Addendum to the Guide to Best Practices in Ocean Acidification Research and Data Reporting, 2015-2016

This addendum provides complementary resources for users of the Guide to Best Practices in Ocean Acidification Research and Data Reporting (Eds: Riebesell U., Fabry V. J., Hansson L. & Gattuso J.-P., 2010. 260 p. Luxembourg: Publications Office of the European Union). It was initiated following discussions within the SOLAS IMBER Ocean Acidification Working Group and the Advisory Board of the IAEA Ocean Acidification International Coordination Centre. Users are strongly recommended to consult the below articles as a complement to the Guide.

Contributors: Jean-Pierre Gattuso, Andrew Dickson, Sam Dupont, Jon Havenhand, Jens Nejstgaard and Ulf Riebesell.

Chapter 1: The carbon dioxide system in seawater: equilibrium chemistry and measurements, by A. G. Dickson

Bockmon, E. E., & Dickson, A. G. 2014. A seawater filtration method suitable for total dissolved carbon and pH analyses. Limnology and Oceanography: Methods 12, 191–195. http://www.aslo.org/lomethods/free/2014/0191.html.

Bockmon, E. E., & Dickson, A. G. 2015. An inter-laboratory comparison assessing the quality of seawater carbon dioxide measurements. Marine Chemistry 171, 36-43. http://www.sciencedirect.com/science/article/pii/S0304420315000213

Hoppe C. J. M., Langer G., Rokitta S. D., Wolf-Gladrow D. A. & Rost B., 2012. Implications of observed inconsistencies in carbonate chemistry measurements for ocean acidification studies. Biogeosciences 9:2401-2405. http://www.biogeosciences.net/9/2401/2012/bg-9-2401-2012.html.

Koeve W., Kim H.-C., Lee K. & Oschlies A., 2012. Potential impact of DOC accumulation on fCO2 and carbonate ion computations in ocean acidification experiments. Biogeosciences 9:3787-3798. http://www.biogeosciences.net/9/3787/2012/bg-9-3787-2012.html.

Martz T.R., Daly K. L., Byrne R. H., Stillman J. H. & Turk D., 2015. Technology for ocean acidification research: Needs and availability. Oceanography 28(2):40–47. http://www.tos.org/oceanography/archive/28-2_martz.html

Orr J. C., Epitalon J.-M. & Gattuso J.-P., 2015. Comparison of ten packages that compute ocean carbonate chemistry. Biogeosciences 12:1483-1510. http://www.biogeosciences.net/12/1483/2015/bg-12-1483-2015.html.

See also Appendix 1 to this Addendum: “Guidelines for reporting ocean acidification data in scientific journals”

Chapter 2: Approaches and tools to manipulate the carbonate chemistry, by J.-P. Gattuso et al.

Bockmon E. E., Frieder C. A., Navarro M. O., White-Kershek L. A. & Dickson A. G., 2013. Technical note: controlled experimental aquarium system for multi-stressor investigation of carbonate chemistry, oxygen saturation, and temperature. Biogeosciences 10:5967-5975. http://www.biogeosciences.net/10/5967/2013/bg-10-5967-2013.html

Cornwall C. E. & Hurd C. L., in press. Experimental design in ocean acidification research: problems and solutions. ICES Journal of Marine Science. http://icesjms.oxfordjournals.org/content/early/2015/07/07/icesjms.fsv118.abstract

Hoffmann L. J., Breitbarth E., McGraw C. M., Law C. S., Currie K. I. & Hunter K. A., 2013. A trace-metal clean, pH-controlled incubator system for ocean acidification incubation studies. Limnology and Oceanography Methods 11:53-61. http://www.aslo.org/lomethods/free/2013/0053.html

Hoppe C. J. M., Langer G., Rokitta S. D., Wolf-Gladrow D. A. & Rost B., 2012. Implications of observed inconsistencies in carbonate chemistry measurements for ocean acidification studies. Biogeosciences 9:2401-2405. http://www.biogeosciences.net/9/2401/2012/bg-9-2401-2012.html.

Jokiel P. L., Bahr K. D. & Rodgers K. S., 2014. Low-cost, high-flow mesocosm system for simulating ocean acidification with CO2 gas. Limnology & Oceanography Methods 12(5):313-322. http://onlinelibrary.wiley.com/doi/10.4319/lom.2014.12.313/abstract

Koeve W., Kim H.-C., Lee K. & Oschlies A., 2012. Potential impact of DOC accumulation on fCO2 and carbonate ion computations in ocean acidification experiments. Biogeosciences 9:3787-3798. http://www.biogeosciences.net/9/3787/2012/bg-9-3787-2012.html

Lunden J. J., Turner J. M., McNicholl C. G., Glynn C. K. & Cordes E. E., 2014. Design, development, and implementation of recirculating aquaria for maintenance and experimentation of deep-sea corals and associated fauna. Limnology and Oceanography: Methods 12(6):363-372. http://onlinelibrary.wiley.com/doi/10.4319/lom.2014.12.363/abstract

MacLeod C. D., Doyle H. L. & Currie K. I., 2015. Technical Note: Maximising accuracy and minimising cost of a potentiometrically regulated ocean acidification simulation system. Biogeosciences 12:713-721. http://www.biogeosciences.net/12/713/2015/bg-12-713-2015.html

Olariaga A., Guallart E. F., Fuentes V., López-Sanz A., Canepa A., Movilla J., Bosch M., Calvo E. & Pelejero C., 2014. Polyp flats, a new system for experimenting with jellyfish polyps, with insights into the effects of ocean acidification. Limnology & Oceanography Methods 12:212-222. http://www.aslo.org/lomethods/free/2014/0212.html

Torres R., Manriquez P. H., Duarte C., Navarro J. M., Lagos N. A., Vargas C. A. & Lardies M. A., 2013. Evaluation of a semi-automatic system for long-term seawater carbonate chemistry manipulation. Revista Chilena de Historia Natural 86(4):443-451. http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-078X2013000400006

Wilcox-Freeburg E., Rhyne A., Robinson W. E., Tlusty M., Bourque B. & Hannigan R. E., 2013. A comparison of two pH-stat carbon dioxide dosing systems for ocean acidification experiments. Limnology and Oceanography: Methods 11:485-494. http://onlinelibrary.wiley.com/doi/10.4319/lom.2013.11.485/abstract.

Chapter 3: Atmospheric CO2 targets for ocean acidification perturbation experiments, by J. P. Barry et al.

Cornwall C. E. & Hurd C. L., in press. Experimental design in ocean acidification research: problems and solutions. ICES Journal of Marine Science. http://icesjms.oxfordjournals.org/content/early/2015/07/07/icesjms.fsv118.abstract

Reum J. C. P., Alin S. R., Harvey C. J., Bednaršek N., Evans W., Feely R. A., Hales B., Lucey N., Mathis J. T., McElhany P., Newton L. & Sabine C. L., in press. Interpretation and design of ocean acidification experiments in upwelling systems in the context of carbonate chemistry co-variation with temperature and oxygen. ICES Journal of Marine Science. http://icesjms.oxfordjournals.org/content/early/2015/01/06/icesjms.fsu231.abstract

Wahl M., Sawall Y. & Saderne V., in press. How good are we at assessing the impact of ocean acidification in coastal systems? Limitations, omissions and strengths of commonly used experimental approaches with a special emphasis on the neglected role of fluctuations. Marine & Freshwater Research.http://www.publish.csiro.au/view/journals/dsp_journals_pip_abstract_Scholar1.cfm?nid=126&pip=MF14154

General book on experimental design:

Quinn G. & Keough M., 2002. Experimental design and data analysis for biologists. Cambridge University Press, http://www.zoology.unimelb.edu.au/qkstats/

Chapter 4: Designing ocean acidification experiments to maximise inference, by J. Havenhand et al.

Anderson D. R., Burnham K. P. & Thompson W. L., 2000. Null hypothesis testing: problems, prevalence, and an alternative. The journal of wildlife management 64(4):912-923. http://www.jstor.org/stable/3803199?seq=1#page_scan_tab_contents

Cornwall C. E. & Hurd C. L., in press. Experimental design in ocean acidification research: problems and solutions. ICES Journal of Marine Science. http://icesjms.oxfordjournals.org/content/early/2015/07/07/icesjms.fsv118.abstract

Ellison A. M., Gotelli N. J., Inouye B. D. & Strong D. R., 2014. P values, hypothesis testing, and model selection: it’s déjà vu all over again 1. Ecology 95:609-610. http://www.esajournals.org/doi/abs/10.1890/13-1911.1

Masson M. E., 2011. A tutorial on a practical Bayesian alternative to null-hypothesis significance testing. Behavior Research Methods 43:679-690. http://rd.springer.com/article/10.3758%2Fs13428-010-0049-5

Smith R. A., Levine T. R., Lachlan K. A. & Fediuk T. A., 2002. The high cost of complexity in experimental design and data analysis: Type I and type II error rates in multiway ANOVA. Human Communication Research 28:515-530. http://onlinelibrary.wiley.com/doi/10.1111/j.1468-2958.2002.tb00821.x/abstract

Veresoglou S. D., 2015. P hacking in biology: An open secret. Proceedings of the National Academy of Sciences of the United States of America (PNAS) 112(37):E5112-E5113. http://www.pnas.org/content/112/37/E5112.full.pdf

Wahl M., Sawall Y. & Saderne, V., in press.. How good are we at assessing the impact of ocean acidification in coastal systems? Limitations, omissions and strengths of commonly used experimental approaches with a special emphasis on the neglected role of fluctuations. Marine and Freshwater Research. http://www.publish.csiro.au/paper/MF14154.htm

Chapter 6: Pelagic mesocosms, by U. Riebesell et al.

Czerny J., Schulz K. G., Boxhammer T., Bellerby R. G. J., Büdenbende, J., Engel A., Krug S. A., Ludwig A., Nachtigall K., Nondal G., Niehoff B., Silyakova A. & Riebesell U., 2013. Implications of elevated CO2 on pelagic carbon fluxes in an Arctic mesocosm study – an elemental mass balance approach. Biogeosciences 10(5):3109–3125. http://www.biogeosciences.net/10/3109/2013/bg-10-3109-2013.html

de Kluijver A., Soetaert K., Czerny J., Schulz K. G., Boxhammer T., Riebesell U. & Middelburg J. J., 2013. A 13C labelling study on carbon fluxes in Arctic plankton communities under elevated CO2 levels. Biogeosciences 10(3):1425–1440. http://www.biogeosciences.net/10/1425/2013/bg-10-1425-2013.html

Guieu C., Dula F., Desboeufs K., Wagener T., Pulido-Villena E., Grisoni J. M., Louis F., Ridame C., Blain S., Brunet C., Bon Nguyen E., Tran S., Labiadh M. & Dominici J. M., 2010. Large clean mesocosms and simulated dust deposition: a new methodology to investigate responses of marine oligotrophic ecosystems to atmospheric inputs. Biogeosciences 7(9):2765–2784. http://www.biogeosciences.net/7/2765/2010/bg-7-2765-2010.html

Kangas P. & Adey W., 1996. Mesocosms and ecological engineering. Ecological Engineering 6:1-5. https://www.infona.pl/resource/bwmeta1.element.elsevier-10c3b6bb-76de-3fdd-b3e2-90cee0aee248/tab/summary

Larsen A., Egge J. K., Nejstgaard J. C., Di Capua I., Thyrhaug R., Bratbak G. & Thingstad T. F., 2015. Contrasting response to nutrient manipulation in Arctic mesocosms are reproduced by a minimum microbial food web model. Limnology and Oceanography 60:360-374. http://onlinelibrary.wiley.com/doi/10.1002/lno.10025/abstract

Petersen J. E., Kennedy V. S., Dennison W. C. & Kemp W. M. (Eds), 2009. Enclosed Experimental Ecosystems and Scale. Tools for Understanding and Managing Coastal Ecosystems. Springer, New York, NY, USA. http://www.springer.com/us/book/9780387767666

Riebesell U., Czerny J., von Bröckel K., Boxhammer T., Büdenbender J., Deckelnick M., Fischer M., Hoffmann D., Krug S. A., Lentz U., Ludwig A., Muche R. & Schulz K. G., 2013. Technical Note: A mobile sea-going mesocosm system – new opportunities for ocean change research. Biogeosciences 10(3):1835–1847. http://www.biogeosciences.net/10/1835/2013/bg-10-1835-2013.html

Thingstad T. F. & Cuevas L. A., 2010. Nutrient pathways through the microbial food web: principles and predictability discussed, based on five different experiments. Aquatic Microbial Ecology 61:249–260. http://www.int-res.com/abstracts/ame/v61/n3/p249-260/

Vadstein O., Andersen T., Reinertsen H. R. & Olsen Y., 2012. Carbon, nitrogen and phosphorus resource supply and utilisation for coastal planktonic heterotrophic bacteria in a gradient of nutrient loading. Marine Ecology Progress Series 447:55–75. http://www.int-res.com/abstracts/meps/v447/p55-75/

Chapter 8: In situ perturbation experiments: natural venting sites, spatial/temporal gradients in ocean pH, manipulative in situ p(CO2) perturbations, by J. P. Barry et al.

Campbell J. E. & Fourqurean J. W., 2011. Novel methodology for in situ carbon dioxide enrichment of benthic ecosystems. Limnology and Oceanography: Methods 9:97-109. http://www.aslo.org/lomethods/free/2011/0097.html

Czerny J., Schulz K. G., Ludwig A. & Riebesell U., 2013. Technical note: a simple method for air–sea gas exchange measurements in mesocosms and its application in carbon budgeting. Biogeosciences 10:1379-1390. http://www.biogeosciences.net/10/1379/2013/bg-10-1379-2013.html

Gattuso J.-P., Kirkwood W., Barry J. P., Cox E., Gazeau F., Hansson L., Hendriks I. E., Kline D. I., Mahacek P., Marker M., Martin S., McElhany P., Peltzer E. T., Reeve J., Roberts D., Saderne V., Tait K., Widdicombe S. & Brewer P., 2014. Free-ocean CO2 enrichment (FOCE) systems: present status and future developments. Biogeosciences 11:4057-4075. http://www.biogeosciences.net/11/4057/2014/bg-11-4057-2014.html

Kirkwood W. J., Walz P. M., Peltzer E. T., Barry J. P., Herlien R. A., Headley K. L., Kecy C., Matsumoto G. I., Maughan T., O’Reilly T. C., Salamy K. A., Shane F. & Brewer P. G., 2015. Design, construction, and operation of an actively controlled deep-sea CO2 enrichment experiment using a cabled observatory system. Deep Sea Research Part I: Oceanographic Research Papers 97:1-9. http://www.sciencedirect.com/science/article/pii/S096706371400209X

Riebesell U., Czerny J., von Bröckel K., Boxhammer T., Büdenbender J., Deckelnick M., Fischer M., Hoffmann D., Krug S. A., Lentz U., Ludwig A., Muche R. & Schulz K. G., 2013. Technical Note: A mobile sea-going mesocosm system – new opportunities for ocean change research. Biogeosciences 10:1835-1847. http://www.biogeosciences.net/10/1835/2013/bg-10-1835-2013.html

Annex 1: Guidelines for reporting ocean acidification data in scientific journals

These guidelines were prepared by J.-P. Gattuso (gattuso@obs-vlfr.fr), H. Garcia (hernan.garcia@noaa.gov), C. J. M. Hoppe (Clara.Hoppe@awi.de), J. Orr (James.Orr@lsce.ipsl.fr), H.-O. Pörtner (Hans.Poertner@awi.de) and Y Yang (yangyan@xmu.edu.cn)

This document was prepared in the framework of the data management activity of the Ocean Acidification International Coordination Centre of the International Atomic Energy Agency (OAICC; http://www.iaea.org/ocean-acidification). Please contact the first author (gattuso@obs-vlfr.fr) in case of any error or omission. It is primarily based on Dickson et al. (2007), Dickson (2010), Nisumaa et al. (2010), Pesant et al. (2010), Pörtner et al. (2010) and Orr et al. (2015).

To ensure reproducibility, it is critical to report at least two variables of the carbonate system of seawater as well as salinity, temperature, and the hydrostatic pressure (if the measurements were not performed at atmospheric pressure). In addition, authors should report concentrations of total dissolved inorganic phosphorus as well as total dissolved inorganic silicon (in μmol kg-1) whenever possible. Furthermore,

– Authors should carefully report how the parameters were measured and, if applicable, which protocol they followed.
– The use of Certified Reference Materials, source, and batch numbers must be mentioned.
– At least two of the following carbonate system parameters should be measured and reported (note the preferred acronyms and units):

  • Dissolved inorganic carbon (CT; μmol kg-1)
  • Total alkalinity (AT; μmol kg-1)
  • pH (it is critical to mention its scale; see below)
  • Partial pressure of carbon dioxide (pCO2; μatm)
  • Fugacity of carbon dioxide (fCO2; μatm)
  • Carbonate ion concentration (CO32-; μmol kg-1)

– The pH scale (NBS, free, total, or seawater) must be mentioned prominently in the manuscript.
– If more than one pH scale is used in a given manuscript, the pH should always be given with the associated scale as a subscript:

  • on the National Bureau of Standards scale (pHNBS)
  • on the seawater scale (pHSWS)
  • on the free scale (pHF)
  • on the total scale (pHT)

– The temperature at the time of sampling and at the time of measurement should both be mentioned, if they differ.

– Salinity is needed (note that it is unitless).
– The formulations used to calculate the following variables should be mentioned:

  • Concentrations of total boron
  • CO2 solubility (K0)
  • Dissociation constants of carbonic acid (K1 and K2), boric acid (Kb), water (Kw), phosphoric acid (Kp1, Kp2, Kp3), silicic acid (Ksi), hydrogen fluoride (Kf), and bisulfate (Ks)
  • Solubility products of calcite (Kspc) and aragonite (Kspa)

– The software package used to calculate the carbonate chemistry, along with its version number, and any associated options must all be mentioned.
– Average reproducibility of the performed measurements (with number of measurements) should be mentioned.
– Finally, it is strongly recommended that the chemistry and biological data are either archived in an on-line database (preferred) or provided along with the paper as supplementary information.

References cited

Dickson, A. G.: The carbon dioxide system in seawater: equilibrium chemistry and measurements, in: Guide to best practices for ocean acidification research and data reporting, edited by: Riebesell, U., Fabry, V. J., Hansson, L., and Gattuso, J.-P., Publications Office of the European Union, Luxembourg, 17–40, 2010.

Dickson, A. G., Sabine, C. L., and Christian J. R.: Guide to best practices for ocean CO2 measurements, PICES Special Publication, 3, 1–191, 2007.

Nisumaa, A.-M., Pesant, S., Bellerby, R. G. J., Delille, B., Middelburg, J. J., Orr, J. C., Riebesell, U., Tyrrell, T., Wolf-Gladrow, D., and Gattuso, J.-P.: EPOCA/EUR-OCEANS data compilation on the biological and biogeochemical responses to ocean acidification, Earth Syst. Sci. Data, 2, 167–175, doi:10.5194/essd-2-167-2010, 2010.

Orr J. C., Epitalon J.-M., and Gattuso J.-P., 2015. Comparison of ten packages that compute ocean carbonate chemistry, Biogeosciences, 12, 1483–1510, 2015.

Pesant, S., Alan Hook, L., Lowry, R., Moncoiffé, G., Nisumaa, A.-M., and Pfeil, B.: Safeguarding and sharing ocean acidification data, in: Guide to best practices for ocean acidification research and data reporting, edited by: Riebesell, U., Fabry, V. J., Hansson, L., and Gattuso, J.-P., Publications Office of the European Union, Luxembourg, 243–258, 2010.

Pörtner H.-O., Dickson A., and Gattuso J.-P.: Terminology and units for parameters relevant to the carbonate system, in: Guide to best practices for ocean acidification research and data reporting, edited by: Riebesell, U., Fabry, V. J., Hansson, L., and Gattuso, J.-P., Publications Office of the European Union, Luxembourg, 18–19, 2010.

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