- About
- Editorial board
- Articles
- Special issues
- Highlight articles
- Manuscript tracking
- Subscribe to alerts
- Peer review
- For authors
- For reviewers
- EGU publications
Journal cover
Journal topic
Biogeosciences
An interactive open-access journal of the European Geosciences Union
Journal topic
- About
- Editorial board
- Articles
- Special issues
- Highlight articles
- Manuscript tracking
- Subscribe to alerts
- Peer review
- For authors
- For reviewers
- EGU publications
Journal metrics
IF3.480
IF 5-year
4.194
4.194
CiteScore
6.7
6.7
SNIP1.143
IPP3.65
SJR1.761
Scimago H
index118
index118
h5-index60
Abstracted/indexed
Abstracted/indexed- Science Citation Index Expanded
- Current Contents/ABE
- Current Contents/PCE
- Scopus
- ADS
- AGRICOLA
- Aquatic Sciences and Fisheries Abstracts
- CAB Abstracts
- Cabell's
- Chemical Abstracts
- CLOCKSS
- CNKI
- DOAJ
- EBSCO
- GBA
- Gale/Cengage
- GeoBase
- GeoRef
- GoOA (CAS)
- Google Scholar
- J-Gate
- Portico
- ProQuest
- World Public Library
Volume 9, issue 6
Biogeosciences, 9, 2177–2193, 2012
https://doi.org/10.5194/bg-9-2177-2012
© Author(s) 2012. This work is distributed under
the Creative Commons Attribution 3.0 License.
https://doi.org/10.5194/bg-9-2177-2012
© Author(s) 2012. This work is distributed under
the Creative Commons Attribution 3.0 License.
Special issue: Molecular biogeochemical provinces in the eastern Atlantic...
Biogeosciences, 9, 2177–2193, 2012
https://doi.org/10.5194/bg-9-2177-2012
© Author(s) 2012. This work is distributed under
the Creative Commons Attribution 3.0 License.
https://doi.org/10.5194/bg-9-2177-2012
© Author(s) 2012. This work is distributed under
the Creative Commons Attribution 3.0 License.
Research article 18 Jun 2012
Research article | 18 Jun 2012
Bacterial assemblages of the eastern Atlantic Ocean reveal both vertical and latitudinal biogeographic signatures
C. J. Friedline et al.
Related subject area
Biodiversity and Ecosystem Function: Marine
Ocean acidification reduces growth and grazing impact of Antarctic heterotrophic nanoflagellates
Dynamics of environmental conditions during the decline of a Cymodocea nodosa meadow
Megafauna community assessment of polymetallic-nodule fields with cameras: platform and methodology comparison
A meta-analysis on environmental drivers of marine phytoplankton C : N : P
Spatial and temporal variability in the response of phytoplankton and prokaryotes to B-vitamin amendments in an upwelling system
Biogeography and community structure of abyssal scavenging Amphipoda (Crustacea) in the Pacific Ocean
Are seamounts refuge areas for fauna from polymetallic nodule fields?
Ocean deoxygenation and copepods: coping with oxygen minimum zone variability
Technical note: Estimating light-use efficiency of benthic habitats using underwater O2 eddy covariance
Unexpected high abyssal ophiuroid diversity in polymetallic nodule fields of the northeast Pacific Ocean and implications for conservation
Population dynamics of modern planktonic foraminifera in the western Barents Sea
Foraminiferal community response to seasonal anoxia in Lake Grevelingen (the Netherlands)
Light availability modulates the effects of warming in a marine N2 fixer
SiR-actin-labelled granules in foraminifera: patterns, dynamics, and hypotheses
Alpha and beta diversity patterns of polychaete assemblages across the nodule province of the eastern Clarion-Clipperton Fracture Zone (equatorial Pacific)
Dimensions of marine phytoplankton diversity
The Arctic picoeukaryote Micromonas pusilla benefits from ocean acidification under constant and dynamic light
Flux variability of phyto- and zooplankton communities in the Mauritanian coastal upwelling between 2003 and 2008
Environmental factors influencing benthic communities in the oxygen minimum zones on the Angolan and Namibian margins
Hypoxia in mangroves: occurrence and impact on valuable tropical fish habitat
Vertical distribution of planktonic foraminifera in the Subtropical South Atlantic: depth hierarchy of controlling factors
Calcification and latitudinal distribution of extant coccolithophores across the Drake Passage during late austral summer 2016
Distribution of free-living marine nematodes in the Clarion–Clipperton Zone: implications for future deep-sea mining scenarios
Characterizing photosymbiosis in modern planktonic foraminifera
Identifying areas prone to coastal hypoxia – the role of topography
Observations of deep-sea fishes and mobile scavengers from the abyssal DISCOL experimental mining area
Ocean acidification and high irradiance stimulate the photo-physiological fitness, growth and carbon production of the Antarctic cryptophyte Geminigera cryophila
Rates and drivers of Red Sea plankton community metabolism
Reviews and syntheses: Insights into deep-sea food webs and global environmental gradients revealed by stable isotope (δ15N, δ13C) and fatty acid trophic biomarkers
Light-dependent calcification in Red Sea giant clam Tridacna maxima
Responses of an abyssal meiobenthic community to short-term burial with crushed nodule particles in the south-east Pacific
A trait-based modelling approach to planktonic foraminifera ecology
Physiological and biochemical responses of Emiliania huxleyi to ocean acidification and warming are modulated by UV radiation
Enhanced microbial nitrogen transformations in association with macrobiota from the rocky intertidal
Meso-zooplankton structure and functioning in the western tropical South Pacific along the 20th parallel south during the OUTPACE survey (February–April 2015)
Impact of carbonate saturation on large Caribbean benthic foraminifera assemblages
Factors influencing test porosity in planktonic foraminifera
Coral reef carbonate budgets and ecological drivers in the central Red Sea – a naturally high temperature and high total alkalinity environment
The ability of macroalgae to mitigate the negative effects of ocean acidification on four species of North Atlantic bivalve
Geophysical and geochemical controls on the megafaunal community of a high Arctic cold seep
The Arctic picoeukaryote Micromonas pusilla benefits synergistically from warming and ocean acidification
Abyssal plain faunal carbon flows remain depressed 26 years after a simulated deep-sea mining disturbance
Dimethyl sulfide dynamics in first-year sea ice melt ponds in the Canadian Arctic Archipelago
Aphotic N2 fixation along an oligotrophic to ultraoligotrophic transect in the western tropical South Pacific Ocean
Functional trait responses to sediment deposition reduce macrofauna-mediated ecosystem functioning in an estuarine mudflat
Dynamics and controls of heterotrophic prokaryotic production in the western tropical South Pacific Ocean: links with diazotrophic and photosynthetic activity
Ocean acidification changes the structure of an Antarctic coastal protistan community
Variability in copepod trophic levels and feeding selectivity based on stable isotope analysis in Gwangyang Bay of the southern coast of the Korean Peninsula
Do pelagic grazers benefit from sea ice? Insights from the Antarctic sea ice proxy IPSO25
Coccolithophore populations and their contribution to carbonate export during an annual cycle in the Australian sector of the Antarctic zone
Stacy Deppeler, Kai G. Schulz, Alyce Hancock, Penelope Pascoe, John McKinlay, and Andrew Davidson
Biogeosciences, 17, 4153–4171, https://doi.org/10.5194/bg-17-4153-2020, https://doi.org/10.5194/bg-17-4153-2020, 2020
Short summary
Short summary
Our study showed how ocean acidification can exert both direct and indirect influences on the interactions among trophic levels within the microbial loop. Microbial grazer abundance was reduced at CO2 concentrations at and above 634 µatm, while microbial communities increased in abundance, likely due to a reduction in being grazed. Such changes in predator–prey interactions with ocean acidification could have significant effects on the food web and biogeochemistry in the Southern Ocean.
Mirjana Najdek, Marino Korlević, Paolo Paliaga, Marsej Markovski, Ingrid Ivančić, Ljiljana Iveša, Igor Felja, and Gerhard J. Herndl
Biogeosciences, 17, 3299–3315, https://doi.org/10.5194/bg-17-3299-2020, https://doi.org/10.5194/bg-17-3299-2020, 2020
Short summary
Short summary
The response of Cymodocea nodosa to environmental changes was reported during a 15-month period. The meadow decline was triggered in spring by the simultaneous reduction of available light in the water column and the creation of anoxic conditions in the rooted area. This disturbance was critical for the plant since it took place during its recruitment phase when metabolic needs are maximal and stored reserves minimal. The loss of such habitat-forming seagrass is a major environmental concern.
Timm Schoening, Autun Purser, Daniel Langenkämper, Inken Suck, James Taylor, Daphne Cuvelier, Lidia Lins, Erik Simon-Lledó, Yann Marcon, Daniel O. B. Jones, Tim Nattkemper, Kevin Köser, Martin Zurowietz, Jens Greinert, and Jose Gomes-Pereira
Biogeosciences, 17, 3115–3133, https://doi.org/10.5194/bg-17-3115-2020, https://doi.org/10.5194/bg-17-3115-2020, 2020
Short summary
Short summary
Seafloor imaging is widely used in marine science and industry to explore and monitor areas of interest. The selection of the most appropriate imaging gear and deployment strategy depends on the target application. This paper compares imaging platforms like autonomous vehicles or towed camera frames and different deployment strategies of those in assessing the megafauna abundance of polymetallic-nodule fields. The deep-sea mining industry needs that information for robust impact monitoring.
Tatsuro Tanioka and Katsumi Matsumoto
Biogeosciences, 17, 2939–2954, https://doi.org/10.5194/bg-17-2939-2020, https://doi.org/10.5194/bg-17-2939-2020, 2020
Short summary
Short summary
We conducted an extensive literature survey (meta-analysis) on how the C : N : P ratio varies with change in key environmental drivers. We found that the expected reduction in nutrients and warming under the future climate change scenario is likely to result in increased C : P and C : N of marine phytoplankton. Further, our findings highlight the greater stoichiometric plasticity of eukaryotes over prokaryotes, which provide us insights on how to understand and model plankton.
Vanessa Joglar, Antero Prieto, Esther Barber-Lluch, Marta Hernández-Ruiz, Emilio Fernández, and Eva Teira
Biogeosciences, 17, 2807–2823, https://doi.org/10.5194/bg-17-2807-2020, https://doi.org/10.5194/bg-17-2807-2020, 2020
Short summary
Short summary
Coastal marine ecosystems are among the most ecologically and economically productive areas providing a large fraction of ecosystem goods and services to human populations, and B vitamins have long been considered important growth factors for phytoplankton. Our findings indicate that the responses of microbial plankton to B-vitamin supply are mainly driven by the bacterial community composition and that microbial plankton in this area seems to be well adapted to cope with B-vitamin shortage.
Tasnim Patel, Henri Robert, Cedric D'Udekem D'Acoz, Koen Martens, Ilse De Mesel, Steven Degraer, and Isa Schön
Biogeosciences, 17, 2731–2744, https://doi.org/10.5194/bg-17-2731-2020, https://doi.org/10.5194/bg-17-2731-2020, 2020
Short summary
Short summary
Exploitation of deep-sea resources in one of the largest ecosystems on the planet has rendered research of its biodiversity more urgent than ever before. We investigated the known habitats and connectivity of deep-sea scavenging amphipods and obtained important knowledge about several species. We also demonstrated that a long-term disturbance experiment has possibly reduced amphipod biodiversity. These data and further sampling expeditions are instrumental for formulating sustainable policies.
Daphne Cuvelier, Pedro A. Ribeiro, Sofia P. Ramalho, Daniel Kersken, Pedro Martinez Arbizu, and Ana Colaço
Biogeosciences, 17, 2657–2680, https://doi.org/10.5194/bg-17-2657-2020, https://doi.org/10.5194/bg-17-2657-2020, 2020
Short summary
Short summary
Polymetallic nodule mining will remove hard substrata from the abyssal deep-sea floor. The only neighbouring ecosystems featuring hard substratum are seamounts, and their inhabiting fauna could aid in recovery post-mining. Nevertheless, first observations of seamount megafauna were very different from nodule-associated megafauna and showed little overlap. The possible uniqueness of these ecosystems implies that they should be included in management plans for the conservation of biodiversity.
Karen F. Wishner, Brad Seibel, and Dawn Outram
Biogeosciences, 17, 2315–2339, https://doi.org/10.5194/bg-17-2315-2020, https://doi.org/10.5194/bg-17-2315-2020, 2020
Short summary
Short summary
Increasing deoxygenation and oxygen minimum zone expansion are consequences of global warming. Copepod species had different vertical distribution strategies and physiologies associated with oxygen profile variability (0–1000 m). Species (1) changed vertical distributions and maximum abundance depth, (2) shifted diapause depth, (3) changed diel vertical migration depths, or (4) changed epipelagic depth range in the aerobic mixed layer. Present-day variability helps predict future scenarios.
Karl M. Attard and Ronnie N. Glud
Biogeosciences Discuss., https://doi.org/10.5194/bg-2020-140, https://doi.org/10.5194/bg-2020-140, 2020
Revised manuscript accepted for BG
Short summary
Short summary
Light-use efficiency defines the ability of primary producers to convert sunlight energy to primary production. This report provides a framework to compute hourly and daily light-use efficiency using underwater eddy covariance, a recent technological development that produces habitat-scale rates of primary production for many different habitat types. The approach, tested on measured flux data, provides a useful means to compare habitat productivity in time and space.
Magdalini Christodoulou, Timothy O'Hara, Andrew F. Hugall, Sahar Khodami, Clara F. Rodrigues, Ana Hilario, Annemiek Vink, and Pedro Martinez Arbizu
Biogeosciences, 17, 1845–1876, https://doi.org/10.5194/bg-17-1845-2020, https://doi.org/10.5194/bg-17-1845-2020, 2020
Short summary
Short summary
Unexpectedly high diversity was revealed in areas licenced for polymetallic nodule mining exploration in the Pacific Ocean. For the first time, a comprehensive reference library including 287 novel ophiuroid sequences allocated to 43 species was produced. Differences in food availability along the nodule province of CCZ were reflected in the biodiversity patterns observed. The APEI3's dissimilarity with the exploration contract areas questions its ability to serve as a biodiversity reservoir.
Julie Meilland, Hélène Howa, Vivien Hulot, Isaline Demangel, Joëlle Salaün, and Thierry Garlan
Biogeosciences, 17, 1437–1450, https://doi.org/10.5194/bg-17-1437-2020, https://doi.org/10.5194/bg-17-1437-2020, 2020
Short summary
Short summary
This study reports on planktonic foraminifera (PF) diversity and distribution in the Barents Sea. The species Globigerinita uvula and Turborotalita quinqueloba dominate the water column while surface sediments are dominated by Neogloboquadrina pachyderma. We hypothesize the unusual dominance of G. uvula in the water to be a seasonal signal or a result of climate forcing. Size-normalized-protein concentrations of PF show a northward decrease, suggesting biomass to vary with the environment.
Julien Richirt, Bettina Riedel, Aurélia Mouret, Magali Schweizer, Dewi Langlet, Dorina Seitaj, Filip J. R. Meysman, Caroline P. Slomp, and Frans J. Jorissen
Biogeosciences, 17, 1415–1435, https://doi.org/10.5194/bg-17-1415-2020, https://doi.org/10.5194/bg-17-1415-2020, 2020
Short summary
Short summary
The paper presents the response of benthic foraminiferal communities to seasonal absence of oxygen coupled with the presence of hydrogen sulfide, considered very harmful for several living organisms.
Our results suggest that the foraminiferal community mainly responds as a function of the duration of the adverse conditions.
This knowledge is especially useful to better understand the ecology of benthic foraminifera but also in the context of palaeoceanographic interpretations.
Xiangqi Yi, Fei-Xue Fu, David A. Hutchins, and Kunshan Gao
Biogeosciences, 17, 1169–1180, https://doi.org/10.5194/bg-17-1169-2020, https://doi.org/10.5194/bg-17-1169-2020, 2020
Short summary
Short summary
Combined effects of warming and light intensity were estimated in N2-fixing cyanobacterium Trichodesmium. Its physiological responses to warming were significantly modulated by light, with growth peaking at 27 °C under the light-saturating condition but being non-responsive across the range of 23–31 °C under the light-limiting condition. Light shortage also weakened the acclimation ability of Trichodesmium to warming, making light-limited Trichodesmium more sensitive to acute temperature change.
Jan Goleń, Jarosław Tyszka, Ulf Bickmeyer, and Jelle Bijma
Biogeosciences, 17, 995–1011, https://doi.org/10.5194/bg-17-995-2020, https://doi.org/10.5194/bg-17-995-2020, 2020
Short summary
Short summary
We studied the organisation and dynamics of actin in foraminifera. Actin is one of the key structural proteins in most lifeforms. Our investigations show that in foraminifera it forms small granules, around 1 µm in diameter, that display rapid movement. This granularity is unusual in comparison to other organisms. We suppose that these granules are most likely involved in the formation of all types of pseudopods responsible for movement, food capturing, biomineralisation, and other functions.
Paulo Bonifácio, Pedro Martínez Arbizu, and Lénaïck Menot
Biogeosciences, 17, 865–886, https://doi.org/10.5194/bg-17-865-2020, https://doi.org/10.5194/bg-17-865-2020, 2020
Short summary
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, https://doi.org/10.5194/bg-17-609-2020, https://doi.org/10.5194/bg-17-609-2020, 2020
Short summary
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, https://doi.org/10.5194/bg-17-635-2020, https://doi.org/10.5194/bg-17-635-2020, 2020
Short summary
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, https://doi.org/10.5194/bg-17-187-2020, https://doi.org/10.5194/bg-17-187-2020, 2020
Short summary
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.
Ulrike Hanz, Claudia Wienberg, Dierk Hebbeln, Gerard Duineveld, Marc Lavaleye, Katriina Juva, Wolf-Christian Dullo, André Freiwald, Leonardo Tamborrino, Gert-Jan Reichart, Sascha Flögel, and Furu Mienis
Biogeosciences, 16, 4337–4356, https://doi.org/10.5194/bg-16-4337-2019, https://doi.org/10.5194/bg-16-4337-2019, 2019
Short summary
Short summary
Along the Namibian and Angolan margins, low oxygen conditions do not meet environmental ranges for cold–water corals and hence are expected to be unsuitable habitats. Environmental conditions show that tidal movements deliver water with more oxygen and high–quality organic matter, suggesting that corals compensate unfavorable conditions with availability of food. With the expected expansion of oxygen minimum zones in the future, this study provides an example how ecosystems cope with extremes.
Alexia Dubuc, Ronald Baker, Cyril Marchand, Nathan J. Waltham, and Marcus Sheaves
Biogeosciences, 16, 3959–3976, https://doi.org/10.5194/bg-16-3959-2019, https://doi.org/10.5194/bg-16-3959-2019, 2019
Short summary
Short summary
Little is known about how hypoxia influences mangrove fish assemblages. In situ video observations reveal species-specific avoidance strategies in response to developing hypoxia in a mangrove forest. Taxa commonly using mangroves could withstand hypoxia, while others usually associated with reef habitats were not recorded below 70 % saturation. These results suggest that hypoxia is an important factor shaping mangrove fish assemblages and could explain the low species richness usually observed.
Douglas Lessa, Raphaël Morard, Lukas Jonkers, Igor M. Venancio, Runa Reuter, Adrian Baumeister, Ana Luiza Albuquerque, and Michal Kucera
Biogeosciences Discuss., https://doi.org/10.5194/bg-2019-355, https://doi.org/10.5194/bg-2019-355, 2019
Revised manuscript accepted for BG
Short summary
Short summary
We observed that living planktonic foraminifera had distinct vertically distributed communities across the Subtropical South Atlantic. In addition, a hierarchic alternation of environmental parameters was measured to control the distribution of planktonic foraminifer's species depending to 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.
Mariem Saavedra-Pellitero, Karl-Heinz Baumann, Miguel Ángel Fuertes, Hartmut Schulz, Yann Marcon, Nele Manon Vollmar, José-Abel Flores, and Frank Lamy
Biogeosciences, 16, 3679–3702, https://doi.org/10.5194/bg-16-3679-2019, https://doi.org/10.5194/bg-16-3679-2019, 2019
Short summary
Short summary
Open ocean phytoplankton include coccolithophore algae, a key element in carbon cycle regulation with important feedbacks to the climate system. We document latitudinal variability in both coccolithophore assemblage and the mass variation in one particular species, Emiliania huxleyi, for a transect across the Drake Passage (in the Southern Ocean). Coccolithophore abundance, diversity and maximum depth habitat decrease southwards, coinciding with changes in the predominant E. huxleyi morphotypes.
Freija Hauquier, Lara Macheriotou, Tania N. Bezerra, Great Egho, Pedro Martínez Arbizu, and Ann Vanreusel
Biogeosciences, 16, 3475–3489, https://doi.org/10.5194/bg-16-3475-2019, https://doi.org/10.5194/bg-16-3475-2019, 2019
Short summary
Short summary
Future mining operations in the deep sea provide a source of scientific uncertainty and call for detailed study of the ecosystem. We investigated one of the most diverse and abundant taxa present in deep-sea sediments, nematodes, and demonstrate the importance of sediment attributes for their communities. Especially species that are less common and have a limited spatial distribution will be vulnerable to mining-induced changes. Our findings can serve as a reference for future impact studies.
Haruka Takagi, Katsunori Kimoto, Tetsuichi Fujiki, Hiroaki Saito, Christiane Schmidt, Michal Kucera, and Kazuyoshi Moriya
Biogeosciences, 16, 3377–3396, https://doi.org/10.5194/bg-16-3377-2019, https://doi.org/10.5194/bg-16-3377-2019, 2019
Short summary
Short summary
Photosymbiosis (endosymbiosis with algae) is an evolutionary important ecology for many marine organisms but has poorly been identified among planktonic foraminifera. In this study, we identified and characterized photosymbiosis of various species of planktonic foraminifera by focusing on their photosynthesis–related features. We finally proposed a new framework showing a potential strength of photosymbiosis, which will serve as a basis for future ecological studies of planktonic foraminifera.
Elina A. Virtanen, Alf Norkko, Antonia Nyström Sandman, and Markku Viitasalo
Biogeosciences, 16, 3183–3195, https://doi.org/10.5194/bg-16-3183-2019, https://doi.org/10.5194/bg-16-3183-2019, 2019
Short summary
Short summary
Our understanding of the drivers of hypoxia fundamentally hinges on patterns of water circulation and vertical mixing that can be difficult to resolve in coastal regions. We identified areas prone to oxygen loss in a complex marine area without knowledge of biogeochemical properties, using only parameters which describe the enclosed seafloors with restricted water exchange. Our approach could help nutrient abatement measures and pinpoint areas where management actions are most urgently needed.
Jeffrey C. Drazen, Astrid B. Leitner, Sage Morningstar, Yann Marcon, Jens Greinert, and Autun Purser
Biogeosciences, 16, 3133–3146, https://doi.org/10.5194/bg-16-3133-2019, https://doi.org/10.5194/bg-16-3133-2019, 2019
Short summary
Short summary
We investigated the fish and scavenger community after a deep seafloor disturbance experiment intended to simulate the effects of deep-sea mining. Fish density returned to background levels after several years; however the dominant fish was rarely found in ploughed habitat after 26 years. Given the significantly larger scale of industrial mining, these results could translate to population-level effects. The abyssal fish community at the site was similar to that in the Clarion–Clipperton Zone.
Scarlett Trimborn, Silke Thoms, Pascal Karitter, and Kai Bischof
Biogeosciences, 16, 2997–3008, https://doi.org/10.5194/bg-16-2997-2019, https://doi.org/10.5194/bg-16-2997-2019, 2019
Short summary
Short summary
Ecophysiological studies on Antarctic cryptophytes to assess whether climatic changes such as ocean acidification and enhanced stratification affect their growth in Antarctic coastal waters in the future are lacking so far. Our results reveal beneficial effects of ocean acidification in conjunction with enhanced irradiance on growth and photosynthesis of the Antarctic cyrptophyte Geminigera cryophila. Hence, cryptophytes such as G. cryophila may be potential winners of these climatic changes.
Daffne C. López-Sandoval, Katherine Rowe, Paloma Carillo-de-Albonoz, Carlos M. Duarte, and Susana Agustí
Biogeosciences, 16, 2983–2995, https://doi.org/10.5194/bg-16-2983-2019, https://doi.org/10.5194/bg-16-2983-2019, 2019
Short summary
Short summary
We addressed how the intertwined effect of temperature and nutrients modulates the metabolic response of planktonic communities in the Red Sea, one of the warmest seas on earth. Our study unveiled that photosynthesis increases at a faster pace than respiration rates for this group of organisms formed by microalgae, bacteria, and drifting animals. This anomaly is likely due to the nature of the basin where the warmest waters are frequently enriched with nutrients, which favours microalgae growth.
Camilla Parzanini, Christopher C. Parrish, Jean-François Hamel, and Annie Mercier
Biogeosciences, 16, 2837–2856, https://doi.org/10.5194/bg-16-2837-2019, https://doi.org/10.5194/bg-16-2837-2019, 2019
Short summary
Short summary
This review synthesized current knowledge of deep-sea food webs and provided a preliminary analysis of global geographic patterns in the biochemical composition of deep-water organisms. Our results revealed both latitudinal and depth wise trends in the biochemical composition of deep-sea animals. In addition, the link across latitudes between surface primary production and deep-water communities was highlighted, which has important implications in the face of global climate change.
Susann Rossbach, Vincent Saderne, Andrea Anton, and Carlos M. Duarte
Biogeosciences, 16, 2635–2650, https://doi.org/10.5194/bg-16-2635-2019, https://doi.org/10.5194/bg-16-2635-2019, 2019
Short summary
Short summary
Giant clams including the species Tridacna maxima are unique among bivalves as they live in symbiosis with unicellular algae and generally function as net photoautotrophs. Light is therefore crucial for these species to thrive. We show that net calcification and photosynthetic rates of T. maxima are light dependent, with maximum rates at conditions comparable to 4 m water depth, reflected also in the depth-related distribution in the Red Sea with maximum abundances in shallow sunlit coral reefs.
Lisa Mevenkamp, Katja Guilini, Antje Boetius, Johan De Grave, Brecht Laforce, Dimitri Vandenberghe, Laszlo Vincze, and Ann Vanreusel
Biogeosciences, 16, 2329–2341, https://doi.org/10.5194/bg-16-2329-2019, https://doi.org/10.5194/bg-16-2329-2019, 2019
Short summary
Short summary
To elucidate the potential effects of crushed nodule particle deposition on abyssal meiobenthos, we covered abyssal soft sediment in the Peru Basin (4200 m depth) with approximately 2 cm of this nodule material for 11 d. About half of the meiobenthos migrated from the sediment into the added material, and nematode feeding type proportions in that added layer were altered. These results considerably contribute to our understanding of the short-term responses of deep-sea meiobenthos to burial.
Maria Grigoratou, Fanny M. Monteiro, Daniela N. Schmidt, Jamie D. Wilson, Ben A. Ward, and Andy Ridgwell
Biogeosciences, 16, 1469–1492, https://doi.org/10.5194/bg-16-1469-2019, https://doi.org/10.5194/bg-16-1469-2019, 2019
Short summary
Short summary
The paper presents a novel study based on the traits of shell size, calcification and feeding behaviour of two planktonic foraminifera life stages using modelling simulations. With the model, we tested the cost and benefit of calcification and explored how the interactions of planktonic foraminifera among other plankton groups influence their biomass under different environmental conditions. Our results provide new insights into environmental controls in planktonic foraminifera ecology.
Shanying Tong, David A. Hutchins, and Kunshan Gao
Biogeosciences, 16, 561–572, https://doi.org/10.5194/bg-16-561-2019, https://doi.org/10.5194/bg-16-561-2019, 2019
Short summary
Short summary
Most previous studies concerning the effects of environmental changes on marine organisms have been carried out under
photosynthetically active radiation onlyconditions, with solar ultraviolet radiation (UVR) not being considered. In this study, we found that UVR can counteract the negative effects of the
greenhousetreatment on the calcification rate to photosynthesis rate ratio, and may be a key stressor when considering the impacts of future greenhouse conditions on E. huxleyi.
Catherine A. Pfister and Mark A. Altabet
Biogeosciences, 16, 193–206, https://doi.org/10.5194/bg-16-193-2019, https://doi.org/10.5194/bg-16-193-2019, 2019
Short summary
Short summary
Microbial assemblages on host plants and animals are an increasingly recognized biological phenomenon. We present evidence that microbes in association with mussels and seaweeds are contributing greatly to nitrogen cycling in coastal marine areas, often many times that of the microbes that are simply free-living in seawater. The addition of dissolved organic carbon increased nutrient uptake by microbes, suggesting that coastal species enhance microbial metabolism through resource provisioning.
François Carlotti, Marc Pagano, Loïc Guilloux, Katty Donoso, Valentina Valdés, Olivier Grosso, and Brian P. V. Hunt
Biogeosciences, 15, 7273–7297, https://doi.org/10.5194/bg-15-7273-2018, https://doi.org/10.5194/bg-15-7273-2018, 2018
Short summary
Short summary
The paper characterizes the zooplankton community and plankton food web processes between New Caledonia and Tahiti (tropical South Pacific) during the austral summer 2015. In this region, the pelagic production depends on N2 fixation by diazotroph microorganisms on which the zooplankton community feeds, supporting a pelagic food chain ending with valuable tuna fisheries. We estimated a contribution of up to 75 % of diazotroph‐derived nitrogen to zooplankton biomass in the Melanesian archipelago.
Ana Martinez, Laura Hernández-Terrones, Mario Rebolledo-Vieyra, and Adina Paytan
Biogeosciences, 15, 6819–6832, https://doi.org/10.5194/bg-15-6819-2018, https://doi.org/10.5194/bg-15-6819-2018, 2018
Short summary
Short summary
Our study at low-pH submarine springs suggests that ocean acidification may reduce the number of Caribbean benthic foraminifera, particularly those species that form carbonate shells. This may have subsequent repercussions on the global carbon cycle and marine food webs that depend on benthic foraminifera.
Janet E. Burke, Willem Renema, Michael J. Henehan, Leanne E. Elder, Catherine V. Davis, Amy E. Maas, Gavin L. Foster, Ralf Schiebel, and Pincelli M. Hull
Biogeosciences, 15, 6607–6619, https://doi.org/10.5194/bg-15-6607-2018, https://doi.org/10.5194/bg-15-6607-2018, 2018
Short summary
Short summary
Metabolic rates are sensitive to environmental conditions and can skew geochemical measurements. However, there is no way to track these rates through time. Here we investigate the controls of test porosity in planktonic foraminifera (organisms commonly used in paleoclimate studies) as a potential proxy for metabolic rate. We found that the porosity varies with body size and temperature, two key controls on metabolic rate, and that it can respond to rapid changes in ambient temperature.
Anna Roik, Till Röthig, Claudia Pogoreutz, Vincent Saderne, and Christian R. Voolstra
Biogeosciences, 15, 6277–6296, https://doi.org/10.5194/bg-15-6277-2018, https://doi.org/10.5194/bg-15-6277-2018, 2018
Short summary
Short summary
In this study we collected in situ accretion/erosion rates and abiotic/biotic variables to estimate carbonate budgets and ecological drivers of coral reef growth in the central Red Sea. Our data suggest that reef growth is comparable to estimates of other regions, but the erosive forces in the Red Sea are not as pronounced. Comparison with recent data suggests that Red Sea reef growth might not have decreased over the past decades, despite warming, calling for more detailed investigations.
Craig S. Young and Christopher J. Gobler
Biogeosciences, 15, 6167–6183, https://doi.org/10.5194/bg-15-6167-2018, https://doi.org/10.5194/bg-15-6167-2018, 2018
Short summary
Short summary
Photosynthetic activity and/or nitrate assimilation by the macroalgae Ulva buffered carbonate chemistry and yielded enhanced growth of bivalves by mitigating the harmful effects of elevated CO2 levels. This benefit was not limited to acidified conditions, as evidenced by increased bivalve growth in the presence of Ulva within ambient CO2 treatments. The ability of macroalgae to buffer carbonate chemistry may be increasingly important for calcifying organisms vulnerable to ocean acidification.
Arunima Sen, Emmelie K. L. Åström, Wei-Li Hong, Alexey Portnov, Malin Waage, Pavel Serov, Michael L. Carroll, and JoLynn Carroll
Biogeosciences, 15, 4533–4559, https://doi.org/10.5194/bg-15-4533-2018, https://doi.org/10.5194/bg-15-4533-2018, 2018
Short summary
Short summary
Diverse benthic communities populate a site of methane seepage on the Arctic shelf. Despite a likely reliance on sulfide as an energy source, Oligobrachia worm distributions did not correlate with sulfide concentrations. We suggest that sulfide and carbon generation linked to microbial activity and high methane fluxes determines their presence or absence. We discuss the site and our results within the context of Arctic ecology and economy as well as the biology of seafloor hydrocarbon seeps.
Clara Jule Marie Hoppe, Clara M. Flintrop, and Björn Rost
Biogeosciences, 15, 4353–4365, https://doi.org/10.5194/bg-15-4353-2018, https://doi.org/10.5194/bg-15-4353-2018, 2018
Short summary
Short summary
Responses of the Arctic microalgae Micromonas pusilla to different pCO2 levels were investigated at two temperatures. We observed that warming and ocean acidification (OA) synergistically increased growth rates. Furthermore, elevated temperature shifted the pCO2 optimum of biomass production to higher levels. This seem to be caused by more efficient photosynthesis under warmer and more acidic conditions. Our findings explain the dominance of picoeukaryotes frequently observed in OA experiments.
Tanja Stratmann, Lidia Lins, Autun Purser, Yann Marcon, Clara F. Rodrigues, Ascensão Ravara, Marina R. Cunha, Erik Simon-Lledó, Daniel O. B. Jones, Andrew K. Sweetman, Kevin Köser, and Dick van Oevelen
Biogeosciences, 15, 4131–4145, https://doi.org/10.5194/bg-15-4131-2018, https://doi.org/10.5194/bg-15-4131-2018, 2018
Short summary
Short summary
Extraction of polymetallic nodules will have negative impacts on the deep-sea ecosystem, but it is not known whether the ecosystem is able to recover from them. Therefore, in 1989 a sediment disturbance experiment was conducted in the Peru Basin to mimic deep-sea mining. Subsequently, the experimental site was re-visited 5 times to monitor the recovery of fauna. We developed food-web models for all 5 time steps and found that, even after 26 years, carbon flow in the system differs significantly.
Margaux Gourdal, Martine Lizotte, Guillaume Massé, Michel Gosselin, Michel Poulin, Michael Scarratt, Joannie Charette, and Maurice Levasseur
Biogeosciences, 15, 3169–3188, https://doi.org/10.5194/bg-15-3169-2018, https://doi.org/10.5194/bg-15-3169-2018, 2018
Short summary
Short summary
Melt ponds (MP) forming over first year ice (FYI) represent a potential source of the climate-relevant gas dimethylsulfide (DMS) to the atmosphere. Nine MP were sampled in the Canadian Arctic Archipelago. DMS concentrations reaching up to 6 nmol L−1, twice the world's surface oceanic mean, were measured. Seawater intrusion appeared to seed MP with DMS-producing communities. DMS flux from Arctic MP is expected to increase in response to the expanding areal and temporal trends of MP on FYI.
Mar Benavides, Katyanne M. Shoemaker, Pia H. Moisander, Jutta Niggemann, Thorsten Dittmar, Solange Duhamel, Olivier Grosso, Mireille Pujo-Pay, Sandra Hélias-Nunige, Alain Fumenia, and Sophie Bonnet
Biogeosciences, 15, 3107–3119, https://doi.org/10.5194/bg-15-3107-2018, https://doi.org/10.5194/bg-15-3107-2018, 2018
Short summary
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.
Sebastiaan Mestdagh, Leila Bagaço, Ulrike Braeckman, Tom Ysebaert, Bart De Smet, Tom Moens, and Carl Van Colen
Biogeosciences, 15, 2587–2599, https://doi.org/10.5194/bg-15-2587-2018, https://doi.org/10.5194/bg-15-2587-2018, 2018
Short summary
Short summary
We studied how invertebrate communities of mudflats are affected by sudden deposition of sediment. We applied sediment layers of different thickness to mudflat communities and studied how their densities, diversity, and behaviour and the exchange of oxygen between the bottom and the water column changed. We found that some species easily diminish in numbers, while others become more active after deposition. The interaction of all species effects influences the environment, i.e. oxygen exchange.
France Van Wambeke, Audrey Gimenez, Solange Duhamel, Cécile Dupouy, Dominique Lefevre, Mireille Pujo-Pay, and Thierry Moutin
Biogeosciences, 15, 2669–2689, https://doi.org/10.5194/bg-15-2669-2018, https://doi.org/10.5194/bg-15-2669-2018, 2018
Short summary
Short summary
The western tropical South Pacific Ocean has recently been shown to be a hotspot for biological nitrogen fixation. In this study, we examined the horizontal and vertical distribution of heterotrophic prokaryotic production alongside photosynthetic rates, nitrogen fixation rates and phosphate turnover times across the western tropical South Pacific Ocean, in order to relate these fluxes to bottom–up controls (related to nitrogen, phosphate and labile C availability).
Alyce M. Hancock, Andrew T. Davidson, John McKinlay, Andrew McMinn, Kai G. Schulz, and Rick L. van den Enden
Biogeosciences, 15, 2393–2410, https://doi.org/10.5194/bg-15-2393-2018, https://doi.org/10.5194/bg-15-2393-2018, 2018
Short summary
Short summary
Absorption of carbon dioxide (CO2) realized by humans is decreasing the ocean pH (ocean acidification). Single-celled organisms (microbes) support the Antarctic ecosystem, yet little is known about their sensitivity to ocean acidification. This study shows a shift in a natural Antarctic microbial community, with CO2 levels exceeding 634 μatm changing the community composition and favouring small cells. This would have significant flow effects for Antarctic food webs and elemental cycles.
Mianrun Chen, Dongyoung Kim, Hongbin Liu, and Chang-Keun Kang
Biogeosciences, 15, 2055–2073, https://doi.org/10.5194/bg-15-2055-2018, https://doi.org/10.5194/bg-15-2055-2018, 2018
Short summary
Short summary
The trophic preference (i.e., food resources and trophic levels) of different copepod groups was assessed along a salinity gradient in the temperate estuarine Gwangyang Bay of Korea, based on a seasonal investigation of taxonomic results in 2015 and stable isotope analysis incorporating multiple linear regression models. Our results depict a simple energy flow of the planktonic food web of Gwangyang Bay.
Katrin Schmidt, Thomas A. Brown, Simon T. Belt, Louise C. Ireland, Kyle W. R. Taylor, Sally E. Thorpe, Peter Ward, and Angus Atkinson
Biogeosciences, 15, 1987–2006, https://doi.org/10.5194/bg-15-1987-2018, https://doi.org/10.5194/bg-15-1987-2018, 2018
Short summary
Short summary
Sea ice cover is declining across the polar regions, but its importance for the food webs is largely unknown. We used certain diatom metabolites to trace ice-derived and ice-conditioned algae production within pelagic grazers. Our results show that zooplankton can feed on ice algae long after their release into the water column, and that the marginal ice zone can act as an important feeding ground. Predictions on future functioning of polar ecosystems need to consider such subtle relationships.
Andrés S. Rigual Hernández, José A. Flores, Francisco J. Sierro, Miguel A. Fuertes, Lluïsa Cros, and Thomas W. Trull
Biogeosciences, 15, 1843–1862, https://doi.org/10.5194/bg-15-1843-2018, https://doi.org/10.5194/bg-15-1843-2018, 2018
Short summary
Short summary
Long-term and annual field observations on key organisms are a critical basis for predicting changes in Southern Ocean ecosystems. Coccolithophores are the most abundant calcium-carbonate-producing phytoplankton and play an important role in Southern Ocean biogeochemical cycles. In this study we document the composition, degree of calcification and annual cycle of coccolithophore communities in one of the largest unexplored regions of the world oceans: the Antarctic zone.
Cited articles
Agogue, H., Lamy, D., Neal, P. R., Sogin, M. L., and Herndl, G. J.: Water mass-specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing, Molecular Ecology, 20, 258–274, 2011.
Altschul, S., Gish, W., Miller, W., Myers, E., and Lipman, D.: Basic local alignment search tool, J. Molecular Biology, 215, 403–410, 1990.
Anderson, B., Arrigo, K., Ward, B., UCI, K., and Van Mooy, B.: The Molecular Biology of Biogeochemistry: Using Molecular Methods to Link Ocean Chemistry with Biological Activity, \urlprefixhttp://www.whoi.edu/sites/molbiogeochem, 2010.
Aristegui, J., Barton, E. D., Alvarez-Salgado, X. A., Santos, A. M. P., Figueiras, F. G., Kifani, S., Hern{á}ndez-Le{ó}n, S., Mason, E., Mach{ú}, E., and Demarcq, H.: Sub-regional ecosystem variability in the Canary Current upwrelling, Prog. Oceanography, 83, 33–48, 2009{a}.
Aristegui, J., Gasol, J. M., Duarte, C. M., and Herndl, G. J.: Microbial oceanography of the dark ocean's pelagic realm, Limnol. Oceanogr., 54, 1501–1529, 2009{b}.
Azam, F., Fenchel, T., Field, J., Gray, J., Meyerreil, L., and Thingstad, F.: The ecological role of water-column microbes in the sea, Marine Ecology-Progress Series, 10, 257–263, 1983.
Baltar, F., Aristegui, J., Gasol, J. M., Sintes, E., and Herndl, G. J.: Evidence of prokaryotic metabolism on suspended particulate organic matter in the dark waters of the subtropical North Atlantic, Limnol. Oceanogr., 54, 182–193, 2009.
Bochdansky, A. B., van Aken, H. M., and Herndl, G. J.: Role of macroscopic particles in deep-sea oxygen consumption, Proc. Natl. Acad. Sci. USA, 107, 8287–8291, 2010.
Breitbart, M., Salamon, P., Andresen, B., Mahaffy, J., Segall, A., Mead, D., Azam, F., and Rohwer, F.: Genomic analysis of uncultured marine viral communities, Proc. Natl. Acad. Sci. USA, 99, 14250–14255, 2002.
Bunge, J.: Estimating the number of species with CatchAll, Pacific Symposium on Biocomputing, 2011.
Carlson, C. A., Giovannoni, S. J., Hansell, D., Goldberg, S., Parsons, R., Otero, M., Vergin, K. L., and Wheeler, B.: Effect of nutrient amendments on bacterioplankton production, community structure, and DOC utilization in the northwestern Sargasso Sea, Aquatic Microbial Ecology, 30, 19–36, 2002.
Cases, I. and de Lorenzo, V.: The grammar of (micro)biological diversity, Environmental Microbiology, 4, 623–627, 2002.
Chao, A.: Nonparametric-estimation of the number of classes in a population, Scandinavian Journal of Statistics, 11, 265–270, 1984.
Chao, A. and Lee, S.: Estimating the Number of Classes via Sample Coverage, Journal of the American Statistical Association, 87, 210–217, 1992.
Chave, J.: Neutral theory and community ecology, Ecology Letters, 7, 241–253, 2004.
Claesson, M. J., O'Sullivan, O., Wang, Q., Nikkilae, J., Marchesi, J. R., Smidt, H., Vos, W. M. D., Ross, R. P., and O'Toole, P. W.: Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine, PLoS One, 4, e6669, 2009.
Clarke, K.: Nonparametric multivariate analyses of changes in community structure, Australian Journal of Ecology, 18, 117–143, 1993.
Cohan, F.: What are bacterial species?, Annual Review of Microbiology, 56, 457–487, 2002.
Cohan, F. M. and Perry, E. B.: A systematics for discovering the fundamental units of bacterial diversity, Current Biology, 17, R373–R386, 2007.
Covert, J. and Moran, M.: Molecular characterization of estuarine bacterial communities that use high- and low-molecular weight fractions of dissolved organic carbon, Aquatic Microbial Ecology, 25, 127–139, 2001.
del Giorgio, P. and Duarte, C.: Respiration in the open ocean, Nature, 420, 379–384, 2002.
DeLong, E. F.: The microbial ocean from genomes to biomes, Nature, 459, 200–206, 2009.
DeLong, E. F., Preston, C., Mincer, T., Rich, V., Hallam, S., Frigaard, N., Martinez, A., Sullivan, M., Edwards, R. A., Brito, B. R., Chisholm, S. W., and Karl, D. M.: Community genomics among stratified microbial assemblages in the ocean's interior, Science, 311, 496–503, 2006.
Ducklow, H. W.: Biogeochemical Provinces: Towards a JGOFS Synthesis, in: Ocean Biogeochemistry, edited by: Fasham, M. J. R., Global Change – The IGBP Series, pp. 3–17, Springer Berlin Heidelberg, 2003.
Eiler, A., Langenheder, S., Bertilsson, S., and Tranvik, L. J.: Heterotrophic bacterial growth efficiency and community structure at different natural organic carbon concentrations, Applied and Environmental Microbiology, 69, 3701–3709, 2003.
Flerus, R., Koch, B. P., Lechtenfeld, O. J., McCallister, S. L., Schmitt-Kopplin, P., Benner, R., Kaiser, K., and Kattner, G.: A molecular perspective on the ageing of marine dissolved organic matter, Biogeosciences Discuss., 8, 11453–11488, https://doi.org/10.5194/bgd-8-11453-2011, 2011.
Fuhrman, J. A.: Microbial community structure and its functional implications, Nature, 459, 193–199, 2009.
Fuhrman, J. and Azam, F.: Thymidine incorporation as a measure of heterotrophic bacterioplankton production in marine surface waters – evaluation and field results, Marine Biology, 66, 109–120, 1982.
Fuhrman, J. and Campbell, L.: Marine ecology - microbial microdiversity, Nature, 393, 410–411, 1998.
Fuhrman, J. A. and Davis, A.: Widespread Archaea and novel Bacteria from the deep sea as shown by 16S rRNA gene sequences, Marine Ecology-Progress Series, 150, 275–285, 1997.
Fuhrman, J. A., Steele, J. A., Hewson, I., Schwalbach, M. S., Brown, M. V., Green, J. L., and Brown, J. H.: A latitudinal diversity gradient in planktonic marine bacteria, Proc. Natl. Acad. Sci. USA, 105, 7774–7778, 2008.
Galand, P. E., Casamayor, E. O., Kirchman, D. L., Potvin, M., and Lovejoy, C.: Unique archaeal assemblages in the Arctic Ocean unveiled by massively parallel tag sequencing, The ISME Journal, 3, 860–869, 2009.
Galand, P. E., Potvin, M., Casamayor, E. O., and Lovejoy, C.: Hydrography shapes bacterial biogeography of the deep Arctic Ocean, The ISME Journal, 4, 564–576, 2010.
Gasol, J. and del Giorgio, P.: Using flow cytometry for counting natural planktonic bacteria and understanding the structure of planktonic bacterial communities, in: Scientia Marina, pp. 197–224, CSIC, Inst Ciencias Mar, Dept Biol Marina & Oceanog, E-08039 Barcelona, Spain, 2000.
Gilbert, J. A., Field, D., Swift, P., Newbold, L., Oliver, A., Smyth, T., Somerfield, P. J., Huse, S., and Joint, I.: The seasonal structure of microbial communities in the Western English Channel, Environmental Microbiology, 11, 3132–3139, 2009.
Gilbert, J. A., Steele, J. A., Caporaso, J. G., Steinbrueck, L., Reeder, J., Temperton, B., Huse, S., Mchardy, A. C., Knight, R., Joint, I., Somerfield, P., Fuhrman, J. A., and Field, D.: Defining seasonal marine microbial community dynamics, The ISME Journal, 6, 298–308, 2012.
Giovannoni, S. J. and Stingl, U.: Molecular diversity and ecology of microbial plankton, Nature, 437, 343–348, 2005.
Giovannoni, S. J., Rapp{é}, M. S., Vergin, K. L., and Adair, N.: 16S rRNA genes reveal stratified open ocean bacterioplankton populations related to the Green Non-Sulfur bacteria, Proc. Natl. Acad. Sci. USA, 93, 7979–7984, 1996.
Giovannoni, S. J., Bibbs, L., Cho, J.-C., Stapels, M. D., Desiderio, R., Vergin, K. L., Rapp{é}, M. S., Laney, S., Wilhelm, L. J., Tripp, H. J., Mathur, E. J., and Barofsky, D. F.: Proteorhodopsin in the ubiquitous marine bacterium SAR11, Nature, 438, 82–85, 2005.
Gobet, A., Quince, C., and Ramette, A.: Multivariate Cutoff Level Analysis (MultiCoLA) of large community data sets, Nucleic Acids Research, 38, e155, 2010.
Gordon, D. A. and Giovannoni, S. J.: Detection of stratified microbial populations related to Chlorobium and Fibrobacter species in the Atlantic and Pacific oceans, Applied and Environmental Microbiology, 62, 1171–1177, 1996.
Gower, J.: General coefficient of similarity and some of its properties, Biometrics, 27, 857–874, 1971.
Hammer, Ø. and Harper, D.: PAST: paleontological statistics software package for education and data analysis, Palaeontologia Electronica, 2001.
Hewson, I., Steele, J., Capone, D., and Fuhrman, J. A.: Remarkable heterogeneity in meso- and bathypelagic bacterioplankton assemblage composition, Limnol. Oceanogr., 51, 1274–1283, 2006.
Hewson, I., Paerl, R. W., Tripp, H. J., Zehr, J. P., and Karl, D. M.: Metagenomic potential of microbial assemblages in the surface waters of the central Pacific Ocean tracks variability in oceanic habitat, Limnol. Oceanogr., 54, 1981–1994, 2009.
Hobbie, J. E., Daley, R. J., and Jasper, S.: Use of nuclepore filters for counting bacteria by fluorescence microscopy, Applied and Environmental Microbiology, 33, 1225–1228, 1977.
Hubbell, S. P.: The Unified Neutral Theory of Biodiversity and Biogeography (MPB-32) (Monographs in Population Biology), Princeton University Press, 2001.
Huber, J. A., Welch, D. M., Morrison, H. G., Huse, S. M., Neal, P. R., Butterfield, D. A., and Sogin, M. L.: Microbial population structures in the deep marine biosphere, Science, 318, 97–100, 2007.
Huelsenbeck, J. and Ronquist, F.: MRBAYES: Bayesian inference of phylogenetic trees, Bioinformatics, 17, 754–755, 2001.
Huse, S. M., Huber, J. A., Morrison, H. G., Sogin, M. L., and Welch, D. M.: Accuracy and quality of massively parallel DNA pyrosequencing, Genome Biology, 8, R143, 2007.
Huse, S. M., Dethlefsen, L., Huber, J. A., Welch, D. M., Relman, D. A., and Sogin, M. L.: Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing, PLoS Genetics, 4, e1000 255, 2008.
Huse, S. M., Welch, D. M., Morrison, H. G., and Sogin, M. L.: Ironing out the wrinkles in the rare biosphere through improved OTU clustering, Environmental Microbiology, 12, 1889–1898, 2010.
Kass, R. and Raftery, A.: Bayes Factors, Journal of the American Statistical Association, 90, 773–795, 1995.
Kerkhof, L., Voytek, M., Sherrell, R., Millie, D., and Schofield, O.: Variability in bacterial community structure during upwelling in the coastal ocean, Hydrobiologia, 401, 139–148, 1999.
Kirchman, D. L., Cottrell, M. T., and Lovejoy, C.: The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes, Environmental Microbiology, 12, 1132–1143, 2010.
Kunin, V., Engelbrektson, A., Ochman, H., and Hugenholtz, P.: Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates, Environmental Microbiology, 12, 118–123, 2010.
Legendre, P. and Legendre, L.: Numerical Ecology, Volume 24, Second Edition (Developments in Environmental Modelling), Elsevier Science, 1998.
Longhurst, A.: Ecological geography of the sea, Academic Press, San Diego, CA, 1998.
Longhurst, A., Sathyendranath, S., Platt, T., and Caverhill, C.: An estimate of global primary production in the ocean from satellite radiometer data, J. Plankton Res., 17, 1245–1271, 1995.
Mart{\'\i}n-Cuadrado, A.-B., L{ó}pez-Garc{\'\i}a, P., Alba, J.-C., Moreira, D., Monticelli, L., Strittmatter, A., Gottschalk, G., and Rodr{\'\i}guez-Valera, F.: Metagenomics of the deep Mediterranean, a warm bathypelagic habitat, PLoS One, 2, e914, 2007.
Martiny, J. B. H., Bohannan, B. J. M., Brown, J., COLWELL, R. K., Fuhrman, J. A., Green, J. L., Horner-Devine, M., Kane, M., Krumins, J., Kuske, C., Morin, P., Naeem, S., Øvreås, L., Reysenbach, A.-L., Smith, V., and Staley, J.: Microbial biogeography: putting microorganisms on the map, Nature Reviews Microbiology, 4, 102–112, 2006a.
Martiny, A. C., Coleman, M. L., and Chisholm, S. W.: Phosphate acquisition genes in Prochlorococcus ecotypes: Evidence for genome-wide adaptation, Proc. Natl. Acad. Sci. USA, 103, 12552–12557, 2006b.
Martiny, A. C., Tai, A. P. K., Veneziano, D., Primeau, F., and Chisholm, S. W.: Taxonomic resolution, ecotypes and the biogeography of Prochlorococcus, Environmental Microbiology, 11, 823–832, 2009.
Massana, R., Karniol, B., Pommier, T., Bodaker, I., and Beja, O.: Metagenomic retrieval of a ribosomal DNA repeat array from an uncultured marine alveolate, Environmental Microbiology, 10, 1335–1343, 2008.
Nagata, T., Fukuda, H., Fukuda, R., and Koike, I.: Bacterioplankton distribution and production in deep Pacific waters: Large-scale geographic variations and possible coupling with sinking particle fluxes, Limnol. Oceanogr., 45, 426–435, 2000.
Nekola, J. and White, P.: The distance decay of similarity in biogeography and ecology, J. Biogeography, 26, 867–878, 1999.
Pinhassi, J., Winding, A., Binnerup, S., Zweifel, U., Riemann, B., and Hagstrom, A.: Spatial variability in bacterioplankton community composition at the Skagerrak-Kattegat Front, Marine Ecology-Progress Series, 255, 1–13, 2003.
Pinhassi, J., Sala, M., Havskum, H., Peters, F., Guadayol, O., Malits, A., and Marrase, C.: Changes in bacterioplankton composition under different phytoplankton regimens, Applied And Environmental Microbiology, 70, 6753–6766, 2004.
Pohl, C., Croot, P., Hennings, U., Daberkow, T., Budeus, G., and Loeff, M.: Synoptic transects on the distribution of trace elements (Hg, Pb, Cd, Cu, Ni, Zn, Co, Mn, Fe, and Al) in surface waters of the Northern-and Southern East Atlantic, J. Marine Syst., 84, 28–41, 2011.
Pommier, T., Canb{ä}ck, B., Riemann, L., Bostr{ö}m, K. H., Simu, K., Lundberg, P., Tunlid, A., and Hagstrom, A.: Global patterns of diversity and community structure in marine bacterioplankton, Molecular Ecology, 16, 867–880, 2006.
Quince, C., Curtis, T. P., and Sloan, W. T.: The rational exploration of microbial diversity, The ISME Journal, 2, 997–1006, 2008.
Reeder, J. and Knight, R.: The `rare biosphere': a reality check, Nature Methods, 6, 636–637, 2009.
Reinthaler, T., van Aken, H. M., and Herndl, G. J.: Major contribution of autotrophy to microbial carbon cycling in the deep North Atlantic's interior, Deep-Sea Res. Part II-Topical Studies in Oceanography, 57, 1572–1580, 2010.
Ricklefs, R. E. and Schluter, D. (Eds.): Species Diversity in Ecological Communities, University Of Chicago Press, Chicago, 1 edn., 1994.
Roesch, L. F., Fulthorpe, R. R., Riva, A., Casella, G., Hadwin, A. K. M., Kent, A. D., Daroub, S. H., Camargo, F. A. O., Farmerie, W. G., and Triplett, E. W.: Pyrosequencing enumerates and contrasts soil microbial diversity, The ISME Journal, 1, 283–290, 2007.
Rossi, J.: Statistical tool for soil biology: Autocorrelogram and Mantel test, European Journal of Soil Biology, 32, 195–203, 1996.
Rusch, D. B., Halpern, A. L., Sutton, G., Heidelberg, K. B., Williamson, S., Yooseph, S., Wu, D., Eisen, J. A., Hoffman, J. M., Remington, K., Beeson, K., Tran, B., Smith, H., Baden-Tillson, H., Stewart, C., Thorpe, J., Freeman, J., Andrews-Pfannkoch, C., Venter, J. E., Li, K., Kravitz, S., Heidelberg, J. F., Utterback, T., Rogers, Y.-H., Falcon, L. I., Souza, V., Bonilla-Rosso, G., Eguiarte, L. E., Karl, D. M., Sathyendranath, S., Platt, T., Bermingham, E., Gallardo, V., Tamayo-Castillo, G., Ferrari, M. R., Strausberg, R. L., Nealson, K., Friedman, R., Frazier, M., and Venter, J. C.: The Sorcerer II global ocean sampling expedition: northwest Atlantic through eastern tropical Pacific, PLoS Biology, 5, 398–431, 2007.
Schattenhofer, M., Fuchs, B. M., Amann, R., Zubkov, M. V., Tarran, G. A., and Pernthaler, J.: Latitudinal distribution of prokaryotic picoplankton populations in the Atlantic Ocean, Environmental Microbiology, 11, 2078–2093, 2009.
Schlitzer, R.: Ocean Data View, \urlprefixhttp://odv/awi.de, 2011.
Schloss, P. D.: A high-throughput DNA sequence aligner for microbial ecology studies., PloS One, 4, e8230–e8230, 2009.
Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., Sahl, J. W., Stres, B., Thallinger, G. G., van Horn, D. J., and Weber, C. F.: Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities, Applied and Environmental Microbiology, 75, 7537–7541, 2009.
Schols, P., D'hondt, C., Geuten, K., Merckx, V., Janssens, S., and Smets, E.: MorphoCode: coding quantitative data for phylogenetic analysis, Phyloinformatics, 4, 1–4, 2004.
Smouse, P., Long, J., and Sokal, R.: Multiple-regression and correlation extensions of the mantel test of matrix correspondence, Systematic Zoology, 35, 627–632, 1986.
Sogin, M. L., Morrison, H. G., Huber, J. A., Welch, D. M., Huse, S. M., Neal, P. R., Arrieta, J. M., and Herndl, G. J.: Microbial diversity in the deep sea and the underexplored "rare biosphere", Proc. Natl. Acad. Sci. USA, 103, 12115–12120, 2006.
Sokal, R. R. and Sneath, P. H. A.: Principles of Numerical Taxonomy (A Series of Books in Biology), W. H. Freeman and Company, 1st edn., 1963.
Sokal, R. R. and Sneath, P. H. A.: Numerical Taxonomy: The Principles and Practice of Numerical Classification, W. H. Freeman and Company, 1973.
Stott, J.: Jcoord, version 1,0, \urlprefixhttp://www.jstott.me.uk/jcoord, 2011.
Taylor, B. B., Torrecilla, E., Bernhardt, A., Taylor, M. H., Peeken, I., Röttgers, R., Piera, J., and Bracher, A.: Bio-optical provinces in the eastern Atlantic Ocean and their biogeographical relevance, Biogeosciences, 8, 3609–3629, https://doi.org/10.5194/bg-8-3609-2011, 2011.
Thiele, K.: The holy grail of the perfect character: the cladistic treatment of morphometric data, Cladistics, 9, 275–304, 1993.
Treusch, A. H., Vergin, K. L., Finlay, L. A., Donatz, M. G., Burton, R. M., Carlson, C. A., and Giovannoni, S. J.: Seasonality and vertical structure of microbial communities in an ocean gyre, The ISME Journal, 3, 1148–1163, 2009.
Van Hannen, E., Zwart, G., Van Agterveld, M., Gons, H., Ebert, J., and Laanbroek, H.: Changes in bacterial and eukaryotic community structure after mass lysis of filamentous cyanobacteria associated with viruses, Applied and Environmental Microbiology, 65, 795–801, 1999.
Varela, M. M., van Aken, H. M., Sintes, E., and Herndl, G. J.: Latitudinal trends of Crenarchaeota and Bacteria in the meso- and bathypelagic water masses of the Eastern North Atlantic, Environmental Microbiology, 10, 110–124, 2007.
Venter, J., Remington, K., Heidelberg, J., Halpern, A., Rusch, D., Eisen, J., Wu, D., Paulsen, I., Nelson, K., Nelson, W., Fouts, D., Levy, S., Knap, A., Lomas, M., Nealson, K., White, O., Peterson, J., Hoffman, J., Parsons, R., Baden-Tillson, H., Pfannkoch, C., Rogers, Y., and Smith, H.: Environmental genome shotgun sequencing of the Sargasso Sea, Science, 304, 66–74, 2004.
VLIZ: Longhurst Biogeographical Provinces, \urlprefixhttp://www.vliz.be/vmdcdata/vlimar/downloads.php, 2009.
Wang, Q., Garrity, G. M., Tiedje, J. M., and Cole, J. R.: Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy, Applied and Environmental Microbiology, 73, 5261–5267, 2007.
West, N. J., Obernosterer, I., Zemb, O., and Lebaron, P.: Major differences of bacterial diversity and activity inside and outside of a natural iron-fertilized phytoplankton bloom in the Southern Ocean, Environmental Microbiology, 10, 738–756, 2008.
Wietz, M., Gram, L., Jorgensen, B., and Schramm, A.: Latitudinal patterns in the abundance of major marine bacterioplankton groups, Aquatic Microbial Ecology, 61, 179–189, 2010.
Wright, T. D., Vergin, K. L., Boyd, P. W., and Giovannoni, S. J.: A novel delta-subdivision proteobacterial lineage from the lower ocean surface layer, Applied and Environmental Microbiology, 63, 1441–1448, 1997.
Xie, Z., Koch, B. P., Möller, A., Sturm, R., and Ebinghaus, R.: Transport and fate of hexachlorocyclohexanes in the oceanic air and surface seawater, Biogeosciences, 8, 2621–2633, https://doi.org/10.5194/bg-8-2621-2011, 2011.
Yokokawa, T., De Corte, D., Sintes, E., and Herndl, G. J.: Spatial patterns of bacterial abundance, activity and community composition in relation to water masses in the eastern Mediterranean Sea, Aquatic Microbial Ecology, 59, 185–195, 2010.
Zinger, L., Amaral-Zettler, L. A., Fuhrman, J. A., Horner-Devine, M. C., Huse, S. M., Welch, D. B. M., Martiny, J. B. H., Sogin, M. L., Boetius, A., and Ramette, A.: Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems, PloS One, 6, e24570, 2011.
Search articles
Download
Biogeosciences
An interactive open-access journal of the European Geosciences Union
All site content, except where otherwise noted, is licensed under the Creative Commons Attribution 4.0 License.