Articles | Volume 8, issue 8
https://doi.org/10.5194/bg-8-2075-2011
© Author(s) 2011. 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-8-2075-2011
© Author(s) 2011. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
Technical note
| 
04 Aug 2011
Technical note |
| 04 Aug 2011
Technical Note: Determination of the metabolically active fraction of benthic foraminifera by means of Fluorescent In Situ Hybridization (FISH)
C. Borrelli
Dipartimento di Scienze della Vita e dell'Ambiente, Polytechnic University of Marche, Via Brecce Bianche, 60122 Ancona, Italy
current address: Department of Earth and Environmental Sciences, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY, 12180, USA
A. Sabbatini
Dipartimento di Scienze della Vita e dell'Ambiente, Polytechnic University of Marche, Via Brecce Bianche, 60122 Ancona, Italy
G. M. Luna
Dipartimento di Scienze della Vita e dell'Ambiente, Polytechnic University of Marche, Via Brecce Bianche, 60122 Ancona, Italy
M. P. Nardelli
Dipartimento di Scienze della Vita e dell'Ambiente, Polytechnic University of Marche, Via Brecce Bianche, 60122 Ancona, Italy
T. Sbaffi
Dipartimento di Scienze della Vita e dell'Ambiente, Polytechnic University of Marche, Via Brecce Bianche, 60122 Ancona, Italy
C. Morigi
Stratigraphy Department, Geological Survey of Denmark and Greenland (GEUS), Øster Voldgade 10, 1350 Copenhagen K, Denmark
R. Danovaro
Dipartimento di Scienze della Vita e dell'Ambiente, Polytechnic University of Marche, Via Brecce Bianche, 60122 Ancona, Italy
A. Negri
Dipartimento di Scienze della Vita e dell'Ambiente, Polytechnic University of Marche, Via Brecce Bianche, 60122 Ancona, Italy
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Biodiversity and Ecosystem Function: Marine
Reefal ostracod assemblages from the Zanzibar Archipelago (Tanzania)
Composite calcite and opal test in Foraminifera (Rhizaria)
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
Planktic foraminifera assemblage composition and flux dynamics inferred from an annual sediment trap record in the Central Mediterranean Sea
Building your own mountain: the effects, limits, and drawbacks of cold-water coral ecosystem engineering
Viability of coastal fish larvae under ocean alkalinity enhancement: from organisms to communities
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
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
Skye Yunshu Tian, Martin Langer, Moriaki Yasuhara, and Chih-Lin Wei
Biogeosciences, 21, 3523–3536, https://doi.org/10.5194/bg-21-3523-2024, https://doi.org/10.5194/bg-21-3523-2024, 2024
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Through the first large-scale study of meiobenthic ostracods from the diverse and productive reef ecosystem in the Zanzibar Archipelago, Tanzania, we found that the diversity and composition of ostracod assemblages as controlled by benthic habitats and human impacts were indicative of overall reef health, and we highlighted the usefulness of ostracods as a model proxy to monitor and understand the degradation of reef ecosystems from the coral-dominated phase to the algae-dominated phase.
Julien Richirt, Satoshi Okada, Yoshiyuki Ishitani, Katsuyuki Uematsu, Akihiro Tame, Kaya Oda, Noriyuki Isobe, Toyoho Ishimura, Masashi Tsuchiya, and Hidetaka Nomaki
Biogeosciences, 21, 3271–3288, https://doi.org/10.5194/bg-21-3271-2024, https://doi.org/10.5194/bg-21-3271-2024, 2024
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We report the first benthic foraminifera with a composite test (i.e. shell) made of opal, which coats the inner part of the calcitic layer. Using comprehensive techniques, we describe the morphology and the composition of this novel opal layer and provide evidence that the opal is precipitated by the foraminifera itself. We explore the potential precipitation process and function(s) of this composite test and further discuss the possible implications for palaeoceanographic reconstructions.
Said Mohamed Hashim, Beth Wangui Waweru, and Agnes Muthumbi
Biogeosciences, 21, 2995–3006, https://doi.org/10.5194/bg-21-2995-2024, https://doi.org/10.5194/bg-21-2995-2024, 2024
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The study investigates the impact of decreasing oxygen in the ocean on macrofaunal communities using the BUS as an example. It identifies distinct shifts in community composition and feeding guilds across oxygen zones, with nematodes dominating dysoxic areas. These findings underscore the complex responses of benthic organisms to oxygen gradients, crucial for understanding ecosystem dynamics in hypoxic environments and their implications for marine biodiversity and sustainability.
Tanguy Soulié, Francesca Vidussi, Justine Courboulès, Marie Heydon, Sébastien Mas, Florian Voron, Carolina Cantoni, Fabien Joux, and Behzad Mostajir
Biogeosciences, 21, 1887–1902, https://doi.org/10.5194/bg-21-1887-2024, https://doi.org/10.5194/bg-21-1887-2024, 2024
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Due to climate change, it is projected that extreme rainfall events, which bring terrestrial matter into coastal seas, will occur more frequently in the Mediterranean region. To test the effects of runoffs of terrestrial matter on plankton communities from Mediterranean coastal waters, an in situ mesocosm experiment was conducted. The simulated runoff affected key processes mediated by plankton, such as primary production and respiration, suggesting major consequences of such events.
Chueh-Chen Tung, Yu-Shih Lin, Jian-Xiang Liao, Tzu-Hsuan Tu, James T. Liu, Li-Hung Lin, Pei-Ling Wang, and Chih-Lin Wei
Biogeosciences, 21, 1729–1756, https://doi.org/10.5194/bg-21-1729-2024, https://doi.org/10.5194/bg-21-1729-2024, 2024
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This study contrasts seabed food webs between a river-fed, high-energy canyon and the nearby slope. We show higher organic carbon (OC) flows through the canyon than the slope. Bacteria dominated the canyon, while seabed fauna contributed more to the slope food web. Due to frequent perturbation, the canyon had a lower faunal stock and OC recycling. Only 4 % of the seabed OC flux enters the canyon food web, suggesting a significant role of the river-fed canyon in transporting OC to the deep sea.
Joost de Vries, Fanny Monteiro, Gerald Langer, Colin Brownlee, and Glen Wheeler
Biogeosciences, 21, 1707–1727, https://doi.org/10.5194/bg-21-1707-2024, https://doi.org/10.5194/bg-21-1707-2024, 2024
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Calcifying phytoplankton (coccolithophores) utilize a life cycle in which they can grow and divide into two different phases. These two phases (HET and HOL) vary in terms of their physiology and distributions, with many unknowns about what the key differences are. Using a combination of lab experiments and model simulations, we find that nutrient storage is a critical difference between the two phases and that this difference allows them to inhabit different nitrogen input regimes.
Theodor Kindeberg, Karl Michael Attard, Jana Hüller, Julia Müller, Cintia Organo Quintana, and Eduardo Infantes
Biogeosciences, 21, 1685–1705, https://doi.org/10.5194/bg-21-1685-2024, https://doi.org/10.5194/bg-21-1685-2024, 2024
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Seagrass meadows are hotspots for biodiversity and productivity, and planting seagrass is proposed as a tool for mitigating biodiversity loss and climate change. We assessed seagrass planted in different years and found that benthic oxygen and carbon fluxes increased as the seabed developed from bare sediments to a mature seagrass meadow. This increase was partly linked to the diversity of colonizing algae which increased the light-use efficiency of the seagrass meadow community.
Thibauld M. Béjard, Andrés S. Rigual-Hernández, Javier P. Tarruella, José A. Flores, Anna Sanchez Vidal, Irene Llamas Cano, and Francisco J. Sierro
EGUsphere, https://doi.org/10.5194/egusphere-2023-3101, https://doi.org/10.5194/egusphere-2023-3101, 2024
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The Mediterranean Sea is considered a climate change hotspot. Documenting planktic foraminifera population is crucial. In the Sicily Strait, 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.
Anna-Selma van der Kaaden, Sandra R. Maier, Siluo Chen, Laurence H. De Clippele, Evert de Froe, Theo Gerkema, Johan van de Koppel, Furu Mienis, Christian Mohn, Max Rietkerk, Karline Soetaert, and Dick van Oevelen
Biogeosciences, 21, 973–992, https://doi.org/10.5194/bg-21-973-2024, https://doi.org/10.5194/bg-21-973-2024, 2024
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Combining hydrodynamic simulations and annotated videos, we separated which hydrodynamic variables that determine reef cover are engineered by cold-water corals and which are not. Around coral mounds, hydrodynamic zones seem to create a typical reef zonation, restricting corals from moving deeper (the expected response to climate warming). But non-engineered downward velocities in winter (e.g. deep winter mixing) seem more important for coral reef growth than coral engineering.
Silvan Urs Goldenberg, Ulf Riebesell, Daniel Brüggemann, Gregor Börner, Michael Sswat, Arild Folkvord, Maria Couret, Synne Spjelkavik, Nicolás Sánchez, Cornelia Jaspers, and Marta Moyano
EGUsphere, https://doi.org/10.5194/egusphere-2024-286, https://doi.org/10.5194/egusphere-2024-286, 2024
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Ocean alkalinity enhancement (OAE) is being evaluated as carbon dioxide removal technology for climate change mitigation. With experiments on single species and species communities, we show that fish larvae can be resilient to the resulting perturbation of seawater. Larvae may hence recruit successfully and continue to support fisheries production in regions of OAE. Our findings for fish and marine food webs help to establish an environmentally safe operating space for this ocean-based solution.
Xiaoke Xin, Giulia Faucher, and Ulf Riebesell
Biogeosciences, 21, 761–772, https://doi.org/10.5194/bg-21-761-2024, https://doi.org/10.5194/bg-21-761-2024, 2024
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Ocean alkalinity enhancement (OAE) is a promising approach to remove CO2 by accelerating natural rock weathering. However, some of the alkaline substances contain trace metals which could be toxic to marine life. By exposing three representative phytoplankton species to Ni released from alkaline materials, we observed varying responses of phytoplankton to nickel concentrations, suggesting caution should be taken and toxic thresholds should be avoided in OAE with Ni-rich materials.
Olmo Miguez-Salas, Angelika Brandt, Henry Knauber, and Torben Riehl
Biogeosciences, 21, 641–655, https://doi.org/10.5194/bg-21-641-2024, https://doi.org/10.5194/bg-21-641-2024, 2024
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In the deep sea, the interaction between benthic fauna (tracemakers) and substrate can be preserved as traces (i.e. lebensspuren), which are common features of seafloor landscapes, rendering them promising proxies for inferring biodiversity from marine images. No general correlation was observed between traces and benthic fauna. However, a local correlation was observed between specific stations depending on unknown tracemakers, tracemaker behaviour, and lebensspuren morphotypes.
Cale A. Miller, Pierre Urrutti, Jean-Pierre Gattuso, Steeve Comeau, Anaïs Lebrun, Samir Alliouane, Robert W. Schlegel, and Frédéric Gazeau
Biogeosciences, 21, 315–333, https://doi.org/10.5194/bg-21-315-2024, https://doi.org/10.5194/bg-21-315-2024, 2024
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This work describes an experimental system that can replicate and manipulate environmental conditions in marine or aquatic systems. Here, we show how the temperature and salinity of seawater delivered from a fjord is manipulated to experimental tanks on land. By constantly monitoring temperature and salinity in each tank via a computer program, the system continuously adjusts automated flow valves to ensure the seawater in each tank matches the targeted experimental conditions.
Rachel A. Kruft Welton, George Hoppit, Daniela N. Schmidt, James D. Witts, and Benjamin C. Moon
Biogeosciences, 21, 223–239, https://doi.org/10.5194/bg-21-223-2024, https://doi.org/10.5194/bg-21-223-2024, 2024
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We conducted a meta-analysis of known experimental literature examining how marine bivalve growth rates respond to climate change. Growth is usually negatively impacted by climate change. Bivalve eggs/larva are generally more vulnerable than either juveniles or adults. Available data on the bivalve response to climate stressors are biased towards early growth stages (commercially important in the Global North), and many families have only single experiments examining climate change impacts.
Vincent Mouchi, Christophe Pecheyran, Fanny Claverie, Cécile Cathalot, Marjolaine Matabos, Yoan Germain, Olivier Rouxel, Didier Jollivet, Thomas Broquet, and Thierry Comtet
Biogeosciences, 21, 145–160, https://doi.org/10.5194/bg-21-145-2024, https://doi.org/10.5194/bg-21-145-2024, 2024
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The impact of deep-sea mining will depend critically on the ability of larval dispersal of hydrothermal mollusks to connect and replenish natural populations. However, assessing connectivity is extremely challenging, especially in the deep sea. Here, we investigate the potential of using the chemical composition of larval shells to discriminate larval origins between multiple hydrothermal sites in the southwest Pacific. Our results confirm that this method can be applied with high accuracy.
Anna-Marie Winter, Nadezda Vasilyeva, and Artem Vladimirov
Biogeosciences, 20, 3683–3716, https://doi.org/10.5194/bg-20-3683-2023, https://doi.org/10.5194/bg-20-3683-2023, 2023
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There is an increasing number of fish in poor state, and many do not recover, even when fishing pressure is ceased. An Allee effect can hinder population recovery because it suppresses the fish's productivity at low abundance. With a model fitted to 17 Atlantic cod stocks, we find that ocean warming and fishing can cause an Allee effect. If present, the Allee effect hinders fish recovery. This shows that Allee effects are dynamic, not uncommon, and calls for precautionary management measures.
Afrah Alothman, Daffne López-Sandoval, Carlos M. Duarte, and Susana Agustí
Biogeosciences, 20, 3613–3624, https://doi.org/10.5194/bg-20-3613-2023, https://doi.org/10.5194/bg-20-3613-2023, 2023
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This study investigates bacterial dissolved inorganic carbon (DIC) fixation in the Red Sea, an oligotrophic ecosystem, using stable-isotope labeling and spectroscopy. The research reveals that bacterial DIC fixation significantly contributes to total DIC fixation, in the surface and deep water. The study demonstrates that as primary production decreases, the role of bacterial DIC fixation increases, emphasizing its importance with photosynthesis in estimating oceanic carbon dioxide production.
Arianna Zampollo, Thomas Cornulier, Rory O'Hara Murray, Jacqueline Fiona Tweddle, James Dunning, and Beth E. Scott
Biogeosciences, 20, 3593–3611, https://doi.org/10.5194/bg-20-3593-2023, https://doi.org/10.5194/bg-20-3593-2023, 2023
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This paper highlights the use of the bottom mixed layer depth (BMLD: depth between the end of the pycnocline and the mixed layer below) to investigate subsurface Chlorophyll a (a proxy of primary production) in temperate stratified shelf waters. The strict correlation between subsurface Chl a and BMLD becomes relevant in shelf-productive waters where multiple stressors (e.g. offshore infrastructure) will change the stratification--mixing balance and related carbon fluxes.
Marco Fusi, Sylvain Rigaud, Giovanna Guadagnin, Alberto Barausse, Ramona Marasco, Daniele Daffonchio, Julie Régis, Louison Huchet, Capucine Camin, Laura Pettit, Cristina Vina-Herbon, and Folco Giomi
Biogeosciences, 20, 3509–3521, https://doi.org/10.5194/bg-20-3509-2023, https://doi.org/10.5194/bg-20-3509-2023, 2023
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Oxygen availability in marine water and freshwater is very variable at daily and seasonal scales. The dynamic nature of oxygen fluctuations has important consequences for animal and microbe physiology and ecology, yet it is not fully understood. In this paper, we showed the heterogeneous nature of the aquatic oxygen landscape, which we defined here as the
oxyscape, and we addressed the importance of considering the oxyscape in the modelling and managing of aquatic ecosystems.
Anne L. Morée, Tayler M. Clarke, William W. L. Cheung, and Thomas L. Frölicher
Biogeosciences, 20, 2425–2454, https://doi.org/10.5194/bg-20-2425-2023, https://doi.org/10.5194/bg-20-2425-2023, 2023
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Ocean temperature and oxygen shape marine habitats together with species’ characteristics. We calculated the impacts of projected 21st-century warming and oxygen loss on the contemporary habitat volume of 47 marine species and described the drivers of these impacts. Most species lose less than 5 % of their habitat at 2 °C of global warming, but some species incur losses 2–3 times greater than that. We also calculate which species may be most vulnerable to climate change and why this is the case.
Markus A. Min, David M. Needham, Sebastian Sudek, Nathan Kobun Truelove, Kathleen J. Pitz, Gabriela M. Chavez, Camille Poirier, Bente Gardeler, Elisabeth von der Esch, Andrea Ludwig, Ulf Riebesell, Alexandra Z. Worden, and Francisco P. Chavez
Biogeosciences, 20, 1277–1298, https://doi.org/10.5194/bg-20-1277-2023, https://doi.org/10.5194/bg-20-1277-2023, 2023
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Emerging molecular methods provide new ways of understanding how marine communities respond to changes in ocean conditions. Here, environmental DNA was used to track the temporal evolution of biological communities in the Peruvian coastal upwelling system and in an adjacent enclosure where upwelling was simulated. We found that the two communities quickly diverged, with the open ocean being one found during upwelling and the enclosure evolving to one found under stratified conditions.
Wojciech Majewski, Witold Szczuciński, and Andrew J. Gooday
Biogeosciences, 20, 523–544, https://doi.org/10.5194/bg-20-523-2023, https://doi.org/10.5194/bg-20-523-2023, 2023
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We studied foraminifera living in the fjords of South Georgia, a sub-Antarctic island sensitive to climate change. As conditions in water and on the seafloor vary, different associations of these microorganisms dominate far inside, in the middle, and near fjord openings. Assemblages in inner and middle parts of fjords are specific to South Georgia, but they may become widespread with anticipated warming. These results are important for interpretating fossil records and monitoring future change.
Allanah Joy Paul, Lennart Thomas Bach, Javier Arístegui, Elisabeth von der Esch, Nauzet Hernández-Hernández, Jonna Piiparinen, Laura Ramajo, Kristian Spilling, and Ulf Riebesell
Biogeosciences, 19, 5911–5926, https://doi.org/10.5194/bg-19-5911-2022, https://doi.org/10.5194/bg-19-5911-2022, 2022
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We investigated how different deep water chemistry and biology modulate the response of surface phytoplankton communities to upwelling in the Peruvian coastal zone. Our results show that the most influential drivers were the ratio of inorganic nutrients (N : P) and the microbial community present in upwelling source water. These led to unexpected and variable development in the phytoplankton assemblage that could not be predicted by the amount of inorganic nutrients alone.
Hanna M. Kauko, Philipp Assmy, Ilka Peeken, Magdalena Różańska-Pluta, Józef M. Wiktor, Gunnar Bratbak, Asmita Singh, Thomas J. Ryan-Keogh, and Sebastien Moreau
Biogeosciences, 19, 5449–5482, https://doi.org/10.5194/bg-19-5449-2022, https://doi.org/10.5194/bg-19-5449-2022, 2022
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This article studies phytoplankton (microscopic
plantsin the ocean capable of photosynthesis) in Kong Håkon VII Hav in the Southern Ocean. Different species play different roles in the ecosystem, and it is therefore important to assess the species composition. We observed that phytoplankton blooms in this area are formed by large diatoms with strong silica armors, which can lead to high silica (and sometimes carbon) export to depth and be important prey for krill.
Chloe Carbonne, Steeve Comeau, Phoebe T. W. Chan, Keyla Plichon, Jean-Pierre Gattuso, and Núria Teixidó
Biogeosciences, 19, 4767–4777, https://doi.org/10.5194/bg-19-4767-2022, https://doi.org/10.5194/bg-19-4767-2022, 2022
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For the first time, our study highlights the synergistic effects of a 9-month warming and acidification combined stress on the early life stages of a Mediterranean azooxanthellate coral, Astroides calycularis. Our results predict a decrease in dispersion, settlement, post-settlement linear extention, budding and survival under future global change and that larvae and recruits of A. calycularis are stages of interest for this Mediterranean coral resistance, resilience and conservation.
Iris E. Hendriks, Anna Escolano-Moltó, Susana Flecha, Raquel Vaquer-Sunyer, Marlene Wesselmann, and Núria Marbà
Biogeosciences, 19, 4619–4637, https://doi.org/10.5194/bg-19-4619-2022, https://doi.org/10.5194/bg-19-4619-2022, 2022
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Seagrasses are marine plants with the capacity to act as carbon sinks due to their high primary productivity, using carbon for growth. This capacity can play a key role in climate change mitigation. We compiled and published data showing that two Mediterranean seagrass species have different metabolic rates, while the study method influences the rates of the measurements. Most communities act as carbon sinks, while the western basin might be more productive than the eastern Mediterranean.
Raúl Tapia, Sze Ling Ho, Hui-Yu Wang, Jeroen Groeneveld, and Mahyar Mohtadi
Biogeosciences, 19, 3185–3208, https://doi.org/10.5194/bg-19-3185-2022, https://doi.org/10.5194/bg-19-3185-2022, 2022
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We report census counts of planktic foraminifera in depth-stratified plankton net samples off Indonesia. Our results show that the vertical distribution of foraminifera species routinely used in paleoceanographic reconstructions varies in hydrographically distinct regions, likely in response to food availability. Consequently, the thermal gradient based on mixed layer and thermocline dwellers also differs for these regions, suggesting potential implications for paleoceanographic reconstructions.
Ricardo González-Gil, Neil S. Banas, Eileen Bresnan, and Michael R. Heath
Biogeosciences, 19, 2417–2426, https://doi.org/10.5194/bg-19-2417-2022, https://doi.org/10.5194/bg-19-2417-2022, 2022
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In oceanic waters, the accumulation of phytoplankton biomass in winter, when light still limits growth, is attributed to a decrease in grazing as the mixed layer deepens. However, in coastal areas, it is not clear whether winter biomass can accumulate without this deepening. Using 21 years of weekly data, we found that in the Scottish coastal North Sea, the seasonal increase in light availability triggers the accumulation of phytoplankton biomass in winter, when light limitation is strongest.
Birgit Koehler, Mårten Erlandsson, Martin Karlsson, and Lena Bergström
Biogeosciences, 19, 2295–2312, https://doi.org/10.5194/bg-19-2295-2022, https://doi.org/10.5194/bg-19-2295-2022, 2022
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Understanding species richness patterns remains a challenge for biodiversity management. We estimated fish species richness over a coastal salinity gradient (3–32) with a method that allowed comparing data from various sources. Species richness was 3-fold higher at high vs. low salinity, and salinity influenced species’ habitat preference, mobility and feeding type. If climate change causes upper-layer freshening of the Baltic Sea, further shifts along the identified patterns may be expected.
Uri Obolski, Thomas Wichard, Alvaro Israel, Alexander Golberg, and Alexander Liberzon
Biogeosciences, 19, 2263–2271, https://doi.org/10.5194/bg-19-2263-2022, https://doi.org/10.5194/bg-19-2263-2022, 2022
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The algal genus Ulva plays a major role in coastal ecosystems worldwide and is a promising prospect as an seagriculture crop. A substantial hindrance to cultivating Ulva arises from sudden sporulation, leading to biomass loss. This process is not yet well understood. Here, we characterize the dynamics of Ulva growth, considering the potential impact of sporulation inhibitors, using a mathematical model. Our findings are an essential step towards understanding the dynamics of Ulva growth.
Emanuela Fanelli, Samuele Menicucci, Sara Malavolti, Andrea De Felice, and Iole Leonori
Biogeosciences, 19, 1833–1851, https://doi.org/10.5194/bg-19-1833-2022, https://doi.org/10.5194/bg-19-1833-2022, 2022
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Zooplankton play a key role in marine ecosystems, forming the base of the marine food web and a link between primary producers and higher-order consumers, such as fish. This aspect is crucial in the Adriatic basin, one of the most productive and overexploited areas of the Mediterranean Sea. A better understanding of community and food web structure and their response to water mass changes is essential under a global warming scenario, as zooplankton are sensitive to climate change.
Masaya Yoshikai, Takashi Nakamura, Rempei Suwa, Sahadev Sharma, Rene Rollon, Jun Yasuoka, Ryohei Egawa, and Kazuo Nadaoka
Biogeosciences, 19, 1813–1832, https://doi.org/10.5194/bg-19-1813-2022, https://doi.org/10.5194/bg-19-1813-2022, 2022
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This study presents a new individual-based vegetation model to investigate salinity control on mangrove productivity. The model incorporates plant hydraulics and tree competition and predicts unique and complex patterns of mangrove forest structures that vary across soil salinity gradients. The presented model does not hold an empirical expression of salinity influence on productivity and thus may provide a better understanding of mangrove forest dynamics in future climate change.
Coulson A. Lantz, William Leggat, Jessica L. Bergman, Alexander Fordyce, Charlotte Page, Thomas Mesaglio, and Tracy D. Ainsworth
Biogeosciences, 19, 891–906, https://doi.org/10.5194/bg-19-891-2022, https://doi.org/10.5194/bg-19-891-2022, 2022
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Coral bleaching events continue to drive the degradation of coral reefs worldwide. In this study we measured rates of daytime coral reef community calcification and photosynthesis during a reef-wide bleaching event. Despite a measured decline in coral health across several taxa, there was no change in overall daytime community calcification and photosynthesis. These findings highlight potential limitations of these community-level metrics to reflect actual changes in coral health.
Hyewon Heather Kim, Jeff S. Bowman, Ya-Wei Luo, Hugh W. Ducklow, Oscar M. Schofield, Deborah K. Steinberg, and Scott C. Doney
Biogeosciences, 19, 117–136, https://doi.org/10.5194/bg-19-117-2022, https://doi.org/10.5194/bg-19-117-2022, 2022
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Heterotrophic marine bacteria are tiny organisms responsible for taking up organic matter in the ocean. Using a modeling approach, this study shows that characteristics (taxonomy and physiology) of bacteria are associated with a subset of ecological processes in the coastal West Antarctic Peninsula region, a system susceptible to global climate change. This study also suggests that bacteria will become more active, in particular large-sized cells, in response to changing climates in the region.
Alice E. Webb, Didier M. de Bakker, Karline Soetaert, Tamara da Costa, Steven M. A. C. van Heuven, Fleur C. van Duyl, Gert-Jan Reichart, and Lennart J. de Nooijer
Biogeosciences, 18, 6501–6516, https://doi.org/10.5194/bg-18-6501-2021, https://doi.org/10.5194/bg-18-6501-2021, 2021
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The biogeochemical behaviour of shallow reef communities is quantified to better understand the impact of habitat degradation and species composition shifts on reef functioning. The reef communities investigated barely support reef functions that are usually ascribed to conventional coral reefs, and the overall biogeochemical behaviour is found to be similar regardless of substrate type. This suggests a decrease in functional diversity which may therefore limit services provided by this reef.
Emmanuel Devred, Andrea Hilborn, and Cornelia Elizabeth den Heyer
Biogeosciences, 18, 6115–6132, https://doi.org/10.5194/bg-18-6115-2021, https://doi.org/10.5194/bg-18-6115-2021, 2021
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A theoretical model of grey seal seasonal abundance on Sable Island (SI) coupled with chlorophyll-a concentration [chl-a] measured by satellite revealed the impact of seal nitrogen fertilization on the surrounding waters of SI, Canada. The increase in seals from about 100 000 in 2003 to about 360 000 in 2018 during the breeding season is consistent with an increase in [chl-a] leeward of SI. The increase in seal abundance explains 8 % of the [chl-a] increase.
Julie Meilland, Michael Siccha, Maike Kaffenberger, Jelle Bijma, and Michal Kucera
Biogeosciences, 18, 5789–5809, https://doi.org/10.5194/bg-18-5789-2021, https://doi.org/10.5194/bg-18-5789-2021, 2021
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Planktonic foraminifera population dynamics has long been assumed to be controlled by synchronous reproduction and ontogenetic vertical migration (OVM). Due to contradictory observations, this concept became controversial. We here test it in the Atlantic ocean for four species of foraminifera representing the main clades. Our observations support the existence of synchronised reproduction and OVM but show that more than half of the population does not follow the canonical trajectory.
Federica Maggioni, Mireille Pujo-Pay, Jérome Aucan, Carlo Cerrano, Barbara Calcinai, Claude Payri, Francesca Benzoni, Yves Letourneur, and Riccardo Rodolfo-Metalpa
Biogeosciences, 18, 5117–5140, https://doi.org/10.5194/bg-18-5117-2021, https://doi.org/10.5194/bg-18-5117-2021, 2021
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Based on current experimental evidence, climate change will affect up to 90 % of coral reefs worldwide. The originality of this study arises from our recent discovery of an exceptional study site where environmental conditions (temperature, pH, and oxygen) are even worse than those forecasted for the future.
While these conditions are generally recognized as unfavorable for marine life, we found a rich and abundant coral reef thriving under such extreme environmental conditions.
Nisan Sariaslan and Martin R. Langer
Biogeosciences, 18, 4073–4090, https://doi.org/10.5194/bg-18-4073-2021, https://doi.org/10.5194/bg-18-4073-2021, 2021
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Analyses of foraminiferal assemblages from the Mamanguape mangrove estuary (northern Brazil) revealed highly diverse, species-rich, and structurally complex biotas. The atypical fauna resembles shallow-water offshore assemblages and are interpreted to be the result of highly saline ocean waters penetrating deep into the estuary. The findings contrast with previous studies, have implications for the fossil record, and provide novel perspectives for reconstructing mangrove environments.
Jutta E. Wollenburg, Jelle Bijma, Charlotte Cremer, Ulf Bickmeyer, and Zora Mila Colomba Zittier
Biogeosciences, 18, 3903–3915, https://doi.org/10.5194/bg-18-3903-2021, https://doi.org/10.5194/bg-18-3903-2021, 2021
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Cultured at in situ high-pressure conditions Cibicides and Cibicidoides taxa develop lasting ectoplasmic structures that cannot be retracted or resorbed. An ectoplasmic envelope surrounds their test and may protect the shell, e.g. versus carbonate aggressive bottom water conditions. Ectoplasmic roots likely anchor the specimens in areas of strong bottom water currents, trees enable them to elevate themselves above ground, and twigs stabilize and guide the retractable pseudopodial network.
Kumar Nimit
Biogeosciences, 18, 3631–3635, https://doi.org/10.5194/bg-18-3631-2021, https://doi.org/10.5194/bg-18-3631-2021, 2021
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The Indian Ocean Rim hosts many of the underdeveloped and emerging economies that depend on ocean resources for the livelihood of millions. Operational ocean information services cater to the requirements of resource managers and end-users to efficiently harness resources, mitigate threats and ensure safety. This paper outlines existing tools and explores the ongoing research that has the potential to convert the findings into operational services in the near- to midterm.
Finn Mielck, Rune Michaelis, H. Christian Hass, Sarah Hertel, Caroline Ganal, and Werner Armonies
Biogeosciences, 18, 3565–3577, https://doi.org/10.5194/bg-18-3565-2021, https://doi.org/10.5194/bg-18-3565-2021, 2021
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Marine sand mining is becoming more and more important to nourish fragile coastlines that face global change. We investigated the largest sand extraction site in the German Bight. The study reveals that after more than 35 years of mining, the excavation pits are still detectable on the seafloor while the sediment composition has largely changed. The organic communities living in and on the seafloor were strongly decimated, and no recovery is observable towards previous conditions.
France Van Wambeke, Elvira Pulido, Philippe Catala, Julie Dinasquet, Kahina Djaoudi, Anja Engel, Marc Garel, Sophie Guasco, Barbara Marie, Sandra Nunige, Vincent Taillandier, Birthe Zäncker, and Christian Tamburini
Biogeosciences, 18, 2301–2323, https://doi.org/10.5194/bg-18-2301-2021, https://doi.org/10.5194/bg-18-2301-2021, 2021
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Michaelis–Menten kinetics were determined for alkaline phosphatase, aminopeptidase and β-glucosidase in the Mediterranean Sea. Although the ectoenzymatic-hydrolysis contribution to heterotrophic prokaryotic needs was high in terms of N, it was low in terms of C. This study points out the biases in interpretation of the relative differences in activities among the three tested enzymes in regard to the choice of added concentrations of fluorogenic substrates.
Oscar E. Romero, Simon Ramondenc, and Gerhard Fischer
Biogeosciences, 18, 1873–1891, https://doi.org/10.5194/bg-18-1873-2021, https://doi.org/10.5194/bg-18-1873-2021, 2021
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Upwelling intensity along NW Africa varies on the interannual to decadal timescale. Understanding its changes is key for the prediction of future changes of CO2 sequestration in the northeastern Atlantic. Based on a multiyear (1988–2009) sediment trap experiment at the site CBmeso, fluxes and the species composition of the diatom assemblage are presented. Our data help in establishing the scientific basis for forecasting and modeling future states of this ecosystem and its decadal changes.
Katharine T. Bigham, Ashley A. Rowden, Daniel Leduc, and David A. Bowden
Biogeosciences, 18, 1893–1908, https://doi.org/10.5194/bg-18-1893-2021, https://doi.org/10.5194/bg-18-1893-2021, 2021
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Turbidity flows – underwater avalanches – are large-scale physical disturbances believed to have profound impacts on productivity and diversity of benthic communities in the deep sea. We reviewed published studies and found that current evidence for changes in productivity is ambiguous at best, but the influence on regional and local diversity is clearer. We suggest study design criteria that may lead to a better understanding of large-scale disturbance effects on deep-sea benthos.
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
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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
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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
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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
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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
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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.
Cited articles
Ainsworth, T. D., Fine, M., Blackall, L. L., and Hoegh-Guldberg, O.: Fluorescence in situ hybridization and spectral imaging of coral-associated bacterial communities, Appl. Environ. Microb., 72, 3016–3020, 2006.
Bentov, S. and Erez, J.: Impact of biomineralization processes on the Mg content of foraminiferal shells: a biological perspective, Geochem. Geophy. Geosy., 7, Q01P08, https://doi.org/10.1029/2005GC001015, 2006.
Bernhard, J. M.: Distinguishing live from dead foraminifera: methods review and proper applications, Micropaleontology, 46, 38–46, 2000.
Bernhard, J. M., Newkirk, S. G., and Bowser, S. S.: Towards a non-terminal viability assay for foraminiferan protists, J. Eukaryot. Microbiol., 42, 357–367, 1995.
Bernhard, J. M., Blanks, J. K., Hintz, C. J., and Chandler, G. T.: Use of the fluorescent calcite marker calcein to label foraminiferal tests, J. Foramin. Res., 34, 96–101, 2004.
Bernhard, J. M., Ostermann, D. R., Williams, D. S., and Blanks, J. K.: Comparison of two methods to identify live benthic foraminifera: a test between Rose Bengal and CellTracker Green with implications for stable isotope paleoreconstructions, Paleoceanography, 21, PA4210, https://doi.org/10.1029/2006PA001290, 2006.
Bernhard, J. M., Sen Gupta, B. K., and Baguley, J. G.: Benthic foraminifera living in Gulf of Mexico bathyal and abyssal sediments: community analysis and comparison to metazoan meiofaunal biomass and density, Deep-Sea Res. Pt. II, 55, 2617–2626, https://doi.org/10.1016/j.dsr2.2008.07.011, 2008.
Booth, B. C.: The use of autofluorescence for analyzing oceanic phytoplankton communities, Bot. Mar., 30, 101–108, 1987.
Christensen, H., Hansen, M., and Sørensen, J.: Counting and size classification of active soil bacteria by Fluorescence In Situ Hybridization with an rRNA oligonucleotide probe, Appl. Environ. Microb., 65, 1753–1761, 1999.
Danovaro, R., Corinaldesi, C., Luna, G. M., Magagnini, M., Manini, E., and Pusceddu, A.: Prokaryote diversity and viral production in deep-sea sediments and seamounts, Deep-Sea Res. Pt. II, 56, 738–747, 2009.
Danovaro, R., Dell'Anno, A., Pusceddu, A., Gambi, C., Heiner, I., and Kristensen, R. M.: The first metazoa living in permanently anoxic conditions, BMC Biol., 8, 30– , 2010.
DeLong, E. F., Wickham, G. S., and Pace, N. R.: Phylogenetic strains: ribosomial RNA-based probes for the identification of single cells, Science, 243, 1360–1363, 1989.
De Nooijer, L. J., Duijnstee, A. P., and Van der Zwaan, G. J.: Novel application of MTT reduction: a viability assay for temperate shallow-water benthic foraminifera, J. Foramin. Res., 36, 195–200, 2006.
De Nooijer, L. J., Toyofuku, T., Oguri, K., Nomaki, H., and Kitazato, H.: Intracellular pH distribution in foraminifera determined by the fluorescent probe HPTS, Limnol. Oceanogr.-Meth., 6, 610-618, 2008.
De Nooijer, L. J., Langer, G., Nehrke, G., and Bijma, J.: Physiological controls on seawater uptake and calcification in the benthic foraminifer Ammonia tepida, Biogeosciences, 6, 2669–2675, https://doi.org/10.5194/bg-6-2669-2009, 2009.
De Stigter, H. C., Jorissen, F. J., and Van der Zwaan, G. J.: Bathymetric distribution and microhabitat partitioning of live (Rose Bengal stained) benthic Foraminifera along a shelf to bathyal transect in the southern Adriatic Sea, J. Foramin. Res., 28, 40–65, 1998.
Dupperon, S., Nadalig, T., Caprais, J. C., Sibuet, M., Fiala-Médioni, A., Amann, R., and Dubilier, N.: Dual symbiosis in a Bathymodiolus sp. mussel from a methane seep on the Gabon continental Margin (Southeast Atlantic): 16S rRNA phylogeny and distribution of the symbionts in gills, Appl. Environ. Microb., 71, 1694–1700, 2005.
Eller, G., Töbe, K., and Medlin, L. K.: Hierarchical probes at various taxonomic levels in the Haptophyta and a new division level probe for the Heterokonta, J. Plankton Res., 29, 629–640, 2007.
Filipsson, H. L., Bernhard, J. M., Lincoln, S. A., and McCorkle, D. C.: A culture-based calibration of benthic foraminiferal paleotemperature proxies: δ18O and Mg/Ca results, Biogeosciences, 7, 1335–1347, https://doi.org/10.5194/bg-7-1335-2010, 2010.
Forge, T. A. and MacGuidwin, A. E.: Nematode autofluorescence and its use as an indicator of viability, J. Nematol., 21, 399–403, 1989.
Frada, M., Not, F., Probert, I., and De Vargas, C.: CaCO3 optical detection with fluorescent in situ hybridization: a new method to identify and quantify calcifying microorganisms from the oceans, J. Phycol., 12, 1162–1169, 2006.
Fried, J., Ludwig, W., Psenner, R., and Heinz, K.: Improvement of ciliate identification and quantification: a new protocol for Fluorescence In Situ Hybridization (FISH) in combination with silver stain techniques, System. Appl. Microbiol., 25, 555–571, 2002.
Garcia-Cuetos, L., Pochon, X., and Pawlowski, J.: Molecular evidence for host-symbiont specificity in soritid foraminifera, Protist, 156, 399–412, 2005.
Gooday, A. J.: Epifaunal and shallow infaunal foraminiferal communities at three abyssal NE Atlantic sites subject to differing phytodetritus input regimes, Deep-Sea Res. Pt. I, 43, 1395–1421, 1996.
Gooday, A. J., Bett, B. J., Shires, R., and Lambshead, P. J. D.: Deep-sea benthic foraminiferal species diversity in the NE Atlantic and NW Arabian Sea: a synthesis, Deep-Sea Res. Pt. II, 45, 165–201, 1998.
Gooday, A. J., Hori, S., Todo, Y., Okamoto, T., Kitazato, H., and Sabbatini, A.: Soft-walled, monothalamous benthic foraminiferans in the Pacific, Indian and Atlantic Oceans: aspects of biodiversity and biogeography, Deep-Sea Res. Pt. I, 51, 33–53, 2004.
Gooday, A. J., Bowser, S. S., Cedhagen, T., Cornelius, N., Hald, M., Korsun, S., and Pawlowski, J.: Monothalamous foraminiferans and gromiids (Protista) from western Svalbard: a preliminary survey, Mar. Biol. Res., 1, 290–312, 2005.
Heinz, P.: Laboratory feeding experiments: response of deep-sea benthic foraminifera to simulated phytoplankton pulses, Revue de Paléobiologie, 20, 643–646, 2001.
Heinz, P., Kitazato, H., Schmiedl, G., and Hemleben, C.: Response of deep-sea benthic foraminifera from the Mediterranean Sea to simulated phytodetritus pulses under laboratory conditions, J. Foramin. Res., 31, 210–227, 2001.
Holzmann, M., Hohenegger, J., Hallock, P., Piller, W. E., and Pawlowski, J.: Molecular phylogeny of larger foraminifera, Mar. Micropaleontol., 43, 57–74, 2001.
Hugenholtz, P., Tyson, G. W., and Blackall, L. L.: Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization, in: Methods in molecular biology, Series n. 179. Gene Probes: Principles and Protocols, edited by: Aquino de Muro, M. and Rapley, R., Humana Press Inc., Totowa, NJ, 272 pp., 2001.
Karner, M. and Fuhrman, J. A.: Determination of active marine bacterioplankton: a comparison of universal 16S rRNA probes, autoradiography, and nucleoid staining, Appl. Environ. Microb., 63, 1208–1213, 1997.
Katz, M. E., Tjalsma, R. C., and Miller, K. G.: Oligocene bathyal to abyssal benthic foraminifera of the Atlantic Ocean, Micropaleontology, 49, 1–45, 2003.
Kerkhof, L. and Ward, B. B.: Comparison of nucleic acid hybridization and fluorometry for measurement of the relationship between RNA/DNA ratio and growth rate in a marine bacterium, Appl. Environ. Microb., 59, 1303–1309, 1993.
Langezaal, A. M., Jannink, N. T., Pierson, E. S., and Van der Zwaan, G. J.: Foraminiferal selectivity towards bacteria: an experimental approach using a cell-permeant stain, J. Sea Res., 54, 256–275, 2005.
Le Cadre, V. and Debenay, J.-P.: Morphological and cytological responses of Ammonia (foraminifera) to copper contamination: Implication for the use of foraminifera as bioindicators of pollution, Environ. Pollut., 143, 304–317, 2006.
Lim, E. L., Amaral, L. A., Caron, D. A., and Delong, E. F.: Application of rRNA-based probes for observing marine nanoplanktonic protists, Appl. Environ. Microb., 59, 1647–1655, 1993.
Lim, E. L., Caron, D. A., and Delong, E. F.: Development and field application of a quantitative method for examining natural assemblages of protists with oligonucleotide probes, Appl. Environ. Microb., 62, 1416–1423, 1996.
Medlin, L. K. and Kooistra, W. H. C. F.: Methods to estimate the diversity in the marine photosynthetic protist community with illustrations from case studies, Diversity, 2, 973–1014, 2010.
Mikulski, C. M., Morton, S. L., and Doucette, G. J.: Development and application of LSU rRNA probes for Karenia brevis in the Gulf of Mexico, USA, Harmful Algae, 4, 49–60, 2005.
Morigi, C.: Benthic environmental changes in the Eastern Mediterranean Sea during sapropel S5 deposition, Palaeogeogr. Palaeocl., 273, 258–271, 2009.
Morigi, C., Jorissen, F. J., Fraticelli, S., Horton, B. P., Principi, M., Sabbatini, A., Capotondi, L., Curzi, P. V., and Negri, A.: Benthic foraminiferal evidence for the formation of the Holocene mud-belt and bathymetrical evolution in the central Adriatic Sea, Mar. Micropaleontol., 57, 25–49, 2005.
Murray, J. W.: Ecology and applications of benthic foraminifera, Cambridge University Press, Cambridge (UK), 426 pp., 2006.
Murray, J. W. and Bowser, S. S.: Mortality, protoplasm decay rate, and reliability of staining techniques to recognize `living' foraminifera: a review, J. Foramin. Res., 30, 66–70, 2000.
Not, F., Simon, N., Biegala, I. C., and Vaulot, D.: Application of fluorescent in situ hybridization coupled with tyramide signal amplification (FISH-TSA) to assess eukaryotic picoplankton composition, Aquat. Microb. Ecol., 28, 157–166, 2002.
Pawlowski, J.: Introduction to the molecular systematic of foraminifera, Micropaleontology, 46, 1–12, 2000.
Pawlowski, J. and Holzmann, M.: Molecular phylogeny of foraminifera – a review, Eur. J. Protistol., 38, 1–10, 2002.
Pernthaler, J., Glöckner, F.O., Schönhuber, W., and Amann, R.: Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes, Method. Microbiol., 30, 207–226, 2001.
Pucci, F., Geslin, E., Barras, C., Morigi, C., Sabbatini, A., Negri, A., and Jorissen, F. J.: Survival of benthic foraminifera under hypoxic conditions. Results of an experimental study using the CellTracker Green method, Mar. Pollut. Bull., 59, 336–351, 2009.
Rice, J., O'Connor, D. C., Sleigh, M. A., Burkill, P. H., Giles, I. G., and Zubkov, M. V.: Fluorescent oligonucleotide rDNA probes that specifically bind to a common nanoflagellate, Paraphysomonas vestita, Microbiology, 143, 1717–1727, 1997a.
Rice, J., Sleigh, M. A., Burkill, P. H., Tarran, G. A., O'Connor, C. D., and Zubkov, M. V.: Flow cytometric analysis of characteristics of hybridization of species-specific fluorescent oligonucleotide probes to rRNA of marine nanoflagellates, Appl. Environ. Microbiol., 63, 938–944, 1997b.
Sabbatini, A., Bonatto, S., Gooday, A. J., Morigi, C., Pancotti, I., Pucci, F., and Negri, A.: Modern benthic foraminifers at Northern shallow sites of Adriatic Sea and soft-walled, monothalamous taxa: a brief overview, Micropaleontol., 56, 359–376, 2010.
Schmiedl, G. and Mackensen, A.: Late Quaternary paleoproductivity and deep water circulation in the Eastern South Atlantic Ocean: evidence from benthic foraminifera, Palaeogeogr. Palaeocl., 130, 43–80, 1997.
Smith, E. M. and del Giorgio, P. A.: Low fractions of active bacteria in natural aquatic communities?, Aquat. Microb. Ecol., 31, 203–208, 2003.
Stoeck, T., Fowle, W. H., and Epstein, S. S.: Methodology of protistan discovery: from rRNA detection to quality scanning electron microscope images, Appl. Environ. Microb., 69, 6856–6863, 2003.
Walton, W. R.: Techniques for recognition of living foraminifera. Contributions from the Cushman Foundation for Foraminiferal Research, 3, 56–60, 1953.
Weiner, S. and Erez, J.: Organic matrix of the shell of the foraminifer Heterostegina depressa, J. Foramin. Res., 14, 206–212, 1984.
Yokouchi, H., Takeyama, H., Miyashita, H., Maruyama, T., and Matsunaga, T.: In situ identification of symbiotic dinoflagellates, the genus Symbiodinium with fluorescent-labeled rRNA-targeted oligonucleotide probes, J. Microbiol. Meth., 53, 327–334, 2003.
