Articles | Volume 14, issue 4
https://doi.org/10.5194/bg-14-901-2017
© Author(s) 2017. 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-14-901-2017
© Author(s) 2017. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
Research article
| 
28 Feb 2017
Research article |
| 28 Feb 2017
Cyanobacterial endobionts within a major marine planktonic calcifier (Globigerina bulloides, Foraminifera) revealed by 16S rRNA metabarcoding
Clare Bird
CORRESPONDING AUTHOR
School of Geosciences, University of Edinburgh, Grant Institute, The
King's Buildings, James Hutton Road, Edinburgh, EH9 3FE, UK
Kate F. Darling
School of Geosciences, University of Edinburgh, Grant Institute, The
King's Buildings, James Hutton Road, Edinburgh, EH9 3FE, UK
School of Geography and Geosciences, University of St Andrews, North
Street, St Andrews, KY16 9AL, UK
Ann D. Russell
Earth and Planetary Sciences, University of California Davis, 2119
Earth and Physical Sciences, One Shields Avenue, Davis, CA 95616, USA
Catherine V. Davis
Earth and Planetary Sciences, University of California Davis, 2119
Earth and Physical Sciences, One Shields Avenue, Davis, CA 95616, USA
Jennifer Fehrenbacher
Earth and Planetary Sciences, University of California Davis, 2119
Earth and Physical Sciences, One Shields Avenue, Davis, CA 95616, USA
College of Earth, Ocean, and Atmospheric Sciences, Oregon State
University, Corvallis, OR 97331, USA
Andrew Free
School of Biological Sciences, University of Edinburgh, Roger Land
Building, The King's Buildings, Alexander Crum Brown Road, Edinburgh, EH9
3FF, UK
Michael Wyman
Biological and Environmental Sciences, Faculty of Natural Sciences,
Cottrell Building, University of Stirling, Stirling, FK9 4LA, UK
Bryne T. Ngwenya
School of Geosciences, University of Edinburgh, Grant Institute, The
King's Buildings, James Hutton Road, Edinburgh, EH9 3FE, UK
Related authors
No articles found.
Flor Vermassen, Clare Bird, Tirza M. Weitkamp, Kate F. Darling, Hanna Farnelid, Céline Heuzé, Allison Y. Hsiang, Salar Karam, Christian Stranne, Marcus Sundbom, and Helen K. Coxall
Biogeosciences, 22, 2261–2286, https://doi.org/10.5194/bg-22-2261-2025, https://doi.org/10.5194/bg-22-2261-2025, 2025
Short summary
Short summary
We provide the first systematic survey of planktonic foraminifera in the high Arctic Ocean. Our results describe the abundance and species composition under summer sea ice. They indicate that the polar specialist N. pachyderma is the only species present, with subpolar species absent. The data set will be a valuable reference for continued monitoring of the state of planktonic foraminifera communities as they respond to the ongoing sea-ice decline and the “Atlantification” of the Arctic Ocean.
Clare Bird, Kate F. Darling, Rabecca Thiessen, and Anna J. Pieńkowski
EGUsphere, https://doi.org/10.5194/egusphere-2024-497, https://doi.org/10.5194/egusphere-2024-497, 2024
Short summary
Short summary
The polar planktonic foraminifer N. pachyderma eats bacteria and diatoms. Unlike other planktonic species, it also keeps the diatom chloroplasts (photosynthesising organelles) inside its cell. In benthic foraminifera this is known as kleptoplasty, and the roles of these stolen chloroplasts are diverse. Their role in N. pachyderma needs to be investigated to find out if stored chloroplasts enable N. pachyderma to live in polar waters and under the ice where no other planktonic species survive.
Jeroen Groeneveld, Helena L. Filipsson, William E. N. Austin, Kate Darling, David McCarthy, Nadine B. Quintana Krupinski, Clare Bird, and Magali Schweizer
J. Micropalaeontol., 37, 403–429, https://doi.org/10.5194/jm-37-403-2018, https://doi.org/10.5194/jm-37-403-2018, 2018
Short summary
Short summary
Current climate and environmental changes strongly affect shallow marine and coastal areas like the Baltic Sea. The combination of foraminiferal geochemistry and environmental parameters demonstrates that in a highly variable setting like the Baltic Sea, it is possible to separate different environmental impacts on the foraminiferal assemblages and therefore use chemical factors to reconstruct how seawater temperature, salinity, and oxygen varied in the past and may vary in the future.
Raphaël Morard, Franck Lejzerowicz, Kate F. Darling, Béatrice Lecroq-Bennet, Mikkel Winther Pedersen, Ludovic Orlando, Jan Pawlowski, Stefan Mulitza, Colomban de Vargas, and Michal Kucera
Biogeosciences, 14, 2741–2754, https://doi.org/10.5194/bg-14-2741-2017, https://doi.org/10.5194/bg-14-2741-2017, 2017
Short summary
Short summary
The exploitation of deep-sea sedimentary archive relies on the recovery of mineralized skeletons of pelagic organisms. Planktonic groups leaving preserved remains represent only a fraction of the total marine diversity. Environmental DNA left by non-fossil organisms is a promising source of information for paleo-reconstructions. Here we show how planktonic-derived environmental DNA preserves ecological structure of planktonic communities. We use planktonic foraminifera as a case study.
Catherine V. Davis, Tessa M. Hill, Ann D. Russell, Brian Gaylord, and Jaime Jahncke
Biogeosciences, 13, 5139–5150, https://doi.org/10.5194/bg-13-5139-2016, https://doi.org/10.5194/bg-13-5139-2016, 2016
Short summary
Short summary
We examine seasonality of planktic foraminifera in an upwelling area to identify species vulnerable to changes in upwelling and ocean acidification and improve interpretation of fossil foraminifera. Of species associated with upwelling on the central California shelf, some are consistent with observations elsewhere while some associations appear to be unique to the region. All species show lunar periodicity and we confirm the presence of foraminifera at very low saturation state of calcite.
T. Bush, I. B. Butler, A. Free, and R. J. Allen
Biogeosciences, 12, 3713–3724, https://doi.org/10.5194/bg-12-3713-2015, https://doi.org/10.5194/bg-12-3713-2015, 2015
Short summary
Short summary
Despite their global importance, redox reactions mediated by microorganisms are often crudely represented in biogeochemical models. We show that including the dynamics of microbial growth in such a model can cause sudden shifts between redox states in response to an environmental change. We identify the conditions required for these redox regime shifts, and predict that they are likely in the modern day sulfur and nitrogen cycles, and potentially the iron cycle in the ancient ocean.
C. V. Davis, M. P. S. Badger, P. R. Bown, and D. N. Schmidt
Biogeosciences, 10, 6131–6139, https://doi.org/10.5194/bg-10-6131-2013, https://doi.org/10.5194/bg-10-6131-2013, 2013
Related subject area
Biodiversity and Ecosystem Function: Marine
The distribution and abundance of planktonic foraminifera under summer sea ice in the Arctic Ocean
Biological response of eelgrass epifauna, Taylor's Sea hare (Phyllaplysia taylori) and eelgrass isopod (Idotea resecata), to elevated ocean alkalinity
Including the invisible: deep depth-integrated chlorophyll estimates from remote sensing may assist in identifying biologically important areas in oligotrophic coastal margins
Growth response of Emiliania huxleyi to ocean alkalinity enhancement
Phytoplankton adaptation to steady or changing environments affects marine ecosystem functioning
Characterizing regional oceanography and bottom environmental conditions at two contrasting sponge grounds on the northern Labrador Shelf
Reviews and Syntheses: Trait-based approach to constrain controls on planktic foraminiferal ecology: key trade-offs and current knowledge gaps
Seasonal foraging behavior of Weddell seals in relation to oceanographic environmental conditions in the Ross Sea, Antarctica
Multifactorial effects of warming, low irradiance, and low salinity on Arctic kelps
Extraordinary bloom of toxin-producing phytoplankton enhanced by strong retention in offshore continental shelf waters
Ideas and perspectives: How sediment archives can improve model projections of marine ecosystem change
Early life stages of fish under ocean alkalinity enhancement in coastal plankton communities
Sedimentary ancient DNA insights into foraminiferal diversity near the grounding line in the western Ross Sea, Antarctica
Planktonic foraminifera assemblage composition and flux dynamics inferred from an annual sediment trap record in the central Mediterranean Sea
Reefal ostracod assemblages from the Zanzibar Archipelago (Tanzania)
Composite calcite and opal test in Foraminifera (Rhizaria)
Multispecies expression of coccolithophore vital effects with changing CO2 concentrations and pH in the laboratory with insights for reconstructing CO2 levels in geological history
Influence of oxygen minimum zone on macrobenthic community structure in the northern Benguela Upwelling System: a macro-nematode perspective
Simulated terrestrial runoff shifts the metabolic balance of a coastal Mediterranean plankton community towards heterotrophy
Contrasting carbon cycling in the benthic food webs between a river-fed, high-energy canyon and an upper continental slope
A critical trade-off between nitrogen quota and growth allows Coccolithus braarudii life cycle phases to exploit varying environment
Structural complexity and benthic metabolism: resolving the links between carbon cycling and biodiversity in restored seagrass meadows
Building your own mountain: the effects, limits, and drawbacks of cold-water coral ecosystem engineering
Phytoplankton response to increased nickel in the context of ocean alkalinity enhancement
Diversity and density relationships between lebensspuren and tracemaking organisms: a study case from abyssal northwest Pacific
Technical note: An autonomous flow-through salinity and temperature perturbation mesocosm system for multi-stressor experiments
Reviews and syntheses: The clam before the storm – a meta-analysis showing the effect of combined climate change stressors on bivalves
A step towards measuring connectivity in the deep sea: elemental fingerprints of mollusk larval shells discriminate hydrothermal vent sites
Spawner weight and ocean temperature drive Allee effect dynamics in Atlantic cod, Gadus morhua: inherent and emergent density regulation
Bacterioplankton dark CO2 fixation in oligotrophic waters
The bottom mixed layer depth as an indicator of subsurface Chlorophyll a distribution
Ideas and perspectives: The fluctuating nature of oxygen shapes the ecology of aquatic habitats and their biogeochemical cycles – the aquatic oxyscape
Impact of deoxygenation and warming on global marine species in the 21st century
Ecological divergence of a mesocosm in an eastern boundary upwelling system assessed with multi-marker environmental DNA metabarcoding
Unique benthic foraminiferal communities (stained) in diverse environments of sub-Antarctic fjords, South Georgia
Upwelled plankton community modulates surface bloom succession and nutrient availability in a natural plankton assemblage
First phytoplankton community assessment of the Kong Håkon VII Hav, Southern Ocean, during austral autumn
Early life stages of a Mediterranean coral are vulnerable to ocean warming and acidification
Mediterranean seagrasses as carbon sinks: methodological and regional differences
Contrasting vertical distributions of recent planktic foraminifera off Indonesia during the southeast monsoon: implications for paleoceanographic reconstructions
The onset of the spring phytoplankton bloom in the coastal North Sea supports the Disturbance Recovery Hypothesis
Species richness and functional attributes of fish assemblages across a large-scale salinity gradient in shallow coastal areas
Modeling the growth and sporulation dynamics of the macroalga Ulva in mixed-age populations in cultivation and the formation of green tides
Spatial changes in community composition and food web structure of mesozooplankton across the Adriatic basin (Mediterranean Sea)
Predicting mangrove forest dynamics across a soil salinity gradient using an individual-based vegetation model linked with plant hydraulics
Will daytime community calcification reflect reef accretion on future, degraded coral reefs?
Modeling polar marine ecosystem functions guided by bacterial physiological and taxonomic traits
Quantifying functional consequences of habitat degradation on a Caribbean coral reef
Enhanced chlorophyll-a concentration in the wake of Sable Island, eastern Canada, revealed by two decades of satellite observations: a response to grey seal population dynamics?
Population dynamics and reproduction strategies of planktonic foraminifera in the open ocean
Flor Vermassen, Clare Bird, Tirza M. Weitkamp, Kate F. Darling, Hanna Farnelid, Céline Heuzé, Allison Y. Hsiang, Salar Karam, Christian Stranne, Marcus Sundbom, and Helen K. Coxall
Biogeosciences, 22, 2261–2286, https://doi.org/10.5194/bg-22-2261-2025, https://doi.org/10.5194/bg-22-2261-2025, 2025
Short summary
Short summary
We provide the first systematic survey of planktonic foraminifera in the high Arctic Ocean. Our results describe the abundance and species composition under summer sea ice. They indicate that the polar specialist N. pachyderma is the only species present, with subpolar species absent. The data set will be a valuable reference for continued monitoring of the state of planktonic foraminifera communities as they respond to the ongoing sea-ice decline and the “Atlantification” of the Arctic Ocean.
Kristin Jones, Lenaïg G. Hemery, Nicholas D. Ward, Peter J. Regier, Mallory C. Ringham, and Matthew D. Eisaman
Biogeosciences, 22, 1615–1630, https://doi.org/10.5194/bg-22-1615-2025, https://doi.org/10.5194/bg-22-1615-2025, 2025
Short summary
Short summary
Ocean alkalinity enhancement is a marine carbon dioxide removal method that aims to mitigate the effects of climate change. This method causes localized increases in ocean pH, but the biological impacts of such changes are not well known. Our study investigated the response of two nearshore invertebrate species to increased pH and found the sea hare to be sensitive to pH changes, whereas the isopod was more resilient. Understanding interactions with biology is important as this field expands.
Renée P. Schoeman, Christine Erbe, and Robert D. McCauley
Biogeosciences, 22, 959–974, https://doi.org/10.5194/bg-22-959-2025, https://doi.org/10.5194/bg-22-959-2025, 2025
Short summary
Short summary
Marine habitat models do not include deep chlorophyll maxima, which may support higher trophic level foraging in (meso-)oligotrophic habitats. We used ocean glider data to show that chlorophyll maxima form off Western Australia in September–April. At least 50 % were biomass maxima, likely supporting local krill growing sufficiently for whale consumption. We suggest including deep chlorophyll maxima in marine habitat models as deep depth-integrated estimates from satellite-derived surface values.
Giulia Faucher, Mathias Haunost, Allanah Joy Paul, Anne Ulrike Christiane Tietz, and Ulf Riebesell
Biogeosciences, 22, 405–415, https://doi.org/10.5194/bg-22-405-2025, https://doi.org/10.5194/bg-22-405-2025, 2025
Short summary
Short summary
Ocean alkalinity enhancement (OAE) is being evaluated for its capacity to absorb atmospheric CO2 in the ocean and store it long term to mitigate climate change. As researchers plan for field tests to gain insights into OAE, sharing knowledge on its environmental impact on marine ecosystems is urgent. Our study examined NaOH-induced OAE in Emiliania huxleyi, a key coccolithophore species, and found that the added total alkalinity (ΔTA) should stay below 600 µmol kg⁻¹ to avoid negative impacts.
Isabell Hochfeld and Jana Hinners
Biogeosciences, 21, 5591–5611, https://doi.org/10.5194/bg-21-5591-2024, https://doi.org/10.5194/bg-21-5591-2024, 2024
Short summary
Short summary
Ecosystem models disagree on future changes in marine ecosystem functioning. We suspect that the lack of phytoplankton adaptation represents a major uncertainty factor, given the key role that phytoplankton play in marine ecosystems. Using an evolutionary ecosystem model, we found that phytoplankton adaptation can notably change simulated ecosystem dynamics. Future models should include phytoplankton adaptation; otherwise they can systematically overestimate future ecosystem-level changes.
Evert de Froe, Igor Yashayaev, Christian Mohn, Johanne Vad, Furu Mienis, Gerard Duineveld, Ellen Kenchington, Erica Head, Steve W. Ross, Sabena Blackbird, George A. Wolff, J. Murray Roberts, Barry MacDonald, Graham Tulloch, and Dick van Oevelen
Biogeosciences, 21, 5407–5433, https://doi.org/10.5194/bg-21-5407-2024, https://doi.org/10.5194/bg-21-5407-2024, 2024
Short summary
Short summary
Deep-sea sponge grounds are distributed globally and are considered hotspots of biological diversity and biogeochemical cycling. To date, little is known about the environmental constraints that control where deep-sea sponge grounds occur and what conditions favour high sponge biomass. Here, we characterize oceanographic conditions at two contrasting sponge grounds. Our results imply that sponges and associated fauna benefit from strong tidal currents and favourable regional ocean currents.
Kirsty Marie Edgar, Maria Grigoratou, Fanny Monteiro, Ruby Barrett, Rui Ying, and Daniela Schmidt
EGUsphere, https://doi.org/10.5194/egusphere-2024-3295, https://doi.org/10.5194/egusphere-2024-3295, 2024
Short summary
Short summary
Planktic foraminifera are microscopic marine organisms whose calcium carbonate shells provide valuable insights into past ocean conditions. A promising means of understanding foraminiferal ecology and their environmental interactions is to constrain their key functional traits relating to feeding, symbioses, motility, calcification and reproduction. Here we review what we know of their functional traits, key gaps in our understanding and suggestions on how to fill them.
Hyunjae Chung, Jikang Park, Mijin Park, Yejin Kim, Unyoung Chun, Sukyoung Yun, Won Sang Lee, Hyun A. Choi, Ji Sung Na, Seung-Tae Yoon, and Won Young Lee
Biogeosciences, 21, 5199–5217, https://doi.org/10.5194/bg-21-5199-2024, https://doi.org/10.5194/bg-21-5199-2024, 2024
Short summary
Short summary
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
Short summary
Short summary
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.
Valeria Ana Guinder, Urban Tillmann, Martin Rivarossa, Carola Ferronato, Fernando Javier Ramirez, Bernd Krock, Haifeng Gu, and Martin Saraceno
EGUsphere, https://doi.org/10.5194/egusphere-2024-3157, https://doi.org/10.5194/egusphere-2024-3157, 2024
Short summary
Short summary
An unusual survey involving two vessels in the Argentine Sea over a ten-day period enabled synoptic observations of a significant bloom of toxic phytoplankton. Simultaneous species characterization of the bloom, along with measurements of surface currents and fronts, provided insights into its development and retention. Interdisciplinary approaches shed light on the biophysical coupling underlying the persistence and horizontal transport of harmful algal blooms in productive marine environments.
Isabell Hochfeld, Ben A. Ward, Anke Kremp, Juliane Romahn, Alexandra Schmidt, Miklós Bálint, Lutz Becks, Jérôme Kaiser, Helge W. Arz, Sarah Bolius, Laura S. Epp, Markus Pfenninger, Christopher A. Klausmeier, Elena Litchman, and Jana Hinners
EGUsphere, https://doi.org/10.5194/egusphere-2024-3297, https://doi.org/10.5194/egusphere-2024-3297, 2024
Short summary
Short summary
Marine ecosystem models (MEMs) are valuable for assessing the threats of global warming to biodiversity and ecosystem functioning, but their predictions vary widely. We argue that MEMs should consider evolutionary processes and undergo independent validation. Here, we present a novel framework for MEM development using validation data from sediment archives, which map long-term environmental and evolutionary change. Our approach is a crucial step towards improving the predictive power of MEMs.
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
Short summary
Short summary
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.
Ewa Demianiuk, Mateusz Baca, Danijela Popović, Inès Barrenechea Angeles, Ngoc-Loi Nguyen, Jan Pawlowski, John B. Anderson, and Wojciech Majewski
EGUsphere, https://doi.org/10.5194/egusphere-2024-2824, https://doi.org/10.5194/egusphere-2024-2824, 2024
Short summary
Short summary
Ancient foraminifera DNA is studied in five Antarctic cores with sediments up to 25 kyr old. We use a standard and a new, more effective marker, which may become the next standard for paleoenvironmental studies. Much less diverse foraminifera occur on slopes of submarine moraines than in open-marine settings. Softly-walled foraminifera, not found in the fossil record, are especially abundant. There is no foraminiferal DNA in tills, suggesting its destruction during glacial redeposition.
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
Short summary
Short summary
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
Short summary
Short summary
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.
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
Short summary
Short summary
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.
Goulwen Le Guevel, Fabrice Minoletti, Carla Geisen, Gwendoline Duong, Virginia Rojas, and Michaël Hermoso
EGUsphere, https://doi.org/10.5194/egusphere-2024-1890, https://doi.org/10.5194/egusphere-2024-1890, 2024
Short summary
Short summary
This study explores the impact of environmental conditions on the chemistry of coccoliths, calcite minerals produced by marine algae, to better understand past climate changes. By cultivating different species of coccolithophores under various CO2 and pH levels, we have shown that the isotopic composition of certain species varies with CO2 concentration and quantified these variations.
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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.
Cited articles
Anand, P., Elderfield, H., and Conte, M. H.: Calibration of Mg ∕ Ca thermometry in planktonic foraminifera from a sediment trap time series, Paleoceanography, 18, 1050 https://doi.org/10.1029/2002PA000846, 2003.
Aldridge, D., Beer, C. J., and Purdie, D. A.: Calcification in the planktonic foraminifera Globigerina bulloides linked to phosphate concentrations in surface waters of the North Atlantic Ocean, Biogeosciences, 9, 1725–1739, https://doi.org/10.5194/bg-9-1725-2012, 2012.
Allers, E., Wright, J. J., Konwar, K. M., Howes, C. G., Beneze, E., Hallam, S. J., and Sullivan, M. B.: Diversity and population structure of Marine Group A bacteria in the Northeast subarctic Pacific Ocean, ISME J., 7, 256–268, https://doi.org/10.1038/ismej.2012.108, 2012.
André, A., Quillévéré, F., Morard, R., Ujiié, Y., Escarguel, G., de Vargas, C., de Garidel-Thoron, T., and Douady, C. J.: SSU rDNA Divergence in Planktonic Foraminifera: Molecular Taxonomy and Biogeographic Implications, Plos One, 9, e104641, https://doi.org/10.1371/journal.pone.0104641, 2014.
Ashton, M., Rosado, W., Govind, N. S., and Tosteson, T. R.: Culturable and nonculturable bacterial symbionts in the toxic benthic dinoflagellate Ostreopsis lenticularis, Toxicon, 42, 419–424, https://doi.org/10.1016/S0041-0101(03)00174-0, 2003.
Apprill, A., McNally, S., Parsons, R., and Weber, L.: Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton, Aquat. Microb. Ecol., 75, 129–137, https://doi.org/10.3354/ame01753, 2015.
Bé, A. W. H., Spero, H. J., and Anderson, O. R.: Effects of symbiont elimination and reinfection on the life processes of the planktonic foraminifer Globigerinoides sacculifer, Mar. Biol., 70, 73–86, https://doi.org/10.1007/BF00397298, 1982.
Beier, C. L., Horn, M., Michel, R., Schweikert, M., Görtz, H.-D., and Wagner, M.: The genus Caedibacter comprises endosymbionts of Paramecium spp. related to the Rickettsiales (Alphaproteobacteria) and to Francisella tularensis (Gammaproteobacteria), Appl. Environ. Microb., 68, 6043–6050, https://doi.org/10.1128/AEM.68.12.6043-6050.2002, 2002.
Bemis, B. E., Spero, H. J., Bijma, J., and Lea, D. W.: Reevaluation of the oxygen isotopic composition of planktonic foraminifera: Experimental results and revised paleotemperature equations, Paleoceanography, 13, 150–160, https://doi.org/10.1029/98PA00070, 1998.
Bemis, B. E., Spero, H. J., Lea, D. W., and Bijma, J.: Temperature influence on the carbon isotopic composition of Globigerina bulloides and Orbulina universa (planktonic foraminifera), Mar. Micropaleontol., 38, 213–228, https://doi.org/10.1016/S0377-8398(00)00006-2, 2000.
Bemis, B. E., Spero, H. J., and Thunell, R. C.: Using species-specific paleotemperature equations with foraminifera: a case study in the Southern California Bight, Mar. Micropaleontol., 46, 405–430, https://doi.org/10.1016/S0377-8398(02)00083-X, 2002.
Bernhard, J. M., Buck, K. R., Farmer, M. A., and Bowser, S. S.: The Santa Barbara Basin is a symbiosis oasis, Nature, 403, 77–80, https://doi.org/10.1038/47476, 2000.
Bernhard, J., Habura, A., and Bowser, S.: An endobiont-bearing allogromiid from the Santa Barbara Basin: Implications for the early diversification of foraminifera, J. Geophys. Res., 111, G03002, https://doi.org/10.1029/2005JG000158, 2006.
Bernhard, J. M., Edgcomb, V. P., Casciotti, K. L., McIlvin, M. R., and Beaudoin, D. J.: Denitrification likely catalyzed by endobionts in an allogromiid foraminifer, ISME J., 6, 951–960, https://doi.org/10.1038/ismej.2011.171, 2012.
Bidigare R. R., Schofield, O., and Prézelin, B. B.: Influence of zeaxanthin on quantum yield of photosynthesis of Synechococcus clone WH7803 (DC2), Mar. Ecol. Prog. Ser., 56, 177–188, https://doi.org/10.3354/meps056177, 1989.
Bijma, J., Erez, J., and Hemleben, C.: Lunar and semi-lunar reproductive cycles in some spinose planktonic foraminifers, J. Formin. Res., 20, 117–127, https://doi.org/10.2113/gsjfr.20.2.117, 1990.
Bijma, J., Hemleben, C., Huber, B. T., Erlenkeuser, H., and Kroon, D.: Experimental determination of the ontogenetic stable isotope variability in two morphotypes of Globigerinella siphonifera (d'Orbigny), Mar. Micropaleontol., 35, 141–160, 1998.
Bijma, J., Spero, H. J., and Lea, D. W.: Reassessing foraminiferal stable isotope geochemistry: Impact of the oceanic carbonate system (experimental results), in: Use of proxies in paleoceanography, edited by: Fischer, G. and Wefer, G., Springer-Verlag, Berlin Heidelberg New York, 489–512, 1999.
Bird, C., Darling, K. F., Russell, A. D., Davis, C. V., Fehrenbacher, J., Free, A., Wyman, M., and Ngwenya, B. T.: Sequencing Read Archive data set, BioProject accession number PRJNA341960, Cyanobacterial endobionts wihtin a major marine planktonic calcifier (Globigerina bulloides, foraminifera) revealed by 16S rRNA metabarcoding, available at: http://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA341960, last access: 23 February 2017.
Bright, M. and Bulgheresi, S.: A complex journey: transmission of microbial symbionts, Nat. Rev. Microbiol., 8, 218–230, https://doi.org/10.1038/nrmicro2262, 2010.
Buck, K. R. and Bentham, W. N.: A novel symbiosis between a cyanobacterium, Synechococcus sp., an aplastidic protist, Solenicola setigera, and a diatom, Leptocylindrus mediterraneus, in the open ocean, Mar. Biol., 132, 349–355, https://doi.org/10.1007/s002270050401, 1998.
Buck, K. R. and Bernhard, J. M.: Protistan-Prokaryotic symbioses in deep-sea sulfidic sediments, in: Symbiosis: mechanisms and model systems, edited by: Seckbach, J., Kluwer Academic Publishers, https://doi.org/10.1007/0-306-48173-1, 2006.
Campbell, L. and Carpenter E. J.: Diel patterns of cell division in marine Synechococcus spp. (Cyanobacteria): use of the frequency of dividing cells technique to measure growth rate, Mar. Ecol. Prog. Ser., 32, 139–148, 1986
Caporaso, G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F., Costello, E., Fierer, N., Peña, A., Goodrich, J., Gordon, J., Huttley, G., Kelley, S., Knights, D., Koenig, J., Ley, R., Lozupone, C., McDonald, D., Muegge, B., Pirrung, M., Reeder, J., Sevinsky, J., Turnbaugh, P., Walters, W., Widmann, J., Yatsunenko, T., Zaneveld, J., and Knight, R.: QIIME allows analysis of high-throughput community sequencing data, Nat. Methods, 7, 335–336, https://doi.org/10.1038/nmeth.f.303, 2010.
Caporaso, G., Lauber, C., Walters, W., Berg-Lyons, D., Huntley, J., Fierer, N., Owens, S., Betley, J., Fraser, L., Bauer, M., Gormley, N., Gilbert, J., Smith, G., and Knight, R.: Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms, ISME J., 6, 1621–1624, https://doi.org/10.1038/ismej.2012.8, 2012.
Caron, D. A., Michaels, A. F., and Swanberg, N. R.: Primary productivity by symbiont-bearing planktonic sarcodines (Acantharia, Radiolaria, Foraminifera) in surface waters near Bermuda, J. Plankton Res., 17, 103–129, https://doi.org/10.1093/plankt/17.1.103, 1995.
Cavalier-Smith, T. and Chao, E. E.: Phylogeny and classification of phylum Cercozoa (Protozoa), Protist, 154, 341–58, https://doi.org/10.1078/143446103322454112, 2003.
Checkley, D. M. and Barth, J. A.: Patterns and processes in the California Current System, Prog. Oceanogr., 83, 49–64, https://doi.org/10.1016/j.pocean.2009.07.028, 2009.
Chow, C.-E. T., Sachdeva, R., Cram, J. A., Steele, J. A., Needham, D. M., Patel, A., Parada, A. E., and Fuhrman, J. A.: Temporal variability and coherence of euphotic zone bacterial communities over a decade in the Southern California Bight, ISME J., 7, 2259–2273, https://doi.org/10.1038/ismej.2013.122, 2013
Cram, J. A., Chow, C.-E. T., Sachdeva, R., Needham, D. M., Parada, A. E., Steele, J. A., and Fuhrman, J. A.: Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years, ISME J., 9, 563–580, https://doi.org/10.1038/ismej.2014.153, 2015.
Curry, W. B. and Matthews, R. K.: Equilibrium 18O fractionation in small size fraction planktic foraminifera: Evidence from recent Indian Ocean sediments, Mar. Micropaleontol., 6, 327–337, 1981.
Darling, K. F., Wade, C. M., Kroon, D., Leigh Brown, A. J., and Bijma, J.: The diversity and distribution of modern planktic foraminiferal small subunit ribosomal RNA genotypes and their potential as tracers of present and past ocean circulations, Paleoceanography, 14, 3–12 https://doi.org/10.1029/1998PA900002, 1999.
Darling, K. F., Wade, C. M., Stewart, I. A., Kroon, D., Dingle, R., and Brown, A. J.: Molecular evidence for genetic mixing of Arctic and Antarctic subpolar populations of planktonic foraminifers, Nature, 405, 43–47, https://doi.org/10.1038/35011002, 2000.
Darling, K. F., Kucera, M., Wade, C. M., von Langen, P., and Pak, D.: Seasonal distribution of genetic types of planktonic foraminifer morphospecies in the Santa Barbara Channel and its paleoceanographic implications, Paleoceanography, 18, 1032–1043, https://doi.org/10.1029/2001PA000723, 2003.
Darling, K. F. and Wade, C.: The genetic diversity of planktic foraminifera and the global distribution of ribosomal RNA genotypes, Mar. Micropaleontol., 67, 216–238, https://doi.org/10.1016/j.marmicro.2008.01.009, 2008.
Davis, C. V., Hill, T. M., Russell, A. D., Gaylord, B. P., and Jahncke, J. and: Seasonality in planktic foraminifera of the central California coastal upwelling region, Biogeosciences, 13, 5139–5150, https://doi.org/10.5194/bg-13-5139-2016, 2016
Decelle, J., Colin, S., and Foster, R. A.: Photosymbiosis in marine planktonic protists, in: Marine Protists: Diversity and Dynamics, edited by: Ohtsuka, S., Suzaki, T., Horiguchi, T., Suzuki, N. and Not, F., Springer Japan, https://doi.org/10.1007/978-4-431-55130-0_19, 2015.
DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu, P., and Andersen, G. L.: Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB, Appl. Environ. Microb., 72, 5069–5072, https://doi.org/10.1128/AEM.03006-05, 2006.
Deuser, W. G., Ross, E. H., Hemleben, C., and Spindler, M.: Seasonal changes in species composition, numbers, mass, size, and isotopic composition of planktonic foraminifera settling into the deep Sargasso Sea, Palaeogeogr., Palaeocl., 33, 103–127, https://doi.org/10.1016/0031-0182(81)90034-1, 1981.
de Vargas, C., Renaud, S., Hilbrecht, H., and Pawlowski, J.: Pleistocene adaptive radiation in Globorotalia truncatulinoides: genetic, morphologic, and environmental evidence, Paleobiology, 27, 104–125, https://doi.org/10.1666/0094-8373(2001)027<0104:PARIGT>2.0.CO;2, 2001.
Edgar, R., Haas, B. J., Clemente, J. C., Quince, C., and Knight, R.: UCHIME improves sensitivity and speed of chimera detection, Bioinformatics, 27, 2194–2200, https://doi.org/10.1093/bioinformatics/btr381, 2011.
Eggins, S. M., Sadekov, A., and De Deckker, P.: Modulation and daily banding of Mg/Ca in Orbulina universa tests by symbiont photosynthesis and respiration: a complication for seawater thermometry?, Earth Planet. Sc. Lett., 225, 411–419, https://doi.org/10.1016/j.epsl.2004.06.019, 2004.
Febvre-Chevalier, C.: Constitution ultrastructural de Globigerina bulloides d' Orbigny (Rhizopoda-Foraminifera), Protistologica, 7, 311–324, 1971.
Feely, R. A., Sabine, C. L., Lee, K., Berelson, W., Kleypas, J., Fabry, V. J., and Millero, F. J.: Impact of anthropogenic CO2 on the CaCO3 system in the oceans, Science, 305, 362–6, https://doi.org/10.1126/science.1097329, 2004.
Field, D. B.: Variability in vertical distributions of planktonic foraminifera in the California Current: Relationships to vertical ocean structure, Paleoceanography, 19, PA2014, https://doi.org/10.1029/2003PA000970, 2004.
Fokin, S. I.: Bacterial endocytobionts of ciliophora and their interactions with the host cell, Int. Rev. Cytol., 236, 181–249, https://doi.org/10.1016/S0074-7696(04)36005-5, 2004.
Fraile, I., Schulz, M., Mulitza, S., and Kucera, M.: Predicting the global distribution of planktonic foraminifera using a dynamic ecosystem model, Biogeosciences, 5, 891–911, https://doi.org/10.5194/bg-5-891-2008, 2008.
Fuller, N. J., Marie, D., Partensky, F., Vaulot, D., Post, A. F., and Scanlan, D. J.: Clade-specific 16S ribosomal DNA oligonucleotides reveal the pre-dominance of a single marine Synechococcus clade throughout a stratified water column in the Red Sea, Appl. Environ. Microb., 69, 2430–2443, https://doi.org/10.1128/AEM.69.5.2430-2443.2003, 2003.
García-Reyes and Largier: Seasonality of coastal upwelling off central and northern California: New insights, including temporal and spatial variability, J. Geophys. Res.-Oceans, 117, C03028, https://doi.org/10.1029/2011jc007629, 2012.
Gast, R. J., Sanders, R. W., and Caron, D. A.: Ecological strategies of protists and their symbiotic relationships with prokaryotic microbes, Trends Microbiol., 17, 563–569, https://doi.org/10.1016/j.tim.2009.09.001, 2009.
Gastrich, M.: Ultrastructure of a new intracellular symbiotic alga found within planktonic foraminifera, J. Phycol., 23, 623–632, https://doi.org/10.1111/j.1529-8817.1987.tb04215.x, 1987.
Gastrich, M. and Bartha, R.: Primary productivity in the planktonic foraminifer Globigerinoides ruber (d'Orbigny), J. Foramin. Res., 18, 137–142, https://doi.org/10.2113/gsjfr.18.2.137, 1988.
Geslin, E., Risgaard-Petersen, N., Lombard, F., Metzger, E., Langlet, D., and Jorissen, F.: Oxygen respiration rates of benthic foraminifera as measured with oxygen microsensors, J. Exp. Mar. Biol. Ecol., 396, 108–114, https://doi.org/10.1016/j.jembe.2010.10.011, 2011.
Gilbert, J. A., Jansson, J. K., and Knight, R.: The Earth Microbiome Project: successes and aspirations, BMC Biol., 12, 69–72, https://doi.org/10.1186/s12915-014-0069-1, 2014.
Gilbert, S. F., Sapp, J., and Tauber, A. I.: A symbiotic view of life: we have never been individuals, Q. Rev. Biol., 87, 325–341 https://doi.org/10.1086/668166, 2012.
Giovannoni, S. J., Britschgi, T. B., Moyer, C. L., and Field, K. G.: Genetic diversity in Sargasso Sea bacterioplankton, Nature, 345, 60–63, https://doi.org/10.1038/345060a0, 1990.
Hannah, F., Rogerson, R., and laybourne-Parry, J.: Respiration rates and biovolumes of common benthic foraminifera (Protozoa), J. Mar. Biol. Assoc. UK, 74, 301–312, https://doi.org/10.1017/S0025315400039345, 1994.
Healy-Williams, N., Ehrlich, R., and Williams, D. F.: Morphometric and stable isotopic evidence for subpopulations of Globorotalia truncatulinoides, J. Foramin. Res., 15, 242–253, https://doi.org/10.2113/gsjfr.15.4.242, 1985.
Hemleben, C., Spindler, M., and Anderson, O. R.: Modern planktonic foraminifera, Springer-Verlag, New York, 1989
Henderson, G. M.: New oceanic proxies for paleoclimate, Earth Planet. Sc. Lett., 203, 1–13, https://doi.org/10.1016/S0012-821X(02)00809-9, 2002.
Holligan, P. M. and Robertson, J. E.: Significance of ocean carbonate budgets for the global carbon cycle, Glob. Change Biol., 2, 85–95, https://doi.org/10.1111/j.1365-2486.1996.tb00053.x, 1996.
Holzmann, M. and Pawlowski, J.: Preservation of foraminifera for DNA extraction and PCR amplification, J. Foramin. Res., 26, 264–267, https://doi.org/10.2113/gsjfr.26.3.264, 1996.
Hönisch, B., Bijma, J., Russell, A. D. and Spero, H. J, Palmer, M. R., Zeebe, R. E., and Eisenhauer, A.: The influence of symbiont photosynthesis on the boron isotopic composition of foraminifera shells, Mar. Micropaleontol., 49, 87–96, https://doi.org/10.1016/S0377-8398(03)00030-6, 2003.
Huber, B. T., Bijma, J., and Darling, K. F.: Cryptic speciation in the living planktonic foraminifer Globigerinella siphonifera (d'Orbigny), Paleobiology, 23, 33–62, https://doi.org/10.1017/S0094837300016638, 1997
Hugenholtz, P., Pitulle, C., Hershberger, K. L., and Pace, N. R.: Novel division level bacterial diversity in a Yellowstone hot spring, J. Bacteriol., 180, 366–376, 1998.
Iglesias-Rodriguez, M. D., Armstrong, R., Feely, R., Hood, R., Kleypas, J., Milliman, J. D., Sabine, C., and Sarmiento, J.: Progress made in study of ocean's calcium carbonate budget, Eos, Tran. Amer. Geophys. Un., 83, 365–375, https://doi.org/10.1029/2002eo000267, 2002.
Jacox, M., Fiechter, J., Moore, A., and Edwards, C.: ENSO and the California Current coastal upwelling response, J. Geophys. Res.-Oceans, 120, 1691–1702, https://doi.org/10.1002/2014jc010650, 2015.
Kahn, M. I. and Williams, D. F.: Oxygen and carbon isotopic composition of living planktonic foraminifera from the northeast Pacific Ocean, Palaeogeogr. Palaeocl., 33, 47–69, https://doi.org/10.1016/0031-0182(81)90032-8, 1981.
Katz, M. E., Cramer, B. S., Franzese, A., Hönisch, B., Miller, K. G., Rosenthal, Y., and Wright, J. D.: Traditional and emerging geochemical proxies in foraminifera, J. Foramin. Res., 40, 165–192, https://doi.org/10.2113/gsjfr.40.2.165, 2010.
Kleijne, A., Kroon, D., and Zevenboom, W.: Phytoplankton and foraminiferal frequencies in northern Indian Ocean and Red Sea surface waters, Neth. J. Sea Res., 24, 531–539, https://doi.org/10.1016/0077-7579(89)90131-2, 1989.
Kozich, J. J., Westcott, S. L., Baxter, N. T., Highlander, S. K., and Schloss, P. D.: Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform, Appl. Environ. Microb., 79, 5112–5120, https://doi.org/10.1128/AEM.01043-13, 2013.
Kroon, D. and Darling, K. F.: Size and upwelling control of the stable isotope composition of Neogloboquadrina dutertrei (d'Orbigny), Globigerinoides ruber (d'Orbigny) and Globigerina bulloides d'Orbigny: examples from the Panama Basin and Arabian Sea, J. Foramin. Res., 25, 39–52, https://doi.org/10.2113/gsjfr.25.1.39, 1995
Kucera, M. and Darling, K. F.: Cryptic species of planktonic foraminifera: their effect on palaeoceanographic reconstructions, Philos. T. Roy. Soc. A, 360, 695–718, https://doi.org/10.1098/rsta.2001.0962, 2002.
Kucera, M. and Kennett, J. P.: Causes and consequences of a middle Pleistocene origin of the modern planktonic foraminifer Neogloboquadrina pachyderma sinistral, Geology, 30, 539–542, https://doi.org/10.1130/0091-7613(2002)030<0539:CACOAM>2.0.CO;2, 2002.
Kucera, M.: Planktonic Foraminifera as Tracers of Past Oceanic Environments, in: Developments in Marine Geology, edited by: Hillaire-Marcel, C. and De Vernal, A., Elsevier, 1, 213–262, https://doi.org/10.1016/S1572-5480(07)01011-1, 2007.
Laurence, M., Hatzis, C., and Brash, D. E.: Common contaminants in next-generation sequencing that hinder discovery of low-abundance microbes, PLoS One, 9, e97876, https://doi.org/10.1371/journal.pone.0097876, 2014.
Lee, J. J., McEnery, M., Pierce, S., Freudenthal, H. D., and Muller, W. A.: Tracer Experiments in Feeding Littoral Foraminifera, J. Eukaryot. Microbiol., 13, 659–670, https://doi.org/10.1111/j.1550-7408.1966.tb01978.x, 1966.
Lombard, F., Erez, J., Michel, E., and Labeyrie, L.: Temperature effect on respiration and photosynthesis of the symbiont-bearing planktonic foraminifera Globigerinoides ruber, Orbulina universa, and Globigerinella siphonifera, Limnol. Oceanogr., 54, 210–218, https://doi.org/10.4319/lo.2009.54.1.0210, 2009.
Lombard, F., Labeyrie, L., Michel, E., Bopp, L., Cortijo, E., Retailleau, S., Howa, H., and Jorissen, F.: Modelling planktic foraminifer growth and distribution using an ecophysiological multi-species approach, Biogeosciences, 8, 853–873, https://doi.org/10.5194/bg-8-853-2011, 2011.
Manno, C, Morato, N., and Bellerby, R.: Effect of ocean acidification and temperature increase on the planktonic foraminifer Neogloboquadrina pachyderma (sinstral), Polar Biol., 35, 1311–1319, https://doi.org/10.1007/s00300-012-1174-7, 2012.
Martin, P., Dyhrman, S. T., Lomas, M. W., Poulton, N. J., and Van Mooy, B. A. S.: Accumulation and enhanced cycling of polyphosphate by Sargasso Sea plankton in response to low phosphorus, P. Natl. Acad. Sci. USA, 111, 8089–8094, https://doi.org/10.1073/pnas.1321719111, 2014.
Mashiotta, T. A., Lea, D. W., and Spero, H. J.: Experimental determination of cadmium uptake in shells of the planktonic foraminifera Orbulina universa and Globigerina bulloides: Implications for surface water paleoreconstructions, Geochim. Cosmochim. Ac., 61, 4053–4065, https://doi.org/10.1016/S0016-7037(97)00206-8, 1997.
Mitra, A., Flynn, K. J., Tillmann, U., Raven, J. A., Caron, D., Stoeker, D. K., Not, F., Hansen, P. J., Hallegraeff, G., Sanders, R., Wilken, S., MacManus, G., Johnson, M., Pitta, P., Våge, S., Berge, T., Calbet, A., Thingstad, F., Jin Jeong, H., Burkholder, J., Glibert, P. M., Granéli, E., and Lundgren, V.: Defining Planktonic Protist Functional Groups on Mechanisms for Energy and Nutrient Acquisition: Incorporation of Diverse Mixotrophic Strategies, Protist, 167, 106–120, https://doi.org/10.1016/l.protis.2016.01.003, 2016.
Morard, R., Quillévéré, F., Escarguel, G., de Garidel-Thoron, T., de Vargas, C., and Kucera, M.: Ecological modeling of the temperature dependence of cryptic species of planktonic Foraminifera in the Southern Hemisphere, Palaeogeogr. Palaeocl., 391, 13–33, https://doi.org/10.1016/l.palaeo.2013.05.011, 2013.
Morris, R. M, Rappé, M. S., Connon, S. A, Vergin, K. L., Siebold, W. A, Carlson, C. A., and Giovannoni, S. J.: SAR11 clade dominates ocean surface bacterioplankton communities, Nature, 420, 806–810, https://doi.org/10.1038/nature01240, 2002.
Mühling, M., Fuller, N. J., Millard, A., Somerfield, P. J., Marie, D., Wilson, W. H., Scanlan, D. J., Post, A. F., Joint, I., and Mann, N. H.: Genetic diversity of marine Synechococcus and co-occurring cyanophage communities: evidence for viral control of phytoplankton, Environ. Microbiol., 7, 499–508, https://doi.org/10.1111/j.1462-2920.2005.00713.x, 2005.
Murray, J.: On the distribution of the pelagic foraminifera at the surface and on the floor of the ocean, Nat. Sci., 11, 17–24, 1897.
Naidu, P. D. and Malmgren, B. A.: Relationship between late Quaternary upwelling history and coiling properties of Neogloboquadrina pachyderma and Globigerina bulloides in the Arabian Sea, J. Foramin. Res., 26, 64–70, https://doi.org/10.2113/gsjfr.26.1.64, 1996.
Nowack, E. C. M. and Melkonian, M.: Endosymbiotic associations within protists, Philos. T. Roy. Soc. B, 365, 699–712, https://doi.org/10.1098/rstb.2009.0188, 2010.
Nübel, U., Garcia-Pichel, F., and Muyzer, G.: PCR primers to amplify 16S rRNA genes from cyanobacteria, Appl. Environ. Microb., 63, 3327–32, 1997.
Orsi, W., Charvet, S., Vd'ačný, P., Bernhard, J. M., and Edgcomb, V. P: Prevalence of partnerships between bacteria and ciliates in oxygen-depleted marine water columns, Front. Microbiol., 3, 341, https://doi.org/10.3389/fmicb.2012.00341, 2012.
Paerl, R. W., Johnson, K. S., Welsh, R. M., Worden, A. Z., Chavez, F. P., and Zehr, J. P.: Differential Distributions of Synechococcus Subgroups Across the California Current System, Front. Microbiol., 2, 59–71, https://doi.org/10.3389/fmicb.2011.00059, 2011.
Padua, R. A., Parrado, A., Larghero, J., and Chomienne, C.: UV and clean air result in contamination-free PCR, Leukemia, 13, 1898–1899, 1999.
Pagaling, E., Strathdee, F., Spears, B. M., Cates, M. E., Allen, R. J., and Free, A.: Community history affects the predictability of microbial ecosystem development, ISME J., 8, 19–30, https://doi.org/10.1038/ismej.2013.150, 2014.
Paoli, A., Celussi, M., Del Negro, P. Umani, S. F., and Talarico, L.: Ecological advantages from light adaptation and heterotrophic-like behavior in Synechococcus harvested from the Gulf of Trieste (Northern Adriatic Sea), FEMS Microbiol. Ecol., 64, 153–327, https://doi.org/10.1111/j.1574-6941.2008.00459.x, 2008.
Parada, A., Needham, D., and Fuhrman, J.: Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples, Environ. Microbiol., 18, 1403–1414, https://doi.org/10.1111/1462-2920.13023, 2016.
Partensky, F., Blanchot, J., and Vaulot, D.: Differential distribution and ecology of Prochlorococcus and Synechococcus in oceanic waters: a review, Bulletin de l'Institut océanographique, available at: http://horizon.documentation.ird.fr/exl-doc/pleins_textes/divers15-02/010019788.pdf (last access: 22 February 2017), 1999.
Rappé, M. S. and Giovannoni, S. J: The uncultured microbial majority, Annu. Rev. Microbiol., 57, 369–394, https://doi.org/10.1146/annurev.micro.57.030502.090759, 2003.
Richardson, T. L. and Jackson, G. A.: Small phytoplankton and carbon export from the surface ocean, Science, 315, 838–40, https://doi.org/10.1126/science.1133471, 2007.
Ridgwell, A. and Zeebe, R. E.: The role of the global carbonate cycle in the regulation and evolution of the Earth system, Earth Planet. Sc. Lett., 234, 299–315, https://doi.org/10.1016/j.epsl.2005.03.006, 2005.
Rink, S., Kühl, M., Bijma, J., and Spero, H. J.: Microsensor studies of photosynthesis and respiration in the symbiotic foraminifer Orbulina universa, Mar. Biol., 131, 583–595, https://doi.org/10.1007/S002270050350, 1998.
Roy, T., Lombard, F., Bopp, L., and Gehlen, M.: Projected impacts of climate change and ocean acidification on the global biogeography of planktonic Foraminifera, Biogeosciences, 12, 2873–2889, https://doi.org/10.5194/bg-12-2873-2015, 2015.
Russell, A. D., Hönisch, B., Spero, H. J., and Lea, D. W.: Effects of seawater carbonate ion concentration and temperature on shell U, Mg, and Sr in cultured planktonic foraminifera, Geochim. Cosmochim. Ac. 68, 4347–4361, https://doi.org/10.1016/j.gca.2004.03.013, 2004.
Sadekov, A., Darling, K. F., Ishimura, T., Wade, C., Kimoto, K., Singh, A., Anand, P., Kroon, D., Jung, S., Ganssen, G., Ganeshram, R., Tsunogai, U., and Elderfield, H.: Geochemical imprints of genotypic variants of Globigerina bulloides in the Arabian Sea, Paleoceanography, 31, 1440–1452, https://doi.org/10.1002/2016pa002947, 2016.
Salter, S. J., Cox, M. J., Turek, E. M., Calus, S. T., Cookson, W. O., Moffatt, M. F., Turner, P., Parkhill, J., Loman, N. J., and Walker, A. W.: Reagent and laboratory contamination can critically impact sequence-based microbiome analyses, BMC Biol., 12, 87–99, https://doi.org/10.1186/S12915-014-0087-Z, 2014.
Sarmiento, J. L. and Gruber, N. (Eds): Ocean Biogeochemical Dynamics. Princeton University Press, New Jersey, 2005.
Sautter, L. R. and Thunell, R. C.: Planktonic foraminiferal response to upwelling and seasonal hydrographic conditions; sediment trap results from San Pedro Basin, Southern California Bight, J. Foramin. Res., 21, 347–363, https://doi.org/10.2113/gsjfr.21.4.347, 1991.
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.
Schiebel, R.: Planktic foraminiferal sedimentation and the marine calcite budget, Global Biogeochem. Cy., 16, 1–21, https://doi.org/10.1029/2001GB001459, 2002.
Schiebel, R., Barker, S., Lendt, R., Thomas, H., and Bollmann, J.: Planktic foraminiferal dissolution in the twilight zone, Deep-Sea. Res. Pt. II, 54, 676–686, https://doi.org/10.1016/j.dsr2.2007.01.009, 2007.
Schweikert, M. and Meyer, B.: Characterization of intracellular bacteria in the freshwater dinoflagellate Peridinium cinctum, Protoplasma, 217, 177–184, https://doi.org/10.1007/BF01283398, 2001.
Seears, H., Darling, K. F., and Wade, C. M.: Ecological partitioning and diversity in tropical planktonic foraminifera, BMC Evol. Biol., 12, 54–69, https://doi.org/10.1186/1471-2148-12-54, 2012.
Six, C., Thomas, J.-C., Garczarek, L., Ostowski, M., Dufresne, A., Blot, N., Scanlan, D. J., and Partensky, F.: Diversity and evolution of phycobilisomes in marine Synechococcus spp.: a comparative genomics study, BMC Genomics, 8, R259, https://doi.org/10.1186/gb-2007-8-12-r259, 2007
Spero, H. J., Lerche, I., and Williams, D. F.: Opening the carbon isotope “vital effect” black box, 2, Quantitative model for interpreting foraminiferal carbon isotope data, Paleoceanography, 6, 639–655, https://doi.org/10.1029/91PA02022, 1991.
Spero, H. J. and Lea, D. W.: Experimental determination of stable isotope variability in Globigerina bulloides: implications for paleoceanographic reconstructions, Mar. Micropaleontol., 28, 231–246, https://doi.org/10.1016/0377-8398(96)00003-5, 1996
Spero, H. J., Bijma, J., Lea, D. W., and Bemis, B. E.: Effect of seawater carbonate concentration on foraminiferal carbon and oxygen isotopes, Nature, 390, 497–500, https://doi.org/10.1038/37333, 1997.
Stewart, D. E. and Farmer, F. H.: Extraction, identification, and quantitation of phycobiliprotein pigments from phototrophic plankton, Limnol. Oceanogr., 29, 392–397, https://doi.org/10.4319/lo.1984.29.2.0392, 1984
Suttle, C. A. and Chan, A. M.: Dynamics and distribution of cyanophages and their effect on marine Synechococcus spp., Appl. Environ. Microbiol., 60, 3167–3174, 1994.
Tai, V. and Palenik, B.: Temporal variation of Synechococcus clades at a coastal Pacific Ocean monitoring site, ISME J., 3, 903–915, https://doi.org/10.1038/ismej.2009.35, 2009.
Tai, V., Burton, R. S., and Palenik, B.: Temporal and spatial distributions of marine Synechococcus in the Southern California Bight assessed by hybridization to bead-arrays, Mar. Ecol. Prog. Ser., 426, 133–147, https://doi.org/10.3354/meps09030, 2011.
Tamura, K., Stecher, G., Peterson, D., Filipski, A., and Kumar, S.: MEGA6: molecular evolutionary genetics analysis version 6.0, Mol. Biol. Evol., 30, 2725–2729, https://doi.org/10.1093/molbev/mst197, 2013.
Thunell, R. and Sautter, L. R.: Planktonic foraminiferal faunal and stable isotopic indices of upwelling: a sediment trap study in the San Pedro Basin, Southern California Bight, Geol. Soc. Lond. Special Publ., 64, 77–91, https://doi.org/10.1144/GSL.SP.1992.064.01.05, 1992.
Toledo, G. and Palenik, B.: Synechococcus diversity in the California current as seen by RNA polymerase (rpoC1) gene sequences of isolated strains, Appl. Environ. Microbiol., 63, 4298–4303, 1997.
Tsuchiya, M., Toyofuku, T., Uematsu, K., Brüchert, V., Collen, J., Yamamoto, H., and Kitazato, H.: Cytologic and Genetic Characteristics of Endobiotic Bacteria and Kleptoplasts of Virgulinella fragilis (Foraminifera), J. Eukaryot. Microbiol., 62, 454–469, https://doi.org/10.1111/jeu.12200, 2015.
Uhle, M. E., Macko, S. A., Spero, H. J., Engel, M. H., and Lea, D. W.: Sources of carbon and nitrogen in modern planktonic foraminifera: the role of algal symbionts as determined by bulk and compound specific stable isotopic analyses, Org. Geochem., 27, 103–113, https://doi.org/10.1016/S0146-6380(97)00075-2, 1997.
Uhle, M. E., Macko, S. A., Spero, H. J., Lea, D. W., Ruddiman, W. F., and Engel, M. H.: The fate of nitrogen in the Orbulina universa foraminifera–symbiont system determined by nitrogen isotope analyses of shell-bound organic matter, Limnol. Oceanogr., 44, 1968–1977, https://doi.org/10.4319/lo.1999.44.8.1968, 1999.
van Hoek, A. H. A. M., van Alen, T. A., Sprakel, V. S. I., Leunissen, J. A. M., Brigge, T., Vogels, G. D., and Hackstein, J. H. P.: Multiple acquisition of methanogenic archaeal symbionts by anaerobic ciliates, Mol. Biol. Evol., 17, 251–258, 2000.
Walters, W., Hyde, E. R., Berg-Lyons, D., Ackermann, G., Humphrey, G., Parada, A., Gilbert, J. A., Jansson, J. K., Caporaso, J. G., Fuhrman, J. A., Apprill, A., and Knight, R.: Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys, Systems, 1, e00009, https://doi.org/10.1128/mSystems.00009-15, 2015.
Waterbury, J. B., Watson, S. W., Guillard, R. R. L., and Brand, L. E.: Widespread occurrence of a unicellular, marine, planktonic, cyanobacterium, Nature, 277, 293–294, https://doi.org/10.1038/277293a0, 1979.
Wernegreen, J. J.: Genome evolution in bacterial endosymbionts of insects, Nat. Rev. Genet., 3, 850–861, https://doi.org/10.1038/nrg931, 2002.
Wolf-Gladrow, D. A., Riebesell, U., Burkhardt, S., and Bijma, J.: Direct effects of CO2 concentration on growth and isotopic composition of marine plankton, Tellus B, 51, 461–476, https://doi.org/10.1034/j.1600-0889.1999.00023.x, 1999.
Wyman, M., Gregory, R. P. F., and Carr, N. G.: Novel role for phycoerythrin in a marine cyanobacterium, Synechococcus strain DC2, Science, 230, 818–820, https://doi.org/10.1126/science.230.4727.818, 1985.
Wyman, M.: An in vivo method for the estimation of phycoerythrin concentrations in marine cyanobacteria (Synechococcus spp.), Limnol. Oceanogr., 37, 1300–1306, https://doi.org/10.4319/lo.1992.37.6.1300, 1992.
Yuasa, T., Horiguchi, T., Mayama, S., Matsuoka, A., and Takahashi, O.: Ultrastructural and molecular characterization of cyanobacterial symbionts in Dictyocoryne profunda (polycystine radiolaria), Symbiosis, 57, 51–55, https://doi.org/10.1007/s13199-012-0174-2, 2012.
Short summary
Accurate ecological data on planktic foraminifera (calcifying microbes that play an important role in the carbon cycle) are important for modelling their response to climate change. We studied the species G. bulloides. A lack of algal symbionts and unusual shell chemistry suggest a different life history compared to other spinose species. We demonstrate that G. bulloides hosts cyanobacterial endobionts. This has implications for modelling this species and for understanding its shell chemistry.
Accurate ecological data on planktic foraminifera (calcifying microbes that play an important...
Altmetrics
Final-revised paper
Preprint