ArticleApplied and environmental microbiology2014
Hot-alkaline DNA extraction method for deep-subseafloor archaeal communities.
Article in Applied and environmental microbiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 51 citations in OpenAlex.
- Preserving Shell Integrity of Microgastropods With the Nondestructive HotSHOT DNA Extraction Method.Ecology and evolution · 2026Article
- Decoding extremophiles: insights from bioinformatics, machine learning, and data-driven approaches.Briefings in bioinformatics · 2026Review
- Oxic Subseafloor Microbial Communities Retain Anabolic Capacity under both Oxic and Oxygen-depleted Conditions.Microbes and environments · 2026Article
- IAA Synthesis Pathway ofMicroorganisms · 2024Article
- Transcriptome profiling of genes regulated by phosphate-solubilizing bacteriaFrontiers in microbiology · 2023Article
- Grinding Beads Influence Microbial DNA Extraction from Organic-Rich Sub-Seafloor Sediment.Microorganisms · 2022Article
- Microbial communities associated with thermogenic gas hydrate-bearing marine sediments in Qiongdongnan Basin, South China Sea.Frontiers in microbiology · 2022Article
- Aerobic microbial life persists in oxic marine sediment as old as 101.5 million years.Nature communications · 2020Article
- Article
- Cultivable microbial community in 2-km-deep, 20-million-year-old subseafloor coalbeds through ~1000 days anaerobic bioreactor cultivation.Scientific reports · 2019Article
- Drivers of Bacterial α- and β-Diversity Patterns and Functioning in Subsurface Hadal Sediments.Frontiers in microbiology · 2019Article
- Microbial Metabolism and Community Dynamics in Hydraulic Fracturing Fluids Recovered From Deep Hydrocarbon-Rich Shale.Frontiers in microbiology · 2019Article
- Microbial Diversity in Sediments from the Bottom of the Challenger Deep, the Mariana Trench.Microbes and environments · 2018Article
- Bioturbation as a key driver behind the dominance of Bacteria over Archaea in near-surface sediment.Scientific reports · 2017Article
- Defining boundaries for the distribution of microbial communities beneath the sediment-buried, hydrothermally active seafloor.The ISME journal · 2017Article
- Aerobic and Anaerobic Methanotrophic Communities Associated with Methane Hydrates Exposed on the Seafloor: A High-Pressure Sampling and Stable Isotope-Incubation Experiment.Frontiers in microbiology · 2017Article
- A Modified SDS-Based DNA Extraction Method for High Quality Environmental DNA from Seafloor Environments.Frontiers in microbiology · 2016Article
- Article
- A modular method for the extraction of DNA and RNA, and the separation of DNA pools from diverse environmental sample types.Frontiers in microbiology · 2015Article
- Influence of DNA extraction method, 16S rRNA targeted hypervariable regions, and sample origin on microbial diversity detected by 454 pyrosequencing in marine chemosynthetic ecosystems.Applied and environmental microbiology · 2014Article
Corrections and comments
- Erratum issued
Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A prerequisite for DNA-based microbial community analysis is even and effective cell disruption for DNA extraction. With a commonly used DNA extraction kit, roughly two-thirds of subseafloor sediment microbial cells remain intact on average (i.e., the cells are not disrupted), indicating that microbial community analyses may be biased at the DNA extraction step, prior to subsequent molecular analyses. To address this issue, we standardized a new DNA extraction method using alkaline treatment and heating. Upon treatment with 1 M NaOH at 98°C for 20 min, over 98% of microbial cells in subseafloor sediment samples collected at different depths were disrupted. However, DNA integrity tests showed that such strong alkaline and heat treatment also cleaved DNA molecules into short fragments that could not be amplified by PCR. Subsequently, we optimized the alkaline and temperature conditions to minimize DNA fragmentation and retain high cell disruption efficiency. The best conditions produced a cell disruption rate of 50 to 80% in subseafloor sediment samples from various depths and retained sufficient DNA integrity for amplification of the complete 16S rRNA gene (i.e., ∼1,500 bp). The optimized method also yielded higher DNA concentrations in all samples tested compared with extractions using a conventional kit-based approach. Comparative molecular analysis using real-time PCR and pyrosequencing of bacterial and archaeal 16S rRNA genes showed that the new method produced an increase in archaeal DNA and its diversity, suggesting that it provides better analytical coverage of subseafloor microbial communities than conventional methods.
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