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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...
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Microbiome as a Tool to Monitor Aquarium Systems.

Wisal A Elmagzoub1, Manfred Weidmann1,2, Marwa H E Elnaiem3

  • 1Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, 04103 Leipzig, Germany.

Veterinary Sciences
|February 26, 2026
PubMed
Summary

Aquarium bacterial communities are unique and change over time, but their essential ammonia-metabolizing function remains stable. Nitrifying bacteria may indicate environmental impacts, aiding aquarium management and fish welfare.

Keywords:
aquatic systemsenvironmental eventsmicrobiome analysisnitrogen cycle

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Area of Science:

  • Aquatic microbiology
  • Environmental science
  • Zoological system management

Background:

  • The bacterial microbiome is crucial for aquarium stability, particularly in metabolizing toxic ammonia.
  • Understanding microbiome dynamics is key to managing artificial aquatic ecosystems effectively.

Purpose of the Study:

  • To monitor changes in aquarium bacterial communities over their first year.
  • To assess the impact of external influences and management interventions on the microbiome.
  • To identify potential microbial indicators of environmental effects.

Main Methods:

  • Collected water and swab samples from seven zoo aquatic systems over one year.
  • Performed bacterial cultivation for total counts.
  • Utilized Oxford Nanopore sequencing for metagenomic analysis.
  • Analyzed taxonomic composition and diversity using EPI2ME software and R.

Main Results:

  • Total bacterial counts increased and stabilized post-inoculation.
  • Significant differences in bacterial diversity were observed between freshwater and saltwater systems.
  • Each aquarium displayed a distinct, dynamic bacterial community.
  • Nitrifying capacity remained stable despite environmental disturbances.

Conclusions:

  • Aquarium microbiomes are unique and resilient, maintaining essential functions despite fluctuations.
  • Nitrifying taxa show promise as indicators for monitoring environmental effects in aquaria.
  • Next-generation sequencing can inform aquarium management for improved fish welfare.