RT Journal Article
SR Electronic
T1 Probing the rare biosphere of the North-West Mediterranean Sea
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 020818
DO 10.1101/020818
A1 Bibiana G. Crespo
A1 Philip J. Wallhead
A1 Ramiro Logares
A1 Carlos Pedrós-Alió
YR 2015
UL http://biorxiv.org/content/early/2015/08/30/020818.abstract
AB The relatively recent development of high-throughput sequencing (HTS) techniques has revealed a wealth of novel sequences found in very low abundance: the rare biosphere. We performed a deep (1 million sequences per sample) pyrosequencing analysis of two marine bacterial samples and isolated a culture collection from one of them. Species data were derived from the sequencing analysis (97% similarity criterion) and various parametric distributions were fitted to the observed counts. Using the best-fitting Sichel distribution we estimate a total richness of 1 568–1 669 (95% CI) and 5027–5196 for surface and deep water samples respectively, implying that 84–89% of the total richness was sequenced. We also predict that a quadrupling of the present sequencing effort should suffice to observe 90% the total richness in both samples. Comparing with isolate sequences we found that isolation retrieved mainly extremely rare taxa which were not obtained by HTS despite the high sequencing effort. Culturing therefore remains a useful tool for mapping marine bacterial diversity, in addition to its other uses for studying the ecology of the rare biosphere.