Soil Microbiome Analysis

One gram of soil is thought to contain around 100 million microorganisms, including bacteria, fungi, viruses and archaea. These microbes are necessary for recycling dead plants and animals and are therefore essential for soil health and agricultural sustainability.

The NucleoSpin Soil kits are designed for the isolation of high molecular weight genomic DNA from microorganisms such as gram-positive and gram-negative bacteria, archaea, fungi, and algae in soil, sludge, and sediment samples. The kits have been tested with a variety of soil matrices covering samples across environments such as forests, bogs, farmland, grassland and more.

Soil is a living ecosystem populated by diverse communities of micro- and macroorganisms. Alongside bacteria, yeasts, and fungi, a wide range of other micro- and macroorganisms contribute to its biological composition. As a result, microbial communities can vary significantly across different soils and environments in composition and mass.

Bacteria

Bacteria are an essential part of the soil ecosystem. They are the last stage of nutrient breakdown before they are released to the plant's root zone.

Fungi

Mycorrhizae, for example, are fungi that help roots and plants absorb water and nutrients.

Actinomycetes

Actinomycetes are prokaryotic organisms that are classified as bacteria, but also very similar to fungi.

Nematodes

Nematodes are microscopic worms. They play an important role in the soil food chain at various trophic levels.

Protozoa

Protozoa are larger microbes that love to consume and be surrounded by bacteria.

Nucleic acid extraction for soil microbiome profiling

The following kits have been optimized for the purification of microbial nucleic acids from a wide range of soil types, including forest, sandy, and agricultural soils. Efficient lysis using ceramic beads combined with an efficient removal of contaminants and typical inhibitors enables reliable characterization of soil microbial communities and the detection of even low-abundance microorganisms.

NucleoSpin Soil Kit (REF 740780)

Soil samples contain different amounts of organic matter and inorganic material (humic substances or polysaccharides) and exhibit different phs, all of which can hinder the consistency of DNA extraction from these sample types. The NucleoSpin Soil kit overcomes these obstacles though the use of highly optimized lysis conditions and mechanical disruption.

NucleoSpin Soil workflow

The sample material is resuspended in Lysis Buffer SL1 or SL2, supplemented with the Enhancer SX, and mechanically disrupted using ceramic beads. Proteins and PCR inhibitors are precipitated with Lysis Buffer SL3 and subsequently pelleted by centrifugation together with the ceramic beads and undissolved sample material. The supernatant is taken off and cleared by passing it through a NucleoSpin® Inhibitor Removal Column. DNA binding conditions are then adjusted by addition of Binding Buffer SB to the flow through and the lysate is loaded onto a NucleoSpin® Soil Binding Column. Residual humic substances, especially humic acids and other PCR inhibitors, are removed by efficient washing with Binding Buffer SB and Wash Buffers SW1 / SW2. After a drying step, ready-to-use DNA can be eluted with Elution Buffer SE (5 mM Tris/HCl, pH 8.5).

Superior DNA yield and purity from various soil types

Due to the highly varying composition of different soils (organic matter, inorganic matter, humic substances, metal ions, polysaccharides, pH, etc.), it is impossible to obtain best results in DNA yield and purity for all sample types with only one single lysis buffer system. Therefore, the NucleoSpin® Soil kit is equipped with two lysis buffers SL1 and SL2 and an Enhancer solution SX. Those three components allow a perfect fine tuning for every type of soil sample for maximum yield and purity. Therefore, both lysis buffers should be tested in parallel for each new sample material. Usually Buffer SL1 in combination with Enhancer SX is more suitable for soil consisting predominantly of minerals while Buffer SL2 is more suitable for soil with a high amount of organic carbon.

Complete removal of PCR inhibitors – PCR results even from undiluted eluates!

DNA was purified with NucleoSpin Soil using Lysis Buffer SL1 and Lysis Buffer SL2 with, and without. Enhancer SX as well as with kits from competitor MP, and MO. Then, 2 μL of undiluted eluate were used as PCR template with fungi specific internal transcribed spacer (ITS) primers. Competitor MP failed to yield DNA pure enough to be used undiluted. DNA, and inhibitor concentration were both low for competitor MO, but the PCR from river sediment samples was still strongly inhibited. With NucleoSpin Soil there were at least two conditions for each soil type yielding plenty of DNA, and working undiluted in PCR.

Efficient lysis system – even suitable for difficult-to-lyse microorganisms

Total DNA from 400 mg cropping soil was purified with NucleoSpin Soil using Lysis Buffer SL2 in combination with Enhancer SX. 2 μl of undiluted eluates were analyzed in PCR using, order specific primer systems.

Lane 1: 1 kbp DNA Ladder (Fermentas) Lane 2: Prokaryotes (16S rRNA gene) Lane 3: Eucaryotes (ITS) Lane 4: Fungi (ITS) Lane 5: Fungi (ß Tubulin) Lane 6: Algae, protozoae, fungi (18S rRNA) Lane 7: Gram+ (B. subtilis, cerA) Lane 8: 1 kbp DNA ladder (Fermentas)

Selected citations

Adamczyk et al. Plant roots increase both decomposition, and stable, organic matter formation in boreal forest soil. Nature Communications, volume 10, 3982 (2019).

Goncalves et al. Microbiota stimulation generates LCMV-specific memory CD8+ T cells in SPF mice, and determines their TCR repertoire during LCMV infection. Molecular Immunology, volume 124, pages 125–141 (2020).

NucleoSpin 96 Soil Kit (REF 740787)

The NucleoSpin 96 Soil kit is optimized for parallel extraction of up to 96 samples. The kit can be used for a wide range of soil or sediment samples using either centrifugation or vacuum processing.

One of the most important procedures in microbiome and metagenomics research is the extraction of high-quality DNA, representative of all species present in a sample. The MACHEREY-NAGEL NucleoSpin® DNA Soil kit enables high-throughput, automation-friendly isolation of microbial DNA from soil samples typically used for microbiome analysis. The inhibitor removal technology ensures efficient removal of contaminants from even challenging soil or fecal samples for superior downstream performance.

NucleoSpin 8 Soil Kit (REF 740779)

One of the most important procedures in microbiome and metagenomics research is the extraction of high-quality DNA, representative of all species presents in a sample. The MACHEREY-NAGEL NucleoSpin® DNA Soil kit enables high-throughput, automation-friendly isolation of microbial DNA from soil samples typically used for microbiome analysis. The inhibitor removal technology ensures efficient removal of contaminants from even challenging soil or fecal samples for superior downstream performance.

NucleoSpin 96 Soil and NucleoSpin 8 Soil use mechanical disruption with ceramic MN Bead Tubes Type A in addition to highly specialized buffer combinations to ensure optimal lysis conditions.

NucleoSpin 96 Soil and NucleoSpin 8 Soil - Ideal for centrifuge or vacuum processing

Our NucleoSpin 96 Soil and NucleoSpin 8 Soil kits are ideal for convenient manual processing of up to 96 samples in parallel. Click here to learn more about processing of 96 well plates and 8 well strips with our NucleoVac 96 Vacuum Manifold.

DNA purification from soil and peat

DNA isolation from Alaskan gelisol.

Bacterial genome copy numbers were determined for DNA that was extracted from 250 mg soil samples derived from active and permafrost layers of Alaska gelisol using the NucleoSpin 96 Soil kit in comparison with a competitor kit from MoBio. Far more bacterial DNA was extracted with the NucleoSpin 96 Soil kit using the combination of Buffer S1 and Buffer SX than with the competitor kit.

DNA isolation from spruce peat

Bacterial genome copy numbers were determined for DNA that was extracted from 500 mg samples of spruce peat using the NucleoSpin 96 Soil kit in comparison with a competitor kit. Far more bacterial DNA was extracted with the NucleoSpin 96 Soil kit using Buffer S1 (with or without SX) than with the competitor kit.

Magnetic bead-based DNA purification from soil samples - NucleoMag DNA Microbiome (REF 744330)

The NucleoMag DNA Microbiome kit enables high throughput, automation friendly isolation of microbial DNA from samples such as soil, stool or biofilm. In combination with the MN Bead tubes or the MN 96 bead Plates an efficient and uniform sample disruption is ensured resulting in high DNA yields. The MACHEREY-NAGEL inhibitory removal technology removes PCR inhibitors even from challenging samples.

NucleoMag DNA Microbiome procedure

The NucleoMag DNA Microbiome kit is designed to purify DNA from a variety of samples, including stool for microbiome and metagenomic analysis and employs unique, patented inhibitor removal technology.

Application notes - Automated DNA purification from soil samples

Automated purification of stool, soil and biofilm samples on the Maelstrom 4800

Automated purification of DNA from soil and stool samples on the Eppendorf® epMotion® 5075t/5073t

Automated DNA purification from biofilm, soil and stool samples on the Hamilton NIMBUS® Presto

Automated DNA isolation from soil, feces and biofilm samples on the Opentrons OT-2

Magnetic bead based isolation of genomic DNA from microorganisms on the MagXtract 3200

Magnetic bead based isolation of genomic DNA from microorganisms on the MultiEX 032

High quality DNA from soil samples

Efficient isolation of DNA from soil microorganisms

Soil samples were subjected to a mechanical lysis procedure with MN Bead Tubes Type A. DNA was purified from the homogenates using the NucleoMag DNA Microbiome kit (MN) and a competitor kit (O) according to the manufac turers instructions. DNA yield and purity were measured photometrically. DNA eluates were diluted 1:10 and used in a qPCR for the bacterial 16s rRNA gene. The NucleoMag DNA Microbiome kit procedure resulted in higher yields, better purities and a better qPCR performance for all soil samples tested

RNA purification from soil samples - NucleoBond RNA Soil (REF 740140 & 740142)

Our NucleoBond RNA Soil and NucleoBond RNA Soil Mini kits enable efficient isolation of high quality RNA and DNA (requires DNA Set for NucleoBond RNA Soil) from any kind of soil or sediment sample. Most soils contain relatively low amounts of RNA, compared to DNA. Therefore we designed our new kit with our proven NucleoBond technology to enable high sample input and pure nucleic acids. With our NucleoSpin Bead Tubes Type A, the optimized Lysis Buffer, and Phenol:Chloroform:Isoamylalcohol an efficient sample disruption is ensured. The optional Buffer OPT enables efficient RNA and DNA purification from mineralic and organic soil samples.

NucleoBond RNA Soil procedure

Application data

High RNA yields with NucleoBond RNA Soil

Different soil samples (clay, shore soil, forest soil) were purified in duplicates according to the standard procedure. For comparison, the samples were applied to a competitor kit from Q. RNA was eluted in 100 μL, and determined photometrically. NucleoBond RNA Soil convinced due to the high RNA yield.

Amplifiable RNA for perfect results with NucleoBond RNA Soil kit.

Duplicates of different soil samples (clay, shore soil, forest soil) were purified in duplicates according to the standard procedure from MN, and Q. 4 μL of eluate was applied to the RT-PCR (amplicon: 466 bp). All MN samples showed lower CP values compared with Q samples, indicating higher RNA yield.