Can Abundance of Protists Be Inferred from Sequence Data: A Case Study of Foraminifera

Article Article scientifique Article Can Abundance of Protists Be Inferred from Sequence Data: A Case Study of Foraminifera eng 2013 author Weber Alexandra 748019 author Pawlowski Jan Wojciech 23432 e56739 10.1371/journal.pone.0056739 1932-6203 http://dx.plos.org/10.1371/journal.pone.0056739 Protists are key players in microbial communities, yet our understanding of their role in ecosystem functioning is seriously impeded by difficulties in identification of protistan species and their quantification. Current microscopy-based methods used for determining the abundance of protists are tedious and often show a low taxonomic resolution. Recent development of next-generation sequencing technologies offered a very powerful tool for studying the richness of protistan communities. Still, the relationship between abundance of species and number of sequences remains subjected to various technical and biological biases. Here, we test the impact of some of these biological biases on sequence abundance of SSU rRNA gene in foraminifera. First, we quantified the rDNA copy number and rRNA expression level of three species of foraminifera by qPCR. Then, we prepared five mock communities with these species, two in equal proportions and three with one species ten times more abundant. The libraries of rDNA and cDNA of the mock communities were constructed, Sanger sequenced and the sequence abundance was calculated. The initial species proportions were compared to the raw sequence proportions as well as to the sequence abundance normalized by rDNA copy number and rRNA expression level per species. Our results showed that without normalization, all sequence data differed significantly from the initial proportions. After normalization, the congruence between the number of sequences and number of specimens was much better. We conclude that without normalization, species abundance determination based on sequence data was not possible because of the effect of biological biases. Nevertheless, by taking into account the variation of rDNA copy number and rRNA expression level we were able to infer species abundance, suggesting that our approach can be successful in controlled conditions. Dewey 590 44 Département de génétique et évolution 162 false PloS one 8 2 7ed25171-069d-4a9e-92ca-55330ee8f859 Article (Published version) Public journal.pone.0056739.pdf 414372 application/pdf CC BY openAccess Faculté des sciences / Section de biologie / Département de génétique et évolution

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Can Abundance of Protists Be Inferred from Sequence Data: A Case Study of Foraminifera	PloS one			2013	537	318

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Weber, Alexandra