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Simultaneous DNA-RNA Extraction from Coastal Sediments and Quantification of 16S rRNA Genes and Transcripts by Real-time PCR
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[Differences Between DNA- and RNA-Based Bacterial Communities in Marine Sediments].

Ming-Yue Li1,2,3, Yu-Hong Yang1,2,3, Tie-Zhu Mi1,2,3

  • 1College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China.

Huan Jing Ke Xue= Huanjing Kexue
|July 2, 2020
PubMed
Summary

Comparing DNA (16S rRNA gene) and RNA (16S rRNA transcript) sequencing in marine sediments reveals distinct bacterial communities. RNA sequencing better reflects active microbial players and their ecological roles in biogeochemical processes.

Keywords:
DNARNAactivebacterial communitysediment

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Area of Science:

  • Marine microbiology
  • Biogeochemistry
  • Molecular ecology

Background:

  • Marine sediments harbor diverse microbial communities vital for global biogeochemical cycles.
  • 16S rRNA gene sequencing (DNA) captures total bacteria, including inactive ones, potentially misrepresenting active community functions.
  • 16S rRNA transcript sequencing (RNA) offers insights into active microorganisms and recent environmental activity.

Purpose of the Study:

  • To investigate the differences between total and active bacterial communities in marine sediments.
  • To compare DNA-based (16S rRNA gene) and RNA-based (16S rRNA transcript) community structures.
  • To assess the accuracy of 16S rRNA gene sequencing in representing bacterial functions in marine environments.

Main Methods:

  • Quantitative real-time polymerase chain reaction (qPCR) for gene and transcript abundance.
  • Illumina high-throughput sequencing for bacterial community structure analysis.
  • Comparative analysis of DNA and RNA extracted from Bohai Sea and South Yellow Sea sediments.

Main Results:

  • 16S rRNA gene abundance significantly exceeded transcript abundance (1-2 orders of magnitude).
  • Total bacterial communities (DNA) were more diverse than active communities (RNA), with notable structural differences.
  • Active bacteria were involved in chemoheterotrophy, sulfate reduction, and nitrification.

Conclusions:

  • 16S rRNA gene sequencing can misestimate key functional microbiota, impacting the understanding of marine sediment bacterial communities.
  • The 'rare biosphere' identified by DNA sequencing may comprise actively transcribing microbes crucial for biogeochemical cycles.
  • Utilizing 16S rRNA sequencing is recommended for accurately reflecting the ecological status of bacterial communities in stable marine sedimentary environments.