Abstract
The exploration of the microbial world has been an exciting series of unanticipated discoveries despite being largely uninformed by rational estimates of the magnitude of task confronting us. However, in the long term, more structured surveys can be achieved by estimating the diversity of microbial communities and the effort required to describe them. The rates of recovery of new microbial taxa in very large samples suggest that many more taxa remain to be discovered in soils and the oceans. We apply a robust statistical method to large gene sequence libraries from these environments to estimate both diversity and the sequencing effort required to obtain a given fraction of that diversity. In the upper ocean, we predict some 1400 phylotypes, and a mere fivefold increase in shotgun reads could yield 90% of the metagenome, that is, all genes from all taxa. However, at deep ocean, hydrothermal vents and diversities in soils can be up to two orders of magnitude larger, and hundreds of times the current number of samples will be required just to obtain 90% of the taxonomic diversity based on 3% difference in 16S rDNA. Obtaining 90% of the metagenome will require tens of thousands of times the current sequencing effort. Although the definitive sequencing of hyperdiverse environments is not yet possible, we can, using taxa-abundance distributions, begin to plan and develop the required methods and strategies. This would initiate a new phase in the exploration of the microbial world.
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Acknowledgements
We thank Aaron Halpern, Alberto Riva, Doug Rusch and Eric W Triplett for providing the soil sequence and GOS cluster data sets. We also thank Sue Huse and Mitchell Sogin for providing a copy of the quickdist program, and Rampal S Etienne for an algorithm used in fitting the log-normal distribution. We thank Mark Bailey, Stephen Giovannoni, and two anonymous reviewers for helpful comments on an earlier version of this article. Chris Quince is supported by a Lord Kelvin Adam Smith Research Fellowship from the University of Glasgow, and Bill Sloan is supported by an Engineering and Physical Sciences Advanced Research Fellowship.
The Bayesian diversity estimation software used in this study is available from the corresponding author upon request or can be downloaded from the website: http://people.civil.gla.ac.uk/~quince/Software/BDES.html.
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Quince, C., Curtis, T. & Sloan, W. The rational exploration of microbial diversity. ISME J 2, 997–1006 (2008). https://doi.org/10.1038/ismej.2008.69
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DOI: https://doi.org/10.1038/ismej.2008.69
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