Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms

BMC Biology
Dominik ForsterEric Bapteste

Abstract

High-throughput sequencing technologies are lifting major limitations to molecular-based ecological studies of eukaryotic microbial diversity, but analyses of the resulting millions of short sequences remain a major bottleneck for these approaches. Here, we introduce the analytical and statistical framework of sequence similarity networks, increasingly used in evolutionary studies and graph theory, into the field of ecology to analyze novel pyrosequenced V4 small subunit rDNA (SSU-rDNA) sequence data sets in the context of previous studies, including SSU-rDNA Sanger sequence data from cultured ciliates and from previous environmental diversity inventories. Our broadly applicable protocol quantified the progress in the description of genetic diversity of ciliates by environmental SSU-rDNA surveys, detected a fundamental historical bias in the tendency to recover already known groups in these surveys, and revealed substantial amounts of hidden microbial diversity. Moreover, network measures demonstrated that ciliates are not globally dispersed, but are structured by habitat and geographical location at intermediate geographical scale, as observed for bacteria, plants, and animals. Currently available 'universal' primers used for ...Continue Reading

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Citations

Jan 17, 2016·European Journal of Protistology·Alessia RossiGiulio Petroni
Apr 21, 2016·European Journal of Protistology·Thomas WeisseDavid J S Montagnes
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Jul 31, 2019·Environmental Microbiology·Dominik ForsterThorsten Stoeck
Jan 4, 2019·History and Philosophy of the Life Sciences·Fridolin GrossRobert Meunier
Apr 22, 2020·BMC Bioinformatics·Thomas HütterNikolaus Augsten
Apr 14, 2018·Microbiology Spectrum·Chloé VigliottiEduardo Corel

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Software Mentioned

BLASTn
Igraph library scripts
Figshare
EGN
Gephi
BLAST
BioMarKs
DNA
cDNA
R

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