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Microbial community characterization in Red Sea-derived samples using a field-deployable DNA extraction system and

Diego J Jiménez1, Tahira Jamil1, Georgios Miliotis2

  • 1Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.

Environmental Microbiome
|November 27, 2025
PubMed
Summary
This summary is machine-generated.

Field DNA extraction using the xTitan system provides more accurate microbial diversity data for Red Sea samples. On-site nucleic acid extraction enhances detection of sensitive microbial taxa, crucial for marine microbiome studies.

Keywords:
BalneolaceaeEndozoicomonadaceaeCoralsHalophilesMangrovesMarine microbiomesSample storage

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Area of Science:

  • Marine microbiology
  • Environmental genomics
  • Molecular ecology

Background:

  • Assessing microbial communities in marine ecosystems like coral reefs and mangroves is vital.
  • Traditional methods involve sample transport, potentially biasing results.
  • Field-deployable nucleic acid extraction systems aim to capture more accurate microbial diversity.

Purpose of the Study:

  • To evaluate the xTitan field-deployable nucleic acid extraction system for Red Sea microbial communities.
  • To compare microbial diversity data from in-field versus in-laboratory DNA extractions.
  • To assess the impact of sample transport and storage on microbial community structure.

Main Methods:

  • Utilized the xTitan automated nucleic acid extraction system in the field and laboratory.
  • Compared DNA extraction using xTitan with a standard commercial kit (Qiagen).
  • Analyzed microbial communities from coral, mangrove sediment, and seawater samples using 16S rRNA gene sequencing.

Main Results:

  • In-field xTitan extraction showed a trend toward higher alpha diversity compared to laboratory methods.
  • Significant differences in beta diversity and functional gene profiles were observed between in-field and in-lab xTitan extractions, especially in mangrove samples.
  • On-site extraction improved detection of certain microbial taxa, including Endozoicomonas acroporae in corals and revealed differential abundance in mangrove-associated species.

Conclusions:

  • The xTitan system is a viable tool for field-based microbial community characterization.
  • On-site DNA extraction minimizes biases associated with sample transport and storage.
  • Field-based extraction is crucial for detecting microbial taxa sensitive to cold storage, enhancing marine microbiome research.