Vega Thurber Rebecca

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Vega Thurber

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Rebecca

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0000-0003-3516-2061

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Expanding Tara oceans protocols for underway, ecosystemic sampling of the ocean-atmosphere interface during Tara Pacific expedition (2016-2018)

(Frontiers Media, 2019-12-11) Gorsky, Gabriel ; Bourdin, Guillaume ; Lombard, Fabien ; Pedrotti, Maria Luiza ; Audrain, Samuel ; Bin, Nicolas ; Boss, Emmanuel S. ; Bowler, Chris ; Cassar, Nicolas ; Caudan, Loic ; Chabot, Genevieve ; Cohen, Natalie R. ; Cron, Daniel ; De Vargas, Colomban ; Dolan, John R. ; Douville, Eric ; Elineau, Amanda ; Flores, J. Michel ; Ghiglione, Jean-Francois ; Haëntjens, Nils ; Hertau, Martin ; John, Seth G. ; Kelly, Rachel L. ; Koren, Ilan ; Lin, Yajuan ; Marie, Dominique ; Moulin, Clémentine ; Moucherie, Yohann ; Pesant, Stephane ; Picheral, Marc ; Poulain, Julie ; Pujo-Pay, Mireille ; Reverdin, Gilles ; Romac, Sarah ; Sullivan, Mathew B. ; Trainic, Miri ; Tressol, Marc ; Troublé, Romain ; Vardi, Assaf ; Voolstra, Christian R. ; Wincker, Patrick ; Agostini, Sylvain ; Banaigs, Bernard ; Boissin, Emilie ; Forcioli, Didier ; Furla, Paola ; Galand, Pierre E. ; Gilson, Eric ; Reynaud, Stephanie ; Sunagawa, Shinichi ; Thomas, Olivier P. ; Vega Thurber, Rebecca ; Zoccola, Didier ; Planes, Serge ; Allemand, Denis ; Karsenti, Eric

Interactions between the ocean and the atmosphere occur at the air-sea interface through the transfer of momentum, heat, gases and particulate matter, and through the impact of the upper-ocean biology on the composition and radiative properties of this boundary layer. The Tara Pacific expedition, launched in May 2016 aboard the schooner Tara, was a 29-month exploration with the dual goals to study the ecology of reef ecosystems along ecological gradients in the Pacific Ocean and to assess inter-island and open ocean surface plankton and neuston community structures. In addition, key atmospheric properties were measured to study links between the two boundary layer properties. A major challenge for the open ocean sampling was the lack of ship-time available for work at “stations”. The time constraint led us to develop new underway sampling approaches to optimize physical, chemical, optical, and genomic methods to capture the entire community structure of the surface layers, from viruses to metazoans in their oceanographic and atmospheric physicochemical context. An international scientific consortium was put together to analyze the samples, generate data, and develop datasets in coherence with the existing Tara Oceans database. Beyond adapting the extensive Tara Oceans sampling protocols for high-resolution underway sampling, the key novelties compared to Tara Oceans’ global assessment of plankton include the measurement of (i) surface plankton and neuston biogeography and functional diversity; (ii) bioactive trace metals distribution at the ocean surface and metal-dependent ecosystem structures; (iii) marine aerosols, including biological entities; (iv) geography, nature and colonization of microplastic; and (v) high-resolution underway assessment of net community production via equilibrator inlet mass spectrometry. We are committed to share the data collected during this expedition, making it an important resource important resource to address a variety of scientific questions.
Algal cover from herbivore exclusion and nutrient enrichment experiments conducted in the Florida Keys National Marine Sanctuary during 2009-2012

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2021-08-05) Burkepile, Deron ; Vega Thurber, Rebecca

This dataset contains summary percent cover data for algal species and other encrusting invertebrates found in the study plots in the Florida Keys National Marine Sanctuary during 2009-2012. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/639509
Algal species ID from herbivore exclusion and nutrient enrichment experiments conducted in the Florida Keys National Marine Sanctuary during 2009-2012 (HERBVRE project)

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2021-08-05) Burkepile, Deron ; Vega Thurber, Rebecca

This dataset contains percent cover data for algal species and other encrusting invertebrates found in the study plots. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/639480
Microbial sample metadata for water samples used in SourceTracker analysis, 2009-2012

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2021-08-10) Burkepile, Deron ; Vega Thurber, Rebecca

This dataset contains microbial sample metadata for water samples used in SourceTracker analysis, from Pickles Reef, Florida Keys National Marine Sanctuary from August of 2011 and 2012. Published in Nature Communications (2016) doi:10.1038/ncomms11833, Supplementary Data 2d. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/674390
Microbial orders comprising the core microbiome across all samples as measured by taxa prevalence, 2009-2012 (HERBVRE project)

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2021-08-05) Burkepile, Deron ; Vega Thurber, Rebecca

This dataset contains microbial orders comprising the core microbiome across all samples as measured by taxa prevalence, from Florida Keys National Marine Sanctuary. Cyanobacteria, Bacteroidetes and Actinobacteria were most abundant in all coral genera, with a core set of 13 bacterial orders in ≥95% of all samples. Published in Nature Communications (2016) doi:10.1038/ncomms11833, Supplementary Data 3a. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/674398
Coral mortality and tissue loss from experiments at Pickles Reef, Florida Keys National Marine Sanctuary, 2009-2012 (HERBVRE project)

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2021-08-05) Burkepile, Deron ; Vega Thurber, Rebecca

This dataset contains data on coral mortality and tissue loss during enclosure experiments at Pickles Reef, Florida Keys National Marine Sanctuary. Published in Nature Communications (2016) doi:10.1038/ncomms11833, Supplementary Data 5a. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/674416
Parrotfish bite annotations from Florida Keys National Marine Sanctuary, 2009-2013

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2021-08-06) Burkepile, Deron ; Vega Thurber, Rebecca

This dataset contains parrotfish bite observations for the study plots at Pickles Reef, Florida Keys National Marine Sanctuary from 2009-2013. Published in Nature Communications (2016) doi:10.1038/ncomms11833, Supplementary Data 2c. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/674439
Microbiome composition of coral species collected from reefs in Mo'orea, French Polynesia and exposed to various experimental treatments in August 2018

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2022-05-24) Thurber, Andrew ; Vega Thurber, Rebecca

Coral samples from reefs in Mo'orea, French Polynesia were exposed to various experimental treatments to quantify how different environmental stressors impact the coral health and microbial community structure of the corals. Environmental stressors included increased temperature and nutrients as well as exudate released from corals when they bleach. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/843188
Microbial sample metadata, sequencing and treatment details, temperature and salinity at Pickles Reef, Florida Keys National Marine Sanctuary from 2009-2012

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2021-08-06) Burkepile, Deron ; Vega Thurber, Rebecca

This dataset contains microbial sample metadata for the study plots including sequencing and treatment details, HCOM temperature and salinity data. The experimental site was in the Florida Keys National Marine Sanctuary from 2009 to 2012. Published in Nature Communications (2016) doi:10.1038/ncomms11833, Supplementary Data 2c. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/674321
Water column temperature measurements from 2017-2019 on coral reefs around the island of Mo’orea, French Polynesia

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2021-07-06) Thurber, Andrew ; Vega Thurber, Rebecca ; Correa, Adrienne Simoes

Water column temperatures were recorded around the island of Mo’orea, French Polynesia from September 2017 through March 2019. Three reef zones (fore reef, back reef, fringing reef) were sampled to help characterize environmental conditions affecting reef health and resilience, and to increase understanding of the factors that trigger viral outbreaks on reefs. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/842938
Natural experiments and long-term monitoring are critical to understand and predict marine host-microbe ecology and evolution

(Public Library of Science, 2021-08-19) Leray, Matthieu ; Wilkins, Laetitia G. E. ; Apprill, Amy ; Bik, Holly M. ; Clever, Friederike ; Connolly, Sean R. ; De León, Marina E. ; Duffy, J. Emmett ; Ezzat, Leïla ; Gignoux-Wolfsohn, Sarah ; Herre, Edward Allen ; Kaye, Jonathan Z. ; Kline, David ; Kueneman, Jordan G. ; McCormick, Melissa K. ; McMillan, W. Owen ; O’Dea, Aaron ; Pereira, Tiago J. ; Petersen, Jillian M. ; Petticord, Daniel F. ; Torchin, Mark ; Vega Thurber, Rebecca ; Videvall, Elin ; Wcislo, William T. ; Yuen, Benedict ; Eisen, Jonathan A.

Marine multicellular organisms host a diverse collection of bacteria, archaea, microbial eukaryotes, and viruses that form their microbiome. Such host-associated microbes can significantly influence the host’s physiological capacities; however, the identity and functional role(s) of key members of the microbiome (“core microbiome”) in most marine hosts coexisting in natural settings remain obscure. Also unclear is how dynamic interactions between hosts and the immense standing pool of microbial genetic variation will affect marine ecosystems’ capacity to adjust to environmental changes. Here, we argue that significantly advancing our understanding of how host-associated microbes shape marine hosts’ plastic and adaptive responses to environmental change requires (i) recognizing that individual host–microbe systems do not exist in an ecological or evolutionary vacuum and (ii) expanding the field toward long-term, multidisciplinary research on entire communities of hosts and microbes. Natural experiments, such as time-calibrated geological events associated with well-characterized environmental gradients, provide unique ecological and evolutionary contexts to address this challenge. We focus here particularly on mutualistic interactions between hosts and microbes, but note that many of the same lessons and approaches would apply to other types of interactions.
The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean

(Public Library of Science, 2019-09-23) Planes, Serge ; Allemand, Denis ; Agostini, Sylvain ; Banaigs, Bernard ; Boissin, Emilie ; Boss, Emmanuel S. ; Bourdin, Guillaume ; Bowler, Chris ; Douville, Eric ; Flores, J. Michel ; Forcioli, Didier ; Furla, Paola ; Galand, Pierre E. ; Ghiglione, Jean-Francois ; Gilson, Eric ; Lombard, Fabien ; Moulin, Clémentine ; Pesant, Stephane ; Poulain, Julie ; Reynaud, Stephanie ; Romac, Sarah ; Sullivan, Matthew B. ; Sunagawa, Shinichi ; Thomas, Olivier P. ; Troublé, Romain ; de Vargas, Colomban ; Vega Thurber, Rebecca ; Voolstra, Christian R. ; Wincker, Patrick ; Tara Pacific Consortium

Coral reefs are the most diverse habitats in the marine realm. Their productivity, structural complexity, and biodiversity critically depend on ecosystem services provided by corals that are threatened because of climate change effects—in particular, ocean warming and acidification. The coral holobiont is composed of the coral animal host, endosymbiotic dinoflagellates, associated viruses, bacteria, and other microeukaryotes. In particular, the mandatory photosymbiosis with microalgae of the family Symbiodiniaceae and its consequences on the evolution, physiology, and stress resilience of the coral holobiont have yet to be fully elucidated. The functioning of the holobiont as a whole is largely unknown, although bacteria and viruses are presumed to play roles in metabolic interactions, immunity, and stress tolerance. In the context of climate change and anthropogenic threats on coral reef ecosystems, the Tara Pacific project aims to provide a baseline of the “-omics” complexity of the coral holobiont and its ecosystem across the Pacific Ocean and for various oceanographically distinct defined areas. Inspired by the previous Tara Oceans expeditions, the Tara Pacific expedition (2016–2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing an east–west transect from Panama to Papua New Guinea and a south–north transect from Australia to Japan, sampling corals throughout 32 island systems with local replicates. Tara Pacific has developed and applied state-of-the-art technologies in very-high-throughput genetic sequencing and molecular analysis to reveal the entire microbial and chemical diversity as well as functional traits associated with coral holobionts, together with various measures on environmental forcing. This ambitious project aims at revealing a massive amount of novel biodiversity, shedding light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs and providing a reference of the biological state of modern coral reefs in the Anthropocene.
Water column nutrients for ambient nutrient conditions from Pickles Reef in Upper Florida Keys, 2009-2012 (HERBVRE project)

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2021-08-05) Burkepile, Deron ; Vega Thurber, Rebecca

This dataset contains summary percent cover data for algal species and other encrusting invertebrates found in the study plots. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/639563
Coral associated microbes on coral, sediment and water sampled from coral reefs in Mo'orea, French Polynesia in 2017 and 2018

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2021-04-23) Thurber, Andrew ; Vega Thurber, Rebecca ; Correa, Adrienne Simoes

Three species of coral, plus water and sediment, were sampled at 21 sites around the island of Mo’orea, French Polynesia during the dry and rainy seasons in 2017 and 2018. Coral associated microbes (bacteria and archaea) were investigated and their community composition characterized through sequencing of the 16S rRNA gene. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/845039
Benthic community composition at Pickles Reef, Florida Keys National Marine Sanctuary from 2009-2013

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2021-08-06) Burkepile, Deron ; Vega Thurber, Rebecca

This dataset contains benthic community composition data for the study plots at Pickles Reef, Florida Keys National Marine Sanctuary from 2009-2013. Published in Nature Communications (2016) doi:10.1038/ncomms11833, Supplementary Data 2c. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/674368
Dominant microbe taxa from Florida Keys National Marine Sanctuary, 2009-2012 (HERBVRE project)

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2021-08-17) Burkepile, Deron ; Vega Thurber, Rebecca

This dataset contains microbial orders that rose to dominate at least one sample. Values quantify the number of samples in which each order was the most abundant, as well as average metadata values for the samples in which that order became most abundant. Metadata values calculated are temperature, overall community evenness, the cover of all upright algae, tall turf algae, or cyanobacteria, and the average abundance of the dominant taxon. Published in Nature Communications (2016) doi:10.1038/ncomms11833, Supplementary Data 3f. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/674407
Relative abundance of phyla from Florida Keys National Marine Sanctuary, 2009-2013

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2021-08-06) Burkepile, Deron ; Vega Thurber, Rebecca

This dataset contains relative abundance data of phyla for the study plots at Pickles Reef, Florida Keys National Marine Sanctuary from 2009-2013. Published in Nature Communications (2016) doi:10.1038/ncomms11833, Supplementary Data 2c. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/674449

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