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Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere
Published on: May 2, 2018
Eukaryotic richness in the abyss: insights from pyrotag sequencing
Jan Pawlowski1, Richard Christen, Béatrice Lecroq
1Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland. Jan.Pawlowski@unige.ch
Plos One
|April 13, 2011
Summary
The deep-sea floor acts as a vast DNA repository, preserving genetic information from both sediment and overlying water. This finding highlights its potential for monitoring past and present environmental changes.
Area of Science:
- Marine Biology
- Genomics
- Ecology
Background:
- The deep sea floor is a highly diverse ecosystem.
- Environmental DNA (eDNA) surveys reveal abundant eukaryotic diversity in deep-sea sediments.
- Previous clone library surveys provided limited sequence data for abyssal eukaryote diversity assessment.
Purpose of the Study:
- To investigate the richness of eukaryotic DNA in Arctic and Southern Ocean deep-sea sediments.
- To utilize massively parallel sequencing for a comprehensive analysis of abyssal eukaryote diversity.
- To assess the potential of deep-sea sediments as a repository for genetic information.
Main Methods:
- Massively parallel sequencing of the 18S ribosomal RNA (rRNA) V9 hypervariable region.
- Analysis of small sediment volumes (0.35–0.7 g).
- Clustering of sequences to identify Operational Taxonomic Units (OTUs).
Main Results:
- Recovered up to 7,499 unique eukaryotic sequences per sample.
- Identified 942 to 1756 OTUs per sample, representing all major eukaryotic groups.
- Dinoflagellates, cercozoans, ciliates, and euglenozoans were predominant.
- Detected 31–71 metazoan OTUs per sample, suggesting a significant portion of DNA may be extracellular or from resting stages.
Conclusions:
- The deep-sea floor functions as a global DNA repository.
- Preserved genetic information reflects organisms in both sediment and water column.
- This DNA repository offers potential for monitoring past and present environmental changes.
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