DNA extraction method affects microbial community profiles from soils and sediment

No abstract is available for this paper.

• Publication year

  2007

• Venue

  Applied Microbiology and Biotechnology

• Publication date

  2007-10-25

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1007/s00253-007-1219-yPMID 17960375
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• DNA extraction procedure: a critical issue for bacterial diversity assessment in marine sediments.

  2006cited by this paper
• Impact of DNA extraction method on bacterial community composition measured by denaturing gradient gel electrophoresis

  2004influential reference
• Assessing shifts in microbial community structure across a range of grasslands of differing management intensity using CLPP, PLFA and community DNA techniques

  2004cited by this paper
• Influence of depth and sampling time on bacterial community structure in an upland grassland soil.

  2003cited by this paper
• Microbial diversity and soil functions

  2003cited by this paper
• A quantitative analysis of DNA extraction and purification from compost.

  2003influential reference
• Efficient recovery of environmental DNA for expression cloning by indirect extraction methods.

  2003influential reference
• Extraction of DNA from soil

  2003influential reference
• Biotechnological prospects from metagenomics.

  2003cited by this paper
• Mechanisms underlying the impact of humic acids on DNA quantification by SYBR Green I and consequences for the analysis of soils and aquatic sediments.

  2003cited by this paper
• Limited resolution of 16S rDNA DGGE caused by melting properties and closely related DNA sequences.

  2003cited by this paper
• Spatial distribution of bacterial communities and their relationships with the micro-architecture of soil.

  2003cited by this paper
• Eubacterial community structure and population size within the soil light fraction, rhizosphere, and heavy fraction of several agricultural systems

  2003cited by this paper
• Microorganisms as indicators of soil health

  2002cited by this paper
• Microbial diversity along a transect of agronomic zones.

  2002cited by this paper
• Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns.

  2002cited by this paper
• Microbial diversity and function in soil: from genes to ecosystems.

  2002cited by this paper
• Evaluation of extraction and purification methods for obtaining PCR-amplifiable DNA from compost for microbial community analysis.

  2002influential reference
• Genetic diversity and strain-typing in cultivated strains of Lentinula edodes (the shii-take mushroom) in Japan by AFLP analysis*

  2002cited by this paper
• Comparison of rapid DNA extraction methods applied to contrasting New Zealand soils

  2001cited by this paper
• Diversity and Seasonal Fluctuations of the Dominant Members of the Bacterial Soil Community in a Wheat Field as Determined by Cultivation and Molecular Methods

  2001cited by this paper
• DNA Extraction from Soils: Old Bias for New Microbial Diversity Analysis Methods

  2001influential reference
• Molecular Cloning: A Laboratory Manual

  2001cited by this paper
• Bacterial abundance and activity in deep-sea sediments from the eastern North Atlantic

  2001cited by this paper
• Effects of tylosin as a disturbance on the soil microbial community

  2001cited by this paper
• Phylogenetic Specificity and Reproducibility and New Method for Analysis of Terminal Restriction Fragment Profiles of 16S rRNA Genes from Bacterial Communities

  2001cited by this paper
• A strategy for optimizing quality and quantity of DNA extracted from soil.

  2001influential reference
• Extraction and purification of microbial DNA from soil and sediment samples

  2001influential reference
• Evaluation of Biological and Physical Protection against Nuclease Degradation of Clay-Bound Plasmid DNA

  2001cited by this paper
• Extraction and purification of DNA in rhizosphere soil samples for PCR-DGGE analysis of bacterial consortia.

  2001influential reference
• Application of polymerase chain reaction-denaturing gradient gel electrophoresis for comparison of direct and indirect extraction methods of soil DNA used for microbial community fingerprinting

  2000cited by this paper
• Soil molecular microbial ecology at age 20: methodological challenges for the future

  2000cited by this paper
• An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics.

  2000cited by this paper
• Rapid Method for Coextraction of DNA and RNA from Natural Environments for Analysis of Ribosomal DNA- and rRNA-Based Microbial Community Composition

  2000influential reference
• METHODS FOR ASSESSING THE COMPOSITION AND DIVERSITY OF SOIL MICROBIAL COMMUNITIES

  2000cited by this paper
• Evaluation and Optimization of DNA Extraction and Purification Procedures for Soil and Sediment Samples

  1999influential reference
• Comparison of different methods for the isolation and purification of total community DNA from soil.

  1999cited by this paper
• Quantification of Bias Related to the Extraction of DNA Directly from Soils

  1999cited by this paper
• Rapid cleanup of bacterial DNA from field samples

  1999cited by this paper
• 16S rDNA methods in soil microbiology

  1999cited by this paper
• Opening the black box of soil microbial diversity

  1999cited by this paper
• Rapid method for fluorometric quantification of DNA in soil

  1998influential reference
• Utility of Green Fluorescent Nucleic Acid Dyes and Aluminum Oxide Membrane Filters for Rapid Epifluorescence Enumeration of Soil and Sediment Bacteria

  1998cited by this paper
• Small-Scale DNA Sample Preparation Method for Field PCR Detection of Microbial Cells and Spores in Soil

  1998cited by this paper
• Rhizosphere carbon flow in trees, in comparison with annual plants: the importance of root exudation and its impact on microbial activity and nutrient availability

  1997cited by this paper
• Seasonal distributions of dominant 16S rRNA-defined populations in a hot spring microbial mat examined by denaturing gradient gel electrophoresis

  1997cited by this paper
• DNA recovery from soils of diverse composition

  1996influential reference
• Total bacterial diversity in soil and sediment communities—A review

  1996cited by this paper
• Phylogenetic identification and in situ detection of individual microbial cells without cultivation.

  1995cited by this paper
• Comparison of methods of DNA extraction from stream sediments

  1995cited by this paper
• Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment

  1994cited by this paper
• Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA

  1993influential reference
• Phylogenetic diversity of aggregate‐attached vs. free‐living marine bacterial assemblages

  1993cited by this paper
• DNA extraction for 16S rRNA gene analysis to determine genetic diversity in deep sediment communities.

  1992cited by this paper
• Rapid method for direct extraction of DNA from soil and sediments

  1991cited by this paper
• Recovery of DNA from soils and sediments

  1988cited by this paper
• Adsorption of DNA to sand and variable degradation rates of adsorbed DNA

  1987cited by this paper
• Microbial ecology and evolution: a ribosomal RNA approach.

  1986cited by this paper
• Isolation of bacterial DNA from soil.

  1980cited by this paper

• Comparing DNA Extraction Protocols for Freshwater Prokaryotic Communities: Impacts on Yield and Microbial Profiling

  2026cites this paper
• Biodiversity and Biological Interactions of Actinobacteria Associated with Deep Sea and Intertidal Marine Invertebrates

  2025cites this paper
• The urinary microbiome: the next frontier of bacterial ecology

  2025cites this paper
• Comparison of Lysis and Amplification Methodologies for Optimal 16S rRNA Gene Profiling for Human and Mouse Microbiome Studies

  2025cites this paper
• Comparative analysis of DNA extraction methods from seamount sediments: evaluation of yield, purity, and fragment integrity

  2025cites this paper
• Prokaryotic diversity, function prediction, and community assembly in the Arabian Sea sediments linked to the extent of mesopelagic hypoxia.

  2025cites this paper
• The urine microbiome: what's normal and what's pathological? Microbiome-based treatment and prevention of urinary tract infections: A review

  2025cites this paper
• Microbiome data integration via shared dictionary learning

  2025cites this paper
• Exploring fungal diversity in Vietnam: A citizen science initiative

  2024cites this paper
• Advancements in DNA Metabarcoding Protocols for Monitoring Zooplankton in Marine and Brackish Environments

  2024cites this paper
• DNA, databases and diet: a case study on the parrotfish Scarus rivulatus

  2024cites this paper
• Estimating the bias related to DNA recovery from hemp stems for retting microbial community investigation

  2023cites this paper
• Anionic nanocellulose as competing agent in microbial DNA extraction from mine process samples.

  2023cites this paper
• Benchmarking DNA isolation methods for marine metagenomics

  2023cites this paper
• Seasonal variation in soil algal community structure in different forest plantations in subtropic China

  2023influential citation
• Pragmatic Considerations When Extracting DNA for Metagenomics Analyses of Clinical Samples

  2023cites this paper
• Through the eDNA looking glass: Responses of fjord benthic foraminiferal communities to contrasting environmental conditions

  2023cites this paper
• Comparison of four DNA extraction kits efficiency for 16SrDNA microbiota profiling of diverse human samples

  2023cites this paper
• Best practice for wildlife gut microbiome research: A comprehensive review of methodology for 16S rRNA gene investigations

  2023cites this paper
• Evaluation and optimization of lysis method for microbial DNA extraction from epiphytic phyllosphere samples.

  2023cites this paper
• Soil sample sizes for DNA extraction substantially affect the examination of microbial diversity and co-occurrence patterns but not abundance

  2023cites this paper
• Qualitative and Quantitative Analysis of DNA from Human Saliva Respectively through Quantitative Polymerase Chain Reaction and UV-Visible Spectrophotometer: A Review

  2022cites this paper
• Next Generation Sequencing genomic analysis of bacteria from soils of the sites with naturally-occurring summer truffle (Tuber aestivum Vittad.)

  2022cites this paper
• A comparison of hard and soft direct methods for DNA extraction from soil

  2022cites this paper
• Optimized sample processing pipeline for PCR-based fungicide resistance quantification of stubble-borne fungal pathogens.

  2022cites this paper
• The Effects of DNA Extraction Kits and Primers on Prokaryotic and Eukaryotic Microbial Community in Freshwater Sediments

  2022cites this paper
• High peatland methane emissions following permafrost thaw : enhanced acetoclastic 1 methanogenesis during early successional stages 2

  2022influential citation
• High peatland methane emissions following permafrost thaw: enhanced acetoclastic methanogenesis during early successional stages

  2022influential citation
• Grinding Beads Influence Microbial DNA Extraction from Organic-Rich Sub-Seafloor Sediment

  2022cites this paper
• Next-Generation Amplicon Sequencing: A Cost-Effective Method for Exploring Microbial Biodiversity

  2022cites this paper
• Dynamics of Bacterial Root Endophytes of Malus domestica Plants Grown in Field Soils Affected by Apple Replant Disease

  2022cites this paper
• The Requirement of Genetic Diagnostic Technologies for Environmental Surveillance of Antimicrobial Resistance

  2021cites this paper
• Identifying biases and their potential solutions in human microbiome studies

  2021cites this paper
• Microbes and Infectious Diseases Impact of Staphylococci DNA extraction methodology on microsatellite-based PCR banding profile

  2021cites this paper
• Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods.

  2021cites this paper
• Evaluation of a Highly Efficient DNA Extraction Method for Bacillus anthracis Endospores

  2020cites this paper
• Robust DNA protocols for tropical soils

  2020cites this paper
• Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from high-mountain streams

  2020cites this paper
• Analysis of the Bacterial and Fungal Community Profiles in Bulk Soil and Rhizospheres of Three Mungbean [Vigna radiata (L.) R. Wilczek] Genotypes through PCR-DGGE

  2020cites this paper
• Microbial Diversity of Soil Ecosystems

  2020cites this paper
• Biomonitoring of aquatic pollution: status and trends from genomics to populations

  2020cites this paper
• Comparing sediment DNA extraction methods for assessing organic enrichment associated with marine aquaculture

  2020cites this paper
• Optimization of a Method for the Concentration of Genetic Material in Bacterial and Fungal Communities on Fresh Apple Peel Surfaces

  2020cites this paper
• Tendentious effects of automated and manual metagenomic DNA purification protocols on broiler gut microbiome taxonomic profiling

  2020cites this paper
• General Geochemistry and Microbiology Techniques

  2019cites this paper
• Environmental DNA metabarcoding studies are critically affected by substrate selection

  2019cites this paper
• Spiking a Silty-Sand Reference Soil with Bacterial DNA: Limits and Pitfalls in the Discrimination of Live and Dead Cells When Applying Ethidium Monoazide (EMA) Treatment

  2019cites this paper
• Optimisation of protocol for effective detachment and selective recovery of the representative bacteria for extraction of metagenomic DNA from Eucalyptus spp. woodchips.

  2018cites this paper
• Long-term agrichemical use leads to alterations in bacterial community diversity.

  2018cites this paper
• Assessing high-throughput environmental DNA extraction methods for meta-barcode characterization of aquatic microbial communities.

  2018cites this paper
• Limited congruence exhibited across microbial, meiofaunal and macrofaunal benthic assemblages in a heterogeneous coastal environment

  2018cites this paper
• Biases in Prokaryotic Community Amplicon Sequencing Affected by DNA Extraction Methods in Both Saline and Non-saline Soil

  2018cites this paper
• Biases during DNA extraction affect characterization of the microbiota associated with larvae of the Pacific white shrimp, Litopenaeus vannamei

  2018cites this paper
• Biases from different DNA extraction methods in intestine microbiome research based on 16S rDNA sequencing: a case in the koi carp, Cyprinus carpio var. Koi

  2018cites this paper
• A modified method for genomic DNA extraction from the fish intestinal microflora

  2018cites this paper
• Isolation of high molecular weight and humic acid-free metagenomic DNA from lignocellulose-rich samples compatible for direct fosmid cloning

  2018cites this paper
• Endophytes of industrial hemp (Cannabis sativa L.) cultivars: identification of culturable bacteria and fungi in leaves, petioles, and seeds.

  2018cites this paper
• Soil Salinity Controls Relative Abundance of Specific Bacterial Groups Involved in the Decomposition of Maize Plant Residues

  2018cites this paper
• Defining the seafloor microbiome of the Gulf of Mexico and its response to oil perturbation

  2018cites this paper
• Inter-laboratory calibration of quantitative analyses of antibiotic resistance genes

  2018cites this paper
• Impact of Different Methods of Soil Sampling and DNA Extraction on the Identification of Soil Bacterial Abundance under Elevated CO2

  2017cites this paper
• Environmental DNA as a valuable and unique source of information about ecological networks in Arctic terrestrial ecosystems

  2017cites this paper
• Biases during DNA extraction affect bacterial and archaeal community profile of anaerobic digestion samples

  2017cites this paper
• Isolation and Diversity Analysis of Soil

  2017cites this paper
• Suitability of various DNA extraction methods for a traditional Chinese paocai system

  2017cites this paper
• The choice of the DNA extraction method may influence the outcome of the soil microbial community structure analysis

  2017cites this paper
• Comparison of two bacterial DNA extraction methods from non-polluted and polluted soils

  2017cites this paper
• META-pipe – Distributed Pipeline Analysis of Marine Metagenomic Sequence Data

  2017cites this paper
• Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing

  2017cites this paper
• Soil DNA Extraction Procedure Influences Protist 18S rRNA Gene Community Profiling Outcome.

  2017cites this paper
• Comparison of Metagenomic DNA Extraction Methods for Soil Sediments of High Elevation Puga Hot Spring in Ladakh, India to Explore Bacterial Diversity

  2017influential citation
• Comparison of ten different DNA extraction procedures with respect to their suitability for environmental samples.

  2017cites this paper
• A method for assessing efficiency of bacterial cell disruption and DNA release

  2016cites this paper
• Carbon amendment and soil depth affect the distribution and abundance of denitrifiers in agricultural soils

  2016cites this paper
• A framework for inferring biological communities from environmental DNA.

  2016cites this paper
• Comparison of Boiling and Robotics Automation Method in DNA Extraction for Metagenomic Sequencing of Human Oral Microbes

  2016cites this paper
• Estimates of Soil Bacterial Ribosome Content and Diversity Are Significantly Affected by the Nucleic Acid Extraction Method Employed

  2016cites this paper
• Examining Biochar Impacts on Soil Abiotic and Biotic Processes and Exploring the Potential for Pyrosequencing Analysis

  2016cites this paper
• Shifts in microbial communities in bioaugmented grease interceptors removing fat, oil, and grease (FOG)

  2016cites this paper
• A comparison of DNA extraction methods for biodiversity studies of eukaryotes in marine sediments

  2015cites this paper
• RNA Preservation Agents and Nucleic Acid Extraction Method Bias Perceived Bacterial Community Composition

  2015cites this paper
• Effort versus Reward: Preparing Samples for Fungal Community Characterization in High-Throughput Sequencing Surveys of Soils

  2015cites this paper
• Functional responses and adaptation of mesophilic microbial communities to psychrophilic anaerobic digestion.

  2015cites this paper
• Sampling, metadata and DNA extraction - important steps in metagenomic studies.

  2015cites this paper
• Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences

  2015influential citation
• Use of pressure cycling technology for cell lysis and recovery of bacterial and fungal communities from soil.

  2015cites this paper
• Fate of Trace Metals in Anaerobic Digestion.

  2015cites this paper
• Next-Generation Sequencing for Pathogen Detection and Identification

  2015cites this paper
• The dynamic interaction between microbial biodiversity, biogeochemical activity and sedimentary geomorphology in the Severn Estuary

  2015cites this paper
• The effect of depth on microbial communities from mesotrophic lake sediments as measured by two DNA extraction methods

  2015influential citation
• Hydrolysis, methanogenesis and bioprocess performance during low-temperature anaerobic digestion of dilute wastewater

  2015cites this paper
• Ancient and modern environmental DNA

  2015cites this paper
• The role of estuarine sediments as a reservoir for pathogenic microorganisms

  2015cites this paper
• Novel methods for comparing and evaluating single and metagenomic assemblies

  2015cites this paper
• Investigation of faecal pollution sources and bacterial transfer hydrodynamics in rural catchments

  2015influential citation
• The Host as the Driver of the Microbiota in the Gut and External Environment of Drosophila melanogaster

  2015cites this paper
• Molecular ecological tools to decipher the role of our microbial mass in obesity.

  2015cites this paper
• It's a Small World: Biogeography and Invasion in the Mouse Intestine

  2015influential citation
• Analyzing the Human Microbiome: A “How To” guide for Physicians

  2014cites this paper
• Rapid extraction of PCR-competent DNA from recalcitrant environmental samples.

  2014cites this paper