title: It's all relative: ranking the diversity of aquatic bacterial communities.
abstract: 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.
authors.affiliation: Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA.
authors.forename: Allison K
authors.initials: AK
authors.lastname: Shaw
authors.forename: Aaron L
authors.initials: AL
authors.lastname: Halpern
authors.forename: Karen
authors.initials: K
authors.lastname: Beeson
authors.forename: Bao
authors.initials: B
authors.lastname: Tran
authors.forename: J Craig
authors.initials: JC
authors.lastname: Venter
authors.forename: Jennifer B H
authors.initials: JB
authors.lastname: Martiny
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics*; D044822:Biodiversity; D004269:DNA, Bacterial / Q000235:genetics; D004784:Environmental Monitoring; D015723:Gene Library; D020459:Genes, rRNA; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D018401:Sample Size; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013223:Statistics as Topic / Q000379:methods*; D014871:Water Microbiology
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S