Access Automation Scripts
For the detection of microorganisms from soil samples
For research use only and NOT intended for in vitro diagnostics.
Details
Supporting Data
Figure 1. Consistent Yield of High Quality of Soil DNA.
Total soil DNA was isolated from gardening top soil samples using Norgen's Soil DNA Isolation 96-Well Kit. For analysis, 10 µL from each 100 µL elution from 10 different wells was run on a 1.2% TAE agarose gel. Lane M is Norgen's High Ranger DNA ladder.
Figure 2. Consistent and high DNA quality.
Total DNA was isolated from gardening top soil using Norgen's Soil DNA Isolation 96-Well Kit. For analysis of DNA quality, 3 µL from each 100 µL elution was used as the template in a real-time PCR reaction (SYBR Green) for the detection of the 16s rDNA. All DNA template from different wells showed a consistent Ct, indicating the consistent high DNA quality and yield. Black circle: NTC.
Figure 3. 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 4. 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 5. 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 6. 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 7. 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 8. 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 9. 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).
Figure 10. Comparison of automated DNA extraction platforms for soil samples using the Soil DNA Isolation Kit (Magnetic Bead System) (Cat. 58100).
DNA was extracted from 250 mg of soil on two automated platforms: Isopure 96 and KingFisher Flex. The bar graph (left) shows average Cq values from 16S rRNA gene qPCR, with Isopure averaging 17.64 and KingFisher averaging 17.94, indicating comparable amplification efficiency. Error bars represent standard deviation (n = 4). The gel image (right) shows 10 µL of eluate from each prep loaded onto a 1% agarose gel (1X TAE buffer). The Norgen UltraRanger 1 kb DNA Ladder (Cat. 12100) was loaded in the first lane. High molecular weight DNA was visible across all samples, with similar band intensity between platforms, suggesting consistent yield and quality of extracted DNA.
Figure 11. Resolution of DNA isolated from 10 g of two different soil types; regular soil (clay) and high humic acid soil (top soil) using Norgen’s Soil DNA Isolation Maxi Kit.
For evaluation, 10 µL from the 1st elution (2 mL) and 2nd elution (2 mL) from each soil sample was run on 1X TAE 1.2% agarose gel. Excellent DNA integrity and yield were observed from the Soil DNA Isolation Maxi Kit. Marker = Norgen’s HighRanger DNA Ladder (Cat. 11900)
Figure 12. Difference in DNA yield between two soil types (clay and top soil) and elutions (1st and 2nd elution).
Ten grams of soil was processed using Norgen’s Soil DNA Isolation Maxi Kit. The second elution increased the total DNA yield by an additional 20-30%.
Figure 13. 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 Maxi Kit to detect 16s rDNA.
The 16s rRNA gene was successfully amplified in both the first elution (red) and second elution (blue) from two soil types (Clay = circle, Top soil = diamond) without PCR inhibition, indicating the excellent soil DNA quality from 10 grams of soil.
Figure 14. Comparison of DNA Yield from Top Soil and Clay Samples.
Norgen’s Soil DNA Isolation Plus Kit (Cat. 64000) and Competitor M’s kit were used to isolate DNA from 250 mg of top soil and clay samples. Following isolation, 10 µL from each 100 µL elution was loaded on 1% TAE agarose gel. Lane M: Norgen's HighRanger 1kb DNA Ladder.
Figure 15. Comparison of DNA Concentration Isolated from Top Soil and Clay Samples.
Norgen’s Soil DNA Isolation Plus Kit (Cat. 64000) and Competitor M’s kit were used to isolate DNA from 250 mg top soil and clay samples. Norgen’s kit showed higher DNA concentrations for both samples in comparison to the competitor kit.
Figure 16. High Quality DNA confirmed by Real-time PCR.
Soil DNA was isolated from 250 mg of clay (containing low humic acids) and top soil (containing high humic acids) samples using Norgen's Soil DNA Isolation Plus Kit and Competitor M's Kit. DNA quality was confirmed by Real-time PCR using 4 µL of soil DNA (total PCR reaction volume was 20 µL) to detect 16s rDNA from different soil samples. The earlier Ct value with Norgen's DNA samples (red lines) compared to Competitor M's samples (green lines) indicated a higher quality of soil DNA for downstream applications.
Figure 17. Microbial profiles from soil samples (clay and top soil) isolated using Norgen’s Soil DNA Isolation Plus Kit (Cat. 64000) and Competitor M's kit.
The relative abundance of phylum-level classifications indicates the efficiency of DNA isolation and the quality of DNA. 16S rRNA genes (v3-4 region) were amplified and the amplicons were sequenced on Illumina® MiSeq™ (MiSeq Reagent Kit v3) using Norgen’s 16S Metagenomic workflow with Illumina 16S Metagenomics Pipeline (v1.0.1).
Figure 18. Abundance of bacterial genera heat map based on phylum level between two DNA soil samples isolation methods.
Norgen’s Soil DNA Isolation Plus Kit (Cat. 64000) and Competitor M's kit. The numbers indicate species count.
| Kit Specifications | |
| Maximum Soil Input | 0.25 g of all soil types |
| Average Yield from 0.25 mL of Soil* | 1–5 μg |
| Average Purity (OD260/280) | 1.7–1.9 |
| Time to Complete 96 Purifications (automated) | 30 minutes (hands-on-time) |
| Time to Complete 96 Purifications (manual) | 90 minutes (hands-on-time) |
* 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. 26560 (192 preps) | Cat. 58100 (50 preps) | Cat. 62800 (2 x 96-well) | Cat. 62000 (10 preps) | Cat. 64000 (50 preps) |
|---|---|---|---|---|---|
| Lysis Buffer D | 1 x 125 mL 1 x 45 mL |
- | - | 1 x 125 mL 1 x 45 mL |
45 mL |
| Lysis Buffer L | - | 60 mL | 1 x 105 mL 1 x 60 mL |
- | |
| Lysis Additive A | 50 mL | 6 mL | 25 mL | 50 mL | 2 x 6 mL |
| Binding Buffer I | 25 mL | 7 mL | 25 mL | 25 mL | 7 mL |
| OSR Solution | 12 mL | 3 mL | 12 mL | 12 mL | 3 mL |
| Lysis Buffer QP | 88 mL | - | - | 88 mL | 25 mL |
| Binding Buffer B | 110 mL | 2 x 12 mL | 85 mL | 110 mL | - |
| Magnetic Beads B | - | 1.1 mL | 2 x 2.2 mL | 1 | - |
| Solution WN | - | 55 mL | 4 x 55 mL | 1 | - |
| Wash Solution A | 2 x 38 mL | - | - | 2 x 38 mL | 18 mL |
| Elution Buffer B | 30 mL | 8 mL | 30 mL | 30 mL | 8 mL |
| Maxi Bead B Tubes | - | - | - | 10 | - |
| Maxi Spin Column | - | - | - | 10 | - |
| Spin Columns | - | - | - | 50 | - |
| Collection Tubes | - | - | - | 50 | - |
| Bead B Tubes | 200 | 2 x 25 | 8 x 25 | 1 | 50 |
| Elution Tubes (1.7 mL) | - | 2 x 25 | - | - | 50 |
| Elution Tubes | - | - | - | 10 | - |
| 96-Well Plate | 2 | - | 2 | 1 | - |
| 96-Well Filter Plate | 2 | - | - | 1 | - |
| 96-Well Collection Plate | 2 | - | - | 1 | - |
| Adhesive Tape | 4 | - | 2 | 1 | - |
| 96-Well Elution Plate | 2 | - | 2 | 1 | - |
| Product Insert | 1 | 1 | 1 | 1 | 1 |
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