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.
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
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
The Bouraké semi-enclosed lagoon (New Caledonia) – a natural laboratory to study the lifelong adaptation of a coral reef ecosystem to extreme environmental conditions
Atypical, high-diversity assemblages of foraminifera in a mangrove estuary in northern Brazil
Permanent ectoplasmic structures in deep-sea Cibicides and Cibicidoides taxa – long-term observations at in situ pressure
Ideas and perspectives: Ushering the Indian Ocean into the UN Decade of Ocean Science for Sustainable Development (UNDOSSD) through marine ecosystem research and operational services – an early career's take
Persistent effects of sand extraction on habitats and associated benthic communities in the German Bight
Spatial patterns of ectoenzymatic kinetics in relation to biogeochemical properties in the Mediterranean Sea and the concentration of the fluorogenic substrate used
A 2-decade (1988–2009) record of diatom fluxes in the Mauritanian coastal upwelling: impact of low-frequency forcing and a two-step shift in the species composition
Review and syntheses: Impacts of turbidity flows on deep-sea benthic communities
Ideas and perspectives: When ocean acidification experiments are not the same, repeatability is not tested
The effect of the salinity, light regime and food source on carbon and nitrogen uptake in a benthic foraminifer
Changes in population depth distribution and oxygen stratification are involved in the current low condition of the eastern Baltic Sea cod (Gadus morhua)
Effects of spatial variability on the exposure of fish to hypoxia: a modeling analysis for the Gulf of Mexico
Plant genotype determines biomass response to flooding frequency in tidal wetlands
Factors controlling the competition between Phaeocystis and diatoms in the Southern Ocean and implications for carbon export fluxes
Characterization of particle-associated and free-living bacterial and archaeal communities along the water columns of the South China Sea
Adult life strategy affects distribution patterns in abyssal isopods – implications for conservation in Pacific nodule areas
Diversity and distribution of nitrogen fixation genes in the oxygen minimum zones of the world oceans
Structure and function of epipelagic mesozooplankton and their response to dust deposition events during the spring PEACETIME cruise in the Mediterranean Sea
Distribution of planktonic foraminifera in the subtropical South Atlantic: depth hierarchy of controlling factors
Technical note: Estimating light-use efficiency of benthic habitats using underwater O2 eddy covariance
Ocean acidification reduces growth and grazing impact of Antarctic heterotrophic nanoflagellates
Dynamics of environmental conditions during the decline of a Cymodocea nodosa meadow
Megafauna community assessment of polymetallic-nodule fields with cameras: platform and methodology comparison
A meta-analysis on environmental drivers of marine phytoplankton C : N : P
Spatial and temporal variability in the response of phytoplankton and prokaryotes to B-vitamin amendments in an upwelling system
Biogeography and community structure of abyssal scavenging Amphipoda (Crustacea) in the Pacific Ocean
Are seamounts refuge areas for fauna from polymetallic nodule fields?
Ocean deoxygenation and copepods: coping with oxygen minimum zone variability
Unexpected high abyssal ophiuroid diversity in polymetallic nodule fields of the northeast Pacific Ocean and implications for conservation
Population dynamics of modern planktonic foraminifera in the western Barents Sea
Foraminiferal community response to seasonal anoxia in Lake Grevelingen (the Netherlands)
Light availability modulates the effects of warming in a marine N2 fixer
SiR-actin-labelled granules in foraminifera: patterns, dynamics, and hypotheses
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.
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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.
Phillip Williamson, Hans-Otto Pörtner, Steve Widdicombe, and Jean-Pierre Gattuso
Biogeosciences, 18, 1787–1792, https://doi.org/10.5194/bg-18-1787-2021, https://doi.org/10.5194/bg-18-1787-2021, 2021
Short summary
Short summary
The reliability of ocean acidification research was challenged in early 2020 when a high-profile paper failed to corroborate previously observed impacts of high CO2 on the behaviour of coral reef fish. We now know the reason why: the
replicatedstudies differed in many ways. Open-minded and collaborative assessment of all research results, both negative and positive, remains the best way to develop process-based understanding of the impacts of ocean acidification on marine organisms.
Michael Lintner, Bianca Lintner, Wolfgang Wanek, Nina Keul, and Petra Heinz
Biogeosciences, 18, 1395–1406, https://doi.org/10.5194/bg-18-1395-2021, https://doi.org/10.5194/bg-18-1395-2021, 2021
Short summary
Short summary
Foraminifera are unicellular marine organisms that play an important role in the marine element cycle. Changes of environmental parameters such as salinity or temperature have a significant impact on the faunal assemblages. Our experiments show that changes in salinity immediately influence the foraminiferal activity. Also the light regime has a significant impact on carbon or nitrogen processing in foraminifera which contain no kleptoplasts.
Michele Casini, Martin Hansson, Alessandro Orio, and Karin Limburg
Biogeosciences, 18, 1321–1331, https://doi.org/10.5194/bg-18-1321-2021, https://doi.org/10.5194/bg-18-1321-2021, 2021
Short summary
Short summary
In the past 20 years the condition of the eastern Baltic cod has dropped, with large implications for the fishery. Our results show that simultaneously the cod population has moved deeper while low-oxygenated waters detrimental for cod growth have become shallower. Cod have thus dwelled more in detrimental waters, explaining the drop in its condition. This study, using long-term fish and hydrological monitoring data, evidences the impact of deoxygenation on fish biology and fishing.
Elizabeth D. LaBone, Kenneth A. Rose, Dubravko Justic, Haosheng Huang, and Lixia Wang
Biogeosciences, 18, 487–507, https://doi.org/10.5194/bg-18-487-2021, https://doi.org/10.5194/bg-18-487-2021, 2021
Short summary
Short summary
The hypoxic zone is an area of low dissolved oxygen (DO) in the Gulf of Mexico. Fish can be killed by exposure to hypoxia and can be negatively impacted by exposure to low, nonlethal DO concentrations (sublethal DO). We found that high sublethal area resulted in higher exposure and DO variability had a small effect on exposure. There was a large variation in exposure among individuals, which when combined with spatial variability of DO, can result in an underestimation of exposure when averaged.
Svenja Reents, Peter Mueller, Hao Tang, Kai Jensen, and Stefanie Nolte
Biogeosciences, 18, 403–411, https://doi.org/10.5194/bg-18-403-2021, https://doi.org/10.5194/bg-18-403-2021, 2021
Short summary
Short summary
By conducting a flooding experiment with two genotypes of the salt-marsh grass Elymus athericus, we show considerable differences in biomass response to flooding within the same species. As biomass production plays a major role in sedimentation processes and thereby salt-marsh accretion, we emphasise the importance of taking intraspecific differences into account when evaluating ecosystem resilience to accelerated sea level rise.
Cara Nissen and Meike Vogt
Biogeosciences, 18, 251–283, https://doi.org/10.5194/bg-18-251-2021, https://doi.org/10.5194/bg-18-251-2021, 2021
Short summary
Short summary
Using a regional Southern Ocean ecosystem model, we find that the relative importance of Phaeocystis and diatoms at high latitudes is controlled by iron and temperature variability, with light levels controlling the seasonal succession in coastal areas. Yet, biomass losses via aggregation and grazing matter as well. We show that the seasonal succession of Phaeocystis and diatoms impacts the seasonality of carbon export fluxes with ramifications for nutrient cycling and food web dynamics.
Jiangtao Li, Lingyuan Gu, Shijie Bai, Jie Wang, Lei Su, Bingbing Wei, Li Zhang, and Jiasong Fang
Biogeosciences, 18, 113–133, https://doi.org/10.5194/bg-18-113-2021, https://doi.org/10.5194/bg-18-113-2021, 2021
Short summary
Short summary
Few studies have focused on the particle-attached (PA) and free-living (FL) microbes of the deep ocean. Here we determined PA and FL microbial communities along depth profiles of the SCS. PA and FL fractions accommodated divergent microbial compositions, and most of them are potentially generalists with PA and FL dual lifestyles. A potential vertical connectivity between surface-specific microbes and those in the deep ocean was indicated, likely through microbial attachment to sinking particles.
Saskia Brix, Karen J. Osborn, Stefanie Kaiser, Sarit B. Truskey, Sarah M. Schnurr, Nils Brenke, Marina Malyutina, and Pedro Martinez Arbizu
Biogeosciences, 17, 6163–6184, https://doi.org/10.5194/bg-17-6163-2020, https://doi.org/10.5194/bg-17-6163-2020, 2020
Short summary
Short summary
The Clarion–Clipperton Fracture Zone (CCZ) located in the Pacific is commercially the most important area of proposed manganese nodule mining. Extraction of this will influence the life and distribution of small deep-sea invertebrates like peracarid crustaceans, of which >90 % are undescribed species new to science. We are doing a species delimitation approach as baseline for an ecological interpretation of species distribution and discuss the results in light of future deep-sea conservation.
Amal Jayakumar and Bess B. Ward
Biogeosciences, 17, 5953–5966, https://doi.org/10.5194/bg-17-5953-2020, https://doi.org/10.5194/bg-17-5953-2020, 2020
Short summary
Short summary
Diversity and community composition of nitrogen-fixing microbes in the three main oxygen minimum zones of the world ocean were investigated using nifH clone libraries. Representatives of three main clusters of nifH genes were detected. Sequences were most diverse in the surface waters. The most abundant OTUs were affiliated with Alpha- and Gammaproteobacteria. The sequences were biogeographically distinct and the dominance of a few OTUs was commonly observed in OMZs in this (and other) studies.
Guillermo Feliú, Marc Pagano, Pamela Hidalgo, and François Carlotti
Biogeosciences, 17, 5417–5441, https://doi.org/10.5194/bg-17-5417-2020, https://doi.org/10.5194/bg-17-5417-2020, 2020
Short summary
Short summary
The impact of Saharan dust deposition events on the Mediterranean Sea ecosystem was studied during a basin-scale survey (PEACETIME cruise, May–June 2017). Short-term responses of the zooplankton community were observed after episodic dust deposition events, highlighting the impact of these events on productivity up to the zooplankton level in the poorly fertilized pelagic ecosystems of the southern Mediterranean Sea.
Douglas Lessa, Raphaël Morard, Lukas Jonkers, Igor M. Venancio, Runa Reuter, Adrian Baumeister, Ana Luiza Albuquerque, and Michal Kucera
Biogeosciences, 17, 4313–4342, https://doi.org/10.5194/bg-17-4313-2020, https://doi.org/10.5194/bg-17-4313-2020, 2020
Short summary
Short summary
We observed that living planktonic foraminifera had distinct vertically distributed communities across the Subtropical South Atlantic. In addition, a hierarchic alternation of environmental parameters was measured to control the distribution of planktonic foraminifer's species depending on the water depth. This implies that not only temperature but also productivity and subsurface processes are signed in fossil assemblages, which could be used to perform paleoceanographic reconstructions.
Karl M. Attard and Ronnie N. Glud
Biogeosciences, 17, 4343–4353, https://doi.org/10.5194/bg-17-4343-2020, https://doi.org/10.5194/bg-17-4343-2020, 2020
Short summary
Short summary
Light-use efficiency defines the ability of primary producers to convert sunlight energy to primary production. This report provides a framework to compute hourly and daily light-use efficiency using underwater eddy covariance, a recent technological development that produces habitat-scale rates of primary production for many different habitat types. The approach, tested on measured flux data, provides a useful means to compare habitat productivity across time and space.
Stacy Deppeler, Kai G. Schulz, Alyce Hancock, Penelope Pascoe, John McKinlay, and Andrew Davidson
Biogeosciences, 17, 4153–4171, https://doi.org/10.5194/bg-17-4153-2020, https://doi.org/10.5194/bg-17-4153-2020, 2020
Short summary
Short summary
Our study showed how ocean acidification can exert both direct and indirect influences on the interactions among trophic levels within the microbial loop. Microbial grazer abundance was reduced at CO2 concentrations at and above 634 µatm, while microbial communities increased in abundance, likely due to a reduction in being grazed. Such changes in predator–prey interactions with ocean acidification could have significant effects on the food web and biogeochemistry in the Southern Ocean.
Mirjana Najdek, Marino Korlević, Paolo Paliaga, Marsej Markovski, Ingrid Ivančić, Ljiljana Iveša, Igor Felja, and Gerhard J. Herndl
Biogeosciences, 17, 3299–3315, https://doi.org/10.5194/bg-17-3299-2020, https://doi.org/10.5194/bg-17-3299-2020, 2020
Short summary
Short summary
The response of Cymodocea nodosa to environmental changes was reported during a 15-month period. The meadow decline was triggered in spring by the simultaneous reduction of available light in the water column and the creation of anoxic conditions in the rooted area. This disturbance was critical for the plant since it took place during its recruitment phase when metabolic needs are maximal and stored reserves minimal. The loss of such habitat-forming seagrass is a major environmental concern.
Timm Schoening, Autun Purser, Daniel Langenkämper, Inken Suck, James Taylor, Daphne Cuvelier, Lidia Lins, Erik Simon-Lledó, Yann Marcon, Daniel O. B. Jones, Tim Nattkemper, Kevin Köser, Martin Zurowietz, Jens Greinert, and Jose Gomes-Pereira
Biogeosciences, 17, 3115–3133, https://doi.org/10.5194/bg-17-3115-2020, https://doi.org/10.5194/bg-17-3115-2020, 2020
Short summary
Short summary
Seafloor imaging is widely used in marine science and industry to explore and monitor areas of interest. The selection of the most appropriate imaging gear and deployment strategy depends on the target application. This paper compares imaging platforms like autonomous vehicles or towed camera frames and different deployment strategies of those in assessing the megafauna abundance of polymetallic-nodule fields. The deep-sea mining industry needs that information for robust impact monitoring.
Tatsuro Tanioka and Katsumi Matsumoto
Biogeosciences, 17, 2939–2954, https://doi.org/10.5194/bg-17-2939-2020, https://doi.org/10.5194/bg-17-2939-2020, 2020
Short summary
Short summary
We conducted an extensive literature survey (meta-analysis) on how the C : N : P ratio varies with change in key environmental drivers. We found that the expected reduction in nutrients and warming under the future climate change scenario is likely to result in increased C : P and C : N of marine phytoplankton. Further, our findings highlight the greater stoichiometric plasticity of eukaryotes over prokaryotes, which provide us insights on how to understand and model plankton.
Vanessa Joglar, Antero Prieto, Esther Barber-Lluch, Marta Hernández-Ruiz, Emilio Fernández, and Eva Teira
Biogeosciences, 17, 2807–2823, https://doi.org/10.5194/bg-17-2807-2020, https://doi.org/10.5194/bg-17-2807-2020, 2020
Short summary
Short summary
Coastal marine ecosystems are among the most ecologically and economically productive areas providing a large fraction of ecosystem goods and services to human populations, and B vitamins have long been considered important growth factors for phytoplankton. Our findings indicate that the responses of microbial plankton to B-vitamin supply are mainly driven by the bacterial community composition and that microbial plankton in this area seems to be well adapted to cope with B-vitamin shortage.
Tasnim Patel, Henri Robert, Cedric D'Udekem D'Acoz, Koen Martens, Ilse De Mesel, Steven Degraer, and Isa Schön
Biogeosciences, 17, 2731–2744, https://doi.org/10.5194/bg-17-2731-2020, https://doi.org/10.5194/bg-17-2731-2020, 2020
Short summary
Short summary
Exploitation of deep-sea resources in one of the largest ecosystems on the planet has rendered research of its biodiversity more urgent than ever before. We investigated the known habitats and connectivity of deep-sea scavenging amphipods and obtained important knowledge about several species. We also demonstrated that a long-term disturbance experiment has possibly reduced amphipod biodiversity. These data and further sampling expeditions are instrumental for formulating sustainable policies.
Daphne Cuvelier, Pedro A. Ribeiro, Sofia P. Ramalho, Daniel Kersken, Pedro Martinez Arbizu, and Ana Colaço
Biogeosciences, 17, 2657–2680, https://doi.org/10.5194/bg-17-2657-2020, https://doi.org/10.5194/bg-17-2657-2020, 2020
Short summary
Short summary
Polymetallic nodule mining will remove hard substrata from the abyssal deep-sea floor. The only neighbouring ecosystems featuring hard substratum are seamounts, and their inhabiting fauna could aid in recovery post-mining. Nevertheless, first observations of seamount megafauna were very different from nodule-associated megafauna and showed little overlap. The possible uniqueness of these ecosystems implies that they should be included in management plans for the conservation of biodiversity.
Karen F. Wishner, Brad Seibel, and Dawn Outram
Biogeosciences, 17, 2315–2339, https://doi.org/10.5194/bg-17-2315-2020, https://doi.org/10.5194/bg-17-2315-2020, 2020
Short summary
Short summary
Increasing deoxygenation and oxygen minimum zone expansion are consequences of global warming. Copepod species had different vertical distribution strategies and physiologies associated with oxygen profile variability (0–1000 m). Species (1) changed vertical distributions and maximum abundance depth, (2) shifted diapause depth, (3) changed diel vertical migration depths, or (4) changed epipelagic depth range in the aerobic mixed layer. Present-day variability helps predict future scenarios.
Magdalini Christodoulou, Timothy O'Hara, Andrew F. Hugall, Sahar Khodami, Clara F. Rodrigues, Ana Hilario, Annemiek Vink, and Pedro Martinez Arbizu
Biogeosciences, 17, 1845–1876, https://doi.org/10.5194/bg-17-1845-2020, https://doi.org/10.5194/bg-17-1845-2020, 2020
Short summary
Short summary
Unexpectedly high diversity was revealed in areas licenced for polymetallic nodule mining exploration in the Pacific Ocean. For the first time, a comprehensive reference library including 287 novel ophiuroid sequences allocated to 43 species was produced. Differences in food availability along the nodule province of CCZ were reflected in the biodiversity patterns observed. The APEI3's dissimilarity with the exploration contract areas questions its ability to serve as a biodiversity reservoir.
Julie Meilland, Hélène Howa, Vivien Hulot, Isaline Demangel, Joëlle Salaün, and Thierry Garlan
Biogeosciences, 17, 1437–1450, https://doi.org/10.5194/bg-17-1437-2020, https://doi.org/10.5194/bg-17-1437-2020, 2020
Short summary
Short summary
This study reports on planktonic foraminifera (PF) diversity and distribution in the Barents Sea. The species Globigerinita uvula and Turborotalita quinqueloba dominate the water column while surface sediments are dominated by Neogloboquadrina pachyderma. We hypothesize the unusual dominance of G. uvula in the water to be a seasonal signal or a result of climate forcing. Size-normalized-protein concentrations of PF show a northward decrease, suggesting biomass to vary with the environment.
Julien Richirt, Bettina Riedel, Aurélia Mouret, Magali Schweizer, Dewi Langlet, Dorina Seitaj, Filip J. R. Meysman, Caroline P. Slomp, and Frans J. Jorissen
Biogeosciences, 17, 1415–1435, https://doi.org/10.5194/bg-17-1415-2020, https://doi.org/10.5194/bg-17-1415-2020, 2020
Short summary
Short summary
The paper presents the response of benthic foraminiferal communities to seasonal absence of oxygen coupled with the presence of hydrogen sulfide, considered very harmful for several living organisms.
Our results suggest that the foraminiferal community mainly responds as a function of the duration of the adverse conditions.
This knowledge is especially useful to better understand the ecology of benthic foraminifera but also in the context of palaeoceanographic interpretations.
Xiangqi Yi, Fei-Xue Fu, David A. Hutchins, and Kunshan Gao
Biogeosciences, 17, 1169–1180, https://doi.org/10.5194/bg-17-1169-2020, https://doi.org/10.5194/bg-17-1169-2020, 2020
Short summary
Short summary
Combined effects of warming and light intensity were estimated in N2-fixing cyanobacterium Trichodesmium. Its physiological responses to warming were significantly modulated by light, with growth peaking at 27 °C under the light-saturating condition but being non-responsive across the range of 23–31 °C under the light-limiting condition. Light shortage also weakened the acclimation ability of Trichodesmium to warming, making light-limited Trichodesmium more sensitive to acute temperature change.
Jan Goleń, Jarosław Tyszka, Ulf Bickmeyer, and Jelle Bijma
Biogeosciences, 17, 995–1011, https://doi.org/10.5194/bg-17-995-2020, https://doi.org/10.5194/bg-17-995-2020, 2020
Short summary
Short summary
We studied the organisation and dynamics of actin in foraminifera. Actin is one of the key structural proteins in most lifeforms. Our investigations show that in foraminifera it forms small granules, around 1 µm in diameter, that display rapid movement. This granularity is unusual in comparison to other organisms. We suppose that these granules are most likely involved in the formation of all types of pseudopods responsible for movement, food capturing, biomineralisation, and other functions.
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