Lanzen A, Jorgensen SL, Bengtsson MM, Jonassen I, Ovreas L, Urich T.. Exploring the composition and diversity of microbial communities at the Jan Mayen hydrothermal vent field using RNA and DNA. FEMS Microbiol Ecol 77: 577-589

Department of Biology and Centre for Geobiology, University of Bergen, Bergen, Norway.
FEMS Microbiology Ecology (Impact Factor: 3.57). 05/2011; 77(3):577-89. DOI: 10.1111/j.1574-6941.2011.01138.x
Source: PubMed


DNA sequencing technology has proven very valuable for analysing the microbiota of poorly accessible ecosystems such as hydrothermal vents. Using a combination of amplicon and shotgun sequencing of small-subunit rRNA and its gene, we examined the composition and diversity of microbial communities from the recently discovered Jan Mayen vent field, located on Mohn's Ridge in the Norwegian-Greenland Sea. The communities were dominated by the epsilonproteobacterial genera Sulfurimonas and Sulfurovum. These are mesophiles involved in sulphur metabolism and typically found in vent fluid mixing zones. Composition and diversity predictions differed systematically between extracted DNA and RNA samples as well as between amplicon and shotgun sequencing. These differences were more substantial than those between two biological replicates. Amplicon vs. shotgun sequencing differences could be explained to a large extent by bias introduced during PCR, caused by preferential primer-template annealing, while DNA vs. RNA differences were thought to be caused by differences between the activity levels of taxa. Further, predicted diversity from RNA samples was consistently lower than that from DNA. In summary, this study illustrates how different methods can provide complementary ecological insights.

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    • "Sequences were filtered using LUCY (Chou and Holmes, 2001) to remove short (< 150 bp) and low-quality sequences (> 0.2% error probability). SSU ribosomal RNA sequences of eukaryotes were identified by MEGAN analysis of BLASTn files against a SSU rRNA reference database (Lanzén et al., 2011; parameters: min. bit score 150, min. "
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    • "Sequences were first filtered using LUCY (Chou and Holmes, 2001), removing short (o150 bp) and low-quality sequences (40.2% error probability). SSU ribosomal RNA sequences of eukaryotes were identified by MEGAN analysis of BLASTn files against a 3-domain SSU rRNA reference database (Lanzén et al., 2011; parameters: min. bit score 150, min. "
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