabarcoding: Which is Better for Characterizing Biological Taxa Found in Surface Soils for Sample Separation?" Genes 10, nr 6 (6.06.2019): 431. http://dx.doi.org/10.3390/genes10060431.

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In forensic geology casework, sample size typically limits routine characterization of material using bulk approaches. To address this, DNA-based characterization of biological taxa has received attention, as the taxa present can be useful for sample-to-sample comparisons and source attribution. In our initial work, low biodiversity was captured when DNA barcodes were Sanger-sequenced from plant and insect fragments isolated from 10 forensic-type surface soils. Considering some forensic laboratories now have access to massively parallel sequencing platforms, we assessed whether biological taxa present in the same surface soils could be better characterized using DNA metabarcoding. To achieve this, plant and animal barcodes were amplified and sequenced on an Illumina® MiniSeq for three different DNA sample types (n = 50): individual fragments used in our initial study, and 250 and 100 mg of bulk soil (from the 10 sites used in the initial study). A total of 572 unique target barcode sequences passed quality filtering and were used in downstream statistical analyses: 54, 321, and 285 for individual fragments, 100 mg, and 250 mg bulk soil samples, respectively. Plant barcodes permitted some spatial separation of sample sites in non-metric multidimensional scaling plots; better separation was obtained for samples prepared from bulk soil. This study confirmed that bulk soil DNA metabarcoding is a better approach for characterizing biological taxa present in surface soils, which could supplement traditional geologic examinations.

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Torsvik, V., J. Goksøyr i F. L. Daae. "High diversity in DNA of soil bacteria." Applied and Environmental Microbiology 56, nr 3 (1990): 782–87. http://dx.doi.org/10.1128/aem.56.3.782-787.1990.

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Bonadei, Martina, Alma Balestrazzi, Barbara Frigerio i Daniela Carbonera. "Soil persistence of DNA from transgenic poplar". Environmental Biosafety Research 8, nr 2 (kwiecień 2009): 79–86. http://dx.doi.org/10.1051/ebr/2009005.

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Pettit, Robin K. "Soil DNA libraries for anticancer drug discovery". Cancer Chemotherapy and Pharmacology 54, nr 1 (8.04.2004): 1–6. http://dx.doi.org/10.1007/s00280-004-0771-8.

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Lartey, R. T., T. C. Caesar-TonThat, A. W. Lenssen, J. Eckhoff, S. L. Hanson i R. G. Evans. "Direct Polymerase Chain Reaction-Based Detection of Cercospora beticola in Field Soils". Plant Disease 94, nr 9 (wrzesień 2010): 1100–1104. http://dx.doi.org/10.1094/pdis-94-9-1100.

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Cercospora beticola, the causal agent of Cercospora leaf spot of sugar beet, survives as pseudostromata in infected sugar beet residues in the soil. Under optimal conditions, overwintering propagules germinate and produce conidia that are dispersed as primary inoculum to initiate infection in sugar beet. We developed a polymerase chain reaction (PCR) technique for rapid detection of C. beticola in field soils. Total DNA was first isolated from soil amended with C. beticola culture using the PowerSoil DNA Kit. The purified DNA was subjected to PCR in Extract-N-Amp PCR mix with CBACTIN primers over 35 cycles. The amplified products were resolved and compared by electrophoresis in 1% agarose gels. The PCR fragment size of C. beticola from the amended field soil correlated in size with the amplicon from control C. beticola culture DNA extract. Additionally, sample soils were collected from sugar beet fields near Sidney, MT and Foxholm, ND. Total DNA was extracted from the samples and subjected to PCR and resolved as previously described. The amplicons were purified from the gels and subjected to BigDye Terminator Cycle sequencing. All sequences from field soils samples, C. beticola-amended field soil, and pure culture were compared by alignment with a C. beticola actin gene sequence from GenBank. The result of the alignment confirmed the amplicons as products from C. beticola. Rapid screening for the presence of C. beticola in the soil by PCR will improve research capabilities in biological control, disease forecasting, and management of this very important sugar beet pathogen.

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Yoo, Seung-Hee, Hang-Yeon Weon, Byung-Yong Kim, Seung-Beom Hong, Soon-Wo Kwon, Yang-Hee Cho, Seung-Joo Go i Erko Stackebrandt. "Devosia soli sp. nov., isolated from greenhouse soil in Korea". International Journal of Systematic and Evolutionary Microbiology 56, nr 11 (1.11.2006): 2689–92. http://dx.doi.org/10.1099/ijs.0.64214-0.

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A Gram-negative, obligately aerobic, rod-shaped bacterium was isolated from greenhouse soil used to cultivate lettuce. The strain, GH2-10T, was characterized on the basis of phenotypic and genotypic data. 16S rRNA gene sequence analysis revealed that the isolate belonged to the genus Devosia, with highest sequence similarity (98.5 %) to Devosia riboflavina IFO 13584T. Sequence similarities with other strains tested were below 97.0 %. Strain GH2-10T had Q-10 as the predominant ubiquinone and C18 : 1 ω7c and C16 : 0 as the major fatty acids. The G+C content of the genomic DNA was 59.5 mol%. The results of DNA–DNA hybridization experiments (47 % relatedness between D. riboflavina DSM 7230T and strain GH2-10T) and physiological and biochemical tests suggested that strain GH2-10T represents a novel species of the genus Devosia, for which the name Devosia soli sp. nov. is proposed. The type strain is GH2-10T (=KACC 11509T=DSM 17780T).

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Gorny, Adrienne M., Frank S. Hay, Xiaohong Wang i Sarah J. Pethybridge. "Isolation of nematode DNA from 100 g of soil using Fe3O4 super paramagnetic nanoparticles". Nematology 20, nr 3 (2018): 271–83. http://dx.doi.org/10.1163/15685411-00003140.

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An economical method for extracting nematode DNA from 100 g of soil was developed to facilitate nematode detection and quantification, and tested using the Northern root-knot nematode,Meloidogyne hapla. The method utilised enzymatic laundry detergent lysis, Fe3O4super paramagnetic iron oxide nanoparticle (SPION) capture, and polyvinylpolypyrrolidone (PVPP) purification. Resultant DNA from this SPION capture method was approximately 100-fold less but of similar quality to DNA obtained from a standard phenol procedure and a commercial DNA extraction kit. An addition of 10 mg of nanoparticles to the extraction lysate was identified to maximise DNA yield while minimising co-capture of contaminants. The detection limit of the SPION capture method was approximately 100 nematodes (100 g soil)−1. The SPION capture method extracted nematode DNA from mineral soils but requires further optimisation for extraction from high organic matter (i.e., ‘muck’) soils. The benefits of this method compared to alternative techniques are discussed.

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Baidoo, Richard, Guiping Yan, Berlin Nelson, Andrea M. Skantar i Senyu Chen. "Use of Chemical Flocculation and Nested PCR for Heterodera glycines Detection in DNA Extracts from Field Soils with Low Population Densities". Plant Disease 101, nr 7 (lipiec 2017): 1153–61. http://dx.doi.org/10.1094/pdis-08-16-1163-re.

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The soybean cyst nematode (SCN) Heterodera glycines is a major pathogen of soybean worldwide. Distinction between SCN and other members of the H. schachtii sensu stricto group based on morphology is a tedious task. A molecular assay was developed to detect SCN in field soils with low population densities and to differentiate SCN from other species. Various numbers of SCN eggs or juveniles were inoculated into 10 g of sterilized soil from which soil DNA was extracted using the PowerSoil DNA Isolation Kit. A specific amplicon was amplified using published SCN-specific primers SCNF1/SCNR1. This primer set was evaluated for the first time to detect SCN directly in soil DNA extracts. The specificity of the primers was confirmed by testing 36 isolates of other nematode species. The PCR assay detected one SCN egg or juvenile added to 10 g of soil. The assay was validated using 35 field soil samples. Grinding the field soil coupled with PCR inhibitor removal by AlNH4(SO4)20.12H2O treatment of soil DNA extracts followed by nested PCR enabled SCN detection as low as 12 SCN eggs/200 g soil. The PCR assay not only provides a sensitive method for SCN detection at low densities but also provides a discrimination method for SCN from other closely related nematodes.

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