Article thumbnail
Location of Repository

How many novel eukaryotic 'kingdoms'? Pitfalls and limitations of environmental DNA surveys

By Cédric Berney, José Fahrni and Jan Pawlowski

Abstract

BACKGROUND: Over the past few years, the use of molecular techniques to detect cultivation-independent, eukaryotic diversity has proven to be a powerful approach. Based on small-subunit ribosomal RNA (SSU rRNA) gene analyses, these studies have revealed the existence of an unexpected variety of new phylotypes. Some of them represent novel diversity in known eukaryotic groups, mainly stramenopiles and alveolates. Others do not seem to be related to any molecularly described lineage, and have been proposed to represent novel eukaryotic kingdoms. In order to review the evolutionary importance of this novel high-level eukaryotic diversity critically, and to test the potential technical and analytical pitfalls and limitations of eukaryotic environmental DNA surveys (EES), we analysed 484 environmental SSU rRNA gene sequences, including 81 new sequences from sediments of the small river, the Seymaz (Geneva, Switzerland). RESULTS: Based on a detailed screening of an exhaustive alignment of eukaryotic SSU rRNA gene sequences and the phylogenetic re-analysis of previously published environmental sequences using Bayesian methods, our results suggest that the number of novel higher-level taxa revealed by previously published EES was overestimated. Three main sources of errors are responsible for this situation: (1) the presence of undetected chimeric sequences; (2) the misplacement of several fast-evolving sequences; and (3) the incomplete sampling of described, but yet unsequenced eukaryotes. Additionally, EES give a biased view of the diversity present in a given biotope because of the difficult amplification of SSU rRNA genes in some taxonomic groups. CONCLUSIONS: Environmental DNA surveys undoubtedly contribute to reveal many novel eukaryotic lineages, but there is no clear evidence for a spectacular increase of the diversity at the kingdom level. After re-analysis of previously published data, we found only five candidate lineages of possible novel high-level eukaryotic taxa, two of which comprise several phylotypes that were found independently in different studies. To ascertain their taxonomic status, however, the organisms themselves have now to be identified

Topics: Research Article
Publisher: BioMed Central
Year: 2004
DOI identifier: 10.1186/1741-7007-2-13
OAI identifier: oai:pubmedcentral.nih.gov:428588
Provided by: PubMed Central

Suggested articles

Citations

  1. (1984). A new method for calculating evolutionary substitution rates.
  2. (2000). An Illustrated Guide to the Protozoa 2nd edition. Lawrence, Kansas: Society of Protozoologists;
  3. (2000). AP: Ancyromonadida: a new phylogenetic lineage among the Protozoa closely related to the common ancestor of Metazoans, Fungi, and Choanoflagellates (Opisthokonta). J Mol Evol
  4. (2003). Autochthonus eukaryotic diversity in hydrothermal sediment and experimental microcolonizers at the Mid-Atlantic ridge. Proc Natl Acad Sci USA
  5. (1978). Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool
  6. (2002). Cavalier-Smith T: Rooting the Eukaryote tree by using a derived gene fusion. Science
  7. (2003). Cavalier-Smith T: The root of the Eukaryote tree pinpointed. Curr Biology
  8. (2003). Chao EEY: Molecular phylogeny of centrohelid Heliozoa, a novel lineage of bikont Eukaryotes that arose by ciliary loss.
  9. (2003). Chao EEY: Phylogeny of Choanozoa, Apusozoa, and other Protozoa and early Eukaryote megaevolution.
  10. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution
  11. (1995). DM: Evaluation of nearestneighbor methods for detection of chimeric small-subunit rRNA sequences. Appl Environ Microbiol
  12. (1994). DM: Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms. Appl Environ Microbiol
  13. (1991). Early evolution and the origin of Eukaryotes. Curr Opin Genet Dev
  14. (2002). Freshwater Foraminiferans revealed by analysis of environmental DNA samples.
  15. (2000). Germot A: Phylogeny of Eukaryotes based on ribosomal RNA: long-branch attraction and models of sequences evolution. Mol Biol Evol
  16. (2000). Introduction to the molecular systematics of Foraminifera. Micropaleontology
  17. (1990). JR: The general stochastic model of nucleotide substitution.
  18. (2003). Keeling PJ: Molecular phylogeny and surface morphology of Colpodella edax (Alveolata): insights into the phagotrophic ancestry of Apicomplexans.
  19. (1999). Laanbroek HJ: Detritus-dependent development of the microbial community in an experimental system: qualitative analysis by denaturing gradient gel electrophoresis. Appl Environ Microbiol
  20. (1999). Long-branch attraction and the rDNA model of early eukaryotic evolution. Mol Biol Evol
  21. (2002). López-García P: The molecular ecology of microbial Eukaryotes unveils a hidden world. Trends Microbiol
  22. (1998). NR: Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity.
  23. (2002). NR: Novel kingdom-level eukaryotic diversity in anoxic environments.
  24. (1996). NR: Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences.
  25. (1990). Nucleic acid sequence phylogeny and random outgroups. Cladistics
  26. (2004). Only six kingdoms of life.
  27. (2000). Opinion: Long branch attraction and protist phylogeny. Protist
  28. (1998). phylogenetic analyses using parsimony (* and other methods) Sunderland, Massachussets: Sinauer Associates;
  29. (2003). Phylogeny of lobose amoebae based on actin and small-subunit ribosomal RNA genes. Mol Biol Evol
  30. (2003). Revised small subunit rRNA analysis provides further evidence that Foraminifera are related to Cercozoa. J Mol Evol
  31. (2001). Ronquist F: MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics
  32. (2002). Simdyanov TG: The phylogeny of Colpodellids (Alveolata) using small subunit rRNA gene sequences suggests they are the free-living sister group to Apicomplexans.
  33. (2002). Sogin ML: Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment.
  34. (2002). Sogin ML: Eukaryotic diversity in Spain's River of Fire. Nature
  35. (2002). Sogin ML: Evolutionary history of "earlydiverging" Eukaryotes: the excavate taxon Carpediemonas is a close relative of Giardia. Mol Biol Evol
  36. (1991). Stackebrandt E: Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed-culture of strict barophilic bacteria. Microb Ecol
  37. (1996). Substitution rate calibration of small subunit ribosomal RNA identifies chlorarachniophyte endosymbionts as remnants of green algae.
  38. (2002). The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proc Natl Acad Sci USA
  39. (2003). The deep roots of Eukaryotes. Science
  40. (2002). The phagotrophic origin of Eukaryotes and phylogenetic classification of Protozoa.
  41. (2004). The twilight of Heliozoa and rise of Rhizaria, a new supergroup of amoeboid Eukaryotes. Proc Natl Acad Sci USA
  42. (1996). Tiedje JM: DNA recovery from soils of diverse composition.
  43. (2003). Tiedje JM: The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res
  44. (2002). Toward the monophyly of Haeckel's Radiolaria: 18S rRNA environmental data support the sisterhood of Polycystinea and Acantharea. Mol Biol Evol
  45. (2001). Unexpected diversity of small Eukaryotes in deep-sea Antarctic plankton. Nature
  46. (2002). Unveiling the organisms behind novel eukaryotic ribosomal DNA sequences from the ocean. Appl Environ Microbiol
  47. (2001). Vaulot D: Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity. Nature
  48. (2000). WF: A kingdomlevel phylogeny of Eukaryotes based on combined protein data. Science
  49. (1993). Woese CR: The ribosomal database project. Nucleic Acids Res

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.