Articles | Volume 8, issue 9
https://doi.org/10.5194/bg-8-2785-2011
© Author(s) 2011. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
https://doi.org/10.5194/bg-8-2785-2011
© Author(s) 2011. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
Research article
| 
29 Sep 2011
Research article |
| 29 Sep 2011
Is the distribution of Prochlorococcus and Synechococcus ecotypes in the Mediterranean Sea affected by global warming?
D. Mella-Flores
UPMC-Université Paris 06, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
CNRS, Observatoire Océanologique, UMR7144, Groupe Plancton Océanique, 29680 Roscoff, France
S. Mazard
Dept. Chemistry and Biomolecular Science, Macquarie University, North Ryde, NSW 2109, Australia
School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
F. Humily
UPMC-Université Paris 06, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
CNRS, Observatoire Océanologique, UMR7144, Groupe Plancton Océanique, 29680 Roscoff, France
F. Partensky
UPMC-Université Paris 06, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
CNRS, Observatoire Océanologique, UMR7144, Groupe Plancton Océanique, 29680 Roscoff, France
F. Mahé
UPMC-Université Paris 06, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
CNRS, Observatoire Océanologique, UMR7144, Groupe Plancton Océanique, 29680 Roscoff, France
L. Bariat
CNRS/INSU and UPMC-Université Paris 06, Laboratoire Arago, UMS2348, Observatoire Océanologique, 66651 Banyuls-sur-mer, France
C. Courties
CNRS/INSU and UPMC-Université Paris 06, Laboratoire Arago, UMS2348, Observatoire Océanologique, 66651 Banyuls-sur-mer, France
D. Marie
UPMC-Université Paris 06, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
CNRS, Observatoire Océanologique, UMR7144, Groupe Plancton Océanique, 29680 Roscoff, France
J. Ras
CNRS and UPMC-Université Paris 06, UMR7093, Laboratoire d'Océanographie de Villefranche, 06234 Villefranche-sur-mer, France
R. Mauriac
Laboratoire d'océanographie physique et biogéochimique, Centre d'océanologie de Marseille, case 901, campus de Luminy, 13288 Marseille cedex 09, France
C. Jeanthon
UPMC-Université Paris 06, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
CNRS, Observatoire Océanologique, UMR7144, Groupe Plancton Océanique, 29680 Roscoff, France
E. Mahdi Bendif
UPMC-Université Paris 06, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
CNRS, Observatoire Océanologique, UMR7144, Groupe Plancton Océanique, 29680 Roscoff, France
M. Ostrowski
Dept. Chemistry and Biomolecular Science, Macquarie University, North Ryde, NSW 2109, Australia
School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
D. J. Scanlan
School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
L. Garczarek
UPMC-Université Paris 06, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
CNRS, Observatoire Océanologique, UMR7144, Groupe Plancton Océanique, 29680 Roscoff, France
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Han Zhang, Guangming Mai, Weicheng Luo, Meng Chen, Ran Duan, and Tuo Shi
Biogeosciences, 21, 2529–2546, https://doi.org/10.5194/bg-21-2529-2024, https://doi.org/10.5194/bg-21-2529-2024, 2024
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We report taxon-specific biogeography of N2-fixing microbes (diazotrophs) driven by Kuroshio intrusion (Kl) into the South China Sea. We show that the composition and distribution of distinct diazotrophic taxa shift with Kl-induced variations in physicochemical parameters of seawater and that Kl shapes diazotrophic community primarily as a stochastic process. This study thus has implications for the distribution of diazotrophs in a future warming ocean, as Kls are projected to intensify.
Celina Rebeca Valença, Luc Beaufort, Gustaaf Marinus Hallegraeff, and Marius Nils Müller
Biogeosciences, 21, 1601–1611, https://doi.org/10.5194/bg-21-1601-2024, https://doi.org/10.5194/bg-21-1601-2024, 2024
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Coccolithophores contribute to the global carbon cycle and their calcite structures (coccoliths) are used as a palaeoproxy to understand past oceanographic conditions. Here, we compared three frequently used methods to estimate coccolith mass from the model species Emiliania huxleyi and the results allow for a high level of comparability between the methods, facilitating future comparisons and consolidation of mass changes observed from ecophysiological and biogeochemical studies.
Ralf Conrad and Peter Claus
Biogeosciences, 21, 1161–1172, https://doi.org/10.5194/bg-21-1161-2024, https://doi.org/10.5194/bg-21-1161-2024, 2024
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Knowledge of carbon isotope fractionation is important for the assessment of the pathways involved in the degradation of organic matter. Formate is an important intermediate during this process. It was mainly converted to carbon dioxide and acetate both in the presence and absence of sulfate. Methane was only a minor product and was mainly formed from the acetate. The acetate was depleted in the heavy carbon atom relative to formate, while the carbon dioxide was enriched.
Adrian Barry-Sosa, Madison K. Flint, Justin C. Ellena, Jonathan B. Martin, and Brent C. Christner
EGUsphere, https://doi.org/10.5194/egusphere-2024-49, https://doi.org/10.5194/egusphere-2024-49, 2024
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This study examined springs in North Central Florida focusing on how interactions between the surface and subsurface affected the properties of groundwater microbes. We found that microbes reproduced at rates that greatly exceed those documented for any other aquifer. Although the groundwater discharged to spring runs contains low concentrations of nutrients, our results indicate that microbes have access to sources of energy and produce new cells at rates similar to surface water bodies.
Mutong Niu, Shu Huang, Wei Hu, Yajie Wang, Wanyun Xu, Wan Wei, Qiang Zhang, Zihan Wang, Donghuan Zhang, Rui Jin, Libin Wu, Junjun Deng, Fangxia Shen, and Pingqing Fu
Biogeosciences, 20, 4915–4930, https://doi.org/10.5194/bg-20-4915-2023, https://doi.org/10.5194/bg-20-4915-2023, 2023
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Sugar compounds in air can trace the source of bioaerosols that affect public health and climate. In rural north China, we observed increased fungal activity at night and less variable bacterial community diversity. Certain night-increasing sugar compounds were more closely related to fungi than bacteria. The fungal community greatly influenced sugar compounds, while bacteria played a limited role. Caution is advised when using sugar compounds to trace airborne microbes, particularly bacteria.
Lucia Fuchslueger, Emily F. Solly, Alberto Canarini, and Albert C. Brangarí
EGUsphere, https://doi.org/10.5194/egusphere-2023-2975, https://doi.org/10.5194/egusphere-2023-2975, 2023
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This overview features empirical, conceptual, and modelling-based studies of the special issue ‘Global change effects on terrestrial biogeochemistry at the plant-soil interface’, summarizing key findings on plants responses to eCO2, soil organisms responses to warming, impacts on soil organic carbon, nitrogen, and mineral nutrient cycling and water level changes affecting greenhouse gas emissions, from the arctic to tropics, crucial for deciphering feedbacks to global change.
David A. Hutchins, Fei-Xue Fu, Shun-Chung Yang, Seth G. John, Stephen J. Romaniello, M. Grace Andrews, and Nathan G. Walworth
Biogeosciences, 20, 4669–4682, https://doi.org/10.5194/bg-20-4669-2023, https://doi.org/10.5194/bg-20-4669-2023, 2023
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Applications of the mineral olivine are a promising means to capture carbon dioxide via coastal enhanced weathering, but little is known about the impacts on important marine phytoplankton. We examined the effects of olivine dissolution products on species from three major phytoplankton groups: diatoms, coccolithophores, and cyanobacteria. Growth and productivity were generally either unaffected or stimulated, suggesting the effects of olivine on key phytoplankton are negligible or positive.
Ze Ren, Shudan Ye, Hongxuan Li, Xilei Huang, and Luyao Chen
Biogeosciences, 20, 4241–4258, https://doi.org/10.5194/bg-20-4241-2023, https://doi.org/10.5194/bg-20-4241-2023, 2023
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Permafrost thaw initiates thermokarst landscape formation, resulting in distinct new habitats, including degraded permafrost soil, thermokarst lake sediments, and lake water. These distinct habitats harbored differentiated bacterial communities that originated from the same source, differing in diversity, assembly mechanisms, and environmental influences. The results imply ecological consequences of permafrost degradation in the face of further climate change.
Caitlyn A. Hall, Andre van Turnhout, Edward Kavazanjian Jr., Leon A. van Paassen, and Bruce Rittmann
Biogeosciences, 20, 2903–2917, https://doi.org/10.5194/bg-20-2903-2023, https://doi.org/10.5194/bg-20-2903-2023, 2023
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Earthquake-induced soil liquefaction poses a significant global threat. Microbially induced desaturation and precipitation (MIDP) via denitrification is a potentially sustainable, non-disruptive bacteria-driven ground improvement technique under existing structures. We developed a next-generation biogeochemical model to understand and predict the behavior of MIDP in the natural environment to design field-based hazard mitigation treatments.
Juan Pablo Almeida, Lorenzo Menichetti, Alf Ekblad, Nicholas P. Rosenstock, and Håkan Wallander
Biogeosciences, 20, 1443–1458, https://doi.org/10.5194/bg-20-1443-2023, https://doi.org/10.5194/bg-20-1443-2023, 2023
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In forests, trees allocate a significant amount of carbon belowground to support mycorrhizal symbiosis. In northern forests nitrogen normally regulates this allocation and consequently mycorrhizal fungi growth. In this study we demonstrate that in a conifer forest from Sweden, fungal growth is regulated by phosphorus instead of nitrogen. This is probably due to an increase in nitrogen deposition to soils caused by decades of human pollution that has altered the ecosystem nutrient regime.
Yong Zhang, Yong Zhang, Shuai Ma, Hanbing Chen, Jiabing Li, Zhengke Li, Kui Xu, Ruiping Huang, Hong Zhang, Yonghe Han, and Jun Sun
Biogeosciences, 20, 1299–1312, https://doi.org/10.5194/bg-20-1299-2023, https://doi.org/10.5194/bg-20-1299-2023, 2023
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We found that increasing light intensity compensates for the negative effects of low phosphorus (P) availability on cellular protein and nitrogen contents. Reduced P availability, increasing light intensity, and ocean acidification act synergistically to increase cellular contents of carbohydrate and POC and the allocation of POC to carbohydrate. These regulation mechanisms in Emiliania huxleyi could provide vital information for evaluating carbon cycle in marine ecosystems under global change.
Beatriz Gill-Olivas, Jon Telling, Mark Skidmore, and Martyn Tranter
Biogeosciences, 20, 929–943, https://doi.org/10.5194/bg-20-929-2023, https://doi.org/10.5194/bg-20-929-2023, 2023
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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 sulfide 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.
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
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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
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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
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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
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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
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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
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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.
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
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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
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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
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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
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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
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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
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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
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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
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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 Hager, 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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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Foraminifera are unicellular marine organisms that play an important role in the marine element cycle. Changes of environmental parameters such as salinity or temperature have a significant impact on the faunal assemblages. Our experiments show that 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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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.
Cited articles
Ahlgren, N. A. and Rocap, G.: Culture isolation and culture-independent clone libraries reveal new marine Synechococcus ecotypes with distinctive light and N physiologies, Appl. Environ. Microbiol., 72, 7193–7204, 2006.
Amann, R. I., Krumholz, L., and Stahl, D. A.: Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic and environmental studies in microbiology, J. Bacteriol., 172, 762–770, 1990.
Belkin, I. M.: Rapid warming of large marine ecosystems, Prog. Oceanogr., 81, 207–213, 2009.
Bertilsson, S., Berglund, O., Karl, D. M., and Chisholm, S. W.: Elemental composition of marine Prochlorococcus and Synechococcus: Implications for the ecological stoichiometry of the sea, Limnol. Oceanogr., 48, 1721–1731, 2003.
Bianchi, C. N.: Biodiversity issues for the forthcoming tropical Mediterranean Sea, Hydrobiologia, 580, 7–21, 2007.
Bonnet, S., Guieu, C., Chiaverini, J., Ras, J., and Stock, A.: Impact of atmospheric inputs on the autotrophic communities in a low nutrient low chlorophyll system, Limnol. Oceanogr., 50, 1810–1819, 2005.
Bouman, H. A., Ulloa, O., Scanlan, D. J., Zwirglmaier, K., Li, W. K., Platt, T., Stuart, V., Barlow, R., Leth, O., Clementson, L., Lutz, V., Fukasawa, M., Watanabe, S., and Sathyendranath, S.: Oceanographic basis of the global surface distribution of Prochlorococcus ecotypes, Science, 312, 918–921, 2006.
Brown, M. V. and Fuhrman, J. A.: Marine bacterial microdiversity as revealed by internal transcribed spacer analysis, Aquat. Microb. Ecol., 41, 15–23, 2005.
Campbell, L., Nolla, H. A., and Vaulot, D.: The importance of Prochlorococcus to community structure in the central North Pacific Ocean, Limnol. Oceanogr., 39, 954-961, 1994.
Campbell, L., Liu, H. B., Nolla, H. A., and Vaulot, D.: Annual variability of phytoplankton and bacteria in the subtropical North Pacific Ocean at Station ALOHA during the 1991-1994 ENSO event, Deep Sea Res. Pt. I, 44, 167–192, 1997.
Chen, F., Wang, K., Kan, J., Suzuki, M. T., and Wommack, K. E.: Diverse and unique picocyanobacteria in Chesapeake Bay, revealed by 16S-23S rRNA internal transcribed spacer sequences, Appl. Environ. Microbiol., 72, 2239–2243, 2006.
Choi, D. H. and Noh, J. H.: Phylogenetic diversity of Synechococcus strains isolated from the East China Sea and the East Sea, FEMS Microbiol. Ecol., 69, 439–448, 2009.
Coleman, M. L. and Chisholm, S. W.: Code and context: Prochlorococcus as a model for cross-scale biology, Trends Microbiol., 15, 399–407, 2007.
Coll, M., Piroddi, C., Steenbeek, J., Kaschner, K., Ben Rais Lasram, F., Aguzzi, J., Ballesteros, E., Bianchi, C. N., Corbera, J., Dailianis, T., Danovaro, R., Estrada, M., Froglia, C., Galil, B. S., Gasol, J. M., Gertwagen, R., Gil, J., Guilhaumon, F., Kesner-Reyes, K., Kitsos, M. S., Koukouras, A., Lampadariou, N., Laxamana, E., Lopez-Fe de la Cuadra, C. M., Lotze, H. K., Martin, D., Mouillot, D., Oro, D., Raicevich, S., Rius-Barile, J., Saiz-Salinas, J. I., San Vicente, C., Somot, S., Templado, J., Turon, X., Vafidis, D., Villanueva, R., and Voultsiadou, E.: The biodiversity of the Mediterranean Sea: estimates, patterns, and threats, PLoS One, 5, e11842, 2010.
Crombet, Y., Leblanc, K., Quéguiner, B., Moutin, T., Rimmelin, P., Ras, J., Claustre, H., Leblond, N., Oriol, L., and Pujo-Pay, M.: Deep silicon maxima in the stratified oligotrophic Mediterranean Sea, Biogeosciences, 8, 459–475, https://doi.org/10.5194/bg-8-459-2011, 2011.
D'Ortenzio, F. and Ribera d'Alcalà, M.: On the trophic regimes of the Mediterranean Sea: a satellite analysis, Biogeosciences, 6, 139–148, https://doi.org/10.5194/bg-6-139-2009, 2009.
Dufresne, A., Ostrowski, M., Scanlan, D. J., Garczarek, L., Mazard, S., Palenik, B. P., Paulsen, I. T., Tandeau de Marsac, N., Wincker, P., Dossat, C., Ferriera, S., Johnson, J., Post, A. F., Hess, W. R., and Partensky, F.: Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria, Genome Biol., 9, R90, 2008.
DuRand, M. D., Olson, R. J., and Chisholm, S. W.: Phytoplankton population dynamics at the Bermuda Atlantic Time-series station in the Sargasso Sea, Deep Sea Res. Pt. II, 48, 1983–2003, 2001.
Eguchi, M., Ostrowski, M., Fegatella, F., Bowman, J., Nichols, D., Nishino, T., and Cavicchioli, R.: Sphingomonas alaskensis strain AFO1, an abundant oligotrophic ultramicrobacterium from the North Pacific, Appl. Environ. Microbiol., 67, 4945–4954, 2001.
Feingersch, R., Suzuki, M. T., Shmoish, M., Sharon, I., Sabehi, G., Partensky, F., and Béjà, O.: Microbial community genomics in eastern Mediterranean Sea surface waters, ISME J., 4, 78–87, 2010.
Felsenstein, J.: PHYLIP – Phylogeny inference package (version 3.2), Cladistics, 5, 164–166, 1989.
Fuller, N. J., Marie, D., Partensky, F., Vaulot, D., Post, A. F., and Scanlan, D. J.: Clade-specific 16S ribosomal DNA oligonucleotides reveal the predominance of a single marine Synechococcus clade throughout a stratified water column in the Red Sea, Appl. Environ. Microbiol., 69, 2430–2443, 2003.
Fuller, N. J., West, N. J., Marie, D., Yallop, M., Rivlin, T., Post, A. F., and Scanlan, D. J.: Dynamics of community structure and phosphate status of picocyanobacterial populations in the Gulf of Aqaba, Red Sea, Limnol. Oceanogr., 50, 363–375, 2005.
Fuller, N. J., Tarran, G. A., Yallop, M., Orcutt, K. M., and Scanlan, D. J.: Molecular analysis of picocyanobacterial community structure along an Arabian Sea transect reveals distinct spatial separation of lineages, Limnol. Oceanogr., 51, 2515–2526, 2006.
Garczarek, L., Dufresne, A., Rousvoal, S., West, N. J., Mazard, S., Marie, D., Claustre, H., Raimbault, P., Post, A. F., Scanlan, D. J., and Partensky, F.: High vertical and low horizontal diversity of Prochlorococcus ecotypes in the Mediterranean Sea in summer, FEMS Microbiol. Ecol., 60, 189–206, 2007.
Goericke, R. and Welschmeyer, N. A.: The marine prochlorophyte Prochlorococcus contributes significantly to phytoplankton biomass and primary production in the Sargasso Sea, Deep Sea Res. Pt. I, 40, 2283–2294, 1993.
Grob, C., Ulloa, O., Li, W. K. W., Alarcon, G., Fukasawa, M., and Watanabe, S.: Picoplankton abundance and biomass across the eastern South Pacific Ocean along latitude 32.5 degrees S, Mar. Ecol. Progr. Ser., 332, 53–62, 2007.
Guindon, S. and Gascuel, O.: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood, System Biol., 52, 696–704, 2003.
Hall, T. A.: BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucl. Acids Symp. Ser., 41, 95–98, 1999.
Hertig, E. and Jacobeit, J.: Downscaling future climate change: Temperature scenarios for the Mediterranean area, Global Planet. Change, 63, 127–131, 2008.
Huelsenbeck, J. P. and Ronquist, F.: MRBAYES: Bayesian inference of phylogenetic trees, Bioinformatics, 17, 754–755, 2001.
Hutchins, D. A., Pustizzi, F., Hare, C. E., and DiTullio, G. R.: A shipboard natural community continuous culture system for ecologically relevant low-level nutrient enrichment experiments, Limnol Oceanogr. Meth., 1, 82–91, 2003.
Johnson, Z. I., Zinser, E. R., Coe, A., McNulty, N. P., Woodward, E. M., and Chisholm, S. W.: Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients, Science, 311, 1737–1740, 2006.
Katoh, K. and Toh, H.: Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework, BMC Bioinfo., 9, 212, 2008.
Kettler, G., Martiny, A. C., Huang, K., Zucker, J., Coleman, M. L., Rodrigue, S., Chen, F., Lapidus, A., Ferriera, S., Johnson, J., Steglich, C., Church, G., Richardson, P., and Chisholm, S. W.: Patterns and implications of gene gain and loss in the evolution of Prochlorococcus, PLoS Genet., 3, e231, 2007.
Lavin, P., González, B., Santibáñez, J., Scanlan, D., and Ulloa, O.: Novel lineages of Prochlorococcus dominate the picocyanobacterial community within the oxygen minimum zone of the eastern tropical South Pacific, Environ. Microbiol. Rep., 2, 728–738, 2010.
Lejeusne, C., Chevaldonné, P., Pergent-Martini, C., Boudouresque, C. F., and Pérez, T.: Climate change effects on a miniature ocean: the highly diverse, highly impacted Mediterranean Sea, Trends Ecol. Evol., 25, 250–260, 2009.
Li, W. K. W., Dickie, P. M., Irwin, B. D., and Wood, A. M.: Biomass of bacteria, cyanobacteria, prochlorophytes and photosynthetic eukaryotes in the Sargasso Sea, Deep Sea Res. Pt. I, 39, 501–519, 1992.
Li, W. K. W.: Primary productivity of prochlorophytes, cyanobacteria, and eukaryotic ultraphytoplankton: measurements from flow cytometric sorting, Limnol. Oceanogr., 39, 169–175, 1994.
Li, W. Z. and Godzik, A.: Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences, Bioinformatics 22, 1658–1659, 2006.
Lindell, D. and Post, A. F.: Ultraphytoplankton succession is triggered by deep winter mixing in the Gulf of Aqaba (Eilat), Red Sea, Limnol. Oceanogr., 40, 1130–1141, 1995.
Mackey, K. R. M., Rivlin, T., Grossman, A. R., Post, A. F., and Paytan, A.: Picophytoplankton responses to changing nutrient and light regimes during a bloom, Mar. Biol., 156, 1531–1546, 2009.
Malmstrom, R. R., Coe, A., Kettler, G. C., Martiny, A. C., Frias-Lopez, J., Zinser, E. R., and Chisholm, S. W.: Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans, ISME J., 4, 1252–1264, 2010.
Mann, E. L., Ahlgren, N., Moffett, J. W., and Chisholm, S. W.: Copper toxicity and cyanobacteria ecology in the Sargasso Sea, Limnol. Oceanogr., 47, 976–988, 2002.
Marie, D., Brussaard, C., Partensky, F., and Vaulot, D.: Flow cytometric analysis of phytoplankton, bacteria and viruses, in: Current Protocols in Cytometry, edited by: Sons, J. W., International Society for Analytical Cytology, 11.11.11-11.11.15., 1999.
Marie, D., Zhu, F., Balagué, V., Ras, J., and Vaulot, D.: Eukaryotic picoplankton communities of the Mediterranean Sea in summer assessed by molecular approaches (DGGE, TTGE, QPCR), FEMS Microbiol. Ecol., 55, 403–415, 2006.
Martiny, A. C., Tai, A. P., Veneziano, D., Primeau, F., and Chisholm, S. W.: Taxonomic resolution, ecotypes and the biogeography of Prochlorococcus, Environ. Microbiol., 11, 823–832, 2009.
Marty, J.-C., Chiavérini, J., Pizay, M. D., and Avril, B.: Seasonal and interannual dynamics of nutrients and phytoplankton pigments in the western Mediterranean Sea at the DYFAMED time-series station (1991–1999) Deep Sea Res. Pt. II, 49, 1965–1985, 2002.
Massana, R., Balague, V., Guillou, L., and Pedros-Alio, C.: Picoeukaryotic diversity in an oligotrophic coastal site studied by molecular and culturing approaches, FEMS Microbiol. Ecol., 50, 231–243, 2004.
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 Bioinfo., 11, 538, 2010.
Mazard, S., Ostrowski, M., Partensky, F., and Scanlan, D. J.: Multiquence analysis, taxonomic resolution and biogeography of marine Synechococcus, Environ. Microbiol., http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02514.x/full, 2011.
Moutin, T., Thingstad, T. F., Van Wambeke, F., Marie, D., Slawyk, G., Raimbault, P., and Claustre, H.: Does competition for nanomolar phosphate supply explain the predominance of the cyanobacterium Synechococcus?, Limnol. Oceanogr., 47, 1562–1567, 2002.
Moutin, T., Van Wambeke, F., and Prieur, L.: The Biogeochemistry from the Oligotrophic to the Ultraoligotrophic Mediterranean (BOUM) experiment, Biogeosciences Discuss., 8, 8091–8160, https://doi.org/10.5194/bgd-8-8091-2011, 2011.
Needleman, S. B. and Wunsch, C. D.: A general method applicable to the search for similarities in the amino acid sequence of two proteins, J. Mol. Biol., 48, 443–453, 1970.
Obernosterer, I., Christaki, U., Lefèvre, D., Catala, P., Van Wambeke, F., and Lebaron, P.: Rapid bacterial mineralization of organic carbon produced during a phytoplankton bloom induced by natural iron fertilization in the Southern Ocean., Deep Sea Res. Pt. II, 55, 777–789, 2008.
Olson, R. J., Chisholm, S. W., Zettler, E. R., and Armbrust, E. V.: Analysis of Synechococcus pigment types in the sea using single and dual beam flow cytometry, Deep Sea Res. Pt. I, 35, 425–440, 1988.
Olson, R. J., Zettler, E. R., Armbrust, E. V., and Chisholm, S. W.: Pigment, size and distribution of Synechococcus in the North Atlantic and Pacific oceans, Limnol. Oceanogr., 35, 45–58, 1990.
Ostrowski, M., Mazard, S., Tetu, S. G., Phillippy, K., Johnson, A., Palenik, B., Paulsen, I. T., and Scanlan, D. J.: PtrA is required for coordinate regulation of gene expression during phosphate stress in a marine Synechococcus, ISME J., 4, 908–921, 2010.
Palenik, B., Brahamsha, B., Larimer, F. W., Land, M., Hauser, L., Chain, P., Lamerdin, J., Regala, W., Allen, E. E., McCarren, J., Paulsen, I., Dufresne, A., Partensky, F., Webb, E. A., and Waterbury, J.: The genome of a motile marine Synechococcus, Nature, 424, 1037–1042, 2003.
Palenik, B., Ren, Q. H., Dupont, C. L., Myers, G. S., Heidelberg, J. F., Badger, J. H., Madupu, R., Nelson, W. C., Brinkac, L. M., Dodson, R. J., Durkin, A. S., Daugherty, S. C., Sullivan, S. A., Khouri, H., Mohamoud, Y., Halpin, R., and Paulsen, I. T.: Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment, Proc. Natl Acad. Sci. USA., 103, 13555–13559, 2006.
Partensky, F., Blanchot, J., Lantoine, F., Neveux, J., and Marie, D.: Vertical structure of picophytoplankton at different trophic sites of the tropical northeastern Atlantic Ocean, Deep Sea Res. Pt. I, 43, 1191–1213, 1996.
Partensky, F., Blanchot, J., and Vaulot, D.: Differential distribution and ecology of Prochlorococcus and Synechococcus in oceanic waters: a review, in: Marine Cyanobacteria, edited by: Charpy, L. and Larkum, A., Musée Océanographique, Monaco, 457–475, 1999.
Partensky, F. and Garczarek, L.: Prochlorococcus: Advantages and limits of minimalism, Ann. Rev. Mar. Sci., 2, 305–331, 2010.
Paytan, A., Mackey, K. R., Chen, Y., Lima, I. D., Doney, S. C., Mahowald, N., Labiosa, R., and Post, A. F.: Toxicity of atmospheric aerosols on marine phytoplankton, Proc. Natl. Acad. Sci. USA., 106, 4601–4605, 2009.
Posada, D.: jModelTest: phylogenetic model averaging, Mol. Biol. Evol., 25, 1253–1256, 2008.
Posada, D.: Selection of models of DNA evolution with jModelTest, Meth. Mol. Biol., 537, 93–112, 2009.
Pujo-Pay, M., Conan, P., Oriol, L., Cornet-Barthaux, V., Falco, C., Ghiglione, J.-F., Goyet, C., Moutin, T., and Prieur, L.: Integrated survey of elemental stoichiometry (C, N, P) from the western to eastern Mediterranean Sea, Biogeosciences, 8, 883–899, https://doi.org/10.5194/bg-8-883-2011, 2011.
Raimbault, P., Slawyk, G., Coste, B., and Fry, J.: Feasibility of using an automated colorimetric procedure for the determination of seawater nitrate in the 0 to 100 nM range: Examples from field and culture, Mar. Biol., 104, 347–351, 1990.
Ras, J., Uitz, J., and Claustre, H.: Spatial variability of phytoplankton pigment distributions in the subtropical South Pacific Ocean: comparison between in situ and modelled data, Biogeosciences, 5, 353-369, 2008.
Reynolds, R. W., Rayner, N. A., Smith, T. M., Stokes, D. C., and Wang, W.: An improved in situ and satellite SST analysis for climate, J. Clim., 15, 1609–1625, 2002.
Rocap, G., Distel, D. L., Waterbury, J. B., and Chisholm, S. W.: Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S-23S ribosomal DNA internal transcribed spacer sequences, Appl. Environ. Microbiol., 68, 1180–1191, 2002.
Rocap, G., Larimer, F. W., Lamerdin, J., Malfatti, S., Chain, P., Ahlgren, N. A., Arellano, A., Coleman, M., Hauser, L., Hess, W. R., Johnson, Z. I., Land, M., Lindell, D., Post, A. F., Regala, W., Shah, M., Shaw, S. L., Steglich, C., Sullivan, M. B., Ting, C. S., Tolonen, A., Webb, E. A., Zinser, E. R., and Chisholm, S. W.: Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation, Nature, 424, 1042–1047, 2003.
Rusch, D. B., Martiny, A. C., Dupont, C. L., Halpern, A. L., and Venter, J. C.: Characterization of Prochlorococcus clades from iron-depleted oceanic regions, Proc. Natl. Acad. Sci. USA, 107, 16184–16189, 2010.
Saaroni, H., Ziv, B., Edelson, J., and Alpert, P.: Long-term variations in summer temperatures over the Eastern Mediterranean, Geophys. Res. Lett., 30, https://doi.org/10.1029/2003GL017742, 2003.
Scanlan, D. J., Ostrowski, M., Mazard, S., Dufresne, A., Garczarek, L., Hess, W. R., Post, A. F., Hagemann, M., Paulsen, I., and Partensky, F.: Ecological genomics of marine picocyanobacteria, Microbiol. Mol. Biol. Rev., 73, 249–299, 2009.
Somot, S., Sevault, F., and Déqué, M.: Transient climate change scenario simulation of the Mediterranean Sea for the Twenty-first century using a high-resolution ocean circulation model, Clim. Dynam., 27, 851–879, 2006.
Stamatakis, A.: RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, 22, 2688–2690, 2006.
Tai, V. and Palenik, B.: Temporal variation of Synechococcus clades at a coastal Pacific Ocean monitoring site, ISME J., 3, 903–915, 2009.
Tai, V., Burton, R. S., and Palenik, B.: Temporal and spatial distributions of marine Synechococcus in the Southern California Bight assessed by hybridization to bead-arrays Mar. Ecol. Prog. Ser., 426, 133–147, 2011.
Tanaka, T., Zohary, T., Krom, M. D., Lawe, C. S., Pitta, P., Psarra, S., Rassoulzadegan, F., Thingstad, T. F., Tselepides, A., Woodward, E. M. S., Flaten, G. A. F., Skjoldal, E. F., and Zodiatis, G.: Microbial community structure and function in the Levantine Basin of the eastern Mediterranean, Deep Sea Res. Pt. I, 54, 1721–1743, 2007.
Tanaka, T., Thingstad, T. F., Christaki, U., Colombet, J., Cornet-Barthaux, V., Courties, C., Grattepanche, J.-D., Lagaria, A., Nedoma, J., Oriol, L., Psarra, S., Pujo-Pay, M., and Van Wambeke, F.: Lack of P-limitation of phytoplankton and heterotrophic prokaryotes in surface waters of three anticyclonic eddies in the stratified Mediterranean Sea, Biogeosciences, 8, 525–538, https://doi.org/10.5194/bg-8-525-2011, 2011
Ternon, E., Guieu, C., Ridame, C., L'Helguen, S., and Catala, P.: Longitudinal variability of the biogeochemical role of Mediterranean aerosols in the Mediterranean Sea, Biogeosciences, 8, 1067–1080, https://doi.org/10.5194/bg-8-1067-2011, 2011.
Tetu, S. G., Brahamsha, B., Johnson, D. A., Tai, V., Phillippy, K., Palenik, B., and Paulsen, I. T.: Microarray analysis of phosphate regulation in the marine cyanobacterium Synechococcus sp. WH8102, ISME J., 3, 835–849, 2009.
Thompson, J. R., Marcelino, L. A., and Polz, M. F.: Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by "reconditioning PCR", Nucl. Acids Res., 30, 2083–2088, 2002.
Toledo, G., Palenik, B., and Brahamsha, B.: Swimming marine Synechococcus strains with widely different photosynthetic pigment ratios form a monophyletic group, Appl. Environ. Microbiol., 65, 5247–5251, 1999.
Toledo, G. and Palenik, B.: A Synechococcus serotype is found preferentially in surface marine waters, Limnol. Oceanogr., 48, 1744–1755, 2003.
West, N. J. and Scanlan, D. J.: Niche-partitioning of Prochlorococcus populations in a stratified water column in the eastern north Atlantic ocean, Appl. Environ. Microbiol., 65, 2585–2591, 1999.
West, N. J., Lebaron, P., Strutton, P. G., and Suzuki, M. T.: A novel clade of Prochlorococcus found in high nutrient low chlorophyll waters in the South and Equatorial Pacific Ocean, ISME J., 5, 933–944, 2010.
Zinser, E. R., Coe, A., Johnson, Z. I., Martiny, A. C., Fuller, N. J., Scanlan, D. J., and Chisholm, S. W.: Prochlorococcus ecotype abundances in the North Atlantic Ocean as revealed by an improved quantitative PCR method, Appl. Environ. Microbiol., 72, 723–732, 2006.
Zinser, E. R., Johnson, Z. I., Coe, A., Karaca, E., Veneziano, D., and Chisholm, S. W.: Influence of light and temperature on Prochlorococcus ecotype distributions in the Atlantic Ocean, Limnol. Oceanogr., 52, 2205–2220, 2007.
Zubkov, M. V., Sleigh, M. A., and Burkill, P. H.: Assaying picoplankton distribution by flow cytometry of underway samples collected along a meridional transect across the Atlantic Ocean, Aquat. Microb. Ecol., 21, 13–20, 2000.
Zwirglmaier, K., Heywood, J. L., Chamberlain, K., Woodward, E. M. S., Zubkov, M. V., and Scanlan, D. J.: Basin-scale distribution patterns lineages in the Atlantic Ocean, Environ. Microbiol., 9, 1278–1290, 2007.
Zwirglmaier, K., Jardillier, L., Ostrowski, M., Mazard, S., Garczarek, L., Vaulot, D., Not, F., Massana, R., Ulloa, O., and Scanlan, D. J.: Global phylogeography of marine Synechococcus and Prochlorococcus reveals a distinct partitioning of lineages among oceanic biomes, Environ. Microbiol., 10, 147–161, 2008.
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