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An assessment of actinobacterial diversity in the marine environment

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Abstract

The 16S rRNA gene sequence diversity within the Phylum Actinobacteria was assessed from four sources: PCR-generated V6 sequence tags derived from seawater samples, metagenomic data from the Global Ocean Sampling (GOS) expedition, marine-derived sequences maintained in the Ribosomal Database Project (RDP), and select cultured strains for which sequence data is not yet available in the RDP. This meta-analysis revealed remarkable levels of phylogenetic diversity and confirms the existence of major, deeply rooted, and as of yet uncharacterized lineages within the phylum. A dramatic incongruence among cultured strains and those detected using culture-independent techniques was also revealed. Redundancy among the actinobacteria detected using culture-independent techniques suggests that greater sequence coverage or improved DNA extraction efficiencies may be required to detect the rare phylotypes that can be readily cultured from marine samples. Conversely, new strategies need to be developed for the cultivation of frequently observed but yet to be cultured marine actinobacteria.

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Acknowledgements

We thank Saul A. Kravitz for his invaluable help in accessing sequence assemblies from the Global Ocean Sampling dataset and Douglas H. Bartlett for generously providing computational resources. P.R.J. acknowledges funding from the National Institutes of Health, International Cooperative Biodiversity Groups program (grant U01-TW007401-01) and NOAA Grant #NAO40AR4170038, California Sea Grant College Program Project #R/MP-98, through NOAA’S National Sea Grant College Program, U.S. Dept. of Commerce. The statements, findings, conclusions and recommendations are those of the author(s) and do necessarily reflect the views of California Sea Grant, NOAA or the U.S. Dept. of Commerce.

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Authors and Affiliations

  1. Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA

    Paul R. Jensen

  2. Environmental Microbiology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, Australia

    Federico M. Lauro

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  1. Paul R. Jensen
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  2. Federico M. Lauro
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Correspondence to Paul R. Jensen.

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Jensen, P.R., Lauro, F.M. An assessment of actinobacterial diversity in the marine environment. Antonie van Leeuwenhoek 94, 51–62 (2008). https://doi.org/10.1007/s10482-008-9239-x

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  • DOI: https://doi.org/10.1007/s10482-008-9239-x

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