ArticlePloS one2014
Improved yield of high molecular weight DNA coincides with increased microbial diversity access from iron oxide cemented sub-surface clay environments.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 32 citations in OpenAlex.
- Optimized Method for Efficient DNA Extraction from Agricultural Soils.Methods and protocols · 2026Article
- Phytoplasma DNA Enrichment from Sugarcane White Leaves for Shotgun Sequencing Improvement.Plants (Basel, Switzerland) · 2024Article
- Metal-oxide precipitation influences microbiome structure in hyporheic zones receiving acid rock drainage.Applied and environmental microbiology · 2024Article
- Improving the efficiency of DNA extraction from iron incrustations and oilfield-produced water.Scientific reports · 2024Article
- RIAM: A Universal Accessible Protocol for the Isolation of High Purity DNA from Various Soils and Other Humic Substances.Methods and protocols · 2022Article
- Improved Protocol for DNA Extraction from Subsoils Using Phosphate Lysis Buffer.Microorganisms · 2020Article
- Validating DNA Extraction Protocols for Bentonite Clay.mSphere · 2019Article
- Nucleic Acid Extraction and Sequencing from Low-Biomass Synthetic Mars Analog Soils forAstrobiology · 2019Article
- Denitrification by Anaeromyxobacter dehalogenans, a Common Soil Bacterium Lacking the Nitrite Reductase GenesApplied and environmental microbiology · 2018Article
- Carbon Amendments Alter Microbial Community Structure and Net Mercury Methylation Potential in Sediments.Applied and environmental microbiology · 2018Article
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- Nucleic Acid Extraction from Synthetic Mars Analog Soils for in situ Life Detection.Astrobiology · 2017Article
- Floc Formation Reduces the pH Stress Experienced by Microorganisms Living in Alkaline Environments.Applied and environmental microbiology · 2017Article
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- Development and Validation of Broad-Range Qualitative and Clade-Specific Quantitative Molecular Probes for Assessing Mercury Methylation in the Environment.Applied and environmental microbiology · 2016Article
- Microbiome composition and geochemical characteristics of deep subsurface high-pressure environment, Pyhäsalmi mine Finland.Frontiers in microbiology · 2015Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
Despite over three decades of progress, extraction of high molecular weight (HMW) DNA from high clay soils or iron oxide cemented clay has remained challenging. HMW DNA is desirable for next generation sequencing as it yields the most comprehensive coverage. Several DNA extraction procedures were compared from samples that exhibit strong nucleic acid adsorption. pH manipulation or use of alternative ion solutions offered no improvement in nucleic acid recovery. Lysis by liquid N2 grinding in concentrated guanidine followed by concentrated sodium phosphate extraction supported HMW DNA recovery from clays high in iron oxides. DNA recovered using 1 M sodium phosphate buffer (PB) as a competitive desorptive wash was 15.22±2.33 µg DNA/g clay, with most DNA consisting of >20 Kb fragments, compared to 2.46±0.25 µg DNA/g clay with the Powerlyzer system (MoBio). Increasing PB concentration in the lysis reagent coincided with increasing DNA fragment length during initial extraction. Rarefaction plots of 16S rRNA (V1-V3 region) pyrosequencing from A-horizon and clay soils showed an ∼80% and ∼400% larger accessed diversity compared to the Powerlyzer soil DNA system, respectively. The observed diversity from the Firmicutes showed the strongest increase with >3-fold more operational taxonomic units (OTU) recovered.
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