ArticleApplied and environmental microbiology2016
Estimates of Soil Bacterial Ribosome Content and Diversity Are Significantly Affected by the Nucleic Acid Extraction Method Employed.
Article in Applied and environmental microbiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
- Comparative evaluation of soil DNA extraction kits for long read metagenomic sequencing.Access microbiology · 2024Article
- Estimating the bias related to DNA recovery from hemp stems for retting microbial community investigation.Applied microbiology and biotechnology · 2023Article
- Metadata harmonization-Standards are the key for a better usage of omics data for integrative microbiome analysis.Environmental microbiome · 2022Article
- Biological Soil Crust From Mesic Forests Promote a Specific Bacteria Community.Frontiers in microbiology · 2022Article
- The Evolution of Ecological Diversity inFrontiers in microbiology · 2022Article
- Effects of DNA preservation solution and DNA extraction methods on microbial community profiling of soil.Folia microbiologica · 2021Article
- Drivers of the composition of active rhizosphere bacterial communities in temperate grasslands.The ISME journal · 2020Article
- Resident and phytometer plants host comparable rhizosphere fungal communities in managed grassland ecosystems.Scientific reports · 2020Article
- Biases in Prokaryotic Community Amplicon Sequencing Affected by DNA Extraction Methods in Both Saline and Non-saline Soil.Frontiers in microbiology · 2018Article
- A Degradome-Based Polymerase Chain Reaction to Resolve the Potential of Environmental Samples for 2,4-Dichlorophenol Biodegradation.Current microbiology · 2017Article
- Differences in Temperature and Water Chemistry Shape Distinct Diversity Patterns in Thermophilic Microbial Communities.Applied and environmental microbiology · 2017Article
- Inferring interactions in complex microbial communities from nucleotide sequence data and environmental parameters.PloS one · 2017Article
- Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests.Scientific reports · 2016Article
- The Hoops, Hopes, and Hypes of Human Microbiome Research.The Yale journal of biology and medicine · 2016Review
- Comparison of six commercial kits to extract bacterial chromosome and plasmid DNA for MiSeq sequencing.Scientific reports · 2016Article
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8 authors.
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Abstract
Modern sequencing technologies allow high-resolution analyses of total and potentially active soil microbial communities based on their DNA and RNA, respectively. In the present study, quantitative PCR and 454 pyrosequencing were used to evaluate the effects of different extraction methods on the abundance and diversity of 16S rRNA genes and transcripts recovered from three different types of soils (leptosol, stagnosol, and gleysol). The quality and yield of nucleic acids varied considerably with respect to both the applied extraction method and the analyzed type of soil. The bacterial ribosome content (calculated as the ratio of 16S rRNA transcripts to 16S rRNA genes) can serve as an indicator of the potential activity of bacterial cells and differed by 2 orders of magnitude between nucleic acid extracts obtained by the various extraction methods. Depending on the extraction method, the relative abundances of dominant soil taxa, in particular Actino bacteria and Proteobacteria, varied by a factor of up to 10. Through this systematic approach, the present study allows guidelines to be deduced for the selection of the appropriate extraction protocol according to the specific soil properties, the nucleic acid of interest, and the target organisms.
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