@article{canesi_sea_2024,
	title = {Sea surface temperature reconstruction in the {Pacific} {Ocean} using multi-elemental proxy in {Porites} and {Diploastrea} corals: {Application} to {Palau} {Archipelago}},
	volume = {645},
	issn = {00092541},
	shorttitle = {Sea surface temperature reconstruction in the {Pacific} {Ocean} using multi-elemental proxy in {Porites} and {Diploastrea} corals},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0009254123005855},
	doi = {10.1016/j.chemgeo.2023.121884},
	language = {en},
	urldate = {2024-09-02},
	journal = {Chemical Geology},
	author = {Canesi, Marine and Douville, Eric and Montagna, Paolo and Bordier, Louise and Caquineau, Sandrine and Pons-Branchu, Edwige and Iwankow, Guillaume and Stolarski, Jarosław and Allemand, Denis and Planes, Serge and Moulin, Clémentine and Lombard, Fabien and Bourdin, Guillaume and Troublé, Romain and Agostini, Sylvain and Banaigs, Bernard and Boissin, Emilie and Boss, Emmanuel and Bowler, Chris and De Vargas, Colomban and Flores, J. Michel and Forcioli, Didier and Furla, Paola and Gilson, Eric and Galand, Pierre E. and Pesant, Stéphane and Sunagawa, Shinichi and Thomas, Olivier P. and Thurber, Rebecca Vega and Voolstra, Christian R. and Wincker, Patrick and Zoccola, Didier and Reynaud, Stéphanie},
	month = feb,
	year = {2024},
	pages = {121884},
}

@article{higuchi_current_2024,
	title = {Current status and potential of coral reef conservation through human interventions: focusing on coral bleaching},
	volume = {26},
	issn = {1345-1421, 1882-5710},
	shorttitle = {Current status and potential of coral reef conservation through human interventions},
	url = {https://www.jstage.jst.go.jp/article/jcrs/26/1/26_19/_article/-char/ja/},
	doi = {10.3755/jcrs.26.19},
	language = {en},
	number = {1},
	urldate = {2025-05-13},
	journal = {Journal of the Japanese Coral Reef Society},
	author = {Higuchi, Tomihiko and Miyajima, Toshihiro and Takagi, Toshiyuki and Yuyama, Ikuko and Agostini, Sylvain and Nakamura, Takashi and Fujimura, Hiroyuki},
	year = {2024},
	pages = {19--37},
}

@article{armstrong_host_2023,
	title = {Host transcriptomic plasticity and photosymbiotic fidelity underpin {Pocillopora} acclimatization across thermal regimes in the {Pacific} {Ocean}},
	volume = {14},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-023-38610-6},
	doi = {10.1038/s41467-023-38610-6},
	abstract = {Abstract
            
              Heat waves are causing declines in coral reefs globally. Coral thermal responses depend on multiple, interacting drivers, such as past thermal exposure, endosymbiont community composition, and host genotype. This makes the understanding of their relative roles in adaptive and/or plastic responses crucial for anticipating impacts of future warming. Here, we extracted DNA and RNA from 102
              Pocillopora
              colonies collected from 32 sites on 11 islands across the Pacific Ocean to characterize host-photosymbiont fidelity and to investigate patterns of gene expression across a historical thermal gradient. We report high host-photosymbiont fidelity and show that coral and microalgal gene expression respond to different drivers. Differences in photosymbiotic association had only weak impacts on host gene expression, which was more strongly correlated with the historical thermal environment, whereas, photosymbiont gene expression was largely determined by microalgal lineage. Overall, our results reveal a three-tiered strategy of thermal acclimatization in
              Pocillopora
              underpinned by host-photosymbiont specificity, host transcriptomic plasticity, and differential photosymbiotic association under extreme warming.},
	language = {en},
	number = {1},
	urldate = {2024-09-02},
	journal = {Nature Communications},
	author = {Armstrong, Eric J. and Lê-Hoang, Julie and Carradec, Quentin and Aury, Jean-Marc and Noel, Benjamin and Hume, Benjamin C. C. and Voolstra, Christian R. and Poulain, Julie and Belser, Caroline and Paz-García, David A. and Cruaud, Corinne and Labadie, Karine and Da Silva, Corinne and Moulin, Clémentine and Boissin, Emilie and Bourdin, Guillaume and Iwankow, Guillaume and Romac, Sarah and Agostini, Sylvain and Banaigs, Bernard and Boss, Emmanuel and Bowler, Chris and De Vargas, Colomban and Douville, Eric and Flores, Michel and Forcioli, Didier and Furla, Paola and Galand, Pierre E. and Gilson, Eric and Lombard, Fabien and Pesant, Stéphane and Reynaud, Stéphanie and Sullivan, Matthew B. and Sunagawa, Shinichi and Thomas, Olivier P. and Troublé, Romain and Thurber, Rebecca Vega and Zoccola, Didier and Planes, Serge and Allemand, Denis and Wincker, Patrick},
	month = jun,
	year = {2023},
	pages = {3056},
}

Abstract Heat waves are causing declines in coral reefs globally. Coral thermal responses depend on multiple, interacting drivers, such as past thermal exposure, endosymbiont community composition, and host genotype. This makes the understanding of their relative roles in adaptive and/or plastic responses crucial for anticipating impacts of future warming. Here, we extracted DNA and RNA from 102 Pocillopora colonies collected from 32 sites on 11 islands across the Pacific Ocean to characterize host-photosymbiont fidelity and to investigate patterns of gene expression across a historical thermal gradient. We report high host-photosymbiont fidelity and show that coral and microalgal gene expression respond to different drivers. Differences in photosymbiotic association had only weak impacts on host gene expression, which was more strongly correlated with the historical thermal environment, whereas, photosymbiont gene expression was largely determined by microalgal lineage. Overall, our results reveal a three-tiered strategy of thermal acclimatization in Pocillopora underpinned by host-photosymbiont specificity, host transcriptomic plasticity, and differential photosymbiotic association under extreme warming.

@article{belser_integrative_2023,
	title = {Integrative omics framework for characterization of coral reef ecosystems from the {Tara} {Pacific} expedition},
	volume = {10},
	issn = {2052-4463},
	url = {https://www.nature.com/articles/s41597-023-02204-0},
	doi = {10.1038/s41597-023-02204-0},
	abstract = {Abstract
            
              Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont,
              i.e
              . the multipartite assemblages comprising the coral host organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene.},
	language = {en},
	number = {1},
	urldate = {2023-06-12},
	journal = {Scientific Data},
	author = {Belser, Caroline and Poulain, Julie and Labadie, Karine and Gavory, Frederick and Alberti, Adriana and Guy, Julie and Carradec, Quentin and Cruaud, Corinne and Da Silva, Corinne and Engelen, Stefan and Mielle, Paul and Perdereau, Aude and Samson, Gaelle and Gas, Shahinaz and {Genoscope Technical Team} and Batisse, Julie and Beluche, Odette and Bertrand, Laurie and Bohers, Chloé and Bordelais, Isabelle and Brun, Elodie and Dubois, Maria and Dumont, Corinne and Zineb, El Hajji and Estrada, Barbara and Ettedgui, Evelyne and Fernandez, Patricia and Garidi, Sonia and Guérin, Thomas and Gorrichon, Kevin and Hamon, Chadia and Kientzel, Lucille and Lebled, Sandrine and Legrain, Chloé and Lenoble, Patricia and Lepretre, Marine and Louesse, Claudine and Magdelenat, Ghislaine and Mahieu, Eric and Martins, Nathalie and Milani, Claire and Orvain, Céline and Oztas, Sophie and Payen, Emilie and Petit, Emmanuelle and Rio, Guillaume and Robert, Dominique and Ronsin, Muriel and Vacherie, Benoit and Voolstra, Christian R. and Galand, Pierre E. and Flores, J. Michel and Hume, Benjamin C. C. and Perna, Gabriela and Ziegler, Maren and Ruscheweyh, Hans-Joachim and Boissin, Emilie and Romac, Sarah and Bourdin, Guillaume and Iwankow, Guillaume and Moulin, Clémentine and Paz García, David A. and Agostini, Sylvain and Banaigs, Bernard and Boss, Emmanuel and Bowler, Chris and De Vargas, Colomban and Douville, Eric and Forcioli, Didier and Furla, Paola and Gilson, Eric and Lombard, Fabien and Pesant, Stéphane and Reynaud, Stéphanie and Sunagawa, Shinichi and Thomas, Olivier P. and Troublé, Romain and Thurber, Rebecca Vega and Zoccola, Didier and Scarpelli, Claude and Jacoby, E’ Krame and Oliveira, Pedro H. and Aury, Jean-Marc and Allemand, Denis and Planes, Serge and Wincker, Patrick},
	month = jun,
	year = {2023},
	pages = {326},
}

Abstract Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e . the multipartite assemblages comprising the coral host organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene.

@article{canesi_differences_2023,
	title = {Differences in carbonate chemistry up-regulation of long-lived reef-building corals},
	volume = {13},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-023-37598-9},
	doi = {10.1038/s41598-023-37598-9},
	abstract = {Abstract
            
              With climate projections questioning the future survival of stony corals and their dominance as tropical reef builders, it is critical to understand the adaptive capacity of corals to ongoing climate change. Biological mediation of the carbonate chemistry of the coral calcifying fluid is a fundamental component for assessing the response of corals to global threats. The
              Tara
              Pacific expedition (2016–2018) provided an opportunity to investigate calcification patterns in extant corals throughout the Pacific Ocean. Cores from colonies of the massive
              Porites
              and
              Diploastrea
              genera were collected from different environments to assess calcification parameters of long-lived reef-building corals. At the basin scale of the Pacific Ocean, we show that both genera systematically up-regulate their calcifying fluid pH and dissolved inorganic carbon to achieve efficient skeletal precipitation. However, while
              Porites
              corals increase the aragonite saturation state of the calcifying fluid (Ω
              cf
              ) at higher temperatures to enhance their calcification capacity,
              Diploastrea
              show a steady homeostatic Ω
              cf
              across the Pacific temperature gradient. Thus, the extent to which
              Diploastrea
              responds to ocean warming and/or acidification is unclear, and it deserves further attention whether this is beneficial or detrimental to future survival of this coral genus.},
	language = {en},
	number = {1},
	urldate = {2024-09-02},
	journal = {Scientific Reports},
	author = {Canesi, Marine and Douville, Eric and Montagna, Paolo and Taviani, Marco and Stolarski, Jarosław and Bordier, Louise and Dapoigny, Arnaud and Coulibaly, Gninwoyo Eric Hermann and Simon, Anne-Catherine and Agelou, Mathieu and Fin, Jonathan and Metzl, Nicolas and Iwankow, Guillaume and Allemand, Denis and Planes, Serge and Moulin, Clémentine and Lombard, Fabien and Bourdin, Guillaume and Troublé, Romain and Agostini, Sylvain and Banaigs, Bernard and Boissin, Emilie and Boss, Emmanuel and Bowler, Chris and De Vargas, Colomban and Flores, Michel and Forcioli, Didier and Furla, Paola and Gilson, Eric and Galand, Pierre E. and Pesant, Stéphane and Sunagawa, Shinichi and Thomas, Olivier P. and Vega Thurber, Rebecca and Voolstra, Christian R. and Wincker, Patrick and Zoccola, Didier and Reynaud, Stéphanie},
	month = jul,
	year = {2023},
	pages = {11589},
}

Abstract With climate projections questioning the future survival of stony corals and their dominance as tropical reef builders, it is critical to understand the adaptive capacity of corals to ongoing climate change. Biological mediation of the carbonate chemistry of the coral calcifying fluid is a fundamental component for assessing the response of corals to global threats. The Tara Pacific expedition (2016–2018) provided an opportunity to investigate calcification patterns in extant corals throughout the Pacific Ocean. Cores from colonies of the massive Porites and Diploastrea genera were collected from different environments to assess calcification parameters of long-lived reef-building corals. At the basin scale of the Pacific Ocean, we show that both genera systematically up-regulate their calcifying fluid pH and dissolved inorganic carbon to achieve efficient skeletal precipitation. However, while Porites corals increase the aragonite saturation state of the calcifying fluid (Ω cf ) at higher temperatures to enhance their calcification capacity, Diploastrea show a steady homeostatic Ω cf across the Pacific temperature gradient. Thus, the extent to which Diploastrea responds to ocean warming and/or acidification is unclear, and it deserves further attention whether this is beneficial or detrimental to future survival of this coral genus.

@article{galand_diversity_2023,
	title = {Diversity of the {Pacific} {Ocean} coral reef microbiome},
	volume = {14},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-023-38500-x},
	doi = {10.1038/s41467-023-38500-x},
	abstract = {Abstract
            
              Coral reefs are among the most diverse ecosystems on Earth. They support high biodiversity of multicellular organisms that strongly rely on associated microorganisms for health and nutrition. However, the extent of the coral reef microbiome diversity and its distribution at the oceanic basin-scale remains to be explored. Here, we systematically sampled 3 coral morphotypes, 2 fish species, and planktonic communities in 99 reefs from 32 islands across the Pacific Ocean, to assess reef microbiome composition and biogeography. We show a very large richness of reef microorganisms compared to other environments, which extrapolated to all fishes and corals of the Pacific, approximates the current estimated total prokaryotic diversity for the entire Earth. Microbial communities vary among and within the 3 animal biomes (coral, fish, plankton), and geographically. For corals, the cross-ocean patterns of diversity are different from those known for other multicellular organisms. Within each coral morphotype, community composition is always determined by geographic distance first, both at the island and across ocean scale, and then by environment. Our unprecedented sampling effort of coral reef microbiomes, as part of the
              Tara
              Pacific expedition, provides new insight into the global microbial diversity, the factors driving their distribution, and the biocomplexity of reef ecosystems.},
	language = {en},
	number = {1},
	urldate = {2023-06-12},
	journal = {Nature Communications},
	author = {Galand, Pierre E. and Ruscheweyh, Hans-Joachim and Salazar, Guillem and Hochart, Corentin and Henry, Nicolas and Hume, Benjamin C. C. and Oliveira, Pedro H. and Perdereau, Aude and Labadie, Karine and Belser, Caroline and Boissin, Emilie and Romac, Sarah and Poulain, Julie and Bourdin, Guillaume and Iwankow, Guillaume and Moulin, Clémentine and Armstrong, Eric J. and Paz-García, David A. and Ziegler, Maren and Agostini, Sylvain and Banaigs, Bernard and Boss, Emmanuel and Bowler, Chris and De Vargas, Colomban and Douville, Eric and Flores, Michel and Forcioli, Didier and Furla, Paola and Gilson, Eric and Lombard, Fabien and Pesant, Stéphane and Reynaud, Stéphanie and Thomas, Olivier P. and Troublé, Romain and Zoccola, Didier and Voolstra, Christian R. and Thurber, Rebecca Vega and Sunagawa, Shinichi and Wincker, Patrick and Allemand, Denis and Planes, Serge},
	month = jun,
	year = {2023},
	pages = {3039},
}

Abstract Coral reefs are among the most diverse ecosystems on Earth. They support high biodiversity of multicellular organisms that strongly rely on associated microorganisms for health and nutrition. However, the extent of the coral reef microbiome diversity and its distribution at the oceanic basin-scale remains to be explored. Here, we systematically sampled 3 coral morphotypes, 2 fish species, and planktonic communities in 99 reefs from 32 islands across the Pacific Ocean, to assess reef microbiome composition and biogeography. We show a very large richness of reef microorganisms compared to other environments, which extrapolated to all fishes and corals of the Pacific, approximates the current estimated total prokaryotic diversity for the entire Earth. Microbial communities vary among and within the 3 animal biomes (coral, fish, plankton), and geographically. For corals, the cross-ocean patterns of diversity are different from those known for other multicellular organisms. Within each coral morphotype, community composition is always determined by geographic distance first, both at the island and across ocean scale, and then by environment. Our unprecedented sampling effort of coral reef microbiomes, as part of the Tara Pacific expedition, provides new insight into the global microbial diversity, the factors driving their distribution, and the biocomplexity of reef ecosystems.

@article{heitzman_seasonal_2023,
	title = {Seasonal coral-algae interactions drive {White} {Mat} {Syndrome} coral disease outbreaks},
	volume = {900},
	issn = {00489697},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0048969723050040},
	doi = {10.1016/j.scitotenv.2023.166379},
	language = {en},
	urldate = {2023-10-31},
	journal = {Science of The Total Environment},
	author = {Heitzman, Joshua M. and Mitushasi, Guinther and Spatafora, Davide and Agostini, Sylvain},
	month = nov,
	year = {2023},
	pages = {166379},
}

@article{hochart_ecology_2023,
	title = {Ecology of {Endozoicomonadaceae} in three coral genera across the {Pacific} {Ocean}},
	volume = {14},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-023-38502-9},
	doi = {10.1038/s41467-023-38502-9},
	abstract = {Abstract
            
              Health and resilience of the coral holobiont depend on diverse bacterial communities often dominated by key marine symbionts of the
              Endozoicomonadaceae
              family. The factors controlling their distribution and their functional diversity remain, however, poorly known. Here, we study the ecology of
              Endozoicomonadaceae
              at an ocean basin-scale by sampling specimens from three coral genera (
              Pocillopora
              ,
              Porites
              ,
              Millepora
              ) on 99 reefs from 32 islands across the Pacific Ocean. The analysis of 2447 metabarcoding and 270 metagenomic samples reveals that each coral genus harbored a distinct new species of
              Endozoicomonadaceae
              . These species are composed of nine lineages that have distinct biogeographic patterns. The most common one, found in
              Pocillopora
              , appears to be a globally distributed symbiont with distinct metabolic capabilities, including the synthesis of amino acids and vitamins not produced by the host. The other lineages are structured partly by the host genetic lineage in
              Pocillopora
              and mainly by the geographic location in
              Porites
              .
              Millepora
              is more rarely associated to
              Endozoicomonadaceae
              . Our results show that different coral genera exhibit distinct strategies of host-
              Endozoicomonadaceae
              associations that are defined at the bacteria lineage level.},
	language = {en},
	number = {1},
	urldate = {2023-06-12},
	journal = {Nature Communications},
	author = {Hochart, Corentin and Paoli, Lucas and Ruscheweyh, Hans-Joachim and Salazar, Guillem and Boissin, Emilie and Romac, Sarah and Poulain, Julie and Bourdin, Guillaume and Iwankow, Guillaume and Moulin, Clémentine and Ziegler, Maren and Porro, Barbara and Armstrong, Eric J. and Hume, Benjamin C. C. and Aury, Jean-Marc and Pogoreutz, Claudia and Paz-García, David A. and Nugues, Maggy M. and Agostini, Sylvain and Banaigs, Bernard and Boss, Emmanuel and Bowler, Chris and De Vargas, Colomban and Douville, Eric and Flores, Michel and Forcioli, Didier and Furla, Paola and Gilson, Eric and Lombard, Fabien and Pesant, Stéphane and Reynaud, Stéphanie and Thomas, Olivier P. and Troublé, Romain and Wincker, Patrick and Zoccola, Didier and Allemand, Denis and Planes, Serge and Thurber, Rebecca Vega and Voolstra, Christian R. and Sunagawa, Shinichi and Galand, Pierre E.},
	month = jun,
	year = {2023},
	pages = {3037},
}

Abstract Health and resilience of the coral holobiont depend on diverse bacterial communities often dominated by key marine symbionts of the Endozoicomonadaceae family. The factors controlling their distribution and their functional diversity remain, however, poorly known. Here, we study the ecology of Endozoicomonadaceae at an ocean basin-scale by sampling specimens from three coral genera ( Pocillopora , Porites , Millepora ) on 99 reefs from 32 islands across the Pacific Ocean. The analysis of 2447 metabarcoding and 270 metagenomic samples reveals that each coral genus harbored a distinct new species of Endozoicomonadaceae . These species are composed of nine lineages that have distinct biogeographic patterns. The most common one, found in Pocillopora , appears to be a globally distributed symbiont with distinct metabolic capabilities, including the synthesis of amino acids and vitamins not produced by the host. The other lineages are structured partly by the host genetic lineage in Pocillopora and mainly by the geographic location in Porites . Millepora is more rarely associated to Endozoicomonadaceae . Our results show that different coral genera exhibit distinct strategies of host- Endozoicomonadaceae associations that are defined at the bacteria lineage level.

@article{hudson_ocean_2022,
	title = {Ocean acidification increases the impact of typhoons on algal communities},
	issn = {00489697},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0048969722083735},
	doi = {10.1016/j.scitotenv.2022.161269},
	language = {en},
	urldate = {2023-01-04},
	journal = {Science of The Total Environment},
	author = {Hudson, Callum J. and Agostini, Sylvain and Wada, Shigeki and Hall-Spencer, Jason M. and Connell, Sean D. and Harvey, Ben P.},
	month = dec,
	year = {2022},
	pages = {161269},
}

@article{lombard_open_2023,
	title = {Open science resources from the {Tara} {Pacific} expedition across coral reef and surface ocean ecosystems},
	volume = {10},
	issn = {2052-4463},
	url = {https://www.nature.com/articles/s41597-022-01757-w},
	doi = {10.1038/s41597-022-01757-w},
	abstract = {Abstract
            
              The
              Tara
              Pacific expedition (2016–2018) sampled coral ecosystems around 32 islands in the Pacific Ocean and the ocean surface waters at 249 locations, resulting in the collection of nearly 58 000 samples. The expedition was designed to systematically study warm-water coral reefs and included the collection of corals, fish, plankton, and seawater samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide a complete description of the sampling methodology, and we explain how to explore and access the different datasets generated by the expedition. Environmental context data were obtained from taxonomic registries, gazetteers, almanacs, climatologies, operational biogeochemical models, and satellite observations. The quality of the different environmental measures has been validated not only by various quality control steps, but also through a global analysis allowing the comparison with known environmental large-scale structures. Such publicly released datasets open the perspective to address a wide range of scientific questions.},
	language = {en},
	number = {1},
	urldate = {2023-06-12},
	journal = {Scientific Data},
	author = {Lombard, Fabien and Bourdin, Guillaume and Pesant, Stéphane and Agostini, Sylvain and Baudena, Alberto and Boissin, Emilie and Cassar, Nicolas and Clampitt, Megan and Conan, Pascal and Da Silva, Ophélie and Dimier, Céline and Douville, Eric and Elineau, Amanda and Fin, Jonathan and Flores, J. Michel and Ghiglione, Jean-François and Hume, Benjamin C. C. and Jalabert, Laetitia and John, Seth G. and Kelly, Rachel L. and Koren, Ilan and Lin, Yajuan and Marie, Dominique and McMinds, Ryan and Mériguet, Zoé and Metzl, Nicolas and Paz-García, David A. and Pedrotti, Maria Luiza and Poulain, Julie and Pujo-Pay, Mireille and Ras, Joséphine and Reverdin, Gilles and Romac, Sarah and Rouan, Alice and Röttinger, Eric and Vardi, Assaf and Voolstra, Christian R. and Moulin, Clémentine and Iwankow, Guillaume and Banaigs, Bernard and Bowler, Chris and De Vargas, Colomban and Forcioli, Didier and Furla, Paola and Galand, Pierre E. and Gilson, Eric and Reynaud, Stéphanie and Sunagawa, Shinichi and Sullivan, Matthew B. and Thomas, Olivier P. and Troublé, Romain and Thurber, Rebecca Vega and Wincker, Patrick and Zoccola, Didier and Allemand, Denis and Planes, Serge and Boss, Emmanuel and Gorsky, Gaby},
	month = jun,
	year = {2023},
	pages = {324},
}

Abstract The Tara Pacific expedition (2016–2018) sampled coral ecosystems around 32 islands in the Pacific Ocean and the ocean surface waters at 249 locations, resulting in the collection of nearly 58 000 samples. The expedition was designed to systematically study warm-water coral reefs and included the collection of corals, fish, plankton, and seawater samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide a complete description of the sampling methodology, and we explain how to explore and access the different datasets generated by the expedition. Environmental context data were obtained from taxonomic registries, gazetteers, almanacs, climatologies, operational biogeochemical models, and satellite observations. The quality of the different environmental measures has been validated not only by various quality control steps, but also through a global analysis allowing the comparison with known environmental large-scale structures. Such publicly released datasets open the perspective to address a wide range of scientific questions.

@article{noel_pervasive_2023,
	title = {Pervasive tandem duplications and convergent evolution shape coral genomes},
	volume = {24},
	issn = {1474-760X},
	url = {https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02960-7},
	doi = {10.1186/s13059-023-02960-7},
	abstract = {Abstract
            
              Background
              Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to coral reef ecosystems, providing habitat to a great diversity of species.
            
            
              Results
              
                In the frame of the Tara Pacific expedition, we assemble two coral genomes,
                Porites lobata
                and
                Pocillopora
                cf.
                effusa,
                with vastly improved contiguity that allows us to study the functional organization of these genomes. We annotate their gene catalog and report a relatively higher gene number than that found in other public coral genome sequences, 43,000 and 32,000 genes, respectively. This finding is explained by a high number of tandemly duplicated genes, accounting for almost a third of the predicted genes. We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to the immune system and disease resistance, which we suggest to be functionally linked to coral host resilience.
              
            
            
              Conclusions
              At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience.},
	language = {en},
	number = {1},
	urldate = {2023-06-12},
	journal = {Genome Biology},
	author = {Noel, Benjamin and Denoeud, France and Rouan, Alice and Buitrago-López, Carol and Capasso, Laura and Poulain, Julie and Boissin, Emilie and Pousse, Mélanie and Da Silva, Corinne and Couloux, Arnaud and Armstrong, Eric and Carradec, Quentin and Cruaud, Corinne and Labadie, Karine and Lê-Hoang, Julie and Tambutté, Sylvie and Barbe, Valérie and Moulin, Clémentine and Bourdin, Guillaume and Iwankow, Guillaume and Romac, Sarah and Agostini, Sylvain and Banaigs, Bernard and Boss, Emmanuel and Bowler, Chris and De Vargas, Colomban and Douville, Eric and Flores, J. Michel and Forcioli, Didier and Furla, Paola and Galand, Pierre E. and Lombard, Fabien and Pesant, Stéphane and Reynaud, Stéphanie and Sullivan, Matthew B. and Sunagawa, Shinichi and Thomas, Olivier P. and Troublé, Romain and Thurber, Rebecca Vega and Allemand, Denis and Planes, Serge and Gilson, Eric and Zoccola, Didier and Wincker, Patrick and Voolstra, Christian R. and Aury, Jean-Marc},
	month = jun,
	year = {2023},
	pages = {123},
}

Abstract Background Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to coral reef ecosystems, providing habitat to a great diversity of species. Results In the frame of the Tara Pacific expedition, we assemble two coral genomes, Porites lobata and Pocillopora cf. effusa, with vastly improved contiguity that allows us to study the functional organization of these genomes. We annotate their gene catalog and report a relatively higher gene number than that found in other public coral genome sequences, 43,000 and 32,000 genes, respectively. This finding is explained by a high number of tandemly duplicated genes, accounting for almost a third of the predicted genes. We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to the immune system and disease resistance, which we suggest to be functionally linked to coral host resilience. Conclusions At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience.

@article{reddy_multi-omics_2023,
	title = {Multi-omics determination of metabolome diversity in natural coral populations in the {Pacific} {Ocean}},
	volume = {4},
	issn = {2662-4435},
	url = {https://www.nature.com/articles/s43247-023-00942-y},
	doi = {10.1038/s43247-023-00942-y},
	abstract = {Abstract
            
              Coral reefs are considered one of the most emblematic ecosystems in our oceans, but their existence is increasingly threatened by climate change. In this study, natural populations of two reef-building coral genera,
              Pocillopora
              spp. and
              Porites
              spp., and one hydrocoral
              Millepora
              cf.
              platyphylla
              from two different marine provinces in the Pacific Ocean were investigated using a multi-omics approach as part of the
              Tara
              Pacific expedition. Here, we propose a standardised method consisting of a biphasic extraction method followed by metabolomics analysis using mass spectrometry for the lipidome and
              1
              H nuclear magnetic resonance for hydrophilic metabolites. Our study assessed a broad range of the metabolome and is the first to identify and add 24 compounds by NMR and over 200 lipids by MS analyses for corals. Metabolic profiles were distinct among genera but not within genotypes of the cnidarian corals. Although endosymbiotic dinoflagellates of the family Symbiodiniaceae are known to play a central role in the metabolomic signature of the coral holobiont, they did not account for all differences. This suggests that a combined effect by different members of the coral holobiont and an interaction with the environment might be at play. Our study provides foundational knowledge on the coral holobiont metabolome.},
	language = {en},
	number = {1},
	urldate = {2024-09-02},
	journal = {Communications Earth \& Environment},
	author = {Reddy, Maggie M. and Goossens, Corentine and Zhou, Yuxiang and Chaib, Slimane and Raviglione, Delphine and Nicolè, Florence and Hume, Benjamin C. C. and Forcioli, Didier and Agostini, Sylvain and Boissin, Emilie and Boss, Emmanuel and Bowler, Chris and De Vargas, Colomban and Douville, Eric and Flores, Michel and Furla, Paola and Galand, Pierre E. and Gilson, Eric and Lombard, Fabien and Pesant, Stéphane and Reynaud, Stéphanie and Sullivan, Matthew B. and Sunagawa, Shinichi and Troublé, Romain and Thurber, Rebecca Vega and Wincker, Patrick and Zoccola, Didier and Voolstra, Christian R. and Allemand, Denis and Planes, Serge and Thomas, Olivier P. and Banaigs, Bernard},
	month = aug,
	year = {2023},
	pages = {281},
}

Abstract Coral reefs are considered one of the most emblematic ecosystems in our oceans, but their existence is increasingly threatened by climate change. In this study, natural populations of two reef-building coral genera, Pocillopora spp. and Porites spp., and one hydrocoral Millepora cf. platyphylla from two different marine provinces in the Pacific Ocean were investigated using a multi-omics approach as part of the Tara Pacific expedition. Here, we propose a standardised method consisting of a biphasic extraction method followed by metabolomics analysis using mass spectrometry for the lipidome and 1 H nuclear magnetic resonance for hydrophilic metabolites. Our study assessed a broad range of the metabolome and is the first to identify and add 24 compounds by NMR and over 200 lipids by MS analyses for corals. Metabolic profiles were distinct among genera but not within genotypes of the cnidarian corals. Although endosymbiotic dinoflagellates of the family Symbiodiniaceae are known to play a central role in the metabolomic signature of the coral holobiont, they did not account for all differences. This suggests that a combined effect by different members of the coral holobiont and an interaction with the environment might be at play. Our study provides foundational knowledge on the coral holobiont metabolome.

@article{reimer_high_2023,
	title = {High abundances of zooxanthellate zoantharians ({Palythoa} and {Zoanthus}) at multiple natural analogues: potential model anthozoans?},
	volume = {42},
	issn = {1432-0975},
	url = {https://doi.org/10.1007/s00338-023-02381-9},
	doi = {10.1007/s00338-023-02381-9},
	abstract = {Whilst natural analogues for future ocean conditions such as CO2 seeps and enclosed lagoons in coral reef regions have received much recent research attention, most efforts in such locations have focused on the effects of prolonged high CO2 levels on scleractinian corals and fishes. Here, we demonstrate that the three species of zooxanthellate zoantharians, hexacorallian non-calcifying “cousins” of scleractinians, are common across five coral reef natural analogue sites with high CO2 levels in the western Pacific Ocean, in Japan (n = 2), Palau, Papua New Guinea, and New Caledonia (n = 1 each). These current observations support previously reported cases of high Palythoa and Zoanthus abundance and dominance on various impacted coral reefs worldwide. The results demonstrate the need for more research on the ecological roles of zooxanthellate zoantharians in coral reef systems, as well as examining other “understudied” taxa that may become increasingly important in the near future under climate change scenarios. Given their abundance in these sites combined with ease in sampling and non-CITES status, some zoantharian species should make excellent hexacoral models for examining potential resilience or resistance mechanisms of anthozoans to future high pCO2 conditions.},
	journal = {Coral Reefs},
	author = {Reimer, James Davis and Agostini, Sylvain and Golbuu, Yimnang and Harvey, Ben P. and Izumiyama, Michael and Jamodiong, Emmeline A. and Kawai, Erina and Kayanne, Hajime and Kurihara, Haruko and Ravasi, Timothy and Wada, Shigeki and Rodolfo-Metalpa, Riccardo},
	month = apr,
	year = {2023},
	pages = {707--715},
}

Whilst natural analogues for future ocean conditions such as CO2 seeps and enclosed lagoons in coral reef regions have received much recent research attention, most efforts in such locations have focused on the effects of prolonged high CO2 levels on scleractinian corals and fishes. Here, we demonstrate that the three species of zooxanthellate zoantharians, hexacorallian non-calcifying “cousins” of scleractinians, are common across five coral reef natural analogue sites with high CO2 levels in the western Pacific Ocean, in Japan (n = 2), Palau, Papua New Guinea, and New Caledonia (n = 1 each). These current observations support previously reported cases of high Palythoa and Zoanthus abundance and dominance on various impacted coral reefs worldwide. The results demonstrate the need for more research on the ecological roles of zooxanthellate zoantharians in coral reef systems, as well as examining other “understudied” taxa that may become increasingly important in the near future under climate change scenarios. Given their abundance in these sites combined with ease in sampling and non-CITES status, some zoantharian species should make excellent hexacoral models for examining potential resilience or resistance mechanisms of anthozoans to future high pCO2 conditions.

@article{rouan_telomere_2023,
	title = {Telomere {DNA} length regulation is influenced by seasonal temperature differences in short-lived but not in long-lived reef-building corals},
	volume = {14},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-023-38499-1},
	doi = {10.1038/s41467-023-38499-1},
	abstract = {Abstract
            
              Telomeres are environment-sensitive regulators of health and aging. Here,we present telomere DNA length analysis of two reef-building coral genera revealing that the long- and short-term water thermal regime is a key driver of between-colony variation across the Pacific Ocean. Notably, there are differences between the two studied genera. The telomere DNA lengths of the short-lived, more stress-sensitive
              Pocillopora
              spp. colonies were largely determined by seasonal temperature variation, whereas those of the long-lived, more stress-resistant
              Porites
              spp. colonies were insensitive to seasonal patterns, but rather influenced by past thermal anomalies. These results reveal marked differences in telomere DNA length regulation between two evolutionary distant coral genera exhibiting specific life-history traits. We propose that environmentally regulated mechanisms of telomere maintenance are linked to organismal performances, a matter of paramount importance considering the effects of climate change on health.},
	language = {en},
	number = {1},
	urldate = {2023-06-12},
	journal = {Nature Communications},
	author = {Rouan, Alice and Pousse, Melanie and Djerbi, Nadir and Porro, Barbara and Bourdin, Guillaume and Carradec, Quentin and Hume, Benjamin Cc. and Poulain, Julie and Lê-Hoang, Julie and Armstrong, Eric and Agostini, Sylvain and Salazar, Guillem and Ruscheweyh, Hans-Joachim and Aury, Jean-Marc and Paz-García, David A. and McMinds, Ryan and Giraud-Panis, Marie-Josèphe and Deshuraud, Romane and Ottaviani, Alexandre and Morini, Lycia Die and Leone, Camille and Wurzer, Lia and Tran, Jessica and Zoccola, Didier and Pey, Alexis and Moulin, Clémentine and Boissin, Emilie and Iwankow, Guillaume and Romac, Sarah and De Vargas, Colomban and Banaigs, Bernard and Boss, Emmanuel and Bowler, Chris and Douville, Eric and Flores, Michel and Reynaud, Stéphanie and Thomas, Olivier P. and Troublé, Romain and Thurber, Rebecca Vega and Planes, Serge and Allemand, Denis and Pesant, Stephane and Galand, Pierre E. and Wincker, Patrick and Sunagawa, Shinichi and Röttinger, Eric and Furla, Paola and Voolstra, Christian R. and Forcioli, Didier and Lombard, Fabien and Gilson, Eric},
	month = jun,
	year = {2023},
	pages = {3038},
}

Abstract Telomeres are environment-sensitive regulators of health and aging. Here,we present telomere DNA length analysis of two reef-building coral genera revealing that the long- and short-term water thermal regime is a key driver of between-colony variation across the Pacific Ocean. Notably, there are differences between the two studied genera. The telomere DNA lengths of the short-lived, more stress-sensitive Pocillopora spp. colonies were largely determined by seasonal temperature variation, whereas those of the long-lived, more stress-resistant Porites spp. colonies were insensitive to seasonal patterns, but rather influenced by past thermal anomalies. These results reveal marked differences in telomere DNA length regulation between two evolutionary distant coral genera exhibiting specific life-history traits. We propose that environmentally regulated mechanisms of telomere maintenance are linked to organismal performances, a matter of paramount importance considering the effects of climate change on health.

@article{seto_potential_2023,
	title = {Potential ecosystem regime shift resulting from elevated {CO}$_{\textrm{2}}$ and inhibition of macroalgal recruitment by turf algae},
	volume = {16},
	issn = {1874-1738, 1874-1746},
	url = {https://link.springer.com/10.1007/s12080-022-00550-0},
	doi = {10.1007/s12080-022-00550-0},
	language = {en},
	urldate = {2023-01-04},
	journal = {Theoretical Ecology},
	author = {Seto, Mayumi and Harvey, Ben P. and Wada, Shigeki and Agostini, Sylvain},
	month = jan,
	year = {2023},
	pages = {1--12},
}

@article{veglia_endogenous_2023,
	title = {Endogenous viral elements reveal associations between a non-retroviral {RNA} virus and symbiotic dinoflagellate genomes},
	volume = {6},
	issn = {2399-3642},
	url = {https://www.nature.com/articles/s42003-023-04917-9},
	doi = {10.1038/s42003-023-04917-9},
	abstract = {Abstract
            
              Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially
              Symbiodinium
              ), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.},
	language = {en},
	number = {1},
	urldate = {2023-06-12},
	journal = {Communications Biology},
	author = {Veglia, Alex J. and Bistolas, Kalia S. I. and Voolstra, Christian R. and Hume, Benjamin C. C. and Ruscheweyh, Hans-Joachim and Planes, Serge and Allemand, Denis and Boissin, Emilie and Wincker, Patrick and Poulain, Julie and Moulin, Clémentine and Bourdin, Guillaume and Iwankow, Guillaume and Romac, Sarah and Agostini, Sylvain and Banaigs, Bernard and Boss, Emmanuel and Bowler, Chris and De Vargas, Colomban and Douville, Eric and Flores, Michel and Forcioli, Didier and Furla, Paola and Galand, Pierre E. and Gilson, Eric and Lombard, Fabien and Pesant, Stéphane and Reynaud, Stéphanie and Sunagawa, Shinichi and Thomas, Olivier P. and Troublé, Romain and Zoccola, Didier and Correa, Adrienne M. S. and Vega Thurber, Rebecca L.},
	month = jun,
	year = {2023},
	pages = {566},
}

Abstract Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium ), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.

@article{voolstra_disparate_2023,
	title = {Disparate genetic divergence patterns in three corals across a pan-{Pacific} environmental gradient highlight species-specific adaptation},
	volume = {2},
	issn = {2731-4243},
	url = {https://www.nature.com/articles/s44185-023-00020-8},
	doi = {10.1038/s44185-023-00020-8},
	abstract = {Abstract
            
              Tropical coral reefs are among the most affected ecosystems by climate change and face increasing loss in the coming decades. Effective conservation strategies that maximize ecosystem resilience must be informed by the accurate characterization of extant genetic diversity and population structure together with an understanding of the adaptive potential of keystone species. Here we analyzed samples from the Tara Pacific Expedition (2016–2018) that completed an 18,000 km longitudinal transect of the Pacific Ocean sampling three widespread corals—
              Pocillopora meandrina
              ,
              Porites lobata
              , and
              Millepora
              cf.
              platyphylla
              —across 33 sites from 11 islands. Using deep metagenomic sequencing of 269 colonies in conjunction with morphological analyses and climate variability data, we can show that despite a targeted sampling the transect encompasses multiple cryptic species. These species exhibit disparate biogeographic patterns and, most importantly, distinct evolutionary patterns in identical environmental regimes. Our findings demonstrate on a basin scale that evolutionary trajectories are species-specific and can only in part be predicted from the environment. This highlights that conservation strategies must integrate multi-species investigations to discern the distinct genomic footprints shaped by selection as well as the genetic potential for adaptive change.},
	language = {en},
	number = {1},
	urldate = {2024-09-02},
	journal = {npj Biodiversity},
	author = {Voolstra, Christian R. and Hume, Benjamin C. C. and Armstrong, Eric J. and Mitushasi, Guinther and Porro, Barbara and Oury, Nicolas and Agostini, Sylvain and Boissin, Emilie and Poulain, Julie and Carradec, Quentin and Paz-García, David A. and Zoccola, Didier and Magalon, Hélène and Moulin, Clémentine and Bourdin, Guillaume and Iwankow, Guillaume and Romac, Sarah and Banaigs, Bernard and Boss, Emmanuel and Bowler, Chris and De Vargas, Colomban and Douville, Eric and Flores, Michel and Furla, Paola and Galand, Pierre E. and Gilson, Eric and Lombard, Fabien and Pesant, Stéphane and Reynaud, Stéphanie and Sullivan, Matthew B. and Sunagawa, Shinichi and Thomas, Olivier P. and Troublé, Romain and Thurber, Rebecca Vega and Wincker, Patrick and Planes, Serge and Allemand, Denis and Forcioli, Didier},
	month = jul,
	year = {2023},
	pages = {15},
}

Abstract Tropical coral reefs are among the most affected ecosystems by climate change and face increasing loss in the coming decades. Effective conservation strategies that maximize ecosystem resilience must be informed by the accurate characterization of extant genetic diversity and population structure together with an understanding of the adaptive potential of keystone species. Here we analyzed samples from the Tara Pacific Expedition (2016–2018) that completed an 18,000 km longitudinal transect of the Pacific Ocean sampling three widespread corals— Pocillopora meandrina , Porites lobata , and Millepora cf. platyphylla —across 33 sites from 11 islands. Using deep metagenomic sequencing of 269 colonies in conjunction with morphological analyses and climate variability data, we can show that despite a targeted sampling the transect encompasses multiple cryptic species. These species exhibit disparate biogeographic patterns and, most importantly, distinct evolutionary patterns in identical environmental regimes. Our findings demonstrate on a basin scale that evolutionary trajectories are species-specific and can only in part be predicted from the environment. This highlights that conservation strategies must integrate multi-species investigations to discern the distinct genomic footprints shaped by selection as well as the genetic potential for adaptive change.

@article{zhao_ocean_2023,
	title = {Ocean acidification stunts molluscan growth at {CO2} seeps},
	volume = {873},
	issn = {00489697},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0048969723009099},
	doi = {10.1016/j.scitotenv.2023.162293},
	language = {en},
	urldate = {2023-02-24},
	journal = {Science of The Total Environment},
	author = {Zhao, Liqiang and Harvey, Ben P. and Higuchi, Tomihiko and Agostini, Sylvain and Tanaka, Kentaro and Murakami-Sugihara, Naoko and Morgan, Holly and Baker, Phoebe and Hall-Spencer, Jason M. and Shirai, Kotaro},
	month = may,
	year = {2023},
	pages = {162293},
}

@article{hall-spencer_decreased_2022,
	title = {Decreased diversity and abundance of marine invertebrates at {CO}$_{\textrm{2}}$ seeps in warm-temperate {Japan}},
	volume = {39},
	issn = {0289-0003},
	url = {https://bioone.org/journals/zoological-science/volume-39/issue-1/zs210061/Decreased-Diversity-and-Abundance-of-Marine-Invertebrates-at-CO2-Seeps/10.2108/zs210061.full},
	doi = {10.2108/zs210061},
	number = {1},
	urldate = {2022-02-02},
	journal = {Zoological Science},
	author = {Hall-Spencer, Jason M. and Belfiore, Giuseppe and Tomatsuri, Morihiko and Porzio, Lucia and Harvey, Ben P. and Agostini, Sylvain and Kon, Koetsu},
	month = jan,
	year = {2022},
	pages = {41--51},
}

@article{heitzman_recurrent_2022,
	title = {Recurrent disease outbreak in a warm temperate marginal coral community},
	volume = {182},
	issn = {0025326X},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0025326X22006361},
	doi = {10.1016/j.marpolbul.2022.113954},
	language = {en},
	urldate = {2022-08-01},
	journal = {Marine Pollution Bulletin},
	author = {Heitzman, Joshua M. and Caputo, Nicolè and Yang, Sung-Yin and Harvey, Ben P. and Agostini, Sylvain},
	month = sep,
	year = {2022},
	pages = {113954},
}

@article{agostini_simplification_2021,
	title = {Simplification, not “tropicalization”, of temperate marine ecosystems under ocean warming and acidification},
	volume = {27},
	issn = {1354-1013, 1365-2486},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/gcb.15749},
	doi = {10.1111/gcb.15749},
	language = {en},
	number = {19},
	urldate = {2021-12-21},
	journal = {Global Change Biology},
	author = {Agostini, Sylvain and Harvey, Ben P. and Milazzo, Marco and Wada, Shigeki and Kon, Koetsu and Floc’h, Nicolas and Komatsu, Kosei and Kuroyama, Mayumi and Hall‐Spencer, Jason M.},
	month = oct,
	year = {2021},
	keywords = {biogeography, climate change, kelp forests, natural analogues, range shift, scleractinian corals, warm-temperate},
	pages = {4771--4784},
}

@article{agostini_greater_2021,
	title = {Greater mitochondrial energy production provides resistance to ocean acidification in “{Winning}” hermatypic corals},
	volume = {7},
	issn = {2296-7745},
	url = {https://www.frontiersin.org/articles/10.3389/fmars.2020.600836/full},
	doi = {10.3389/fmars.2020.600836},
	abstract = {Coral communities around the world are projected to be negatively affected by ocean acidification. Not all coral species will respond in the same manner to rising CO
              2
              levels. Evidence from naturally acidified areas such as CO
              2
              seeps have shown that although a few species are resistant to elevated CO
              2
              , most lack sufficient resistance resulting in their decline. This has led to the simple grouping of coral species into “winners” and “losers,” but the physiological traits supporting this ecological assessment are yet to be fully understood. Here using CO
              2
              seeps, in two biogeographically distinct regions, we investigated whether physiological traits related to energy production [mitochondrial electron transport systems (ETSAs) activities] and biomass (protein contents) differed between winning and losing species in order to identify possible physiological traits of resistance to ocean acidification and whether they can be acquired during short-term transplantations. We show that winning species had a lower biomass (protein contents per coral surface area) resulting in a higher potential for energy production (biomass specific ETSA: ETSA per protein contents) compared to losing species. We hypothesize that winning species inherently allocate more energy toward inorganic growth (calcification) compared to somatic (tissue) growth. In contrast, we found that losing species that show a higher biomass under reference
              p
              CO
              2
              experienced a loss in biomass and variable response in area-specific ETSA that did not translate in an increase in biomass-specific ETSA following either short-term (4–5 months) or even life-long acclimation to elevated
              p
              CO
              2
              conditions. Our results suggest that resistance to ocean acidification in corals may not be acquired within a single generation or through the selection of physiologically resistant individuals. This reinforces current evidence suggesting that ocean acidification will reshape coral communities around the world, selecting species that have an inherent resistance to elevated
              p
              CO
              2
              .},
	urldate = {2021-07-27},
	journal = {Frontiers in Marine Science},
	author = {Agostini, Sylvain and Houlbrèque, Fanny and Biscéré, Tom and Harvey, Ben P. and Heitzman, Joshua M. and Takimoto, Risa and Yamazaki, Wataru and Milazzo, Marco and Rodolfo-Metalpa, Riccardo},
	month = jan,
	year = {2021},
	pages = {600836},
}

Coral communities around the world are projected to be negatively affected by ocean acidification. Not all coral species will respond in the same manner to rising CO 2 levels. Evidence from naturally acidified areas such as CO 2 seeps have shown that although a few species are resistant to elevated CO 2 , most lack sufficient resistance resulting in their decline. This has led to the simple grouping of coral species into “winners” and “losers,” but the physiological traits supporting this ecological assessment are yet to be fully understood. Here using CO 2 seeps, in two biogeographically distinct regions, we investigated whether physiological traits related to energy production [mitochondrial electron transport systems (ETSAs) activities] and biomass (protein contents) differed between winning and losing species in order to identify possible physiological traits of resistance to ocean acidification and whether they can be acquired during short-term transplantations. We show that winning species had a lower biomass (protein contents per coral surface area) resulting in a higher potential for energy production (biomass specific ETSA: ETSA per protein contents) compared to losing species. We hypothesize that winning species inherently allocate more energy toward inorganic growth (calcification) compared to somatic (tissue) growth. In contrast, we found that losing species that show a higher biomass under reference p CO 2 experienced a loss in biomass and variable response in area-specific ETSA that did not translate in an increase in biomass-specific ETSA following either short-term (4–5 months) or even life-long acclimation to elevated p CO 2 conditions. Our results suggest that resistance to ocean acidification in corals may not be acquired within a single generation or through the selection of physiologically resistant individuals. This reinforces current evidence suggesting that ocean acidification will reshape coral communities around the world, selecting species that have an inherent resistance to elevated p CO 2 .

@article{allen_species_2021,
	title = {Species turnover underpins the effect of elevated {CO}$_{\textrm{2}}$ on biofilm communities through early succession},
	volume = {2},
	issn = {26669005},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2666900521000174},
	doi = {10.1016/j.ecochg.2021.100017},
	language = {en},
	urldate = {2021-07-27},
	journal = {Climate Change Ecology},
	author = {Allen, Ro J. and Summerfield, Tina C. and Harvey, Ben P. and Agostini, Sylvain and Rastrick, Samuel P.S. and Hall-Spencer, Jason M. and Hoffmann, Linn J.},
	month = dec,
	year = {2021},
	pages = {100017},
}

@article{harvey_feedback_2021,
	title = {Feedback mechanisms stabilise degraded turf algal systems at a {CO}$_{\textrm{2}}$ seep site},
	volume = {4},
	issn = {2399-3642},
	url = {http://www.nature.com/articles/s42003-021-01712-2},
	doi = {10.1038/s42003-021-01712-2},
	abstract = {Abstract
            Human activities are rapidly changing the structure and function of coastal marine ecosystems. Large-scale replacement of kelp forests and coral reefs with turf algal mats is resulting in homogenous habitats that have less ecological and human value. Ocean acidification has strong potential to substantially favour turf algae growth, which led us to examine the mechanisms that stabilise turf algal states. Here we show that ocean acidification promotes turf algae over corals and macroalgae, mediating new habitat conditions that create stabilising feedback loops (altered physicochemical environment and microbial community, and an inhibition of recruitment) capable of locking turf systems in place. Such feedbacks help explain why degraded coastal habitats persist after being initially pushed past the tipping point by global and local anthropogenic stressors. An understanding of the mechanisms that stabilise degraded coastal habitats can be incorporated into adaptive management to better protect the contribution of coastal systems to human wellbeing.},
	language = {en},
	number = {1},
	urldate = {2021-07-27},
	journal = {Communications Biology},
	author = {Harvey, Ben P. and Allen, Ro and Agostini, Sylvain and Hoffmann, Linn J. and Kon, Koetsu and Summerfield, Tina C. and Wada, Shigeki and Hall-Spencer, Jason M.},
	month = dec,
	year = {2021},
	pages = {219},
}

Abstract Human activities are rapidly changing the structure and function of coastal marine ecosystems. Large-scale replacement of kelp forests and coral reefs with turf algal mats is resulting in homogenous habitats that have less ecological and human value. Ocean acidification has strong potential to substantially favour turf algae growth, which led us to examine the mechanisms that stabilise turf algal states. Here we show that ocean acidification promotes turf algae over corals and macroalgae, mediating new habitat conditions that create stabilising feedback loops (altered physicochemical environment and microbial community, and an inhibition of recruitment) capable of locking turf systems in place. Such feedbacks help explain why degraded coastal habitats persist after being initially pushed past the tipping point by global and local anthropogenic stressors. An understanding of the mechanisms that stabilise degraded coastal habitats can be incorporated into adaptive management to better protect the contribution of coastal systems to human wellbeing.

@article{harvey_ocean_2021,
	title = {Ocean acidification locks algal communities in a species‐poor early successional stage},
	volume = {27},
	issn = {1354-1013, 1365-2486},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/gcb.15455},
	doi = {10.1111/gcb.15455},
	language = {en},
	number = {10},
	urldate = {2021-07-27},
	journal = {Global Change Biology},
	author = {Harvey, Ben P. and Kon, Koetsu and Agostini, Sylvain and Wada, Shigeki and Hall‐Spencer, Jason M.},
	month = may,
	year = {2021},
	pages = {2174--2187},
}

@article{pena_major_2021,
	title = {Major loss of coralline algal diversity in response to ocean acidification},
	volume = {27},
	issn = {1354-1013, 1365-2486},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/gcb.15757},
	doi = {10.1111/gcb.15757},
	language = {en},
	number = {19},
	urldate = {2021-12-21},
	journal = {Global Change Biology},
	author = {Peña, Viviana and Harvey, Ben P. and Agostini, Sylvain and Porzio, Lucia and Milazzo, Marco and Horta, Paulo and Le Gall, Line and Hall‐Spencer, Jason M.},
	month = oct,
	year = {2021},
	pages = {4785--4798},
}

@article{wada_ocean_2021,
	title = {Ocean acidification increases phytobenthic carbon fixation and export in a warm-temperate system},
	volume = {250},
	issn = {02727714},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0272771420308441},
	doi = {10.1016/j.ecss.2020.107113},
	language = {en},
	urldate = {2021-07-27},
	journal = {Estuarine, Coastal and Shelf Science},
	author = {Wada, Shigeki and Agostini, Sylvain and Harvey, Ben P. and Omori, Yuko and Hall-Spencer, Jason M.},
	month = mar,
	year = {2021},
	pages = {107113},
}

@article{cattano_changes_2020,
	title = {Changes in fish communities due to benthic habitat shifts under ocean acidification conditions},
	volume = {725},
	issn = {00489697},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0048969720320143},
	doi = {10.1016/j.scitotenv.2020.138501},
	language = {en},
	urldate = {2021-07-27},
	journal = {Science of The Total Environment},
	author = {Cattano, Carlo and Agostini, Sylvain and Harvey, Ben P. and Wada, Shigeki and Quattrocchi, Federico and Turco, Gabriele and Inaba, Kazuo and Hall-Spencer, Jason M. and Milazzo, Marco},
	month = jul,
	year = {2020},
	pages = {138501},
}

@article{flores_tara_2020,
	title = {Tara {Pacific} {Expedition}’s {Atmospheric} {Measurements} of {Marine} {Aerosols} across the {Atlantic} and {Pacific} {Oceans}: {Overview} and {Preliminary} {Results}},
	volume = {101},
	issn = {0003-0007, 1520-0477},
	shorttitle = {Tara {Pacific} {Expedition}’s {Atmospheric} {Measurements} of {Marine} {Aerosols} across the {Atlantic} and {Pacific} {Oceans}},
	url = {https://journals.ametsoc.org/view/journals/bams/101/5/bams-d-18-0224.1.xml},
	doi = {10.1175/BAMS-D-18-0224.1},
	abstract = {Abstract
            
              Marine aerosols play a significant role in the global radiative budget, in clouds’ processes, and in the chemistry of the marine atmosphere. There is a critical need to better understand their production mechanisms, composition, chemical properties, and the contribution of ocean-derived biogenic matter to their mass and number concentration. Here we present an overview of a new dataset of in situ measurements of marine aerosols conducted over the 2.5-yr
              Tara
              Pacific Expedition over 110,000 km across the Atlantic and Pacific Oceans. Preliminary results are presented here to describe the new dataset that will be built using this novel set of measurements. It will characterize marine aerosols properties in detail and will open a new window to study the marine aerosol link to the water properties and environmental conditions.},
	number = {5},
	urldate = {2021-07-27},
	journal = {Bulletin of the American Meteorological Society},
	author = {Flores, J. M. and Bourdin, G. and Altaratz, O. and Trainic, M. and Lang-Yona, N. and Dzimban, E. and Steinau, S. and Tettich, F. and Planes, S. and Allemand, D. and Agostini, S. and Banaigs, B. and Boissin, E. and Boss, E. and Douville, E. and Forcioli, D. and Furla, P. and Galand, P. E. and Sullivan, M. B. and Gilson, É. and Lombard, F. and Moulin, C. and Pesant, S. and Poulain, J. and Reynaud, S. and Romac, S. and Sunagawa, S. and Thomas, O. P. and Troublé, R. and de Vargas, C. and Thurber, R. Vega and Voolstra, C. R. and Wincker, P. and Zoccola, D. and Bowler, C. and Gorsky, G. and Rudich, Y. and Vardi, A. and Koren, I.},
	month = may,
	year = {2020},
	pages = {E536--E554},
}

Abstract Marine aerosols play a significant role in the global radiative budget, in clouds’ processes, and in the chemistry of the marine atmosphere. There is a critical need to better understand their production mechanisms, composition, chemical properties, and the contribution of ocean-derived biogenic matter to their mass and number concentration. Here we present an overview of a new dataset of in situ measurements of marine aerosols conducted over the 2.5-yr Tara Pacific Expedition over 110,000 km across the Atlantic and Pacific Oceans. Preliminary results are presented here to describe the new dataset that will be built using this novel set of measurements. It will characterize marine aerosols properties in detail and will open a new window to study the marine aerosol link to the water properties and environmental conditions.

@article{kang_origin_2020,
	title = {The {Origin} of the {Subtropical} {Coral} \textit{{Alveopora} japonica} ({Scleractinia}: {Acroporidae}) in {High}-{Latitude} {Environments}},
	volume = {8},
	issn = {2296-701X},
	shorttitle = {The {Origin} of the {Subtropical} {Coral} {Alveopora} japonica ({Scleractinia}},
	url = {https://www.frontiersin.org/article/10.3389/fevo.2020.00012/full},
	doi = {10.3389/fevo.2020.00012},
	urldate = {2021-07-27},
	journal = {Frontiers in Ecology and Evolution},
	author = {Kang, Ji Hyoun and Jang, Ji Eun and Kim, Jae Hwan and Kim, Sangil and Keshavmurthy, Shashank and Agostini, Sylvain and Reimer, James D. and Chen, Chaolun Allen and Choi, Kwang-Sik and Park, Sang Rul and Lee, Hyuk Je},
	month = feb,
	year = {2020},
	pages = {12},
}

@article{kerfahi_responses_2020,
	title = {Responses of {Intertidal} {Bacterial} {Biofilm} {Communities} to {Increasing} {pCO}$_{\textrm{2}}$},
	volume = {22},
	issn = {1436-2228, 1436-2236},
	url = {http://link.springer.com/10.1007/s10126-020-09958-3},
	doi = {10.1007/s10126-020-09958-3},
	language = {en},
	number = {6},
	urldate = {2021-07-27},
	journal = {Marine Biotechnology},
	author = {Kerfahi, Dorsaf and Harvey, Ben P. and Agostini, Sylvain and Kon, Koetsu and Huang, Ruiping and Adams, Jonathan M. and Hall-Spencer, Jason M.},
	month = dec,
	year = {2020},
	pages = {727--738},
}

@article{gorsky_expanding_2019,
	title = {Expanding {Tara} {Oceans} {Protocols} for {Underway}, {Ecosystemic} {Sampling} of the {Ocean}-{Atmosphere} {Interface} {During} {Tara} {Pacific} {Expedition} (2016–2018)},
	volume = {6},
	issn = {2296-7745},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2019.00750/full},
	doi = {10.3389/fmars.2019.00750},
	urldate = {2021-07-27},
	journal = {Frontiers in Marine Science},
	author = {Gorsky, Gabriel and Bourdin, Guillaume and Lombard, Fabien and Pedrotti, Maria Luiza and Audrain, Samuel and Bin, Nicolas and Boss, Emmanuel and Bowler, Chris and Cassar, Nicolas and Caudan, Loic and Chabot, Genevieve and Cohen, Natalie R. and Cron, Daniel and De Vargas, Colomban and Dolan, John R. and Douville, Eric and Elineau, Amanda and Flores, J. Michel and Ghiglione, Jean Francois and Haëntjens, Nils and Hertau, Martin and John, Seth G. and Kelly, Rachel L. and Koren, Ilan and Lin, Yajuan and Marie, Dominique and Moulin, Clémentine and Moucherie, Yohann and Pesant, Stéphane and Picheral, Marc and Poulain, Julie and Pujo-Pay, Mireille and Reverdin, Gilles and Romac, Sarah and Sullivan, Mathew B. and Trainic, Miri and Tressol, Marc and Troublé, Romain and Vardi, Assaf and Voolstra, Christian R. and Wincker, Patrick and Agostini, Sylvain and Banaigs, Bernard and Boissin, Emilie and Forcioli, Didier and Furla, Paola and Galand, Pierre E. and Gilson, Eric and Reynaud, Stéphanie and Sunagawa, Shinichi and Thomas, Olivier P. and Thurber, Rebecca Lisette Vega and Zoccola, Didier and Planes, Serge and Allemand, Denis and Karsenti, Eric},
	month = dec,
	year = {2019},
	pages = {750},
}

@article{harvey_diatoms_2019,
	title = {Diatoms {Dominate} and {Alter} {Marine} {Food}-{Webs} {When} {CO}$_{\textrm{2}}$ {Rises}},
	volume = {11},
	issn = {1424-2818},
	url = {https://www.mdpi.com/1424-2818/11/12/242},
	doi = {10.3390/d11120242},
	abstract = {Diatoms are so important in ocean food-webs that any human induced changes in their abundance could have major effects on the ecology of our seas. The large chain-forming diatom Biddulphia biddulphiana greatly increases in abundance as pCO2 increases along natural seawater CO2 gradients in the north Pacific Ocean. In areas with reference levels of pCO2, it was hard to find, but as seawater carbon dioxide levels rose, it replaced seaweeds and became the main habitat-forming species on the seabed. This diatom algal turf supported a marine invertebrate community that was much less diverse and completely differed from the benthic communities found at present-day levels of pCO2. Seawater CO2 enrichment stimulated the growth and photosynthetic efficiency of benthic diatoms, but reduced the abundance of calcified grazers such as gastropods and sea urchins. These observations suggest that ocean acidification will shift photic zone community composition so that coastal food-web structure and ecosystem function are homogenised, simplified, and more strongly affected by seasonal algal blooms.},
	language = {en},
	number = {12},
	urldate = {2021-07-27},
	journal = {Diversity},
	author = {Harvey, Ben P. and Agostini, Sylvain and Kon, Koetsu and Wada, Shigeki and Hall-Spencer, Jason M.},
	month = dec,
	year = {2019},
	pages = {242},
}

Diatoms are so important in ocean food-webs that any human induced changes in their abundance could have major effects on the ecology of our seas. The large chain-forming diatom Biddulphia biddulphiana greatly increases in abundance as pCO2 increases along natural seawater CO2 gradients in the north Pacific Ocean. In areas with reference levels of pCO2, it was hard to find, but as seawater carbon dioxide levels rose, it replaced seaweeds and became the main habitat-forming species on the seabed. This diatom algal turf supported a marine invertebrate community that was much less diverse and completely differed from the benthic communities found at present-day levels of pCO2. Seawater CO2 enrichment stimulated the growth and photosynthetic efficiency of benthic diatoms, but reduced the abundance of calcified grazers such as gastropods and sea urchins. These observations suggest that ocean acidification will shift photic zone community composition so that coastal food-web structure and ecosystem function are homogenised, simplified, and more strongly affected by seasonal algal blooms.

@article{nakabayashi_potential_2019,
	title = {The potential role of temperate {Japanese} regions as refugia for the coral \textit{{Acropora} hyacinthus} in the face of climate change},
	volume = {9},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/s41598-018-38333-5},
	doi = {10.1038/s41598-018-38333-5},
	language = {en},
	number = {1},
	urldate = {2021-07-27},
	journal = {Scientific Reports},
	author = {Nakabayashi, Aki and Yamakita, Takehisa and Nakamura, Takashi and Aizawa, Hiroaki and Kitano, Yuko F and Iguchi, Akira and Yamano, Hiroya and Nagai, Satoshi and Agostini, Sylvain and Teshima, Kosuke M. and Yasuda, Nina},
	month = dec,
	year = {2019},
	pages = {1892},
}

@article{planes_tara_2019,
	title = {The {Tara} {Pacific} expedition—{A} pan-ecosystemic approach of the “-omics” complexity of coral reef holobionts across the {Pacific} {Ocean}},
	volume = {17},
	issn = {1545-7885},
	url = {https://dx.plos.org/10.1371/journal.pbio.3000483},
	doi = {10.1371/journal.pbio.3000483},
	language = {en},
	number = {9},
	urldate = {2021-07-27},
	journal = {PLOS Biology},
	author = {Planes, Serge and Allemand, Denis and Agostini, Sylvain and Banaigs, Bernard and Boissin, Emilie and Boss, Emmanuel and Bourdin, Guillaume and Bowler, Chris and Douville, Eric and Flores, J. Michel and Forcioli, Didier and Furla, Paola and Galand, Pierre E. and Ghiglione, Jean-François and Gilson, Eric and Lombard, Fabien and Moulin, Clémentine and Pesant, Stephane and Poulain, Julie and Reynaud, Stéphanie and Romac, Sarah and Sullivan, Matthew B. and Sunagawa, Shinichi and Thomas, Olivier P. and Troublé, Romain and de Vargas, Colomban and Vega Thurber, Rebecca and Voolstra, Christian R. and Wincker, Patrick and Zoccola, Didier and {the Tara Pacific Consortium}},
	month = sep,
	year = {2019},
	pages = {e3000483},
}

@article{witkowski_validation_2019,
	title = {Validation of carbon isotope fractionation in algal lipids as a \textit{p}{CO}$_{\textrm{2}}$ proxy using a natural {CO}$_{\textrm{2}}$ seep ({Shikine} {Island}, {Japan})},
	volume = {16},
	issn = {1726-4189},
	url = {https://bg.copernicus.org/articles/16/4451/2019/},
	doi = {10.5194/bg-16-4451-2019},
	abstract = {Abstract. Carbon dioxide concentrations in the atmosphere play an
integral role in many Earth system dynamics, including its influence on
global temperature. The past can provide insights into these dynamics, but
unfortunately reconstructing long-term trends of atmospheric carbon dioxide
(expressed in partial pressure; pCO2) remains a challenge in
paleoclimatology. One promising approach for reconstructing past pCO2
utilizes the isotopic fractionation associated with CO2 fixation during
photosynthesis into organic matter (εp). Previous studies have focused
primarily on testing estimates of εp derived from the δ13C
of species-specific alkenone compounds in laboratory cultures and mesocosm
experiments. Here, we analyze εp derived from the δ13C of
more general algal biomarkers, i.e., compounds derived from a multitude of
species from sites near a CO2 seep off the coast of Shikine Island
(Japan), a natural environment with CO2 concentrations ranging from
ambient (ca. 310 µatm) to elevated (ca. 770 µatm) pCO2. We observed
strong, consistent δ13C shifts in several algal biomarkers from
a variety of sample matrices over the steep CO2 gradient. Of the three
general algal biomarkers explored here, namely loliolide, phytol, and
cholesterol, εp positively correlates with pCO2, in agreement with
εp theory and previous culture studies. pCO2 reconstructed from the
εp of general algal biomarkers show the same trends throughout, as well
as the correct control values, but with lower absolute reconstructed values
than the measured values at the elevated pCO2 sites. Our results show
that naturally occurring CO2 seeps may provide useful testing grounds
for pCO2 proxies and that general algal biomarkers show promise for
reconstructing past pCO2.},
	language = {en},
	number = {22},
	urldate = {2021-07-27},
	journal = {Biogeosciences},
	author = {Witkowski, Caitlyn R. and Agostini, Sylvain and Harvey, Ben P. and van der Meer, Marcel T. J. and Sinninghe Damsté, Jaap S. and Schouten, Stefan},
	month = nov,
	year = {2019},
	pages = {4451--4461},
}

Abstract. Carbon dioxide concentrations in the atmosphere play an integral role in many Earth system dynamics, including its influence on global temperature. The past can provide insights into these dynamics, but unfortunately reconstructing long-term trends of atmospheric carbon dioxide (expressed in partial pressure; pCO2) remains a challenge in paleoclimatology. One promising approach for reconstructing past pCO2 utilizes the isotopic fractionation associated with CO2 fixation during photosynthesis into organic matter (εp). Previous studies have focused primarily on testing estimates of εp derived from the δ13C of species-specific alkenone compounds in laboratory cultures and mesocosm experiments. Here, we analyze εp derived from the δ13C of more general algal biomarkers, i.e., compounds derived from a multitude of species from sites near a CO2 seep off the coast of Shikine Island (Japan), a natural environment with CO2 concentrations ranging from ambient (ca. 310 µatm) to elevated (ca. 770 µatm) pCO2. We observed strong, consistent δ13C shifts in several algal biomarkers from a variety of sample matrices over the steep CO2 gradient. Of the three general algal biomarkers explored here, namely loliolide, phytol, and cholesterol, εp positively correlates with pCO2, in agreement with εp theory and previous culture studies. pCO2 reconstructed from the εp of general algal biomarkers show the same trends throughout, as well as the correct control values, but with lower absolute reconstructed values than the measured values at the elevated pCO2 sites. Our results show that naturally occurring CO2 seeps may provide useful testing grounds for pCO2 proxies and that general algal biomarkers show promise for reconstructing past pCO2.

@article{agostini_ocean_2018,
	title = {Ocean acidification drives community shifts towards simplified non-calcified habitats in a subtropical−temperate transition zone},
	volume = {8},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/s41598-018-29251-7},
	doi = {10.1038/s41598-018-29251-7},
	language = {en},
	number = {1},
	urldate = {2021-07-27},
	journal = {Scientific Reports},
	author = {Agostini, Sylvain and Harvey, Ben P. and Wada, Shigeki and Kon, Koetsu and Milazzo, Marco and Inaba, Kazuo and Hall-Spencer, Jason M.},
	month = dec,
	year = {2018},
	pages = {11354},
}

@article{harvey_dissolution_2018,
	title = {Dissolution: {The} {Achilles}’ {Heel} of the {Triton} {Shell} in an {Acidifying} {Ocean}},
	volume = {5},
	issn = {2296-7745},
	shorttitle = {Dissolution},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2018.00371/full},
	doi = {10.3389/fmars.2018.00371},
	urldate = {2021-07-27},
	journal = {Frontiers in Marine Science},
	author = {Harvey, Ben P. and Agostini, Sylvain and Wada, Shigeki and Inaba, Kazuo and Hall-Spencer, Jason M.},
	month = oct,
	year = {2018},
	pages = {371},
}

@article{agostini_mitochondrial_2016,
	title = {Mitochondrial electron transport activity and metabolism of experimentally bleached hermatypic corals},
	volume = {475},
	issn = {00220981},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0022098115300629},
	doi = {10.1016/j.jembe.2015.11.012},
	language = {en},
	urldate = {2021-07-27},
	journal = {Journal of Experimental Marine Biology and Ecology},
	author = {Agostini, Sylvain and Fujimura, Hiroyuki and Hayashi, Hiroyuki and Fujita, Kazuhiko},
	month = feb,
	year = {2016},
	pages = {100--107},
}

@article{agostini_geochemistry_2015,
	title = {Geochemistry of two shallow {CO}$_{\textrm{2}}$ seeps in {Shikine} {Island} ({Japan}) and their potential for ocean acidification research},
	volume = {2},
	issn = {23524855},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2352485515000298},
	doi = {10.1016/j.rsma.2015.07.004},
	language = {en},
	urldate = {2021-07-27},
	journal = {Regional Studies in Marine Science},
	author = {Agostini, Sylvain and Wada, Shigeki and Kon, Koetsu and Omori, Akihito and Kohtsuka, Hisanori and Fujimura, Hiroyuki and Tsuchiya, Yasutaka and Sato, Toshihiko and Shinagawa, Hideo and Yamada, Yutaro and Inaba, Kazuo},
	month = nov,
	year = {2015},
	pages = {45--53},
}

@article{higuchi_biotic_2014,
	title = {Biotic {Control} of {Skeletal} {Growth} by {Scleractinian} {Corals} in {Aragonite}–{Calcite} {Seas}},
	volume = {9},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0091021},
	doi = {10.1371/journal.pone.0091021},
	language = {en},
	number = {3},
	urldate = {2021-07-27},
	journal = {PLoS ONE},
	author = {Higuchi, Tomihiko and Fujimura, Hiroyuki and Yuyama, Ikuko and Harii, Saki and Agostini, Sylvain and Oomori, Tamotsu},
	editor = {Roberts, John Murray},
	month = mar,
	year = {2014},
	pages = {e91021},
}

@article{agostini_respiratory_2013,
	title = {Respiratory electron transport system activity in symbiotic corals and its link to calcification},
	volume = {18},
	issn = {1864-7782, 1864-7790},
	url = {http://www.int-res.com/abstracts/ab/v18/n2/p125-139/},
	doi = {10.3354/ab00496},
	language = {en},
	number = {2},
	urldate = {2021-07-27},
	journal = {Aquatic Biology},
	author = {Agostini, S and Fujimura, H and Fujita, K and Suzuki, Y and Nakano, Y},
	month = apr,
	year = {2013},
	keywords = {wrongNakano},
	pages = {125--139},
}

@article{agostini_effects_2013,
	title = {The effects of thermal and high-{CO}$_{\textrm{2}}$ stresses on the metabolism and surrounding microenvironment of the coral \textit{{Galaxea} fascicularis}},
	volume = {336},
	issn = {16310691},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1631069113001455},
	doi = {10.1016/j.crvi.2013.07.003},
	language = {en},
	number = {8},
	urldate = {2021-07-27},
	journal = {Comptes Rendus Biologies},
	author = {Agostini, Sylvain and Fujimura, Hiroyuki and Higuchi, Tomihiko and Yuyama, Ikuko and Casareto, Beatriz E. and Suzuki, Yoshimi and Nakano, Yoshikatsu},
	month = aug,
	year = {2013},
	keywords = {wrongNakano},
	pages = {384--391},
}

@article{higuchi_bacterial_2013,
	title = {Bacterial enhancement of bleaching and physiological impacts on the coral \textit{{Montipora} digitata}},
	volume = {440},
	issn = {00220981},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0022098112004030},
	doi = {10.1016/j.jembe.2012.11.011},
	language = {en},
	urldate = {2021-07-27},
	journal = {Journal of Experimental Marine Biology and Ecology},
	author = {Higuchi, Tomihiko and Agostini, Sylvain and Casareto, Beatriz Estela and Yoshinaga, Koichi and Suzuki, Toshiyuki and Nakano, Yoshikatsu and Fujimura, Hiroyuki and Suzuki, Yoshimi},
	month = feb,
	year = {2013},
	keywords = {wrongNakano},
	pages = {54--60},
}