title: Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  Currently 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.
authors.affiliation: Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger-Straße 14, Kaiserslautern, D-67633, Germany. dforster@rhrk.uni-kl.de.
authors.forename: Dominik
authors.initials: D
authors.lastname: Forster
authors.affiliation: Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger-Straße 14, Kaiserslautern, D-67633, Germany. lucie.bittner@gmail.com.|CNRS, FR3631, Institut de Biologie Paris-Seine, Paris, F-75005, France. lucie.bittner@gmail.com.|Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), Paris, F-75005, France. lucie.bittner@gmail.com.
authors.forename: Lucie
authors.initials: L
authors.lastname: Bittner
authors.affiliation: Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), Paris, F-75005, France. karkar.slim@gmail.com.|CNRS, UMR7138, Institut de Biologie Paris-Seine, Paris, F-75005, France. karkar.slim@gmail.com.
authors.forename: Slim
authors.initials: S
authors.lastname: Karkar
authors.affiliation: Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger-Straße 14, Kaiserslautern, D-67633, Germany. dunthorn@rhrk.uni-kl.de.
authors.forename: Micah
authors.initials: M
authors.lastname: Dunthorn
authors.affiliation: CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, F-29680, France. romac@sb-roscoff.fr.|Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, F-29680, France. romac@sb-roscoff.fr.
authors.forename: Sarah
authors.initials: S
authors.lastname: Romac
authors.affiliation: CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, F-29680, France. stephane.audic@sb-roscoff.fr.|Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, F-29680, France. stephane.audic@sb-roscoff.fr.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Audic
authors.affiliation: Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), Paris, F-75005, France. philippe.lopez@upmc.fr.|CNRS, UMR7138, Institut de Biologie Paris-Seine, Paris, F-75005, France. philippe.lopez@upmc.fr.
authors.forename: Philippe
authors.initials: P
authors.lastname: Lopez
authors.affiliation: Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger-Straße 14, Kaiserslautern, D-67633, Germany. stoeck@rhrk.uni-kl.de.
authors.forename: Thorsten
authors.initials: T
authors.lastname: Stoeck
authors.affiliation: Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), Paris, F-75005, France. epbapteste@gmail.com.|CNRS, UMR7138, Institut de Biologie Paris-Seine, Paris, F-75005, France. epbapteste@gmail.com.
authors.forename: Eric
authors.initials: E
authors.lastname: Bapteste
mesh_terms: D025041:Animal Migration / Q000502:physiology*; D000818:Animals; D001483:Base Sequence; D016798:Ciliophora / Q000235:genetics* / Q000502:physiology; D018076:DNA, Complementary / Q000235:genetics; D030541:Databases, Genetic; D017753:Ecosystem; D053263:Gene Regulatory Networks; D014644:Genetic Variation; D005843:Geography; D008954:Models, Biological; D012689:Sequence Homology, Nucleic Acid
chemical_list: D018076:DNA, Complementary