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Related Concept Videos

Methods to Assess Microbial Populations01:30

Methods to Assess Microbial Populations

Assessing microbial populations is crucial for understanding microbial roles in health, ecology, and industry. Various complementary techniques—both culture-based and molecular—enable detailed analysis of microbial abundance, diversity, and function.Viable Plate CountThe viable plate count is a traditional culture-based method used to estimate the number of living microbes in a sample. After serial dilution, the sample is spread onto nutrient agar plates. Each viable cell forms a visible...
Microbial Growth Measurement: Indirect Methods01:27

Microbial Growth Measurement: Indirect Methods

Estimating microbial growth is essential for understanding population dynamics and environmental adaptations. Indirect methods provide valuable insights by measuring parameters such as turbidity, metabolic activity, and biomass, enabling efficient and reproducible assessments.During exponential growth, microbial cells scatter light proportionally to their biomass, a principle used in turbidity measurements. About one million cells per milliliter produce detectable scattering, which a...
Deep Sea Microbial Ecology01:18

Deep Sea Microbial Ecology

The deep ocean and its underlying sediments represent vast, largely unexplored microbial habitats that extend far beyond the sunlit photic zone. The photic (euphotic) zone typically spans the upper ~100–200 meters of pelagic waters in the open ocean, but its depth varies geographically and seasonally, where sufficient light supports photosynthetic life. Below this lies the deep sea, spanning roughly 1000–6000 meters (bathypelagic to abyssal zones), with deeper hadal trenches extending beyond...
Microbial Growth Measurement: Direct Methods01:23

Microbial Growth Measurement: Direct Methods

Direct methods for measuring microbial populations in a culture are essential tools in microbiology, providing quantitative data for various applications. Among these, microscopic counts, plate counts, and serial dilution are widely used techniques, each with unique principles and applications.Microscopic CountsMicroscopic counting involves the use of a Petroff-Hausser chamber, a specialized microscope slide with a grid and defined depth. By observing a liquid culture under a microscope,...
Microbial Biosensors01:17

Microbial Biosensors

Microbial biosensors are analytical devices that utilize living microbes to detect specific substances through measurable signals. These devices consist of two main components: biosensing organisms and signal-transducing elements. Biosensing organisms, such as Escherichia coli or Saccharomyces cerevisiae, are typically housed in multiwell plates connected to transducers, enabling rapid, real-time detection of target analytes.Signal Generation MechanismWhen a target analyte—such as...
Automated Microbial Diagnostics01:24

Automated Microbial Diagnostics

Automated diagnostic analyzers have transformed clinical microbiology by providing rapid and reliable methods for pathogen identification and antibiotic susceptibility testing. Among these systems, the Vitek 2 is widely used because it automates the traditionally labor-intensive processes of microbial identification (ID) and antibiotic susceptibility testing (AST), delivering standardized and timely results that are essential for effective patient care.Microbial Identification with ID CardsThe...

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Updated: May 29, 2026

Quantifying Microorganisms at Low Concentrations Using Digital Holographic Microscopy (DHM)
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Published on: November 1, 2017

Detection and quantification of microbial cells in subsurface sediments.

Jens Kallmeyer1

  • 1Earth and Environmental Sciences, Geomicrobiology Group, University of Potsdam, Potsdam, Germany. kallm@geo.uni-potsdam.de

Advances in Applied Microbiology
|September 20, 2011
PubMed
Summary

Accurate quantification of subsurface microbial life requires careful sample processing to avoid contamination. This review examines the entire workflow, from sample collection to fluorescence microscopy, for reliable cell enumeration.

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Area of Science:

  • Subsurface microbiology
  • Geomicrobiology
  • Microbial ecology

Background:

  • Quantifying total cell abundance is crucial for understanding subsurface life.
  • Fluorescence microscopy is the standard method for cell enumeration, despite advances in molecular techniques.
  • Reliable results depend on meticulous attention to the entire sample processing chain.

Purpose of the Study:

  • To review and evaluate all steps involved in enumerating cells in subsurface sediments.
  • To identify potential sources of contamination throughout the sample processing workflow.
  • To discuss strategies for contamination control in subsurface microbiology studies.

Main Methods:

  • Comprehensive review of existing literature on sample collection, processing, and analysis.
  • Discussion of various contamination control methods and tracers.
  • Analysis of challenges encountered at drill sites and field camps versus laboratory settings.

Main Results:

  • Numerous potential contamination sources exist from sample retrieval to final analysis.
  • Contamination control is essential, as some level is unavoidable.
  • Early-stage contamination at field sites poses significant challenges to accurate cell enumeration.

Conclusions:

  • Optimizing the entire sample processing chain is critical for accurate subsurface cell quantification.
  • Effective contamination control strategies must be implemented at all stages, especially during initial sample handling.
  • Further research into robust field-based contamination assessment and mitigation is warranted.