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Related Concept Videos

DNA Isolation01:34

DNA Isolation

DNA from cells is required for many biotechnology and research applications, such as molecular cloning. To remove and purify DNA from cells, researchers use various methods of DNA extraction. While the specifics of different protocols may vary, some general concepts underlie the process of DNA extraction.
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Overview Of Cell Separation And Isolation

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Related Experiment Video

Updated: May 27, 2026

Extraction and Analysis of Microbial Phospholipid Fatty Acids in Soils
10:03

Extraction and Analysis of Microbial Phospholipid Fatty Acids in Soils

Published on: August 26, 2016

A cell extraction method for oily sediments.

Michael Lappé1, Jens Kallmeyer

  • 1Geomicrobiology Group, Institute of Earth and Environmental Science, University of Potsdam Potsdam, Germany.

Frontiers in Microbiology
|November 30, 2011
PubMed
Summary

This study presents a modified method to extract microbial cells from hydrocarbon-contaminated sediments. The new protocol effectively removes hydrocarbons, reducing background fluorescence and improving cell enumeration accuracy for environmental monitoring.

Keywords:
cell enumerationcell separationhydrocarbonssubsurface microbiology

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Area of Science:

  • Environmental microbiology
  • Biogeochemistry
  • Analytical chemistry

Background:

  • Hydrocarbons are crucial carbon sources for microbes but pose challenges in cell enumeration due to fluorescence interference.
  • Existing cell extraction methods, like Kallmeyer et al. (2008), are not optimized for oily sediments, leading to inaccurate cell counts.
  • Accurate microbial cell enumeration is vital for understanding hydrocarbon biodegradation and environmental impact.

Purpose of the Study:

  • To develop and optimize a modified cell extraction method for hydrocarbon-contaminated sediments.
  • To reduce background fluorescence caused by hydrocarbons for improved microscopic cell identification and enumeration.
  • To determine optimal solvents and ratios for maximizing hydrocarbon removal while minimizing cell lysis.

Main Methods:

  • A modified cell extraction protocol involving pre-treatment to remove hydrocarbons before cell separation.
  • Testing various solvents (n-hexane, methanol) and volumetric ratios (1:2-1:5) for hydrocarbon extraction efficiency and cell viability.
  • Validation using spiked samples (E. coli) and samples with varying oil biodegradation levels.

Main Results:

  • The modified method significantly increased cell counts compared to the original Kallmeyer et al. (2008) protocol.
  • n-Hexane and methanol were identified as effective solvents, with methanol being more suitable for mature oils.
  • An optimal solvent-to-sample ratio of 1:2-1:5 was established to balance hydrocarbon removal and cell preservation, achieving 30-50% extraction efficiency.

Conclusions:

  • The developed method provides a clearer microscopic image, enabling easier and more accurate microbial cell enumeration in oily sediments.
  • The choice of solvent (n-hexane vs. methanol) depends on the oil's biodegradation level for optimal results.
  • This optimized protocol offers reproducible and reliable cell counts for diverse hydrocarbon-contaminated samples.