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Response of an Arctic Sediment Nitrogen Cycling Community to Increased CO2

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Abstract

Ocean acidification influences sediment/water nitrogen fluxes, possibly by impacting on the microbial process of ammonia oxidation. To investigate this further, undisturbed sediment cores collected from Ny Alesund harbour (Svalbard) were incubated with seawater adjusted to CO2 concentrations of 380, 540, 760, 1,120 and 3,000 µatm. DNA and RNA were extracted from the sediment surface after 14 days' exposure and the abundance of bacterial and archaeal ammonia oxidising (amoA) genes and transcripts quantified using quantitative polymerase chain reaction. While there was no change to the abundance of bacterial amoA genes, an increase to 760 µatm pCO2 reduced the abundance of bacterial amoA transcripts by 65 %, and this was accompanied by a shift in the composition of the active community. In contrast, archaeal amoA gene and transcript abundance both doubled at 3,000 µatm, with an increase in species richness also apparent. This suggests that ammonia oxidising bacteria and archaea in marine sediments have different pH optima, and the impact of elevated CO2 on N cycling may be dependent on the relative abundances of these two major microbial groups. Further evidence of a shift in the balance of key N cycling groups was also evident: the abundance of nirS-type denitrifier transcripts decreased alongside bacterial amoA transcripts, indicating that NO3 − produced by bacterial nitrification fuelled denitrification. An increase in the abundance of Planctomycete-specific 16S rRNA, the vast majority of which grouped with known anammox bacteria, was also apparent at 3,000 µatm pCO2. This could indicate a possible shift from coupled nitrification–denitrification to anammox activity at elevated CO2.

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Acknowledgments

This work was funded by the European Project on Ocean Acidification (EPOCA), funded by the European Community's Seventh Framework Programme (FP7/2007-2013) under grant agreement no. 211384, and was also supported by the NERC funded programme Oceans 2025 (Theme 3 – Coastal and Shelf Processes). B.L. acknowledges funding from an NERC Algorithm PhD Studentship (NE/F008864/1). We thank Helen Findlay and Hannah Wood for setting up the mesocosm system, Fred Gazeau, Peter van Rijswijk, Lara Pozzato, Marie-Dominique Pizay and Jean-Pierre Gattuso for providing the carbonate and nutrient data, Max Schwanitz, Sandra Treydte and Julian Mönnich for collecting the sediment cores, Vas Kitidis and Bess Ward for useful discussions and Paul Somerfield for advice on statistical analyses.

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  1. Bonnie Laverock

    Present address: UWA Oceans Institute, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia

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  1. Plymouth Marine Laboratory, Prospect Place, Plymouth, PL1 3DH, UK

    Karen Tait, Bonnie Laverock & Stephen Widdicombe

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Fig. S1

DGGE gel images of bacterial amoA (a) and archaeal amoA (b) transcripts. Numbers represent sediments cores, and each lane is combined from the PCR products from four replicate RNA extractions from each core (JPEG 43 kb)

High resolution image (TIFF 40099 kb)

Fig. S2

Phylogenetic tree of nirS transcripts from OTU data (80 % similarity) retrieved from the different pCO2 treatments (filled triangle 8.1, filled square 7.7, filled circle 7.2), shown alongside previously reported environmental sequences. The number of sequences derived from each pCO2 treatment is also shown for each OTU. The tree topology is based on neighbour-joining and bootstrap analysis was performed with 1,000 replications (MEGA 5). The accession numbers of the reference sequences are shown in parentheses (JPEG 606 kb)

High resolution image (EPS 521 kb)

Supplementary Table 1

Environmental conditions in the cores averaged over the 14 day experimental period, values are means (n = 5) (± 95 % confidence intervals). pH, temperature (ºC), salinity and total alkalinity (TA, μmol kg-1) were measured and used to calculate pCO2 (μatm), dissolved inorganic carbon (DIC, μmol kg-1), and saturation states for calcite (ΩC) and aragonite (ΩA). Details of how these values were measured and calculated can be found in Gazeau et al. (manuscript in revision). (DOC 34 kb)

Supplementary Table 2

Primer pairs and reaction conditions used for q-PCR and RT-qPCR assays (DOC 49 kb)

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Tait, K., Laverock, B. & Widdicombe, S. Response of an Arctic Sediment Nitrogen Cycling Community to Increased CO2 . Estuaries and Coasts 37, 724–735 (2014). https://doi.org/10.1007/s12237-013-9709-x

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