scholarly journals Innovative Methods for Soil DNA Purification Tested in Soils with Widely Differing Characteristics

2008 ◽  
Vol 74 (9) ◽  
pp. 2902-2907 ◽  
Author(s):  
Marketa Sagova-Mareckova ◽  
Ladislav Cermak ◽  
Jitka Novotna ◽  
Kamila Plhackova ◽  
Jana Forstova ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Soil Ph ◽  
Vegetation Cover ◽  
Organic Matter Content ◽  
Clay Content ◽  
Matter Content ◽  
Soil Dna ◽  
Innovative Methods ◽  
Soil Dna Extraction ◽  
Extraction And Purification

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.

scholarly journals Effect of Clay, Soil Organic Matter, and Soil pH on Initial and Residual Weed Control with Flumioxazin

Agronomy ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1326
Author(s):  
Calvin F. Glaspie ◽  
Eric A. L. Jones ◽  
Donald Penner ◽  
John A. Pawlak ◽  
Wesley J. Everman
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Weed Control ◽  
Soil Ph ◽  
Organic Matter Content ◽  
Amaranthus Retroflexus ◽  
Matter Content ◽  
Weed Species ◽  
Soil Organic Matter Content ◽  
Field Soils

Greenhouse studies were conducted to evaluate the effects of soil organic matter content and soil pH on initial and residual weed control with flumioxazin by planting selected weed species in various lab-made and field soils. Initial control was determined by planting weed seeds into various lab-made and field soils treated with flumioxazin (71 g ha−1). Seeds of Echinochloa crus-galli (barnyard grass), Setaria faberi (giant foxtail), Amaranthus retroflexus (redroot pigweed), and Abutilon theophrasti (velvetleaf) were incorporated into the top 1.3 cm of each soil at a density of 100 seeds per pot, respectively. Emerged plants were counted and removed in both treated and non-treated pots two weeks after planting and each following week for six weeks. Flumioxazin control was evaluated by calculating percent emergence of weeds in treated soils compared to the emergence of weeds in non-treated soils. Clay content was not found to affect initial flumioxazin control of any tested weed species. Control of A. theophrasti, E. crus-galli, and S. faberi was reduced as soil organic matter content increased. The control of A. retroflexus was not affected by organic matter. Soil pH below 6 reduced flumioxazin control of A. theophrasti, and S. faberi but did not affect the control of A. retroflexus and E. crus-galli. Flumioxazin residual control was determined by planting selected weed species in various lab-made and field soils 0, 2, 4, 6, and 8 weeks after treatment. Eight weeks after treatment, flumioxazin gave 0% control of A. theophrasti and S. faberi in all soils tested. Control of A. retroflexus and Chenopodium album (common lambsquarters) was 100% for the duration of the experiment, except when soil organic matter content was greater than 3% or the soil pH 7. Eight weeks after treatment, 0% control was only observed for common A. retroflexus and C. album in organic soil (soil organic matter > 80%) or when soil pH was above 7. Control of A. theophrasti and S. faberi decreased as soil organic matter content and soil pH increased. Similar results were observed when comparing lab-made soils to field soils; however, differences in control were observed between lab-made organic matter soils and field organic matter soils. Results indicate that flumioxazin can provide control ranging from 75–100% for two to six weeks on common weed species.

Near-infrared spectroscopy as a potential method for routine sediment analysis to improve rapidity and efficiency

1998 ◽  
Vol 37 (6-7) ◽  
pp. 181-188 ◽  
Author(s):  
Diane F. Malley
Keyword(s):  
Near Infrared ◽  
Organic Matter Content ◽  
Aggregate Size ◽  
Clay Content ◽  
Analytical Techniques ◽  
Matter Content ◽  
Near Infrared Reflectance ◽  
Organic C ◽  
Analytical Technique ◽  
Sediment Analysis

The potential for improvement in the rapidity, cost-effectiveness, and efficiency of sediment analysis by the application of near-infrared reflectance spectroscopy (NIRS) is recognized. The rapid (<2 min), non-chemical, non-destructive analytical technique of near-infrared (700–2500 nm) spectroscopy combines applied spectroscopy and complex statistics. It has been used for the experimental analysis of various constituents and functions of soils since the 1960s, and applications for the analysis of sediments are currently being explored. For application of NIRS, sediment samples require little preparation, other than drying, and the samples are not subject to the manipulations of conventional analytical techniques. The spectral information recorded in a 2 min scan can be used to predict numerous constituents and parameters on the samples once appropriate calibration equations have been prepared from sets of samples analyzed by both NIRS and conventional analytical techniques. Constituents and properties of soil and/or sediment analyzed by NIRS technology include moisture, organic matter content, organic C, CO3=, N, P, S, K, Ca, Mg, clay content, humic acids, lignin, cellulose, metal oxides, heavy metals, aggregate size, and inferred past pH of lakes. Several areas are identified where further research is needed to prepare for the application of NIRS to the routine analysis of sediments.

scholarly journals Factors Affecting Microbial Formation of Nitrate-Nitrogen in Soil and Their Effects on Fertilizer Nitrogen Use Efficiency

2001 ◽  
Vol 1 ◽  
pp. 122-129 ◽  
Author(s):  
Alan Olness ◽  
Dian Lopez ◽  
David Archer ◽  
Jason Cordes ◽  
Colin Sweeney ◽  
...  
Keyword(s):  
Organic Matter ◽  
Decision Aid ◽  
Pore Space ◽  
Organic Matter Content ◽  
Clay Content ◽  
Matter Content ◽  
N Fertilizer ◽  
Nitrate N ◽  
Soil Clay ◽  
Soil Clay Content

Mineralization of soil organic matter is governed by predictable factors with nitrate-N as the end product. Crop production interrupts the natural balance, accelerates mineralization of N, and elevates levels of nitrate-N in soil. Six factors determine nitrate-N levels in soils: soil clay content, bulk density, organic matter content, pH, temperature, and rainfall. Maximal rates of N mineralization require an optimal level of air-filled pore space. Optimal air-filled pore space depends on soil clay content, soil organic matter content, soil bulk density, and rainfall. Pore space is partitioned into water- and air-filled space. A maximal rate of nitrate formation occurs at a pH of 6.7 and rather modest mineralization rates occur at pH 5.0 and 8.0. Predictions of the soil nitrate-N concentrations with a relative precision of 1 to 4 μg N g–1of soil were obtained with a computerized N fertilizer decision aid. Grain yields obtained using the N fertilizer decision aid were not measurably different from those using adjacent farmer practices, but N fertilizer use was reduced by >10%. Predicting mineralization in this manner allows optimal N applications to be determined for site-specific soil and weather conditions.

scholarly journals A small rainfall simulator for the determination of soil erodibility.

1987 ◽  
Vol 35 (3) ◽  
pp. 407-415 ◽  
Author(s):  
A. Kamphorst
Keyword(s):  
Organic Matter ◽  
Soil Conservation ◽  
Standard Procedure ◽  
Organic Matter Content ◽  
Clay Content ◽  
Matter Content ◽  
Soil Erodibility ◽  
Rainfall Simulator ◽  
Highly Sensitive

A small rainfall simulator is described, which can be used in the field as well as in the laboratory for the determination of infiltration and erosion characterisitcs of soils. It is particularly suitable for soil conservation surveys, as it is light to carry and easy to handle in the field. A description is given of a standard procedure for the determination of topsoil erodibilities in the field and some results are presented. The method appears to be highly sensitive to soil properties influencing soil erodibility, such as clay content, organic matter content and soil pH. (Abstract retrieved from CAB Abstracts by CABI’s permission)

scholarly journals Different Methods of Soil DNA Extraction

BIO-PROTOCOL ◽  
2020 ◽  
Vol 10 (2) ◽  
Author(s):  
Asmita Kamble ◽  
Harinder Singh
Keyword(s):  
Dna Extraction ◽  
Soil Dna ◽  
Soil Dna Extraction

scholarly journals Comparative value of various methods of approximating the permanent wilting percentage

1969 ◽  
Vol 36 (2) ◽  
pp. 122-133
Author(s):  
M. A. Lugo López
Keyword(s):  
Puerto Rico ◽  
Organic Matter Content ◽  
Clay Content ◽  
Matter Content ◽  
Regression Equations ◽  
Accurate Approximation ◽  
Time Saving ◽  
Laboratory Equipment ◽  
Pressure Plate ◽  
Humid Region

Very accurate estimations of the permanent wilting percentage can be obtained for soils of all regions of Puerto Rico by use of regression equations based on the hygroscopic coefficient. Reliable estimates can also be obtained for humid-region soils by using the clay content as a basis. Attempts to correlate permanent wilting-percentage values with moisture equivalents and organic-matter content did not give such satisfactory results. The 15-atmosphere percentage as determined by using pressure plates gives an accurate approximation of permanent wilting-percentage values. It is time-saving, but initial expense in laboratory equipment is rather high. This approach is to be preferred whenever feasible. A regression equation is given relating pressure-plate values to the permanent wilting percentage. Whenever less precise estimates are acceptable and time is not a factor, advantage should be taken of the established correlation between the hygroscopic coefficient and the permanent wilting percentage.

Surfactant Effects on Picloram Adsorption by Soils

Weed Science ◽  
1976 ◽  
Vol 24 (6) ◽  
pp. 549-552 ◽  
Author(s):  
J. D. Gaynor ◽  
V. V. Volk
Keyword(s):  
Organic Matter ◽  
Cationic Surfactant ◽  
Anionic Surfactant ◽  
Organic Matter Content ◽  
Clay Content ◽  
Surfactant Solution ◽  
Matter Content ◽  
Adsorption Sites ◽  
Surfactant Solutions ◽  
Extractable Al

The effects of soil organic matter, clay, extractable Al, cation exchange capacity, and pH on the adsorption of picloram (4-amino-3,5,6-trichloropicolinic acid) from aqueous and surfactant solutions were investigated. Linear adsorption isotherms for the soils were obtained with the Freundlich equation. Of the five soil properties investigated, Freundlich K values correlated with extractable Al and clay content. Picloram adsorption from aqueous solutions and from the non-ionic and anionic surfactant solutions was greater on the soils at pH 5 than at pH 7. The anionic surfactant competed with picloram for adsorption sites on the soils at pH 5. Picloram adsorption from solutions containing 0.1 and 1% cationic surfactant was greater than that from aqeuous and anionic and nonionic surfactant solutions. Picloram adsorption from the 10% cationic surfactant solution was similar on soils with pH 5 and 7 and increased with decreased organic matter content.

scholarly journals Relationship of soil properties to fractionation, bioavailability and mobility of lead and zinc in soil

2008 ◽  
Vol 53 (No. 5) ◽  
pp. 225-238 ◽  
Author(s):  
N. Finžgar ◽  
P. Tlustoš ◽  
D. Leštan
Keyword(s):  
Organic Matter ◽  
Regression Analysis ◽  
Soil Organic Matter ◽  
Soil Properties ◽  
Multiple Regression ◽  
Contaminated Soils ◽  
Organic Matter Content ◽  
Clay Content ◽  
Exchange Capacity ◽  
Matter Content

Sequential extractions, metal uptake by <i>Taraxacum officinale</i>, Ruby&rsquo;s physiologically based extraction test (PBET) and toxicity characteristic leaching procedure (TCLP), were used to assess the risk of Pb and Zn in contaminated soils, and to determine relationships among soil characteristics, heavy metals soil fractionation, bioavailability and leachability. Regression analysis using linear and 2nd order polynomial models indicated relationships between Pb and Zn contamination and soil properties, although of small significance (<i>P</i> < 0.05). Statistically highly significant correlations (<i>P</i> < 0.001) were obtained using multiple regression analysis. A correlation between soil cation exchange capacity (CEC) and soil organic matter and clay content was expected. The proportion of Pb in the PBET intestinal phase correlated with total soil Pb and Pb bound to soil oxides and the organic matter fraction. The leachable Pb, extracted with TCLP, correlated with the Pb bound to carbonates and soil organic matter content (<i>R</i><sup>2</sup> = 69%). No highly significant correlations (<i>P</i> < 0.001) for Zn with soil properties or Zn fractionation were obtained using multiple regression.

Hardsetting in the surface horizons of sandy soils and Its implications for soil classification and management

Soil Research ◽  
1994 ◽  
Vol 32 (3) ◽  
pp. 603 ◽  
Author(s):  
RJ Harper ◽  
RJ Gilkes
Keyword(s):  
Organic Matter Content ◽  
Sandy Soils ◽  
Clay Content ◽  
Soil Classification ◽  
Matter Content ◽  
Arid Area ◽  
Plant Performance ◽  
Classification Schemes ◽  
Surface Conditions ◽  
Measured Strength

Marked variations in hardsetting occur in the sandy surface horizons of duplex deep sandy soils in a semi-arid area of Western Australia. Hardsetting by definition only occurs in dry soils and increases with field texture. Soil strength measured on remoulded samples in the laboratory conformed with field assessments of strength (consistence). Most (79%) of the variation in strength between Ap horizon samples was explained by clay content, with small differences in clay content resulting in large differences in strength. Half of the maximum measured strength in the Ap horizons was achieved at a clay content of only 8%. The A2 horizons were markedly stronger than corresponding Ap horizons, despite similar clay contents, and this difference in strength is related to the larger organic matter content of the Ap horizons. Hardsetting of these sandy soils may be explained in terms of the cementing action provided by clay which forms bridges between particles. Organic material weakens these bridges. Hardsetting may affect the wind erodibility of sandy soils, through differences in surface conditions (i.e. loose v. compact) and by increasing the resistance to abrasion by saltating sand. It is not clear what effect it will have on plant performance. Hardsetting is a continuous, rather than discrete soil attribute, and if it is to be described in the field, and used in soil classification schemes, objectives class limits should be defined, perhaps using dry consistence ratings.

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