Articles | Volume 13, issue 14
https://doi.org/10.5194/bg-13-4135-2016
© Author(s) 2016. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
https://doi.org/10.5194/bg-13-4135-2016
© Author(s) 2016. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
Research article
| 
19 Jul 2016
Research article |
| 19 Jul 2016
Global analysis of gene expression dynamics within the marine microbial community during the VAHINE mesocosm experiment in the southwest Pacific
Ulrike Pfreundt
Institute for Biology III, University of Freiburg, Freiburg, Germany
Dina Spungin
Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel
Sophie Bonnet
Aix Marseille Université, CNRS/INSU, Université de
Toulon, IRD, Mediterranean Institute of Oceanography (MIO), Marseille, France
Institut de Recherche pour le Développement, AMU/
CNRS/INSU, Université de Toulon, Mediterranean Institute of Oceanography
(MIO) Nouméa, New Caledonia, France
Ilana Berman-Frank
Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel
Wolfgang R. Hess
CORRESPONDING AUTHOR
Institute for Biology III, University of Freiburg, Freiburg, Germany
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Nir Haim, Vika Grigorieva, Rotem Soffer, Boaz Mayzel, Timor Katz, Ronen Alkalay, Eli Biton, Ayah Lazar, Hezi Gildor, Ilana Berman-Frank, Yishai Weinstein, Barak Herut, and Yaron Toledo
Earth Syst. Sci. Data, 16, 2659–2668, https://doi.org/10.5194/essd-16-2659-2024, https://doi.org/10.5194/essd-16-2659-2024, 2024
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This paper outlines the process of creating an open-access surface wave dataset, drawing from deep-sea research station observations located 50 km off the coast of Israel. The discussion covers the wave monitoring procedure, from instrument configuration to wave field retrieval, and aspects of quality assurance. The dataset presented spans over 5 years, offering uncommon in situ wave measurements in the deep sea, and addresses the existing gap in wave information within the region.
Zhibo Shao, Yangchun Xu, Hua Wang, Weicheng Luo, Lice Wang, Yuhong Huang, Nona Sheila R. Agawin, Ayaz Ahmed, Mar Benavides, Mikkel Bentzon-Tilia, Ilana Berman-Frank, Hugo Berthelot, Isabelle C. Biegala, Mariana B. Bif, Antonio Bode, Sophie Bonnet, Deborah A. Bronk, Mark V. Brown, Lisa Campbell, Douglas G. Capone, Edward J. Carpenter, Nicolas Cassar, Bonnie X. Chang, Dreux Chappell, Yuh-ling Lee Chen, Matthew J. Church, Francisco M. Cornejo-Castillo, Amália Maria Sacilotto Detoni, Scott C. Doney, Cecile Dupouy, Marta Estrada, Camila Fernandez, Bieito Fernández-Castro, Debany Fonseca-Batista, Rachel A. Foster, Ken Furuya, Nicole Garcia, Kanji Goto, Jesús Gago, Mary R. Gradoville, M. Robert Hamersley, Britt A. Henke, Cora Hörstmann, Amal Jayakumar, Zhibing Jiang, Shuh-Ji Kao, David M. Karl, Leila R. Kittu, Angela N. Knapp, Sanjeev Kumar, Julie LaRoche, Hongbin Liu, Jiaxing Liu, Caroline Lory, Carolin R. Löscher, Emilio Marañón, Lauren F. Messer, Matthew M. Mills, Wiebke Mohr, Pia H. Moisander, Claire Mahaffey, Robert Moore, Beatriz Mouriño-Carballido, Margaret R. Mulholland, Shin-ichiro Nakaoka, Joseph A. Needoba, Eric J. Raes, Eyal Rahav, Teodoro Ramírez-Cárdenas, Christian Furbo Reeder, Lasse Riemann, Virginie Riou, Julie C. Robidart, Vedula V. S. S. Sarma, Takuya Sato, Himanshu Saxena, Corday Selden, Justin R. Seymour, Dalin Shi, Takuhei Shiozaki, Arvind Singh, Rachel E. Sipler, Jun Sun, Koji Suzuki, Kazutaka Takahashi, Yehui Tan, Weiyi Tang, Jean-Éric Tremblay, Kendra Turk-Kubo, Zuozhu Wen, Angelicque E. White, Samuel T. Wilson, Takashi Yoshida, Jonathan P. Zehr, Run Zhang, Yao Zhang, and Ya-Wei Luo
Earth Syst. Sci. Data, 15, 3673–3709, https://doi.org/10.5194/essd-15-3673-2023, https://doi.org/10.5194/essd-15-3673-2023, 2023
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N2 fixation by marine diazotrophs is an important bioavailable N source to the global ocean. This updated global oceanic diazotroph database increases the number of in situ measurements of N2 fixation rates, diazotrophic cell abundances, and nifH gene copy abundances by 184 %, 86 %, and 809 %, respectively. Using the updated database, the global marine N2 fixation rate is estimated at 223 ± 30 Tg N yr−1, which triplicates that using the original database.
Siqi Wu, Moge Du, Xianhui Sean Wan, Corday Selden, Mar Benavides, Sophie Bonnet, Robert Hamersley, Carolin R. Löscher, Margaret R. Mulholland, Xiuli Yan, and Shuh-Ji Kao
Biogeosciences Discuss., https://doi.org/10.5194/bg-2021-104, https://doi.org/10.5194/bg-2021-104, 2021
Preprint withdrawn
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Nitrogen (N2) fixation is one of the most important nutrient sources to the ocean. Here, we report N2 fixation in the deep, dark ocean in the South China Sea via a highly sensitive new method and elaborate controls, showing the overlooked importance of N2 fixation in the deep ocean. By global data compilation, we also provide an easy measured basic parameter to estimate deep N2 fixation. Our study may help to expand the area limit of N2 fixation studies and better constrain global N2 fixation.
Angela M. Kuhn, Katja Fennel, and Ilana Berman-Frank
Biogeosciences, 15, 7379–7401, https://doi.org/10.5194/bg-15-7379-2018, https://doi.org/10.5194/bg-15-7379-2018, 2018
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Recent studies demonstrate that marine N2 fixation can be carried out without light. However, direct measurements of N2 fixation in dark environments are relatively scarce. This study uses a model that represents biogeochemical cycles at a deep-ocean location in the Gulf of Aqaba (Red Sea). Different model versions are used to test assumptions about N2 fixers. Relaxing light limitation for marine N2 fixers improved the similarity between model results and observations of deep nitrate and oxygen.
Sophie Bonnet, Mathieu Caffin, Hugo Berthelot, Olivier Grosso, Mar Benavides, Sandra Helias-Nunige, Cécile Guieu, Marcus Stenegren, and Rachel Ann Foster
Biogeosciences, 15, 4215–4232, https://doi.org/10.5194/bg-15-4215-2018, https://doi.org/10.5194/bg-15-4215-2018, 2018
Dina Spungin, Natalia Belkin, Rachel A. Foster, Marcus Stenegren, Andrea Caputo, Mireille Pujo-Pay, Nathalie Leblond, Cécile Dupouy, Sophie Bonnet, and Ilana Berman-Frank
Biogeosciences, 15, 3893–3908, https://doi.org/10.5194/bg-15-3893-2018, https://doi.org/10.5194/bg-15-3893-2018, 2018
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The way marine organisms die can determine the fate of organic matter (OM) in the ocean. We investigated whether a form of auto-induced programmed cell death (PCD) influenced phytoplankton mortality and fate of OM. Our results from high biomass blooms of the cyanobacterium Trichodesmium show evidence for PCD and high production of sticky carbon material termed transparent exopolymeric particles (TEP) that facilitates cellular aggregation and enhances the vertical flux of OM to depth.
Mathieu Caffin, Hugo Berthelot, Véronique Cornet-Barthaux, Aude Barani, and Sophie Bonnet
Biogeosciences, 15, 3795–3810, https://doi.org/10.5194/bg-15-3795-2018, https://doi.org/10.5194/bg-15-3795-2018, 2018
Mar Benavides, Katyanne M. Shoemaker, Pia H. Moisander, Jutta Niggemann, Thorsten Dittmar, Solange Duhamel, Olivier Grosso, Mireille Pujo-Pay, Sandra Hélias-Nunige, Alain Fumenia, and Sophie Bonnet
Biogeosciences, 15, 3107–3119, https://doi.org/10.5194/bg-15-3107-2018, https://doi.org/10.5194/bg-15-3107-2018, 2018
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We measured N2 fixation rates and identified diazotrophic phylotypes in the mesopelagic layer along a transect spanning from New Caledonia to French Polynesia. N2 fixation rates were low but consistently detected across all depths and stations. A distinct diazotrophic phylotype dominated at 650 dbar, coinciding with the oxygenated Subantarctic Mode Water (SAMW) and suggesting that the distribution of aphotic diazotroph communities is to some extent controlled by water mass structure.
Angela N. Knapp, Kelly M. McCabe, Olivier Grosso, Nathalie Leblond, Thierry Moutin, and Sophie Bonnet
Biogeosciences, 15, 2619–2628, https://doi.org/10.5194/bg-15-2619-2018, https://doi.org/10.5194/bg-15-2619-2018, 2018
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The spatial distribution of biological N2 fixation fluxes to the ocean remains poorly constrained. Here we use nitrogen isotope budgets to identify significant N2 fixation inputs to the western tropical South Pacific (WTSP), where N2 fixation supports > 50 % of export production at stations proximal to iron sources. The significant N2 fixation inputs in the WTSP may offset nitrogen loss in the oxygen-deficient zones of the eastern tropical South Pacific.
Mathieu Caffin, Thierry Moutin, Rachel Ann Foster, Pascale Bouruet-Aubertot, Andrea Michelangelo Doglioli, Hugo Berthelot, Cécile Guieu, Olivier Grosso, Sandra Helias-Nunige, Nathalie Leblond, Audrey Gimenez, Anne Alexandra Petrenko, Alain de Verneil, and Sophie Bonnet
Biogeosciences, 15, 2565–2585, https://doi.org/10.5194/bg-15-2565-2018, https://doi.org/10.5194/bg-15-2565-2018, 2018
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We performed N budgets to assess the role of N2 fixation on production and export in the western tropical South Pacific Ocean. We deployed a combination of techniques including high-sensitivity measurements of N input and sediment traps deployment. We demonstrated that N2 fixation was the major source of new N before atmospheric deposition and upward nitrate fluxes. It contributed significantly to organic matter export, indicating a high efficiency of this region to export carbon.
Marcus Stenegren, Andrea Caputo, Carlo Berg, Sophie Bonnet, and Rachel A. Foster
Biogeosciences, 15, 1559–1578, https://doi.org/10.5194/bg-15-1559-2018, https://doi.org/10.5194/bg-15-1559-2018, 2018
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We successfully performed quantitative PCR at sea. The qPCR data were procured within 3 h and used in decisions on further sampling on site. We designed and applied a new primer and probe set for quantifying the UCYN-A1 host and observed discrepancies between host and symbiont, which contradict previous studies. Lastly, we observed a clear vertical separation between a subsurface group (UCYN-A with hosts) and a surface group (remaining diazotrophs), mainly separated by temperature.
Yangyang Lu, Zuozhu Wen, Dalin Shi, Mingming Chen, Yao Zhang, Sophie Bonnet, Yuhang Li, Jiwei Tian, and Shuh-Ji Kao
Biogeosciences, 15, 1–12, https://doi.org/10.5194/bg-15-1-2018, https://doi.org/10.5194/bg-15-1-2018, 2018
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We investigated the light response of field Trichodesmium N2 fixation and net dissolved nitrogen release behavior. Our results suggest that N2 fixation was a function of light intensity, and the light requirement of Trichodesmium nitrogen fixation was high relative to its photosynthetic light demand. Meanwhile, light is a crucial parameter driving the physiological state of Trichodesmium, which subsequently determined the C / N metabolism and net dissolved nitrogen release.
Thierry Moutin, Andrea Michelangelo Doglioli, Alain de Verneil, and Sophie Bonnet
Biogeosciences, 14, 3207–3220, https://doi.org/10.5194/bg-14-3207-2017, https://doi.org/10.5194/bg-14-3207-2017, 2017
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The overall goal of OUTPACE was to obtain a successful representation of the interactions between planktonic organisms and the cycle of biogenic elements in the western tropical South Pacific Ocean across trophic and N2 fixation gradients. The international OUTPACE cruise took place between 18 February and 3 April 2015 aboard the RV L’Atalante and involved 60 scientists. The transect covered ~4 000 km from the western part of the Melanesian archipelago to the western boundary of the gyre.
Audrey Gimenez, Melika Baklouti, Sophie Bonnet, and Thierry Moutin
Biogeosciences, 13, 5103–5120, https://doi.org/10.5194/bg-13-5103-2016, https://doi.org/10.5194/bg-13-5103-2016, 2016
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In the context of the VAHINE mesocosm experiment in the Nouméa lagoon (New Caledonia), a 1-D vertical biogeochemical mechanistic model was used together with the in situ experiment to complement our comprehension of the planktonic ecosystem dynamics and the main biogeochemical carbon, nitrogen and phosphate fluxes. The model also showed the fate of fixed N2 by providing, over time, the proportion of diazotroph-derived nitrogen (DDN) in each compartment (mineral and organic) of the model.
Angela N. Knapp, Sarah E. Fawcett, Alfredo Martínez-Garcia, Nathalie Leblond, Thierry Moutin, and Sophie Bonnet
Biogeosciences, 13, 4645–4657, https://doi.org/10.5194/bg-13-4645-2016, https://doi.org/10.5194/bg-13-4645-2016, 2016
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The goal of this manuscript was to track the fate of newly fixed nitrogen (N) in large volume mesocosms in the coastal waters of New Caledonia. We used a N isotope ("δ15N") budget and found a shift in the δ15N of sinking particulate N over the 23-day experiment, indicating that nitrate supported export production at the beginning of the experiment, but that nitrogen fixation supported export at the end. We infer that nitrogen fixation supported export production by a release of dissolved N.
Sophie Bonnet, Melika Baklouti, Audrey Gimenez, Hugo Berthelot, and Ilana Berman-Frank
Biogeosciences, 13, 4461–4479, https://doi.org/10.5194/bg-13-4461-2016, https://doi.org/10.5194/bg-13-4461-2016, 2016
Dina Spungin, Ulrike Pfreundt, Hugo Berthelot, Sophie Bonnet, Dina AlRoumi, Frank Natale, Wolfgang R. Hess, Kay D. Bidle, and Ilana Berman-Frank
Biogeosciences, 13, 4187–4203, https://doi.org/10.5194/bg-13-4187-2016, https://doi.org/10.5194/bg-13-4187-2016, 2016
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The marine cyanobacterium Trichodesmium spp. forms massive blooms important to carbon and nitrogen cycling in the oceans that often collapse abruptly. We investigated a Trichodesmium bloom in the lagoon waters of New Caledonia to specifically elucidate the cellular processes mediating the bloom decline. We demonstrate physiological, biochemical, and genetic evidence for nutrient and oxidative stress that induced a genetically controlled programmed cell death (PCD) pathway leading to bloom demise.
Hugo Berthelot, Sophie Bonnet, Olivier Grosso, Véronique Cornet, and Aude Barani
Biogeosciences, 13, 4005–4021, https://doi.org/10.5194/bg-13-4005-2016, https://doi.org/10.5194/bg-13-4005-2016, 2016
Ilana Berman-Frank, Dina Spungin, Eyal Rahav, France Van Wambeke, Kendra Turk-Kubo, and Thierry Moutin
Biogeosciences, 13, 3793–3805, https://doi.org/10.5194/bg-13-3793-2016, https://doi.org/10.5194/bg-13-3793-2016, 2016
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In the marine environment, sticky sugar-containing gels, termed transparent exopolymeric particles (TEP), are produced from biological sources and physical and chemical processes. These compounds are essential vectors enhancing downward flow of organic matter and its storage at depth. Spatial and temporal dynamics of TEPs were followed for 23 days during the VAHINE mesocosm experiment that investigated the fate of nitrogen and carbon derived from organisms fixing atmospheric N2 (diazotrophs).
France Van Wambeke, Ulrike Pfreundt, Aude Barani, Hugo Berthelot, Thierry Moutin, Martine Rodier, Wolfgang R. Hess, and Sophie Bonnet
Biogeosciences, 13, 3187–3202, https://doi.org/10.5194/bg-13-3187-2016, https://doi.org/10.5194/bg-13-3187-2016, 2016
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The phytoplankton is at the base of the plankton food web in large parts of oceanic "deserts" such as the South Pacific Ocean, where nitrogen sources limit activity. Mesocosms were fertilized with phosphorus to stimulate diazotrophy (atmospheric N2 fixation). Mostly diazotroph-derived nitrogen fuelled the heterotrophic bacterial community through indirect processes generating dissolved organic matter and detritus, such as mortality, lysis and grazing of both diazotrophs and non-diazotrophs.
Brian P. V. Hunt, Sophie Bonnet, Hugo Berthelot, Brandon J. Conroy, Rachel A. Foster, and Marc Pagano
Biogeosciences, 13, 3131–3145, https://doi.org/10.5194/bg-13-3131-2016, https://doi.org/10.5194/bg-13-3131-2016, 2016
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Biological nitrogen (N) fixation is an important source of N for food webs in tropical and subtropical oceans. However, uptake pathways remain poorly understood. This study found that fixed N contributed a third of total zooplankton N in the New Caledonia lagoon. Fixed N reached the zooplankton through 1) direct grazing on N fixers and 2) grazing on phytoplankton that had taken up N released by fixers. We report the first record of direct zooplankton grazing on the unicellular N fixer UCYN-C.
Sophie Bonnet, Thierry Moutin, Martine Rodier, Jean-Michel Grisoni, Francis Louis, Eric Folcher, Bertrand Bourgeois, Jean-Michel Boré, and Armelle Renaud
Biogeosciences, 13, 2803–2814, https://doi.org/10.5194/bg-13-2803-2016, https://doi.org/10.5194/bg-13-2803-2016, 2016
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e main goal of the VAHINE project was to study the fate of N2 fixation in the ocean. Three large-volume (~ 50 m3) mesocosms were deployed in a tropical oligotrophic ecosystem (the New Caledonia lagoon, south-eastern Pacific). This introductory paper describes the scientific objectives of the project in detail as well as the implementation plan: the mesocosm description and deployment, the selection of the study site, and the logistical and sampling strategy.
Sophie Bonnet, Hugo Berthelot, Kendra Turk-Kubo, Sarah Fawcett, Eyal Rahav, Stéphane L'Helguen, and Ilana Berman-Frank
Biogeosciences, 13, 2653–2673, https://doi.org/10.5194/bg-13-2653-2016, https://doi.org/10.5194/bg-13-2653-2016, 2016
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N2 fixation rates were measured daily in ~ 50 m3 mesocosms deployed in New Caledonia to investigate the high-frequency dynamics of diazotrophy and the fate of diazotroph-derived nitrogen (DDN) oligotrophic ecosystems. ~ 10 % of UCYN-C from the water column were exported daily to the traps, representing as much as 22.4 ± 5.5 % of the total POC exported at the height of the UCYN-C bloom. 16 ± 6 % of the DDN was released to the dissolved pool and 21 ± 4 % was transferred to non-diazotrophic plankton.
Ulrike Pfreundt, France Van Wambeke, Mathieu Caffin, Sophie Bonnet, and Wolfgang R. Hess
Biogeosciences, 13, 2319–2337, https://doi.org/10.5194/bg-13-2319-2016, https://doi.org/10.5194/bg-13-2319-2016, 2016
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The Southwest Pacific has one of the highest N2 fixation rates in the global ocean, yet information is scarce on the bacterioplankton interrelationships. We detected high microbial diversity in the New Caledonia lagoon and inside a 50 000 L experimental enclosure of the same water mass over 3 weeks and give evidence for previously unknown niche partitioning. Phosphate fertilization promoted the growth of efficient N2 fixing cyanobacteria triggering the growth of most heterotrophic bacteria.
K. A. Turk-Kubo, I. E. Frank, M. E. Hogan, A. Desnues, S. Bonnet, and J. P. Zehr
Biogeosciences, 12, 7435–7452, https://doi.org/10.5194/bg-12-7435-2015, https://doi.org/10.5194/bg-12-7435-2015, 2015
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-A shift from diatom-associated diazotrophs (DDAs) to unicellular cyanobacterial group C (UCYN-C) in response to DIP fertilization was captured in a large-scale mesocosm experiment in the Noumea lagoon (NL), a low-nutrient low-chlorophyll coastal environment. -First report of in situ net growth and mortality rates for unicellular diazotrophs UCYN-A2, and UCYN-C. -First quantitative abundance data for diazotrophs in NL indicate that DDAs and UCYN-A1/A2 may be important N2 fixers in this region.
H. Berthelot, T. Moutin, S. L'Helguen, K. Leblanc, S. Hélias, O. Grosso, N. Leblond, B. Charrière, and S. Bonnet
Biogeosciences, 12, 4099–4112, https://doi.org/10.5194/bg-12-4099-2015, https://doi.org/10.5194/bg-12-4099-2015, 2015
C. Ridame, J. Dekaezemacker, C. Guieu, S. Bonnet, S. L'Helguen, and F. Malien
Biogeosciences, 11, 4783–4800, https://doi.org/10.5194/bg-11-4783-2014, https://doi.org/10.5194/bg-11-4783-2014, 2014
E. Rahav, B. Herut, M. R. Mulholland, B. Voß, D. Stazic, C. Steglich, W. R. Hess, and I. Berman-Frank
Biogeosciences Discuss., https://doi.org/10.5194/bgd-10-10327-2013, https://doi.org/10.5194/bgd-10-10327-2013, 2013
Revised manuscript has not been submitted
E. Rahav, B. Herut, A. Levi, M. R. Mulholland, and I. Berman-Frank
Ocean Sci., 9, 489–498, https://doi.org/10.5194/os-9-489-2013, https://doi.org/10.5194/os-9-489-2013, 2013
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Understanding how marine animals adapt to variations in marine environmental conditions is paramount. In this paper, we investigated the influence of changes in seawater and light conditions on the seasonal foraging behavior of Weddell seals in the Ross Sea, Antarctica. Our findings could serve as a baseline and establish a foundational understanding for future research, particularly concerning the impact of marine environmental changes on the ecosystem of the Ross Sea Marine Protected Area.
Anaïs Lebrun, Cale A. Miller, Marc Meynadier, Steeve Comeau, Pierre Urrutti, Samir Alliouane, Robert Schlegel, Jean-Pierre Gattuso, and Frédéric Gazeau
Biogeosciences, 21, 4605–4620, https://doi.org/10.5194/bg-21-4605-2024, https://doi.org/10.5194/bg-21-4605-2024, 2024
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We tested the effects of warming, low salinity, and low irradiance on Arctic kelps. We show that growth rates were similar across species and treatments. Alaria esculenta is adapted to low-light conditions. Saccharina latissima exhibited nitrogen limitation, suggesting coastal erosion and permafrost thawing could be beneficial. Laminaria digitata did not respond to the treatments. Gene expression of Hedophyllum nigripes and S. latissima indicated acclimation to the experimental treatments.
Silvan Urs Goldenberg, Ulf Riebesell, Daniel Brüggemann, Gregor Börner, Michael Sswat, Arild Folkvord, Maria Couret, Synne Spjelkavik, Nicolás Sánchez, Cornelia Jaspers, and Marta Moyano
Biogeosciences, 21, 4521–4532, https://doi.org/10.5194/bg-21-4521-2024, https://doi.org/10.5194/bg-21-4521-2024, 2024
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Ocean alkalinity enhancement (OAE) is being evaluated as a carbon dioxide removal technology for climate change mitigation. With an experiment on species communities, we show that larval and juvenile fish can be resilient to the resulting perturbation of seawater. Fish may hence recruit successfully and continue to support fisheries' production in regions of OAE. Our findings help to establish an environmentally safe operating space for this ocean-based solution.
Thibauld M. Béjard, Andrés S. Rigual-Hernández, Javier P. Tarruella, José-Abel Flores, Anna Sanchez-Vidal, Irene Llamas-Cano, and Francisco J. Sierro
Biogeosciences, 21, 4051–4076, https://doi.org/10.5194/bg-21-4051-2024, https://doi.org/10.5194/bg-21-4051-2024, 2024
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The Mediterranean Sea is regarded as a climate change hotspot. Documenting the population of planktonic foraminifera is crucial. In the Sicily Channel, fluxes are higher during winter and positively linked with chlorophyll a concentration and cool temperatures. A comparison with other Mediterranean sites shows the transitional aspect of the studied zone. Finally, modern populations significantly differ from those in the sediment, highlighting a possible effect of environmental change.
Skye Yunshu Tian, Martin Langer, Moriaki Yasuhara, and Chih-Lin Wei
Biogeosciences, 21, 3523–3536, https://doi.org/10.5194/bg-21-3523-2024, https://doi.org/10.5194/bg-21-3523-2024, 2024
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Through the first large-scale study of meiobenthic ostracods from the diverse and productive reef ecosystem in the Zanzibar Archipelago, Tanzania, we found that the diversity and composition of ostracod assemblages as controlled by benthic habitats and human impacts were indicative of overall reef health, and we highlighted the usefulness of ostracods as a model proxy to monitor and understand the degradation of reef ecosystems from the coral-dominated phase to the algae-dominated phase.
Giulia Faucher, Mathias Haunost, Allanah Joy Paul, Anne Ulrike Christiane Tietz, and Ulf Riebesell
EGUsphere, https://doi.org/10.5194/egusphere-2024-2201, https://doi.org/10.5194/egusphere-2024-2201, 2024
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OAE is being evaluated for its capacity to absorb atmospheric CO2 in the ocean, storing it long-term to mitigate climate change. As researchers plan for field tests to gain practical insights into OAE, sharing knowledge on its environmental impact on marine ecosystems is urgent. Our study examined NaOH-induced alkalinity increases on Emiliania huxleyi, a key coccolithophore species. We found that to prevent negative impacts on this species, the increase in ΔTA should not exceed 600 µmol kg-1.
Julien Richirt, Satoshi Okada, Yoshiyuki Ishitani, Katsuyuki Uematsu, Akihiro Tame, Kaya Oda, Noriyuki Isobe, Toyoho Ishimura, Masashi Tsuchiya, and Hidetaka Nomaki
Biogeosciences, 21, 3271–3288, https://doi.org/10.5194/bg-21-3271-2024, https://doi.org/10.5194/bg-21-3271-2024, 2024
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We report the first benthic foraminifera with a composite test (i.e. shell) made of opal, which coats the inner part of the calcitic layer. Using comprehensive techniques, we describe the morphology and the composition of this novel opal layer and provide evidence that the opal is precipitated by the foraminifera itself. We explore the potential precipitation process and function(s) of this composite test and further discuss the possible implications for palaeoceanographic reconstructions.
Said Mohamed Hashim, Beth Wangui Waweru, and Agnes Muthumbi
Biogeosciences, 21, 2995–3006, https://doi.org/10.5194/bg-21-2995-2024, https://doi.org/10.5194/bg-21-2995-2024, 2024
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The study investigates the impact of decreasing oxygen in the ocean on macrofaunal communities using the BUS as an example. It identifies distinct shifts in community composition and feeding guilds across oxygen zones, with nematodes dominating dysoxic areas. These findings underscore the complex responses of benthic organisms to oxygen gradients, crucial for understanding ecosystem dynamics in hypoxic environments and their implications for marine biodiversity and sustainability.
Tanguy Soulié, Francesca Vidussi, Justine Courboulès, Marie Heydon, Sébastien Mas, Florian Voron, Carolina Cantoni, Fabien Joux, and Behzad Mostajir
Biogeosciences, 21, 1887–1902, https://doi.org/10.5194/bg-21-1887-2024, https://doi.org/10.5194/bg-21-1887-2024, 2024
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Due to climate change, it is projected that extreme rainfall events, which bring terrestrial matter into coastal seas, will occur more frequently in the Mediterranean region. To test the effects of runoffs of terrestrial matter on plankton communities from Mediterranean coastal waters, an in situ mesocosm experiment was conducted. The simulated runoff affected key processes mediated by plankton, such as primary production and respiration, suggesting major consequences of such events.
Chueh-Chen Tung, Yu-Shih Lin, Jian-Xiang Liao, Tzu-Hsuan Tu, James T. Liu, Li-Hung Lin, Pei-Ling Wang, and Chih-Lin Wei
Biogeosciences, 21, 1729–1756, https://doi.org/10.5194/bg-21-1729-2024, https://doi.org/10.5194/bg-21-1729-2024, 2024
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This study contrasts seabed food webs between a river-fed, high-energy canyon and the nearby slope. We show higher organic carbon (OC) flows through the canyon than the slope. Bacteria dominated the canyon, while seabed fauna contributed more to the slope food web. Due to frequent perturbation, the canyon had a lower faunal stock and OC recycling. Only 4 % of the seabed OC flux enters the canyon food web, suggesting a significant role of the river-fed canyon in transporting OC to the deep sea.
Joost de Vries, Fanny Monteiro, Gerald Langer, Colin Brownlee, and Glen Wheeler
Biogeosciences, 21, 1707–1727, https://doi.org/10.5194/bg-21-1707-2024, https://doi.org/10.5194/bg-21-1707-2024, 2024
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Calcifying phytoplankton (coccolithophores) utilize a life cycle in which they can grow and divide into two different phases. These two phases (HET and HOL) vary in terms of their physiology and distributions, with many unknowns about what the key differences are. Using a combination of lab experiments and model simulations, we find that nutrient storage is a critical difference between the two phases and that this difference allows them to inhabit different nitrogen input regimes.
Theodor Kindeberg, Karl Michael Attard, Jana Hüller, Julia Müller, Cintia Organo Quintana, and Eduardo Infantes
Biogeosciences, 21, 1685–1705, https://doi.org/10.5194/bg-21-1685-2024, https://doi.org/10.5194/bg-21-1685-2024, 2024
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Seagrass meadows are hotspots for biodiversity and productivity, and planting seagrass is proposed as a tool for mitigating biodiversity loss and climate change. We assessed seagrass planted in different years and found that benthic oxygen and carbon fluxes increased as the seabed developed from bare sediments to a mature seagrass meadow. This increase was partly linked to the diversity of colonizing algae which increased the light-use efficiency of the seagrass meadow community.
Anna-Selma van der Kaaden, Sandra R. Maier, Siluo Chen, Laurence H. De Clippele, Evert de Froe, Theo Gerkema, Johan van de Koppel, Furu Mienis, Christian Mohn, Max Rietkerk, Karline Soetaert, and Dick van Oevelen
Biogeosciences, 21, 973–992, https://doi.org/10.5194/bg-21-973-2024, https://doi.org/10.5194/bg-21-973-2024, 2024
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Combining hydrodynamic simulations and annotated videos, we separated which hydrodynamic variables that determine reef cover are engineered by cold-water corals and which are not. Around coral mounds, hydrodynamic zones seem to create a typical reef zonation, restricting corals from moving deeper (the expected response to climate warming). But non-engineered downward velocities in winter (e.g. deep winter mixing) seem more important for coral reef growth than coral engineering.
Xiaoke Xin, Giulia Faucher, and Ulf Riebesell
Biogeosciences, 21, 761–772, https://doi.org/10.5194/bg-21-761-2024, https://doi.org/10.5194/bg-21-761-2024, 2024
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Ocean alkalinity enhancement (OAE) is a promising approach to remove CO2 by accelerating natural rock weathering. However, some of the alkaline substances contain trace metals which could be toxic to marine life. By exposing three representative phytoplankton species to Ni released from alkaline materials, we observed varying responses of phytoplankton to nickel concentrations, suggesting caution should be taken and toxic thresholds should be avoided in OAE with Ni-rich materials.
Olmo Miguez-Salas, Angelika Brandt, Henry Knauber, and Torben Riehl
Biogeosciences, 21, 641–655, https://doi.org/10.5194/bg-21-641-2024, https://doi.org/10.5194/bg-21-641-2024, 2024
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In the deep sea, the interaction between benthic fauna (tracemakers) and substrate can be preserved as traces (i.e. lebensspuren), which are common features of seafloor landscapes, rendering them promising proxies for inferring biodiversity from marine images. No general correlation was observed between traces and benthic fauna. However, a local correlation was observed between specific stations depending on unknown tracemakers, tracemaker behaviour, and lebensspuren morphotypes.
Cale A. Miller, Pierre Urrutti, Jean-Pierre Gattuso, Steeve Comeau, Anaïs Lebrun, Samir Alliouane, Robert W. Schlegel, and Frédéric Gazeau
Biogeosciences, 21, 315–333, https://doi.org/10.5194/bg-21-315-2024, https://doi.org/10.5194/bg-21-315-2024, 2024
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This work describes an experimental system that can replicate and manipulate environmental conditions in marine or aquatic systems. Here, we show how the temperature and salinity of seawater delivered from a fjord is manipulated to experimental tanks on land. By constantly monitoring temperature and salinity in each tank via a computer program, the system continuously adjusts automated flow valves to ensure the seawater in each tank matches the targeted experimental conditions.
Rachel A. Kruft Welton, George Hoppit, Daniela N. Schmidt, James D. Witts, and Benjamin C. Moon
Biogeosciences, 21, 223–239, https://doi.org/10.5194/bg-21-223-2024, https://doi.org/10.5194/bg-21-223-2024, 2024
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We conducted a meta-analysis of known experimental literature examining how marine bivalve growth rates respond to climate change. Growth is usually negatively impacted by climate change. Bivalve eggs/larva are generally more vulnerable than either juveniles or adults. Available data on the bivalve response to climate stressors are biased towards early growth stages (commercially important in the Global North), and many families have only single experiments examining climate change impacts.
Vincent Mouchi, Christophe Pecheyran, Fanny Claverie, Cécile Cathalot, Marjolaine Matabos, Yoan Germain, Olivier Rouxel, Didier Jollivet, Thomas Broquet, and Thierry Comtet
Biogeosciences, 21, 145–160, https://doi.org/10.5194/bg-21-145-2024, https://doi.org/10.5194/bg-21-145-2024, 2024
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The impact of deep-sea mining will depend critically on the ability of larval dispersal of hydrothermal mollusks to connect and replenish natural populations. However, assessing connectivity is extremely challenging, especially in the deep sea. Here, we investigate the potential of using the chemical composition of larval shells to discriminate larval origins between multiple hydrothermal sites in the southwest Pacific. Our results confirm that this method can be applied with high accuracy.
Anna-Marie Winter, Nadezda Vasilyeva, and Artem Vladimirov
Biogeosciences, 20, 3683–3716, https://doi.org/10.5194/bg-20-3683-2023, https://doi.org/10.5194/bg-20-3683-2023, 2023
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There is an increasing number of fish in poor state, and many do not recover, even when fishing pressure is ceased. An Allee effect can hinder population recovery because it suppresses the fish's productivity at low abundance. With a model fitted to 17 Atlantic cod stocks, we find that ocean warming and fishing can cause an Allee effect. If present, the Allee effect hinders fish recovery. This shows that Allee effects are dynamic, not uncommon, and calls for precautionary management measures.
Afrah Alothman, Daffne López-Sandoval, Carlos M. Duarte, and Susana Agustí
Biogeosciences, 20, 3613–3624, https://doi.org/10.5194/bg-20-3613-2023, https://doi.org/10.5194/bg-20-3613-2023, 2023
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This study investigates bacterial dissolved inorganic carbon (DIC) fixation in the Red Sea, an oligotrophic ecosystem, using stable-isotope labeling and spectroscopy. The research reveals that bacterial DIC fixation significantly contributes to total DIC fixation, in the surface and deep water. The study demonstrates that as primary production decreases, the role of bacterial DIC fixation increases, emphasizing its importance with photosynthesis in estimating oceanic carbon dioxide production.
Arianna Zampollo, Thomas Cornulier, Rory O'Hara Murray, Jacqueline Fiona Tweddle, James Dunning, and Beth E. Scott
Biogeosciences, 20, 3593–3611, https://doi.org/10.5194/bg-20-3593-2023, https://doi.org/10.5194/bg-20-3593-2023, 2023
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This paper highlights the use of the bottom mixed layer depth (BMLD: depth between the end of the pycnocline and the mixed layer below) to investigate subsurface Chlorophyll a (a proxy of primary production) in temperate stratified shelf waters. The strict correlation between subsurface Chl a and BMLD becomes relevant in shelf-productive waters where multiple stressors (e.g. offshore infrastructure) will change the stratification--mixing balance and related carbon fluxes.
Marco Fusi, Sylvain Rigaud, Giovanna Guadagnin, Alberto Barausse, Ramona Marasco, Daniele Daffonchio, Julie Régis, Louison Huchet, Capucine Camin, Laura Pettit, Cristina Vina-Herbon, and Folco Giomi
Biogeosciences, 20, 3509–3521, https://doi.org/10.5194/bg-20-3509-2023, https://doi.org/10.5194/bg-20-3509-2023, 2023
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Oxygen availability in marine water and freshwater is very variable at daily and seasonal scales. The dynamic nature of oxygen fluctuations has important consequences for animal and microbe physiology and ecology, yet it is not fully understood. In this paper, we showed the heterogeneous nature of the aquatic oxygen landscape, which we defined here as the
oxyscape, and we addressed the importance of considering the oxyscape in the modelling and managing of aquatic ecosystems.
Anne L. Morée, Tayler M. Clarke, William W. L. Cheung, and Thomas L. Frölicher
Biogeosciences, 20, 2425–2454, https://doi.org/10.5194/bg-20-2425-2023, https://doi.org/10.5194/bg-20-2425-2023, 2023
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Ocean temperature and oxygen shape marine habitats together with species’ characteristics. We calculated the impacts of projected 21st-century warming and oxygen loss on the contemporary habitat volume of 47 marine species and described the drivers of these impacts. Most species lose less than 5 % of their habitat at 2 °C of global warming, but some species incur losses 2–3 times greater than that. We also calculate which species may be most vulnerable to climate change and why this is the case.
Markus A. Min, David M. Needham, Sebastian Sudek, Nathan Kobun Truelove, Kathleen J. Pitz, Gabriela M. Chavez, Camille Poirier, Bente Gardeler, Elisabeth von der Esch, Andrea Ludwig, Ulf Riebesell, Alexandra Z. Worden, and Francisco P. Chavez
Biogeosciences, 20, 1277–1298, https://doi.org/10.5194/bg-20-1277-2023, https://doi.org/10.5194/bg-20-1277-2023, 2023
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Emerging molecular methods provide new ways of understanding how marine communities respond to changes in ocean conditions. Here, environmental DNA was used to track the temporal evolution of biological communities in the Peruvian coastal upwelling system and in an adjacent enclosure where upwelling was simulated. We found that the two communities quickly diverged, with the open ocean being one found during upwelling and the enclosure evolving to one found under stratified conditions.
Wojciech Majewski, Witold Szczuciński, and Andrew J. Gooday
Biogeosciences, 20, 523–544, https://doi.org/10.5194/bg-20-523-2023, https://doi.org/10.5194/bg-20-523-2023, 2023
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We studied foraminifera living in the fjords of South Georgia, a sub-Antarctic island sensitive to climate change. As conditions in water and on the seafloor vary, different associations of these microorganisms dominate far inside, in the middle, and near fjord openings. Assemblages in inner and middle parts of fjords are specific to South Georgia, but they may become widespread with anticipated warming. These results are important for interpretating fossil records and monitoring future change.
Allanah Joy Paul, Lennart Thomas Bach, Javier Arístegui, Elisabeth von der Esch, Nauzet Hernández-Hernández, Jonna Piiparinen, Laura Ramajo, Kristian Spilling, and Ulf Riebesell
Biogeosciences, 19, 5911–5926, https://doi.org/10.5194/bg-19-5911-2022, https://doi.org/10.5194/bg-19-5911-2022, 2022
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We investigated how different deep water chemistry and biology modulate the response of surface phytoplankton communities to upwelling in the Peruvian coastal zone. Our results show that the most influential drivers were the ratio of inorganic nutrients (N : P) and the microbial community present in upwelling source water. These led to unexpected and variable development in the phytoplankton assemblage that could not be predicted by the amount of inorganic nutrients alone.
Hanna M. Kauko, Philipp Assmy, Ilka Peeken, Magdalena Różańska-Pluta, Józef M. Wiktor, Gunnar Bratbak, Asmita Singh, Thomas J. Ryan-Keogh, and Sebastien Moreau
Biogeosciences, 19, 5449–5482, https://doi.org/10.5194/bg-19-5449-2022, https://doi.org/10.5194/bg-19-5449-2022, 2022
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This article studies phytoplankton (microscopic
plantsin the ocean capable of photosynthesis) in Kong Håkon VII Hav in the Southern Ocean. Different species play different roles in the ecosystem, and it is therefore important to assess the species composition. We observed that phytoplankton blooms in this area are formed by large diatoms with strong silica armors, which can lead to high silica (and sometimes carbon) export to depth and be important prey for krill.
Chloe Carbonne, Steeve Comeau, Phoebe T. W. Chan, Keyla Plichon, Jean-Pierre Gattuso, and Núria Teixidó
Biogeosciences, 19, 4767–4777, https://doi.org/10.5194/bg-19-4767-2022, https://doi.org/10.5194/bg-19-4767-2022, 2022
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For the first time, our study highlights the synergistic effects of a 9-month warming and acidification combined stress on the early life stages of a Mediterranean azooxanthellate coral, Astroides calycularis. Our results predict a decrease in dispersion, settlement, post-settlement linear extention, budding and survival under future global change and that larvae and recruits of A. calycularis are stages of interest for this Mediterranean coral resistance, resilience and conservation.
Iris E. Hendriks, Anna Escolano-Moltó, Susana Flecha, Raquel Vaquer-Sunyer, Marlene Wesselmann, and Núria Marbà
Biogeosciences, 19, 4619–4637, https://doi.org/10.5194/bg-19-4619-2022, https://doi.org/10.5194/bg-19-4619-2022, 2022
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Seagrasses are marine plants with the capacity to act as carbon sinks due to their high primary productivity, using carbon for growth. This capacity can play a key role in climate change mitigation. We compiled and published data showing that two Mediterranean seagrass species have different metabolic rates, while the study method influences the rates of the measurements. Most communities act as carbon sinks, while the western basin might be more productive than the eastern Mediterranean.
Raúl Tapia, Sze Ling Ho, Hui-Yu Wang, Jeroen Groeneveld, and Mahyar Mohtadi
Biogeosciences, 19, 3185–3208, https://doi.org/10.5194/bg-19-3185-2022, https://doi.org/10.5194/bg-19-3185-2022, 2022
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We report census counts of planktic foraminifera in depth-stratified plankton net samples off Indonesia. Our results show that the vertical distribution of foraminifera species routinely used in paleoceanographic reconstructions varies in hydrographically distinct regions, likely in response to food availability. Consequently, the thermal gradient based on mixed layer and thermocline dwellers also differs for these regions, suggesting potential implications for paleoceanographic reconstructions.
Ricardo González-Gil, Neil S. Banas, Eileen Bresnan, and Michael R. Heath
Biogeosciences, 19, 2417–2426, https://doi.org/10.5194/bg-19-2417-2022, https://doi.org/10.5194/bg-19-2417-2022, 2022
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In oceanic waters, the accumulation of phytoplankton biomass in winter, when light still limits growth, is attributed to a decrease in grazing as the mixed layer deepens. However, in coastal areas, it is not clear whether winter biomass can accumulate without this deepening. Using 21 years of weekly data, we found that in the Scottish coastal North Sea, the seasonal increase in light availability triggers the accumulation of phytoplankton biomass in winter, when light limitation is strongest.
Birgit Koehler, Mårten Erlandsson, Martin Karlsson, and Lena Bergström
Biogeosciences, 19, 2295–2312, https://doi.org/10.5194/bg-19-2295-2022, https://doi.org/10.5194/bg-19-2295-2022, 2022
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Understanding species richness patterns remains a challenge for biodiversity management. We estimated fish species richness over a coastal salinity gradient (3–32) with a method that allowed comparing data from various sources. Species richness was 3-fold higher at high vs. low salinity, and salinity influenced species’ habitat preference, mobility and feeding type. If climate change causes upper-layer freshening of the Baltic Sea, further shifts along the identified patterns may be expected.
Uri Obolski, Thomas Wichard, Alvaro Israel, Alexander Golberg, and Alexander Liberzon
Biogeosciences, 19, 2263–2271, https://doi.org/10.5194/bg-19-2263-2022, https://doi.org/10.5194/bg-19-2263-2022, 2022
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The algal genus Ulva plays a major role in coastal ecosystems worldwide and is a promising prospect as an seagriculture crop. A substantial hindrance to cultivating Ulva arises from sudden sporulation, leading to biomass loss. This process is not yet well understood. Here, we characterize the dynamics of Ulva growth, considering the potential impact of sporulation inhibitors, using a mathematical model. Our findings are an essential step towards understanding the dynamics of Ulva growth.
Emanuela Fanelli, Samuele Menicucci, Sara Malavolti, Andrea De Felice, and Iole Leonori
Biogeosciences, 19, 1833–1851, https://doi.org/10.5194/bg-19-1833-2022, https://doi.org/10.5194/bg-19-1833-2022, 2022
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Zooplankton play a key role in marine ecosystems, forming the base of the marine food web and a link between primary producers and higher-order consumers, such as fish. This aspect is crucial in the Adriatic basin, one of the most productive and overexploited areas of the Mediterranean Sea. A better understanding of community and food web structure and their response to water mass changes is essential under a global warming scenario, as zooplankton are sensitive to climate change.
Masaya Yoshikai, Takashi Nakamura, Rempei Suwa, Sahadev Sharma, Rene Rollon, Jun Yasuoka, Ryohei Egawa, and Kazuo Nadaoka
Biogeosciences, 19, 1813–1832, https://doi.org/10.5194/bg-19-1813-2022, https://doi.org/10.5194/bg-19-1813-2022, 2022
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This study presents a new individual-based vegetation model to investigate salinity control on mangrove productivity. The model incorporates plant hydraulics and tree competition and predicts unique and complex patterns of mangrove forest structures that vary across soil salinity gradients. The presented model does not hold an empirical expression of salinity influence on productivity and thus may provide a better understanding of mangrove forest dynamics in future climate change.
Coulson A. Lantz, William Leggat, Jessica L. Bergman, Alexander Fordyce, Charlotte Page, Thomas Mesaglio, and Tracy D. Ainsworth
Biogeosciences, 19, 891–906, https://doi.org/10.5194/bg-19-891-2022, https://doi.org/10.5194/bg-19-891-2022, 2022
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Coral bleaching events continue to drive the degradation of coral reefs worldwide. In this study we measured rates of daytime coral reef community calcification and photosynthesis during a reef-wide bleaching event. Despite a measured decline in coral health across several taxa, there was no change in overall daytime community calcification and photosynthesis. These findings highlight potential limitations of these community-level metrics to reflect actual changes in coral health.
Hyewon Heather Kim, Jeff S. Bowman, Ya-Wei Luo, Hugh W. Ducklow, Oscar M. Schofield, Deborah K. Steinberg, and Scott C. Doney
Biogeosciences, 19, 117–136, https://doi.org/10.5194/bg-19-117-2022, https://doi.org/10.5194/bg-19-117-2022, 2022
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Heterotrophic marine bacteria are tiny organisms responsible for taking up organic matter in the ocean. Using a modeling approach, this study shows that characteristics (taxonomy and physiology) of bacteria are associated with a subset of ecological processes in the coastal West Antarctic Peninsula region, a system susceptible to global climate change. This study also suggests that bacteria will become more active, in particular large-sized cells, in response to changing climates in the region.
Alice E. Webb, Didier M. de Bakker, Karline Soetaert, Tamara da Costa, Steven M. A. C. van Heuven, Fleur C. van Duyl, Gert-Jan Reichart, and Lennart J. de Nooijer
Biogeosciences, 18, 6501–6516, https://doi.org/10.5194/bg-18-6501-2021, https://doi.org/10.5194/bg-18-6501-2021, 2021
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The biogeochemical behaviour of shallow reef communities is quantified to better understand the impact of habitat degradation and species composition shifts on reef functioning. The reef communities investigated barely support reef functions that are usually ascribed to conventional coral reefs, and the overall biogeochemical behaviour is found to be similar regardless of substrate type. This suggests a decrease in functional diversity which may therefore limit services provided by this reef.
Emmanuel Devred, Andrea Hilborn, and Cornelia Elizabeth den Heyer
Biogeosciences, 18, 6115–6132, https://doi.org/10.5194/bg-18-6115-2021, https://doi.org/10.5194/bg-18-6115-2021, 2021
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A theoretical model of grey seal seasonal abundance on Sable Island (SI) coupled with chlorophyll-a concentration [chl-a] measured by satellite revealed the impact of seal nitrogen fertilization on the surrounding waters of SI, Canada. The increase in seals from about 100 000 in 2003 to about 360 000 in 2018 during the breeding season is consistent with an increase in [chl-a] leeward of SI. The increase in seal abundance explains 8 % of the [chl-a] increase.
Julie Meilland, Michael Siccha, Maike Kaffenberger, Jelle Bijma, and Michal Kucera
Biogeosciences, 18, 5789–5809, https://doi.org/10.5194/bg-18-5789-2021, https://doi.org/10.5194/bg-18-5789-2021, 2021
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Planktonic foraminifera population dynamics has long been assumed to be controlled by synchronous reproduction and ontogenetic vertical migration (OVM). Due to contradictory observations, this concept became controversial. We here test it in the Atlantic ocean for four species of foraminifera representing the main clades. Our observations support the existence of synchronised reproduction and OVM but show that more than half of the population does not follow the canonical trajectory.
Federica Maggioni, Mireille Pujo-Pay, Jérome Aucan, Carlo Cerrano, Barbara Calcinai, Claude Payri, Francesca Benzoni, Yves Letourneur, and Riccardo Rodolfo-Metalpa
Biogeosciences, 18, 5117–5140, https://doi.org/10.5194/bg-18-5117-2021, https://doi.org/10.5194/bg-18-5117-2021, 2021
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Based on current experimental evidence, climate change will affect up to 90 % of coral reefs worldwide. The originality of this study arises from our recent discovery of an exceptional study site where environmental conditions (temperature, pH, and oxygen) are even worse than those forecasted for the future.
While these conditions are generally recognized as unfavorable for marine life, we found a rich and abundant coral reef thriving under such extreme environmental conditions.
Nisan Sariaslan and Martin R. Langer
Biogeosciences, 18, 4073–4090, https://doi.org/10.5194/bg-18-4073-2021, https://doi.org/10.5194/bg-18-4073-2021, 2021
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Analyses of foraminiferal assemblages from the Mamanguape mangrove estuary (northern Brazil) revealed highly diverse, species-rich, and structurally complex biotas. The atypical fauna resembles shallow-water offshore assemblages and are interpreted to be the result of highly saline ocean waters penetrating deep into the estuary. The findings contrast with previous studies, have implications for the fossil record, and provide novel perspectives for reconstructing mangrove environments.
Jutta E. Wollenburg, Jelle Bijma, Charlotte Cremer, Ulf Bickmeyer, and Zora Mila Colomba Zittier
Biogeosciences, 18, 3903–3915, https://doi.org/10.5194/bg-18-3903-2021, https://doi.org/10.5194/bg-18-3903-2021, 2021
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Cultured at in situ high-pressure conditions Cibicides and Cibicidoides taxa develop lasting ectoplasmic structures that cannot be retracted or resorbed. An ectoplasmic envelope surrounds their test and may protect the shell, e.g. versus carbonate aggressive bottom water conditions. Ectoplasmic roots likely anchor the specimens in areas of strong bottom water currents, trees enable them to elevate themselves above ground, and twigs stabilize and guide the retractable pseudopodial network.
Kumar Nimit
Biogeosciences, 18, 3631–3635, https://doi.org/10.5194/bg-18-3631-2021, https://doi.org/10.5194/bg-18-3631-2021, 2021
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The Indian Ocean Rim hosts many of the underdeveloped and emerging economies that depend on ocean resources for the livelihood of millions. Operational ocean information services cater to the requirements of resource managers and end-users to efficiently harness resources, mitigate threats and ensure safety. This paper outlines existing tools and explores the ongoing research that has the potential to convert the findings into operational services in the near- to midterm.
Finn Mielck, Rune Michaelis, H. Christian Hass, Sarah Hertel, Caroline Ganal, and Werner Armonies
Biogeosciences, 18, 3565–3577, https://doi.org/10.5194/bg-18-3565-2021, https://doi.org/10.5194/bg-18-3565-2021, 2021
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Marine sand mining is becoming more and more important to nourish fragile coastlines that face global change. We investigated the largest sand extraction site in the German Bight. The study reveals that after more than 35 years of mining, the excavation pits are still detectable on the seafloor while the sediment composition has largely changed. The organic communities living in and on the seafloor were strongly decimated, and no recovery is observable towards previous conditions.
France Van Wambeke, Elvira Pulido, Philippe Catala, Julie Dinasquet, Kahina Djaoudi, Anja Engel, Marc Garel, Sophie Guasco, Barbara Marie, Sandra Nunige, Vincent Taillandier, Birthe Zäncker, and Christian Tamburini
Biogeosciences, 18, 2301–2323, https://doi.org/10.5194/bg-18-2301-2021, https://doi.org/10.5194/bg-18-2301-2021, 2021
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Michaelis–Menten kinetics were determined for alkaline phosphatase, aminopeptidase and β-glucosidase in the Mediterranean Sea. Although the ectoenzymatic-hydrolysis contribution to heterotrophic prokaryotic needs was high in terms of N, it was low in terms of C. This study points out the biases in interpretation of the relative differences in activities among the three tested enzymes in regard to the choice of added concentrations of fluorogenic substrates.
Oscar E. Romero, Simon Ramondenc, and Gerhard Fischer
Biogeosciences, 18, 1873–1891, https://doi.org/10.5194/bg-18-1873-2021, https://doi.org/10.5194/bg-18-1873-2021, 2021
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Upwelling intensity along NW Africa varies on the interannual to decadal timescale. Understanding its changes is key for the prediction of future changes of CO2 sequestration in the northeastern Atlantic. Based on a multiyear (1988–2009) sediment trap experiment at the site CBmeso, fluxes and the species composition of the diatom assemblage are presented. Our data help in establishing the scientific basis for forecasting and modeling future states of this ecosystem and its decadal changes.
Katharine T. Bigham, Ashley A. Rowden, Daniel Leduc, and David A. Bowden
Biogeosciences, 18, 1893–1908, https://doi.org/10.5194/bg-18-1893-2021, https://doi.org/10.5194/bg-18-1893-2021, 2021
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Turbidity flows – underwater avalanches – are large-scale physical disturbances believed to have profound impacts on productivity and diversity of benthic communities in the deep sea. We reviewed published studies and found that current evidence for changes in productivity is ambiguous at best, but the influence on regional and local diversity is clearer. We suggest study design criteria that may lead to a better understanding of large-scale disturbance effects on deep-sea benthos.
Cited articles
Aylward, F. O., Eppley, J. M., Smith, J. M., Chavez, F. P., Scholin, C. A., and DeLong, E. F.: Microbial community transcriptional networks are conserved in three domains at ocean basin scales, P. Natl. Acad. Sci. USA, 112, 5443–5448, https://doi.org/10.1073/pnas.1502883112, 2015.
Berthelot, H., Moutin, T., L'Helguen, S., Leblanc, K., Hélias, S., Grosso, O., Leblond, N., Charrière, B., and Bonnet, S.: Dinitrogen fixation and dissolved organic nitrogen fueled primary production and particulate export during the VAHINE mesocosm experiment (New Caledonia lagoon), Biogeosciences, 12, 4099–4112, https://doi.org/10.5194/bg-12-4099-2015, 2015.
Bonnet, S., Berthelot, H., Turk-Kubo, K., Fawcett, S., Rahav, E., L'Helguen, S., and Berman-Frank, I.: Dynamics of N2 fixation and fate of diazotroph-derived nitrogen in a low-nutrient, low-chlorophyll ecosystem: results from the VAHINE mesocosm experiment (New Caledonia), Biogeosciences, 13, 2653–2673, https://doi.org/10.5194/bg-13-2653-2016, 2016a.
Bonnet, S., Moutin, T., Rodier, M., Grisoni, J.-M., Louis, F., Folcher, E., Bourgeois, B., Boré, J.M., and Renaud, A.: Introduction to the project VAHINE: VAriability of vertical and tropHIc transfer of diazotroph derived N in the south wEst Pacific, Biogeosciences, 13, 2803–2814, https://doi.org/10.5194/bg-13-2803-2016, 2016b.
Buchfink, B., Xie, C., and Huson, D. H.: Fast and sensitive protein alignment using DIAMOND, Nat. Methods, 12, 59–60, https://doi.org/10.1038/nmeth.3176, 2015.
Cho, J.-C. and Giovannoni, S. J.: Cultivation and growth characteristics of a diverse group of oligotrophic marine Gammaproteobacteria, Appl. Environ. Microbiol., 70, 432–440, 2004.
Dufresne, A., Ostrowski, M., Scanlan, D. J., Garczarek, L., Mazard, S., Palenik, B. P., Paulsen, I. T., de Marsac, N. T., Wincker, P., Dossat, C., Ferriera, S., Johnson, J., Post, A. F., Hess, W. R., and Partensky, F.: Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria, Genome Biol., 9, R90, https://doi.org/10.1186/gb-2008-9-5-r90, 2008.
Dupont, C. L., Rusch, D. B., Yooseph, S., Lombardo, M.-J., Alexander Richter, R., Valas, R., Novotny, M., Yee-Greenbaum, J., Selengut, J. D., Haft, D. H., Halpern, A. L., Lasken, R. S., Nealson, K., Friedman, R., and Craig Venter, J.: Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage, ISME J., 6, 1186–1199, https://doi.org/10.1038/ismej.2011.189, 2012.
Edgar, R. C.: Search and clustering orders of magnitude faster than BLAST, Bioinformatics, 26, 2460–2461, https://doi.org/10.1093/bioinformatics/btq461, 2010.
Forchhammer, K.: P(II) signal transducers: novel functional and structural insights, Trends Microbiol., 16, 65–72, https://doi.org/10.1016/j.tim.2007.11.004, 2008.
Foster, R. A., Kuypers, M. M. M., Vagner, T., Paerl, R. W., Musat, N., and Zehr, J. P.: Nitrogen fixation and transfer in open ocean diatom-cyanobacterial symbioses, ISME J., 5, 1484–1493, https://doi.org/10.1038/ismej.2011.26, 2011.
Frank, J. A., Lorimer, D., Youle, M., Witte, P., Craig, T., Abendroth, J., Rohwer, F., Edwards, R. A., Segall, A. M., and Burgin, A. B.: Structure and function of a cyanophage-encoded peptide deformylase, ISME J., 7, 1150–1160, https://doi.org/10.1038/ismej.2013.4, 2013.
Frias-Lopez, J., Shi, Y., Tyson, G. W., Coleman, M. L., Schuster, S. C., Chisholm, S. W., and Delong, E. F.: Microbial community gene expression in ocean surface waters, P. Natl. Acad. Sci. USA, 105, 3805–3810, https://doi.org/10.1073/pnas.0708897105, 2008.
Ganesh, S., Bristow, L. A., Larsen, M., Sarode, N., Thamdrup, B. and Stewart, F. J.: Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone, ISME J., 9, 2682–2696, https://doi.org/10.1038/ismej.2015.44, 2015.
García-Martínez, J., Acinas, S. G., Massana, R., and Rodríguez-Valera, F.: Prevalence and microdiversity of Alteromonas macleodii-like microorganisms in different oceanic regions, Environ. Microbiol., 4, 42–50, 2002.
Georg, J., Dienst, D., Schürgers, N., Wallner, T., Kopp, D., Stazic, D., Kuchmina, E., Klähn, S., Lokstein, H., Hess, W. R., and Wilde, A.: The Small Regulatory RNA SyR1/PsrR1 Controls Photosynthetic Functions in Cyanobacteria, Plant Cell Online, 26, 3661–3679, https://doi.org/10.1105/tpc.114.129767, 2014.
Gifford, S. M., Sharma, S., and Moran, M. A.: Linking activity and function to ecosystem dynamics in a coastal bacterioplankton community, Front. Microbiol., 5, 185, https://doi.org/10.3389/fmicb.2014.00185, 2014.
Gómez-Consarnau, L., Akram, N., Lindell, K., Pedersen, A., Neutze, R., Milton, D. L., González, J. M., and Pinhassi, J.: Proteorhodopsin phototrophy promotes survival of marine bacteria during starvation, PLoS Biol., 8, e1000358, https://doi.org/10.1371/journal.pbio.1000358, 2010.
Haas, B. J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P. D., Bowden, J., Couger, M. B., Eccles, D., Li, B., Lieber, M., Macmanes, M. D., Ott, M., Orvis, J., Pochet, N., Strozzi, F., Weeks, N., Westerman, R., William, T., Dewey, C. N., Henschel, R., Leduc, R. D., Friedman, N., and Regev, A.: De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis, Nat. Protoc., 8, 1494–1512, https://doi.org/10.1038/nprot.2013.084, 2013.
Hewson, I., Poretsky, R. S., Tripp, H. J., Montoya, J. P., and Zehr, J. P.: Spatial patterns and light-driven variation of microbial population gene expression in surface waters of the oligotrophic open ocean, Environ. Microbiol., 12, 1940–1956, https://doi.org/10.1111/j.1462-2920.2010.02198.x, 2010.
Hilton, J. A., Satinsky, B. M., Doherty, M., Zielinski, B., and Zehr, J. P.: Metatranscriptomics of N2-fixing cyanobacteria in the Amazon River plume, ISME J., 9, 1557–1569, https://doi.org/10.1038/ismej.2014.240, 2015.
Huergo, L. F., Chandra, G., and Merrick, M.: P(II) signal transduction proteins: nitrogen regulation and beyond, FEMS Microbiol. Rev., 37, 251–283, https://doi.org/10.1111/j.1574-6976.2012.00351.x, 2013.
Hunt, D. E., Lin, Y., Church, M. J., Karl, D. M., Tringe, S. G., Izzo, L. K., and Johnson, Z. I.: Relationship between Abundance and Specific Activity of Bacterioplankton in Open Ocean Surface Waters, Appl. Environ. Microbiol., 79, 177–184, https://doi.org/10.1128/AEM.02155-12, 2013.
Huson, D. H. and Weber, N.: Microbial community analysis using MEGAN, Methods Enzymol., 531, 465–485, https://doi.org/10.1016/B978-0-12-407863-5.00021-6, 2013.
Ivars-Martinez, E., Martin-Cuadrado, A.-B., D'Auria, G., Mira, A., Ferriera, S., Johnson, J., Friedman, R., and Rodriguez-Valera, F.: Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter, ISME J., 2, 1194–1212, https://doi.org/10.1038/ismej.2008.74, 2008.
Jones, D. S., Flood, B. E., and Bailey, J. V.: Metatranscriptomic insights into polyphosphate metabolism in marine sediments, ISME J., 10, 1015–1019, https://doi.org/10.1038/ismej.2015.169, 2015.
Kimura, H., Young, C. R., Martinez, A., and Delong, E. F.: Light-induced transcriptional responses associated with proteorhodopsin-enhanced growth in a marine flavobacterium, ISME J., 5, 1641–1651, https://doi.org/10.1038/ismej.2011.36, 2011.
Klähn, S., Schaal, C., Georg, J., Baumgartner, D., Knippen, G., Hagemann, M., Muro-Pastor, A. M., and Hess, W. R.: The sRNA NsiR4 is involved in nitrogen assimilation control in cyanobacteria by targeting glutamine synthetase inactivating factor IF7, P. Natl. Acad. Sci. USA, 112, E6243–6252, https://doi.org/10.1073/pnas.1508412112, 2015.
Knapp, A. N., Fawcett, S. E., Martínez-Garcia, A., Leblond, N., Moutin, T., and Bonnet, S.: Nitrogen isotopic evidence for a shift from nitrate- to diazotroph-fueled export production in VAHINE mesocosm experiments, Biogeosciences Discuss., 12, 19901–19939, https://doi.org/10.5194/bgd-12-19901-2015, 2015.
Kopylova, E., Noé, L., and Touzet, H.: SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data, Bioinforma. Oxf. Engl., 28, 3211–3217, https://doi.org/10.1093/bioinformatics/bts611, 2012.
Lami, R., Cottrell, M. T., Campbell, B. J., and Kirchman, D. L.: Light-dependent growth and proteorhodopsin expression by Flavobacteria and SAR11 in experiments with Delaware coastal waters, Environ. Microbiol., 11, 3201–3209, https://doi.org/10.1111/j.1462-2920.2009.02028.x, 2009.
Langmead, B.: Aligning short sequencing reads with Bowtie, Curr. Protoc. Bioinforma. Ed. Board Andreas Baxevanis Al, Chapter 11, Unit 11.7, https://doi.org/10.1002/0471250953.bi1107s32, 2010.
Leblanc, K., Cornet, V., Caffin, M., Rodier, M., Desnues, A., Berthelot, H., Turk-Kubo, K., and Heliou, J.: Phytoplankton community structure in the VAHINE MESOCOSM experiment, Biogeosciences Discuss., https://doi.org/10.5194/bg-2015-605, in review, 2016.
Li, B. and Dewey, C. N.: RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome, BMC Bioinformatics, 12, 323, https://doi.org/10.1186/1471-2105-12-323, 2011.
Lindell, D. and Post, A. F.: Ecological aspects of ntcA gene expression and its use as an indicator of the nitrogen status of marine Synechococcus spp, Appl. Environ. Microbiol., 67, 3340–3349, https://doi.org/10.1128/AEM.67.8.3340-3349.2001, 2001.
López-Pérez, M., Gonzaga, A., Martin-Cuadrado, A.-B., Onyshchenko, O., Ghavidel, A., Ghai, R., and Rodriguez-Valera, F.: Genomes of surface isolates of Alteromonas macleodii: the life of a widespread marine opportunistic copiotroph, Sci. Rep., 2, 696, https://doi.org/10.1038/srep00696, 2012.
Lott, S. C., Voß, B., Hess, W. R., and Steglich, C.: CoVennTree: a new method for the comparative analysis of large datasets, Front. Genet., 6, 43, https://doi.org/10.3389/fgene.2015.00043, 2015.
Luo, Y.-W., Doney, S. C., Anderson, L. A., Benavides, M., Berman-Frank, I., Bode, A., Bonnet, S., Boström, K. H., Böttjer, D., Capone, D. G., Carpenter, E. J., Chen, Y. L., Church, M. J., Dore, J. E., Falcón, L. I., Fernández, A., Foster, R. A., Furuya, K., Gómez, F., Gundersen, K., Hynes, A. M., Karl, D. M., Kitajima, S., Langlois, R. J., LaRoche, J., Letelier, R. M., Marañón, E., McGillicuddy Jr., D. J., Moisander, P. H., Moore, C. M., Mouriño-Carballido, B., Mulholland, M. R., Needoba, J. A., Orcutt, K. M., Poulton, A. J., Rahav, E., Raimbault, P., Rees, A. P., Riemann, L., Shiozaki, T., Subramaniam, A., Tyrrell, T., Turk-Kubo, K. A., Varela, M., Villareal, T. A., Webb, E. A., White, A. E., Wu, J., and Zehr, J. P.: Database of diazotrophs in global ocean: abundance, biomass and nitrogen fixation rates, Earth Syst. Sci. Data, 4, 47–73, https://doi.org/10.5194/essd-4-47-2012, 2012.
Ma, Y., Allen, L. Z., and Palenik, B.: Diversity and genome dynamics of marine cyanophages using metagenomic analyses, Environ. Microbiol. Rep., 6, 583–594, 2014.
Markowitz, V. M., Chen, I.-M. A., Chu, K., Pati, A., Ivanova, N. N., and Kyrpides, N. C.: Ten Years of Maintaining and Expanding a Microbial Genome and Metagenome Analysis System, Trends Microbiol., https://doi.org/10.1016/j.tim.2015.07.012, 2015.
Martin-Cuadrado, A.-B., Garcia-Heredia, I., Moltó, A. G., López-Úbeda, R., Kimes, N., López-García, P., Moreira, D., and Rodriguez-Valera, F.: A new class of marine Euryarchaeota group II from the Mediterranean deep chlorophyll maximum, ISME J., 9, 1619–1634, https://doi.org/10.1038/ismej.2014.249, 2015.
Moore, R. B., Oborník, M., Janouskovec, J., Chrudimský, T., Vancová, M., Green, D. H., Wright, S. W., Davies, N. W., Bolch, C. J. S., Heimann, K., Slapeta, J., Hoegh-Guldberg, O., Logsdon, J. M., and Carter, D. A.: A photosynthetic alveolate closely related to apicomplexan parasites, Nature, 451, 959–963, https://doi.org/10.1038/nature06635, 2008.
Moran, M. A., Satinsky, B., Gifford, S. M., Luo, H., Rivers, A., Chan, L.-K., Meng, J., Durham, B. P., Shen, C., Varaljay, V. A., Smith, C. B., Yager, P. L., and Hopkinson, B. M.: Sizing up metatranscriptomics, ISME J., 7, 237–243, https://doi.org/10.1038/ismej.2012.94, 2013.
Nakayama, T., Kamikawa, R., Tanifuji, G., Kashiyama, Y., Ohkouchi, N., Archibald, J. M., and Inagaki, Y.: Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle, P. Natl. Acad. Sci. USA, 111, 11407–11412, https://doi.org/10.1073/pnas.1405222111, 2014.
Oborník, M., Modrý, D., Lukeš, M., Cernotíková-Stříbrná, E., Cihlář, J., Tesařová, M., Kotabová, E., Vancová, M., Prášil, O., and Lukeš, J.: Morphology, ultrastructure and life cycle of Vitrella brassicaformis n. sp., n. gen., a novel chromerid from the Great Barrier Reef, Protist, 163, 306–323, https://doi.org/10.1016/j.protis.2011.09.001, 2012.
Oksanen, J., Blanchet, F. G., Kindt, R., Legendre, P., Minchin, P. R., O'Hara, R. B., Simpson, G. L., Solymos, P., Stevens, M. H. H., and Wagner, H.: vegan: Community Ecology Package, available at: http://CRAN.R-project.org/package=vegan (last access: 7 February 2016), 2015.
Pfreundt, U., Miller, D., Adusumilli, L., Stambler, N., Berman-Frank, I., and Hess, W. R.: Depth dependent metatranscriptomes of the marine pico-/nanoplanktonic communities in the Gulf of Aqaba/Eilat during seasonal deep mixing, Mar. Genomics, 18 Pt B, 93–95, https://doi.org/10.1016/j.margen.2014.06.005, 2014.
Pfreundt, U., Spungin, D., Berman-Frank, I., Bonnet, S., and Hess, W. R.: 16S rRNA gene amplicon and metatranscriptomic datasets from the VAHINE mesocosm experiment in the New Caledonian Lagoon, South West Pacific, http://www.ncbi.nlm.nih.gov/bioproject/PRJNA304389/, 2015.
Pfreundt, U., Van Wambeke, F., Caffin, M., Bonnet, S., and Hess, W. R.: Succession within the prokaryotic communities during the VAHINE mesocosms experiment in the New Caledonia lagoon, Biogeosciences, 13, 2319–2337, https://doi.org/10.5194/bg-13-2319-2016, 2016.
Pinto, F. L., Thapper, A., Sontheim, W., and Lindblad, P.: Analysis of current and alternative phenol based RNA extraction methodologies for cyanobacteria, BMC Mol. Biol., 10, 79, https://doi.org/10.1186/1471-2199-10-79, 2009.
Poretsky, R. S., Hewson, I., Sun, S., Allen, A. E., Zehr, J. P., and Moran, M. A.: Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre, Environ. Microbiol., 11, 1358–1375, https://doi.org/10.1111/j.1462-2920.2008.01863.x, 2009.
Prechtl, J., Kneip, C., Lockhart, P., Wenderoth, K., and Maier, U.-G.: Intracellular spheroid bodies of rhopalodia gibba have nitrogen-fixing apparatus of cyanobacterial origin, Mol. Biol. Evol., 21, 1477–1481, https://doi.org/10.1093/molbev/msh086, 2004.
Robinson, M. D., McCarthy, D. J., and Smyth, G. K.: edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, 26, 139–140, https://doi.org/10.1093/bioinformatics/btp616, 2010.
Scanlan, D. J., Ostrowski, M., Mazard, S., Dufresne, A., Garczarek, L., Hess, W. R., Post, A. F., Hagemann, M., Paulsen, I., and Partensky, F.: Ecological genomics of marine picocyanobacteria, Microbiol. Mol. Biol. Rev., 73, 249–299, https://doi.org/10.1128/MMBR.00035-08, 2009.
Schäfer, H., Servais, P., and Muyzer, G.: Successional changes in the genetic diversity of a marine bacterial assemblage during confinement, Arch. Microbiol., 173, 138–145, 2000.
Shi, Y., Tyson, G. W., and DeLong, E. F.: Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column, Nature, 459, 266–269, https://doi.org/10.1038/nature08055, 2009.
Spring, S., Riedel, T., Spröer, C., Yan, S., Harder, J., and Fuchs, B. M.: Taxonomy and evolution of bacteriochlorophyll a-containing members of the OM60/NOR5 clade of marine gammaproteobacteria: description of Luminiphilus syltensis gen. nov., sp. nov., reclassification of Haliea rubra as Pseudohaliea rubra gen. nov., comb. nov., and emendation of Chromatocurvus halotolerans, BMC Microbiol., 13, 118, https://doi.org/10.1186/1471-2180-13-118, 2013.
Steglich, C., Stazic, D., Lott, S. C., Voigt, K., Greengrass, E., Lindell, D., and Hess, W. R.: Dataset for metatranscriptome analysis of Prochlorococcus-rich marine picoplankton communities in the Gulf of Aqaba, Red Sea, Mar. Genomics, 19, 5–7, 2015.
Tolonen, A. C., Aach, J., Lindell, D., Johnson, Z. I., Rector, T., Steen, R., Church, G. M., and Chisholm, S. W.: Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability, Mol. Syst. Biol., 2, 53, https://doi.org/10.1038/msb4100087, 2006.
Turk-Kubo, K. A., Frank, I. E., Hogan, M. E., Desnues, A., Bonnet, S., and Zehr, J. P.: Diazotroph community succession during the VAHINE mesocosm experiment (New Caledonia lagoon), Biogeosciences, 12, 7435–7452, https://doi.org/10.5194/bg-12-7435-2015, 2015.
Van Mooy, B. A. S., Rocap, G., Fredricks, H. F., Evans, C. T. and Devol, A. H.: Sulfolipids dramatically decrease phosphorus demand by picocyanobacteria in oligotrophic marine environments, P. Natl. Acad. Sci. USA, 103, 8607–8612, https://doi.org/10.1073/pnas.0600540103, 2006.
Van Mooy, B. A. S., Fredricks, H. F., Pedler, B. E., Dyhrman, S. T., Karl, D. M., Koblízek, M., Lomas, M. W., Mincer, T. J., Moore, L. R., Moutin, T., Rappé, M. S., and Webb, E. A.: Phytoplankton in the ocean use non-phosphorus lipids in response to phosphorus scarcity, Nature, 458, 69–72, https://doi.org/10.1038/nature07659, 2009.
Van Wambeke, F., Pfreundt, U., Barani, A., Berthelot, H., Moutin, T., Rodier, M., Hess, W. R., and Bonnet, S.: Heterotrophic bacterial production and metabolic balance during the VAHINE mesocosm experiment in the New Caledonia lagoon, Biogeosciences, 13, 3187–3202, https://doi.org/10.5194/bg-13-3187-2016, 2016.
Voigt, K., Sharma, C. M., Mitschke, J., Joke Lambrecht, S., Voß, B., Hess, W. R., and Steglich, C.: Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity, ISME J., 8, 2056–2068, https://doi.org/10.1038/ismej.2014.57, 2014.
Wemheuer, B., Wemheuer, F., Hollensteiner, J., Meyer, F.-D., Voget, S., and Daniel, R.: The green impact: bacterioplankton response toward a phytoplankton spring bloom in the southern North Sea assessed by comparative metagenomic and metatranscriptomic approaches, Front. Microbiol., 6, 805, https://doi.org/10.3389/fmicb.2015.00805, 2015.
Short summary
The VAHINE experiment in the New Caledonia lagoon (SW Pacific) targeted the dynamics of nutrient pools and fluxes, N2 fixation, and the composition and productivity of the microbial communities. To connect this information to the actual activities of diverse microbial taxa, we present the analysis of the community-wide gene expression for 23 days. The results from this experiment provide insight into the microbial activities in a low-nutrient, low-chlorophyll ecosystem and within a mesocosm.
The VAHINE experiment in the New Caledonia lagoon (SW Pacific) targeted the dynamics of nutrient...
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