Soil DNA Isolation Kit (Magnetic Bead System)

Features and Benefits

Fast and easy processing using a magnetic bead system
Robust lysis system (chemical lysis combined with a mechanical homogenization)
Isolate high quality genomic DNA
High yields - Consistent, high yields of inhibitor-free DNA up to 50 kb plus
Isolate sequencing quality total DNA from a variety of microorganisms including bacteria, fungi and algae
Also available in a 96-well format that can be integrated with a robotic automation system

Norgen’s Soil DNA Isolation Kit (Magnetic Bead System) provides a fast and reproducible method for isolating genomic DNA from soil samples. All types of soil samples can be processed with this kit, including common soil samples and difficult soil samples with high humic acid content such as compost and manure. The kit removes all traces of humic acid using the provided the OSR (Organic Substance Removal) Solution. Total genomic DNA can be isolated and purified from all the various microorganisms found in soil, such as bacteria, fungi and algae. The purified DNA is of the highest quality and is fully compatible with downstream PCR applications, as all humic acid substances and PCR inhibitors are removed during the isolation.

Norgen's Soil DNA Isolation Kit (Magnetic Bead System) is also available in a 96-well format for high throughput applications. Purification with the 96-well plates can be integrated with a robotic automation system.

Details

Supporting Data

Figure 1. Resolution of DNA isolated from two different types of soil samples DNA was isolated from high humic acid soil (top soil) and regular soil (clay) using Norgen’s column-based Soil DNA Isolation Kit (Red C) and Norgen's Soil DNA Isolation Kit (Magnetic Bead System) (Mag Bead). For evaluation, 10 µL from the 75 µL elution was run on 1X TAE 1.2% agarose gel. Excellent DNA integrity and yield were observed from the Soil DNA Isolation Kit (Magnetic Bead System), indicating the robust performance comparable to the column based method. Marker = Norgen’s HighRanger DNA Ladder.

Figure 2. Two of Norgen’s soil DNA isolation methods (Column vs Magnetic Bead System) were compared for DNA concentration. All DNA elutions isolated using Norgen’s Soil DNA Isolation Kit (Magnetic Bead System) [A to E] showed a comparable DNA concentration to Norgen’s Soil DNA Isolation Kit (Column Method; Cat. 26500), indicating the consistent and robust performance of the Soil DNA Isolation Kit (Magnetic Bead System).

Figure 3. High soil DNA quality was confirmed by real-time PCR using 8 µL of soil DNA (total PCR reaction volume was 20 µL) isolated using Norgen’s Soil DNA Isolation Kit (Magnetic Bead System) to detect 16s rDNA. PCR results from Norgen's Soil DNA Isolation Kit (Magnetic Bead System) (circle) were comparable to Norgen’s column based Soil DNA Isolation Kit (cross) and showed the successful 16s rDNA detection without PCR inhibition, indicating the excellent soil DNA quality using Norgen’s Soil DNA Isolation Kit (Magnetic Bead System).

Figure 4. Hierarchical Clustering Dendrogram. High quality of soil DNA was successfully isolated from the 5 challenging soil types using Norgen's Soil DNA Isolation Kits (A: Soil DNA Isolation Kit (Magnetic Bead System) and B: Soil DNA Isolation Kit Spin Column) respectively. The Hierarchical Clustering Dendrogram is based on genus-level classifications and shows the relative abundance of its genus-level classifications among soil types.

Figure 5. Principal Coordinate Analysis (PCoA) generated by Illumina MiSeq. Principal Coordinate Analysis of 20 samples (25-28: Mulch, 29-32: Clay, 33-36: Potting soil, 76-78: Top soil, 79-82: Compost) showing differences in the distribution of taxonomic classifications between samples up to species level. Each soil type is clearly clustered together and away from other types.

Figure 6. Resolution of DNA Isolated from Top Soil. DNA was isolated from high humic acid soil (top soil) using Norgen's Soil DNA Isolation 96-Well Kit (Magnetic Bead System). For evaluation, 10 µL from the 75 µL elution was run on 1X TAE 1.2% agarose gel. Excellent DNA integrity, consistency and yield were observed from the Soil DNA Isolation 96-Well Kit (Magnetic Bead System). Marker = Norgen’s HighRanger DNA Ladder (Cat. 11900).

Figure 7. High Soil DNA Quality Was Confirmed By Real-time PCR Using 2 µL of Soil DNA (Total PCR Reaction Volume Was 20 µL) Isolated Using Norgen’s Soil DNA Isolation 96-Well Kit (Magnetic Bead System) to Detect 16s rRNA. PCR results from Norgen's Soil DNA Isolation 96-Well Kit (Magnetic Bead System) showed the successful 16s rRNA detection without PCR inhibition, indicating the excellent soil DNA quality using Norgen’s Soil DNA Isolation 96-Well Kit (Magnetic Bead System).

Kit Specifications
Maximum Soil Input	0.25 g
Type of Soil Processed	All types of soil
Average Yield from 0.25 mL of Soil*	1 - 5 μg
Average Purity (OD260/280)	1.7 - 1.8
Time to Complete Purifications	40 minutes (Cat. 58100) 50 minutes (Cat. 62800)

* Average DNA yields will vary depending upon soil sample types

Storage Conditions and Product Stability
All solutions should be kept tightly sealed and stored at room temperature. This kit is stable for 1 year after the date of shipment.

Component	Cat. 58100 (50 preps)	Cat. 62800 (2 x 96-well)
Lysis Buffer G	100 mL	1 x 100 mL 1 x 45 mL
Lysis Additive A	6 mL	25 mL
Binding Buffer I	7 mL	25 mL
OSR Solution	3 mL	12 mL
Binding Buffer B	2 x 12 mL	85 mL
Magnetic Bead Suspension	2 x 1.1 mL	8.5 mL
Buffer SK	30 mL	1 x 40 mL 1 x 60 mL
Elution Buffer B	8 mL	15 mL
Elution Tubes (1.7 mL)	50	-
Bead Tubes	50	196
96-Well Plate	-	2
96-Well Elution Plate	-	2
Adhesive Tape	-	2
Product Insert	1	1

Documentation

PROTOCOLS

(58100) Soil DNA Isolation Kit (Magnetic Bead System) - Protocol (50 prep)

(62800) Soil DNA Isolation 96-Well Kit (High Throughput Magnetic Bead System) - Protocol (2 x 96-well)

SAFETY DATA SHEETS

58100 - Soil DNA Isolation Kit (Magnetic Bead System - 50 Preps) - SDS

62800 - Soil DNA Isolation Kit (Magnetic Bead System - 2x96 Well Plates) - SDS

FLYERS

Flyer

FAQs

Magnetic Bead System, High Throughput Magnetic Bead System

What if magnetic beads were accidentally pipetted up with the supernatant?

If the magnetic beads were accidently pipetted up with the supernatant, the pipette tip was placed too close to the magnetic beads while pipetting. Simply return the magnetic beads and the supernatant back into the sample well. Mix well, and place the plate back onto the magnetic separation plate for the specified time. Carefully remove the supernatant without touching the magnetic beads

Why do I have a low genomic DNA yield?

A low genomic DNA yield may be caused by the following:

Incomplete lysis of cells.
Ensure that Lysis Additive A is added. Also, incubation at 65ºC may result in increased yields.
Amount of magnetic beads added was not sufficient.
Ensure that the magnetic bead suspension is mixed well prior to use to avoid any inconsistency in DNA isolation.
DNA concentration in the soil sample being used is low.
Some soil types contain very little target DNA. Incubation at 65ºC may result in increased yields.

Why is the purified DNA not performing well in downstream applications?

If the DNA does not perform well in downstream applications, it may be due to one or more of the following:

Eluted DNA sample is brown.
The elution contains high humic acids. Ensure that the OSR Solution was added to the clean lysate.
DNA was not washed with the provided Buffer SK.
Traces of humic acids or salt from the binding step may remain in the sample if the magnetic beads are not washed with the provided Buffer SK. Humic acids and salt may interfere with downstream applications and thus must be washed from the magnetic beads.
Ethanol carryover.
Ensure that the drying step after the 70% ethanol wash steps is performed in order to remove traces of ethanol prior to elution. Ethanol is known to interfere with many downstream applications.

Why is RNA present in eluted DNA?

Ran can get co-eluted with DNA. Carry out a digestion with RNase A on the elution if the RNA present will interfere with downstream applications. Refer to manufacturer’s instructions regarding amount of enzyme to use, optimal incubation time and temperature.

Citations

Title	Arbuscular mycorrhizal fungal diversity and potential association networks among African tropical forest trees
Citation	Mycorrhiza 2024.
Authors	Damilola Olanipon, Margaux Boeraeve & Hans Jacquemyn

Title	Symbiotic microbiota vary with breeding group membership in a highly social joint-nesting bird
Citation	Behavioral Ecology 2023.
Authors	Leanne A Grieves, Gregory B Gloor, James S Quinn

Title	Acclimatization of a mixed-animal manure inoculum to the anaerobic digestion of Axonopus compressus reveals the putative importance of Mesotoga infera and Methanosaeta concilii as elucidated by DGGE and Illumina MiSeq
Citation	Bioresource Technology 2017.
Authors	Lee, J. T., He, J., & Tong, Y. W. (2017).

Title	Selection of a Very Active Microbial Community for the Coupled Treatment of Tetramethylammonium Hydroxide and Photoresist in Aqueous Solutions
Citation	International Journal of Environmental Research and Public Health 2017.
Authors	Moretti, G., Matteucci, F., Saraullo, M., Vegliò, F., & del Gallo, M. (2017).

Title	It takes an individual plant to raise a community: TRFLP analysis of the rhizosphere microbial community of two pairs of high-and low-metal-accumulating plants
Citation	Soil Biology and Biochemistry 2014.
Authors	MP Columbus, SM Macfie

Soil DNA Isolation Kit (Magnetic Bead System)