Impacts of bioturbation on temporal variation in bacterial and archaeal nitrogen-cycling gene abundance in coastal sediments
Version of Record online: 19 NOV 2013
© 2013 The Authors. Environmental Microbiology Reports published by Society for Applied Microbiology and John Wiley & Sons Ltd.
This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Environmental Microbiology Reports
Volume 6, Issue 1, pages 113–121, February 2014
How to Cite
Laverock, B., Tait, K., Gilbert, J. A., Osborn, A. M. and Widdicombe, S. (2014), Impacts of bioturbation on temporal variation in bacterial and archaeal nitrogen-cycling gene abundance in coastal sediments. Environmental Microbiology Reports, 6: 113–121. doi: 10.1111/1758-2229.12115
- Issue online: 20 JAN 2014
- Version of Record online: 19 NOV 2013
- Accepted manuscript online: 22 OCT 2013 10:07PM EST
- Manuscript Accepted: 11 OCT 2013
- Manuscript Received: 1 AUG 2013
- NERC Algorithm PhD Studentship. Grant Number: NE/F008864/1
- NERC-funded programme Oceans 2025
Fig. S1. Variation in monthly pelagic nutrient concentrations in Jennycliff Bay (5.3497 N, 04.1331 W) in the Western English Channel. (A) nitrite, (B) nitrate, (C) ammonium, (D) silicate, (E) phosphate. Inset legends show water depth in metres. Data are from the PML Benthic Survey Data Inventory (Woodward et al., 2013). (F) Variation in monthly temperature (closed circles; black line) and salinity (open diamonds; grey line) for the L4 site (50.225 N, 04.1944 W), in the Western English Channel, with lines connecting the average value for each month. Data are from the Western Channel Observatory Data Inventory (Fishwick, 2013).
Table S1. Sediment sampling strategy.
Table S2. Primer pairs and reaction conditions used for quantitative polymerase chain reaction (q-PCR) assays. q-PCR amplification and detection for all assays was carried out using an ABI 7000 sequence detection system (Applied Biosystems, Carlsbad CA, USA) with an initial denaturation for 5 min at 95°C, followed by 40 cycles of 95°C for 15 s and annealing temperatures as listed below for 1 min. All reactions were carried out in 25 μl final volume; final primer concentrations are shown for this reaction volume. For each reaction, the standard curve was calculated using the ABI Prism 7000 sequence detection software. From the standard curve, the slope (m), y intercept and coefficient of determination (r2) recorded and used to calculate the efficiency of the amplification (E) using the equation E = (101/m − 1) × 100. Values for calculating the efficiency of each reaction are given, as well as the threshold cycle value (CT), which was determined using automatic analysis settings.
Table S3. Seasonal variation in the average gene abundance (gene copies g−1 wet sediment) in burrow (B) and surface (S) sediments, and comparison to abundances reported in the literature for similar marine environments and using similar gene primers. Full data are available from the Dryad Digital Repository (doi: to be confirmed). Absolute gene abundances were calculated from standard curves using the r2, y intercept and efficiency values given in Table S2.
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