Environmental rRNA inventories miss over half of protistan diversity

Title:
Environmental rRNA inventories miss over half of protistan diversity
Creator:
Jeon, Sunok (Author)
Bunge, John (Author)
Leslin, Chesley (Author)
Stoeck, Thorsten (Author)
Hong, Sunhee (Author)
Epstein, Slava S. (Author)
Language:
English
Publisher:
BioMedCentral
Copyright date:
2008
Type of resource:
Text
Genre:
Articles
Format:
electronic
Digital origin:
born digital
Abstract/Description:

Background


The main tool to discover novel microbial eukaryotes is the rRNA approach. This approach has important biases, including PCR discrimination against certain rRNA gene species, which makes molecular inventories skewed relative to the source communities. The degree of this bias has not been quantified, and it remains unclear whether species missed from clone libraries could be recovered by increasing sequencing efforts, or whether they cannot be detected in principle. Here we attempt to discriminate between these possibilities by statistically analysing four protistan inventories obtained using different general eukaryotic PCR primers.

Results


We show that each PCR primer set-specific clone library is not a sample from the community diversity but rather from a fraction of this diversity. Therefore, even sequencing such clone libraries to saturation would only recover that fraction, which, according to the parametric models, varies between 17 ± 4% to 49 ± 10%, depending on the set of primers. The pooled data is thus qualitatively richer than individual libraries, even if normalized to the same sequencing effort.

Conclusion


The use of a single pair of primers leads to significant underestimation of the true community richness at all levels of taxonomic hierarchy. The majority of available protistan rRNA gene surveys likely sampled less than half of the target diversity, and might have completely missed the rest. The use of multiple PCR primers reduces this bias but does not necessarily eliminate it.
Comments:
Originally published in BMC Microbiology 8:222 (2008). doi:10.1186/1471-2180-8-222
This study was supported by NSF Grant MCB-0348341 to SSE and by the Deutsche Forschungsgemeinschaft grant STO414/2-1 to TS.
Subjects and keywords:
Protista - Variation
rRna
molecular inventories
novel microbial eukaryotes
PCR primers
Microbiology

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