Articles | Volume 16, issue 20
https://doi.org/10.5194/bg-16-4113-2019
© Author(s) 2019. 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-16-4113-2019
© Author(s) 2019. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
28 Oct 2019
Research article |
| 28 Oct 2019
| 28 Oct 2019
Effects of sea animal colonization on the coupling between dynamics and activity of soil ammonia-oxidizing bacteria and archaea in maritime Antarctica
Qing Wang
Anhui Province Key Laboratory of Polar Environment and Global Change,
School of Earth and Space Sciences, University of Science and Technology of
China, Hefei 230026, China
Anhui Province Key Laboratory of Polar Environment and Global Change,
School of Earth and Space Sciences, University of Science and Technology of
China, Hefei 230026, China
Yanling Zheng
State Key Laboratory of Estuarine and Coastal Research, East China
Normal University, Shanghai 200062, China
Tao Bao
Anhui Province Key Laboratory of Polar Environment and Global Change,
School of Earth and Space Sciences, University of Science and Technology of
China, Hefei 230026, China
Lijun Hou
CORRESPONDING AUTHOR
State Key Laboratory of Estuarine and Coastal Research, East China
Normal University, Shanghai 200062, China
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Interdisciplinary strategy to assess the impact of meteorological variables on the biochemical composition of the rain and the dynamics of a small eutrophic lake under rain forcing
Depth-related patterns in microbial community responses to complex organic matter in the western North Atlantic Ocean
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Eddy-enhanced primary production sustains heterotrophic microbial activities in the Eastern Tropical North Atlantic
Composition and niche-specific characteristics of microbial consortia colonizing Marsberg copper mine in the Rhenish Massif
Abrasion of sedimentary rocks as a source of hydrogen peroxide and nutrients to subglacial ecosystems
Diversity and assembly processes of microbial eukaryotic communities in Fildes Peninsula Lakes (West Antarctica)
Nitrophobic ectomycorrhizal fungi are associated with enhanced hydrophobicity of soil organic matter in a Norway spruce forest
Physiological control on carbon isotope fractionation in marine phytoplankton
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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.
Beatriz Gill-Olivas, Jon Telling, Mark Skidmore, and Martyn Tranter
EGUsphere, https://doi.org/10.5194/egusphere-2022-908, https://doi.org/10.5194/egusphere-2022-908, 2022
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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 sulphide minerals, along with previously weathered silicate minerals, produces a range of compounds and nutrients which can be utilised by the diverse suite of microbes that inhabit glacier beds.
Chunmei Zhang, Huirong Li, Yinxin Zeng, Haitao Ding, Bin Wang, Yangjie Li, Zhongqiang Ji, Yonghong Bi, and Wei Luo
Biogeosciences, 19, 4639–4654, https://doi.org/10.5194/bg-19-4639-2022, https://doi.org/10.5194/bg-19-4639-2022, 2022
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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 Wells, and James C. Stegen
Biogeosciences, 18, 4773–4789, https://doi.org/10.5194/bg-18-4773-2021, https://doi.org/10.5194/bg-18-4773-2021, 2021
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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.
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.
Nimrod Wieler, Hanan Ginat, Osnat Gillor, and Roey Angel
Biogeosciences, 16, 1133–1145, https://doi.org/10.5194/bg-16-1133-2019, https://doi.org/10.5194/bg-16-1133-2019, 2019
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In stony deserts, when rocks are exposed to atmospheric conditions, they undergo weathering. The cavernous (honeycomb) weathering pattern is one of the most common, but it is still unclear exactly how it is formed. We show that microorganisms, which differ from the surrounding soil and dust, form biological crusts on exposed rock surfaces. These microbes secrete polymeric substances that mitigate weathering by reducing evaporation rates and, consequently, salt transport rates through the rock.
Yang Li, Zhaojun Wu, Xingchen Dong, Zifu Xu, Qixin Zhang, Haiyan Su, Zhongjun Jia, and Qingye Sun
Biogeosciences, 16, 573–583, https://doi.org/10.5194/bg-16-573-2019, https://doi.org/10.5194/bg-16-573-2019, 2019
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This paper contributes to the study of bacterial carbon sequestration in mine tailings. Previous studies focused on carbonate mineral precipitation, while the role of autotrophs in carbon sequestration has been neglected. Carbon sequestration in two mine tailings treated with FeS2 was analyzed using 13C isotope labeling, pyrosequencing, and DNA SIP to identify carbon fixers. This paper is the first to investigate carbon sequestration by autotrophic groups in mine tailings.
Dong-Hun Lee, Jung-Hyun Kim, Yung Mi Lee, Alina Stadnitskaia, Young Keun Jin, Helge Niemann, Young-Gyun Kim, and Kyung-Hoon Shin
Biogeosciences, 15, 7419–7433, https://doi.org/10.5194/bg-15-7419-2018, https://doi.org/10.5194/bg-15-7419-2018, 2018
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In this study, we provide first evidence of lipid biomarker patterns and phylogenetic identities of key microbes mediating anaerobic oxidation of methane (AOM) communities in active mud volcanoes (MVs) on the continental slope of the Canadian Beaufort Sea. Our lipid and 16S rRNA results indicate that archaea of the ANME-2c and ANME-3 clades are involved in AOM in the MVs investigated.
Joshua F. Dean, Jurgen R. van Hal, A. Johannes Dolman, Rien Aerts, and James T. Weedon
Biogeosciences, 15, 7141–7154, https://doi.org/10.5194/bg-15-7141-2018, https://doi.org/10.5194/bg-15-7141-2018, 2018
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Lakes, rivers, ponds and streams are significant contributors of the greenhouse gas carbon dioxide to the atmosphere. This is partly due to the decomposition of plant and soil organic matter transported through these aquatic systems by microbial communities. In determining how vulnerable this organic material is to decomposition during aquatic transport, we show that standardized treatments in experiments can affect the way microbial communities behave and potentially the experimental outcome.
Xi Wen, Viktoria Unger, Gerald Jurasinski, Franziska Koebsch, Fabian Horn, Gregor Rehder, Torsten Sachs, Dominik Zak, Gunnar Lischeid, Klaus-Holger Knorr, Michael E. Böttcher, Matthias Winkel, Paul L. E. Bodelier, and Susanne Liebner
Biogeosciences, 15, 6519–6536, https://doi.org/10.5194/bg-15-6519-2018, https://doi.org/10.5194/bg-15-6519-2018, 2018
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Rewetting drained peatlands may lead to prolonged emission of the greenhouse gas methane, but the underlying factors are not well described. In this study, we found two rewetted fens with known high methane fluxes had a high ratio of microbial methane producers to methane consumers and a low abundance of methane consumers compared to pristine wetlands. We therefore suggest abundances of methane-cycling microbes as potential indicators for prolonged high methane emissions in rewetted peatlands.
Kyle R. Frischkorn, Andreas Krupke, Cécile Guieu, Justine Louis, Mónica Rouco, Andrés E. Salazar Estrada, Benjamin A. S. Van Mooy, and Sonya T. Dyhrman
Biogeosciences, 15, 5761–5778, https://doi.org/10.5194/bg-15-5761-2018, https://doi.org/10.5194/bg-15-5761-2018, 2018
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Trichodesmium is a keystone genus of marine cyanobacteria that is estimated to supply nearly half of the ocean’s fixed nitrogen, fuelling primary productivity and the cycling of carbon and nitrogen in the ocean. In our study we characterize Trichodesmium ecology across the western tropical South Pacific using gene and genome sequencing and geochemistry. We detected genes for phosphorus reduction, providing a mechanism for the noted importance of this organism in the ocean's phosphorus cycle.
Audrey Lallement, Ludovic Besaury, Elise Tixier, Martine Sancelme, Pierre Amato, Virginie Vinatier, Isabelle Canet, Olga V. Polyakova, Viatcheslay B. Artaev, Albert T. Lebedev, Laurent Deguillaume, Gilles Mailhot, and Anne-Marie Delort
Biogeosciences, 15, 5733–5744, https://doi.org/10.5194/bg-15-5733-2018, https://doi.org/10.5194/bg-15-5733-2018, 2018
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The main objective of this work was to evaluate the potential degradation of phenol, a highly toxic pollutant, by cloud microorganisms. Phenol concentrations measured on five cloud samples collected at the PUY station in France were from 0.15 to 0.74 µg L−1. Metatranscriptomic analysis suggested that phenol could be biodegraded directly in clouds, likely by Gammaproteobacteria. A large screening showed that 93 % of 145 bacterial strains isolated from clouds were able to degrade phenol.
Sara J. Bender, Dawn M. Moran, Matthew R. McIlvin, Hong Zheng, John P. McCrow, Jonathan Badger, Giacomo R. DiTullio, Andrew E. Allen, and Mak A. Saito
Biogeosciences, 15, 4923–4942, https://doi.org/10.5194/bg-15-4923-2018, https://doi.org/10.5194/bg-15-4923-2018, 2018
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Phaeocystis antarctica is an important phytoplankter of the Antarctic coastal environment where it dominates the early season bloom after sea ice retreat. Iron nutrition was found to be an important factor that results in Phaeocystis colony formation and a large restructuring of the proteome, including changes associated with the flagellate to colonial transition and adaptive responses to iron scarcity. Analysis of Phaeocystis proteins from the Ross Sea revealed the presence of both cell types.
Sophie Bonnet, Mathieu Caffin, Hugo Berthelot, Olivier Grosso, Mar Benavides, Sandra Helias-Nunige, Cécile Guieu, Marcus Stenegren, and Rachel Ann Foster
Biogeosciences, 15, 4215–4232, https://doi.org/10.5194/bg-15-4215-2018, https://doi.org/10.5194/bg-15-4215-2018, 2018
Dina Spungin, Natalia Belkin, Rachel A. Foster, Marcus Stenegren, Andrea Caputo, Mireille Pujo-Pay, Nathalie Leblond, Cécile Dupouy, Sophie Bonnet, and Ilana Berman-Frank
Biogeosciences, 15, 3893–3908, https://doi.org/10.5194/bg-15-3893-2018, https://doi.org/10.5194/bg-15-3893-2018, 2018
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The way marine organisms die can determine the fate of organic matter (OM) in the ocean. We investigated whether a form of auto-induced programmed cell death (PCD) influenced phytoplankton mortality and fate of OM. Our results from high biomass blooms of the cyanobacterium Trichodesmium show evidence for PCD and high production of sticky carbon material termed transparent exopolymeric particles (TEP) that facilitates cellular aggregation and enhances the vertical flux of OM to depth.
Christian Nyrop Albers, Magnus Kramshøj, and Riikka Rinnan
Biogeosciences, 15, 3591–3601, https://doi.org/10.5194/bg-15-3591-2018, https://doi.org/10.5194/bg-15-3591-2018, 2018
Natasha A. Gafar and Kai G. Schulz
Biogeosciences, 15, 3541–3560, https://doi.org/10.5194/bg-15-3541-2018, https://doi.org/10.5194/bg-15-3541-2018, 2018
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Emiliania huxleyi and Gephyrocapsa oceanica are the most prolific calcifying phytoplankton in today's oceans. We compare their sensitivity to combined anthropogenic stressors of temperature, light and CO2. For the future, we project a niche contraction for G. oceanica. Furthermore, there was good correlation of our new metric, the CaCO3 production potential, with satellite-derived concentrations in the modern ocean, indicating means of assessing overall coccolithophorid success in the future.
Cited articles
Alves, R. J. E., Wanek, W., Zappe, A., Richter, A., Svenning, M. M.,
Schleper, C., and Urich, T.: Nitrification rates in Arctic soils are
associated with functionally distinct populations of ammonia-oxidizing
archaea, ISME J., 7, 1620–1631, https://doi.org/10.1038/ ismej.2013.35, 2013.
Ayton, J., Aislabie, J., Barker, G. M., Saul, D., and Turner, S.:
Crenarchaeota affiliated with group 1.1 b are prevalent in coastal mineral
soils of the Ross Sea region of Antarctica, Environ. Microbiol., 12, 689–703,
https://doi.org/10.1111/j.14622920.2009.02111.x, 2010.
Baker, B. J., Lesniewski, R. A., and Dick, G. J.: Genome-enabled
transcriptomics reveals archaeal populations that drive nitrification in a
deep-sea hydrothermal plume, ISME J., 6, 2269–2279,
https://doi.org/10.1038/ismej.2012.64, 2012.
Belser, L. W. and Schmidt, E. L.: Diversity in the ammonia-oxidizing
nitrifier population of a soil, Appl. Environ. Microbiol., 36, 584–588, 1978.
Beman, J. M., Popp, B. N., and Francis, C. A.: Molecular and biogeochemical
evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of
California,ISME J., 2, 429–441, 2008.
Blackall, T. D., Wilson, L. J., Theobald, M. R., Milford, C., Nemitz, E.,
Bull, J., and Sutton, M. A.: Ammonia emissions from seabird colonies,
Geophys. Res. Lett., 34, L10801, https://doi.org/10.1029/2006GL028928, 2007.
Bouskill, N. J., Eveillard, D., Chien, D., Jayakumar, A., and Ward, B. B.:
Environmental factors determining ammoniaoxidizing organism distribution and
diversity in marine environments, Environ. Microbiol., 14, 714–729,
https://doi.org/10.1111/j.1462-2920.2011.02623.x, 2012.
Boyd, E. S., Lange, R. K., Mitchell, A. C., Havig, J. R., Hamilton, T. L.,
Lafrenière, M. J., Shock, E. L., Peters, J. W., and Skidmore, M.: Diversity, abundance, and potential activity
of nitrifying and nitrate-reducing microbial assemblages in a subglacial
ecosystem, Appl. Environ. Microbiol., 77, 4778–4787, https://doi.org/10.1128/AEM.00376-11, 2011.
Cowan, D. A., Ramond, J. B., Makhalanyane, T. P., and De Maayer, P.:
Metagenomics of extreme environments, Curr. Opin. Microbiol., 25, 97–102,
https://doi.org/10.1016/j.mib.2015.05.005, 2015.
Daebeler, A., Abell, G. C., Bodelier, P. L., Bodrossy, L., Frampton, D. M.,
Hefting, M. M., and Laanbroek, H. J.: Archaeal dominated ammonia-oxidizing
communities in Icelandic grassland soils are moderately affected by
long-term N fertilization and geothermal heating, Front. Microbiol., 3, 352,
https://doi.org/10.3389/fmicb.2012.00352, 2012.
Daebeler, A., Bodelier, P. L., Hefting, M. M., Rütting, T., Jia, Z., and
Laanbroek, H. J.: Soil warming and fertilization altered rates of nitrogen
transformation processes and selected for adapted ammonia-oxidizing archaea
in sub-arctic grassland soil, Soil Biol. Biochem., 107, 114–124,
https://doi.org/10.1016/j.soilbio.2016.12.013, 2017.
Dang, H., Zhang, X., Sun, J., Li, T., Zhang, Z., and Yang, G.: Diversity and
spatial distribution of sediment ammonia-oxidizing crenarchaeota in response
to estuarine and environmental gradients in the Changjiang Estuary and East
China Sea, Microbiology, 154, 2084–2095, https://doi.org/10.1099/mic.0.2007/013581-0,
2008.
Di, H. J., Cameron, K. C., Shen, J. P., Winefield, C. S., O'callaghan, M.,
Bowatte, S., and He, J. Z.: Nitrification driven by bacteria and not archaea
in nitrogen-rich grassland soils, Nat. Geosci., 2, 621–624,
https://doi.org/10.1038/ngeo613, 2009.
Edgar, R. C.: MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucl. Acid. Res., 32, 1792–1797, 2004.
Fan, F., Yang, Q., Li, Z., Wei, D., Cui, X. A., and Liang, Y.: Impacts of
organic and inorganic fertilizers on nitrification in a cold climate soil
are linked to the bacterial ammonia oxidizer community, Microb. Ecol., 62, 982–990,
https://doi.org/10.1007/s00248-011-9897-5, 2011.
Francis, C. A., Roberts, K. J., Beman, J. M., Santoro, A. E., and Oakley, B.
B.: Ubiquity and diversity of ammonia-oxidizing archaea in water columns and
sediments of the ocean, P. Natl. Acad. Sci. USA, 102, 14683–14688,
https://doi.org/10.1073/pnas.0506625102, 2005.
Gao, Y. S., Yang, L. J., Wang, J. J., Xie, Z. Q., Wang, Y. H., and Sun, L.
G.: Penguin colonization following the last glacial-interglacial transition
in the Vestfold Hills, East Antarctica, Palaeogeogr. Palaeocl., 490, 629–639, https://doi.org/10.1016/j.palaeo.2017.11.053, 2018.
Glaser, K., Hackl, E., Inselsbacher, E., Strauss, J., Wanek, W.,
Zechmeister-Boltenstern, S., and Sessitsch, A.: Dynamics of
ammonia-oxidizing communities in barley-planted bulk soil and rhizosphere
following nitrate and ammonium fertilizer amendment, FEMS Microbiol. Ecol., 74, 575–591,
https://doi.org/10.1111/j.1574-6941.2010.00970.x, 2010.
Gubry-Rangin, C., Novotnik, B., Mandič-Mulec, I., Nicol, G. W., and
Prosser, J. I.: Temperature responses of soil ammonia-oxidising archaea
depend on pH, Soil Biol. Biochem., 106, 61–68, https://doi.org/10.1016/j.soilbio.2016.12.007,
2017.
Habteselassie, M. Y., Xu, L., and Norton, J. M.: Ammonia-oxidizer
communities in an agricultural soil treated with contrasting nitrogen
sources, Front. Microbiol., 4, 326, https://doi.org/10.3389/fmicb.2013.00326, 2013.
Hatzenpichler, R.: Diversity, physiology, and niche differentiation of
ammonia-oxidizing archaea, Appl. Environ. Microbiol., 78, 7501–7510, https://doi.org/10.1128/AEM.01960-12, 2012.
Hatzenpichler, R., Lebedeva, E. V., Spieck, E., Stoecker, K., Richter, A.,
Daims, H., and Wagner, M.: A moderately thermophilic ammonia-oxidizing
crenarchaeote from a hot spring, P. Natl. Acad. Sci. USA, 105, 2134–2139,
https://doi.org/10.1073/pnas.0708857105, 2008.
Jung, J., Yeom, J., Kim, J., Han, J., Lim, H. S., Park, H., Hyun, S., and Park, W.: Change
in gene abundance in the nitrogen biogeochemical cycle with temperature and
nitrogen addition in Antarctic
soils, Res. Microbiol., 162, 1018–1026, https://doi.org/10.1016/j.resmic.2011.07.007, 2011.
Kalanetra, K. M., Bano, N., and Hollibaugh, J. T.: Ammonia-oxidizing Archaea
in the Arctic Ocean and Antarctic coastal waters, Environ. Microbiol., 11, 2434–2445,
https://doi.org/10.1111/j.1462-2920.2009.01974.x, 2009.
Könneke, M., Bernhard, A. E., José, R., Walker, C. B., Waterbury, J.
B., and Stahl, D. A.: Isolation of an autotrophic ammonia-oxidizing marine
archaeon, Nature, 437, 543–546, https://doi.org/10.1038/nature03911, 2005.
Kurola, J., Salkinoja-Salonen, M., Aarnio, T., Hultman, J., and
Romantschuk, M.: Activity, diversity and population size of ammoniaoxidising
bacteria in oilcontaminated landfarming soil, FEMS Microbiol. Lett., 250, 33–38,
https://doi.org/10.1016/j.femsle.2005.06.057, 2005.
Lam, P., Jensen, M. M., Lavik, G., McGinnis, D. F., Müller, B.,
Schubert, C. J., Amann, R., Thamdrup, B., and Kuypers, M. M.: Linking crenarchaeal and bacterial nitrification to
anammox in the Black Sea, P. Natl. Acad. Sci. USA, 104, 7104–7109,
https://doi.org/10.1073/pnas.0611081104, 2007.
Le Roux, X., Poly, F., Currey, P., Commeaux, C., Hai, B., Nicol, G. W., Prosser, J. I., Schloter, M., Attard, E., and Klumpp, K.: Effects of aboveground grazing on coupling among nitrifier activity,
abundance and community structure, ISME J., 2, 221–232,
https://doi.org/10.1038/ismej.2007.109, 2008
Leininger, S., Urich, T., Schloter, M., Schwark, L., Qi, J., Nicol, G. W.,
Prosser, J. I., Schuster, S. C., and Schleper, C.: Archaea predominate among ammonia-oxidizing prokaryotes in
soils, Nature, 442, 806–809, https://doi.org/10.1038/nature04983, 2006.
Li, J., Nedwell, D. B., Beddow, J., Dumbrell, A. J., McKew, B. A., Thorpe,
E. L., and Whitby, C.: amoA gene abundances and nitrification potential
rates suggest that benthic ammonia-oxidizing bacteria and not archaea
dominate N cycling in the Colne Estuary, United Kingdom, Appl. Environ. Microbiol., 81, 159–165,
https://doi.org/10.1128/AEM.02654-14, 2015.
Lindeboom, H. J.: The nitrogen pathway in a penguin
rookery, Ecology, 65, 269–277, https://doi.org/10.2307/1939479, 1984.
Ma, D. W., Zhu, R. B., Ding, W., Shen, C. C., Chu, H. Y., and Lin, X. G.:
Ex-situ enzyme activity and bacterial community diversity through soil depth
profiles in penguin and seal colonies on Vestfold Hills, East
Antarctica, Pol. Biol., 36, 1347–1361, https://doi.org/10.1007/s00300-013-1355-z,
2013.
Madden, T.: The BLAST Sequence Analysis Tool, in: The NCBI Handbook, edited by: McEntyre, J. and Ostell, J., Bethesda (MD), National Center for Biotechnology Information (US), Chap. 16,
Bookshelf ID: NBK21097, 2002.
Magalhães, C. M., Machado, A., Frank-Fahle, B., Lee, C. K., and Cary, S.
C.: The ecological dichotomy of ammonia-oxidizing archaea and bacteria in
the hyper-arid soils of the Antarctic Dry Valleys, Front. Microbiol., 5, 515, https://doi.org/10.3389/fmicb.2014.00515, 2014.
Martens-Habbena, W., Berube, P. M., Urakawa, H., José, R., and Stahl, D.
A.: Ammonia oxidation kinetics determine niche separation of nitrifying
Archaea and Bacteria, Nature, 461, 976–979, https://doi.org/10.1038/nature08465,
2009.
Mintie, A. T., Heichen, R. S., Cromack Jr, K., Myrold, D. D., and
Bottomley, P. J.: Ammonia-oxidizing bacteria along meadow-to-forest
transects in the Oregon Cascade Mountains, Appl. Environ. Microbiol., 69, 3129–3136,
https://doi.org/10.1128/AEM.69.6.3129-3136.2003, 2003.
Mosier, A. C. and Francis, C. A.: Relative abundance and diversity of
ammonia-oxidizing archaea and bacteria in the San Francisco Bay
estuary, Environ. Microbiol., 10, 3002–3016,
https://doi.org/10.1111/j.1462-2920.2008.01764.x, 2008.
Nunes-Alves, C.: Do it yourself nitrification, Nat. Rev. Microbiol., 14, 61, https://doi.org/10.1038/nrmicro.2015.20, 2016.
Otero, X. L., Peña-Lastra, S., Pérez-Alberti, A., Ferreira, T. O.,
and Huerta-Diaz, M. A.: Seabird colonies as important global drivers in the
nitrogen and phosphorus cycles, Nat. Commun., 9, 246,
https://doi.org/0.1038/s41467-017-02446-8, 2018.
Ouyang, Y., Norton, J. M., Stark, J. M., Reeve, J. R., and Habteselassie, M.
Y.: Ammonia-oxidizing bacteria are more responsive than archaea to nitrogen
source in an agricultural soil, Soil Biol. Biochem., 96, 4–15,
https://doi.org/10.1016/j.soilbio.2016.01.012, 2016.
Pan, H., Xie, K. X., Zhang, Q. C., Jia, Z. J., Xu, J. M., Di, H. J., and Li,
Y.: Archaea and bacteria respectively dominate nitrification in lightly and
heavily grazed soil in a grassland system, Biol. Fert. Soils, 54, 41–54,
https://doi.org/10.1007/s00374-017-1236-7, 2018.
Park, J. H., Day, T. A., Strauss, S., and Ruhland, C. T.: Biogeochemical
pools and fluxes of carbon and nitrogen in a maritime tundra near penguin
colonies along the Antarctic Peninsula, Pol. Biol., 30, 199–207,
https://doi.org/10.1007/s00300-006-0173-y, 2007.
Prosser, J. I. and Nicol, G. W.: Archaeal and bacterial ammonia-oxidisers
in soil: the quest for niche specialisation and differentiation, Trends Microbiol., 20,
523–531, https://doi.org/10.1016/j.tim.2012.08.001, 2012.
Richter, I., Herbold, C. W., Lee, C. K., McDonald, I. R., Barrett, J. E.,
and Cary, S. C.: Influence of soil properties on archaeal diversity and
distribution in the McMurdo Dry Valleys, Antarctica, FEMS Microbiol. Ecol., 89, 347–359,
https://doi.org/10.1111/1574-6941.12322, 2014.
Riddick, S. N., Dragosits, U., Blackall, T. D., Daunt, F., Wanless, S., and
Sutton, M. A.: The global distribution of ammonia emissions from seabird
colonies, Atmos. Environ., 55, 319–327, https://doi.org/10.1016/j.atmosenv.2012.02.052,
2012.
Rotthauwe, J. H., Witzel, K. P., and Liesack, W.: The ammonia monooxygenase
structural gene amoA as a functional marker: molecular fine-scale analysis
of natural ammonia-oxidizing populations, Appl. Environ. Microbiol., 63, 4704–4712, 1997.
Santoro, A. E., Buchwald, C., McIlvin, M. R., and Casciotti, K. L.: Isotopic
signature of N2O produced by marine ammonia-oxidizing
archaea, Science, 333, 1282–1285, https://doi.org/10.1126/science.1208239, 2011.
Schloss, P. D., Westcott, S., Ryabin, T., Hall, J., Hartmann, M., Hollister,
E., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., Sahl, J. W., Stres, B., Thallinger, G. G., Van Horn, D. J., and Weber, C. F.: Introducing mothur: Open-source, platform-independent,
community-supported software for describing and comparing microbial
communities, Appl. Environ. Microbiol., 75, 7537–7541, https://doi.org/10.1128/AEM.01541-09, 2009.
Shen, J. P., Zhang, L. M., Di, H. J., and He, J. Z.: A review of
ammonia-oxidizing bacteria and archaea in Chinese soils, Front. Microbiol., 3, 296,
https://doi.org/10.3389/fmicb.2012.00296, 2012.
Simas, F. N. B., Schaefer, C. E. G. R. , Melo, V. F., Albuquerque-Filho, M.
R. A., Michel, R. F. M., Pereira, V. V., Gomes, M. R. M., and da Costa, L. M.: Ornithogenic cryosols from
Maritime Antarctica: Phosphatization as a soil forming
process, Geoderma, 138, 191–203, https://doi.org/10.1016/j.geoderma.2006.11.011, 2007.
Silva, A. F., Carvalho, G., Oehmen, A., Lousada-Ferreira, M., van
Nieuwenhuijzen, A., Reis, M. A., and Crespo, M. T. B.: Microbial population
analysis of nutrient removal-related organisms in membrane bioreactors.
Appl. Microbiol. Biotechnol., 93, 2171–2180,
https://doi.org/10.1007/s00253-011-3499-5, 2012.
Silva, M. C., Poly, F., Guillaumaud, N., van Elsas, J. D., and Falcão
Salles, J.: Fluctuations in ammonia oxidizing communities across
agricultural soils are driven by soil structure and pH, Front. Microbiol., 3, 77,
https://doi.org/10.3389/fmicb.2012.00077, 2012.
Sterngren, A. E., Hallin, S., and Bengtson, P.: Archaeal ammonia oxidizers
dominate in numbers, but bacteria drive gross nitrification in N-amended
grassland soil, Front. Microbiol., 6, 1350, https://doi.org/10.3389/fmicb.2015.01350, 2015.
Stieglmeier, M., Mooshammer, M., Kitzler, B., Wanek, W.,
Zechmeister-Boltenstern, S., Richter, A., and Schleper, C.: Aerobic nitrous
oxide production through N-nitrosating hybrid formation in ammonia-oxidizing
archaea, ISME J., 8, 1135–1146, 2014.
Stopnišek, N., Gubry-Rangin, C., Höfferle, Š., Nicol, G. W.,
Mandič-Mulec, I., and Prosser, J. I. : Thaumarchaeal ammonia oxidation
in an acidic forest peat soil is not influenced by ammonium amendment,
Appl. Environ. Microbiol., 76, 7626–7634, https://doi.org/10.1128/AEM.00595-10, 2010.
Sun, L. G., Liu, X. D., Yin, X. B., Zhu, R. B., Xie, Z. Q., and Wang, Y. H.:
A 1,500-year record of Antarctic seal populations in response to climate
change, Pol. Biol., 27, 495–501, https://doi.org/10.1007/s00300-004-0608-2, 2004.
Sun, L. G., Xie, Z. Q., and Zhao, J. L.: Palaeoecology: A 3,000-year record
of penguin populations, Nature, 407, 858, https://doi.org/10.1038/35038163, 2000.
Sun, L., Zhu, R., Xie, Z., and Xing, G.: Emissions of nitrous oxide and
methane from Antarctic tundra: role of penguin dropping
deposition, Atmos. Environ., 36, 4977–4982,
https://doi.org/10.1016/S1352-2310(02)00340-0, 2002.
Tatur, A., Myrcha, A., and Niegodzisz, J.: Formation of abandoned penguin
rookery ecosystems in the maritime Antarctic, Pol. Biol., 17, 405–417,
https://doi.org/10.1007/s003000050135, 1997.
Tolar, B. B., Ross, M. J., Wallsgrove, N. J., Liu, Q., Aluwihare, L. I.,
Popp, B. N., and Hollibaugh, J. T.: Contribution of ammonia oxidation to
chemoautotrophy in Antarctic coastal waters, ISME J., 10, 2605,
https://doi.org/10.1038/ismej.2016.61, 2016.
Verhamme, D. T., Prosser, J. I., and Nicol, G. W.: Ammonia concentration
determines differential growth of ammonia-oxidising archaea and bacteria in
soil microcosms, ISME J., 5, 1067–1071, https://doi.org/10.1038/ismej.2010.191,
2011.
Wang, B. Z., Zhao, J., Guo, Z. Y., Ma, J., Xu, H., and Jia, Z. J.:
Differential contributions of ammonia oxidizers and nitrite oxidizers to
nitrification in four paddy soils, ISME J., 9, 1062–1075,
https://doi.org/10.1038/ismej.2014.194, 2015.
Wang, Q.: Table. Effects of sea animal colonization on the coupling between dynamics and activity of soil ammonia-oxidizing bacteria and archaea in maritime Antarctica, https://doi.org/10.5281/zenodo.1260292, 2018.
Wessén, E., Söderström, M., Stenberg, M., Bru, D., Hellman, M.,
Welsh, A., Thomsen, F., Klemedtson, L., Philippot, L., and Hallim, S.: Spatial distribution of ammonia-oxidizing bacteria and
archaea across a 44-hectare farm related to ecosystem functioning, ISME J., 5,
1213–1225, https://doi.org/10.1038/ismej.2010.206, 2011.
Wuchter, C., Abbas, B., Coolen, M. J. L., Herfort, L., van Bleijswijk, J.,
Timmers, P., Strous, M., Teira, E., Herndl, G. J., Middelburg, J. J., Schouten, S., and Sinninghe Damsté, J. S.: Archaeal nitrification in the ocean, P. Natl. Acad. Sci. USA, 103,
12317–12322, https://doi.org/10.1073/pnas.0600756103, 2006.
Xia, Y., Zhu, Y. G., Gu, Q., and He, J. Z.: Does long-term fertilization
treatment affect the response of soil ammonia-oxidizing bacterial
communities to Zn contamination?, Plant Soil, 301, 245–254, https://doi.org/10.1007/s11104-007-9441-z, 2007.
Xie, Z., Le Roux, X., Wang, C., Gu, Z., An, M., Nan, H., Chen, B. Z., Li, F., Liu, Y. J., Du, G. Z., Feng, H. Y., and Ma, X. J.: Identifying
response groups of soil nitrifiers and denitrifiers to grazing and
associated soil environmental drivers in Tibetan alpine meadows, Soil Biol. Biochem., 77,
89–99, https://doi.org/10.1016/j.soilbio.2014.06.024, 2014.
Yang, Y., Shan, J., Zhang, J., Zhang, X., Xie, S., and Liu, Y.: Ammonia-and
methane-oxidizing microorganisms in high-altitude wetland sediments and
adjacent agricultural soils, Appl. Microbiol. Biotechnol., 98,
10197–10209, https://doi.org/10.1007/s00253-014-5942-x, 2014.
Yao, H. Y., Gao, Y. M., Nicol, G. W., Campbell, C. D., Prosser, J. I.,
Zhang, L. M., Han, W. Y., and Singh, B. K.: Links between ammonia oxidizer community structure,
abundance, and nitrification potential in acidic soils, Appl. Environ. Microbiol., 77, 4618–4625,
https://doi.org/10.1128/AEM.00136-11, 2011.
Yergeau, E., Kang, S., He, Z., Zhou, J., and Kowalchuk, G. A.: Functional
microarray analysis of nitrogen and carbon cycling genes across an Antarctic
latitudinal transect, ISME J., 1, 163–179,
https://doi.org/10.1038/ismej.2007.24, 2007.
Zhang, L. M., Wang, M., Prosser, J. I., Zheng, Y. M., and He, J. Z.:
Altitude ammonia-oxidizing bacteria and archaea in soils of Mount
Everest, FEMS Microbiol. Ecol., 70, 208–217, https://doi.org/10.1111/j.1574-6941.2009.00775.x,
2009.
Zhao, K., Kong, W. D., Khan, A., Liu, J. B., Guo, G. X., Muhanmmad, S., Zhao, X. Z., and Dong, X. B.: Elevational diversity and distribution of ammonia-oxidizing archaea
community in meadow soils on the Tibetan Plateau, Appl. Microbiol. Biotechnol., 101, 7065–7074,
https://doi.org/10.1007/s00253-017-8435-x, 2017.
Zhao, X., Wang, S., and Xing, G.: Nitrification, acidification, and nitrogen
leaching from subtropical cropland soils as affected by rice straw-based
biochar: laboratory incubation and column leaching studies, J. Soil. Sediment., 14, 471–482,
2014.
Zheng, Y. K., Wang, X. B., Gu, Y. F., and Zhang, X. P.: Diversity of
ammonia-oxidizing archaea in Tibetan Zoige plateau wetland, Acta Microbiol. Sin., 54,
1090–1096, 2014.
Zheng, Y. L., Hou, L. J., Liu, M., Lu, M., Zhao, H., Yin, G. Y., and Zhou,
J. L.: Diversity, abundance, and activity of ammonia-oxidizing bacteria and
archaea in Chongming eastern intertidal sediments, Appl. Microbiol. Biotechnol., 97, 8351–8363,
https://doi.org/10.1007/s00253-012-4512-3, 2013.
Zheng, Y. L., Hou, L. J., Newell, S., Liu, M., Zhou, J. L., Zhao, H., You,
L. L., and Cheng, X. L.:. Community dynamics and activity of
ammonia-oxidizing prokaryotes in intertidal sediments of the Yangtze
estuary, Appl. Environ. Microbiol., 80, 408–149, https://doi.org/10.1128/AEM.03035-13, 2014.
Zhu, R. B., Liu, Y. S., Xu, H., Ma, J., Zhao, S. P., and Sun, L. G.: Nitrous
oxide emissions from sea animal colonies in the maritime
Antarctic, Geophys. Res. Lett., 35, L09807, https://doi.org/10.1029/2007GL032541, 2008.
Zhu, R. B., Sun, J. J., Liu, Y. S., Gong, Z. J., and Sun, L. G.: Potential
ammonia emissions from penguin guano, ornithogenic soils and seal colony
soils in coastal Antarctica: effects of freezing-thawing cycles and selected
environmental variables, Antarct. Sci., 23, 78–92,
https://doi.org/10.1017/S0954102010000623, 2011.
Zhu, R. B., Liu, Y. S., Xu, H., Ma, D. W., and Jiang, S.: Marine animals
significantly increase tundra N2O and CH4 emissions in maritime
Antarctica, J. Geophys. Res.-Biogeo., 118, 1773–1792, https://doi.org/10.1002/2013JG002398, 2013.
Zhu, R. B., Wang, Q., Ding, W., Wang, C., Hou, L. J., and Ma, D. W.:
Penguins significantly increased phosphine formation and phosphorus
contribution in maritime Antarctic soils, Sci. Rep., 4, 7055,
https://doi.org/10.1038/srep07055, 2014.
Zhu, R. B., Shi, Y., Ma, D. W., Wang, C., Xu, H., and Chu, H. Y.: Bacterial
diversity is strongly associated with historical penguin activity in an
Antarctic lake sediment profile, Sci. Rep., 5, 17231,
https://doi.org/10.1038/srep17231, 2015.
Short summary
We investigated abundance, potential activity, and diversity of soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) in five Antarctic tundra patches, including penguin colony, seal colony, and tundra marsh. We have found (1) sea animal colonization increased AOB population size.; (2) AOB contributed to ammonia oxidation rates more than AOA in sea animal colonies; (3) community structures of AOB and AOA were closely related to soil biogeochemical processes associated with animal activities.
We investigated abundance, potential activity, and diversity of soil ammonia-oxidizing archaea...
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