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Can abundance of protists be inferred from sequence data: a case study of foraminifera


, : Can abundance of protists be inferred from sequence data: a case study of foraminifera. Plos One 8(2): E56739-E56739

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.

US$19.90

PMID: 23431390

DOI: 10.1371/journal.pone.0056739


Other references

Sessions, Stanley K., 1999: Deformed frogs What does the evidence tell us?. AAAS Annual Meeting & Science Innovation Exposition 165: A 15, 21-26 January

Tsai H J.; Satou M.; Shiraishi A.; Ueda K., 1987: Effects of moving structured background on the neuronal activities of optic tectum in the japanese toad. Zoological Science (Tokyo) 4(6): 970

Chesalina, T.L.; Chesalin, M.V., 2001: Hybridization between striped mullet and haarder in the Black Sea. Journal of Morphology 248(3): 216, June

Jensen, G.M.; Shepard, K.F.; Gwyer, J.; Hack, L.M., 1992: Attribute dimensions that distinguish master and novice physical therapy clinicians in orthopedic settings. The purpose of this qualitative case study was to further investigate the work of master and novice clinicians within the practice setting. The sample consisted of three master clinicians and three novice clinicians practicing in orthopedic outpat...

Callingham, B.A., 1989: Biochemical aspects of the pharmacology of moclobemide. The implications of animal studies. Administration of moclobemide--a relatively short-acting, reversible inhibitor of monoamine oxidase-A (MAO-A)--to experimental animals potentiates the pressor responses to intravenously injected tyramine, but such effects are moderate, short-lived...

Kaidash A.S.; Shinkarev V.P.; Afonin S.P., 1975: Increase of the degree of visible infection of wheat plants by yellow rust due to growth of mycelium in leaves. Mikologiya i Fitopatologiya 9(1): 57-60

Tan, A.S., 1998: Genetics of hairiness of sesame (Sesamum indicum L.). The objectives of this study were to: (i) investigate inheritance of hairiness in sesame using the hairy genotypes TR38106-1, TR42804-1 and TR50235-1 in crosses with 3 non-hairy genotypes; (ii) study allelism among the hairy accessions, and (iii)...

Singh, P.R.; Katti, K.V.; Lusiak, P.; Berning, D.; Katti, K.K.; Higginbotham, C.; Hoffman, T.; Ketring, A.R.; Volkert, W.A., 1995: Tc-99m chelates of novel amines and carboxylates. Journal of Nuclear Medicine 36(5 SUPPL ): 146P-147P

Podliachouk, L.; Wroblewski, A., 1957: Study of substance A from the saliva of swine. Comptes Rendus Hebdomadaires des Seances de L'academie des Sciences 244(23): 2867-2869

Gill, C.J.; Murphy, M.A.; Hamer, D.H., 2002: Treatment of Staphylococcus epidermidis ventriculo-peritoneal shunt infection with linezolid. Gram-positive bacterial meningitis frequently complicates ventriculo-peritoneal (VP) shunts used for hydrocephalus. Linezolid, an oxazolidinone, is active against Gram-positive cocci, and has excellent CSF penetration. We present a 22-year-old wom...