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Archaeal amoA gene diversity points to distinct biogeography of ammonia-oxidizing Crenarchaeota in the ocean
Article first published online: 12 JUN 2012
© 2012 Society for Applied Microbiology and Blackwell Publishing Ltd
Special Issue: Marine Microbial Ecophysiology and Metagenomics
Volume 15, Issue 5, pages 1647–1658, May 2013
How to Cite
Sintes, E., Bergauer, K., De Corte, D., Yokokawa, T. and Herndl, G. J. (2013), Archaeal amoA gene diversity points to distinct biogeography of ammonia-oxidizing Crenarchaeota in the ocean. Environmental Microbiology, 15: 1647–1658. doi: 10.1111/j.1462-2920.2012.02801.x
- Issue published online: 18 APR 2013
- Article first published online: 12 JUN 2012
- Received 13 October, 2011; revised 11 May, 2012; accepted 15 May, 2012.
Fig. S1. Location of the two sampling areas: (A) the tropical Atlantic and (B) stations occupied in the coastal Arctic off Ny Ålesund (Kongsfjorden, Spitsbergen, Norway).
Fig. S2. Depth profile of prokaryotic abundance (PA) and heterotrophic activity (PHA, measured via leucine incorporation) obtained in (A) the coastal Arctic and (B) the tropical Atlantic. (C) Dark dissolved inorganic carbon fixation (DIC) in the water column of the coastal Arctic and tropical Atlantic.
Fig. S3. Proportion of HAC- or LAC- clones added to a DNA mixture as compared with the proportion of HAC or LAC-amoA measured with the corresponding primer in the mixture.
Fig. S4. Distribution of archaeal amoA copy numbers along the Romanche Fracture Zone of the tropical Atlantic (see Fig. S1 for sample location and stations) obtained with (A) the ‘high-ammonia concentration’ primer set, (B) the ‘low-ammonia concentration’ primer set and (C) the ratio between archaeal amoA copy numbers determined with the ‘high’ versus ‘low ammonia concentration’ primer sets (1:1 line is indicated at around 100 m depth).
Fig. S5. Distribution of (A) abundance of Marine Crenarcheaota Group I (MCGI) genes along a transect through the Romanche Fracture Zone in the tropical Atlantic and the ratio archaeal amoA to MCGI obtained with (B) the ‘high ammonia concentration’ and (C) the ‘low ammonia concentration’ primer set.
Fig. S6. Depth profile of the ratio between total archaeal amoA (sum of HAC- and LAC-amoA) and 16S rRNA of MCGI for the Arctic (open circles) and the Atlantic (full circles).
Fig. S7. Rarefaction curves for the archaeal amoA gene obtained with the ‘high ammonia concentration’ (HAC) and the ‘low ammonia concentration’ (LAC) primer sets at 100, 250, 1750 and 7000 m depth in the tropical Atlantic.
Fig. S8. Scatter plot for the first two principal components (PCA) obtained for the phylogenetic composition with the ‘high-ammonia concentration’ (HAC) and ‘low-ammonia concentration’ (LAC) primer set at different depth layers in the Romanche Fracture Zone of the tropical Atlantic (UniFrac analysis). Numbers next to dots indicate depth in m of the sample.
Fig. S9. Ammonium (A, C) and nitrite (B, D) concentration throughout the water column in the Arctic (A, B) and Atlantic (C, D).
Table S1. Median and range (max–min) of the percentage of recovery of archaeal amoA originating from clones belonging to the ‘high ammonia concentration’ (HAC) and the ‘low ammonia concentration’ (LAC) cluster as measured with the two primer sets used in this study.
Table S2. Depth-averaged concentrations (in μM) of ammonium (NH4+), nitrite (NO2-) and nitrate (NO3-) and the abundance of crenarchaeal genes (HAC amoA, LAC amoA, total amoA and MCGI), and the corresponding ratios obtained in the coastal Arctic.
Table S3. Depth-averaged concentrations (in μM) of ammonium (NH4+), nitrite (NO2-), nitrate (NO3-) and oxygen (O2) and the abundance of crenarchaeal genes (HAC amoA, LAC amoA, total amoA and MCGI), and the corresponding ratios obtained in the tropical Atlantic.
Table S4. Clones of the NCBI database (as for 30 March 2010) containing the exact sequence from the reverse primer of the LAC-amoA or the HAC-amoA and their origin.
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