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Acknowledgements Although this paper is not linked to any of the research carried out by, or on behalf of, the James Hutton Institute, some parts of it were written during the first author’s allocated work time. Rachel Creaney is grateful to the James Hutton Institute for giving her this opportunity. The authors would also like to thank Dr Tavis Potts (University of Aberdeen) for proofreading the first draft of the paper and providing valuable comments on its flow, structure and contents. Finally, the authors are grateful to Emily Hastings and Doug Wardell-Johnson from the James Hutton Institute for their assistance with obtaining some of the data used in this paper.

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ACKNOWLEDGEMENTS The authors are grateful to the following bodies that provided financial support for the project: (i) China Scholarship Council, (ii) National Natural Science Foundation of China (Grant No. U1334201 and (iii) UK Engineering and Physical Sciences Research Council (Grant No. EP/G069441/1).

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Acknowledgements The authors would like to thank staff at Marine Scotland Science Patricia White, Rebecca McIntosh, Julia Black and Mark Fordyce for their technical assistance and invaluable feedback on the project. Thanks also go to Alex Douglas at the University of Aberdeen for his advice on data analysis and statistics. For feedback on the manuscript thanks to Lesley McEvoy and Rhiannon Inkster at the NAFC Marine Centre. The study was supported by the Marine Collaborations Forum (MarCRF) which aims to develop cross-disciplinary research between the University of Aberdeen and Marine Scotland Science. Finally, thanks are also due to Scottish Fishermen's Trust for a student support bursary.

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Acknowledgements This work was funded by the projects HAR2013-43701-P (Spanish Economy and Competitiveness Ministry) and CGL2010-20672 (Spanish Ministry of Science and Innovation). This research was also partially developed with Xunta de Galicia funding (grants R2014/001 and GPC2014/009). N. Silva-Sánchez is currently supported by a FPU pre-doctoral grant (AP2010-3264) funded by the Spanish Government. We are grateful to Ana Moreno, Mariano Barriendos and Gerardo Benito who kindly provide us data included in Figure 5a. We also want to thank constructive comments from two anonymous reviewers.

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Funding Some of author A’s research alluded to here was conducted while on a Leverhulme Senior Research Fellowship. Author B’s research is supported by the ESRC Research Centre XXX.

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Acknowledgement The authors are grateful to Prof. Siegfried Schmauder and Prof. Erdogan Madenci for the useful discussions that occurred throughout the realization of this study and acknowledge the Defence Science and Technology Laboratory (DSTL) for the financial support. A special thanks go to the anonymous reviewers, whose time and contribution have been highly appreciated. Results were obtained using the EPSRC funded ARCHIE-WeSt High Performance Computer (www.archie-west.ac.uk). EPSRC grant no. EP/K000586/1.

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Acknowledgements BP Exploration Co. is thanked for funding, and particularly the Carbonate Team (Anna Matthews, Teresa Sabato Ceraldi, and Darryl G. Green) for supporting this research and for fruitful discussions. Mark Anderson, Kim Rosewell, and Tony Sinclair (University of Hull) are thanked for laboratory assistance, and for SEM sample preparation and set-up respectively. The technical and human support from Prof. Jörg Hardege and Maggy A. Harley (University of Hull) was key to perform these experiments. We would like to acknowledge an anonymous reviewer for the detailed and constructive comments, and Brian Jones's editorial handling of the manuscript which is greatly appreciated.

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Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://crea tivecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

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Peer reviewed

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We thank EPSRC and the Scottish Imaging Network (SINAPSE) for grants. DO’H thanks the Royal Society for a Wolfson Research Merit Award and ST is grateful to the John and Kathleen Watson Scholarship for financial support. We are grateful to Dr Catherine Botting and Dr Sally Shirran of the St Andrews Mass Spectrometry Service for MALDI-MS acquisitions. We also thank Dr Sally Pimlott of the University of Glasgow for the use of radiochemistry facilities.

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Acknowledgements The research described here is supported by the award made by the RCUK Digital Economy programme to the dot.rural Digital Economy Research Hub; award reference: EP/G066051/1. Further, we would like to acknowledge the RCUK research grant EP/J000604/2.

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Acknowledgements: We would like to thank Hanna Bensch and Hannes Weise for assistance with the collection of samples in the field. This work was supported by the Biodiversity and Ecosystem Services in a Changing Climate (BECC; a joint Lund-Gothenburg University initiative), the Swedish Research Council (EIS, BH), the Crafoord Foundation (EIS, BH), the Swedish Royal Society (EIS), ‘Gyllenstiernska Krapperupstiftelsen (EIS), the Wenner-Gren Foundations (postdoctoral stipend to RYD), EU FP7 (Marie Curie International Incoming Fellowship to RYD), the Kungliga Fysiografiska Sällskapet i Lund (MW) and the Helge Ax:son Johnson Stiftelse (MW). B.H. and E.I.S. conceived of the study. L.L. developed the hypotheses to be tested. L.L. and R.D. collected the field data and samples. All six authors contributed to planning RNA-seq analyses. P.C. and L.L. analysed the data. L.L. wrote the manuscript, which all six authors edited.

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We thank Prof. David O’Hagan and Dr Qingzhi Zhang (University of St Andrews, UK) for their helpful discussion and for providing the synthetic 50 -FDA sample. This work is supported by National Natural Science Foundation of China (No. 81503086), a starting funding (No. 20140520) from Tianjin University of Science & Technology, a research funding of “1000 Talents Plan” of Tianjin (to LM) and Foundation of Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education and Tianjin Key Lab of Industrial Microbiology (No. 2015IM106)

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This work was supported by the Fluvial Systems Research Group sponsors BG Group, BP, Chevron, ConocoPhilips, and Total. We thank reviews from Martin Stokes, an anonymous reviewer and Editor Stuart Jones.

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Acknowledgements This work was supported by funding of the Academy of Finland (259505), Helsinki University Research grant (490085) and ESCMID grant (4720572) to D.P.F., University of Pittsburgh Central Research Development Fund to X.L., Technology Strategy Board grant (131181) to W.H., M.J. and J.H.N. National Programme of Sustainability I of the Ministry of Education of the Czech Republic I grant (LO1416) to T.G.