Online citations, reference lists, and bibliographies.

Quantitative Cell Lysis Of Indigenous Microorganisms And Rapid Extraction Of Microbial DNA From Sediment.

Margret Irmgard Moré, James B. Herrick, Maurizete Cruz Silva, William C. Ghiorse, Eugene L. Madsen
Published 1994 · Biology, Medicine
Cite This
Download PDF
Analyze on Scholarcy
Share
This study reports improvements in two of the key steps, lysis of indigenous cells and DNA purification, required for achieving a rapid nonselective protocol for extracting nucleic acids directly from sodium dodecyl sulfate (SDS)-treated sediment rich in organic matter. Incorporation of bead-mill homogenization into the DNA extraction procedure doubled the densitometrically determined DNA yield (11.8 micrograms of DNA.g [dry weight] of sediment-1) relative to incorporation of three cycles of freezing and thawing (5.2 micrograms of DNA.g [dry weight] of sediment-1). The improved DNA extraction efficiency was attributed to increased cell lysis, measured by viable counts of sediment microorganisms which showed that 2 and 8%, respectively, survived the bead-mill homogenization and freeze-thaw procedures. Corresponding measurements of suspensions of viable Bacillus endospores demonstrated that 2 and 94% of the initial number survived. Conventional, laser scanning epifluorescence phase-contrast, and differential interference-contrast microscopy revealed that small coccoid bacterial cells (1.2 to 0.3 micron long) were left intact after combined SDS and bead-mill homogenization of sediment samples. Estimates of the residual fraction of the fluorescently stained cell numbers indicated that 6% (2.2 x 10(8) cells.g [dry weight] of sediment-1) of the original population (3.8 x 10(9) cells.g [dry weight] of sediment-1) remained after treatment with SDS and bead-mill homogenization. Thus, lysis of total cells was less efficient than that of cells which could be cultured. The extracted DNA was used to successfully amplify nahR, the regulatory gene for naphthalene catabolism in Pseudomonas putida G7, by PCR.(ABSTRACT TRUNCATED AT 250 WORDS)



This paper is referenced by
Fonctionnement et qualité des sols soumis à des perturbations physiques et chimiques d'origines anthropiques: réponses du sol, de la flore et de la microflore bactérienne tellurique
Raphaël Gros (2002)
Izolacja kwasów nukleinowych ze środowiska - pierwszy krok w analizie metagenomu
Jacek Kozdrój (2010)
10.1007/s002840010223
Improved Method for Detection of Methanotrophic Bacteria in Forest Soils by PCR
Ralph Steinkamp (2001)
10.1007/978-1-4939-3185-9_21
Nucleic Acid Purification from Soil and Environmental Sources
Moogega Cooper (2016)
10.1128/AEM.02339-09
PCR Inhibitor Levels in Concentrates of Biosolid Samples Predicted by a New Method Based on Excitation-Emission Matrix Spectroscopy
Channah M Rock (2010)
Electrophoresis and Temperature Gradient Gel PCR-Amplified Genes Encoding 18 S rRNA Rhizosphere by Sequencing of Cloned Analysis of Fungal Diversity in the Wheat
Eric Smit (1998)
10.1128/aem.61.2.763-768.1995
Isolation and characterization of RNA from low-biomass deep-subsurface sediments.
Andrew V. Ogram (1995)
Assessment of DNA contents of soil fungi
T. H. Anderson (2008)
10.1016/j.mimet.2014.04.005
Isolation of PCR quality microbial community DNA from heavily contaminated environments.
Manjula Gunawardana (2014)
10.1128/aem.65.5.1980-1990.1999
Molecular Analyses of the Methane-Oxidizing Microbial Community in Rice Field Soil by Targeting the Genes of the 16S rRNA, Particulate Methane Monooxygenase, and Methanol Dehydrogenase
Thilo Henckel (1999)
Soil and Sediment Samples Extraction and Purification Procedures for Evaluation and Optimization of DNA
Daniel N. Miller (1999)
Molecular approaches to assessing fungal diversity in the natural environment
Ecy Liew (1998)
10.1016/S1164-5563(03)00033-5
Extraction of DNA from soil
Patrick Robe (2003)
10.1016/B978-0-12-370519-8.00008-0
Environmental Sample Collection and Processing
I. Pepper (2009)
10.1139/w05-003
A survey of the methods for the characterization of microbial consortia and communities.
Dan Spiegelman (2005)
10.1111/jam.12420
An efficient and economical method for extraction of DNA amenable to biotechnological manipulations, from diverse soils and sediments.
S Sharma (2014)
10.1007/s00253-002-1072-y
Recent developments in molecular techniques for identification and monitoring of xenobiotic-degrading bacteria and their catabolic genes in bioremediation
Jaka Widada (2002)
10.1128/aem.65.7.3240-3243.1999
In Situ Detection of the Clostridium botulinum Type C1 Toxin Gene in Wetland Sediments with a Nested PCR Assay
Judy L. Williamson (1999)
10.1134/S0026261714060174
Analysis of endophytic bacterial community composition by 16S rDNA clone library in Achnatherum inebrians
Ying Shi (2014)
Phylogenetic diversity and community structure of sulfate-reducing bacteria in a salt marsh sediment
R Varga (1997)
10.1080/00275514.2001.12063212
Extraction and PCR amplification of DNA from minute ectoparasitic fungi
Alex Weir (2001)
10.1080/15440478.2014.897669
Cultivation of Fiber and Oil Flax (Linum usitatissimum L.) in No-Tillage and Conventional Systems. Part II. Influence of No-Tillage and Use of Herbicides on Yield and Weed Infestation of Oil Flax and the Physical and Biological Properties of the Soil
K Pudelko (2013)
10.1128/AEM.67.9.4365-4371.2001
Diversity and Distribution in Hypersaline Microbial Mats of Bacteria Related to Chloroflexusspp
Ulrich Nübel (2001)
Sediments by a Novel Hydroxyapatite Rapid Extraction of DNA and rRNA from
Kevin J. Purdy (1996)
10.1080/10837450.2018.1425885
Evaluation of anionic surfactants effects on the skin barrier function based on skin permeability
Mana Okasaka (2019)
Screening for aerobic endospore-forming bacteria as biocontrol agents for powdery mildew disease of cucurbits.
Heather Rayne. Tredgold (2015)
10.1155/2014/518960
An Improved Method for Soil DNA Extraction to Study the Microbial Assortment within Rhizospheric Region
Faria Fatima (2014)
10.1007/S11274-011-0713-7
Dehalogenase gene detection and microbial diversity of a chlorinated hydrocarbon contaminated site
Algasan Govender (2011)
10.1080/01490450903060814
Bacterial and Archaeal DNA Extracted from Inoculated Experiments: Implication for the Optimization of DNA Extraction from Deep-Sea Basalts
Hongmei Wang (2009)
10.1080/00032710802162186
A Parametric Study of Sample Lysis and DNA Purification Techniques for Use in Automated Devices
J. Edward Hu (2008)
10.1111/j.1550-7408.2003.tb00132.x
Detection of Naegleria sp. in a Thermal, Acidic Stream in Yellowstone National Park
Kathy B. Sheehan (2003)
Community of Yellowstone National Park the Octopus Spring Microbial Mat Isolates Typical of Those Predominating in Synechococcus of and Photosynthesis by Effect of Temperature and Light on Growth
Jessica P. Allewalt (2005)
See more
Semantic Scholar Logo Some data provided by SemanticScholar