Publications

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2019
Stark, JS, Peltzer ET, Kline DI, Queiros AM, Cox TE, Headley K, Barry J, Gazeau F, Runcie JW, Widdicombe S, Milnes M, Roden NP, Black J, Whiteside S, Johnstone G, Ingels J, Shaw E, Bodrossy L, Gaitan-Espitia JD, Kirkwood W, Gattuso J.  2019.  Free Ocean CO2 Enrichment (FOCE) experiments: Scientific and technical recommendations for future in situ ocean acidification projects. Progress in Oceanography. 172:89-107.   10.1016/j.pocean.2019.01.006   AbstractWebsite

Free Ocean CO2 Enrichment (FOCE) experiments are a relatively recent development in ocean acidification research, designed to address the need for in situ, long-term, community level experiments. FOCE studies have been conducted across different marine benthic habitats and regions, from Antarctica to the tropics. Based on this previous research we have formed some core operating principles that will aid those embarking on future FOCE experiments. FOCE studies have potential to provide important insight into the effects of ocean acidification that can add to or refine conclusions drawn from laboratory or single species studies because they are conducted in situ on intact assemblages. Scaling up from sub-organismal and individual effects to also include indirect impacts on the ecosystem and ecosystem services, make FOCE experiments essential in filling in current knowledge gaps in our understanding of ocean acidification. While FOCE systems are complex, relatively costly, and somewhat difficult to operate, the challenges they pose are tractable and they have proven to be a useful approach in ocean acidification research. The aim of this paper is to draw from the experiences of past FOCE experiments and provide practical advice for designing, building and operating a FOCE experiment. Some of the most important recommendations include: field testing the system design; having a backup power supply; using replicate treatment enclosures; monitoring and maintaining the chemistry appropriately; allowing sufficient time to achieve near CO2 equilibrium conditions; and having a scientific focus with a core set of hypotheses. Future FOCE experiments could focus on longer durations, multiple factors, and testing more intact benthic marine communities and ecosystems. We hope this paper will encourage further FOCE deployments and experiments, as well as provide some guidelines to improve future FOCE studies and advance ocean acidification research.

2018
Cyronak, T, Andersson AJ, Langdon C, Albright R, Bates NR, Caldeira K, Carlton R, Corredor JE, Dunbar RB, Enochs I, Erez J, Eyre BD, Gattuso JP, Gledhill D, Kayanne H, Kline DI, Koweek DA, Lantz C, Lazar B, Manzello D, McMahon A, Melendez M, Page HN, Santos IR, Schulz KG, Shaw E, Silverman J, Suzuki A, Teneva L, Watanabe A, Yamamoto S.  2018.  Taking the metabolic pulse of the world's coral reefs. Plos One. 13   10.1371/journal.pone.0190872   AbstractWebsite

Worldwide, coral reef ecosystems are experiencing increasing pressure from a variety of anthropogenic perturbations including ocean warming and acidification, increased sedimentation, eutrophication, and overfishing, which could shift reefs to a condition of net calcium carbonate (CaCO3) dissolution and erosion. Herein, we determine the net calcification potential and the relative balance of net organic carbon metabolism (net community production; NCP) and net inorganic carbon metabolism (net community calcification; NCC) within 23 coral reef locations across the globe. In light of these results, we consider the suitability of using these two metrics developed from total alkalinity (TA) and dissolved inorganic carbon (DIC) measurements collected on different spatiotemporal scales to monitor coral reef biogeochemistry under anthropogenic change. All reefs in this study were net calcifying for the majority of observations as inferred from alkalinity depletion relative to offshore, although occasional observations of net dissolution occurred at most locations. However, reefs with lower net calcification potential (i.e., lower TA depletion) could shift towards net dissolution sooner than reefs with a higher potential. The percent influence of organic carbon fluxes on total changes in dissolved inorganic carbon (DIC) (i.e., NCP compared to the sum of NCP and NCC) ranged from 32% to 88% and reflected inherent biogeochemical differences between reefs. Reefs with the largest relative percentage of NCP experienced the largest variability in seawater pH for a given change in DIC, which is directly related to the reefs ability to elevate or suppress local pH relative to the open ocean. This work highlights the value of measuring coral reef carbonate chemistry when evaluating their susceptibility to ongoing global environmental change and offers a baseline from which to guide future conservation efforts aimed at preserving these valuable ecosystems.

Du, N, Gholami P, Kline DI, Dupont CL, Dickson AG, Mendola D, Martz T, Allen AE, Mitchell GB.  2018.  Simultaneous quantum yield measurements of carbon uptake and oxygen evolution in microalgal cultures. PloS one. 13(6):e0199125.: Public Library of Science   10.1371/journal.pone.0199125   Abstract

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Gormley, K, McLellan F, McCabe C, Hinton C, Ferris J, Kline DI, Scott BE.  2018.  Automated Image Analysis of Offshore Infrastructure Marine Biofouling. Journal of Marine Science and Engineering. 6(1):2.: Multidisciplinary Digital Publishing Institute Abstract
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2015
Beijbom, O, Edmunds PJ, Roelfsema C, Smith J, Kline DI, Neal BP, Dunlap MJ, Moriarty V, Fan TY, Tan CJ, Chan S, Treibitz T, Gamst A, Mitchell BG, Kriegman D.  2015.  Towards automated annotation of benthic survey images: Variability of human experts and operational modes of automation. Plos One. 10   10.1371/journal.pone.0130312   AbstractWebsite

Global climate change and other anthropogenic stressors have heightened the need to rapidly characterize ecological changes in marine benthic communities across large scales. Digital photography enables rapid collection of survey images to meet this need, but the subsequent image annotation is typically a time consuming, manual task. We investigated the feasibility of using automated point-annotation to expedite cover estimation of the 17 dominant benthic categories from survey-images captured at four Pacific coral reefs. Inter- and intra- annotator variability among six human experts was quantified and compared to semi- and fully- automated annotation methods, which are made available at coralnet.ucsd. edu. Our results indicate high expert agreement for identification of coral genera, but lower agreement for algal functional groups, in particular between turf algae and crustose coralline algae. This indicates the need for unequivocal definitions of algal groups, careful training of multiple annotators, and enhanced imaging technology. Semi-automated annotation, where 50% of the annotation decisions were performed automatically, yielded cover estimate errors comparable to those of the human experts. Furthermore, fully-automated annotation yielded rapid, unbiased cover estimates but with increased variance. These results show that automated annotation can increase spatial coverage and decrease time and financial outlay for image-based reef surveys.

Georgiou, L, Falter J, Trotter J, Kline DI, Holcomb M, Dove SG, Hoegh-Guldberg O, McCulloch M.  2015.  pH homeostasis during coral calcification in a Free Ocean CO2 Enrichment (FOCE) experiment, Heron Island reef flat, Great Barrier Reef. . Proceedings of the National Academy of Sciences . 112(43):13219-13224.   10.1073/pnas.1505586112  
Andersson, AJ, Kline DI, Edmunds PJ, Archer SD, Bednaršek N, Carpenter RC, Chadsey M, Goldstein P, Grottoli AG, Hurst TP.  2015.  Understanding ocean acidification impacts on organismal to ecological scales. Oceanography. 28(2):16-27. Abstract
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2014
Gonzalez-Rivero, M, Bongaerts P, Beijbom O, Pizarro O, Friedman A, Rodriguez-Ramirez A, Upcroft B, Laffoley D, Kline D, Bailhache C, Vevers R, Hoegh-Guldberg O.  2014.  The Catlin Seaview Survey - kilometre-scale seascape assessment, and monitoring of coral reef ecosystems. Aquatic Conservation-Marine and Freshwater Ecosystems. 24:184-198.   10.1002/aqc.2505   AbstractWebsite

Marine ecosystems provide critically important goods and services to society, and hence their accelerated degradation underpins an urgent need to take rapid, ambitious and informed decisions regarding their conservation and management.The capacity, however, to generate the detailed field data required to inform conservation planning at appropriate scales is limited by time and resource consuming methods for collecting and analysing field data at the large scales required.The Catlin Seaview Survey', described here, introduces a novel framework for large-scale monitoring of coral reefs using high-definition underwater imagery collected using customized underwater vehicles in combination with computer vision and machine learning. This enables quantitative and geo-referenced outputs of coral reef features such as habitat types, benthic composition, and structural complexity (rugosity) to be generated across multiple kilometre-scale transects with a spatial resolution ranging from 2 to 6m(2).The novel application of technology described here has enormous potential to contribute to our understanding of coral reefs and associated impacts by underpinning management decisions with kilometre-scale measurements of reef health.Imagery datasets from an initial survey of 500km of seascape are freely available through an online tool called the Catlin Global Reef Record. Outputs from the image analysis using the technologies described here will be updated on the online repository as work progresses on each dataset.Case studies illustrate the utility of outputs as well as their potential to link to information from remote sensing. The potential implications of the innovative technologies on marine resource management and conservation are also discussed, along with the accuracy and efficiency of the methodologies deployed.10.1002/(ISSN)1099-0755 Copyright (c) 2014 John Wiley & Sons, Ltd.

Gattuso, JP, Kirkwood W, Barry JP, Cox E, Gazeau F, Hansson L, Hendriks I, Kline DI, Mahacek P, Martin S, McElhany P, Peltzer ET, Reeve J, Roberts D, Saderne V, Tait K, Widdicombe S, Brewer PG.  2014.  Free-ocean CO2 enrichment (FOCE) systems: present status and future developments. Biogeosciences. 11:4057-4075.   10.5194/bg-11-4057-2014   AbstractWebsite

Free-ocean CO2 enrichment (FOCE) systems are designed to assess the impact of ocean acidification on biological communities in situ for extended periods of time (weeks to months). They overcome some of the drawbacks of laboratory experiments and field observations by enabling (1) precise control of CO2 enrichment by monitoring pH as an offset of ambient pH, (2) consideration of indirect effects such as those mediated through interspecific relationships and food webs, and (3) relatively long experiments with intact communities. Bringing perturbation experiments from the laboratory to the field is, however, extremely challenging. The main goal of this paper is to provide guidelines on the general design, engineering, and sensor options required to conduct FOCE experiments. Another goal is to introduce xFOCE, a community-led initiative to promote awareness, provide resources for in situ perturbation experiments, and build a user community. Present and existing FOCE systems are briefly described and examples of data collected presented. Future developments are also addressed as it is anticipated that the next generation of FOCE systems will include, in addition to pH, options for oxygen and/or temperature control. FOCE systems should become an important experimental approach for projecting the future response of marine ecosystems to environmental change.

2013
Nash, MC, Opdyke BN, Troitzsch U, Russell BD, Adey WH, Kato A, Diaz-Pulido G, Brent C, Gardner M, Prichard J, Kline DI.  2013.  Dolomite rich coral reef coralline algae resist dissolution in acidified conditions.. Nature Climate Change. 3:268-272.   10.1038/nclimate1760   Abstract

Coral reef ecosystems develop best in high-flow environments but their fragile frameworks are also vulnerable to high wave energy. Wave-resistant algal rims, predominantly made up of the crustose coralline algae (CCA) Porolithon onkodes and P. pachydermum1, 2, are therefore critical structural elements for the survival of many shallow coral reefs. Concerns are growing about the susceptibility of CCA to ocean acidification because CCA Mg-calcite skeletons are more susceptible to dissolution under low pH conditions than coral aragonite skeletons3. However, the recent discovery4 of dolomite (Mg0.5Ca0.5(CO3)), a stable carbonate5, in P. onkodes cells necessitates a reappraisal of the impacts of ocean acidification on these CCA. Here we show, using a dissolution experiment, that dried dolomite-rich CCA have 6–10 times lower rates of dissolution than predominantly Mg-calcite CCA in both high-CO2 (~ 700 ppm) and control (~ 380 ppm) environments, respectively. We reveal this stabilizing mechanism to be a combination of reduced porosity due to dolomite infilling and selective dissolution of other carbonate minerals. Physical break-up proceeds by dissolution of Mg-calcite walls until the dolomitized cell eventually drops out intact. Dolomite-rich CCA frameworks are common in shallow coral reefs globally and our results suggest that it is likely that they will continue to provide protection and stability for coral reef frameworks as CO2

2010
Eakin, CM, Morgan JA, Heron SF, Smith TB, Liu G, Alvarez-Filip L, Baca B, Bartels E, Bastidas C, Bouchon C, Brandt M, Bruckner AW, Bunkley-Williams L, Cameron A, Causey BD, Chiappone M, Christensen TRL, Crabbe MJC, Day O, de la Guardia E, Diaz-Pulido G, DiResta D, Gil-Agudelo DL, Gilliam DS, Ginsburg RN, Gore S, Guzman HM, Hendee JC, Hernandez-Delgado EA, Husain E, Jeffrey CFG, Jones RJ, Jordan-Dahlgren E, Kaufman LS, Kline DI, Kramer PA, Lang JC, Lirman D, Mallela J, Manfrino C, Marechal JP, Marks K, Mihaly J, Miller WJ, Mueller EM, Muller EM, Toro CAO, Oxenford HA, Ponce-Taylor D, Quinn N, Ritchie KB, Rodriguez S, Ramirez AR, Romano S, Samhouri JF, Sanchez JA, Schmahl GP, Shank BV, Skirving WJ, Steiner SCC, Villamizar E, Walsh SM, Walter C, Weil E, Williams EH, Roberson KW, Yusuf Y.  2010.  Caribbean Corals in Crisis: Record Thermal Stress, Bleaching, and Mortality in 2005. Plos One. 5   10.1371/journal.pone.0013969   AbstractWebsite

Background: The rising temperature of the world's oceans has become a major threat to coral reefs globally as the severity and frequency of mass coral bleaching and mortality events increase. In 2005, high ocean temperatures in the tropical Atlantic and Caribbean resulted in the most severe bleaching event ever recorded in the basin. Methodology/Principal Findings: Satellite-based tools provided warnings for coral reef managers and scientists, guiding both the timing and location of researchers' field observations as anomalously warm conditions developed and spread across the greater Caribbean region from June to October 2005. Field surveys of bleaching and mortality exceeded prior efforts in detail and extent, and provided a new standard for documenting the effects of bleaching and for testing nowcast and forecast products. Collaborators from 22 countries undertook the most comprehensive documentation of basin-scale bleaching to date and found that over 80% of corals bleached and over 40% died at many sites. The most severe bleaching coincided with waters nearest a western Atlantic warm pool that was centered off the northern end of the Lesser Antilles. Conclusions/Significance: Thermal stress during the 2005 event exceeded any observed from the Caribbean in the prior 20 years, and regionally-averaged temperatures were the warmest in over 150 years. Comparison of satellite data against field surveys demonstrated a significant predictive relationship between accumulated heat stress (measured using NOAA Coral Reef Watch's Degree Heating Weeks) and bleaching intensity. This severe, widespread bleaching and mortality will undoubtedly have long-term consequences for reef ecosystems and suggests a troubled future for tropical marine ecosystems under a warming climate.

2006
Kline, DI, Bryant J, Kisflaudy E, Rohwer G, Nostropaur F, Grayson J, Knowlton N, Rohwer F.  2006.  The aquatic automated dosing and maintenance system (AADAMS). Limnology and Oceanography-Methods. 4:184-192. AbstractWebsite

The maintenance and dosing of aquatic organisms, such as corals and mollusks, are essential for ecotoxicology studies, yet it is difficult to maintain many of these sensitive organisms for an extended period. Consequently, many previous aquatic ecotoxicology experiments have been limited in their number of replicates and maintained in one or a few experimental aquaria, with only a limited number of stressors tested in each experiment. Here we describe a modular system that overcomes many of the difficulties of maintaining large numbers of sensitive aquatic organisms in separate containers, and allows testing of a large suite of stressors in each experiment. The AADAMS (aquatic automated dosing and maintenance system) allows testing of 40 independent stressors with 10 independent replicates per stressor (400 individuals total). The AADAMS provides surge and regular water changes simultaneously with accurate dosing via Venturi valves. In a series of experiments over a 1-year period, the AADAMS was used to test the effects of various factors affecting water quality on Caribbean coral reefs. Roofing tar and road asphalt were two of the most damaging pollutants tested, with LD50 values (lethal dose that killed 50% of the corals) of 0.013 g L-1 and 0.079 g L-1, respectively, thus suggesting that runoff from roads and near-shore construction could be contributing to reef decline. The AADAMS is an accurate, reliable system for highly replicated ecotoxicological studies of sensitive aquatic organisms, which are important indicators of ecosystem health.