scholarly journals The effects of humic substances on DNA isolation from soils

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9378
Author(s):  
Ewa Wnuk ◽  
Adam Waśko ◽  
Anna Walkiewicz ◽  
Piotr Bartmiński ◽  
Romualda Bejger ◽  
...  
Keyword(s):  
Humic Substances ◽  
Dna Isolation ◽  
Arable Land ◽  
Soil Layer ◽  
Soil Samples ◽  
Total Carbon ◽  
High Concentration ◽  
Soil Dna ◽  
Total Carbon Content ◽  
Direct Cell

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.

scholarly journals Transformation of organic carbon in alluvial soils under different land uses

2020 ◽  
Vol 27 (1) ◽  
Author(s):  
Alvyra Šlepetienė ◽  
Kazimiež Duchovski ◽  
Jonas Volungevičius
Keyword(s):  
Land Use ◽  
Organic Carbon ◽  
Total Organic Carbon ◽  
Arable Land ◽  
Soil Layer ◽  
Soil Samples ◽  
Plant Residues ◽  
Land Uses ◽  
Forest Land ◽  
Alluvial Deposits

The aim of this study – to evaluate the status of organic carbon (OC) under different land uses of soils formed in alluvial deposits. The soil samples were collected from 0–10, 10–20 and 20–30 cm depths in three field replicates.Three land uses were investigated: arable land, grassland and forest. The experimental site is situated near Surviliškis, Kėdainiai District (55°26′08.37′′N, 24°02′27.75′′Y) in Central Lowland of Lithuania. A total of 27 soil samples, collected from 0–10, 10–20 and 20–30 cm depths in three field replicates, were analysed for OC. The samples were prepared for analysis by removing plant residues, grinding and sieving through a 0.25 mm sieve. For all land uses, the highest content of OC was found in the upper 0–10 cm soil layer of the soil, with the highest values found in the forest land use. Fast-growing deciduous trees are an effective means to increase the content of OC in alluvial soil, especially in the 0–10 cm layer. The distribution of OC in the soil layers depended on the land use. Grassland and forest land uses allow OC to be preserved throughout the 0–30 cm layer, with less OC differentiation than in arable land. This could be attributed to the specificities of organic matter accumulation and degradation in different land uses. Not only the amount of labile organic carbon (similar to total organic carbon) was highest (0.392 g kg–1) in forest soil in the 0–10 cm layer, it also had a higher relative share in the total organic carbon (2.9%) than in other land uses – arable land and grassland (2.3–2.4%).

Evaluation of the Mechanical Strength of Disturbed Military Training Areas based on the Physical and Chemical Parameters of Soil

2021 ◽  
Author(s):  
Kersti Vennik ◽  
Tõnu Tõnutare ◽  
Kadri Krebstein
Keyword(s):  
Mechanical Strength ◽  
Bulk Density ◽  
Military Training ◽  
Soil Layer ◽  
Total Carbon ◽  
Soil Conditions ◽  
Cone Penetrometer ◽  
Chemical Parameters ◽  
Total Carbon Content ◽  
Military Training Areas

<p>Military training areas have to sustain the intensive usage of tracked and wheeled vehicles and the dismounted movement of soldiers. The periodic nature of training activities causes heavy loads, including a high number of loading repetitions on the soil; this makes the mechanical strength and recovery of soil a consequential issue. In many cases, the preparation of new training areas involves field preparations, e.g. earthmoving or deforestation activities that lead to serious disturbance of soil, especially its natural mechanical strength. The goal of this study was to investigate the potential methods to determine the conditions of previously disturbed military training areas. Soil measurements were carried out two years after deforestation works. Within this study, soil samples were collected and the mechanical strength of soil was determined in July and November 2020, with the aim to characterize soil conditions during dry and wet periods. Soil bulk density as well as cone penetrometer and dynamic cone penetrometer measurements were carried out.  In chemical parameters of soil, the total carbon content was measured as an indicator of uniformity by mixing organic matter in the soil surface (25 cm) layer. As the development of plant cover and especially its tight root system is very important for increasing the mechanical strength of soil, the content of plant available nutrients (P, K, Mg and Ca) was also measured. To evaluate the uniformity of blended upper soil layer, the soil was divided into 5 different layers of 5 cm thick each. The bulk density was determined for each layer. The chemical parameters of soil were determined for each layer separately and a diagram of element content in profile was created according to obtained results. This presentation will address the preliminary results of field measurements.</p>

scholarly journals  Humus content and quality under different soil tillage systems

2010 ◽  
Vol 5 (No. 3) ◽  
pp. 90-95
Author(s):  
Ľ. Pospíšilová ◽  
N. Fasurová ◽  
V. Petrášová
Keyword(s):  
Carbon Content ◽  
Humic Substances ◽  
Humus Content ◽  
Total Carbon ◽  
Soil Tillage ◽  
Soil Types ◽  
Total Carbon Content ◽  
Minimum Tillage ◽  
Spectroscopic Characteristics ◽  
Non Destructive

The main objective of our study was to compare the contents and quality of humic substances in selected soil types under different tillage regimes (deep, reduced, minimum). Non destructive spectroscopic methods such as UV-VIS and synchronous fluorescence spectroscopy were applied. After three years of experiments, no statistically significant differences in the total carbon content, labile carbon content, and humic substances carbon content were found. Humic substances quality and the absorbance in UV-VIS spectral range was the highest in Haplic Chernozem (minimum tillage). Fluorescence intensity varied in dependence on the soil types, however, the same main fluorophores in all samples were detected. Fluorescence of humic substances was the highest in Haplic Chernozem (minimum tillage). The determination of HS spectroscopic characteristics was found as a sensitive indicator for HS quality assessment.

scholarly journals The Influence of Afforestation on Upland Soils: The Use of ‘Bomb 14C’ Enrichment as a Quantitative Tracer for Changes in Organic Status

Radiocarbon ◽  
1989 ◽  
Vol 31 (03) ◽  
pp. 637-643 ◽  
Author(s):  
D D Harkness ◽  
A F Harrison
Keyword(s):  
Organic Matter ◽  
Carbon Content ◽  
Growth Period ◽  
Soil Samples ◽  
Total Carbon ◽  
Soil Horizons ◽  
Total Carbon Content ◽  
Soil Carbon Content ◽  
Fresh Organic Matter ◽  
Carbon Inventory

A series of soil samples were collected in November 1984 from five stands of Sitka spruce planted at recorded times between 1951 and 1968. Within a comprehensive program of ecologic and biogeochemical analyses, natural 14C measurements on selected organic components of the 0 to 5cm soil horizons serve to quantify progressive changes induced in the organic carbon inventory and relative to that of the original grassland. Points of particular interest are: 1) an enhanced input of fresh organic matter in the years immediately following planting; this, in parallel with a net decrease in the total carbon content of the topsoil; 2) this freshly introduced carbon predominates in the soil profile even after 30 years of afforestation; 3) during the 15- to 30-year growth period, the soil carbon content remains constant but progressive changes occur in its biogeochemical composition and rate of turnover.

Sulfur processing in forest soil and litter along an elevational and vegetative gradient

1986 ◽  
Vol 16 (4) ◽  
pp. 689-695 ◽  
Author(s):  
Mary E. Watwood ◽  
John W. Fitzgerald ◽  
James R. Gosz
Keyword(s):  
New Mexico ◽  
Moisture Content ◽  
Soil Ph ◽  
Soil Samples ◽  
Total Carbon ◽  
Santa Fe ◽  
Sulfate Adsorption ◽  
Total Carbon Content ◽  
Organic S ◽  
Pool Sizes

O2 litter and A1 horizon soil samples from various locations within the Santa Fe and Cibola National Forests of New Mexico were assayed for sulfate adsorption, organic S formation, and organic S solubilization and mineralization (mobilization). During a 48-h incubation, samples of O2 litter were found to adsorb between 1.6 and 4.1 nmol g−1 of added sulfate S and to form 2.0 to 9.8 nmol g−1 of organic S from this anion. Between 17 and 48% of this organic S was mobilized within 24 h. A1 horizon soils adsorbed 1.2 to 4.9 nmol g−1 of added sulfate S and formed between 1.6 and 4.8 nmol g−1 of organic S during 48 h. Between 20 and 50% of this organic S was mobilized within 24 h. Estimations of S-accumulation potentials for both horizons were made from these determinations. Intrinsic S pools were quantified to determine the S status of the samples prior to incubation. Carbon-bonded forms of S were found to predominate in samples from both horizons, while ester sulfate accounted for most of the remaining S. Sample pH, moisture content, and total carbon content were also determined. Attempts were made to correlate these characteristics and S pool sizes with laboratory determined potentials for sulfate adsorption, organic S formation, and mobilization. For some sites, relationships were established between sulfate adsorption, soil pH, and total C, whereas the total S and organic S content of most samples agreed well with organic S formation potentials.

scholarly journals Total carbon content and humic substances quality in selected subtypes of Cambisols

2009 ◽  
Vol 57 (4) ◽  
pp. 73-82
Author(s):  
Veronika Petrášová ◽  
Jiří Martinec ◽  
Ľubica Pospíšilová
Keyword(s):  
Organic Carbon ◽  
Humic Substances ◽  
Spectral Range ◽  
Synchronous Fluorescence ◽  
Arable Soil ◽  
Spectral Lines ◽  
Total Carbon ◽  
Total Carbon Content ◽  
Vis Spectroscopy ◽  
C Nmr

Cambisols cover an estimated 45% of agricultural soils in the Czech Republic. We aimed our work at stabile forms of organic carbon and humic substances quality in Cambisols under different types of soil management (grassland and arable soil). Object of our study were the following subtypes of Cambisols: Eutric Cambisol (locality Vatín – arable soil), Eutric Cambisol (locality Vatín – grassland), Haplic Cambisol (locality Náměšť n/Oslavou – arable soil), Leptic Cambisol (locality Ocmanice – grassland), Haplic Cambisol (locality Nové Město na Moravě – arable soil), Haplic Cambisol (locality Přemyslov – Tři Kameny – grassland), Arenic Cambisol (locality Pocoucov – arable soil), Dystric Cambisol (locality Sněžné – arable soil), Dystric Cambisol (locality Velká Skrovnice – arable soil), Dystric Cambisol (locality Vojnův Městec – arable soil). Non-destructive spectroscopic methods such as UV-VIS spectroscopy, synchronous fluorescence spectroscopy (SFS) and 13C NMR spectroscopy for humic substances (HS) quality assessment were used. Total organic carbon (TOC) content was determined by oxidimetric titration. Fractionation of HS was made by short fractionation method. Isolation of pure humic ­acids (HA) preparation was made according to the standard IHSS method.Results showed that TOC and humus content varied from 2.70 % (grassland) to 1.3 % (arable soil). Ave­ra­ge HS sum was 8.4 mg / kg in grassland and 6.4 mg / kg in arable soil. Average HA sum was 3.6 mg / kg in grassland and 3 mg / kg in arable soil. Fulvic acids (FA) content was 4.7 mg / kg in grassland and 3.7 mg / kg in arable soil. HS quality was low and very similar for all studied samples. HA/FA ratio low (< 1). HS absorbance in UV-VIS spectral range was low and similar in all studied samples. Higher absorption in this spectral range was closely connected with higher HS content. Also in 2D-synchronous fluorescence scan spectra similar shape of spectral lines was detected. Relative fluorescence intensity strongly depended on HA and FA content. Five main fluorescence peaks for HA and FA presence at λex./ λem.: 468/488, 482/502, 450/470, 376/396, 340/360 at constant difference of ∆λ=20 nm were measured. 13C NMR spectra of HA isolated from Eutric Cambisol showed low aromaticity degree and high content of aliphatic moieties. HA were young (= less aromatic compounds in HA molecule) and no differences in HA structure were detected to compare arable soil and grassland.

scholarly journals LAMP Detection of Four Plant-Pathogenic Oomycetes and Its Application in Lettuce Fields

Plant Disease ◽  
2019 ◽  
Vol 103 (2) ◽  
pp. 298-307 ◽  
Author(s):  
Wenzhuo Feng ◽  
Ayaka Hieno ◽  
Mikio Kusunoki ◽  
Haruhisa Suga ◽  
Koji Kageyama
Keyword(s):  
Dna Isolation ◽  
Detection Method ◽  
Control Strategies ◽  
Extraction Methods ◽  
Soil Samples ◽  
Lamp Method ◽  
Pythium Irregulare ◽  
Soil Dna ◽  
Plant Culture ◽  
Dna Extraction Methods

In Kagawa Prefecture, Japan, the pathogens Phytophthora pseudolactucae, Pythium irregulare, Pythium uncinulatum, and Pythium spinosum have caused huge losses in lettuce production. We used loop-mediated isothermal amplification (LAMP) to analyze soil and plants in lettuce fields for the presence of these four pathogens. To develop an effective on-site detection method, we contrasted the Plant-LAMP and Plant Culture-LAMP procedures for plant samples, and five soil DNA extraction methods for soil samples. Plant-LAMP and a Soil DNA Isolation kit were selected to analyze three fields for the pathogen species present, infected sites, and level of soil contamination. We found that the same wilting symptoms could be caused by Phytophthora or Pythium, or a mixture of species from both genera. Ph. pseudolactucae infects the pith of the lettuce in aboveground parts, whereas Pythium spp. mainly infect roots. Ph. pseudolactucae and Py. uncinulatum caused disease more frequently than the other two pathogens. Furthermore, not all of the pathogens existed in the soil near infected lettuce plants. Therefore, the LAMP method can be used to diagnose pathogenic oomycetes in the field, and will be useful in the development of control strategies in lettuce production.

scholarly journals Transformation of organic substances in the conjugate series of surface waters of North Karelia

2019 ◽  
Vol 46 (1) ◽  
pp. 43-50
Author(s):  
O. Yu. Drozdova ◽  
S. M. Ilina ◽  
N. A. Anokhina ◽  
Yu. A. Zavgorodnyaya ◽  
V. V. Demin ◽  
...  
Keyword(s):  
Organic Matter ◽  
Humic Substances ◽  
Organic Compounds ◽  
Natural Waters ◽  
Weighted Average ◽  
Water Soluble ◽  
Total Carbon ◽  
Benzoic Acids ◽  
Total Carbon Content ◽  
Conjugate Series

In this study, compositions of organic matter were investigated in the conjugate series of natural waters, including that from soil water, wetlands, streams, and lakes. In determinations of compositions of aliphatic and benzoic acids and humic substances, humic substances comprised the bulk of dissolved organic carbon, with 28% in lake waters and 57% in waters of wetlands and a weighted average molecular mass of 1 kDa. Aliphatic and benzoic acids comprised ≤ 2% of the total carbon content of water-soluble organic compounds. Transformations of dissolved organic matter occurred in a series of surveyed waters. Specifically, compositions and specific characteristics are dynamic, and increases in the fraction with a molecular weight of < 1 kDa were associated with photo- and bio-degradation of macromolecular organic compounds.

Transport of soluble organic and inorganic carbon in sandy soils under nitrogen fertilization

1999 ◽  
Vol 79 (2) ◽  
pp. 303-310 ◽  
Author(s):  
F. L. Wang ◽  
A. K. Alva
Keyword(s):  
Nitrogen Fertilization ◽  
Inorganic Carbon ◽  
Average Rate ◽  
Sandy Soils ◽  
Water Soluble ◽  
Total Carbon ◽  
Total Carbon Content ◽  
Water Soluble Organic Carbon ◽  
Isobutylidene Diurea ◽  
Leaching Condition

Leaching of water soluble soil carbon plays an important role in downward transport of soil nutrients and pollutants and may be influenced by soil and management factors. We examined the leaching of water soluble carbon from two sandy soils under nitrogen fertilization by adapting an intermittent leaching-incubation technique using packed soil columns (94 × 10 cm). After 30 d, cumulative amounts of water-soluble organic carbon (SOC) leached from the Candler and Wabasso sand for various treatments in mg C column−1 were: 77 and 302 (NH4NO3), 64 and 265 (control), and 45 and 239 (isobutylidene diurea, IBDU), respectively. The IBDU and NH4NO3 treatments increased the leaching of water-soluble inorganic carbon (SIC), which ranged from 2 to 38 mg C column−1 over 30 d. At the end of eight cycles of leaching/incubation, the total carbon content increased at depth (control and NH4NO3 treatment) in the Candler sand, but decreased in the Wabasso sand. In the first leaching event, the average rate of SOC leaching from the Wabasso sand was 26 mg C column−1 d−1 which dropped rapidly to about 5 mg C column−1 d−1 towards the end of the experiment. The rate of SOC leaching from the Candler sand was much lower (<8 mg C column−1 d−1) than the rate of SOC leaching from the Wabasso sand. Compared with the unamended treatments, application of NH4NO3 increased and IBDU decreased the leaching of SOC in both soils. These effects of N application were considerable during the initial two to three leaching events only. Our results suggest that the initial rainfalls that follow a dry period may be critical for transporting SOC from the upper layer of these sandy soils. Key words: C leaching, sandy soil, intermittent leaching condition, isobutylidene

Sign in / Sign up

Export Citation Format

Share Document