Soil microbiome
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.
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.
Mycorrhizae, for example, are fungi that help roots and plants absorb water and nutrients.
Actinomycetes are prokaryotic organisms that are classified as bacteria, but also very similar to fungi.
Nematodes are microscopic worms. They play an important role in the soil food chain at various trophic levels.
Protozoa are larger microbes that love to consume and be surrounded by bacteria.
Nucleic acid extraction for soil microbiome profiling
The following MACHEREY-NAGEL kits have been optimized for purifying microbial nucleic acids from a variety of soil types, including forest soil, sandy soil and cropping soil. Superior inhibitor removal and efficient lysis with ceramic beads will allow you to characterize the diversity of soil microbial communities and identify even low-abundant microorganisms.
Click below for more information about our soil kits
NucleoSpin Soil
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 procedure
Superior DNA yield and purity from various soil types
Two different lysis buffer options plus optional addition of the chemical additive Enhancer SX allow fine tuning for maximum yield and purity.
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.
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
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.
NucleoSpin 8 Soil
The NucleoSpin 8 Soil kit is optimized for parallel extraction of 8 to 48 samples.
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
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
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
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.