Articles | Volume 19, issue 5
https://doi.org/10.5194/bg-19-1469-2022
© Author(s) 2022. 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-19-1469-2022
© Author(s) 2022. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
14 Mar 2022
Research article |
| 14 Mar 2022
| 14 Mar 2022
Implementation of mycorrhizal mechanisms into soil carbon model improves the prediction of long-term processes of plant litter decomposition
Weilin Huang
CORRESPONDING AUTHOR
Environmental Biology, Institute of Environmental Sciences, Leiden
University, Einsteinweg 2, 2333CC Leiden, the Netherlands
Centre for Environmental Sciences, Hasselt University, Martelarenlaan
42, 3500 Hasselt, Belgium
Invited contribution by Weilin Huang, recipient of the EGU Energy, Resources and the Environment Virtual Outstanding Student and PhD candidate Presentation Awards 2021.
Peter M. van Bodegom
Environmental Biology, Institute of Environmental Sciences, Leiden
University, Einsteinweg 2, 2333CC Leiden, the Netherlands
Toni Viskari
Climate System Research Department, Finnish Meteorological Institute, 00101 Helsinki, Finland
Jari Liski
Climate System Research Department, Finnish Meteorological Institute, 00101 Helsinki, Finland
Nadejda A. Soudzilovskaia
Environmental Biology, Institute of Environmental Sciences, Leiden
University, Einsteinweg 2, 2333CC Leiden, the Netherlands
Centre for Environmental Sciences, Hasselt University, Martelarenlaan
42, 3500 Hasselt, Belgium
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Wen Wen, Joris Timmermans, Qi Chen, and Peter M. van Bodegom
Hydrol. Earth Syst. Sci., 26, 4537–4552, https://doi.org/10.5194/hess-26-4537-2022, https://doi.org/10.5194/hess-26-4537-2022, 2022
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A novel approach for evaluating individual and combined impacts of drought and salinity in real-life settings is proposed using Sentinel-2. We found that crop responses to drought and salinity differ between growth stages. Compared to salinity, crop growth is most strongly affected by drought stress and is, in general, further exacerbated when co-occurring with salinity stress. Our approach facilitates a way to monitor crop health under multiple stresses with potential large-scale applications.
Jarmo Mäkelä, Laura Arppe, Hannu Fritze, Jussi Heinonsalo, Kristiina Karhu, Jari Liski, Markku Oinonen, Petra Straková, and Toni Viskari
Biogeosciences, 19, 4305–4313, https://doi.org/10.5194/bg-19-4305-2022, https://doi.org/10.5194/bg-19-4305-2022, 2022
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Soils account for the largest share of carbon found in terrestrial ecosystems, and accurate depiction of soil carbon decomposition is essential in understanding how permanent these carbon storages are. We present a straightforward way to include carbon isotope concentrations into soil decomposition and carbon storages for the Yasso model, which enables the model to use 13C as a natural tracer to track changes in the underlying soil organic matter decomposition.
Niel Verbrigghe, Niki I. W. Leblans, Bjarni D. Sigurdsson, Sara Vicca, Chao Fang, Lucia Fuchslueger, Jennifer L. Soong, James T. Weedon, Christopher Poeplau, Cristina Ariza-Carricondo, Michael Bahn, Bertrand Guenet, Per Gundersen, Gunnhildur E. Gunnarsdóttir, Thomas Kätterer, Zhanfeng Liu, Marja Maljanen, Sara Marañón-Jiménez, Kathiravan Meeran, Edda S. Oddsdóttir, Ivika Ostonen, Josep Peñuelas, Andreas Richter, Jordi Sardans, Páll Sigurðsson, Margaret S. Torn, Peter M. Van Bodegom, Erik Verbruggen, Tom W. N. Walker, Håkan Wallander, and Ivan A. Janssens
Biogeosciences, 19, 3381–3393, https://doi.org/10.5194/bg-19-3381-2022, https://doi.org/10.5194/bg-19-3381-2022, 2022
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In subarctic grassland on a geothermal warming gradient, we found large reductions in topsoil carbon stocks, with carbon stocks linearly declining with warming intensity. Most importantly, however, we observed that soil carbon stocks stabilised within 5 years of warming and remained unaffected by warming thereafter, even after > 50 years of warming. Moreover, in contrast to the large topsoil carbon losses, subsoil carbon stocks remained unaffected after > 50 years of soil warming.
Toni Viskari, Janne Pusa, Istem Fer, Anna Repo, Julius Vira, and Jari Liski
Geosci. Model Dev., 15, 1735–1752, https://doi.org/10.5194/gmd-15-1735-2022, https://doi.org/10.5194/gmd-15-1735-2022, 2022
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We wanted to examine how the chosen measurement data and calibration process affect soil organic carbon model calibration. In our results we found that there is a benefit in using data from multiple litter-bag decomposition experiments simultaneously, even with the required assumptions. Additionally, due to the amount of noise and uncertainties in the system, more advanced calibration methods should be used to parameterize the models.
Olli Nevalainen, Olli Niemitalo, Istem Fer, Antti Juntunen, Tuomas Mattila, Olli Koskela, Joni Kukkamäki, Layla Höckerstedt, Laura Mäkelä, Pieta Jarva, Laura Heimsch, Henriikka Vekuri, Liisa Kulmala, Åsa Stam, Otto Kuusela, Stephanie Gerin, Toni Viskari, Julius Vira, Jari Hyväluoma, Juha-Pekka Tuovinen, Annalea Lohila, Tuomas Laurila, Jussi Heinonsalo, Tuula Aalto, Iivari Kunttu, and Jari Liski
Geosci. Instrum. Method. Data Syst., 11, 93–109, https://doi.org/10.5194/gi-11-93-2022, https://doi.org/10.5194/gi-11-93-2022, 2022
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Better monitoring of soil carbon sequestration is needed to understand the best carbon farming practices in different soils and climate conditions. We, the Field Observatory Network (FiON), have therefore established a methodology for monitoring and forecasting agricultural carbon sequestration by combining offline and near-real-time field measurements, weather data, satellite imagery, and modeling. To disseminate our work, we built a website called the Field Observatory (fieldobservatory.org).
Laura Heimsch, Annalea Lohila, Juha-Pekka Tuovinen, Henriikka Vekuri, Jussi Heinonsalo, Olli Nevalainen, Mika Korkiakoski, Jari Liski, Tuomas Laurila, and Liisa Kulmala
Biogeosciences, 18, 3467–3483, https://doi.org/10.5194/bg-18-3467-2021, https://doi.org/10.5194/bg-18-3467-2021, 2021
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CO2 and H2O fluxes were measured at a newly established eddy covariance site in southern Finland for 2 years from 2018 to 2020. This agricultural grassland site focuses on the conversion from intensive towards more sustainable agricultural management. The first summer experienced prolonged dry periods, and notably larger fluxes were observed in the second summer. The field acted as a net carbon sink during both study years.
Alexey N. Shiklomanov, Michael C. Dietze, Istem Fer, Toni Viskari, and Shawn P. Serbin
Geosci. Model Dev., 14, 2603–2633, https://doi.org/10.5194/gmd-14-2603-2021, https://doi.org/10.5194/gmd-14-2603-2021, 2021
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Airborne and satellite images are a great resource for calibrating and evaluating computer models of ecosystems. Typically, researchers derive ecosystem properties from these images and then compare models against these derived properties. Here, we present an alternative approach where we modify a model to predict what the satellite would see more directly. We then show how this approach can be used to calibrate model parameters using airborne data from forest sites in the northeastern US.
Toni Viskari, Maisa Laine, Liisa Kulmala, Jarmo Mäkelä, Istem Fer, and Jari Liski
Geosci. Model Dev., 13, 5959–5971, https://doi.org/10.5194/gmd-13-5959-2020, https://doi.org/10.5194/gmd-13-5959-2020, 2020
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The research here established whether a Bayesian statistical method called state data assimilation could be used to improve soil organic carbon (SOC) forecasts. Our test case was a fallow experiment where SOC content was measured over several decades from a plot where all vegetation was removed. Our results showed that state data assimilation improved projections and allowed for the detailed model state be updated with coarse total carbon measurements.
Tea Thum, Julia E. M. S. Nabel, Aki Tsuruta, Tuula Aalto, Edward J. Dlugokencky, Jari Liski, Ingrid T. Luijkx, Tiina Markkanen, Julia Pongratz, Yukio Yoshida, and Sönke Zaehle
Biogeosciences, 17, 5721–5743, https://doi.org/10.5194/bg-17-5721-2020, https://doi.org/10.5194/bg-17-5721-2020, 2020
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Global vegetation models are important tools in estimating the impacts of global climate change. The fate of soil carbon is of the upmost importance as its emissions will enhance the atmospheric carbon dioxide concentration. To evaluate the skill of global vegetation models to model the soil carbon and its responses to environmental factors, it is important to use different data sources. We evaluated two different soil carbon models by using atmospheric carbon dioxide concentrations.
Jarmo Mäkelä, Jürgen Knauer, Mika Aurela, Andrew Black, Martin Heimann, Hideki Kobayashi, Annalea Lohila, Ivan Mammarella, Hank Margolis, Tiina Markkanen, Jouni Susiluoto, Tea Thum, Toni Viskari, Sönke Zaehle, and Tuula Aalto
Geosci. Model Dev., 12, 4075–4098, https://doi.org/10.5194/gmd-12-4075-2019, https://doi.org/10.5194/gmd-12-4075-2019, 2019
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We assess the differences of six stomatal conductance formulations, embedded into a land–vegetation model JSBACH, on 10 boreal coniferous evergreen forest sites. We calibrate the model parameters using all six functions in a multi-year experiment, as well as for a separate drought event at one of the sites, using the adaptive population importance sampler. The analysis reveals weaknesses in the stomatal conductance formulation-dependent model behaviour that we are able to partially amend.
Zhun Mao, Delphine Derrien, Markus Didion, Jari Liski, Thomas Eglin, Manuel Nicolas, Mathieu Jonard, and Laurent Saint-André
Biogeosciences, 16, 1955–1973, https://doi.org/10.5194/bg-16-1955-2019, https://doi.org/10.5194/bg-16-1955-2019, 2019
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In a context of global changes, modeling and predicting the dynamics of soil carbon stocks in forest ecosystems are vital but challenging. Yasso07 is considered to be one of the most promising models for such a purpose. We examine the accuracy of its prediction of soil carbon dynamics over the whole French metropolitan territory at a decennial timescale. We revealed how the bottleneck in soil carbon modeling is linked with the lack of knowledge on soil carbon quality and fine-root litter.
Anna B. Harper, Peter M. Cox, Pierre Friedlingstein, Andy J. Wiltshire, Chris D. Jones, Stephen Sitch, Lina M. Mercado, Margriet Groenendijk, Eddy Robertson, Jens Kattge, Gerhard Bönisch, Owen K. Atkin, Michael Bahn, Johannes Cornelissen, Ülo Niinemets, Vladimir Onipchenko, Josep Peñuelas, Lourens Poorter, Peter B. Reich, Nadjeda A. Soudzilovskaia, and Peter van Bodegom
Geosci. Model Dev., 9, 2415–2440, https://doi.org/10.5194/gmd-9-2415-2016, https://doi.org/10.5194/gmd-9-2415-2016, 2016
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Dynamic global vegetation models (DGVMs) are used to predict the response of vegetation to climate change. We improved the representation of carbon uptake by ecosystems in a DGVM by including a wider range of trade-offs between nutrient allocation to photosynthetic capacity and leaf structure, based on observed plant traits from a worldwide data base. The improved model has higher rates of photosynthesis and net C uptake by plants, and more closely matches observations at site and global scales.
M. Baudena, S. C. Dekker, P. M. van Bodegom, B. Cuesta, S. I. Higgins, V. Lehsten, C. H. Reick, M. Rietkerk, S. Scheiter, Z. Yin, M. A. Zavala, and V. Brovkin
Biogeosciences, 12, 1833–1848, https://doi.org/10.5194/bg-12-1833-2015, https://doi.org/10.5194/bg-12-1833-2015, 2015
A. Loew, P. M. van Bodegom, J.-L. Widlowski, J. Otto, T. Quaife, B. Pinty, and T. Raddatz
Biogeosciences, 11, 1873–1897, https://doi.org/10.5194/bg-11-1873-2014, https://doi.org/10.5194/bg-11-1873-2014, 2014
B. Ringeval, S. Houweling, P. M. van Bodegom, R. Spahni, R. van Beek, F. Joos, and T. Röckmann
Biogeosciences, 11, 1519–1558, https://doi.org/10.5194/bg-11-1519-2014, https://doi.org/10.5194/bg-11-1519-2014, 2014
L. M. Verheijen, V. Brovkin, R. Aerts, G. Bönisch, J. H. C. Cornelissen, J. Kattge, P. B. Reich, I. J. Wright, and P. M. van Bodegom
Biogeosciences, 10, 5497–5515, https://doi.org/10.5194/bg-10-5497-2013, https://doi.org/10.5194/bg-10-5497-2013, 2013
R. Wania, J. R. Melton, E. L. Hodson, B. Poulter, B. Ringeval, R. Spahni, T. Bohn, C. A. Avis, G. Chen, A. V. Eliseev, P. O. Hopcroft, W. J. Riley, Z. M. Subin, H. Tian, P. M. van Bodegom, T. Kleinen, Z. C. Yu, J. S. Singarayer, S. Zürcher, D. P. Lettenmaier, D. J. Beerling, S. N. Denisov, C. Prigent, F. Papa, and J. O. Kaplan
Geosci. Model Dev., 6, 617–641, https://doi.org/10.5194/gmd-6-617-2013, https://doi.org/10.5194/gmd-6-617-2013, 2013
J. R. Melton, R. Wania, E. L. Hodson, B. Poulter, B. Ringeval, R. Spahni, T. Bohn, C. A. Avis, D. J. Beerling, G. Chen, A. V. Eliseev, S. N. Denisov, P. O. Hopcroft, D. P. Lettenmaier, W. J. Riley, J. S. Singarayer, Z. M. Subin, H. Tian, S. Zürcher, V. Brovkin, P. M. van Bodegom, T. Kleinen, Z. C. Yu, and J. O. Kaplan
Biogeosciences, 10, 753–788, https://doi.org/10.5194/bg-10-753-2013, https://doi.org/10.5194/bg-10-753-2013, 2013
T. Viskari, E. Asmi, P. Kolmonen, H. Vuollekoski, T. Petäjä, and H. Järvinen
Atmos. Chem. Phys., 12, 11767–11779, https://doi.org/10.5194/acp-12-11767-2012, https://doi.org/10.5194/acp-12-11767-2012, 2012
T. Viskari, E. Asmi, A. Virkkula, P. Kolmonen, T. Petäjä, and H. Järvinen
Atmos. Chem. Phys., 12, 11781–11793, https://doi.org/10.5194/acp-12-11781-2012, https://doi.org/10.5194/acp-12-11781-2012, 2012
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Mutong Niu, Shu Huang, Wei Hu, Yajie Wang, Wanyun Xu, Wan Wei, Qiang Zhang, Zihan Wang, Donghuan Zhang, Rui Jin, Libin Wu, Junjun Deng, Fangxia Shen, and Pingqing Fu
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Sugar compounds in air can trace the source of bioaerosols that affect public health and climate. In rural north China, we observed increased fungal activity at night and less variable bacterial community diversity. Certain night-increasing sugar compounds were more closely related to fungi than bacteria. The fungal community greatly influenced sugar compounds, while bacteria played a limited role. Caution is advised when using sugar compounds to trace airborne microbes, particularly bacteria.
David A. Hutchins, Fei-Xue Fu, Shun-Chung Yang, Seth G. John, Stephen J. Romaniello, M. Grace Andrews, and Nathan G. Walworth
Biogeosciences, 20, 4669–4682, https://doi.org/10.5194/bg-20-4669-2023, https://doi.org/10.5194/bg-20-4669-2023, 2023
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Biogeosciences, 20, 4241–4258, https://doi.org/10.5194/bg-20-4241-2023, https://doi.org/10.5194/bg-20-4241-2023, 2023
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Caitlyn A. Hall, Andre van Turnhout, Edward Kavazanjian Jr., Leon A. van Paassen, and Bruce Rittmann
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Juan Pablo Almeida, Lorenzo Menichetti, Alf Ekblad, Nicholas P. Rosenstock, and Håkan Wallander
Biogeosciences, 20, 1443–1458, https://doi.org/10.5194/bg-20-1443-2023, https://doi.org/10.5194/bg-20-1443-2023, 2023
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Yong Zhang, Yong Zhang, Shuai Ma, Hanbing Chen, Jiabing Li, Zhengke Li, Kui Xu, Ruiping Huang, Hong Zhang, Yonghe Han, and Jun Sun
Biogeosciences, 20, 1299–1312, https://doi.org/10.5194/bg-20-1299-2023, https://doi.org/10.5194/bg-20-1299-2023, 2023
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Beatriz Gill-Olivas, Jon Telling, Mark Skidmore, and Martyn Tranter
Biogeosciences, 20, 929–943, https://doi.org/10.5194/bg-20-929-2023, https://doi.org/10.5194/bg-20-929-2023, 2023
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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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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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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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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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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.
Julie Dinasquet, Estelle Bigeard, Frédéric Gazeau, Farooq Azam, Cécile Guieu, Emilio Marañón, Céline Ridame, France Van Wambeke, Ingrid Obernosterer, and Anne-Claire Baudoux
Biogeosciences, 19, 1303–1319, https://doi.org/10.5194/bg-19-1303-2022, https://doi.org/10.5194/bg-19-1303-2022, 2022
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Saharan dust deposition of nutrients and trace metals is crucial to microbes in the Mediterranean Sea. Here, we tested the response of microbial and viral communities to simulated dust deposition under present and future conditions of temperature and pH. Overall, the effect of the deposition was dependent on the initial microbial assemblage, and future conditions will intensify microbial responses. We observed effects on trophic interactions, cascading all the way down to viral processes.
Ralf Conrad, Pengfei Liu, and Peter Claus
Biogeosciences, 18, 6533–6546, https://doi.org/10.5194/bg-18-6533-2021, https://doi.org/10.5194/bg-18-6533-2021, 2021
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Acetate is an important intermediate during the anaerobic degradation of organic matter. It is consumed by methanogenic and sulfidogenic microorganisms accompanied by stable carbon isotope fractionation. We determined isotope fractionation under different conditions in two paddy soils and two lake sediments and also determined the composition of the microbial communities. Despite a relatively wide range of experimental conditions, the range of fractionation factors was quite moderate.
Natalie R. Cohen, Abigail E. Noble, Dawn M. Moran, Matthew R. McIlvin, Tyler J. Goepfert, Nicholas J. Hawco, Christopher R. German, Tristan J. Horner, Carl H. Lamborg, John P. McCrow, Andrew E. Allen, and Mak A. Saito
Biogeosciences, 18, 5397–5422, https://doi.org/10.5194/bg-18-5397-2021, https://doi.org/10.5194/bg-18-5397-2021, 2021
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A previous study documented an intense hydrothermal plume in the South Pacific Ocean; however, the iron release associated with this plume and the impact on microbiology were unclear. We describe metal concentrations associated with multiple hydrothermal plumes in this region and protein signatures of plume-influenced microbes. Our findings demonstrate that resources released from these systems can be transported away from their source and may alter the physiology of surrounding microbes.
Sabyasachi Bhattacharya, Tarunendu Mapder, Svetlana Fernandes, Chayan Roy, Jagannath Sarkar, Moidu Jameela Rameez, Subhrangshu Mandal, Abhijit Sar, Amit Kumar Chakraborty, Nibendu Mondal, Sumit Chatterjee, Bomba Dam, Aditya Peketi, Ranadhir Chakraborty, Aninda Mazumdar, and Wriddhiman Ghosh
Biogeosciences, 18, 5203–5222, https://doi.org/10.5194/bg-18-5203-2021, https://doi.org/10.5194/bg-18-5203-2021, 2021
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Physicochemical determinants of microbiome architecture across continental shelves–slopes are unknown, so we explored the geomicrobiology along 3 m sediment horizons of seasonal (shallow coastal) and perennial (deep sea) hypoxic zones of the Arabian Sea. Nature, concentration, and fate of the organic matter delivered to the sea floor were found to shape the microbiome across the western Indian margin, under direct–indirect influence of sedimentation rate and water column O2 level.
Aditi Sengupta, Sarah J. Fansler, Rosalie K. Chu, Robert E. Danczak, Vanessa A. Garayburu-Caruso, Lupita Renteria, Hyun-Seob Song, Jason Toyoda, Jacqueline Hager, and James C. Stegen
Biogeosciences, 18, 4773–4789, https://doi.org/10.5194/bg-18-4773-2021, https://doi.org/10.5194/bg-18-4773-2021, 2021
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Conceptual models link microbes with the environment but are untested. We test a recent model using riverbed sediments. We exposed sediments to disturbances, going dry and becoming wet again. As the length of dry conditions got longer, there was a sudden shift in the ecology of microbes, chemistry of organic matter, and rates of microbial metabolism. We propose a new model based on feedbacks initiated by disturbance that cascade across biological, chemical, and functional aspects of the system.
Cora Hörstmann, Eric J. Raes, Pier Luigi Buttigieg, Claire Lo Monaco, Uwe John, and Anya M. Waite
Biogeosciences, 18, 3733–3749, https://doi.org/10.5194/bg-18-3733-2021, https://doi.org/10.5194/bg-18-3733-2021, 2021
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Microbes are the main drivers of productivity and nutrient cycling in the ocean. We present a combined approach assessing C and N uptake and microbial community diversity across ecological provinces in the Southern Ocean and southern Indian Ocean. Provinces showed distinct genetic fingerprints, but microbial activity varied gradually across regions, correlating with nutrient concentrations. Our study advances the biogeographic understanding of microbial diversity across C and N uptake regimes.
Nimrod Wieler, Tali Erickson Gini, Osnat Gillor, and Roey Angel
Biogeosciences, 18, 3331–3342, https://doi.org/10.5194/bg-18-3331-2021, https://doi.org/10.5194/bg-18-3331-2021, 2021
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Biological rock crusts (BRCs) are common microbial-based assemblages covering rocks in drylands. BRCs play a crucial role in arid environments because of the limited activity of plants and soil. Nevertheless, BRC development rates have never been dated. Here we integrated archaeological, microbiological and geological methods to provide a first estimation of the growth rate of BRCs under natural conditions. This can serve as an affordable dating tool in archaeological sites in arid regions.
Michal Elul, Maxim Rubin-Blum, Zeev Ronen, Itay Bar-Or, Werner Eckert, and Orit Sivan
Biogeosciences, 18, 2091–2106, https://doi.org/10.5194/bg-18-2091-2021, https://doi.org/10.5194/bg-18-2091-2021, 2021
Mindaugas Zilius, Irma Vybernaite-Lubiene, Diana Vaiciute, Donata Overlingė, Evelina Grinienė, Anastasija Zaiko, Stefano Bonaglia, Iris Liskow, Maren Voss, Agneta Andersson, Sonia Brugel, Tobia Politi, and Paul A. Bukaveckas
Biogeosciences, 18, 1857–1871, https://doi.org/10.5194/bg-18-1857-2021, https://doi.org/10.5194/bg-18-1857-2021, 2021
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In fresh and brackish waters, algal blooms are often dominated by cyanobacteria, which have the ability to utilize atmospheric nitrogen. Cyanobacteria are also unusual in that they float to the surface and are dispersed by wind-driven currents. Their patchy and dynamic distribution makes it difficult to track their abundance and quantify their effects on nutrient cycling. We used remote sensing to map the distribution of cyanobacteria in a large Baltic lagoon and quantify their contributions.
Saly Jaber, Muriel Joly, Maxence Brissy, Martin Leremboure, Amina Khaled, Barbara Ervens, and Anne-Marie Delort
Biogeosciences, 18, 1067–1080, https://doi.org/10.5194/bg-18-1067-2021, https://doi.org/10.5194/bg-18-1067-2021, 2021
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Our study is of interest to atmospheric scientists and environmental microbiologists, as we show that clouds can be considered a medium where bacteria efficiently degrade and transform amino acids, in competition with chemical processes. As current atmospheric multiphase models are restricted to chemical degradation of organic compounds, our conclusions motivate further model development.
Kahina Djaoudi, France Van Wambeke, Aude Barani, Nagib Bhairy, Servanne Chevaillier, Karine Desboeufs, Sandra Nunige, Mohamed Labiadh, Thierry Henry des Tureaux, Dominique Lefèvre, Amel Nouara, Christos Panagiotopoulos, Marc Tedetti, and Elvira Pulido-Villena
Biogeosciences, 17, 6271–6285, https://doi.org/10.5194/bg-17-6271-2020, https://doi.org/10.5194/bg-17-6271-2020, 2020
Romie Tignat-Perrier, Aurélien Dommergue, Alban Thollot, Olivier Magand, Timothy M. Vogel, and Catherine Larose
Biogeosciences, 17, 6081–6095, https://doi.org/10.5194/bg-17-6081-2020, https://doi.org/10.5194/bg-17-6081-2020, 2020
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The adverse atmospheric environmental conditions do not appear suited for microbial life. We conducted the first global comparative metagenomic analysis to find out if airborne microbial communities might be selected by their ability to resist these adverse conditions. The relatively higher concentration of fungi led to the observation of higher proportions of stress-related functions in air. Fungi might likely resist and survive atmospheric physical stress better than bacteria.
Yanhong Lu, Shunyan Cheung, Ling Chen, Shuh-Ji Kao, Xiaomin Xia, Jianping Gan, Minhan Dai, and Hongbin Liu
Biogeosciences, 17, 6017–6032, https://doi.org/10.5194/bg-17-6017-2020, https://doi.org/10.5194/bg-17-6017-2020, 2020
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Through a comprehensive investigation, we observed differential niche partitioning among diverse ammonia-oxidizing archaea (AOA) sublineages in a typical subtropical estuary. Distinct AOA communities observed at DNA and RNA levels suggested that a strong divergence in ammonia-oxidizing activity among different AOA groups occurs. Our result highlights the importance of identifying major ammonia oxidizers at RNA level in future studies.
Anna-Neva Visser, Scott D. Wankel, Pascal A. Niklaus, James M. Byrne, Andreas A. Kappler, and Moritz F. Lehmann
Biogeosciences, 17, 4355–4374, https://doi.org/10.5194/bg-17-4355-2020, https://doi.org/10.5194/bg-17-4355-2020, 2020
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This study focuses on the chemical reaction between Fe(II) and nitrite, which has been reported to produce high levels of the greenhouse gas N2O. We investigated the extent to which dead biomass and Fe(II) minerals might enhance this reaction. Here, nitrite reduction was highest when both additives were present but less pronounced if only Fe(II) minerals were added. Both reaction systems show distinct differences, rather low N2O levels, and indicated the abiotic production of N2.
Lisa Tanet, Séverine Martini, Laurie Casalot, and Christian Tamburini
Biogeosciences, 17, 3757–3778, https://doi.org/10.5194/bg-17-3757-2020, https://doi.org/10.5194/bg-17-3757-2020, 2020
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Bioluminescent bacteria, the most abundant light-emitting organisms in the ocean, can be free-living, be symbiotic or colonize organic particles. This review suggests that they act as a visual target and may indirectly influence the sequestration of biogenic carbon in oceans by increasing the attraction rate for consumers. We summarize the instrumentation available to quantify this impact in future studies and propose synthetic figures integrating these ecological and biogeochemical concepts.
Michael Lintner, Bianca Biedrawa, Julia Wukovits, Wolfgang Wanek, and Petra Heinz
Biogeosciences, 17, 3723–3732, https://doi.org/10.5194/bg-17-3723-2020, https://doi.org/10.5194/bg-17-3723-2020, 2020
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Foraminifera are unicellular marine organisms that play an important role in the marine element cycle. Changes of environmental parameters such as salinity or temperature have a significant impact on the faunal assemblages. Our experiments show that changing salinity in the German Wadden Sea immediately influences the foraminiferal community. It seems that A. tepida is better adapted to salinity fluctuations than H. germanica.
Kathrin Busch, Ulrike Hanz, Furu Mienis, Benjamin Mueller, Andre Franke, Emyr Martyn Roberts, Hans Tore Rapp, and Ute Hentschel
Biogeosciences, 17, 3471–3486, https://doi.org/10.5194/bg-17-3471-2020, https://doi.org/10.5194/bg-17-3471-2020, 2020
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Seamounts are globally abundant submarine structures that offer great potential to study the impacts and interactions of environmental gradients at a single geographic location. In an exemplary way, we describe potential mechanisms by which a seamount can affect the structure of pelagic and benthic (sponge-)associated microbial communities. We conclude that the geology, physical oceanography, biogeochemistry, and microbiology of seamounts are even more closely linked than currently appreciated.
Alexander Bratek, Justus E. E. van
Beusekom, Andreas Neumann, Tina Sanders, Jana Friedrich, Kay-Christian Emeis, and Kirstin Dähnke
Biogeosciences, 17, 2839–2851, https://doi.org/10.5194/bg-17-2839-2020, https://doi.org/10.5194/bg-17-2839-2020, 2020
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The following paper highlights the importance of benthic N-transformation rates in different sediment types in the southern North Sea as a source of fixed nitrogen for primary producers and also as a sink of fixed nitrogen. Sedimentary fluxes of dissolved inorganic nitrogen support ∼7 to 59 % of the average annual primary production. Semi-permeable and permeable sediments contribute ∼68 % of the total benthic N2 production rates, counteracting eutrophication in the southern North Sea.
Sabine Haalboom, David M. Price, Furu Mienis, Judith D. L. van Bleijswijk, Henko C. de Stigter, Harry J. Witte, Gert-Jan Reichart, and Gerard C. A. Duineveld
Biogeosciences, 17, 2499–2519, https://doi.org/10.5194/bg-17-2499-2020, https://doi.org/10.5194/bg-17-2499-2020, 2020
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Mineral mining in deep-sea hydrothermal settings will lead to the formation of plumes of fine-grained, chemically reactive, suspended matter. Understanding how natural hydrothermal plumes evolve as they disperse from their source, and how they affect their surrounding environment, may help in characterising the behaviour of the diluted part of mining plumes. The natural plume provided a heterogeneous, geochemically enriched habitat conducive to the development of a distinct microbial ecology.
Noelle A. Held, Eric A. Webb, Matthew M. McIlvin, David A. Hutchins, Natalie R. Cohen, Dawn M. Moran, Korinna Kunde, Maeve C. Lohan, Claire Mahaffey, E. Malcolm S. Woodward, and Mak A. Saito
Biogeosciences, 17, 2537–2551, https://doi.org/10.5194/bg-17-2537-2020, https://doi.org/10.5194/bg-17-2537-2020, 2020
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Trichodesmium is a globally important marine nitrogen fixer that stimulates primary production in the surface ocean. We surveyed metaproteomes of Trichodesmium populations across the North Atlantic and other oceans, and we found that they experience simultaneous phosphate and iron stress because of the biophysical limits of nutrient uptake. Importantly, nitrogenase was most abundant during co-stress, indicating the potential importance of this phenotype to global nitrogen and carbon cycling.
Helmke Hepach, Claire Hughes, Karen Hogg, Susannah Collings, and Rosie Chance
Biogeosciences, 17, 2453–2471, https://doi.org/10.5194/bg-17-2453-2020, https://doi.org/10.5194/bg-17-2453-2020, 2020
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Tropospheric iodine takes part in numerous atmospheric chemical cycles, including tropospheric ozone destruction and aerosol formation. Due to its significance for atmospheric processes, it is crucial to constrain its sources and sinks. This paper aims at investigating and understanding features of biogenic iodate-to-iodide reduction in microalgal monocultures. We find that phytoplankton senescence may play a crucial role in the release of iodide to the marine environment.
Roger D. Finlay, Shahid Mahmood, Nicholas Rosenstock, Emile B. Bolou-Bi, Stephan J. Köhler, Zaenab Fahad, Anna Rosling, Håkan Wallander, Salim Belyazid, Kevin Bishop, and Bin Lian
Biogeosciences, 17, 1507–1533, https://doi.org/10.5194/bg-17-1507-2020, https://doi.org/10.5194/bg-17-1507-2020, 2020
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Effects of biological activity on mineral weathering operate at scales ranging from short-term, microscopic interactions to global, evolutionary timescale processes. Microorganisms have had well-documented effects at large spatio-temporal scales, but to establish the quantitative significance of microscopic measurements for field-scale processes, higher-resolution studies of liquid chemistry at local weathering sites and improved upscaling to soil-scale dissolution rates are still required.
Christine Rooks, James Kar-Hei Fang, Pål Tore Mørkved, Rui Zhao, Hans Tore Rapp, Joana R. Xavier, and Friederike Hoffmann
Biogeosciences, 17, 1231–1245, https://doi.org/10.5194/bg-17-1231-2020, https://doi.org/10.5194/bg-17-1231-2020, 2020
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Sponge grounds are known as nutrient sources, providing nitrate and ammonium to the ocean. We found that they also can do the opposite: in six species from Arctic and North Atlantic sponge grounds, we measured high rates of denitrification, which remove these nutrients from the sea. Rates were highest when the sponge tissue got low in oxygen, which happens when sponges stop pumping because of stress. Sponge grounds may become nutrient sinks when exposed to stress.
Cheng Li, Clare E. Reimers, and Yvan Alleau
Biogeosciences, 17, 597–607, https://doi.org/10.5194/bg-17-597-2020, https://doi.org/10.5194/bg-17-597-2020, 2020
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Novel filamentous cable bacteria that grow in the top layer of intertidal mudflat sediment were attracted to electrodes poised at a positive electrical potential. Several diverse morphologies of Desulfobulbaceae filaments, cells, and colonies were observed on the electrode surface. These observations provide information to suggest conditions that will induce cable bacteria to perform electron donation to an electrode, informing future experiments that culture cable bacteria outside of sediment.
Marie Maßmig, Jan Lüdke, Gerd Krahmann, and Anja Engel
Biogeosciences, 17, 215–230, https://doi.org/10.5194/bg-17-215-2020, https://doi.org/10.5194/bg-17-215-2020, 2020
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Little is known about the rates of bacterial element cycling in oxygen minimum zones (OMZs). We measured bacterial production and rates of extracellular hydrolytic enzymes at various in situ oxygen concentrations in the OMZ off Peru. Our field data show unhampered bacterial activity at low oxygen concentrations. Meanwhile bacterial degradation of organic matter substantially contributed to the formation of the OMZ.
Anna T. Kunert, Mira L. Pöhlker, Kai Tang, Carola S. Krevert, Carsten Wieder, Kai R. Speth, Linda E. Hanson, Cindy E. Morris, David G. Schmale III, Ulrich Pöschl, and Janine Fröhlich-Nowoisky
Biogeosciences, 16, 4647–4659, https://doi.org/10.5194/bg-16-4647-2019, https://doi.org/10.5194/bg-16-4647-2019, 2019
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A screening of more than 100 strains from 65 different species revealed that the ice nucleation activity within the fungal genus Fusarium is more widespread than previously assumed. Filtration experiments suggest that the single cell-free Fusarium IN is smaller than 100 kDa (~ 6 nm) and that aggregates can be formed in solution. Exposure experiments, freeze–thaw cycles, and long-term storage tests demonstrate a high stability of Fusarium IN under atmospherically relevant conditions.
Qing Wang, Renbin Zhu, Yanling Zheng, Tao Bao, and Lijun Hou
Biogeosciences, 16, 4113–4128, https://doi.org/10.5194/bg-16-4113-2019, https://doi.org/10.5194/bg-16-4113-2019, 2019
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We investigated abundance, potential activity, and diversity of soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) in five Antarctic tundra patches, including penguin colony, seal colony, and tundra marsh. We have found (1) sea animal colonization increased AOB population size.; (2) AOB contributed to ammonia oxidation rates more than AOA in sea animal colonies; (3) community structures of AOB and AOA were closely related to soil biogeochemical processes associated with animal activities.
Yalda Vasebi, Marco E. Mechan Llontop, Regina Hanlon, David G. Schmale III, Russell Schnell, and Boris A. Vinatzer
Biogeosciences, 16, 1675–1683, https://doi.org/10.5194/bg-16-1675-2019, https://doi.org/10.5194/bg-16-1675-2019, 2019
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Ice nucleation particles (INPs) help ice form at temperatures as high as −4 °C and contribute to the formation of precipitation. Leaf litter contains a high concentration of INPs, but the organisms that produce them are unknown. Here, we cultured two bacteria and one fungus from leaf litter that produce INPs similar to those found in leaf litter. This suggests that leaf litter may be an important habitat of these organisms and supports a role of these organisms as producers of atmospheric INPs.
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.
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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.
This work focuses on one of the essential pathways of mycorrhizal impact on C cycles: the...
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