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Culturing captures members of the soil rare biosphere
Article first published online: 13 JUL 2012
© 2012 Society for Applied Microbiology and Blackwell Publishing Ltd
Special Issue: Microbial Communities - Structure, Behaviour, Evolution
Volume 14, Issue 9, pages 2247–2252, September 2012
How to Cite
Shade, A., Hogan, C. S., Klimowicz, A. K., Linske, M., McManus, P. S. and Handelsman, J. (2012), Culturing captures members of the soil rare biosphere. Environmental Microbiology, 14: 2247–2252. doi: 10.1111/j.1462-2920.2012.02817.x
- Issue published online: 4 SEP 2012
- Article first published online: 13 JUL 2012
- Received 23 April, 2012; revised 26 May, 2012; accepted 31 May, 2012.
Figure S1. Rank abundance distribution of OTUs from singleton-omitted, rarefied dataset from soil.
Figure S2. Heatmap visualizations of the 26 most abundant OTUs within the (A) culture-based and (B) culture-independent communities, and organized within each map by similar response patterns. Columns are communities, and rows are OTUs. Please note differences in scale of relative abundances for A and B. Variovorax (OTU 550) was the only abundant OTU shared across both cultured-based and culture-independent communities. OTUs marked with an asterisk could not be resolved to the Order level.
Figure S3. Frequency of OTUs across Bacteria phyla and Proteobacteria class for (A) culture-independent and (B) culture-based communities.
Figure S4. Comparison of taxa detected in rhizosphere isolation medium (RIM) and 0.1× tryptic soy agar (TSA) at the (A) phylum level and (B) Proteobacteria class. (C) Venn analysis of OTUs detected on each type of medium. OTU assignments were made with Ribosomal Database Project assignment of full-length 16S RNA gene sequences from clone libraries of metagenomic DNA extracted from a pool of isolates for each culturing media. RIM was ultimately selected for cultivation because it inhibited the growth of filamentous Bacillus mycoides, which often obscured quantification of smaller, non-filamentous colonies on TSA.
Table S1. Summary of sequencing effort and number of OTUs detected in culture-based, culture-independent, and the total dataset. Note that the total is not necessarily the sum of the culture-based and culture-independent (e.g. some OTUs were shared across both communities).
Appendix S1. Supplemental methods.
|EMI_2817_sm_SuppInfor.pdf||1436K||Supporting info item|
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