Articles | Volume 13, issue 14
Biogeosciences, 13, 4135–4149, 2016
© Author(s) 2016. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
19 Jul 2016
Research article | 19 Jul 2016
Global analysis of gene expression dynamics within the marine microbial community during the VAHINE mesocosm experiment in the southwest Pacific
Ulrike Pfreundt et al.
No articles found.
Siqi Wu, Moge Du, Xianhui Sean Wan, Corday Selden, Mar Benavides, Sophie Bonnet, Robert Hamersley, Carolin R. Löscher, Margaret R. Mulholland, Xiuli Yan, and Shuh-Ji Kao
Preprint under review for BGShort summary
Nitrogen (N2) fixation is one of the most important nutrient sources to the ocean. Here, we report N2 fixation in the deep, dark ocean in the South China Sea via a highly sensitive new method and elaborate controls, showing the overlooked importance of N2 fixation in the deep ocean. By global data compilation, we also provide an easy measured basic parameter to estimate deep N2 fixation. Our study may help to expand the area limit of N2 fixation studies and better constrain global N2 fixation.
Angela M. Kuhn, Katja Fennel, and Ilana Berman-Frank
Biogeosciences, 15, 7379–7401,Short summary
Recent studies demonstrate that marine N2 fixation can be carried out without light. However, direct measurements of N2 fixation in dark environments are relatively scarce. This study uses a model that represents biogeochemical cycles at a deep-ocean location in the Gulf of Aqaba (Red Sea). Different model versions are used to test assumptions about N2 fixers. Relaxing light limitation for marine N2 fixers improved the similarity between model results and observations of deep nitrate and oxygen.
Sophie Bonnet, Mathieu Caffin, Hugo Berthelot, Olivier Grosso, Mar Benavides, Sandra Helias-Nunige, Cécile Guieu, Marcus Stenegren, and Rachel Ann Foster
Biogeosciences, 15, 4215–4232,
Dina Spungin, Natalia Belkin, Rachel A. Foster, Marcus Stenegren, Andrea Caputo, Mireille Pujo-Pay, Nathalie Leblond, Cécile Dupouy, Sophie Bonnet, and Ilana Berman-Frank
Biogeosciences, 15, 3893–3908,Short summary
The way marine organisms die can determine the fate of organic matter (OM) in the ocean. We investigated whether a form of auto-induced programmed cell death (PCD) influenced phytoplankton mortality and fate of OM. Our results from high biomass blooms of the cyanobacterium Trichodesmium show evidence for PCD and high production of sticky carbon material termed transparent exopolymeric particles (TEP) that facilitates cellular aggregation and enhances the vertical flux of OM to depth.
Mathieu Caffin, Hugo Berthelot, Véronique Cornet-Barthaux, Aude Barani, and Sophie Bonnet
Biogeosciences, 15, 3795–3810,
Mar Benavides, Katyanne M. Shoemaker, Pia H. Moisander, Jutta Niggemann, Thorsten Dittmar, Solange Duhamel, Olivier Grosso, Mireille Pujo-Pay, Sandra Hélias-Nunige, Alain Fumenia, and Sophie Bonnet
Biogeosciences, 15, 3107–3119,Short summary
We measured N2 fixation rates and identified diazotrophic phylotypes in the mesopelagic layer along a transect spanning from New Caledonia to French Polynesia. N2 fixation rates were low but consistently detected across all depths and stations. A distinct diazotrophic phylotype dominated at 650 dbar, coinciding with the oxygenated Subantarctic Mode Water (SAMW) and suggesting that the distribution of aphotic diazotroph communities is to some extent controlled by water mass structure.
Angela N. Knapp, Kelly M. McCabe, Olivier Grosso, Nathalie Leblond, Thierry Moutin, and Sophie Bonnet
Biogeosciences, 15, 2619–2628,Short summary
The spatial distribution of biological N2 fixation fluxes to the ocean remains poorly constrained. Here we use nitrogen isotope budgets to identify significant N2 fixation inputs to the western tropical South Pacific (WTSP), where N2 fixation supports > 50 % of export production at stations proximal to iron sources. The significant N2 fixation inputs in the WTSP may offset nitrogen loss in the oxygen-deficient zones of the eastern tropical South Pacific.
Mathieu Caffin, Thierry Moutin, Rachel Ann Foster, Pascale Bouruet-Aubertot, Andrea Michelangelo Doglioli, Hugo Berthelot, Cécile Guieu, Olivier Grosso, Sandra Helias-Nunige, Nathalie Leblond, Audrey Gimenez, Anne Alexandra Petrenko, Alain de Verneil, and Sophie Bonnet
Biogeosciences, 15, 2565–2585,Short summary
We performed N budgets to assess the role of N2 fixation on production and export in the western tropical South Pacific Ocean. We deployed a combination of techniques including high-sensitivity measurements of N input and sediment traps deployment. We demonstrated that N2 fixation was the major source of new N before atmospheric deposition and upward nitrate fluxes. It contributed significantly to organic matter export, indicating a high efficiency of this region to export carbon.
Marcus Stenegren, Andrea Caputo, Carlo Berg, Sophie Bonnet, and Rachel A. Foster
Biogeosciences, 15, 1559–1578,Short summary
We successfully performed quantitative PCR at sea. The qPCR data were procured within 3 h and used in decisions on further sampling on site. We designed and applied a new primer and probe set for quantifying the UCYN-A1 host and observed discrepancies between host and symbiont, which contradict previous studies. Lastly, we observed a clear vertical separation between a subsurface group (UCYN-A with hosts) and a surface group (remaining diazotrophs), mainly separated by temperature.
Yangyang Lu, Zuozhu Wen, Dalin Shi, Mingming Chen, Yao Zhang, Sophie Bonnet, Yuhang Li, Jiwei Tian, and Shuh-Ji Kao
Biogeosciences, 15, 1–12,Short summary
We investigated the light response of field Trichodesmium N2 fixation and net dissolved nitrogen release behavior. Our results suggest that N2 fixation was a function of light intensity, and the light requirement of Trichodesmium nitrogen fixation was high relative to its photosynthetic light demand. Meanwhile, light is a crucial parameter driving the physiological state of Trichodesmium, which subsequently determined the C / N metabolism and net dissolved nitrogen release.
Thierry Moutin, Andrea Michelangelo Doglioli, Alain de Verneil, and Sophie Bonnet
Biogeosciences, 14, 3207–3220,Short summary
The overall goal of OUTPACE was to obtain a successful representation of the interactions between planktonic organisms and the cycle of biogenic elements in the western tropical South Pacific Ocean across trophic and N2 fixation gradients. The international OUTPACE cruise took place between 18 February and 3 April 2015 aboard the RV L’Atalante and involved 60 scientists. The transect covered ~4 000 km from the western part of the Melanesian archipelago to the western boundary of the gyre.
Audrey Gimenez, Melika Baklouti, Sophie Bonnet, and Thierry Moutin
Biogeosciences, 13, 5103–5120,Short summary
In the context of the VAHINE mesocosm experiment in the Nouméa lagoon (New Caledonia), a 1-D vertical biogeochemical mechanistic model was used together with the in situ experiment to complement our comprehension of the planktonic ecosystem dynamics and the main biogeochemical carbon, nitrogen and phosphate fluxes. The model also showed the fate of fixed N2 by providing, over time, the proportion of diazotroph-derived nitrogen (DDN) in each compartment (mineral and organic) of the model.
Angela N. Knapp, Sarah E. Fawcett, Alfredo Martínez-Garcia, Nathalie Leblond, Thierry Moutin, and Sophie Bonnet
Biogeosciences, 13, 4645–4657,Short summary
The goal of this manuscript was to track the fate of newly fixed nitrogen (N) in large volume mesocosms in the coastal waters of New Caledonia. We used a N isotope ("δ15N") budget and found a shift in the δ15N of sinking particulate N over the 23-day experiment, indicating that nitrate supported export production at the beginning of the experiment, but that nitrogen fixation supported export at the end. We infer that nitrogen fixation supported export production by a release of dissolved N.
Sophie Bonnet, Melika Baklouti, Audrey Gimenez, Hugo Berthelot, and Ilana Berman-Frank
Biogeosciences, 13, 4461–4479,
Dina Spungin, Ulrike Pfreundt, Hugo Berthelot, Sophie Bonnet, Dina AlRoumi, Frank Natale, Wolfgang R. Hess, Kay D. Bidle, and Ilana Berman-Frank
Biogeosciences, 13, 4187–4203,Short summary
The marine cyanobacterium Trichodesmium spp. forms massive blooms important to carbon and nitrogen cycling in the oceans that often collapse abruptly. We investigated a Trichodesmium bloom in the lagoon waters of New Caledonia to specifically elucidate the cellular processes mediating the bloom decline. We demonstrate physiological, biochemical, and genetic evidence for nutrient and oxidative stress that induced a genetically controlled programmed cell death (PCD) pathway leading to bloom demise.
Hugo Berthelot, Sophie Bonnet, Olivier Grosso, Véronique Cornet, and Aude Barani
Biogeosciences, 13, 4005–4021,
Ilana Berman-Frank, Dina Spungin, Eyal Rahav, France Van Wambeke, Kendra Turk-Kubo, and Thierry Moutin
Biogeosciences, 13, 3793–3805,Short summary
In the marine environment, sticky sugar-containing gels, termed transparent exopolymeric particles (TEP), are produced from biological sources and physical and chemical processes. These compounds are essential vectors enhancing downward flow of organic matter and its storage at depth. Spatial and temporal dynamics of TEPs were followed for 23 days during the VAHINE mesocosm experiment that investigated the fate of nitrogen and carbon derived from organisms fixing atmospheric N2 (diazotrophs).
France Van Wambeke, Ulrike Pfreundt, Aude Barani, Hugo Berthelot, Thierry Moutin, Martine Rodier, Wolfgang R. Hess, and Sophie Bonnet
Biogeosciences, 13, 3187–3202,Short summary
The phytoplankton is at the base of the plankton food web in large parts of oceanic "deserts" such as the South Pacific Ocean, where nitrogen sources limit activity. Mesocosms were fertilized with phosphorus to stimulate diazotrophy (atmospheric N2 fixation). Mostly diazotroph-derived nitrogen fuelled the heterotrophic bacterial community through indirect processes generating dissolved organic matter and detritus, such as mortality, lysis and grazing of both diazotrophs and non-diazotrophs.
Brian P. V. Hunt, Sophie Bonnet, Hugo Berthelot, Brandon J. Conroy, Rachel A. Foster, and Marc Pagano
Biogeosciences, 13, 3131–3145,Short summary
Biological nitrogen (N) fixation is an important source of N for food webs in tropical and subtropical oceans. However, uptake pathways remain poorly understood. This study found that fixed N contributed a third of total zooplankton N in the New Caledonia lagoon. Fixed N reached the zooplankton through 1) direct grazing on N fixers and 2) grazing on phytoplankton that had taken up N released by fixers. We report the first record of direct zooplankton grazing on the unicellular N fixer UCYN-C.
Sophie Bonnet, Thierry Moutin, Martine Rodier, Jean-Michel Grisoni, Francis Louis, Eric Folcher, Bertrand Bourgeois, Jean-Michel Boré, and Armelle Renaud
Biogeosciences, 13, 2803–2814,Short summary
e main goal of the VAHINE project was to study the fate of N2 fixation in the ocean. Three large-volume (~ 50 m3) mesocosms were deployed in a tropical oligotrophic ecosystem (the New Caledonia lagoon, south-eastern Pacific). This introductory paper describes the scientific objectives of the project in detail as well as the implementation plan: the mesocosm description and deployment, the selection of the study site, and the logistical and sampling strategy.
Sophie Bonnet, Hugo Berthelot, Kendra Turk-Kubo, Sarah Fawcett, Eyal Rahav, Stéphane L'Helguen, and Ilana Berman-Frank
Biogeosciences, 13, 2653–2673,Short summary
N2 fixation rates were measured daily in ~ 50 m3 mesocosms deployed in New Caledonia to investigate the high-frequency dynamics of diazotrophy and the fate of diazotroph-derived nitrogen (DDN) oligotrophic ecosystems. ~ 10 % of UCYN-C from the water column were exported daily to the traps, representing as much as 22.4 ± 5.5 % of the total POC exported at the height of the UCYN-C bloom. 16 ± 6 % of the DDN was released to the dissolved pool and 21 ± 4 % was transferred to non-diazotrophic plankton.
Ulrike Pfreundt, France Van Wambeke, Mathieu Caffin, Sophie Bonnet, and Wolfgang R. Hess
Biogeosciences, 13, 2319–2337,Short summary
The Southwest Pacific has one of the highest N2 fixation rates in the global ocean, yet information is scarce on the bacterioplankton interrelationships. We detected high microbial diversity in the New Caledonia lagoon and inside a 50 000 L experimental enclosure of the same water mass over 3 weeks and give evidence for previously unknown niche partitioning. Phosphate fertilization promoted the growth of efficient N2 fixing cyanobacteria triggering the growth of most heterotrophic bacteria.
K. A. Turk-Kubo, I. E. Frank, M. E. Hogan, A. Desnues, S. Bonnet, and J. P. Zehr
Biogeosciences, 12, 7435–7452,Short summary
-A shift from diatom-associated diazotrophs (DDAs) to unicellular cyanobacterial group C (UCYN-C) in response to DIP fertilization was captured in a large-scale mesocosm experiment in the Noumea lagoon (NL), a low-nutrient low-chlorophyll coastal environment. -First report of in situ net growth and mortality rates for unicellular diazotrophs UCYN-A2, and UCYN-C. -First quantitative abundance data for diazotrophs in NL indicate that DDAs and UCYN-A1/A2 may be important N2 fixers in this region.
H. Berthelot, T. Moutin, S. L'Helguen, K. Leblanc, S. Hélias, O. Grosso, N. Leblond, B. Charrière, and S. Bonnet
Biogeosciences, 12, 4099–4112,
C. Ridame, J. Dekaezemacker, C. Guieu, S. Bonnet, S. L'Helguen, and F. Malien
Biogeosciences, 11, 4783–4800,
E. Rahav, B. Herut, M. R. Mulholland, B. Voß, D. Stazic, C. Steglich, W. R. Hess, and I. Berman-Frank
Revised manuscript has not been submitted
E. Rahav, B. Herut, A. Levi, M. R. Mulholland, and I. Berman-Frank
Ocean Sci., 9, 489–498,
Related subject area
Biodiversity and Ecosystem Function: MarineContrasting vertical distributions of recent planktic foraminifera off Indonesia during the southeast monsoon: implications for paleoceanographic reconstructionsEarly life stages of a Mediterranean coral are vulnerable to ocean warming and acidificationThe onset of the spring phytoplankton bloom in the coastal North Sea supports the Disturbance Recovery HypothesisSpecies richness and functional attributes of fish assemblages across a large-scale salinity gradient in shallow coastal areasModeling the growth and sporulation dynamics of the macroalga Ulva in mixed-age populations in cultivation and the formation of green tidesSpatial 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 hydraulicsWill daytime community calcification reflect reef accretion on future, degraded coral reefs?Modeling polar marine ecosystem functions guided by bacterial physiological and taxonomic traitsQuantifying functional consequences of habitat degradation on a Caribbean coral reefEnhanced 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 oceanThe Bouraké semi-enclosed lagoon (New Caledonia) – a natural laboratory to study the lifelong adaptation of a coral reef ecosystem to extreme environmental conditionsAtypical, high-diversity assemblages of foraminifera in a mangrove estuary in northern BrazilPermanent ectoplasmic structures in deep-sea Cibicides and Cibicidoides taxa – long-term observations at in situ pressureIdeas 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 takePersistent effects of sand extraction on habitats and associated benthic communities in the German BightSpatial patterns of ectoenzymatic kinetics in relation to biogeochemical properties in the Mediterranean Sea and the concentration of the fluorogenic substrate usedMediterranean seagrasses as carbon sinks: Methodological and regional differencesA 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 compositionReview and syntheses: Impacts of turbidity flows on deep-sea benthic communitiesIdeas and perspectives: When ocean acidification experiments are not the same, repeatability is not testedThe effect of the salinity, light regime and food source on carbon and nitrogen uptake in a benthic foraminiferChanges 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 MexicoPlant genotype determines biomass response to flooding frequency in tidal wetlandsFactors controlling the competition between Phaeocystis and diatoms in the Southern Ocean and implications for carbon export fluxesCharacterization of particle-associated and free-living bacterial and archaeal communities along the water columns of the South China SeaAdult life strategy affects distribution patterns in abyssal isopods – implications for conservation in Pacific nodule areasDiversity and distribution of nitrogen fixation genes in the oxygen minimum zones of the world oceansStructure and function of epipelagic mesozooplankton and their response to dust deposition events during the spring PEACETIME cruise in the Mediterranean SeaDistribution of planktonic foraminifera in the subtropical South Atlantic: depth hierarchy of controlling factorsTechnical note: Estimating light-use efficiency of benthic habitats using underwater O2 eddy covarianceOcean acidification reduces growth and grazing impact of Antarctic heterotrophic nanoflagellatesDynamics of environmental conditions during the decline of a Cymodocea nodosa meadowMegafauna community assessment of polymetallic-nodule fields with cameras: platform and methodology comparisonA meta-analysis on environmental drivers of marine phytoplankton C : N : PSpatial and temporal variability in the response of phytoplankton and prokaryotes to B-vitamin amendments in an upwelling systemBiogeography and community structure of abyssal scavenging Amphipoda (Crustacea) in the Pacific OceanAre seamounts refuge areas for fauna from polymetallic nodule fields?Ocean deoxygenation and copepods: coping with oxygen minimum zone variabilityUnexpected high abyssal ophiuroid diversity in polymetallic nodule fields of the northeast Pacific Ocean and implications for conservationPopulation dynamics of modern planktonic foraminifera in the western Barents SeaForaminiferal community response to seasonal anoxia in Lake Grevelingen (the Netherlands)Light availability modulates the effects of warming in a marine N2 fixerSiR-actin-labelled granules in foraminifera: patterns, dynamics, and hypothesesAlpha and beta diversity patterns of polychaete assemblages across the nodule province of the eastern Clarion-Clipperton Fracture Zone (equatorial Pacific)Dimensions of marine phytoplankton diversityThe Arctic picoeukaryote Micromonas pusilla benefits from ocean acidification under constant and dynamic lightFlux variability of phyto- and zooplankton communities in the Mauritanian coastal upwelling between 2003 and 2008
Raúl Tapia, Sze Ling Ho, Hui-Yu Wang, Jeroen Groeneveld, and Mahyar Mohtadi
Biogeosciences, 19, 3185–3208,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.
Chloe Carbonne, Steeve Comeau, Phoebe T. W. Chan, Keyla Plichon, Jean-Pierre Gattuso, and Núria Teixidó
For the first time, our study highlights the synergistic and additive effects 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 of dispersion, settlement, post-settlement growth 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.
Ricardo González-Gil, Neil S. Banas, Eileen Bresnan, and Michael R. Heath
Biogeosciences, 19, 2417–2426,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,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,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,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,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,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,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,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,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,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,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,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,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.
Biogeosciences, 18, 3631–3635,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,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,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.
Anna Escolano-Moltó, Susana Flecha, Raquel Vaquer-Sunyer, Marlene Wesselmann, Núria Marbà, and Iris Eline Hendriks
Revised manuscript accepted for BGShort 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 published and own data and show two Mediterranean seagrass species have different metabolic rates and the method used influences the rates of the measurements. Also the Eastern basin is more productive compared to the Western Mediterranean while most communities act as carbon sinks.
Oscar E. Romero, Simon Ramondenc, and Gerhard Fischer
Biogeosciences, 18, 1873–1891,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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.
Paulo Bonifácio, Pedro Martínez Arbizu, and Lénaïck Menot
Biogeosciences, 17, 865–886,Short summary
The patterns observed in the composition of polychaete assemblages were attributed to variations in food supply at the regional scale and nodule density at the local scale. The high levels of species replacement were mainly driven by rare species, leading to regional species pool estimates between 498 and 240 000 species. The high proportion of singletons seems reflect an under-sampling bias that is currently preventing the assessment of potential biodiversity loss due to nodule mining.
Stephanie Dutkiewicz, Pedro Cermeno, Oliver Jahn, Michael J. Follows, Anna E. Hickman, Darcy A. A. Taniguchi, and Ben A. Ward
Biogeosciences, 17, 609–634,Short summary
Phytoplankton are an essential component of the marine food web and earth's carbon cycle. We use observations, ecological theory and a unique trait-based ecosystem model to explain controls on patterns of marine phytoplankton biodiversity. We find that different dimensions of diversity (size classes, biogeochemical functional groups, thermal norms) are controlled by a disparate combination of mechanisms. This may explain why previous studies of phytoplankton diversity had conflicting results.
Emily White, Clara J. M. Hoppe, and Björn Rost
Biogeosciences, 17, 635–647,Short summary
The Arctic picoeukaryote Micromonas pusilla was acclimated to two pCO2 levels under a constant and a dynamic light, simulating more realistic light fields. M. pusilla was able to benefit from ocean acidification with an increase in growth rate, irrespective of the light regime. In dynamic light M. pusilla optimised its photophysiology for effective light usage during both low- and high-light periods. This highlights M. pusilla is likely to cope well with future conditions in the Arctic Ocean.
Oscar E. Romero, Karl-Heinz Baumann, Karin A. F. Zonneveld, Barbara Donner, Jens Hefter, Bambaye Hamady, Vera Pospelova, and Gerhard Fischer
Biogeosciences, 17, 187–214,Short summary
Monitoring of the multiannual evolution of populations representing different trophic levels allows for obtaining insights into the impact of climate variability in marine coastal upwelling ecosystems. By using a multiyear, continuous (1,900 d) sediment trap record, we assess the dynamics and fluxes of calcareous, organic and siliceous microorganisms off Mauritania (NW Africa). The experiment allowed for the recognition of a general sequence of seasonal variations of the main populations.
Aylward, F. O., Eppley, J. M., Smith, J. M., Chavez, F. P., Scholin, C. A., and DeLong, E. F.: Microbial community transcriptional networks are conserved in three domains at ocean basin scales, P. Natl. Acad. Sci. USA, 112, 5443–5448, https://doi.org/10.1073/pnas.1502883112, 2015.
Berthelot, H., Moutin, T., L'Helguen, S., Leblanc, K., Hélias, S., Grosso, O., Leblond, N., Charrière, B., and Bonnet, S.: Dinitrogen fixation and dissolved organic nitrogen fueled primary production and particulate export during the VAHINE mesocosm experiment (New Caledonia lagoon), Biogeosciences, 12, 4099–4112, https://doi.org/10.5194/bg-12-4099-2015, 2015.
Bonnet, S., Berthelot, H., Turk-Kubo, K., Fawcett, S., Rahav, E., L'Helguen, S., and Berman-Frank, I.: Dynamics of N2 fixation and fate of diazotroph-derived nitrogen in a low-nutrient, low-chlorophyll ecosystem: results from the VAHINE mesocosm experiment (New Caledonia), Biogeosciences, 13, 2653–2673, https://doi.org/10.5194/bg-13-2653-2016, 2016a.
Bonnet, S., Moutin, T., Rodier, M., Grisoni, J.-M., Louis, F., Folcher, E., Bourgeois, B., Boré, J.M., and Renaud, A.: Introduction to the project VAHINE: VAriability of vertical and tropHIc transfer of diazotroph derived N in the south wEst Pacific, Biogeosciences, 13, 2803–2814, https://doi.org/10.5194/bg-13-2803-2016, 2016b.
Buchfink, B., Xie, C., and Huson, D. H.: Fast and sensitive protein alignment using DIAMOND, Nat. Methods, 12, 59–60, https://doi.org/10.1038/nmeth.3176, 2015.
Cho, J.-C. and Giovannoni, S. J.: Cultivation and growth characteristics of a diverse group of oligotrophic marine Gammaproteobacteria, Appl. Environ. Microbiol., 70, 432–440, 2004.
Dufresne, A., Ostrowski, M., Scanlan, D. J., Garczarek, L., Mazard, S., Palenik, B. P., Paulsen, I. T., de Marsac, N. T., Wincker, P., Dossat, C., Ferriera, S., Johnson, J., Post, A. F., Hess, W. R., and Partensky, F.: Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria, Genome Biol., 9, R90, https://doi.org/10.1186/gb-2008-9-5-r90, 2008.
Dupont, C. L., Rusch, D. B., Yooseph, S., Lombardo, M.-J., Alexander Richter, R., Valas, R., Novotny, M., Yee-Greenbaum, J., Selengut, J. D., Haft, D. H., Halpern, A. L., Lasken, R. S., Nealson, K., Friedman, R., and Craig Venter, J.: Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage, ISME J., 6, 1186–1199, https://doi.org/10.1038/ismej.2011.189, 2012.
Edgar, R. C.: Search and clustering orders of magnitude faster than BLAST, Bioinformatics, 26, 2460–2461, https://doi.org/10.1093/bioinformatics/btq461, 2010.
Forchhammer, K.: P(II) signal transducers: novel functional and structural insights, Trends Microbiol., 16, 65–72, https://doi.org/10.1016/j.tim.2007.11.004, 2008.
Foster, R. A., Kuypers, M. M. M., Vagner, T., Paerl, R. W., Musat, N., and Zehr, J. P.: Nitrogen fixation and transfer in open ocean diatom-cyanobacterial symbioses, ISME J., 5, 1484–1493, https://doi.org/10.1038/ismej.2011.26, 2011.
Frank, J. A., Lorimer, D., Youle, M., Witte, P., Craig, T., Abendroth, J., Rohwer, F., Edwards, R. A., Segall, A. M., and Burgin, A. B.: Structure and function of a cyanophage-encoded peptide deformylase, ISME J., 7, 1150–1160, https://doi.org/10.1038/ismej.2013.4, 2013.
Frias-Lopez, J., Shi, Y., Tyson, G. W., Coleman, M. L., Schuster, S. C., Chisholm, S. W., and Delong, E. F.: Microbial community gene expression in ocean surface waters, P. Natl. Acad. Sci. USA, 105, 3805–3810, https://doi.org/10.1073/pnas.0708897105, 2008.
Ganesh, S., Bristow, L. A., Larsen, M., Sarode, N., Thamdrup, B. and Stewart, F. J.: Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone, ISME J., 9, 2682–2696, https://doi.org/10.1038/ismej.2015.44, 2015.
García-Martínez, J., Acinas, S. G., Massana, R., and Rodríguez-Valera, F.: Prevalence and microdiversity of Alteromonas macleodii-like microorganisms in different oceanic regions, Environ. Microbiol., 4, 42–50, 2002.
Georg, J., Dienst, D., Schürgers, N., Wallner, T., Kopp, D., Stazic, D., Kuchmina, E., Klähn, S., Lokstein, H., Hess, W. R., and Wilde, A.: The Small Regulatory RNA SyR1/PsrR1 Controls Photosynthetic Functions in Cyanobacteria, Plant Cell Online, 26, 3661–3679, https://doi.org/10.1105/tpc.114.129767, 2014.
Gifford, S. M., Sharma, S., and Moran, M. A.: Linking activity and function to ecosystem dynamics in a coastal bacterioplankton community, Front. Microbiol., 5, 185, https://doi.org/10.3389/fmicb.2014.00185, 2014.
Gómez-Consarnau, L., Akram, N., Lindell, K., Pedersen, A., Neutze, R., Milton, D. L., González, J. M., and Pinhassi, J.: Proteorhodopsin phototrophy promotes survival of marine bacteria during starvation, PLoS Biol., 8, e1000358, https://doi.org/10.1371/journal.pbio.1000358, 2010.
Haas, B. J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P. D., Bowden, J., Couger, M. B., Eccles, D., Li, B., Lieber, M., Macmanes, M. D., Ott, M., Orvis, J., Pochet, N., Strozzi, F., Weeks, N., Westerman, R., William, T., Dewey, C. N., Henschel, R., Leduc, R. D., Friedman, N., and Regev, A.: De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis, Nat. Protoc., 8, 1494–1512, https://doi.org/10.1038/nprot.2013.084, 2013.
Hewson, I., Poretsky, R. S., Tripp, H. J., Montoya, J. P., and Zehr, J. P.: Spatial patterns and light-driven variation of microbial population gene expression in surface waters of the oligotrophic open ocean, Environ. Microbiol., 12, 1940–1956, https://doi.org/10.1111/j.1462-2920.2010.02198.x, 2010.
Hilton, J. A., Satinsky, B. M., Doherty, M., Zielinski, B., and Zehr, J. P.: Metatranscriptomics of N2-fixing cyanobacteria in the Amazon River plume, ISME J., 9, 1557–1569, https://doi.org/10.1038/ismej.2014.240, 2015.
Huergo, L. F., Chandra, G., and Merrick, M.: P(II) signal transduction proteins: nitrogen regulation and beyond, FEMS Microbiol. Rev., 37, 251–283, https://doi.org/10.1111/j.1574-6976.2012.00351.x, 2013.
Hunt, D. E., Lin, Y., Church, M. J., Karl, D. M., Tringe, S. G., Izzo, L. K., and Johnson, Z. I.: Relationship between Abundance and Specific Activity of Bacterioplankton in Open Ocean Surface Waters, Appl. Environ. Microbiol., 79, 177–184, https://doi.org/10.1128/AEM.02155-12, 2013.
Huson, D. H. and Weber, N.: Microbial community analysis using MEGAN, Methods Enzymol., 531, 465–485, https://doi.org/10.1016/B978-0-12-407863-5.00021-6, 2013.
Ivars-Martinez, E., Martin-Cuadrado, A.-B., D'Auria, G., Mira, A., Ferriera, S., Johnson, J., Friedman, R., and Rodriguez-Valera, F.: Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter, ISME J., 2, 1194–1212, https://doi.org/10.1038/ismej.2008.74, 2008.
Jones, D. S., Flood, B. E., and Bailey, J. V.: Metatranscriptomic insights into polyphosphate metabolism in marine sediments, ISME J., 10, 1015–1019, https://doi.org/10.1038/ismej.2015.169, 2015.
Kimura, H., Young, C. R., Martinez, A., and Delong, E. F.: Light-induced transcriptional responses associated with proteorhodopsin-enhanced growth in a marine flavobacterium, ISME J., 5, 1641–1651, https://doi.org/10.1038/ismej.2011.36, 2011.
Klähn, S., Schaal, C., Georg, J., Baumgartner, D., Knippen, G., Hagemann, M., Muro-Pastor, A. M., and Hess, W. R.: The sRNA NsiR4 is involved in nitrogen assimilation control in cyanobacteria by targeting glutamine synthetase inactivating factor IF7, P. Natl. Acad. Sci. USA, 112, E6243–6252, https://doi.org/10.1073/pnas.1508412112, 2015.
Knapp, A. N., Fawcett, S. E., Martínez-Garcia, A., Leblond, N., Moutin, T., and Bonnet, S.: Nitrogen isotopic evidence for a shift from nitrate- to diazotroph-fueled export production in VAHINE mesocosm experiments, Biogeosciences Discuss., 12, 19901–19939, https://doi.org/10.5194/bgd-12-19901-2015, 2015.
Kopylova, E., Noé, L., and Touzet, H.: SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data, Bioinforma. Oxf. Engl., 28, 3211–3217, https://doi.org/10.1093/bioinformatics/bts611, 2012.
Lami, R., Cottrell, M. T., Campbell, B. J., and Kirchman, D. L.: Light-dependent growth and proteorhodopsin expression by Flavobacteria and SAR11 in experiments with Delaware coastal waters, Environ. Microbiol., 11, 3201–3209, https://doi.org/10.1111/j.1462-2920.2009.02028.x, 2009.
Langmead, B.: Aligning short sequencing reads with Bowtie, Curr. Protoc. Bioinforma. Ed. Board Andreas Baxevanis Al, Chapter 11, Unit 11.7, https://doi.org/10.1002/0471250953.bi1107s32, 2010.
Leblanc, K., Cornet, V., Caffin, M., Rodier, M., Desnues, A., Berthelot, H., Turk-Kubo, K., and Heliou, J.: Phytoplankton community structure in the VAHINE MESOCOSM experiment, Biogeosciences Discuss., https://doi.org/10.5194/bg-2015-605, in review, 2016.
Li, B. and Dewey, C. N.: RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome, BMC Bioinformatics, 12, 323, https://doi.org/10.1186/1471-2105-12-323, 2011.
Lindell, D. and Post, A. F.: Ecological aspects of ntcA gene expression and its use as an indicator of the nitrogen status of marine Synechococcus spp, Appl. Environ. Microbiol., 67, 3340–3349, https://doi.org/10.1128/AEM.67.8.3340-3349.2001, 2001.
López-Pérez, M., Gonzaga, A., Martin-Cuadrado, A.-B., Onyshchenko, O., Ghavidel, A., Ghai, R., and Rodriguez-Valera, F.: Genomes of surface isolates of Alteromonas macleodii: the life of a widespread marine opportunistic copiotroph, Sci. Rep., 2, 696, https://doi.org/10.1038/srep00696, 2012.
Lott, S. C., Voß, B., Hess, W. R., and Steglich, C.: CoVennTree: a new method for the comparative analysis of large datasets, Front. Genet., 6, 43, https://doi.org/10.3389/fgene.2015.00043, 2015.
Luo, Y.-W., Doney, S. C., Anderson, L. A., Benavides, M., Berman-Frank, I., Bode, A., Bonnet, S., Boström, K. H., Böttjer, D., Capone, D. G., Carpenter, E. J., Chen, Y. L., Church, M. J., Dore, J. E., Falcón, L. I., Fernández, A., Foster, R. A., Furuya, K., Gómez, F., Gundersen, K., Hynes, A. M., Karl, D. M., Kitajima, S., Langlois, R. J., LaRoche, J., Letelier, R. M., Marañón, E., McGillicuddy Jr., D. J., Moisander, P. H., Moore, C. M., Mouriño-Carballido, B., Mulholland, M. R., Needoba, J. A., Orcutt, K. M., Poulton, A. J., Rahav, E., Raimbault, P., Rees, A. P., Riemann, L., Shiozaki, T., Subramaniam, A., Tyrrell, T., Turk-Kubo, K. A., Varela, M., Villareal, T. A., Webb, E. A., White, A. E., Wu, J., and Zehr, J. P.: Database of diazotrophs in global ocean: abundance, biomass and nitrogen fixation rates, Earth Syst. Sci. Data, 4, 47–73, https://doi.org/10.5194/essd-4-47-2012, 2012.
Ma, Y., Allen, L. Z., and Palenik, B.: Diversity and genome dynamics of marine cyanophages using metagenomic analyses, Environ. Microbiol. Rep., 6, 583–594, 2014.
Markowitz, V. M., Chen, I.-M. A., Chu, K., Pati, A., Ivanova, N. N., and Kyrpides, N. C.: Ten Years of Maintaining and Expanding a Microbial Genome and Metagenome Analysis System, Trends Microbiol., https://doi.org/10.1016/j.tim.2015.07.012, 2015.
Martin-Cuadrado, A.-B., Garcia-Heredia, I., Moltó, A. G., López-Úbeda, R., Kimes, N., López-García, P., Moreira, D., and Rodriguez-Valera, F.: A new class of marine Euryarchaeota group II from the Mediterranean deep chlorophyll maximum, ISME J., 9, 1619–1634, https://doi.org/10.1038/ismej.2014.249, 2015.
Moore, R. B., Oborník, M., Janouskovec, J., Chrudimský, T., Vancová, M., Green, D. H., Wright, S. W., Davies, N. W., Bolch, C. J. S., Heimann, K., Slapeta, J., Hoegh-Guldberg, O., Logsdon, J. M., and Carter, D. A.: A photosynthetic alveolate closely related to apicomplexan parasites, Nature, 451, 959–963, https://doi.org/10.1038/nature06635, 2008.
Moran, M. A., Satinsky, B., Gifford, S. M., Luo, H., Rivers, A., Chan, L.-K., Meng, J., Durham, B. P., Shen, C., Varaljay, V. A., Smith, C. B., Yager, P. L., and Hopkinson, B. M.: Sizing up metatranscriptomics, ISME J., 7, 237–243, https://doi.org/10.1038/ismej.2012.94, 2013.
Nakayama, T., Kamikawa, R., Tanifuji, G., Kashiyama, Y., Ohkouchi, N., Archibald, J. M., and Inagaki, Y.: Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle, P. Natl. Acad. Sci. USA, 111, 11407–11412, https://doi.org/10.1073/pnas.1405222111, 2014.
Oborník, M., Modrý, D., Lukeš, M., Cernotíková-Stříbrná, E., Cihlář, J., Tesařová, M., Kotabová, E., Vancová, M., Prášil, O., and Lukeš, J.: Morphology, ultrastructure and life cycle of Vitrella brassicaformis n. sp., n. gen., a novel chromerid from the Great Barrier Reef, Protist, 163, 306–323, https://doi.org/10.1016/j.protis.2011.09.001, 2012.
Oksanen, J., Blanchet, F. G., Kindt, R., Legendre, P., Minchin, P. R., O'Hara, R. B., Simpson, G. L., Solymos, P., Stevens, M. H. H., and Wagner, H.: vegan: Community Ecology Package, available at: http://CRAN.R-project.org/package=vegan (last access: 7 February 2016), 2015.
Pfreundt, U., Miller, D., Adusumilli, L., Stambler, N., Berman-Frank, I., and Hess, W. R.: Depth dependent metatranscriptomes of the marine pico-/nanoplanktonic communities in the Gulf of Aqaba/Eilat during seasonal deep mixing, Mar. Genomics, 18 Pt B, 93–95, https://doi.org/10.1016/j.margen.2014.06.005, 2014.
Pfreundt, U., Spungin, D., Berman-Frank, I., Bonnet, S., and Hess, W. R.: 16S rRNA gene amplicon and metatranscriptomic datasets from the VAHINE mesocosm experiment in the New Caledonian Lagoon, South West Pacific, http://www.ncbi.nlm.nih.gov/bioproject/PRJNA304389/, 2015.
Pfreundt, U., Van Wambeke, F., Caffin, M., Bonnet, S., and Hess, W. R.: Succession within the prokaryotic communities during the VAHINE mesocosms experiment in the New Caledonia lagoon, Biogeosciences, 13, 2319–2337, https://doi.org/10.5194/bg-13-2319-2016, 2016.
Pinto, F. L., Thapper, A., Sontheim, W., and Lindblad, P.: Analysis of current and alternative phenol based RNA extraction methodologies for cyanobacteria, BMC Mol. Biol., 10, 79, https://doi.org/10.1186/1471-2199-10-79, 2009.
Poretsky, R. S., Hewson, I., Sun, S., Allen, A. E., Zehr, J. P., and Moran, M. A.: Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre, Environ. Microbiol., 11, 1358–1375, https://doi.org/10.1111/j.1462-2920.2008.01863.x, 2009.
Prechtl, J., Kneip, C., Lockhart, P., Wenderoth, K., and Maier, U.-G.: Intracellular spheroid bodies of rhopalodia gibba have nitrogen-fixing apparatus of cyanobacterial origin, Mol. Biol. Evol., 21, 1477–1481, https://doi.org/10.1093/molbev/msh086, 2004.
Robinson, M. D., McCarthy, D. J., and Smyth, G. K.: edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, 26, 139–140, https://doi.org/10.1093/bioinformatics/btp616, 2010.
Scanlan, D. J., Ostrowski, M., Mazard, S., Dufresne, A., Garczarek, L., Hess, W. R., Post, A. F., Hagemann, M., Paulsen, I., and Partensky, F.: Ecological genomics of marine picocyanobacteria, Microbiol. Mol. Biol. Rev., 73, 249–299, https://doi.org/10.1128/MMBR.00035-08, 2009.
Schäfer, H., Servais, P., and Muyzer, G.: Successional changes in the genetic diversity of a marine bacterial assemblage during confinement, Arch. Microbiol., 173, 138–145, 2000.
Shi, Y., Tyson, G. W., and DeLong, E. F.: Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column, Nature, 459, 266–269, https://doi.org/10.1038/nature08055, 2009.
Spring, S., Riedel, T., Spröer, C., Yan, S., Harder, J., and Fuchs, B. M.: Taxonomy and evolution of bacteriochlorophyll a-containing members of the OM60/NOR5 clade of marine gammaproteobacteria: description of Luminiphilus syltensis gen. nov., sp. nov., reclassification of Haliea rubra as Pseudohaliea rubra gen. nov., comb. nov., and emendation of Chromatocurvus halotolerans, BMC Microbiol., 13, 118, https://doi.org/10.1186/1471-2180-13-118, 2013.
Steglich, C., Stazic, D., Lott, S. C., Voigt, K., Greengrass, E., Lindell, D., and Hess, W. R.: Dataset for metatranscriptome analysis of Prochlorococcus-rich marine picoplankton communities in the Gulf of Aqaba, Red Sea, Mar. Genomics, 19, 5–7, 2015.
Tolonen, A. C., Aach, J., Lindell, D., Johnson, Z. I., Rector, T., Steen, R., Church, G. M., and Chisholm, S. W.: Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability, Mol. Syst. Biol., 2, 53, https://doi.org/10.1038/msb4100087, 2006.
Turk-Kubo, K. A., Frank, I. E., Hogan, M. E., Desnues, A., Bonnet, S., and Zehr, J. P.: Diazotroph community succession during the VAHINE mesocosm experiment (New Caledonia lagoon), Biogeosciences, 12, 7435–7452, https://doi.org/10.5194/bg-12-7435-2015, 2015.
Van Mooy, B. A. S., Rocap, G., Fredricks, H. F., Evans, C. T. and Devol, A. H.: Sulfolipids dramatically decrease phosphorus demand by picocyanobacteria in oligotrophic marine environments, P. Natl. Acad. Sci. USA, 103, 8607–8612, https://doi.org/10.1073/pnas.0600540103, 2006.
Van Mooy, B. A. S., Fredricks, H. F., Pedler, B. E., Dyhrman, S. T., Karl, D. M., Koblízek, M., Lomas, M. W., Mincer, T. J., Moore, L. R., Moutin, T., Rappé, M. S., and Webb, E. A.: Phytoplankton in the ocean use non-phosphorus lipids in response to phosphorus scarcity, Nature, 458, 69–72, https://doi.org/10.1038/nature07659, 2009.
Van Wambeke, F., Pfreundt, U., Barani, A., Berthelot, H., Moutin, T., Rodier, M., Hess, W. R., and Bonnet, S.: Heterotrophic bacterial production and metabolic balance during the VAHINE mesocosm experiment in the New Caledonia lagoon, Biogeosciences, 13, 3187–3202, https://doi.org/10.5194/bg-13-3187-2016, 2016.
Voigt, K., Sharma, C. M., Mitschke, J., Joke Lambrecht, S., Voß, B., Hess, W. R., and Steglich, C.: Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity, ISME J., 8, 2056–2068, https://doi.org/10.1038/ismej.2014.57, 2014.
Wemheuer, B., Wemheuer, F., Hollensteiner, J., Meyer, F.-D., Voget, S., and Daniel, R.: The green impact: bacterioplankton response toward a phytoplankton spring bloom in the southern North Sea assessed by comparative metagenomic and metatranscriptomic approaches, Front. Microbiol., 6, 805, https://doi.org/10.3389/fmicb.2015.00805, 2015.
The VAHINE experiment in the New Caledonia lagoon (SW Pacific) targeted the dynamics of nutrient pools and fluxes, N2 fixation, and the composition and productivity of the microbial communities. To connect this information to the actual activities of diverse microbial taxa, we present the analysis of the community-wide gene expression for 23 days. The results from this experiment provide insight into the microbial activities in a low-nutrient, low-chlorophyll ecosystem and within a mesocosm.
The VAHINE experiment in the New Caledonia lagoon (SW Pacific) targeted the dynamics of nutrient...