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Efficient recovery and DNA extraction for algae-associated microbial communities.

Elizaveta Chevokina1, Daria Sibiryakina1, Andrey Sobolev1

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This study benchmarks methods for extracting microbial DNA from marine algae biofilms. The GeneJET kit offered the best balance of DNA quantity and quality for metagenomic sequencing.

Keywords:
DNA extractionalgaebiofilmsmetagenomicsmicrobial communities

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Area of Science:

  • Microbiology
  • Marine Biology
  • Molecular Biology

Background:

  • High-quality microbial DNA extraction from environmental samples is crucial for metagenomic sequencing.
  • Biofilm matrix and algal symbionts pose challenges to DNA recovery and purity.
  • Existing DNA purification methods vary in efficiency and suitability for different sample types.

Purpose of the Study:

  • To benchmark methods for microbial cell recovery from marine macroalgae biofilms.
  • To evaluate commercial DNA purification kits for DNA yield and quality for sequencing.
  • To provide guidance on selecting optimal DNA extraction procedures for algae-associated microbial communities.

Main Methods:

  • Five methods were used to recover microbial cells from red, brown, and green macroalgae biofilms.
  • Six commercial DNA purification kits were systematically evaluated for DNA extraction.
  • Extracted DNA quality and quantity were assessed for 16S rRNA gene and shotgun sequencing suitability.

Main Results:

  • A trade-off between DNA quantity and quality was universally observed across methods.
  • Whole-sample homogenization led to high chloroplast contamination; buffer washing resulted in low DNA recovery.
  • The GeneJET Genomic DNA Purification Kit demonstrated the most versatile performance across algal species.

Conclusions:

  • Detergent use improved DNA yields, while cell washing alone decreased recovery.
  • DNA extraction kit efficiency significantly varied depending on the algal species.
  • This study offers a benchmark for selecting DNA extraction methods for marine algae-associated microbial studies.