Diel gene expression profiles of a phosphorus limited mountain lake using metatranscriptomics
Article first published online: 26 NOV 2012
© 2012 Society for Applied Microbiology and Blackwell Publishing Ltd
Volume 15, Issue 4, pages 1190–1203, April 2013
How to Cite
Vila-Costa, M., Sharma, S., Moran, M. A. and Casamayor, E. O. (2013), Diel gene expression profiles of a phosphorus limited mountain lake using metatranscriptomics. Environmental Microbiology, 15: 1190–1203. doi: 10.1111/1462-2920.12033
- Issue published online: 4 APR 2013
- Article first published online: 26 NOV 2012
- Accepted manuscript online: 2 NOV 2012 03:34AM EST
- Manuscript Accepted: 25 OCT 2012
- Manuscript Revised: 24 SEP 2012
- Manuscript Received: 24 APR 2012
- 7th Framework Programme (FP7) Marie Curie Fellowship. Grant Number: GenS FP7-MC-IOF-219811
- Ministry of Spanish Office of Science and Innovation (MICINN)
- Gordon and Betty Moore Foundation
- MICINN. Grant Numbers: PIRENA CGL2009-13318, DARKNESS CGL2012-32747
Fig. S1. Cluster analysis based on Bray-Curtis distance matrices of COG functional categories from day and night samples from Lake Llebreta (LLB, night: N1, D1, N2, day: D2), Pacific Ocean HOT station (from Poretsky et al., 2010) and Sapelo Island coastal seawater (SAP, from Poretsky et al., 2009a).
Fig. S2. Relative abundance of transcripts for phosphorus-related functional gene categories expressed during the night and day. Gene key: pst operon, high-affinity Pi transport; pitA, low-affinity Pi transport; AlkP, alkaline phosphatases (phoX, phoA, phoD); phn operon, phosphonate uptake and utilization; ugp operon, glycerol-3-phosphate transport; phoB and phoR, phosphate regulon transcriptional regulatory protein; ppx, polyphosphate utilization; ppk, polyphosphate kinase. Phylum key: BCF, Bacteroidetes; BETA, Betaproteobacteria; ACTINO, Actinobacteria; ALPHA, Alphaproteobacteria. See Table S2 for more details.
Fig. S3. Rarefaction curves for COG functional categories for day and night samples of Lake Llebreta, Pacific Ocean HOT, and Sapelo Island coastal seawater. Inset: Lake Llebreta samples replotted at a different scale.
Fig. S4. Relative abundance of COG functional categories for Lake Llebreta, Pacific ocean HOT, and Sapelo Island coastal seawater metatranscriptomes at night (N) and during the day (D). Each axis of the radial graph represents a COG category.
Table S1. Pair-wise comparisons of COGs significantly enriched in each metatranscriptome (P < 0.05, Xipe comparison).
Table S2. Set of diagnostic biogeochemical genes in the phosphorus (P) cycle from marine environments (extracted from Gifford et al., 2011) and orthologues of those genes in the three most active bacterial phyla in the metatranscriptomic libraries.
Table S3. COG categories enriched in freshwater (Lake Llebreta) and marine (HOT and SAPELO) transcript libraries.
Table S4. Environmental data for freshwater Lake Llebreta and marine sites at HOT (Hawaii Ocean Time-series) and Sapelo Island (Sapelo).
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