Microbial Ecology

, Volume 71, Issue 1, pp 29–43 | Cite as

Expansion of Cultured Bacterial Diversity by Large-Scale Dilution-to-Extinction Culturing from a Single Seawater Sample

Microbiology of Aquatic Systems

Abstract

High-throughput cultivation (HTC) based on a dilution-to-extinction method has been applied broadly to the cultivation of marine bacterial groups, which has often led to the repeated isolation of abundant lineages such as SAR11 and oligotrophic marine gammaproteobacteria (OMG). In this study, to expand the phylogenetic diversity of HTC isolates, we performed a large-scale HTC with a single surface seawater sample collected from the East Sea, the Western Pacific Ocean. Phylogenetic analyses of the 16S rRNA genes from 847 putative pure cultures demonstrated that some isolates were affiliated with not-yet-cultured clades, including the OPB35 and Puniceicoccaceae marine group of Verrucomicrobia and PS1 of Alphaproteobacteria. In addition, numerous strains were obtained from abundant clades, such as SAR11, marine Roseobacter clade, OMG (e.g., SAR92 and OM60), OM43, and SAR116, thereby increasing the size of available culture resources for representative marine bacterial groups. Comparison between the composition of HTC isolates and the bacterial community structure of the seawater sample used for HTC showed that diverse marine bacterial groups exhibited various growth capabilities under our HTC conditions. The growth response of many bacterial groups, however, was clearly different from that observed with conventional plating methods, as exemplified by numerous isolates of the SAR11 clade and Verrucomicrobia. This study showed that a large number of novel bacterial strains could be obtained by an extensive HTC from even a small number of samples.

Keywords

Dilution-to-extinction High-throughput cultivation Pyrosequencing Marine Roseobacter clade SAR11 Verrucomicrobia 

Notes

Acknowledgments

This research was supported by a grant from the Marine Biotechnology Program (PJT200620, Genome Analysis of Marine Organisms and Development of Functional Applications) funded by the Ministry of Oceans and Fisheries, Korea and also by Mid-Career Research Program through National Research Foundation funded by the Ministry of Science, ICT and Future Planning (NRF-2013R1A2A2A01068004). The authors declare that they have no conflicts of interest.

Supplementary material

248_2015_695_MOESM1_ESM.pdf (365 kb)
Fig. S1Neighbor-joining phylogenetic tree of the HTC isolates based on 16S rRNA gene sequences. This tree is a combined and extended version of the two trees presented in Fig. 2 and includes strain ID of all HTC isolates (PDF 364 kb)
248_2015_695_MOESM2_ESM.xlsx (78 kb)
Table S1Detailed taxonomic information on the HTC isolates (spreadsheet 1) and representatives of pyrosequencing reads from the pooled HTC cultures (spreadsheet 2) (XLSX 78 kb)
248_2015_695_MOESM3_ESM.pdf (75 kb)
Table S2The number of genus-level taxa found in the three sets of growth-positive HTC wells (PDF 74 kb)

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Department of Biological SciencesInha UniversityIncheonRepublic of Korea

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