Present address: Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
It's all relative: ranking the diversity of aquatic bacterial communities
Article first published online: 14 JUL 2008
© 2008 The Authors. Journal compilation © 2008 Society for Applied Microbiology and Blackwell Publishing Ltd
Volume 10, Issue 9, pages 2200–2210, September 2008
How to Cite
Shaw, A. K., Halpern, A. L., Beeson, K., Tran, B., Venter, J. C. and Martiny, J. B. H. (2008), It's all relative: ranking the diversity of aquatic bacterial communities. Environmental Microbiology, 10: 2200–2210. doi: 10.1111/j.1462-2920.2008.01626.x
- Issue published online: 12 AUG 2008
- Article first published online: 14 JUL 2008
- Received 3 October, 2007; revised 11 February 2008; accepted 21 February, 2008.
The study of microbial diversity patterns is hampered by the enormous diversity of microbial communities and the lack of resources to sample them exhaustively. For many questions about richness and evenness, however, one only needs to know the relative order of diversity among samples rather than total diversity. We used 16S libraries from the Global Ocean Survey to investigate the ability of 10 diversity statistics (including rarefaction, non-parametric, parametric, curve extrapolation and diversity indices) to assess the relative diversity of six aquatic bacterial communities. Overall, we found that the statistics yielded remarkably similar rankings of the samples for a given sequence similarity cut-off. This correspondence, despite the different underlying assumptions of the statistics, suggests that diversity statistics are a useful tool for ranking samples of microbial diversity. In addition, sequence similarity cut-off influenced the diversity ranking of the samples, demonstrating that diversity statistics can also be used to detect differences in phylogenetic structure among microbial communities. Finally, a subsampling analysis suggests that further sequencing from these particular clone libraries would not have substantially changed the richness rankings of the samples.