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Modification of a High-Throughput Automatic Microbial Cell Enumeration System for Shipboard Analyses.

Christin M Bennke1, Greta Reintjes1, Martha Schattenhofer1,2

  • 1Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.

Applied and Environmental Microbiology
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We developed an automated system for microbial cell enumeration, improving accuracy and efficiency for marine ecology studies. This robust system works even on research vessels, enabling rapid analysis of microbial communities at sea.

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Area of Science:

  • Microbial Ecology
  • Oceanography
  • Bio-imaging

Background:

  • Accurate microbial cell enumeration is crucial for understanding microbial ecology, especially in complex marine environments.
  • Traditional microscopic quantification, while effective for specific clades using methods like fluorescence in situ hybridization (FISH), can be labor-intensive and challenging under field conditions.

Purpose of the Study:

  • To improve an existing automated image acquisition and cell enumeration system for robust performance on oceanographic research vessels.
  • To adapt and validate the system for high-seas deployment, ensuring accurate microbial cell counts in planktonic samples under dynamic conditions.

Main Methods:

  • An automated image acquisition and cell enumeration system was enhanced and adapted for shipboard use.
  • System settings (minimal pixel area, exposure times) were optimized ashore before at-sea testing under varying wind and wave conditions.
  • Performance was evaluated by comparing automated counts with manual counts and assessing image quality under ship movement (up to 3m heave, 6.3° pitch/roll).

Main Results:

  • The system demonstrated robustness, producing high-quality images despite significant ship motion.
  • Approximately 25% of acquired images from plankton samples were suitable for automated cell enumeration.
  • Automated cell counts showed a high correlation with manual counts (r² > 0.9), successfully enumerating even small microbes like SAR11.
  • The system enabled accurate and reproducible microbial cell counts, including specific clades, within hours of sample collection.

Conclusions:

  • The developed automated system provides a reliable method for microbial cell enumeration in planktonic samples, even under challenging oceanic conditions.
  • This technology facilitates real-time insights into microbial abundance and distribution at sea, supporting targeted sampling and a better understanding of marine microbial ecology.
  • The system's adaptability and accuracy enhance the capacity for large-scale '-omics' studies and microbial community analysis in marine research.