New insights into the diversity of marine picoeukaryotes

Over the last decade, culture-independent surveys of marine picoeukaryotic diversity based on 18S ribosomal DNA clone libraries have unveiled numerous sequences of novel high-rank taxa. This newfound diversity has significantly altered our understanding of marine microbial food webs and the evolutio...

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Bibliographic Details
Published in:PloS one 2009-09, Vol.4 (9), p.e7143-e7143
Main Authors: Not, Fabrice, del Campo, Javier, Balagué, Vanessa, de Vargas, Colomban, Massana, Ramon
Format: Article
Language:English
Subjects:
Animals
Biodiversity
Biological products
Cell culture
Cell size
Ciliates
Ciliophora - physiology
Cloning
Cloning, Molecular
Computational Biology
Copy number
Datasets
Deoxyribonucleic acid
DNA
DNA, Ribosomal - analysis
DNA, Ribosomal - genetics
Ecology/Marine and Freshwater Ecology
Environment
Environmental DNA
Environmental Sciences
Eukaryota
Eukaryotes
Evolution
Evolutionary Biology/Evolutionary Ecology
Expeditions
Food chains
Food webs
Gene sequencing
Genes
Genetic Variation
Life Sciences
Marine and Aquatic Sciences
Marine and Aquatic Sciences/Biological Oceanography
Marine and Aquatic Sciences/Ecology
Marine and Aquatic Sciences/Genetics, Genomics, and Barcoding
Marine and Aquatic Sciences/Microbiology
Marine Biology - methods
Marine ecology
Metabolism
Microbiology/Environmental Microbiology
Microbiology/Microbial Evolution and Genomics
Microorganisms
Molecular biology
Multiculturalism
Nucleotide sequence
Oxytricha
Phylogenetics
Phylogeny
Polls & surveys
Polymerase Chain Reaction
Prasinophyceae
Rankings
RNA
RNA, Ribosomal, 18S - genetics
rRNA 18S
Seawater
Sequence Analysis, DNA
Studies
Stylonychia
Surveys
Taxa
Taxonomy
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Summary:Over the last decade, culture-independent surveys of marine picoeukaryotic diversity based on 18S ribosomal DNA clone libraries have unveiled numerous sequences of novel high-rank taxa. This newfound diversity has significantly altered our understanding of marine microbial food webs and the evolution of eukaryotes. However, the current picture of marine eukaryotic biodiversity may be significantly skewed by PCR amplification biases, occurrence of rDNA genes in multiple copies within a single cell, and the capacity of DNA to persist as extracellular material. In this study we performed an analysis of the metagenomic dataset from the Global Ocean Survey (GOS) expedition, seeking eukaryotic ribosomal signatures. This PCR-free approach revealed similar phylogenetic patterns to clone library surveys, suggesting that PCR steps do not impose major biases in the exploration of environmental DNA. The different cell size fractions within the GOS dataset, however, displayed a distinct picture. High protistan diversity in the
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0007143