Present address: Dept. of Biology/Aquatic Ecology, Lund University, Sölvegatan 37, 22362 Lund, Sweden.
Which sequencing depth is sufficient to describe patterns in bacterial α- and β-diversity?
Article first published online: 23 APR 2012
© 2012 Society for Applied Microbiology and Blackwell Publishing Ltd
Environmental Microbiology Reports
Volume 4, Issue 3, pages 367–372, June 2012
How to Cite
Lundin, D., Severin, I., Logue, J. B., Östman, Ö., Andersson, A. F. and Lindström, E. S. (2012), Which sequencing depth is sufficient to describe patterns in bacterial α- and β-diversity?. Environmental Microbiology Reports, 4: 367–372. doi: 10.1111/j.1758-2229.2012.00345.x
- Issue published online: 10 MAY 2012
- Article first published online: 23 APR 2012
- Received 19 January, 2012; accepted 25 March, 2012.
Supplementary experimental procedures.
Fig. S1. Analysis of α-diversity in relation to sequencing depth. (A, D, G) Shannon index; (B, E, H) Chao1 richness; (C, F, I) Pielou's evenness; (A, B, C) 15 lakes (‘Water07’); (D, E, F) 10 sediment samples (‘Sediments’) and (G, H, I) 5 lakes and 1 stream (‘Water10’).
Fig. S2. Analysis of β-diversity. (A) Bray-Curtis values of 15 lakes in relation to sequencing depth (‘Water07’); (B) DCA plot of the Water07 samples using 20 000 sequences per sample; (C) Bray-Curtis values of 10 sediment samples in relation to sequencing depth (‘Sediments’); (D) DCA plot of the sediment samples using 15 000 sequences per sample; (E) Bray-Curtis values of five lakes and 1 stream in relation to sequencing depth (‘Water10’); (F) DCA plot of the Water10 samples using 15 000 sequences per sample. Abbreviations in DCA plots are the same as in Table S1.
Fig. S3. Design of the study.
Table S1. Physicochemical and biological characteristics of the study systems.
Table S2. The loss of sequences due to the perseus Chimera check step. # sequences denotes the number of sequences in each sample before chimera check. Within each data set and sequencing depth each sample was resampled to the minimum number of sequences according to the table.
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