title: Probing the Rare Biosphere of the North-West Mediterranean Sea: An Experiment with High Sequencing Effort.
abstract: High-throughput sequencing (HTS) techniques have suggested the existence of a wealth of species with very low relative abundance: the rare biosphere. We attempted to exhaustively map this rare biosphere in two water samples by performing an exceptionally deep pyrosequencing analysis (~500,000 final reads per sample). Species data were derived by a 97% identity criterion and various parametric distributions were fitted to the observed counts. Using the best-fitting Sichel distribution we estimate a total species richness of 1,568-1,669 (95% Credible Interval) and 5,027-5,196 for surface and deep water samples respectively, implying that 84-89% of the total richness in those two samples was sequenced, and we predict that a quadrupling of the present sequencing effort would suffice to observe 90% of the total richness in both samples. Comparing the HTS results with a culturing approach we found that most of the cultured taxa were not obtained by HTS, despite the high sequencing effort. Culturing therefore remains a useful tool for uncovering marine bacterial diversity, in addition to its other uses for studying the ecology of marine bacteria.
authors.affiliation: Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (ICM-CSIC), Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain.
authors.forename: Bibiana G
authors.initials: BG
authors.lastname: Crespo
authors.affiliation: Norwegian Institute for Water Research (NIVA), Thormøhlens gate 53D, N-5006 Bergen, Norway.
authors.forename: Philip J
authors.initials: PJ
authors.lastname: Wallhead
authors.affiliation: Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (ICM-CSIC), Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain.
authors.forename: Ramiro
authors.initials: R
authors.lastname: Logares
authors.affiliation: Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (ICM-CSIC), Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain.
authors.forename: Carlos
authors.initials: C
authors.lastname: Pedrós-Alió
mesh_terms: D001419:Bacteria / Q000302:isolation & purification; D001483:Base Sequence; D044822:Biodiversity; D030541:Databases, Genetic; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008522:Mediterranean Sea; D013045:Species Specificity