Name: electrostatic method to remove particulate organic matter from soil
Uploaded: 2021-02-10T13:30:00.000+00:00
Duration: 4 min 40 s
Description: Watch this Scientific Journal Video about Electrostatic Method to Remove Particulate Organic Matter from Soil at JoVE.com

This work was supported solely by USDA-ARS base funding. The authors greatly appreciate Mikayla Kelly, Caroline J. Melle, Alex Lasher, Emmi Klarer, and Katherine Son for their technical help.

1. Soil preparation
<ol>
	<li>Collect soil samples to the desired depth. Thoroughly dry the soil at 40 &#176;C or following lab-specific standard protocols.</li>
	<li>Sieve the soil through appropriate-sized soil sieves to obtain approximately 10-25 g of sieved soil. Many studies use a 1- or 2-mm sieve. The amount of soil is based on the mass required for the downstream analyses and will impact the number of times the electrostatic removal step will need to be repeated.</li>
	<li>Place the soil in a clean, dry metal or glass flat-bottomed pan that is large enough for soil to be spread thin (at least 20 cm in diameter). Gently shake the pan horizontally to distribute the soil evenly in as thin a layer as possible.</li>
</ol>
2. Charge an electrostatic surface
<ol>
	<li>Hold a 100 mm diameter glass or polystyrene Petri dish top or bottom in one hand and vigorously rub the outer surface with a clean piece of nylon cloth, cotton cloth, or polystyrene foam several times. Perform the surface charging away from the sample to prevent fabric fragments from being introduced into the sample.</li>
	<li>Inspect the surface of the Petri dish to make sure it is clean.</li>
</ol>
3. Remove particulate organic matter
<ol>
	<li>Lower the charged surface to within 0.5 cm to 2 cm above the soil and move it horizontally to pick up as much particulate material as possible. Attraction to the surface can be noted visually and audibly.</li>
	<li>When the Petri dish no longer attracts additional particles, move the dish away from the sample.</li>
</ol>
4. Clean the electrostatic surface
<ol>
	<li>Hold the charged surface over a collection dish and use a fine brush to transfer the electrostatically attracted material from the Petri dish surface into the collection dish. A camel hairbrush works well.</li>
</ol>
5. Repeat until the yield of particulates decreases
<ol>
	<li>Repeat steps 2 through 4 until the number of organic matter particles being picked up decreases. Redistribute the soil sample by horizontal shaking of the soil pan to expose new material at the surface and continue electrostatic collection. 
	NOTE: The endpoint is arbitrary and depends on the judgement of the researcher. Inspection of the charged surface after exposure to the soil gives a visual indication of whether a significant amount of organic particulates are still being removed from the soil. The final products are soil with reduced particulate content, and concentrated POM containing a small amount of electrostatically removed soil.</li>
</ol>

<ol>
	<li>Gosling, P., Parsons, N., Bending, G. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=What+are+the+primary+factors+controlling+the+light+fraction+and+particulate+soil+organic+matter+content+of+agricultural+soils.">What are the primary factors controlling the light fraction and particulate soil organic matter content of agricultural soils.</a> Biology and Fertility of Soils. 49 (8), 1001-1014 (2013).</li><li>Gollany, H. T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Soil+organic+carbon+accretion+vs.+sequestration+using+physicochemical+fractionation+and+CQESTR+simulation.">Soil organic carbon accretion vs. sequestration using physicochemical fractionation and CQESTR simulation.</a> Soil Science Society of America Journal. 77 (2), 618-629 (2013).</li><li>Cambardella, C. A., Gajda, A. M., Doran, J. W., Wienhold, B. J., Kettler, T. A., Kimble, J. M., Lal, R., Follett, R. F., Stewart, B. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Assessment methods for soil carbon. , 349-359 (2001).</li><li>Wander, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Soil organic matter in sustainable agriculture. , 67-102 (2004).</li><li>Curtin, D., Beare, M. H., Qiu, W., Sharp, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Does+particulate+organic+matter+fraction+meet+the+criteria+for+a+model+soil+organic+matter+pool.">Does particulate organic matter fraction meet the criteria for a model soil organic matter pool.</a> Pedosphere. 29 (2), 195-203 (2019).</li><li>Kirkby, C. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stable+soil+organic+matter:+A+comparison+of+C:N:P:S+ratios+in+Australian+and+other+world+soils.">Stable soil organic matter: A comparison of C:N:P:S ratios in Australian and other world soils.</a> Geoderma. 163 (3-4), 197-208 (2011).</li><li>Strickland, T. C., Sollins, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Improved+method+for+separating+light-+and+heavy-fraction+organic+material+from+soil.">Improved method for separating light- and heavy-fraction organic material from soil.</a> Soil Science Society of America Journal. 51 (5), 1390-1393 (1987).</li><li>Golchin, A., Oades, J. M., Skjemstad, J. O., Clarke, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Study+of+free+and+occluded+particulate+organic+matter+in+soils+by+solid+state+13C+Cp/MAS+NMR+spectroscopy+and+scanning+electron+microscopy.">Study of free and occluded particulate organic matter in soils by solid state 13C Cp/MAS NMR spectroscopy and scanning electron microscopy.</a> Soil Research. 32 (2), 285-309 (1994).</li><li>Theodorou, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nitrogen+transformations+in+particle+size+fractions+from+a+second+rotation+pine+forest+soil.">Nitrogen transformations in particle size fractions from a second rotation pine forest soil.</a> Communications in Soil Science and Plant Analysis. 21 (5-6), 407-413 (1990).</li><li>Kaiser, M., Ellerbrock, R. H., Sommer, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Separation+of+coarse+organic+particles+from+bulk+surface+soil+samples+by+electrostatic+attraction.">Separation of coarse organic particles from bulk surface soil samples by electrostatic attraction.</a> Soil Science Society of America Journal. 73 (6), 2118-2130 (2009).</li><li>Kuzyakov, Y., Biriukova, O., Turyabahika, F., Stahr, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Electrostatic+method+to+separate+roots+from+soil.">Electrostatic method to separate roots from soil.</a> Journal of Plant Nutrition and Soil Science. 164 (5), 541 (2001).</li><li>Schneider, C. A., Rasband, W. S., Eliceiri, K. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=NIH+Image+to+ImageJ:+25+years+of+image+analysis.">NIH Image to ImageJ: 25 years of image analysis.</a> Nature Methods. 9 (7), 671-675 (2012).</li></ol>

The authors have nothing to disclose.

The electrostatic attraction method was effective in removing POM from the silt loam soils. The method described here is slightly different from Kaiser, et al.10 which used a combination of glass/cotton. We treated all but the finest soil fraction and used polystyrene rather than glass due to the triboelectric difference, which for polystyrene/nylon is 100 nC/J compared to glass/ cotton at 20 nC/J12. Glass and polystyrene foam have proven effective and convenient in more re...

Accurate estimates of soil organic carbon (SOC) are important in evaluating changes resulting from agricultural management or the environment. Particulate organic matter (POM) has important functions in the ecology and physics of a soil but it is often short lived and varies based on several factors including season, moisture conditions, aeration, sample collection techniques, recent soil management, vegetation life cycle, and others1. These temporally unstable sources can confound estimates of long-term trends in stable and truly sequestered soil organic carbon2.
Despite being well-defined, common, and important, POM is not easily separated from soil nor is it easy to measure quantitatively. Particulate organic matter has been measured as that which floats in liquids (light fraction, typically 1.4-2.2 g cm-3), or as that which can be separated by size (e.g., &#62; 53-250 &#181;m or &#62; 250 &#181;m), or a combination of the two3,4,5. Both size-based and density-based techniques can influence the quantitative and chemical outcomes of POM measurement4. A careful visual inspection of soil that has been size-fractionated using routine methods often reveals long, narrow structures like roots and slivers of leaf or stem that have passed through the screen. Simply removing these structures by hand has been shown to substantially reduce measurements of total SOC2,6 but the method is notably subject to the diligence and visual acuity of the operator. POM separation from a soil sample as the light fraction during flotation in a dense liquid7 does not capture all POM, and excessive shaking during the flotation process can actually reduce the amount of light fraction recovered from a sample8. Flotation requires many steps and exposes the soil to chemical solutions which can change the chemical characteristics or dissolve and remove constituents that may be of interest4.
Alternative methods for removing POM have been used to avoid or augment the use of dense aqueous solutions. Kirkby, et al.6 compared light fraction removal using two flotation procedures to a dry sieving/winnowing method9. Winnowing was performed by passing a light current of air across a thin layer of soil to gently lift away the light from the heavy fraction. The dry sieving/winnowing performed similarly to the two flotation methods with regard to C, N, P, and S content; however, the authors suggest that dry sieving/winnowing produced &#34;slightly cleaner&#34; soils6. POM has also been separated from soil using electrostatic attraction10,11 in which organic particles are isolated by passing an electrostatically charged surface above the soil. The electrostatic attraction method successfully recovered POM, referred to as course organic particles, from dried, sieved (&#62; 0.315 mm) soils with statistical repeatability comparable to other methods of size and density fractionation10.
Here we demonstrate how electrostatic attraction can be used to remove POM of sizes ranging from visible to microscopic. Unlike other reported methods, electrostatic attraction of fine soil also removes a small portion of mineral and aggregated soil which is visibly like the remaining soil. Given our results to date, it is reasonable to assume that the removal of a small portion of non-POM soil will have no substantial effect on the downstream analyses; however, this assumption should be verified for a specific soil if large proportions of the total soil sample are being removed electrostatically. The methods and examples provided here were performed on silt loam loess soils from a semi-arid environment.
This method may not be suitable for all soil types but has the advantages of being quick and efficient in removing particulate organic matter too small to remove manually or by an air current. Process speed is important in reducing fatigue, ensuring consistency, and encouraging greater replication for better accuracy of conclusions. Additionally, the ability to remove very small particulates is important in avoiding bias toward soils with larger rather than small particulate sizes.

<table><tbody><tr><td>brush, camel-hair</td><td></td><td></td><td></td></tr><tr><td>petri dish, glass or plastic</td><td></td><td></td><td></td></tr><tr><td>polystyrene foam, cotton or nylon cloth</td><td></td><td></td><td></td></tr><tr><td>soil</td><td></td><td></td><td></td></tr><tr><td>soil sieves</td><td></td><td></td><td></td></tr></tbody></table>

electrostatic method to remove particulate organic matter from soil

Estimations of soil organic carbon are dependent on soil processing methods including removal of undecomposed plant material. Inadequate separation of roots and plant material from soil can result in highly variable carbon measurements. Methods to remove the plant material are often limited to the largest, most visible plant materials. In this manuscript we describe how electrostatic attraction can be used to remove plant material from a soil sample. An electrostatically charged surface passed close to dry soil naturally attracts both undecomposed and partially decomposed plant particles, along with a small quantity of mineral and aggregated soil. The soil sample is spread in a thin layer on a flat surface or a soil sieve. A plastic or glass Petri dish is electrostatically charged by rubbing with polystyrene foam or nylon or cotton cloth. The charged dish is passed repeatedly over the soil. The dish is then brushed clean and recharged. Re-spreading the soil and repeating the procedure eventually results in a diminishing yield of particulates. The process removes about 1 to 5% of the soil sample, and about 2 to 3 times that proportion in organic carbon. Like other particulate removal methods, the endpoint is arbitrary and not all free particulates are removed. The process takes approximately 5 min and does not require a chemical process as do density flotation methods. Electrostatic attraction consistently removes material with higher than average C concentration and C:N ratio, and much of the material can be visually identified as plant or faunal material under a microscope.

The results presented here are based on the analysis of silt loam soils from agricultural sites in the Pacific Northwest (Table 1). Soils were collected to depths of 0-20 cm or 0-30 cm, dried at 40 &#176;C, passed through a 2 mm sieve, and treated using a polystyrene surface charged with a nylon cloth.
The amount of soil electrostatically removed from a sample varied. About 1% to 6% of the total soil mass was re...

Watch this Scientific Journal Video about Electrostatic Method to Remove Particulate Organic Matter from Soil at JoVE.com

Electrostatic Method to Remove Particulate Organic Matter from Soil

Removing recently deposited and incompletely decomposed plant material from soil samples reduces the influence of temporary seasonal inputs on soil organic carbon measurements. Attraction to an electrostatically charged surface can be used to quickly remove a substantial amount of particulate organic matter.

Estimations of soil organic carbon are dependent on soil processing methods including removal of undecomposed plant material. Inadequate separation of ...

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Universidad San Sebastian

Research

JoVE Journal

Environment

4.7K Views.  USDA-Agricultural Research Service, Soil and Water Conservation Research Unit. Removing recently deposited and incompletely decomposed plant material from soil samples reduces the influence of temporary seasonal inputs on soil organic carbon measurements. Attraction to an electrostatically charged surface can be used to quickly remove a substantial amount of particulate organic matter.

Video: Electrostatic Method to Remove Particulate Organic Matter from Soil

A Lipid Extraction and Analysis Method for Characterizing Soil Microbes in Experiments with Many Samples

Microbial communities are important drivers and regulators of ecosystem processes. To understand how management of ecosystems may affect microbial communities, a relatively precise but effort-intensive technique to assay microbial community composition is phospholipid fatty acid (PLFA) analysis. PLFA was developed to analyze phospholipid biomarkers, which can be used as indicators of microbial biomass and the composition of broad functional groups of fungi and bacteria. It has commonly been used to compare soils under alternative plant communities, ecology, and management regimes. The PLFA method has been shown to be sensitive to detecting shifts in microbial community composition.
An alternative method, fatty acid methyl ester extraction and analysis (MIDI-FA) was developed for rapid extraction of total lipids, without separation of the phospholipid fraction, from pure cultures as a microbial identification technique. This method is rapid but is less suited for soil samples because it lacks an initial step separating soil particles and begins instead with a saponification reaction that likely produces artifacts from the background organic matter in the soil. 
This article describes a method that increases throughput while balancing effort and accuracy for extraction of lipids from the cell membranes of microorganisms for use in characterizing both total lipids and the relative abundance of indicator lipids to determine soil microbial community structure in studies with many samples. The method combines the accuracy achieved through PLFA profiling by extracting and concentrating soil lipids as a first step, and a reduction in effort by saponifying the organic material extracted and processing with the MIDI-FA method as a second step.

The article describes a method that increases throughput while balancing effort and accuracy for extraction of lipids from the cell membranes of microorganisms for use in characterizing both total lipids and the relative abundance of indicator lipids to determine soil microbial community structure in studies with many samples.

Microbial communities are important drivers and regulators of ecosystem processes. To understand how management of ecosystems may affect microbial ...

Improving Infrared Spectroscopy Characterization of Soil Organic Matter with Spectral Subtractions

Soil organic matter (SOM) underlies numerous soil processes and functions. Fourier transform infrared (FTIR) spectroscopy detects infrared-active organic bonds that constitute the organic component of soils. However, the relatively low organic matter content of soils (commonly &#60; 5% by mass) and absorbance overlap of mineral and organic functional groups in the mid-infrared (MIR) region (4,000-400 cm-1) engenders substantial interference by dominant mineral absorbances, challenging or even preventing interpretation of spectra for SOM characterization. Spectral subtractions, a post-hoc mathematical treatment of spectra, can reduce mineral interference and enhance resolution of spectral regions corresponding to organic functional groups by mathematically removing mineral absorbances. This requires a mineral-enriched reference spectrum, which can be empirically obtained for a given soil sample by removing SOM. The mineral-enriched reference spectrum is subtracted from the original (untreated) spectrum of the soil sample to produce a spectrum representing SOM absorbances. Common SOM removal methods include high-temperature combustion (&#39;ashing&#39;) and chemical oxidation. Selection of the SOM removal method carries two considerations: (1) the amount of SOM removed, and (2) absorbance artifacts in the mineral reference spectrum and thus the resulting subtraction spectrum. These potential issues can, and should, be identified and quantified in order to avoid fallacious or biased interpretations of spectra for organic functional group composition of SOM. Following SOM removal, the resulting mineral-enriched sample is used to collect a mineral reference spectrum. Several strategies exist to perform subtractions depending on the experimental goals and sample characteristics, most notably the determination of the subtraction factor. The resulting subtraction spectrum requires careful interpretation based on the aforementioned methodology. For many soil and other environmental samples containing substantial mineral components, subtractions have strong potential to improve FTIR spectroscopic characterization of organic matter composition.

SOM underlies many soil functions and processes, but its characterization by FTIR spectroscopy is often challenged by mineral interferences. The described method can increase the utility of SOM analysis by FTIR spectroscopy by subtracting mineral interferences in soil spectra using empirically obtained mineral reference spectra.

Soil organic matter (SOM) underlies numerous soil processes and functions. Fourier transform infrared (FTIR) spectroscopy detects infrared-active organic ...

Combined Size and Density Fractionation of Soils for Investigations of Organo-Mineral Interactions

Combined size and density fractionation (CSDF) is a method used to physically separate soil into fractions differing in particle size and mineralogy. CSDF relies on sequential density separation and sedimentation steps to isolate (1) the free light fraction (uncomplexed organic matter), (2) the occluded light fraction (uncomplexed organic matter trapped in soil aggregates) and (3) a variable number of heavy fractions (soil minerals and their associated organic matter) differing in composition. Provided that the parameters of the CSDF (dispersion energy, density cut-offs, sedimentation time) are properly selected, the method yields heavy fractions of relatively homogeneous mineral composition. Each of these fractions is expected to have a different complexing ability towards organic matter, rendering this a useful method to isolate and study the nature of organo-mineral interactions. Combining density and particle size separation brings an improved resolution compared to simple size or density fractionation methods, allowing the separation of heavy components according to both mineralogy and size (related to surface area) criteria. As is the case for all physical fractionation methods, it may be considered as less disruptive or aggressive than chemically-based extraction methods. However, CSDF is a time-consuming method and furthermore, the quantity of material obtained in some fractions can be limiting for subsequent analysis. Following CSDF, the fractions may be analyzed for mineralogical composition, soil organic carbon concentration and organic matter chemistry. The method provides quantitative information about organic carbon distribution within a soil sample and brings light to the sorptive capacity of the different, naturally-occurring mineral phases, thus providing mechanistic information about the preferential nature of organo-mineral interactions in soils (i.e., which minerals, what type of organic matter).

Combined size and density fractionation (CSDF) is a method to physically separate soil into fractions differing in texture (particle size) and mineralogy (density). The purpose is to isolate fractions with different reactivities towards soil organic matter (SOM), in order to better understand organo-mineral interactions and SOM dynamics.

Combined size and density fractionation (CSDF) is a method used to physically separate soil into fractions differing in particle size and mineralogy. CSDF ...

Single-throughput Complementary High-resolution Analytical Techniques for Characterizing Complex Natural Organic Matter Mixtures

Natural organic matter (NOM) is composed of a highly complex mixture of thousands of organic compounds which, historically, proved difficult to characterize. However, to understand the thermodynamic and kinetic controls on greenhouse gas (carbon dioxide [CO2] and methane [CH4]) production resulting from the decomposition of NOM, a molecular-level characterization coupled with microbial proteome analyses is necessary. Further, climate and environmental changes are expected to perturb natural ecosystems, potentially upsetting complex interactions that influence both the supply of organic matter substrates and the microorganisms performing the transformations. A detailed molecular characterization of the organic matter, microbial proteomics, and the pathways and transformations by which organic matter is decomposed will be necessary to predict the direction and magnitude of the effects of environmental changes. This article describes a methodological throughput for comprehensive metabolite characterization in a single sample by direct injection Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), gas chromatography mass spectrometry (GC-MS), nuclear magnetic resonance (NMR) spectroscopy, liquid chromatography mass spectrometry (LC-MS), and proteomics analysis. This approach results in a fully-paired dataset which improves statistical confidence for inferring pathways of organic matter decomposition, the resulting CO2 and CH4 production rates, and their responses to environmental perturbation. Herein we present results of applying this method to NOM samples collected from peatlands; however, the protocol is applicable to any NOM sample (e.g., peat, forested soils, marine sediments, etc.).

This protocol describes a single throughput for complementary analytical and omics techniques culminating in a fully-paired characterization of natural organic matter and microbial proteomics in different ecosystems. This approach permits robust comparisons for identifying metabolic pathways and transformations important for describing greenhouse gas production and predicting responses to environmental change.

Natural organic matter (NOM) is composed of a highly complex mixture of thousands of organic compounds which, historically, proved difficult to ...

The MPLEx Protocol for Multi-omic Analyses of Soil Samples

Mass spectrometry (MS)-based integrated metaproteomic, metabolomic, and lipidomic (multi-omic) studies are transforming our ability to understand and characterize microbial communities in environmental and biological systems. These measurements are even enabling enhanced analyses of complex soil microbial communities, which are the most complex microbial systems known to date. Multi-omic analyses, however, do have sample preparation challenges, since separate extractions are typically needed for each omic study, thereby greatly amplifying the preparation time and amount of sample required. To address this limitation, a 3-in-1 method for the simultaneous extraction of metabolites, proteins, and lipids (MPLEx) from the same soil sample was created by adapting a solvent-based approach. This MPLEx protocol has proven to be both simple and robust for many sample types, even when utilized for limited quantities of complex soil samples. The MPLEx method also greatly enabled the rapid multi-omic measurements needed to gain a better understanding of the members of each microbial community, while evaluating the changes taking place upon biological and environmental perturbations.

A protocol is presented for simultaneously extracting metabolites, proteins, and lipids from a single soil sample, allowing reduced sample preparation times and enabling multi-omic mass spectrometry analyses of samples with limited quantities.

Mass spectrometry (MS)-based integrated metaproteomic, metabolomic, and lipidomic (multi-omic) studies are transforming our ability to understand and ...

Chemistry

Utilizing Soil Density Fractionation to Separate Distinct Soil Carbon Pools

Soil organic matter (SOM) is a complicated mixture of different compounds that span the range from free, partially degraded plant components to more microbially altered compounds held in the soil aggregates to highly processed microbial by-products with strong associations with reactive soil minerals. Soil scientists have struggled to find ways to separate soil into fractions that are easily measurable and useful for soil carbon (C) modeling. Fractionating soil based on density is increasingly being used, and it is easy to perform and yields C pools based on the degree of association between the SOM and different minerals; thus, soil density fractionation can help to characterize the SOM and identify SOM stabilization mechanisms. However, the reported soil density fractionation protocols vary significantly, making the results from different studies and ecosystems hard to compare. Here, we describe a robust density fractionation procedure that separates particulate and mineral-associated organic matter and explain the benefits and drawbacks of separating soil into two, three, or more density fractions. Such fractions often differ in their chemical and mineral composition, turnover time, and degree of microbial processing, as well as the degree of mineral stabilization.

Soil density fractionation separates soil organic matter into distinct pools with differing stabilization mechanisms, chemistries, and turnover times. Sodium polytungstate solutions with specific densities allow the separation of free particulate organic matter and mineral-associated organic matter, resulting in organic matter fractions suitable for describing the soil response to management and climate change.

Soil organic matter (SOM) is a complicated mixture of different compounds that span the range from free, partially degraded plant components to more ...

Extraction of High Molecular Weight Genomic DNA from Soils and Sediments

The soil microbiome is a vast and relatively unexplored reservoir of genomic diversity and metabolic innovation that is intimately associated with nutrient and energy flow within terrestrial ecosystems. Cultivation-independent environmental genomic, also known as metagenomic, approaches promise unprecedented access to this genetic information with respect to pathway reconstruction and functional screening for high value therapeutic and biomass conversion processes. However, the soil microbiome still remains a challenge largely due to the difficulty in obtaining high molecular weight DNA of sufficient quality for large insert library production. Here we introduce a protocol for extracting high molecular weight, microbial community genomic DNA from soils and sediments. The quality of isolated genomic DNA is ideal for constructing large insert environmental genomic libraries for downstream sequencing and screening applications. 
The procedure starts with cell lysis. Cell walls and membranes of microbes are lysed by both mechanical (grinding) and chemical forces (&beta;-mercaptoethanol). Genomic DNA is then isolated using extraction buffer, chloroform-isoamyl alcohol and isopropyl alcohol. The buffers employed for the lysis and extraction steps include guanidine isothiocyanate and hexadecyltrimethylammonium bromide (CTAB) to preserve the integrity of the high molecular weight genomic DNA. Depending on your downstream application, the isolated genomic DNA can be further purified using cesium chloride (CsCl) gradient ultracentrifugation, which reduces impurities including humic acids. The first procedure, extraction, takes approximately 8 hours, excluding DNA quantification step. The CsCl gradient ultracentrifugation, is a two days process. During the entire procedure, genomic DNA should be treated gently to prevent shearing, avoid severe vortexing, and repetitive harsh pipetting.

A methodology to isolate high molecular weight and high quality genomic DNA from soil microbial community is described.

The soil microbiome is a vast and relatively unexplored reservoir of genomic diversity and metabolic innovation that is intimately associated with ...

Biology

Separation and Identification of Conventional Microplastics from Farmland Soils

Microplastics (MPs) pollution in the terrestrial environment has received increasing attention over the last decade, with increasing studies describing the numbers and types of MPs in different soil systems and their impacts on soil and crop health. However, different MPs extraction and analytical methods are used, limiting opportunities to compare results and generate reliable evidence for industry advice and policymakers. Here, we present a protocol that describes the methodology for sampling, separation, and chemical identification of conventional MPs&#160;from soil. The method is low-cost, and the materials are readily available. This enhances operational ease and may help with widespread adoption. The protocol provides detailed information on sample collection from the top 0-30 cm of soil using plastic-free utensils; simulation of different soil types through the use of various solid media (such as bentonite clay, silicon dioxide, and non-contaminated soil), with the addition of the same mass&#160;of polyethylene(PE)-MPs for subsequent quantification; density separation of plastic particles utilizing saturated sodium chloride (NaCl) solution and digestion of organic impurities in the supernatant using 4 M sodium hydroxide (NaOH) solution; quantification of particles using fluorescent microscopy after Nile Red staining; and polymer identification using micro&#160;Fourier-Transform Infrared Spectroscopy (&#956;-FTIR) or Laser-Direct Infrared (LDIR) spectroscopy. The MPs recovery rate ranged from 83% - 90% for the abovementioned media. This protocol presents an efficient method for soil MPs analysis that is optimized for feasibility, applicability, and cost-effectiveness. Moreover, the video accompanied can guide the process of analyzing the soil MPs step-by-step virtually. This study is dedicated to standardizing the methods for soil MPs analysis, enhancing the connectivity and comparability of measurements, and establishing a foundation for more standardized and scientific research.

Presented here is a method for extracting microplastics from soil and identifying their polymer types. The method has been optimized for execution, applicability, and cost-effectiveness. It lays a scientific foundation for standardizing the analytical method to identify microplastics in soils.

Microplastics (MPs) pollution in the terrestrial environment has received increasing attention over the last decade, with increasing studies describing ...

Analysis of Organochlorine Pesticides in a Soil Sample by a Modified QuEChERS Approach Using Ammonium Formate

Currently, the QuEChERS method represents the most widely used sample preparation protocol worldwide for analyzing pesticide residues in a broad variety of matrices both in official and non-official laboratories. The QuEChERS method using ammonium formate has previously proven to be advantageous compared to the original and the two official versions. On the one hand, the simple addition of 0.5 g of ammonium formate per gram of sample is sufficient to induce phase separation and achieve good analytical performance. On the other hand, ammonium formate reduces the need for maintenance in routine analyses. Here, a modified QuEChERS method using ammonium formate was applied for the simultaneous analysis of organochlorine pesticide (OCP) residues in agricultural soil. Specifically, 10 g of the sample was hydrated with 10 mL of water and then extracted with 10 mL of acetonitrile. Next, phase separation was carried out using 5 g of ammonium formate. After centrifugation, the supernatant was subjected to a dispersive solid-phase extraction clean-up step with anhydrous magnesium sulfate, primary-secondary amine, and octadecylsilane. Gas chromatography-mass spectrometry was used as the analytical technique. The QuEChERS method using ammonium formate is demonstrated as a successful alternative for extracting OCP residues from a soil sample.

The present protocol describes the utilization of ammonium formate for phase partitioning in QuEChERS, together with gas chromatography-mass spectrometry, to successfully determine organochlorine pesticide residues in a soil sample.

Currently, the QuEChERS method represents the most widely used sample preparation protocol worldwide for analyzing pesticide residues in a broad variety ...

Precise Electrochemical Sizing of Individual Electro-Inactive Particles

Nanoimpact electrochemistry enables the time-resolved in situ characterization (e.g., size, catalytic activity) of single nanomaterial units, providing a means of elucidating heterogeneities that would be masked in ensemble studies. To implement this technique with redox inactive particles, a solution-phase redox reaction is used to produce a steady-state background current on a disk ultramicroelectrode. When a particle adsorbs onto the electrode, it produces a stepwise reduction in the exposed electrode area, which produces, in turn, a stepwise decrease in the current commensurate with the size of the adsorbing species. Historically, however, nanoimpact electrochemistry has suffered from &#34;edge effects,&#34; in which the radial diffusion layer formed at the circumference of the ultramicroelectrodes renders the step size dependent not only on the size of the particle but also on where it lands on the electrode. The introduction of electrocatalytic current generation, however, mitigates the heterogeneity caused by edge effects, thus improving the measurement precision. In this approach, termed &#34;electrocatalytic interruption,&#34; a substrate that regenerates the redox probe at the diffusion layer is introduced. This shifts the rate-limiting step of the current generation from diffusion to the homogeneous reaction rate constant, thus reducing flux heterogeneity and increasing the precision of particle sizing by an order of magnitude. The protocol described here explains the set-up and data collection employed in nanoimpact experiments implementing this effect for improved precision in the sizing of redox in-active materials.

As an analytical technique, nanoimpact electrochemistry, an increasingly important approach to counting and characterizing nanometer-scale, electro-inactive particles, suffers from poor precision due to the heterogeneous current distributions that arise from its use of ultramicroelectrodes. Outlined here is a generalized approach, termed "electrocatalytic interruption," that enhances precision in such measurements.

Nanoimpact electrochemistry enables the time-resolved in situ characterization (e.g., size, catalytic activity) of single nanomaterial units, providing a ...