Articles | Volume 22, issue 3
https://doi.org/10.5194/bg-22-625-2025
© Author(s) 2025. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/bg-22-625-2025
© Author(s) 2025. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
04 Feb 2025
Research article |
| 04 Feb 2025
| 04 Feb 2025
Grazing mortality as a controlling factor in the uncultured non-cyanobacterial diazotroph (Gamma A) around the Kuroshio region
Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
present address: Institute for Chemical Research, Kyoto University, Kyoto, 611-0011, Japan
Tamaha Yamaguchi
Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Kanagawa, 236-8648, Japan
Kiyotaka Hidaka
Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Kanagawa, 236-8648, Japan
Sayaka Sogawa
Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Kanagawa, 236-8648, Japan
Takashi Setou
Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Kanagawa, 236-8648, Japan
Taketoshi Kodama
Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Kanagawa, 236-8648, Japan
present address: Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
Takuhei Shiozaki
Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan
Kazutaka Takahashi
Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
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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
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Federico Fabisik, Benoit Guieysse, Jonathan Procter, and Maxence Plouviez
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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.
Cited articles
Amir, A., McDonald, D., Navas-Molina, J. A., Kopylova, E., Morton, J. T., Zech Xu, Z., Kightley, E. P., Thompson, L. R., Hyde, E. R., Gonzalez, A., and Knight, R.: Deblur rapidly resolves single-nucleotide community sequence patterns, mSystems, 2, e00191, https://doi.org/10.1128/mSystems.00191-16, 2017.
Bates, D., Mächler, M., Bolker, B., and Walker, S.: Fitting Linear Mixed-Effects Models Using lme4, J. Stat. Softw., 67, 1–48, https://doi.org/10.18637/jss.v067.i01, 2015.
Benavides, M., Moisander, P. H., Daley, M. C., Bode, A., and Arístegui, J.: Longitudinal variability of diazotroph abundances in the subtropical North Atlantic Ocean, J. Plankton Res., 38, 662–672, 2016.
Bird, C., Martinez, J. M., O'Donnell, A. G., and Wyman, M.: Spatial distribution and transcriptional activity of an uncultured clade of planktonic diazotrophic γ-proteobacteria in the Arabian Sea, Appl. Environ. Microbiol., 71, 2079–2085, https://doi.org/10.1128/AEM.71.4.2079-2085.2005, 2005.
Blais, M., Tremblay, J. É., Jungblut, A. D., Gagnon, J., Martin, J., Thaler, M., and Lovejoy, C.: Nitrogen fixation and identification of potential diazotrophs in the Canadian Arctic, Global Biogeochem. Cy., 26, GB3022, https://doi.org/10.1029/2011GB004096, 2012.
Bombar, D., Paerl, R. W., and Riemann, L.: Marine non-cyanobacterial diazotrophs: moving beyond molecular detection, Trend. Microbiol., 24, 916–927, https://doi.org/10.1016/j.tim.2016.07.002, 2016.
Chang, J., Chiang, K.-P., and Gong, G.-C.: Seasonal variation and cross-shelf distribution of the nitrogen-fixing cyanobacterium, Trichodesmium, in southern East China Sea, Cont. Shelf Res., 20, 479–492, https://doi.org/10.1016/s0278-4343(99)00082-5, 2000.
Chen, M., Lu, Y., Jiao, N., Tian, J., Kao, S. J., and Yao, Z.: Biogeographic drivers of diazotrophs in the western Pacific Ocean, Limnol. Oceanogr., 64, 1403–1421, https://doi.org/10.1002/lno.11123, 2019.
Chen, Y. L. L., Chen, H. Y., Tuo, S. H., and Ohki, K.: Seasonal dynamics of new production from Trichodesmium N2 fixation and nitrate uptake in the upstream Kuroshio and South China Sea basin, Limnol. Oceanogr., 53, 1705–1721, https://doi.org/10.4319/LO.2008.53.5.1705, 2009.
Cheung, S., Suzuki, K., Xia, X., and Liu, H.: Transportation of diazotroph community from the upstream to downstream of the Kuroshio, J. Geophys. Res.-Biogeo., 124, 2680–2693, https://doi.org/10.1029/2018jg004960, 2019.
Cheung, S., Nitanai, R., Tsurumoto, C., Endo, H., Nakaoka, S., Cheah, W., Lorda, J. F., Xia, X. M., Liu, H. B., and Suzuki, K.: Physical forcing controls the basin-scale occurrence of nitrogen-fixing organisms in the North Pacific Ocean, Global Biogeochem. Cy., 34, e2019GB006452, https://doi.org/10.1029/2019GB006452, 2020.
Cheung, S., Liu, K., Turk-Kubo, K. A., Nishioka, J., Suzuki, K., Landry, M. R., Zehr, J. P., Leung, S., Deng, L., and Liu, H.: High biomass turnover rates of endosymbiotic nitrogen-fixing cyanobacteria in the western Bering Sea, Limnol. Oceanogr. Lett., 7, 501–509, https://doi.org/10.1002/lol2.10267, 2022.
Cornejo-Castillo, F. M. and Zehr, J. P.: Intriguing size distribution of the uncultured and globally widespread marine non-cyanobacterial diazotroph Gamma-A, ISME J., 15, 124–128, https://doi.org/10.1038/s41396-020-00765-1, 2021.
Delmont, T. O., Quince, C., Shaiber, A., Esen, O. C., Lee, S. T. M., Rappe, M. S., MacLellan, S. L., Lucker, S., and Eren, A. M.: Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes, Nat. Microbiol., 3, 804–813, https://doi.org/10.1038/s41564-018-0176-9, 2018.
Delmont, T. O., Pierella Karlusich, J. J., Veseli, I., Fuessel, J., Murat, E. A., Foster, R. A., Bowler, C., Wincker, P., and Pelletier, E.: Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean, ISME J., 16, 927–936, https://doi.org/10.1038/s41396-021-01135-1, 2022.
Deng, L., Cheung, S., and Liu, H.: Protistal grazers increase grazing on unicellular cyanobacteria diazotroph at night, Front. Mar. Sci., 7, 135, https://doi.org/10.3389/fmars.2020.00135, 2020.
Deng, L., Cheung, S., Xu, Z., Liu, K., and Liu, H.: Microzooplankton grazing exerts a strong top-down control on unicellular cyanobacterial diazotrophs, J. Geophys. Res.-Biogeo., 128, e2023JG007824, https://doi.org/10.1029/2023jg007824, 2023.
Ding, C., Wu, C., Li, L., Pujari, L., Zhang, G., and Sun, J.: Comparison of diazotrophic composition and distribution in the South China Sea and the Western Pacific Ocean, Biology, 10, 555, https://doi.org/10.3390/biology10060555, 2021.
Dutkiewicz, S., Follows, M. J., and Bragg, J. G.: Modeling the coupling of ocean ecology and biogeochemistry, Global Biogeochem. Cy., 23, GB4017, https://doi.org/10.1029/2008GB003405, 2009.
Edler, L.: Recommendation on methods of marine biological studies in the Baltic Sea: Phytoplankton and chlorophyll, Bal. Mar. Biolog. Publ., 5, 1–38, 1979.
Farnelid, H., Andersson, A. F., Bertilsson, S., Abu Al-Soud, W., Hansen, L. H., Sorensen, S., Steward, G. F., Hagstrom, A., and Riemann, L.: Nitrogenase gene amplicons from global marine surface waters are dominated by genes of non-cyanobacteria, PLoS ONE, 6, e19223, https://doi.org/10.1371/journal.pone.0019223, 2011.
Gradoville, M. R., Farnelid, H., White, A. E., Turk-Kubo, K. A., Stewart, B., Ribalet, F., Ferrón, S., Pinedo-Gonzalez, P., Armbrust, E. V., Karl, D. M., John, S., and Zehr, J. P.: Latitudinal constraints on the abundance and activity of the cyanobacterium UCYN-A and other marine diazotrophs in the North Pacific, Limnol. Oceanogr., 65, 1858–1875, https://doi.org/10.1002/lno.11423, 2020.
Gruber, N. and Galloway, J. N.: An Earth-system perspective of the global nitrogen cycle, Nature, 451, 293–296, https://doi.org/10.1038/nature06592, 2008.
Halm, H., Lam, P., Ferdelman, T. G., Lavik, G., Dittmar, T., LaRoche, J., D'Hondt, S., and Kuypers, M. M. M.: Heterotrophic organisms dominate nitrogen fixation in the South Pacific Gyre, ISME J., 6, 1238–1249, https://doi.org/10.1038/ismej.2011.182, 2012.
Hansen, B., Bjornsen, P. K., and Hansen, P. J.: The size ratio between planktonic predators and their prey, Limnol. Oceanogr., 39, 395–403, https://doi.org/10.4319/lo.1994.39.2.0395, 1994.
Harding, K. J.: Insights into marine unicellular cyanobacterial and noncyanobacterial diazotrophs through single-cell analyses, Ph.D. thesis, University of California Santa Cruz, ark:/13030/m522946f, https://escholarship.org/uc/item/9886g5gm (last access: 31 January 2025), 2021.
Hasegawa, D.: Island Mass Effect, in: Kuroshio Current, Physical, Biogeochemical and Ecosystem Dynamics, edited by: Nagai, T., Saito, H., Suzuki, K., and Takahashi, M., Geophysical Monograph 243, John Wiley & Sons, Hoboken, 163–174, https://doi.org/10.1002/9781119428428.ch10, 2019.
Itoh, S., Kaneko, H., Kouketsu, S., Okunishi, T., Tsutsumi, E., Ogawa, H., and Yasuda, I.: Vertical eddy diffusivity in the subsurface pycnocline across the Pacific, J. Oceanogr., 77, 185–197, https://doi.org/10.1007/s10872-020-00589-9, 2021.
Jiang, Z., Li, H., Zhai, H., Zhou, F., Chen, Q., Chen, J., Zhang, D., and Yan, X.: Seasonal and spatial changes in Trichodesmium associated with physicochemical properties in East China Sea and southern Yellow Sea, J. Geophys. Res.-Biogeo., 123, 509–530, https://doi.org/10.1002/2017jg004275, 2018.
Jiang, Z., Zhu, Y., Sun, Z., Zhai, H., Zhou, F., Yan, X., Zeng, J., Chen, J., and Chen, Q.: Enhancement of summer nitrogen fixation by the Kuroshio intrusion in the East China Sea and southern Yellow Sea, J. Geophys. Res.-Biogeosci., 128, e2022JG007287, https://doi.org/10.1029/2022jg007287, 2023.
John, E. H. and Davidson, K.: Prey selectivity and the influence of prey carbon: Nitrogen ratio on microflagellate grazing, J. Exp. Mar. Biol. Ecol., 260, 93–111, https://doi.org/10.1016/S0022-0981(01)00244-1, 2001.
Kanayama, T., Kobari, T., Suzuki, K., Yoshie, N., Honma, T., Karu, F., and Kume, G.: Impact of microzooplankton grazing on the phytoplankton community in the Kuroshio of the East China sea: A major trophic pathway of the Kuroshio ecosystem, Deep-Sea Res. Pt. I, 163, 103337, https://doi.org/10.1016/j.dsr.2020.103337, 2020.
Kaneko, H., Yasuda, I., Komatsu, K., and Itoh, S.: Observations of vertical turbulent nitrate flux across the Kuroshio, Geophys. Res. Lett., 40, 3123–3127, https://doi.org/10.1002/grl.50613, 2013.
Kaneko, H., Yasuda, I., Itoh, S., and Ito, S.-I.: Vertical turbulent nitrate flux from direct measurements in the western subarctic and subtropical gyres of the North Pacific, J. Oceanogr., 77, 29–44, https://doi.org/10.1007/s10872-020-00576-0, 2021.
Karl, D., Letelier, R., Tupas, L., Dore, J., Christian, J., and Hebel, D.: The role of nitrogen fixation in biogeochemical cycling in the subtropical North Pacific Ocean, Nature, 388, 533–538, https://doi.org/10.1038/41474, 1997.
Kobari, T., Honma, T., Hasegawa, D., Yoshie, N., Tsutsumi, E., Matsuno, T., Nagai, T., Kanayama, T., Karu, F., Suzuki, K., Tanaka, T., Guo, X., Kume, G., Nishina, A., and Nakamura, H.: Phytoplankton growth and consumption by microzooplankton stimulated by turbulent nitrate flux suggest rapid trophic transfer in the oligotrophic Kuroshio, Biogeosciences, 17, 2441–2452, https://doi.org/10.5194/bg-17-2441-2020, 2020.
Kodama, T., Shimizu, Y., Ichikawa, T., Hiroe, Y., Kusaka, A., Morita, H., Shimizu, M., and Hidaka, K.: Seasonal and spatial contrast in the surface layer nutrient content around the Kuroshio along 138° E, observed between 2002 and 2013, J. Oceanogr., 70, 489–503, https://doi.org/10.1007/s10872-014-0245-5, 2014.
Kodama, T., Nishimoto, A., Horii, S., Ito, D., Yamaguchi, T., Hidaka, K., Setou, T., and Ono, T.: Spatial and seasonal variations of stable isotope ratios of particulate organic carbon and nitrogen in the surface water of the Kuroshio, J. Geophys. Res.-Ocean., 126, e2021JC017175, https://doi.org/10.1029/2021jc017175, 2021.
Landry, M. R. and Hassett, R. P.: Estimating the grazing impact of marine microzooplankton, Mar. Biol., 67, 283–288, https://doi.org/10.1007/BF00397668, 1982.
Landry, M. R., Brown, S. L., Campbell, L., Constantinou, J., and Liu, H.: Spatial patterns in phytoplankton growth and microzooplankton grazing in the Arabian Sea during monsoon forcing, Deep-Sea Res. Pt. II, 45, 2353–2368, https://doi.org/10.1016/s0967-0645(98)00074-5, 1998.
Landry, M. R., Brown, S. L., Neveux, J., Dupouy, C., Blanchot, J., Christensen, S., and Bidigare, R. R.: Phytoplankton growth and microzooplankton grazing in high nutrient, low-chlorophyll waters of the equatorial Pacific: community and taxonspecific rate assessments from pigment and flow cytometric analyses, J. Geophys. Res.-Ocean., 108, 8142, https://doi.org/10.1029/2000jc000744, 2003.
Langlois, R., Mills, M., Ridame, C., Croot, P., and LaRoche, J.: Diazotrophic bacteria respond to Saharan dust additions, Mar. Ecol. Prog. Ser., 470, 1–14, https://doi.org/10.3354/meps10109, 2012.
Langlois, R., Großkopf, T., Mills, M., Takeda, S., and LaRoche, J.: Widespread distribution and expression of Gamma A (UMB), an uncultured, diazotrophic, γ-proteobacterial nifH phylotype, PLoS One, 10, e0128912, https://doi.org/10.1371/journal.pone.0128912, 2015.
Luo, Y. W., Doney, S. C., Anderson, L. A., Benavides, M., Berman-Frank, I., Bode, A., Bonnet, S., Boström, K. H., Böttjer, D., Capone, D. G. C., E. J., Chen, Y. L., Church, M. J., Dore, J. E., Falcón, L. I., Fernández, A., Foster, R. A., Furuya, K., Gómez, F., Gundersen, K., Hynes, A. M., Karl, D. M., Kitajima, S., Langlois, R. J., LaRoche, J., Letelier, R. M., Marañón, E., McGillicuddy Jr., D. J. M., P. H., Moore, C. M., Mouriño-Carballido, B. M., M. R. Needoba, J. A., Orcutt, K. M., Poulton, A. J., Rahav, E., Raimbault, P., Rees, A. P., Riemann, L., Shiozaki, T., Subramaniam, A., Tyrrell, T., Turk-Kubo, K. A., Varela, M., Villareal, T. A., Webb, E. A., White, A. E., Wu, J., and Zehr, J. P.: Database of diazotrophs in global ocean: Abundance, biomass and nitrogen fixation rates, Earth Syst. Sci. Data, 4, 47–73, https://doi.org/10.5194/essd-4-47-2012, 2012.
Marumo, R. and Nagasawa, S.: Seasonal variation of the standing crop of a pelagic blue green alga, Trichodesmium in the Kuroshio water, Bull. Plank. Soc. Jpn., 23, 1925, https://doi.org/10.1016/0304-3770(83)90088-8, 1976.
Moisander, P. H., Beinart, R. A., Voss, M., and Zehr, J. P.: Diversity and abundance of diazotrophic microorganisms in the South China Sea during intermonsoon, ISME J., 2, 954–967, https://doi.org/10.1038/ismej.2008.51, 2008.
Moisander, P. H., Zhang, R., Boyle, E. A., Hewson, I., Montoya, J. P., and Zehr, J. P.: Analogous nutrient limitations in unicellular diazotrophs and Prochlorococcus in the South Pacific Ocean, ISME J., 6, 733–744, https://doi.org/10.1038/ismej.2011.152, 2012.
Moisander, P. H., Serros, T., Paerl, R. W., Beinart, R. A., and Zehr, J. P.: Gammaproteobacterial diazotrophs and nifH gene expression in surface waters of the South Pacific Ocean, ISME J., 8, 1962–1973, https://doi.org/10.1038/ismej.2014.49, 2014.
Mullin, M. M.: Production of zooplankton in the ocean: the present status and problems, Oceanogr. Mar. Biol. Annu. Rev., 7, 293–310, 1969.
Nagai, T., Clayton, S., and Uchiyama, Y.: Multiscale routes to supply nutrients through the Kuroshio nutrient stream,in: Kuroshio Current, Physical, Biogeochemical and Ecosystem Dynamics, edited by: Nagai, T., Saito, H., Suzuki, K., and Takahashi, M., Geophysical Monograph 243, John Wiley & Sons, Hoboken, 105–125, https://doi.org/10.1002/9781119428428.ch6, 2019a.
Nagai, T., Durán, G. S., Otero, D. A., Mori, Y., Yoshie, N., Ohgi, K., Hasegawa, D., Nishina, A., and Kobari, T.: How the Kuroshio Current delivers nutrients to sunlit layers on the continental shelves with aid of near-inertial waves and turbulence, Geophys. Res. Lett., 46, 6726–6735, https://doi.org/10.1029/2019gl082680, 2019b.
Putt, M. and Stoecker, D. K.: An experimentally determined carbon: volume ratio for marine “oligotrichous” ciliates from estuarine and coastal waters, Limnol. Oceanogr., 34, 1097–1103, https://doi.org/10.4319/lo.1989.34.6.1097, 1989.
R Core Team: R: A language and environment for statistical computing, R Foundation for Statistical Computing, Vienna, Austria, https://www.R-project.org/ (last access: 27 January 2025), 2024.
Salazar, G., Paoli, L., Alberti, A., Huerta-Cepas, J., Ruscheweyh, H.-J., Cuenca, M., Field, C. M., Coelho, L. P., Cruaud, C., Engelen, S., Gregory, A. C., Labadie, K., Marec, C., Pelletier, E., Royo-Llonch, M., Roux, S., Sánchez, P., Uehara, H., Zayed, A. A., Zeller, G., Carmichael, M., Dimier, C., Ferland, J., Kandels, S., Picheral, M., Pisarev, S., Poulain, J., Acinas, S. G., Babin, M., Bork, P., Bowler, C., De Vargas, C., Guidi, L., Hingamp, P., Iudicone, D., Karp-Boss, L., Karsenti, E., Ogata, H., Pesant, S., Speich, S., Sullivan, M. B., Wincker, P., Sunagawa, S., Acinas, S. G., Babin, M., Bork, P., Boss, E., Bowler, C., Cochrane, G., De Vargas, C., Follows, M., Gorsky, G., Grimsley, N., Guidi, L., Hingamp, P., Iudicone, D., Jaillon, O., Kandels-Lewis, S., Karp-Boss, L., Karsenti, E., Not, F., Ogata, H., Pesant, S., Poulton, N., Raes, J., Sardet, C., Speich, S., Stemmann, L., Sullivan, M. B., Sunagawa, S., and Wincker, P.: Gene expression changes and community turnover differentially shape the global ocean metatranscriptome, Cell, 179, 1068, https://doi.org/10.1016/j.cell.2019.10.014, 2019.
T. Sato.: Grazing mortality as a controlling factor on the non-cyanobacterial diazotroph (Gamma A) around the Kuroshio region, the UTokyo Repository [data set], https://doi.org/10.15083/0002009919, 2024.
Sato, T., Shiozaki, T., Taniuchi, Y., Kasai, H., and Takahashi, K.: Nitrogen fixation and diazotroph community in the subarctic Sea of Japan and Sea of Okhotsk, J. Geophys. Res.-Ocean., 126, e2020JC017071, https://doi.org/10.1029/2020JC017071, 2021.
Sato, T., Shiozaki, T., Hashihama, F., Sato, M., Murara, A., Sasaoka, K., Umeda, S.-I., and Takahashi, K.: Low nitrogen fixation related to shallow nitracline across the eastern Indian Ocean, J. Geophys. Res.-Biogeo., 127, e2022JG007104, https://doi.org/10.1029/2022JG007104, 2022.
Scavotto, R. E., Dziallas, C., Bentzon-Tilia, M., Riemann, L., and Moisander, P. H.: Nitrogen-fixing bacteria associated with copepods in coastal waters of the North Atlantic Ocean, Environ. Microbiol., 17, 3754–3765, https://doi.org/10.1111/1462-2920.12777, 2015.
Shao, Z. and Luo, Y.-W.: Controlling factors on the global distribution of a representative marine non-cyanobacterial diazotroph phylotype (Gamma A), Biogeosciences, 19, 2939–2952, https://doi.org/10.5194/bg-19-2939-2022, 2022.
Shao, Z., Xu, Y., Wang, H., Luo, W., Wang, L., Huang, Y., Agawin, N. S. R., Ahmed, A., Benavides, M., Bentzon-Tilia, M., Berman-Frank, I., Berthelot, H., Biegala, I. C., Bif, M. B., Bode, A., Bonnet, S., Bronk, D. A., Brown, M. V., Campbell, L., Capone, D. G., Carpenter, E. J., Cassar, N., Chang, B. X., Chappell, D., Chen, Y.-l. L., Church, M. J., Cornejo-Castillo, F. M., Detoni, A. M. S., Doney, S. C., Dupouy, C., Estrada, M., Fernandez, C., Fernández-Castro, B., Fonseca-Batista, D., Foster, R. A., Furuya, K., Garcia, N., Goto, K., Gago, J., Gradoville, M. R., Hamersley, M. R., Henke, B. A., Hörstmann, C., Jayakumar, A., Jiang, Z., Kao, S.-J., Karl, D. M., Kittu, L. R., Knapp, A. N., Kumar, S., LaRoche, J., Liu, H., Liu, J., Lory, C., Löscher, C. R., Marañón, E., Messer, L. F., Mills, M. M., Mohr, W., Moisander, P. H., Mahaffey, C., Moore, R., Mouriño-Carballido, B., Mulholland, M. R., Nakaoka, S.-I., Needoba, J. A., Raes, E. J., Rahav, E., Ramírez-Cárdenas, T., Reeder, C. F., Riemann, L., Riou, V., Robidart, J. C., Sarma, V. V. S. S., Sato, T., Saxena, H., Selden, C., Seymour, J. R., Shi, D., Shiozaki, T., Singh, A., Sipler, R. E., Sun, J., Suzuki, K., Takahashi, K., Tan, Y., Tang, W., Tremblay, J.-É., Turk-Kubo, K., Wen, Z., White, A. E., Wilson, S. T., Yoshida, T., Zehr, J. P., Zhang, R., Zhang, Y., and Luo, Y.-W.: Global oceanic diazotroph database version 2 and elevated estimate of global oceanic N2 fixation, Earth Syst. Sci. Data, 15, 3673–3709, https://doi.org/10.5194/essd-15-3673-2023, 2023.
Shiozaki, T., Ijichi, M., Kodama, T., Takeda, S., and Furuya, K.: Heterotrophic bacteria as major nitrogen fixers in the euphotic zone of the Indian Ocean, Global Biogeochem. Cy., 28, 1096–1110, https://doi.org/10.1002/2014GB004886, 2014a.
Shiozaki, T., Chen, Y. L. L., Lin, Y. H., Taniuchi, Y., Sheu, D. S., Furuya, K., and Chen, H. Y.: Seasonal variations of unicellular diazotroph groups A and B, and Trichodesmium in the northern South China Sea and neighboring upstream Kuroshio Current, Cont. Shelf Res., 80, 20–31, https://doi.org/10.1016/j.csr.2014.02.015, 2014b.
Shiozaki, T., Nagata, T., Ijichi, M., and Furuya, K.: Nitrogen fixation and the diazotroph community in the temperate coastal region of the northwestern North Pacific, Biogeosciences, 12, 4751–4764, https://doi.org/10.5194/bg-12-4751-2015, 2015a.
Shiozaki, T., Takeda, S., Itoh, S., Kodama, T., Liu, X., Hashihama, F., and Furuya, K.: Why is Trichodesmium abundant in the Kuroshio?, Biogeosciences, 12, 6931–6943, https://doi.org/10.5194/bg-12-6931-2015, 2015b.
Shiozaki, T., Bombar, D., Riemann, L., Hashihama, F., Takeda, S., Yamaguchi, T., Ehama, M., Hamasaki, K., and Furuya, K.: Basin scale variability of active diazotrophs and nitrogen fixation in the North Pacific, from the tropics to the subarctic Bering Sea, Global Biogeochem. Cy., 31, 996–1009, https://doi.org/10.1002/2017gb005681, 2017.
Shiozaki, T., Kondo, Y., Yuasa, D., and Takeda, S.: Distribution of major diazotrophs in the surface water of the Kuroshio from northeastern Taiwan to south of mainland Japan, J. Plankton Res., 40, 407–419, https://doi.org/10.1093/plankt/fby027, 2018a.
Shiozaki, T., Fujiwara, A., Ijichi, M., Harada, N., Nishino, S., Nishi, S., Nagata, T., and Hamasaki, K.: Diazotroph community structure and the role of nitrogen fixation in the nitrogen cycle in the Chukchi Sea (western Arctic Ocean), Limnol. Oceanogr., 63, 2191–2205, https://doi.org/10.1002/lno.10933, 2018b.
Shiozaki, T., Nishimura, Y., Yoshizawa, S., Takami, H., Hamasaki, K., Fujiwara, A., Nishino, S., and Harada, N.: Distribution and survival strategies of endemic and cosmopolitan diazotrophs in the Arctic Ocean, ISME J., 17, 1340–1350, https://doi.org/10.1038/s41396-023-01424-x, 2023.
Staniewski, M. A. and Short, S. M.: Methodological review and meta-analysis of dilution assays for estimates of virus- and grazer-mediated phytoplankton mortality, Limnol. Oceanogr. Method., 16, 649–668, https://doi.org/10.1002/lom3.10273, 2018.
Tschitschko, B., Esti, M., Philippi, M., Kidane, A. T., Littmann, S., Kitzinger, K., Speth, D. R., Li, S., Kraberg, A., Tienken, D., Marchant, H. K., Kartal, B., Milucka, J., Mohr, W., and Kuypers, M. M. M.: Rhizobia–diatom symbiosis fixes missing nitrogen in the ocean, Nature, 630, 899–904, https://doi.org/10.1038/s41586-024-07495-w, 2024.
Tsutsumi, E., Matsuno, T., Lien, R. C., Nakamura, H., Senjyu, T., and Guo, X.: Turbulent mixing within the Kuroshio in the Tokara Strait, J. Geophys. Res.-Ocean., 122, 7082–7094, https://doi.org/10.1002/2017jc013049, 2017.
Turk-Kubo, K. A., Connell, P., Caron, D., Hogan, M. E., Farnelid, H. M., and Zehr, J. P.: In situ diazotroph population dynamics under different resource ratios in the North Pacific subtropical gyre, Front. Microbiol., 9, 1616, https://doi.org/10.3389/fmicb.2018.01616, 2018.
Turk-Kubo, K. A., Frank, I. E., Hogan, M. E., Desnues, A., Bonnet, S., and Zehr, J. P.: Diazotroph community succession during the VAHINE mesocosm experiment (New Caledonia lagoon), Biogeosciences, 12, 7435–7452, https://doi.org/10.5194/bg-12-7435-2015, 2015.
Turk-Kubo, K. A., Gradoville, M. R., Cheung, S., Cornejo-Castillo, F. M., Harding, K. J., Morando, M., Mills, M., and Zehr, J. P.: Non-cyanobacterial diazotrophs: global diversity, distribution, ecophysiology, and activity in marine waters, FEMS Microbiol. Rev., 47, fuac046, https://doi.org/10.1093/femsre/fuac046, 2023.
Verity, P. G. and Lagdon, C.: Relationships between lorica volume, carbon, nitrogen, and ATP content of tintinnids In Narragansett Bay, J. Plankton Res., 6, 859–868, https://doi.org/10.1093/plankt/6.5.859, 1984.
Wang, H. and Luo, Y.-W.: Top-down control on major groups of global marine diazotrophs, Acta Oceanol. Sin., 41, 111–119, https://doi.org/10.1007/s13131-021-1956-2, 2022.
Wang, W. L., Moore, J. K., Martiny, A. C., and Primeau, F. W.: Convergent estimates of marine nitrogen fixation, Nature, 566, 205–211, https://doi.org/10.1038/s41586-019-0911-2, 2019.
Ward, B. A., Dutkiewicz, S., Moore, C. M., and Follows, M. J.: Iron, phosphorus, and nitrogen supply ratios define the biogeography of nitrogen fixation, Limnol. Oceanogr., 58, 2059–2075, https://doi.org/10.4319/lo.2013.58.6.2059, 2013.
Wen, Z., Browning, T. J., Dai, R., Wu, W., Li, W., Hu, X., Lin, W., Wang, L., Liu, X., Cao, Z., Hong, H., and Shi, D.: The response of diazotrophs to nutrient amendment in the South China Sea and western North Pacific, Biogeosciences, 19, 5237–5250, https://doi.org/10.5194/bg-19-5237-2022, 2022a.
Wen, Z., Browning, T. J., Cai, Y., Dai, R., Zhang, R., Du, C., Jiang, R., Lin, W., Liu, X., Cao, Z., Hong, H., Dai, M., and Shi, D.: Nutrient regulation of biological nitrogen fixation across the tropical western North Pacific, Sci. Adv., 8, 7564, https://doi.org/10.1126/SCIADV.ABL7564, 2022b.
Wilson, S. T., Aylward, F. O., Ribalet, F., Barone, B., Casey, J. R., Ferrón, S., Connell, P., Eppley, J. M., Fitzsimmons, J. M., Hayes, C. T., Romano, A. E., Turk-Kubo, K., Vislova, A., Armbrust, E. V., Caron, D. A., Church, M. J., Zehr, J. P., Karl, D. M., and Delong, E. F.: Coordinated regulation of growth, activity and transcription in natural populations of the unicellular nitrogen-fixing cyanobacterium Crocosphaera, Nat. Microbiol., 2, 17118, https://doi.org/10.1038/nmicrobiol.2017.118, 2017.
Zehr, J. P.: Nitrogen fixation by marine cyanobacteria, Trends Microbiol., 19, 162–173, https://doi.org/10.1016/j.tim.2010.12.004, 2011.
Zehr, J. P. and Capone, D. G.: Marine nitrogen fixation, Springer Nature, https://doi.org/10.1007/978-3-030-67746-6, 2021.
Zehr, J. P. and Turner, P. J.: Nitrogen fixation: Nitrogenase genes and gene expression, Methods Microbiol., 30, 271–286, https://doi.org/10.1016/S0580-9517(01)30049-1, 2001.
Zehr, J. P., Mellon, M. T., and Zani, S.: New nitrogen-fixing microorganisms detected in oligotrophic oceans by amplification of nitrogenase (nifH) genes, Appl. Environ. Microbiol., 64, 3444–3450, https://doi.org/10.1128/AEM.64.9.3444-3450.1998, 1998.
Zehr, J. P., Jenkins, B. D., Short, S. M., and Steward, G. F.: Nitrogenase gene diversity and microbial community structure: a cross-system comparison, Environ. Microbiol., 5, 539–554, https://doi.org/10.1046/j.1462-2920.2003.00451.x, 2003.
Short summary
Gamma A is a widespread non-cyanobacterial diazotroph that plays a crucial role in marine ecosystems, but its controlling factors are still largely unknown. This study, for the first time, quantified microzooplankton grazing on Gamma A and revealed the significance of grazing pressure on Gamma A distribution around the Kuroshio region. It highlights the importance of top-down controls on Gamma A abundance and the associated nitrogen cycle.
Gamma A is a widespread non-cyanobacterial diazotroph that plays a crucial role in marine...
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