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

BMC Biology

Research Article

Sarah Romac¹  Stéphane Audic¹  Dominik Forster²  Micah Dunthorn²  Thorsten Stoeck²  Lucie Bittner³  Eric Bapteste⁴  Philippe Lopez⁴  Slim Karkar⁴ 

[1] CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, F-29680, Roscoff, France;Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, F-29680, Roscoff, France;Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger-Straße 14, D-67633, Kaiserslautern, Germany;Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger-Straße 14, D-67633, Kaiserslautern, Germany;CNRS, FR3631, Institut de Biologie Paris-Seine, F-75005, Paris, France;Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), F-75005, Paris, France;Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), F-75005, Paris, France;CNRS, UMR7138, Institut de Biologie Paris-Seine, F-75005, Paris, France;

关键词: Biogeography;    Microbial diversity;    High-throughput sequencing;    Environmental rDNA sequencing;    Protist;   

DOI  :  10.1186/s12915-015-0125-5

 received in 2014-08-12, accepted in 2015-01-28,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundHigh-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.ResultsOur 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.ConclusionsCurrently available ‘universal’ primers used for local in-depth sequencing surveys provide little hope to exhaust the significantly higher ciliate (and most likely microbial) diversity than previously thought. Network analyses such as presented in this study offer a promising way to guide the design of novel primers and to further explore this vast and structured microbial diversity.

【 授权许可】

Unknown   
© Forster et al.; licensee BioMed Central. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

【 图 表 】

Fig. 1