Articles | Volume 10, issue 6
https://doi.org/10.5194/bg-10-4273-2013
© Author(s) 2013. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
https://doi.org/10.5194/bg-10-4273-2013
© Author(s) 2013. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
Research article
| 
27 Jun 2013
Research article |
| 27 Jun 2013
Upper Arctic Ocean water masses harbor distinct communities of heterotrophic flagellates
A. Monier
Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Québec-Océan, Université Laval, Québec, QC, Canada
Takuvik Joint International Laboratory, Université Laval (Canada) – CNRS UMI3376 (France), Québec, QC, Canada
R. Terrado
Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Québec-Océan, Université Laval, Québec, QC, Canada
M. Thaler
Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Québec-Océan, Université Laval, Québec, QC, Canada
A. Comeau
Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Québec-Océan, Université Laval, Québec, QC, Canada
E. Medrinal
Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Québec-Océan, Université Laval, Québec, QC, Canada
C. Lovejoy
Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Québec-Océan, Université Laval, Québec, QC, Canada
Takuvik Joint International Laboratory, Université Laval (Canada) – CNRS UMI3376 (France), Québec, QC, Canada
Related authors
No articles found.
Philippe Massicotte, Rainer M. W. Amon, David Antoine, Philippe Archambault, Sergio Balzano, Simon Bélanger, Ronald Benner, Dominique Boeuf, Annick Bricaud, Flavienne Bruyant, Gwenaëlle Chaillou, Malik Chami, Bruno Charrière, Jing Chen, Hervé Claustre, Pierre Coupel, Nicole Delsaut, David Doxaran, Jens Ehn, Cédric Fichot, Marie-Hélène Forget, Pingqing Fu, Jonathan Gagnon, Nicole Garcia, Beat Gasser, Jean-François Ghiglione, Gaby Gorsky, Michel Gosselin, Priscillia Gourvil, Yves Gratton, Pascal Guillot, Hermann J. Heipieper, Serge Heussner, Stanford B. Hooker, Yannick Huot, Christian Jeanthon, Wade Jeffrey, Fabien Joux, Kimitaka Kawamura, Bruno Lansard, Edouard Leymarie, Heike Link, Connie Lovejoy, Claudie Marec, Dominique Marie, Johannie Martin, Jacobo Martín, Guillaume Massé, Atsushi Matsuoka, Vanessa McKague, Alexandre Mignot, William L. Miller, Juan-Carlos Miquel, Alfonso Mucci, Kaori Ono, Eva Ortega-Retuerta, Christos Panagiotopoulos, Tim Papakyriakou, Marc Picheral, Louis Prieur, Patrick Raimbault, Joséphine Ras, Rick A. Reynolds, André Rochon, Jean-François Rontani, Catherine Schmechtig, Sabine Schmidt, Richard Sempéré, Yuan Shen, Guisheng Song, Dariusz Stramski, Eri Tachibana, Alexandre Thirouard, Imma Tolosa, Jean-Éric Tremblay, Mickael Vaïtilingom, Daniel Vaulot, Frédéric Vaultier, John K. Volkman, Huixiang Xie, Guangming Zheng, and Marcel Babin
Earth Syst. Sci. Data, 13, 1561–1592, https://doi.org/10.5194/essd-13-1561-2021, https://doi.org/10.5194/essd-13-1561-2021, 2021
Short summary
Short summary
The MALINA oceanographic expedition was conducted in the Mackenzie River and the Beaufort Sea systems. The sampling was performed across seven shelf–basin transects to capture the meridional gradient between the estuary and the open ocean. The main goal of this research program was to better understand how processes such as primary production are influencing the fate of organic matter originating from the surrounding terrestrial landscape during its transition toward the Arctic Ocean.
J. Comte, C. Lovejoy, S. Crevecoeur, and W. F. Vincent
Biogeosciences, 13, 175–190, https://doi.org/10.5194/bg-13-175-2016, https://doi.org/10.5194/bg-13-175-2016, 2016
Short summary
Short summary
Thaw ponds and lakes varied in their bacterial community structure. A small number of taxa occurred in high abundance and dominated many of the communities. Nevertheless, there were taxonomic differences among different valleys implying some degree of habitat selection. Association networks were composed of a limited number of highly connected OTUs. These "keystone species" were not merely the abundant taxa, whose loss would greatly alter the structure and functioning of these aquatic ecosystem.
A. Przytulska, J. Comte, S. Crevecoeur, C. Lovejoy, I. Laurion, and W. F. Vincent
Biogeosciences, 13, 13–26, https://doi.org/10.5194/bg-13-13-2016, https://doi.org/10.5194/bg-13-13-2016, 2016
Short summary
Short summary
Permafrost thaw lakes are a subject of increasing research interest given their abundance across the northern landscape. Our aim in the present study was to characterize the photosynthetic communities in a range of subarctic thaw lakes using a combination of HPLC analysis of algal and bacterial pigments, flow cytometry and molecular analysis. Our results showed that the thaw lakes contain diverse phototrophic communities and are a previously unrecognized habitat for abundant picophotoautotrophs.
Related subject area
Biogeochemistry: Environmental Microbiology
Nitrous oxide (N2O) synthesis by the freshwater cyanobacterium Microcystis aeruginosa
Interdisciplinary strategy to assess the impact of meteorological variables on the biochemical composition of the rain and the dynamics of a small eutrophic lake under rain forcing
Depth-related patterns in microbial community responses to complex organic matter in the western North Atlantic Ocean
Assessing the influence of ocean alkalinity enhancement on a coastal phytoplankton community
Eddy-enhanced primary production sustains heterotrophic microbial activities in the Eastern Tropical North Atlantic
Composition and niche-specific characteristics of microbial consortia colonizing Marsberg copper mine in the Rhenish Massif
Abrasion of sedimentary rocks as a source of hydrogen peroxide and nutrients to subglacial ecosystems
Diversity and assembly processes of microbial eukaryotic communities in Fildes Peninsula Lakes (West Antarctica)
Nitrophobic ectomycorrhizal fungi are associated with enhanced hydrophobicity of soil organic matter in a Norway spruce forest
Physiological control on carbon isotope fractionation in marine phytoplankton
Implementation of mycorrhizal mechanisms into soil carbon model improves the prediction of long-term processes of plant litter decomposition
Impact of dust addition on the microbial food web under present and future conditions of pH and temperature
Fractionation of stable carbon isotopes during acetate consumption by methanogenic and sulfidogenic microbial communities in rice paddy soils and lake sediments
Hydrothermal trace metal release and microbial metabolism in the northeastern Lau Basin of the South Pacific Ocean
Sedimentation rate and organic matter dynamics shape microbiomes across a continental margin
Disturbance triggers non-linear microbe–environment feedbacks
Hydrographic fronts shape productivity, nitrogen fixation, and microbial community composition in the southern Indian Ocean and the Southern Ocean
Microbial and geo-archaeological records reveal the growth rate, origin and composition of desert rock surface communities
Metagenomic insights into the metabolism of microbial communities that mediate iron and methane cycling in Lake Kinneret iron-rich methanic sediments
Spatiotemporal patterns of N2 fixation in coastal waters derived from rate measurements and remote sensing
Biotic and abiotic transformation of amino acids in cloud water: experimental studies and atmospheric implications
Potential bioavailability of organic matter from atmospheric particles to marine heterotrophic bacteria
Microbial functional signature in the atmospheric boundary layer
New insight to niche partitioning and ecological function of ammonia oxidizing archaea in subtropical estuarine ecosystem
Impact of reactive surfaces on the abiotic reaction between nitrite and ferrous iron and associated nitrogen and oxygen isotope dynamics
Reviews and syntheses: Bacterial bioluminescence – ecology and impact in the biological carbon pump
Salinity-dependent algae uptake and subsequent carbon and nitrogen metabolisms of two intertidal foraminifera (Ammonia tepida and Haynesina germanica)
On giant shoulders: how a seamount affects the microbial community composition of seawater and sponges
Spatial variations in sedimentary N-transformation rates in the North Sea (German Bight)
Patterns of (trace) metals and microorganisms in the Rainbow hydrothermal vent plume at the Mid-Atlantic Ridge
Co-occurrence of Fe and P stress in natural populations of the marine diazotroph Trichodesmium
Senescence as the main driver of iodide release from a diverse range of marine phytoplankton
Reviews and syntheses: Biological weathering and its consequences at different spatial levels – from nanoscale to global scale
Deep-sea sponge grounds as nutrient sinks: denitrification is common in boreo-Arctic sponges
Inducing the attachment of cable bacteria on oxidizing electrodes
Bacterial degradation activity in the eastern tropical South Pacific oxygen minimum zone
Macromolecular fungal ice nuclei in Fusarium: effects of physical and chemical processing
Effects of sea animal colonization on the coupling between dynamics and activity of soil ammonia-oxidizing bacteria and archaea in maritime Antarctica
Comprehensive characterization of an aspen (Populus tremuloides) leaf litter sample that maintained ice nucleation activity for 48 years
The origin and role of biological rock crusts in rocky desert weathering
Pyrite oxidization accelerates bacterial carbon sequestration in copper mine tailings
Biogeochemical evidence of anaerobic methane oxidation on active submarine mud volcanoes on the continental slope of the Canadian Beaufort Sea
Filtration artefacts in bacterial community composition can affect the outcome of dissolved organic matter biolability assays
Predominance of methanogens over methanotrophs in rewetted fens characterized by high methane emissions
Trichodesmium physiological ecology and phosphate reduction in the western tropical South Pacific
Potential for phenol biodegradation in cloud waters
Colony formation in Phaeocystis antarctica: connecting molecular mechanisms with iron biogeochemistry
In-depth characterization of diazotroph activity across the western tropical South Pacific hotspot of N2 fixation (OUTPACE cruise)
Programmed cell death in diazotrophs and the fate of organic matter in the western tropical South Pacific Ocean during the OUTPACE cruise
Rapid mineralization of biogenic volatile organic compounds in temperate and Arctic soils
Federico Fabisik, Benoit Guieysse, Jonathan Procter, and Maxence Plouviez
Biogeosciences, 20, 687–693, https://doi.org/10.5194/bg-20-687-2023, https://doi.org/10.5194/bg-20-687-2023, 2023
Short summary
Short summary
We show, for the first time, that pure cultures of the cyanobacterium Microcystis aeruginosa can synthesize the potent greenhouse gas N2O using nitrite as substrate. Our findings have broad environmental implications because M. aeruginosa is globally found in freshwater ecosystems and is often the dominant species found in algae blooms. Further research is now needed to determine the occurrence and significance of N2O emissions from ecosystems rich with M. aeruginosa.
Fanny Noirmain, Jean-Luc Baray, Frédéric Tridon, Philippe Cacault, Hermine Billard, Guillaume Voyard, Joël Van Baelen, and Delphine Latour
Biogeosciences, 19, 5729–5749, https://doi.org/10.5194/bg-19-5729-2022, https://doi.org/10.5194/bg-19-5729-2022, 2022
Short summary
Short summary
We present a study linking rain, meteorology, and mountain lake phytoplankton dynamics on the basis of a case study at Aydat (France) in September 2020. The air mass origin mainly influences the rain chemical composition, which depends on the type of rain, convective or stratiform. Our results also highlighted a non-negligible presence of photosynthetic cells in rainwater. The impact of the atmospheric forcing on the lake could play a key role in phytoplankton dynamics in the temperate zone.
Sarah A. Brown, John Paul Balmonte, Adrienne Hoarfrost, Sherif Ghobrial, and Carol Arnosti
Biogeosciences, 19, 5617–5631, https://doi.org/10.5194/bg-19-5617-2022, https://doi.org/10.5194/bg-19-5617-2022, 2022
Short summary
Short summary
Bacteria use extracellular enzymes to cut large organic matter to sizes small enough for uptake. We compared the enzymatic response of surface, mid-water, and deep-ocean bacteria to complex natural substrates. Bacteria in surface and mid-depth waters produced a much wider range of enzymes than those in the deep ocean and may therefore consume a broader range of organic matter. The extent to which organic matter is recycled by bacteria depends in part on its residence time at different depths.
Aaron Ferderer, Zanna Chase, Fraser Kennedy, Kai G. Schulz, and Lennart T. Bach
Biogeosciences, 19, 5375–5399, https://doi.org/10.5194/bg-19-5375-2022, https://doi.org/10.5194/bg-19-5375-2022, 2022
Short summary
Short summary
Ocean alkalinity enhancement has the capacity to remove vast quantities of carbon from the atmosphere, but its effect on marine ecosystems is largely unknown. We assessed the effect of increased alkalinity on a coastal phytoplankton community when seawater was equilibrated and not equilibrated with atmospheric CO2. We found that the phytoplankton community was moderately affected by increased alkalinity and equilibration with atmospheric CO2 had little influence on this effect.
Quentin Devresse, Kevin W. Becker, Arne Bendinger, Johannes Hahn, and Anja Engel
Biogeosciences, 19, 5199–5219, https://doi.org/10.5194/bg-19-5199-2022, https://doi.org/10.5194/bg-19-5199-2022, 2022
Short summary
Short summary
Eddies are ubiquitous in the ocean and alter physical, chemical, and biological processes. However, how they affect organic carbon production and consumption is largely unknown. Here we show how an eddy triggers a cascade effect on biomass production and metabolic activities of phyto- and bacterioplankton. Our results may contribute to the improvement of biogeochemical models used to estimate carbon fluxes in the ocean.
Sania Arif, Heiko Nacke, Elias Schliekmann, Andreas Reimer, Gernot Arp, and Michael Hoppert
Biogeosciences, 19, 4883–4902, https://doi.org/10.5194/bg-19-4883-2022, https://doi.org/10.5194/bg-19-4883-2022, 2022
Short summary
Short summary
The natural enrichment of Chloroflexi (Ktedonobacteria) at the Kilianstollen Marsberg copper mine rocks being exposed to the acidic sulfate-rich leachate led to an investigation of eight metagenomically assembled genomes (MAGs) involved in copper and other transition heavy metal resistance in addition to low pH resistance and aromatic compounds degradation. The present study offers functional insights about a novel cold-adapted Ktedonobacteria MAG extremophily along with other phyla MAGs.
Beatriz Gill-Olivas, Jon Telling, Mark Skidmore, and Martyn Tranter
EGUsphere, https://doi.org/10.5194/egusphere-2022-908, https://doi.org/10.5194/egusphere-2022-908, 2022
Short summary
Short summary
Microbial ecosystems have been found in all subglacial environments sampled to date. Yet, little is known of the sources of energy and nutrients that sustain these microbial populations. This study shows that crushing of sedimentary rocks, which contain organic carbon, carbonate and sulphide minerals, along with previously weathered silicate minerals, produces a range of compounds and nutrients which can be utilised by the diverse suite of microbes that inhabit glacier beds.
Chunmei Zhang, Huirong Li, Yinxin Zeng, Haitao Ding, Bin Wang, Yangjie Li, Zhongqiang Ji, Yonghong Bi, and Wei Luo
Biogeosciences, 19, 4639–4654, https://doi.org/10.5194/bg-19-4639-2022, https://doi.org/10.5194/bg-19-4639-2022, 2022
Short summary
Short summary
The unique microbial eukaryotic community structure and lower diversity have been demonstrated in five freshwater lakes of the Fildes Peninsula, Antarctica. Stochastic processes and biotic co-occurrence patterns were shown to be important in shaping microbial eukaryotic communities in the area. Our study provides a better understanding of the dynamic patterns and ecological assembly processes of microbial eukaryotic communities in Antarctic oligotrophic lakes (Fildes Peninsula).
Juan Pablo Almeida, Nicholas P. Rosenstock, Susanne K. Woche, Georg Guggenberger, and Håkan Wallander
Biogeosciences, 19, 3713–3726, https://doi.org/10.5194/bg-19-3713-2022, https://doi.org/10.5194/bg-19-3713-2022, 2022
Short summary
Short summary
Fungi living in symbiosis with tree roots can accumulate belowground, forming special tissues than can repel water. We measured the water repellency of organic material incubated belowground and correlated it with fungal growth. We found a positive association between water repellency and root symbiotic fungi. These results are important because an increase in soil water repellency can reduce the release of CO2 from soils into the atmosphere and mitigate the effects of greenhouse gasses.
Karen M. Brandenburg, Björn Rost, Dedmer B. Van de Waal, Mirja Hoins, and Appy Sluijs
Biogeosciences, 19, 3305–3315, https://doi.org/10.5194/bg-19-3305-2022, https://doi.org/10.5194/bg-19-3305-2022, 2022
Short summary
Short summary
Reconstructions of past CO2 concentrations rely on proxy estimates, with one line of proxies relying on the CO2-dependence of stable carbon isotope fractionation in marine phytoplankton. Culturing experiments provide insights into which processes may impact this. We found, however, that the methods with which these culturing experiments are performed also influence 13C fractionation. Caution should therefore be taken when extrapolating results from these experiments to proxy applications.
Weilin Huang, Peter M. van Bodegom, Toni Viskari, Jari Liski, and Nadejda A. Soudzilovskaia
Biogeosciences, 19, 1469–1490, https://doi.org/10.5194/bg-19-1469-2022, https://doi.org/10.5194/bg-19-1469-2022, 2022
Short summary
Short summary
This work focuses on one of the essential pathways of mycorrhizal impact on C cycles: the mediation of plant litter decomposition. We present a model based on litter chemical quality which precludes a conclusive examination of mycorrhizal impacts on soil C. It improves long-term decomposition predictions and advances our understanding of litter decomposition dynamics. It creates a benchmark in quantitatively examining the impacts of plant–microbe interactions on soil C dynamics.
Julie Dinasquet, Estelle Bigeard, Frédéric Gazeau, Farooq Azam, Cécile Guieu, Emilio Marañón, Céline Ridame, France Van Wambeke, Ingrid Obernosterer, and Anne-Claire Baudoux
Biogeosciences, 19, 1303–1319, https://doi.org/10.5194/bg-19-1303-2022, https://doi.org/10.5194/bg-19-1303-2022, 2022
Short summary
Short summary
Saharan dust deposition of nutrients and trace metals is crucial to microbes in the Mediterranean Sea. Here, we tested the response of microbial and viral communities to simulated dust deposition under present and future conditions of temperature and pH. Overall, the effect of the deposition was dependent on the initial microbial assemblage, and future conditions will intensify microbial responses. We observed effects on trophic interactions, cascading all the way down to viral processes.
Ralf Conrad, Pengfei Liu, and Peter Claus
Biogeosciences, 18, 6533–6546, https://doi.org/10.5194/bg-18-6533-2021, https://doi.org/10.5194/bg-18-6533-2021, 2021
Short summary
Short summary
Acetate is an important intermediate during the anaerobic degradation of organic matter. It is consumed by methanogenic and sulfidogenic microorganisms accompanied by stable carbon isotope fractionation. We determined isotope fractionation under different conditions in two paddy soils and two lake sediments and also determined the composition of the microbial communities. Despite a relatively wide range of experimental conditions, the range of fractionation factors was quite moderate.
Natalie R. Cohen, Abigail E. Noble, Dawn M. Moran, Matthew R. McIlvin, Tyler J. Goepfert, Nicholas J. Hawco, Christopher R. German, Tristan J. Horner, Carl H. Lamborg, John P. McCrow, Andrew E. Allen, and Mak A. Saito
Biogeosciences, 18, 5397–5422, https://doi.org/10.5194/bg-18-5397-2021, https://doi.org/10.5194/bg-18-5397-2021, 2021
Short summary
Short summary
A previous study documented an intense hydrothermal plume in the South Pacific Ocean; however, the iron release associated with this plume and the impact on microbiology were unclear. We describe metal concentrations associated with multiple hydrothermal plumes in this region and protein signatures of plume-influenced microbes. Our findings demonstrate that resources released from these systems can be transported away from their source and may alter the physiology of surrounding microbes.
Sabyasachi Bhattacharya, Tarunendu Mapder, Svetlana Fernandes, Chayan Roy, Jagannath Sarkar, Moidu Jameela Rameez, Subhrangshu Mandal, Abhijit Sar, Amit Kumar Chakraborty, Nibendu Mondal, Sumit Chatterjee, Bomba Dam, Aditya Peketi, Ranadhir Chakraborty, Aninda Mazumdar, and Wriddhiman Ghosh
Biogeosciences, 18, 5203–5222, https://doi.org/10.5194/bg-18-5203-2021, https://doi.org/10.5194/bg-18-5203-2021, 2021
Short summary
Short summary
Physicochemical determinants of microbiome architecture across continental shelves–slopes are unknown, so we explored the geomicrobiology along 3 m sediment horizons of seasonal (shallow coastal) and perennial (deep sea) hypoxic zones of the Arabian Sea. Nature, concentration, and fate of the organic matter delivered to the sea floor were found to shape the microbiome across the western Indian margin, under direct–indirect influence of sedimentation rate and water column O2 level.
Aditi Sengupta, Sarah J. Fansler, Rosalie K. Chu, Robert E. Danczak, Vanessa A. Garayburu-Caruso, Lupita Renteria, Hyun-Seob Song, Jason Toyoda, Jacqueline Wells, and James C. Stegen
Biogeosciences, 18, 4773–4789, https://doi.org/10.5194/bg-18-4773-2021, https://doi.org/10.5194/bg-18-4773-2021, 2021
Short summary
Short summary
Conceptual models link microbes with the environment but are untested. We test a recent model using riverbed sediments. We exposed sediments to disturbances, going dry and becoming wet again. As the length of dry conditions got longer, there was a sudden shift in the ecology of microbes, chemistry of organic matter, and rates of microbial metabolism. We propose a new model based on feedbacks initiated by disturbance that cascade across biological, chemical, and functional aspects of the system.
Cora Hörstmann, Eric J. Raes, Pier Luigi Buttigieg, Claire Lo Monaco, Uwe John, and Anya M. Waite
Biogeosciences, 18, 3733–3749, https://doi.org/10.5194/bg-18-3733-2021, https://doi.org/10.5194/bg-18-3733-2021, 2021
Short summary
Short summary
Microbes are the main drivers of productivity and nutrient cycling in the ocean. We present a combined approach assessing C and N uptake and microbial community diversity across ecological provinces in the Southern Ocean and southern Indian Ocean. Provinces showed distinct genetic fingerprints, but microbial activity varied gradually across regions, correlating with nutrient concentrations. Our study advances the biogeographic understanding of microbial diversity across C and N uptake regimes.
Nimrod Wieler, Tali Erickson Gini, Osnat Gillor, and Roey Angel
Biogeosciences, 18, 3331–3342, https://doi.org/10.5194/bg-18-3331-2021, https://doi.org/10.5194/bg-18-3331-2021, 2021
Short summary
Short summary
Biological rock crusts (BRCs) are common microbial-based assemblages covering rocks in drylands. BRCs play a crucial role in arid environments because of the limited activity of plants and soil. Nevertheless, BRC development rates have never been dated. Here we integrated archaeological, microbiological and geological methods to provide a first estimation of the growth rate of BRCs under natural conditions. This can serve as an affordable dating tool in archaeological sites in arid regions.
Michal Elul, Maxim Rubin-Blum, Zeev Ronen, Itay Bar-Or, Werner Eckert, and Orit Sivan
Biogeosciences, 18, 2091–2106, https://doi.org/10.5194/bg-18-2091-2021, https://doi.org/10.5194/bg-18-2091-2021, 2021
Mindaugas Zilius, Irma Vybernaite-Lubiene, Diana Vaiciute, Donata Overlingė, Evelina Grinienė, Anastasija Zaiko, Stefano Bonaglia, Iris Liskow, Maren Voss, Agneta Andersson, Sonia Brugel, Tobia Politi, and Paul A. Bukaveckas
Biogeosciences, 18, 1857–1871, https://doi.org/10.5194/bg-18-1857-2021, https://doi.org/10.5194/bg-18-1857-2021, 2021
Short summary
Short summary
In fresh and brackish waters, algal blooms are often dominated by cyanobacteria, which have the ability to utilize atmospheric nitrogen. Cyanobacteria are also unusual in that they float to the surface and are dispersed by wind-driven currents. Their patchy and dynamic distribution makes it difficult to track their abundance and quantify their effects on nutrient cycling. We used remote sensing to map the distribution of cyanobacteria in a large Baltic lagoon and quantify their contributions.
Saly Jaber, Muriel Joly, Maxence Brissy, Martin Leremboure, Amina Khaled, Barbara Ervens, and Anne-Marie Delort
Biogeosciences, 18, 1067–1080, https://doi.org/10.5194/bg-18-1067-2021, https://doi.org/10.5194/bg-18-1067-2021, 2021
Short summary
Short summary
Our study is of interest to atmospheric scientists and environmental microbiologists, as we show that clouds can be considered a medium where bacteria efficiently degrade and transform amino acids, in competition with chemical processes. As current atmospheric multiphase models are restricted to chemical degradation of organic compounds, our conclusions motivate further model development.
Kahina Djaoudi, France Van Wambeke, Aude Barani, Nagib Bhairy, Servanne Chevaillier, Karine Desboeufs, Sandra Nunige, Mohamed Labiadh, Thierry Henry des Tureaux, Dominique Lefèvre, Amel Nouara, Christos Panagiotopoulos, Marc Tedetti, and Elvira Pulido-Villena
Biogeosciences, 17, 6271–6285, https://doi.org/10.5194/bg-17-6271-2020, https://doi.org/10.5194/bg-17-6271-2020, 2020
Romie Tignat-Perrier, Aurélien Dommergue, Alban Thollot, Olivier Magand, Timothy M. Vogel, and Catherine Larose
Biogeosciences, 17, 6081–6095, https://doi.org/10.5194/bg-17-6081-2020, https://doi.org/10.5194/bg-17-6081-2020, 2020
Short summary
Short summary
The adverse atmospheric environmental conditions do not appear suited for microbial life. We conducted the first global comparative metagenomic analysis to find out if airborne microbial communities might be selected by their ability to resist these adverse conditions. The relatively higher concentration of fungi led to the observation of higher proportions of stress-related functions in air. Fungi might likely resist and survive atmospheric physical stress better than bacteria.
Yanhong Lu, Shunyan Cheung, Ling Chen, Shuh-Ji Kao, Xiaomin Xia, Jianping Gan, Minhan Dai, and Hongbin Liu
Biogeosciences, 17, 6017–6032, https://doi.org/10.5194/bg-17-6017-2020, https://doi.org/10.5194/bg-17-6017-2020, 2020
Short summary
Short summary
Through a comprehensive investigation, we observed differential niche partitioning among diverse ammonia-oxidizing archaea (AOA) sublineages in a typical subtropical estuary. Distinct AOA communities observed at DNA and RNA levels suggested that a strong divergence in ammonia-oxidizing activity among different AOA groups occurs. Our result highlights the importance of identifying major ammonia oxidizers at RNA level in future studies.
Anna-Neva Visser, Scott D. Wankel, Pascal A. Niklaus, James M. Byrne, Andreas A. Kappler, and Moritz F. Lehmann
Biogeosciences, 17, 4355–4374, https://doi.org/10.5194/bg-17-4355-2020, https://doi.org/10.5194/bg-17-4355-2020, 2020
Short summary
Short summary
This study focuses on the chemical reaction between Fe(II) and nitrite, which has been reported to produce high levels of the greenhouse gas N2O. We investigated the extent to which dead biomass and Fe(II) minerals might enhance this reaction. Here, nitrite reduction was highest when both additives were present but less pronounced if only Fe(II) minerals were added. Both reaction systems show distinct differences, rather low N2O levels, and indicated the abiotic production of N2.
Lisa Tanet, Séverine Martini, Laurie Casalot, and Christian Tamburini
Biogeosciences, 17, 3757–3778, https://doi.org/10.5194/bg-17-3757-2020, https://doi.org/10.5194/bg-17-3757-2020, 2020
Short summary
Short summary
Bioluminescent bacteria, the most abundant light-emitting organisms in the ocean, can be free-living, be symbiotic or colonize organic particles. This review suggests that they act as a visual target and may indirectly influence the sequestration of biogenic carbon in oceans by increasing the attraction rate for consumers. We summarize the instrumentation available to quantify this impact in future studies and propose synthetic figures integrating these ecological and biogeochemical concepts.
Michael Lintner, Bianca Biedrawa, Julia Wukovits, Wolfgang Wanek, and Petra Heinz
Biogeosciences, 17, 3723–3732, https://doi.org/10.5194/bg-17-3723-2020, https://doi.org/10.5194/bg-17-3723-2020, 2020
Short summary
Short summary
Foraminifera are unicellular marine organisms that play an important role in the marine element cycle. Changes of environmental parameters such as salinity or temperature have a significant impact on the faunal assemblages. Our experiments show that changing salinity in the German Wadden Sea immediately influences the foraminiferal community. It seems that A. tepida is better adapted to salinity fluctuations than H. germanica.
Kathrin Busch, Ulrike Hanz, Furu Mienis, Benjamin Mueller, Andre Franke, Emyr Martyn Roberts, Hans Tore Rapp, and Ute Hentschel
Biogeosciences, 17, 3471–3486, https://doi.org/10.5194/bg-17-3471-2020, https://doi.org/10.5194/bg-17-3471-2020, 2020
Short summary
Short summary
Seamounts are globally abundant submarine structures that offer great potential to study the impacts and interactions of environmental gradients at a single geographic location. In an exemplary way, we describe potential mechanisms by which a seamount can affect the structure of pelagic and benthic (sponge-)associated microbial communities. We conclude that the geology, physical oceanography, biogeochemistry, and microbiology of seamounts are even more closely linked than currently appreciated.
Alexander Bratek, Justus E. E. van
Beusekom, Andreas Neumann, Tina Sanders, Jana Friedrich, Kay-Christian Emeis, and Kirstin Dähnke
Biogeosciences, 17, 2839–2851, https://doi.org/10.5194/bg-17-2839-2020, https://doi.org/10.5194/bg-17-2839-2020, 2020
Short summary
Short summary
The following paper highlights the importance of benthic N-transformation rates in different sediment types in the southern North Sea as a source of fixed nitrogen for primary producers and also as a sink of fixed nitrogen. Sedimentary fluxes of dissolved inorganic nitrogen support ∼7 to 59 % of the average annual primary production. Semi-permeable and permeable sediments contribute ∼68 % of the total benthic N2 production rates, counteracting eutrophication in the southern North Sea.
Sabine Haalboom, David M. Price, Furu Mienis, Judith D. L. van Bleijswijk, Henko C. de Stigter, Harry J. Witte, Gert-Jan Reichart, and Gerard C. A. Duineveld
Biogeosciences, 17, 2499–2519, https://doi.org/10.5194/bg-17-2499-2020, https://doi.org/10.5194/bg-17-2499-2020, 2020
Short summary
Short summary
Mineral mining in deep-sea hydrothermal settings will lead to the formation of plumes of fine-grained, chemically reactive, suspended matter. Understanding how natural hydrothermal plumes evolve as they disperse from their source, and how they affect their surrounding environment, may help in characterising the behaviour of the diluted part of mining plumes. The natural plume provided a heterogeneous, geochemically enriched habitat conducive to the development of a distinct microbial ecology.
Noelle A. Held, Eric A. Webb, Matthew M. McIlvin, David A. Hutchins, Natalie R. Cohen, Dawn M. Moran, Korinna Kunde, Maeve C. Lohan, Claire Mahaffey, E. Malcolm S. Woodward, and Mak A. Saito
Biogeosciences, 17, 2537–2551, https://doi.org/10.5194/bg-17-2537-2020, https://doi.org/10.5194/bg-17-2537-2020, 2020
Short summary
Short summary
Trichodesmium is a globally important marine nitrogen fixer that stimulates primary production in the surface ocean. We surveyed metaproteomes of Trichodesmium populations across the North Atlantic and other oceans, and we found that they experience simultaneous phosphate and iron stress because of the biophysical limits of nutrient uptake. Importantly, nitrogenase was most abundant during co-stress, indicating the potential importance of this phenotype to global nitrogen and carbon cycling.
Helmke Hepach, Claire Hughes, Karen Hogg, Susannah Collings, and Rosie Chance
Biogeosciences, 17, 2453–2471, https://doi.org/10.5194/bg-17-2453-2020, https://doi.org/10.5194/bg-17-2453-2020, 2020
Short summary
Short summary
Tropospheric iodine takes part in numerous atmospheric chemical cycles, including tropospheric ozone destruction and aerosol formation. Due to its significance for atmospheric processes, it is crucial to constrain its sources and sinks. This paper aims at investigating and understanding features of biogenic iodate-to-iodide reduction in microalgal monocultures. We find that phytoplankton senescence may play a crucial role in the release of iodide to the marine environment.
Roger D. Finlay, Shahid Mahmood, Nicholas Rosenstock, Emile B. Bolou-Bi, Stephan J. Köhler, Zaenab Fahad, Anna Rosling, Håkan Wallander, Salim Belyazid, Kevin Bishop, and Bin Lian
Biogeosciences, 17, 1507–1533, https://doi.org/10.5194/bg-17-1507-2020, https://doi.org/10.5194/bg-17-1507-2020, 2020
Short summary
Short summary
Effects of biological activity on mineral weathering operate at scales ranging from short-term, microscopic interactions to global, evolutionary timescale processes. Microorganisms have had well-documented effects at large spatio-temporal scales, but to establish the quantitative significance of microscopic measurements for field-scale processes, higher-resolution studies of liquid chemistry at local weathering sites and improved upscaling to soil-scale dissolution rates are still required.
Christine Rooks, James Kar-Hei Fang, Pål Tore Mørkved, Rui Zhao, Hans Tore Rapp, Joana R. Xavier, and Friederike Hoffmann
Biogeosciences, 17, 1231–1245, https://doi.org/10.5194/bg-17-1231-2020, https://doi.org/10.5194/bg-17-1231-2020, 2020
Short summary
Short summary
Sponge grounds are known as nutrient sources, providing nitrate and ammonium to the ocean. We found that they also can do the opposite: in six species from Arctic and North Atlantic sponge grounds, we measured high rates of denitrification, which remove these nutrients from the sea. Rates were highest when the sponge tissue got low in oxygen, which happens when sponges stop pumping because of stress. Sponge grounds may become nutrient sinks when exposed to stress.
Cheng Li, Clare E. Reimers, and Yvan Alleau
Biogeosciences, 17, 597–607, https://doi.org/10.5194/bg-17-597-2020, https://doi.org/10.5194/bg-17-597-2020, 2020
Short summary
Short summary
Novel filamentous cable bacteria that grow in the top layer of intertidal mudflat sediment were attracted to electrodes poised at a positive electrical potential. Several diverse morphologies of Desulfobulbaceae filaments, cells, and colonies were observed on the electrode surface. These observations provide information to suggest conditions that will induce cable bacteria to perform electron donation to an electrode, informing future experiments that culture cable bacteria outside of sediment.
Marie Maßmig, Jan Lüdke, Gerd Krahmann, and Anja Engel
Biogeosciences, 17, 215–230, https://doi.org/10.5194/bg-17-215-2020, https://doi.org/10.5194/bg-17-215-2020, 2020
Short summary
Short summary
Little is known about the rates of bacterial element cycling in oxygen minimum zones (OMZs). We measured bacterial production and rates of extracellular hydrolytic enzymes at various in situ oxygen concentrations in the OMZ off Peru. Our field data show unhampered bacterial activity at low oxygen concentrations. Meanwhile bacterial degradation of organic matter substantially contributed to the formation of the OMZ.
Anna T. Kunert, Mira L. Pöhlker, Kai Tang, Carola S. Krevert, Carsten Wieder, Kai R. Speth, Linda E. Hanson, Cindy E. Morris, David G. Schmale III, Ulrich Pöschl, and Janine Fröhlich-Nowoisky
Biogeosciences, 16, 4647–4659, https://doi.org/10.5194/bg-16-4647-2019, https://doi.org/10.5194/bg-16-4647-2019, 2019
Short summary
Short summary
A screening of more than 100 strains from 65 different species revealed that the ice nucleation activity within the fungal genus Fusarium is more widespread than previously assumed. Filtration experiments suggest that the single cell-free Fusarium IN is smaller than 100 kDa (~ 6 nm) and that aggregates can be formed in solution. Exposure experiments, freeze–thaw cycles, and long-term storage tests demonstrate a high stability of Fusarium IN under atmospherically relevant conditions.
Qing Wang, Renbin Zhu, Yanling Zheng, Tao Bao, and Lijun Hou
Biogeosciences, 16, 4113–4128, https://doi.org/10.5194/bg-16-4113-2019, https://doi.org/10.5194/bg-16-4113-2019, 2019
Short summary
Short summary
We investigated abundance, potential activity, and diversity of soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) in five Antarctic tundra patches, including penguin colony, seal colony, and tundra marsh. We have found (1) sea animal colonization increased AOB population size.; (2) AOB contributed to ammonia oxidation rates more than AOA in sea animal colonies; (3) community structures of AOB and AOA were closely related to soil biogeochemical processes associated with animal activities.
Yalda Vasebi, Marco E. Mechan Llontop, Regina Hanlon, David G. Schmale III, Russell Schnell, and Boris A. Vinatzer
Biogeosciences, 16, 1675–1683, https://doi.org/10.5194/bg-16-1675-2019, https://doi.org/10.5194/bg-16-1675-2019, 2019
Short summary
Short summary
Ice nucleation particles (INPs) help ice form at temperatures as high as −4 °C and contribute to the formation of precipitation. Leaf litter contains a high concentration of INPs, but the organisms that produce them are unknown. Here, we cultured two bacteria and one fungus from leaf litter that produce INPs similar to those found in leaf litter. This suggests that leaf litter may be an important habitat of these organisms and supports a role of these organisms as producers of atmospheric INPs.
Nimrod Wieler, Hanan Ginat, Osnat Gillor, and Roey Angel
Biogeosciences, 16, 1133–1145, https://doi.org/10.5194/bg-16-1133-2019, https://doi.org/10.5194/bg-16-1133-2019, 2019
Short summary
Short summary
In stony deserts, when rocks are exposed to atmospheric conditions, they undergo weathering. The cavernous (honeycomb) weathering pattern is one of the most common, but it is still unclear exactly how it is formed. We show that microorganisms, which differ from the surrounding soil and dust, form biological crusts on exposed rock surfaces. These microbes secrete polymeric substances that mitigate weathering by reducing evaporation rates and, consequently, salt transport rates through the rock.
Yang Li, Zhaojun Wu, Xingchen Dong, Zifu Xu, Qixin Zhang, Haiyan Su, Zhongjun Jia, and Qingye Sun
Biogeosciences, 16, 573–583, https://doi.org/10.5194/bg-16-573-2019, https://doi.org/10.5194/bg-16-573-2019, 2019
Short summary
Short summary
This paper contributes to the study of bacterial carbon sequestration in mine tailings. Previous studies focused on carbonate mineral precipitation, while the role of autotrophs in carbon sequestration has been neglected. Carbon sequestration in two mine tailings treated with FeS2 was analyzed using 13C isotope labeling, pyrosequencing, and DNA SIP to identify carbon fixers. This paper is the first to investigate carbon sequestration by autotrophic groups in mine tailings.
Dong-Hun Lee, Jung-Hyun Kim, Yung Mi Lee, Alina Stadnitskaia, Young Keun Jin, Helge Niemann, Young-Gyun Kim, and Kyung-Hoon Shin
Biogeosciences, 15, 7419–7433, https://doi.org/10.5194/bg-15-7419-2018, https://doi.org/10.5194/bg-15-7419-2018, 2018
Short summary
Short summary
In this study, we provide first evidence of lipid biomarker patterns and phylogenetic identities of key microbes mediating anaerobic oxidation of methane (AOM) communities in active mud volcanoes (MVs) on the continental slope of the Canadian Beaufort Sea. Our lipid and 16S rRNA results indicate that archaea of the ANME-2c and ANME-3 clades are involved in AOM in the MVs investigated.
Joshua F. Dean, Jurgen R. van Hal, A. Johannes Dolman, Rien Aerts, and James T. Weedon
Biogeosciences, 15, 7141–7154, https://doi.org/10.5194/bg-15-7141-2018, https://doi.org/10.5194/bg-15-7141-2018, 2018
Short summary
Short summary
Lakes, rivers, ponds and streams are significant contributors of the greenhouse gas carbon dioxide to the atmosphere. This is partly due to the decomposition of plant and soil organic matter transported through these aquatic systems by microbial communities. In determining how vulnerable this organic material is to decomposition during aquatic transport, we show that standardized treatments in experiments can affect the way microbial communities behave and potentially the experimental outcome.
Xi Wen, Viktoria Unger, Gerald Jurasinski, Franziska Koebsch, Fabian Horn, Gregor Rehder, Torsten Sachs, Dominik Zak, Gunnar Lischeid, Klaus-Holger Knorr, Michael E. Böttcher, Matthias Winkel, Paul L. E. Bodelier, and Susanne Liebner
Biogeosciences, 15, 6519–6536, https://doi.org/10.5194/bg-15-6519-2018, https://doi.org/10.5194/bg-15-6519-2018, 2018
Short summary
Short summary
Rewetting drained peatlands may lead to prolonged emission of the greenhouse gas methane, but the underlying factors are not well described. In this study, we found two rewetted fens with known high methane fluxes had a high ratio of microbial methane producers to methane consumers and a low abundance of methane consumers compared to pristine wetlands. We therefore suggest abundances of methane-cycling microbes as potential indicators for prolonged high methane emissions in rewetted peatlands.
Kyle R. Frischkorn, Andreas Krupke, Cécile Guieu, Justine Louis, Mónica Rouco, Andrés E. Salazar Estrada, Benjamin A. S. Van Mooy, and Sonya T. Dyhrman
Biogeosciences, 15, 5761–5778, https://doi.org/10.5194/bg-15-5761-2018, https://doi.org/10.5194/bg-15-5761-2018, 2018
Short summary
Short summary
Trichodesmium is a keystone genus of marine cyanobacteria that is estimated to supply nearly half of the ocean’s fixed nitrogen, fuelling primary productivity and the cycling of carbon and nitrogen in the ocean. In our study we characterize Trichodesmium ecology across the western tropical South Pacific using gene and genome sequencing and geochemistry. We detected genes for phosphorus reduction, providing a mechanism for the noted importance of this organism in the ocean's phosphorus cycle.
Audrey Lallement, Ludovic Besaury, Elise Tixier, Martine Sancelme, Pierre Amato, Virginie Vinatier, Isabelle Canet, Olga V. Polyakova, Viatcheslay B. Artaev, Albert T. Lebedev, Laurent Deguillaume, Gilles Mailhot, and Anne-Marie Delort
Biogeosciences, 15, 5733–5744, https://doi.org/10.5194/bg-15-5733-2018, https://doi.org/10.5194/bg-15-5733-2018, 2018
Short summary
Short summary
The main objective of this work was to evaluate the potential degradation of phenol, a highly toxic pollutant, by cloud microorganisms. Phenol concentrations measured on five cloud samples collected at the PUY station in France were from 0.15 to 0.74 µg L−1. Metatranscriptomic analysis suggested that phenol could be biodegraded directly in clouds, likely by Gammaproteobacteria. A large screening showed that 93 % of 145 bacterial strains isolated from clouds were able to degrade phenol.
Sara J. Bender, Dawn M. Moran, Matthew R. McIlvin, Hong Zheng, John P. McCrow, Jonathan Badger, Giacomo R. DiTullio, Andrew E. Allen, and Mak A. Saito
Biogeosciences, 15, 4923–4942, https://doi.org/10.5194/bg-15-4923-2018, https://doi.org/10.5194/bg-15-4923-2018, 2018
Short summary
Short summary
Phaeocystis antarctica is an important phytoplankter of the Antarctic coastal environment where it dominates the early season bloom after sea ice retreat. Iron nutrition was found to be an important factor that results in Phaeocystis colony formation and a large restructuring of the proteome, including changes associated with the flagellate to colonial transition and adaptive responses to iron scarcity. Analysis of Phaeocystis proteins from the Ross Sea revealed the presence of both cell types.
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, https://doi.org/10.5194/bg-15-4215-2018, https://doi.org/10.5194/bg-15-4215-2018, 2018
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, https://doi.org/10.5194/bg-15-3893-2018, https://doi.org/10.5194/bg-15-3893-2018, 2018
Short summary
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.
Christian Nyrop Albers, Magnus Kramshøj, and Riikka Rinnan
Biogeosciences, 15, 3591–3601, https://doi.org/10.5194/bg-15-3591-2018, https://doi.org/10.5194/bg-15-3591-2018, 2018
Cited articles
Adl, S. M., Simpson, A. G. B., Lane, C. E., Lukeš, J., Bass, D., Bowser, S. S., Brown, M. W., Burki, F., Dunthorn, M., Hampl, V., Heiss, A., Hoppenrath, M., Lara, E., le Gall, L., Lynn, D. H., McManus, H., Mitchell, E. A. D., Mozley-Stanridge, S. E., Parfrey, L. W., Pawlowski, J., Rueckert, S., Shadwick, L., Schoch, C. L., Smirnov, A., and Spiegel, F. W.: The Revised Classification of Eukaryotes, J. Eukaryotic. Microbiol., 59, 429–514, https://doi.org/10.1111/j.1550-7408.2012.00644.x, 2012.
Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic. Acids. Res., 25, 3389–3402, https://doi.org/10.1093/nar/25.17.3389, 1997.
Azam, F. and Malfatti, F.: Microbial structuring of marine ecosystems, Nat. Rev. Microbiol., 5, 782–791, https://doi.org/10.1038/nrmicro1747, 2007.
Bachy, C., López-García, P., Vereshchaka, A., and Moreira, D.: Diversity and vertical distribution of microbial eukaryotes in the snow, sea ice and seawater near the north pole at the end of the polar night, Front. Microbiol., 2, 106, https://doi.org/10.3389/fmicb.2011.00106, 2011.
Barberán, A., Bates, S. T., Casamayor, E. O., and Fierer, N.: Using network analysis to explore co-occurrence patterns in soil microbial communities, ISME J., 6, 343–351, https://doi.org/10.1038/ismej.2011.119, 2011.
Berger, S. A. and Stamatakis, A.: Aligning short reads to reference alignments and trees, Bioinformatics, 27, 2068–2075, https://doi.org/10.1093/bioinformatics/btr320, 2011.
Bjorklund, K. R., Kruglikova, S. B., and Anderson, O. R.: Modern incursions of tropical Radiolaria into the Arctic Ocean, J. Micropalaeontol., 31, 139–158, https://doi.org/10.1144/0262-821X11-030, 2012.
Bråte, J., Klaveness, D., Rygh, T., Jakobsen, K. S., and Shalchian-Tabrizi, K.: Telonemia-specific environmental 18S rDNA PCR reveals unknown diversity and multiple marine-freshwater colonizations, BMC Microbiol., 10, 168, https://doi.org/10.1186/1471-2180-10-168, 2010.
Burki, F., Kudryavtsev, A., Matz, M. V., Aglyamova, G. V., Bulman, S., Fiers, M., Keeling, P. J., and Pawlowski, J.: Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists, BMC Evol. Biol., 10, 377, https://doi.org/10.1186/1471-2148-10-377, 2010.
Carmack, E. C.: The alpha/beta ocean distinction: A perspective on freshwater fluxes, convection, nutrients and productivity in high-latitude seas, Deep-Sea Res. Pt. II, 54, 2578–2598, https://doi.org/10.1016/j.dsr2.2007.08.018, 2007
Carmack, E. C. and Macdonald, R. W.: Oceanography of the Canadian shelf of the Beaufort Sea: a setting for marine life, Arctic, 55, 29–45, 2002.
Cavalier-Smith, T.: Protist phylogeny and the high-level classification of Protozoa, Europ. J. Protistol., 39, 338–348, https://doi.org/10.1078/0932-4739-00002, 2003.
Chaffron, S., Rehrauer, H., Pernthaler, J., and Mering, von, C.: A global network of coexisting microbes from environmental and whole-genome sequence data, Genome Res., 20, 947–959, https://doi.org/10.1101/gr.104521.109, 2010.
Comeau, A. M., Li, W. K. W., Tremblay, J.-É., Carmack, E. C., and Lovejoy, C.: Arctic Ocean Microbial Community Structure before and after the 2007 Record Sea Ice Minimum, PLoS ONE, 6, e27492, https://doi.org/10.1371/journal.pone.0027492, 2011.
Comeau, A. M., Philippe, B., Thaler, M., Gosselin, M., Poulin, M., and Lovejoy, C.: Protists in Arctic drift and land-fast sea ice, J. Phycol., 49, 229–240, https://doi.org/10.1111/jpy.12026, 2013.
Countway, P. D., Gast, R. J., Dennett, M. R., Savai, P., Rose, J. M., and Caron, D. A.: Distinct protistan assemblages characterize the euphotic zone and deep sea (2500 m) of the western North Atlantic (Sargasso Sea and Gulf Stream), Environ. Microbiol., 9, 1219–1232, https://doi.org/10.1111/j.1462-2920.2007.01243.x, 2007.
Cuvelier, M. L., Ortiz, A., Kim, E., Moehlig, H., Richardson, D. E., Heidelberg, J. F., Archibald, J. M., and Worden, A. Z.: Widespread distribution of a unique marine protistan lineage, Environ. Microbiol., 10, 1621–1634, https://doi.org/10.1111/j.1462-2920.2008.01580.x, 2008.
Del Campo, J. and Massana, R.: Emerging Diversity within Chrysophytes, Choanoflagellates and Bicosoecids Based on Molecular Surveys, Protist, 2011.
Demir-Hilton, E., Sudek, S., Cuvelier, M. L., Gentemann, C. L., Zehr, J. P., and Worden, A. Z.: Global distribution patterns of distinct clades of the photosynthetic picoeukaryote Ostreococcus, ISME J, 5, 1095–1107, https://doi.org/10.1038/ismej.2010.209, 2011.
Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C., and Knight, R.: UCHIME improves sensitivity and speed of chimera detection, Bioinformatics, 27, 2194–2200, https://doi.org/10.1093/bioinformatics/btr381, 2011.
Forest, A., Babin, M., Stemmann, L., Picheral, M., Sampei, M., Fortier, L., Gratton, Y., Bélanger, S., Devred, E., Sahlin, J., Doxaran, D., Joux, F., Ortega-Retuerta, E., Martín, J., Jeffrey, W. H., Gasser, B., and Carlos Miquel, J.: Ecosystem function and particle flux dynamics across the Mackenzie Shelf (Beaufort Sea, Arctic Ocean): an integrative analysis of spatial variability and biophysical forcings, Biogeosciences, 10, 2833–2866, https://doi.org/10.5194/bg-10-2833-2013, 2013.
Galand, P. E., Casamayor, E. O., Kirchman, D. L., and Lovejoy, C.: Ecology of the rare microbial biosphere of the Arctic Ocean, Proc. Natl. Acad. Sci. USA, 106, 22427–22432, https://doi.org/10.1073/pnas.0908284106, 2009a.
Galand, P. E., Potvin, M., Casamayor, E. O., and Lovejoy C.: Hydrography shapes bacterial biogeography of the deep Arctic Ocean, ISME J., 4, 564–576, https://doi.org/10.1038/ismej.2009.134, 2009b.
Ghiglione, J. F. and Murray, A. E.: Pronounced summer to winter differences and higher wintertime richness in coastal Antarctic marine bacterioplankton, Environ. Microbiol., 14, 617–629, https://doi.org/10.1111/j.1462-2920.2011.02601.x, 2011.
Giovannoni, S. J. and Vergin, K. L.: Seasonality in ocean microbial communities, Science, 335, 671–676, https://doi.org/10.1126/science.1198078, 2012.
Gómez, F., Moreira, D., Benzerara, K., and López-García, P.: Solenicola setigera is the first characterized member of the abundant and cosmopolitan uncultured marine stramenopile group MAST-3, Environ. Microbiol., 13, 193–202, https://doi.org/10.1111/j.1462-2920.2010.02320.x, 2011.
Gouy, M., Guindon, S., and Gascuel, O.: SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building, Mol. Biol. Evol., 27, 221–224, https://doi.org/10.1093/molbev/msp259, 2010.
Hamady, M., Lozupone, C., and Knight, R.: Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data, ISME J., 4, 17–27, https://doi.org/10.1038/ismej.2009.97, 2010.
Hamilton, A. K., Lovejoy, C., Galand, P. E., and Ingram, R. G.: Water masses and biogeography of picoeukaryote assemblages in a cold hydrographically complex system, Limnol. Oceanogr., 53, 922–935, 2008.
Hawlitschek, O., Hendrich, L., Espeland, M., Toussaint, E. F. A., Genner, M. J., and Balke, M.: Pleistocene climate change promoted rapid diversification of aquatic invertebrates in Southeast Australia, BMC Evol. Biol., 12, 142, https://doi.org/10.1186/1471-2148-12-142, 2012.
Ikävalko, J. and Gradinger, R.: Flagellates and heliozoans in the Greenland Sea ice studied alive using light microscopy, Polar Biol., 17, 473–481, https://doi.org/10.1007/s003000050145, 1997.
Jackson, J. M., Williams, W. J., and Carmack, E. C.: Winter sea-ice melt in the Canada Basin, Arctic Ocean, Geophys. Res. Lett., 39, L03603, https://doi.org/10.1029/2011GL050219, 2012.
Johnson, Z. I., Zinser, E. R., Coe, A., McNulty, N. P., Woodward, E. M. S., and Chisholm, S. W.: Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients, Science, 311, 1737–1740, https://doi.org/10.1126/science.1118052, 2006.
Jones, S. E. and Lennon, J. T.: Dormancy contributes to the maintenance of microbial diversity, Proc Natl Acad Sci USA, 107, 5881–5886, https://doi.org/10.1073/pnas.0912765107, 2010.
Jürgens, K. and Massana, R.: Protist grazing on marine bacterioplankon, edited by: Kirchman, D. L., Microbial Ecology of the Oceans, second edition, John Wiley & Sons, Inc., New York, USA, 383–441, 2008.
Kim, E., Harrison, J. W., Sudek, S., Jones, M. D. M., Wilcox, H. M., Richards, T. A., Worden, A. Z., and Archibald, J. M.: Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life, Proc. Natl. Acad. Sci. USA, 108, 1496–1500, https://doi.org/10.1073/pnas.1013337108, 2011.
King, N., Young ,S. L., Abedin, M., Carr, M., and Leadbeater, B. S. C.: The choanoflagellates: heterotrophic nanoflagellates and sister group of the metazoa, Cold Spring Harb. Protoc., 4, https://doi.org/10.1101/pdb.emo116, 2009.
Kiørboe, T.: How zooplankton feed: mechanisms, traits and trade-offs, Biol. Rev., 86, 311–339, https://doi.org/10.1111/j.1469-185X.2010.00148.x, 2011.
Li, W. K. W., McLaughlin, F. A., Lovejoy, C., and Carmack, E. C.: Smallest algae thrive as the Arctic Ocean freshens, Science, 326, p. 539, https://doi.org/10.1126/science.1179798, 2009.
Lin, Y.-C., Campbell, T., Chung, C.-C., Gong, G.-C., Chiang, K.-P., and Worden, A. Z.: Distribution patterns and phylogeny of marine stramenopiles in the north pacific ocean, Appl. Environ. Microbiol., 78, 3387–3399, https://doi.org/10.1128/AEM.06952-11, 2012.
Logares, R., Audic, S., Santini, S., Pernice, M. C., de Vargas, C., and Massana, R.: Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing, ISME J, 6, 1823–1833, https://doi.org/10.1038/ismej.2012.36, 2012.
Lovejoy, C. and Potvin, M.: Microbial eukaryotic distribution in a dynamic Beaufort Sea and the Arctic Ocean, J. Plank. Res., 33, 431–444, https://doi.org/10.1093/plankt/fbq124, 2011.
Lovejoy, C., Legendre, L., Martineau, M.-J., Bâcle, J., and von Quillfeldt, C. H.: Distribution of phytoplankton and other protists in the North Water, Deep-Sea Res. Pt. II, 49, 5027–5047, https://doi.org/10.1016/S0967-0645(02)00176-5, 2002.
Lovejoy, C., Massana, R., and Pedrós-Alió, C.: Diversity and distribution of marine microbial eukaryotes in the Arctic Ocean and adjacent seas, Appl. Environ. Microbiol., 72, 3085–3095, https://doi.org/10.1128/AEM.72.5.3085-3095.2006, 2006.
Lovejoy, C., Vincent, W. F., Bonilla, S., Roy, S., Martineau, M.-J., Terrado, R., Potvin, M., Massana, R., and Pedrós-Alió, C.: Distribution, phylogeny, and growth of cold-adapted picoprasinophytes in Arctic seas, J. Phycol., 43, 78–89, https://doi.org/10.1111/j.1529-8817.2006.00310.x, 2007.
Lozupone, C. and Knight, R.: UniFrac: a new phylogenetic method for comparing microbial communities, Appl. Environ. Microbiol., 71, 8228–8235, https://doi.org/10.1128/AEM.71.12.8228-8235.2005, 2005.
Majaneva, M., Rintala, J.-M., Piisilä, M., Fewer, D. P., and Blomster, J.: Comparison of wintertime eukaryotic community from sea ice and open water in the Baltic Sea, based on sequencing of the 18S rRNA gene, Polar Biol., 35, 875–889, https://doi.org/10.1007/s00300-011-1132-9, 2011.
Marchant, H. J. and Scott, F. J.: Uptake of sub-micrometre particles and dissolved organic material by Antarctic choanoflagellates, Mar. Ecol. Prog. Ser., 92, 59–64, https://doi.org/10.3354/meps092059, 1993.
Martin, J., Tremblay, J. É., Gagnon, J., Tremblay, G., Lapoussière, A., Jose, C., Poulin, M., Gosselin, M., Gratton, Y., and Michel, C.: Prevalence, structure and properties of subsurface chlorophyll maxima in Canadian Arctic waters, Mar. Ecol. Prog. Ser., 412, 69–84, https://doi.org/10.3354/meps08666, 2010.
Massana, R.: Eukaryotic picoplankton in surface oceans, Annu. Rev. Microbiol., 65, 91–110, https://doi.org/10.1146/annurev-micro-090110-102903, 2011.
Massana, R., Castresana, J., Balagué, V., Guillou, L., Romari, K., Groisillier, A., Valentin, K., and Pedrós-Alió, C.: Phylogenetic and Ecological Analysis of Novel Marine Stramenopiles, Appl. Environ. Microbiol., 70, 3528–3534, https://doi.org/10.1128/AEM.70.6.3528-3534.2004, 2004.
Massana, R., Terrado, R., Forn, I., Lovejoy, C., and Pedrós-Alió, C.: Distribution and abundance of uncultured heterotrophic flagellates in the world oceans, Environ. Microbiol., 8, 1515–1522, https://doi.org/10.1111/j.1462-2920.2006.01042.x, 2006.
Matsen, F. A., Kodner, R. B., and Armbrust, E. V.: pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree, BMC Bioinformatics, 11, 538, https://doi.org/10.1186/1471-2105-11-538, 2010.
Matsuoka, A., Huot, Y., Shimada, K., Saitoh, S.-I., and Babin, M.: Bio-optical characteristics of the western Arctic Ocean: implications for ocean color algorithms, Can. J. Remote Sens., 33, 503–518, https://doi.org/10.5589/m07-059, 2007.
Matsuoka, A., Bricaud, A., Benner, R., Para, J., Sempéré, R., Prieur, L., Bélanger, S., and Babin, M.: Tracing the transport of colored dissolved organic matter in water masses of the Southern Beaufort Sea: relationship with hydrographic characteristics, Biogeosciences, 9, 925–940, https://doi.org/10.5194/bg-9-925-2012, 2012.
McLaughlin, F., Shimada, K., Carmack, E., Itoh, M., and Nishino, S.: The hydrography of the southern Canada Basin, 2002, Polar Biol., 28, 182–189, https://doi.org/10.1007/s00300-004-0701-6, 2005.
Monier, A., Claverie, J.-M., and Ogata, H.: Taxonomic distribution of large DNA viruses in the sea, Genome Biol., 9, R106, https://doi.org/10.1186/gb-2008-9-7-r106, 2008.
Not, F., Valentin, K., Romari, K., Lovejoy, C., Massana, R., Tobe, K., Vaulot, D., and Medlin, L. K.: Picobiliphytes: a marine picoplanktonic algal group with unknown affinities to other eukaryotes, Science, 315, 253–255, https://doi.org/10.1126/science.1136264, 2007.
Piwosz, K. and Pernthaler, J.: Seasonal population dynamics and trophic role of planktonic nanoflagellates in coastal surface waters of the Southern Baltic Sea, Environ. Microbiol., 12, 364–377, https://doi.org/10.1111/j.1462-2920.2009.02074.x, 2010.
Poulin, F. J. and Franks, P. J. S.: Size-structured planktonic ecosystems: constraints, controls and assembly instructions, J. Plankt. Res., 32, 1121–1130, https://doi.org/10.1093/plankt/fbp145, 2010.
Price, M. N., Dehal, P. S., and Arkin, A. P.: FastTree 2–approximately maximum-likelihood trees for large alignments, PLoS ONE, 5, e9490, https://doi.org/10.1371/journal.pone.0009490, 2010.
Pruesse, E., Quast, C., Knittel, K., Fuchs, B. M., Ludwig, W., Peplies, J., and Gloeckner, F. O.: SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB, Nucleic Acids Res, 35, 7188–7196, https://doi.org/10.1093/nar/gkm864, 2007.
Rainville, L., Lee, C. M., and Woodgate, R. A.: Impact of Wind-Driven Mixing in the Arctic Ocean, Oceanography, 24, 136–145, https://doi.org/10.5670/oceanog.2011.65, 2011.
Riedel, A., Michel, C., and Gosselin M.: Seasonal study of sea-ice exopolymeric substances on the Mackenzie shelf: implications for transport of sea-ice bacteria and algae, Aq. Microb. Ecol., 45, 195–206, https://doi.org/10.3354/ame045195, 2006.
Rodríguez-Martínez, R., Labrenz, M., del Campo, J., Forn, I., Jürgens, K., and Massana, R.: Distribution of the uncultured protist MAST-4 in the Indian Ocean, Drake Passage and Mediterranean Sea assessed by real-time quantitative PCR, Environ. Microbiol., 11, 397–408, https://doi.org/10.1111/j.1462-2920.2008.01779.x, 2009.
Ró\.za\'nska, M., Poulin, M., and Gosselin, M.: Protist entrapment in newly formed sea ice in the Coastal Arctic Ocean, J. Mar. Sys., 74, 887–901, https://doi.org/10.1016/j.jmarsys.2007.11.009, 2008.
Russell, F. S.: The vertical distribution of plankton in the sea, Biol. Rev., 2, 213–262, https://doi.org/10.1111/j.1469-185X.1927.tb00878.x, 1927.
Sazhin, A. F., Rat'kova, T. N., and Kosobokova, K. N.: Inhabitants of the White Sea coastal ice during the early spring period, Russ. Acad. Sci. Oceanol., 44, 82–89, 2004.
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, Appl. Environ. Microbiol., 75, 7537–7541, https://doi.org/10.1128/AEM.01541-09, 2009.
Seenivasan, R., Sausen, N., Medlin, L. K., and Melkonian, M.: Picomonas judraskeda Gen. Et Sp. Nov.: The First Identified Member of the Picozoa Phylum Nov., a Widespread Group of Picoeukaryotes, Formerly Known as "Picobiliphytes", PLoS ONE, 8, e59565, https://doi.org/10.1371/journal.pone.0059565, 2013.
Shalchian-Tabrizi, K., Kauserud, H., Massana, R., Klaveness, D., and Jakobsen, K. S.: Analysis of environmental 18S ribosomal RNA sequences reveals unknown diversity of the cosmopolitan phylum Telonemia, Protist, 158, 173–180, https://doi.org/10.1016/j.protis.2006.10.003, 2007.
Sherr, E. B. and Sherr, B. F.: Bacterivory and herbivory – Key roles of phagotrophic protists in pelagic food webs, Microb. Ecol., 28, 223–235, https://doi.org/10.1007/BF00166812, 1994.
Sherr, E. B. and Sherr, B. F.: Capacity of herbivorous protists to control initiation and development of mass phytoplankton blooms, Aquat. Microb. Ecol., 57, 253–262, https://doi.org/10.3354/ame01358, 2009.
Sogin, M. L., Morrison, H. G., Huber, J. A., Mark Welch, D., 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, https://doi.org/10.1073/pnas.0605127103, 2006.
Stamatakis, A.: RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, 22, 2688–2690, https://doi.org/10.1093/bioinformatics/btl446, 2006.
Stoupin, D., Kiss, A. K., Arndt, H., Shatilovich, A. V., Gilichinsky, D. A., and Nitsche, F.: Cryptic diversity within the choanoflagellate morphospecies complex Codosiga botrytis – Phylogeny and morphology of ancient and modern isolates, Europ. J. Protistol., 48, 263–273, https://doi.org/10.1016/j.ejop.2012.01.004, 2012.
Terrado, R., Lovejoy, C., Massana, R., and Vincent, W. F.: Microbial food web responses to light and nutrients beneath the coastal Arctic Ocean sea ice during the winter–spring transition, J. Mar. Syst., 74, 964–977, https://doi.org/10.1016/j.jmarsys.2007.11.001, 2008.
Terrado, R., Vincent, W. F., and Lovejoy, C.: Mesopelagic protists: diversity and succession in a coastal Arctic ecosystem, Aquat. Microb. Ecol., 56, 25–40, https://doi.org/10.3354/ame01327, 2009.
Terrado, R., Medrinal, E., Dasilva, C., Thaler, M., Vincent, W. F., and Lovejoy, C.: Protist community composition during spring in an Arctic flaw lead polynya, Polar Biol., 34, 1901–1914, https://doi.org/10.1007/s00300-011-1039-5, 2011.
Thaler, M. and Lovejoy, C.: Distribution and diversity of a protist predator Cryothecomonas (Cercozoa) in Arctic marine waters, J. Eukaryot. Microbiol., 59, 291–299, https://doi.org/10.1111/j.1550-7408.2012.00631.x, 2012.
Tremblay, G., Belzile, C., Gosselin, M., Poulin, M., Roy, S., and Tremblay, J. É.: Late summer phytoplankton distribution along a 3500 km transect in Canadian Arctic waters: strong numerical dominance by picoeukaryotes, Aquat. Microb. Ecol., 54, 55–70, https://doi.org/10.3354/ame01257, 2009.
Treusch, A. H., Demir-Hilton, E., Vergin, K. L., Worden, A. Z., Carlson, C. A., Donatz, M. G., Burton, R. M., and Giovannoni, S. J.: Phytoplankton distribution patterns in the northwestern Sargasso Sea revealed by small subunit rRNA genes from plastids, ISME J., 6, 481–492, https://doi.org/10.1038/ismej.2011.117, 2011.
Tsubouchi, T., Bacon, S., Naveira Garabato, A. C., Aksenov, Y., Laxon, S. W., Fahrbach, E., Beszczynska-Möller, A., Hansen, E., Lee, C. M., and Ingvaldsen, R. B.: The Arctic Ocean in summer: A quasi-synoptic inverse estimate of boundary fluxes and water mass transformation, J. Geophys. Res., 117, C01024, https://doi.org/10.1029/2011JC007174, 2012.
Vørs, N.: Heterotrophic amoebae, flagellates and heliozoa from Arctic marine waters (North West Territories, Canada and West Greenland), Polar Biol., 13, 113–126, https://doi.org/10.1007/BF00238544, 1993.
Waleron, M., Waleron, K., Vincent, W. F., and Wilmotte, A.: Allochthonous inputs of riverine picocyanobacteria to coastal waters in the Arctic Ocean, FEMS Microbiol. Ecol., 59, 356–365, https://doi.org/10.1111/j.1574-6941.2006.00236.x, 2006.
Werner, I., Ikävalko, J., and Schünemann, H.: Sea-ice algae in Arctic pack ice during late winter, Polar Biol., 30, 1493–1504, https://doi.org/10.1007/s00300-007-0310-2, 2007.
Wickham, H.: ggplot2, Springer-Verlag New York Inc, 2009.
Wilkins, D., Lauro, F. M., Williams, T. J., Demaere, M. Z., Brown, M. V., Hoffman, J. M., Andrews-Pfannkoch, C., McQuaid, J. B., Riddle, M. J., Rintoul, S. R., and Cavicchioli, R.: Biogeographic partitioning of Southern Ocean microorganisms revealed by metagenomics, Environ. Microbiol., 15, 1462–2920, https://doi.org/10.1111/1462-2920.12035, 2012.
Yoon, H. S., Price, D. C., Stepanauskas, R., Rajah, V. D., Sieracki, M. E., Wilson, W. H., Yang, E. C., Duffy, S., and Bhattacharya, D.: Single-cell genomics reveals organismal interactions in uncultivated marine protists, Science, 332, 714–717, https://doi.org/10.1126/science.1203163, 2011.
Altmetrics
Final-revised paper
Preprint