Articles | Volume 17, issue 6
https://doi.org/10.5194/bg-17-1507-2020
© Author(s) 2020. 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-17-1507-2020
© Author(s) 2020. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Reviews and syntheses
| 
25 Mar 2020
Reviews and syntheses |
| 25 Mar 2020
| 25 Mar 2020
Reviews and syntheses: Biological weathering and its consequences at different spatial levels – from nanoscale to global scale
Uppsala BioCenter, Department of Forest Mycology and Plant Pathology,
Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
Shahid Mahmood
Uppsala BioCenter, Department of Forest Mycology and Plant Pathology,
Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
Nicholas Rosenstock
Department of Biology, Lund University, Box 117, 221 00 Lund,
Sweden
Emile B. Bolou-Bi
Université Felix Houphouët-Boigny, UFR des Sciences de la
Terre et des Ressources Minières, Departement des Sciences du sol, BP
582 Abidjan 22, Côte D'Ivoire
Stephan J. Köhler
Soil-Water-Environment Center, Department of Aquatic Sciences and
Assessment, Swedish University of Agricultural Sciences, 750 07 Uppsala,
Sweden
Zaenab Fahad
Uppsala BioCenter, Department of Forest Mycology and Plant Pathology,
Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
Department of Ecology and Genetics, EBC, Uppsala University 752 36
Uppsala, Sweden
Anna Rosling
Department of Ecology and Genetics, EBC, Uppsala University 752 36
Uppsala, Sweden
Håkan Wallander
Department of Biology, Lund University, Box 117, 221 00 Lund,
Sweden
Salim Belyazid
Department of Physical Geography, Stockholm University, 106 91
Stockholm, Sweden
Kevin Bishop
Soil-Water-Environment Center, Department of Aquatic Sciences and
Assessment, Swedish University of Agricultural Sciences, 750 07 Uppsala,
Sweden
College of Marine Sciences and Engineering, Nanjing Normal University,
Nanjing 210023, China
Related authors
Cecilia Akselsson, Salim Belyazid, Johan Stendahl, Roger Finlay, Bengt A. Olsson, Martin Erlandsson Lampa, Håkan Wallander, Jon Petter Gustafsson, and Kevin Bishop
Biogeosciences, 16, 4429–4450, https://doi.org/10.5194/bg-16-4429-2019, https://doi.org/10.5194/bg-16-4429-2019, 2019
Short summary
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The release of elements from soil through weathering is an important process, controlling nutrient availability for plants and recovery from acidification. However, direct measurements cannot be done, and present estimates are burdened with high uncertainties. In this paper we use different approaches to quantify weathering rates in different scales in Sweden and discuss the pros and cons. The study contributes to more robust assessments of sustainable harvesting of forest biomass.
Nicholas P. Rosenstock, Patrick A. W. van Hees, Petra M. A. Fransson, Roger D. Finlay, and Anna Rosling
Biogeosciences, 16, 3637–3649, https://doi.org/10.5194/bg-16-3637-2019, https://doi.org/10.5194/bg-16-3637-2019, 2019
Short summary
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We examined the effects of elevated CO2, pine seedlings, and ectomycorrhizal fungi on mineral weathering. Seedlings significantly increased mineral weathering, while elevated CO2 increased plant growth and organic acid concentrations but had no effect on weathering. Ectomycorrhial fungi showed some tendency to increase weathering. We conclude that nutrient uptake, which reduces transport limitation to weathering, is the primary mechanism by which plants enhanced weathering in this system.
Daniel Escobar, Stefano Manzoni, Jeimar Tapasco, and Salim Belyazid
EGUsphere, https://doi.org/10.5194/egusphere-2024-2754, https://doi.org/10.5194/egusphere-2024-2754, 2024
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We studied carbon dynamics in afforested, drained peatlands using the ForSAFE-Peat model over two forest rotations. Our simulations showed that while trees store carbon, significant soil carbon losses occur, particularly early on, indicating that forest growth may not fully offset these losses once carbon time dynamics are considered. This emphasizes the need to consider both soil and harvested wood products when evaluating the climate impact of such systems.
Erik Schwarz, Samia Ghersheen, Salim Belyazid, and Stefano Manzoni
Biogeosciences, 21, 3441–3461, https://doi.org/10.5194/bg-21-3441-2024, https://doi.org/10.5194/bg-21-3441-2024, 2024
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The occurrence of unstable equilibrium points (EPs) could impede the applicability of microbial-explicit soil organic carbon models. For archetypal model versions we identify when instability can occur and describe mathematical conditions to avoid such unstable EPs. We discuss implications for further model development, highlighting the important role of considering basic ecological principles to ensure biologically meaningful models.
Veronika Kronnäs, Klas Lucander, Giuliana Zanchi, Nadja Stadlinger, Salim Belyazid, and Cecilia Akselsson
Biogeosciences, 20, 1879–1899, https://doi.org/10.5194/bg-20-1879-2023, https://doi.org/10.5194/bg-20-1879-2023, 2023
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In a future climate, extreme droughts might become more common. Climate change and droughts can have negative effects on soil weathering and plant health.
In this study, climate change effects on weathering were studied on sites in Sweden using the model ForSAFE, a climate change scenario and an extreme drought scenario. The modelling shows that weathering is higher during summer and increases with global warming but that weathering during drought summers can become as low as winter weathering.
Jana Erdbrügger, Ilja van Meerveld, Jan Seibert, and Kevin Bishop
Earth Syst. Sci. Data, 15, 1779–1800, https://doi.org/10.5194/essd-15-1779-2023, https://doi.org/10.5194/essd-15-1779-2023, 2023
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Groundwater can respond quickly to precipitation and is the main source of streamflow in most catchments in humid, temperate climates. To better understand shallow groundwater dynamics, we installed a network of groundwater wells in two boreal headwater catchments in Sweden. We recorded groundwater levels in 75 wells for 2 years and sampled the water and analyzed its chemical composition in one summer. This paper describes these datasets.
Juan Pablo Almeida, Lorenzo Menichetti, Alf Ekblad, Nicholas P. Rosenstock, and Håkan Wallander
Biogeosciences, 20, 1443–1458, https://doi.org/10.5194/bg-20-1443-2023, https://doi.org/10.5194/bg-20-1443-2023, 2023
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In forests, trees allocate a significant amount of carbon belowground to support mycorrhizal symbiosis. In northern forests nitrogen normally regulates this allocation and consequently mycorrhizal fungi growth. In this study we demonstrate that in a conifer forest from Sweden, fungal growth is regulated by phosphorus instead of nitrogen. This is probably due to an increase in nitrogen deposition to soils caused by decades of human pollution that has altered the ecosystem nutrient regime.
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.
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.
Gustaf Granath, Christopher D. Evans, Joachim Strengbom, Jens Fölster, Achim Grelle, Johan Strömqvist, and Stephan J. Köhler
Biogeosciences, 18, 3243–3261, https://doi.org/10.5194/bg-18-3243-2021, https://doi.org/10.5194/bg-18-3243-2021, 2021
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We measured element losses and impacts on water quality following a wildfire in Sweden. We observed the largest carbon and nitrogen losses during the fire and a strong pulse of elements 1–3 months after the fire that showed a fast (weeks) and a slow (months) release from the catchments. Total carbon export through water did not increase post-fire. Overall, we observed a rapid recovery of the biogeochemical cycling of elements within 3 years but still an annual net release of carbon dioxide.
Martin Erlandsson Lampa, Harald U. Sverdrup, Kevin H. Bishop, Salim Belyazid, Ali Ameli, and Stephan J. Köhler
SOIL, 6, 231–244, https://doi.org/10.5194/soil-6-231-2020, https://doi.org/10.5194/soil-6-231-2020, 2020
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In this study, we demonstrate how new equations describing base cation release from mineral weathering can reproduce patterns in observations from stream and soil water. This is a major step towards modeling base cation cycling on the catchment scale, which would be valuable for defining the highest sustainable rates of forest harvest and levels of acidifying deposition.
Harald Ulrik Sverdrup, Eric H. Oelkers, Martin Erlandsson Lampa, Salim Belyazid, Daniel Kurz, and Cecilia Akselsson
Biogeosciences Discuss., https://doi.org/10.5194/bg-2019-464, https://doi.org/10.5194/bg-2019-464, 2020
Manuscript not accepted for further review
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Equations, parameters and constants describing mineral dissolution kinetics have now been obtained for 113 minerals from 12 major structural groups, comprising all types of minerals encountered in most soils. The PROFILE and ForSAFE weathering sub-model was extended to cover two-dimensional catchments, both in the vertical and the horizontal direction, including the hydrology.
Nicholas P. Rosenstock, Johan Stendahl, Gregory van der Heijden, Lars Lundin, Eric McGivney, Kevin Bishop, and Stefan Löfgren
SOIL, 5, 351–366, https://doi.org/10.5194/soil-5-351-2019, https://doi.org/10.5194/soil-5-351-2019, 2019
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Biofuel harvests from forests involve large removals of available nutrients, necessitating accurate measurements of soil nutrient stocks. We found that dilute hydrochloric acid extractions from soils released far more Ca, Na, and K than classical salt–extracted exchangeable nutrient pools. The size of these acid–extractable pools may indicate that forest ecosystems could sustain greater biomass extractions of Ca, Mg, and K than are predicted from salt–extracted exchangeable base cation pools.
Cecilia Akselsson, Salim Belyazid, Johan Stendahl, Roger Finlay, Bengt A. Olsson, Martin Erlandsson Lampa, Håkan Wallander, Jon Petter Gustafsson, and Kevin Bishop
Biogeosciences, 16, 4429–4450, https://doi.org/10.5194/bg-16-4429-2019, https://doi.org/10.5194/bg-16-4429-2019, 2019
Short summary
Short summary
The release of elements from soil through weathering is an important process, controlling nutrient availability for plants and recovery from acidification. However, direct measurements cannot be done, and present estimates are burdened with high uncertainties. In this paper we use different approaches to quantify weathering rates in different scales in Sweden and discuss the pros and cons. The study contributes to more robust assessments of sustainable harvesting of forest biomass.
Nicholas P. Rosenstock, Patrick A. W. van Hees, Petra M. A. Fransson, Roger D. Finlay, and Anna Rosling
Biogeosciences, 16, 3637–3649, https://doi.org/10.5194/bg-16-3637-2019, https://doi.org/10.5194/bg-16-3637-2019, 2019
Short summary
Short summary
We examined the effects of elevated CO2, pine seedlings, and ectomycorrhizal fungi on mineral weathering. Seedlings significantly increased mineral weathering, while elevated CO2 increased plant growth and organic acid concentrations but had no effect on weathering. Ectomycorrhial fungi showed some tendency to increase weathering. We conclude that nutrient uptake, which reduces transport limitation to weathering, is the primary mechanism by which plants enhanced weathering in this system.
Salim Belyazid, Cecilia Akselsson, and Giuliana Zanchi
Biogeosciences Discuss., https://doi.org/10.5194/bg-2019-44, https://doi.org/10.5194/bg-2019-44, 2019
Revised manuscript not accepted
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The release of base cations from mineral weathering is expected to increase in response to higher temperatures associated with climate change. By considering the effect of changes in moisture, this study shows that climate change will lead to an increase in weathering rates, but to lower extent than expected due to water limitation. The study uses an integrated forest ecosystem model that simultaneously simulates changes in soil and vegetation and the feedbacks between them.
Harald Ulrik Sverdrup, Eric Oelkers, Martin Erlandsson Lampa, Salim Belyazid, Daniel Kurz, and Cecilia Akselsson
Biogeosciences Discuss., https://doi.org/10.5194/bg-2019-38, https://doi.org/10.5194/bg-2019-38, 2019
Revised manuscript not accepted
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The present publication documents the kinetic parameterisation of the related PROFILE (steady state) and ForSAFE (integrated dynamics) models. It gives the full coefficient database for about 100 minerals occurring in most soils. The text outlines the principles and methods used in setting the coefficient values. It outlines how the models with the parameterisation based on laboratory kinetics, is successful in estimating field weathering rates similar to what is being observed.
Eric McGivney, Jon Petter Gustafsson, Salim Belyazid, Therese Zetterberg, and Stefan Löfgren
SOIL, 5, 63–77, https://doi.org/10.5194/soil-5-63-2019, https://doi.org/10.5194/soil-5-63-2019, 2019
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Forest management may lead to long-term soil acidification due to the removal of base cations during harvest. By means of the HD-MINTEQ model, we compared the acidification effects of harvesting with the effects of historical acid rain at three forested sites in Sweden. The effects of harvesting on pH were predicted to be much smaller than those resulting from acid deposition during the 20th century. There were only very small changes in predicted weathering rates due to acid rain or harvest.
Veronika Kronnäs, Cecilia Akselsson, and Salim Belyazid
SOIL, 5, 33–47, https://doi.org/10.5194/soil-5-33-2019, https://doi.org/10.5194/soil-5-33-2019, 2019
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Weathering rates in forest soils are important for sustainable forestry but cannot be measured. In this paper, we have modelled weathering with the commonly used PROFILE model as well as with the dynamic model ForSAFE, better suited to a changing climate with changing human activities but never before tested for weathering calculations. We show that ForSAFE gives comparable weathering rates to PROFILE and that it shows the variation in weathering with time and works well for scenario modelling.
Jon Petter Gustafsson, Salim Belyazid, Eric McGivney, and Stefan Löfgren
SOIL, 4, 237–250, https://doi.org/10.5194/soil-4-237-2018, https://doi.org/10.5194/soil-4-237-2018, 2018
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This paper investigates how different dynamic soil chemistry models describe the processes governing aluminium and base cations in acid soil waters. We find that traditional cation-exchange equations, which are still used in many models, diverge from state-of-the-art complexation submodels such as WHAM, SHM, and NICA-Donnan when large fluctuations in pH or ionic strength occur. In conclusion, the complexation models provide a better basis for the modelling of chemical dynamics in acid soils.
Lixin Wang, Xiaohua Wei, Kevin Bishop, Alison D. Reeves, Nadia Ursino, and Rita Winkler
Hydrol. Earth Syst. Sci., 22, 1731–1734, https://doi.org/10.5194/hess-22-1731-2018, https://doi.org/10.5194/hess-22-1731-2018, 2018
Fredrik Lidman, Åsa Boily, Hjalmar Laudon, and Stephan J. Köhler
Biogeosciences, 14, 3001–3014, https://doi.org/10.5194/bg-14-3001-2017, https://doi.org/10.5194/bg-14-3001-2017, 2017
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The riparian zone is the narrow strip of land that lines a watercourse. This is the last soil that the groundwater is in contact with before it enters the stream and it therefore has a high impact on the water quality. In this paper we show that many elements occur in elevated concentrations in the peat-like riparian zone of boreal headwaters and that this also leads to elevated concentrations in the streams. Hence, understanding riparian soils is crucial for a sustainable management of streams.
S. Osterwalder, J. Fritsche, C. Alewell, M. Schmutz, M. B. Nilsson, G. Jocher, J. Sommar, J. Rinne, and K. Bishop
Atmos. Meas. Tech., 9, 509–524, https://doi.org/10.5194/amt-9-509-2016, https://doi.org/10.5194/amt-9-509-2016, 2016
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Human activities have increased mercury (Hg) cycling between land and atmosphere. To define landscapes as sinks or sources of Hg we have developed an advanced REA system for long-term measurements of gaseous elemental Hg exchange. It was tested in two contrasting environments: above Basel, Switzerland, and a peatland in Sweden. Both landscapes showed net Hg emission (15 and 3 ng m−2 h−1, respectively). The novel system will help to advance our understanding of Hg exchange on an ecosystem scale.
J. Temnerud, C. von Brömssen, J. Fölster, I. Buffam, J.-O. Andersson, L. Nyberg, and K. Bishop
Biogeosciences, 13, 399–413, https://doi.org/10.5194/bg-13-399-2016, https://doi.org/10.5194/bg-13-399-2016, 2016
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In this study we test whether river outlet chemistry can be used as an additional source of information to improve the prediction of the total organic carbon (TOC) of headwaters, relative to models based on map information alone. Including river outlet TOC as a predictor in the models gave 5-15 % lower prediction errors than using map information alone. Thus, data on water chemistry measured at river outlets offer information which can complement GIS-based modelling of headwaters chemistry.
F. I. Leith, K. J. Dinsmore, M. B. Wallin, M. F. Billett, K. V. Heal, H. Laudon, M. G. Öquist, and K. Bishop
Biogeosciences, 12, 1881–1892, https://doi.org/10.5194/bg-12-1881-2015, https://doi.org/10.5194/bg-12-1881-2015, 2015
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Carbon dioxide transport between the terrestrial and aquatic systems was dominated by export from the near-stream riparian zone. Over the year, riparian export was highest during autumn storms and the spring snowmelt event. This resulted in high downstream export during these periods with vertical evasion from the stream surface accounting for 60% of the total stream water export, highlighting the importance of evasion to carbon export via the aquatic conduit.
M. Dietzel, A. Leis, R. Abdalla, J. Savarino, S. Morin, M. E. Böttcher, and S. Köhler
Biogeosciences, 11, 3149–3161, https://doi.org/10.5194/bg-11-3149-2014, https://doi.org/10.5194/bg-11-3149-2014, 2014
J. L. J. Ledesma, T. Grabs, M. N. Futter, K. H. Bishop, H. Laudon, and S. J. Köhler
Biogeosciences, 10, 3849–3868, https://doi.org/10.5194/bg-10-3849-2013, https://doi.org/10.5194/bg-10-3849-2013, 2013
S. K. Oni, M. N. Futter, K. Bishop, S. J. Köhler, M. Ottosson-Löfvenius, and H. Laudon
Biogeosciences, 10, 2315–2330, https://doi.org/10.5194/bg-10-2315-2013, https://doi.org/10.5194/bg-10-2315-2013, 2013
Related subject area
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Overview: Global change effects on terrestrial biogeochemistry at the plant–soil interface
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Grazing mortality as a controlling factor in the uncultured non-cyanobacterial diazotroph (Gamma A) around the Kuroshio region
Changes in diazotrophic community structure associated with Kuroshio succession in the northern South China Sea
Technical note: A comparison of methods for estimating coccolith mass
Fractionation of stable carbon isotopes during formate consumption in anoxic rice paddy soils and lake sediments
Characteristics of bacterial and fungal communities and their associations with sugar compounds in atmospheric aerosols at a rural site in northern China
Responses of globally important phytoplankton species to olivine dissolution products and implications for carbon dioxide removal via ocean alkalinity enhancement
Differentiation of cognate bacterial communities in thermokarst landscapes: implications for ecological consequences of permafrost degradation
A multi-phase biogeochemical model for mitigating earthquake-induced liquefaction via microbially induced desaturation and calcium carbonate precipitation
Phosphorus regulates ectomycorrhizal fungi biomass production in a Norway spruce forest
Reallocation of elemental content and macromolecules in the coccolithophore Emiliania huxleyi to acclimate to climate change
Abrasion of sedimentary rocks as a source of hydrogen peroxide and nutrients to subglacial ecosystems
Nitrous oxide (N2O) synthesis by the freshwater cyanobacterium Microcystis aeruginosa
Interdisciplinary strategy to assess the impact of meteorological variables on the biochemical composition of the rain and the dynamics of a small eutrophic lake under rain forcing
Depth-related patterns in microbial community responses to complex organic matter in the western North Atlantic Ocean
Assessing the influence of ocean alkalinity enhancement on a coastal phytoplankton community
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Composition and niche-specific characteristics of microbial consortia colonizing Marsberg copper mine in the Rhenish Massif
Diversity and assembly processes of microbial eukaryotic communities in Fildes Peninsula Lakes (West Antarctica)
Nitrophobic ectomycorrhizal fungi are associated with enhanced hydrophobicity of soil organic matter in a Norway spruce forest
Physiological control on carbon isotope fractionation in marine phytoplankton
Implementation of mycorrhizal mechanisms into soil carbon model improves the prediction of long-term processes of plant litter decomposition
Impact of dust addition on the microbial food web under present and future conditions of pH and temperature
Fractionation of stable carbon isotopes during acetate consumption by methanogenic and sulfidogenic microbial communities in rice paddy soils and lake sediments
Hydrothermal trace metal release and microbial metabolism in the northeastern Lau Basin of the South Pacific Ocean
Sedimentation rate and organic matter dynamics shape microbiomes across a continental margin
Disturbance triggers non-linear microbe–environment feedbacks
Hydrographic fronts shape productivity, nitrogen fixation, and microbial community composition in the southern Indian Ocean and the Southern Ocean
Microbial and geo-archaeological records reveal the growth rate, origin and composition of desert rock surface communities
Metagenomic insights into the metabolism of microbial communities that mediate iron and methane cycling in Lake Kinneret iron-rich methanic sediments
Spatiotemporal patterns of N2 fixation in coastal waters derived from rate measurements and remote sensing
Biotic and abiotic transformation of amino acids in cloud water: experimental studies and atmospheric implications
Potential bioavailability of organic matter from atmospheric particles to marine heterotrophic bacteria
Microbial functional signature in the atmospheric boundary layer
New insight to niche partitioning and ecological function of ammonia oxidizing archaea in subtropical estuarine ecosystem
Impact of reactive surfaces on the abiotic reaction between nitrite and ferrous iron and associated nitrogen and oxygen isotope dynamics
Reviews and syntheses: Bacterial bioluminescence – ecology and impact in the biological carbon pump
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Adrian Barry-Sosa, Madison K. Flint, Justin C. Ellena, Jonathan B. Martin, and Brent C. Christner
Biogeosciences, 21, 3965–3984, https://doi.org/10.5194/bg-21-3965-2024, https://doi.org/10.5194/bg-21-3965-2024, 2024
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This study examined springs in north central Florida focusing on how interactions between the surface and subsurface affected the properties of groundwater microbes. We found that microbes reproduced at rates that greatly exceed those documented for any other aquifer. Although the groundwater discharged to spring runs contains low concentrations of nutrients, our results indicate that microbes have access to sources of energy and produce new cells at rates similar to surface waterbodies.
Lucia Fuchslueger, Emily Francesca Solly, Alberto Canarini, and Albert Carles Brangarí
Biogeosciences, 21, 3959–3964, https://doi.org/10.5194/bg-21-3959-2024, https://doi.org/10.5194/bg-21-3959-2024, 2024
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This overview of the special issue “Global change effects on terrestrial biogeochemistry at the plant–soil interface” features empirical, conceptual and modelling-based studies and outlines key findings on plant responses to elevated CO2; soil organism responses to warming; impacts on soil organic carbon, nitrogen and mineral nutrient cycling; and water level changes affecting greenhouse gas emissions, from the Arctic to the tropics, which are crucial for deciphering feedbacks to global change.
Barbara Ervens, Pierre Amato, Kifle Aregahegn, Muriel Joly, Amina Khaled, Tiphaine Labed-Veydert, Frédéric Mathonat, Leslie Nuñez López, Raphaëlle Péguilhan, and Minghui Zhang
EGUsphere, https://doi.org/10.5194/egusphere-2024-2377, https://doi.org/10.5194/egusphere-2024-2377, 2024
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Atmospheric microorganisms are a small fraction of Earth's microbiome, with bacteria being a significant part. Aerosolized bacteria are airborne for a few days encountering unique chemical and physical conditions affecting stress levels and survival. We explore chemical and microphysical conditions bacteria encounter, highlighting potential nutrient and oxidant limitations and diverse effects by pollutants, which may ultimately impact the microbiome's role in global ecosystems and biodiversity.
Takuya Sato, Tamaha Yamaguchi, Kiyotaka Hidataka, Sayaka Sogawa, Takashi Setou, Taketoshi Kodama, Takuhei Shiozaki, and Kazutaka Takahashi
EGUsphere, https://doi.org/10.5194/egusphere-2024-1294, https://doi.org/10.5194/egusphere-2024-1294, 2024
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Gamma A is a widespread non-cyanobacterial diazotroph and plays a crucial role for marine ecosystems, but its controlling factors are still largely unknown. This study, for the first time, quantified microzooplankton grazing on Gamma A and revealed significance of grazing pressure on Gamma A distribution around the Kuroshio region. It highlights the importance of top-down controls on Gamma A abundance and the associated nitrogen cycle.
Han Zhang, Guangming Mai, Weicheng Luo, Meng Chen, Ran Duan, and Tuo Shi
Biogeosciences, 21, 2529–2546, https://doi.org/10.5194/bg-21-2529-2024, https://doi.org/10.5194/bg-21-2529-2024, 2024
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We report taxon-specific biogeography of N2-fixing microbes (diazotrophs) driven by Kuroshio intrusion (Kl) into the South China Sea. We show that the composition and distribution of distinct diazotrophic taxa shift with Kl-induced variations in physicochemical parameters of seawater and that Kl shapes diazotrophic community primarily as a stochastic process. This study thus has implications for the distribution of diazotrophs in a future warming ocean, as Kls are projected to intensify.
Celina Rebeca Valença, Luc Beaufort, Gustaaf Marinus Hallegraeff, and Marius Nils Müller
Biogeosciences, 21, 1601–1611, https://doi.org/10.5194/bg-21-1601-2024, https://doi.org/10.5194/bg-21-1601-2024, 2024
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Coccolithophores contribute to the global carbon cycle and their calcite structures (coccoliths) are used as a palaeoproxy to understand past oceanographic conditions. Here, we compared three frequently used methods to estimate coccolith mass from the model species Emiliania huxleyi and the results allow for a high level of comparability between the methods, facilitating future comparisons and consolidation of mass changes observed from ecophysiological and biogeochemical studies.
Ralf Conrad and Peter Claus
Biogeosciences, 21, 1161–1172, https://doi.org/10.5194/bg-21-1161-2024, https://doi.org/10.5194/bg-21-1161-2024, 2024
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Knowledge of carbon isotope fractionation is important for the assessment of the pathways involved in the degradation of organic matter. Formate is an important intermediate during this process. It was mainly converted to carbon dioxide and acetate both in the presence and absence of sulfate. Methane was only a minor product and was mainly formed from the acetate. The acetate was depleted in the heavy carbon atom relative to formate, while the carbon dioxide was enriched.
Mutong Niu, Shu Huang, Wei Hu, Yajie Wang, Wanyun Xu, Wan Wei, Qiang Zhang, Zihan Wang, Donghuan Zhang, Rui Jin, Libin Wu, Junjun Deng, Fangxia Shen, and Pingqing Fu
Biogeosciences, 20, 4915–4930, https://doi.org/10.5194/bg-20-4915-2023, https://doi.org/10.5194/bg-20-4915-2023, 2023
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Sugar compounds in air can trace the source of bioaerosols that affect public health and climate. In rural north China, we observed increased fungal activity at night and less variable bacterial community diversity. Certain night-increasing sugar compounds were more closely related to fungi than bacteria. The fungal community greatly influenced sugar compounds, while bacteria played a limited role. Caution is advised when using sugar compounds to trace airborne microbes, particularly bacteria.
David A. Hutchins, Fei-Xue Fu, Shun-Chung Yang, Seth G. John, Stephen J. Romaniello, M. Grace Andrews, and Nathan G. Walworth
Biogeosciences, 20, 4669–4682, https://doi.org/10.5194/bg-20-4669-2023, https://doi.org/10.5194/bg-20-4669-2023, 2023
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Applications of the mineral olivine are a promising means to capture carbon dioxide via coastal enhanced weathering, but little is known about the impacts on important marine phytoplankton. We examined the effects of olivine dissolution products on species from three major phytoplankton groups: diatoms, coccolithophores, and cyanobacteria. Growth and productivity were generally either unaffected or stimulated, suggesting the effects of olivine on key phytoplankton are negligible or positive.
Ze Ren, Shudan Ye, Hongxuan Li, Xilei Huang, and Luyao Chen
Biogeosciences, 20, 4241–4258, https://doi.org/10.5194/bg-20-4241-2023, https://doi.org/10.5194/bg-20-4241-2023, 2023
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Permafrost thaw initiates thermokarst landscape formation, resulting in distinct new habitats, including degraded permafrost soil, thermokarst lake sediments, and lake water. These distinct habitats harbored differentiated bacterial communities that originated from the same source, differing in diversity, assembly mechanisms, and environmental influences. The results imply ecological consequences of permafrost degradation in the face of further climate change.
Caitlyn A. Hall, Andre van Turnhout, Edward Kavazanjian Jr., Leon A. van Paassen, and Bruce Rittmann
Biogeosciences, 20, 2903–2917, https://doi.org/10.5194/bg-20-2903-2023, https://doi.org/10.5194/bg-20-2903-2023, 2023
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Earthquake-induced soil liquefaction poses a significant global threat. Microbially induced desaturation and precipitation (MIDP) via denitrification is a potentially sustainable, non-disruptive bacteria-driven ground improvement technique under existing structures. We developed a next-generation biogeochemical model to understand and predict the behavior of MIDP in the natural environment to design field-based hazard mitigation treatments.
Juan Pablo Almeida, Lorenzo Menichetti, Alf Ekblad, Nicholas P. Rosenstock, and Håkan Wallander
Biogeosciences, 20, 1443–1458, https://doi.org/10.5194/bg-20-1443-2023, https://doi.org/10.5194/bg-20-1443-2023, 2023
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In forests, trees allocate a significant amount of carbon belowground to support mycorrhizal symbiosis. In northern forests nitrogen normally regulates this allocation and consequently mycorrhizal fungi growth. In this study we demonstrate that in a conifer forest from Sweden, fungal growth is regulated by phosphorus instead of nitrogen. This is probably due to an increase in nitrogen deposition to soils caused by decades of human pollution that has altered the ecosystem nutrient regime.
Yong Zhang, Yong Zhang, Shuai Ma, Hanbing Chen, Jiabing Li, Zhengke Li, Kui Xu, Ruiping Huang, Hong Zhang, Yonghe Han, and Jun Sun
Biogeosciences, 20, 1299–1312, https://doi.org/10.5194/bg-20-1299-2023, https://doi.org/10.5194/bg-20-1299-2023, 2023
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We found that increasing light intensity compensates for the negative effects of low phosphorus (P) availability on cellular protein and nitrogen contents. Reduced P availability, increasing light intensity, and ocean acidification act synergistically to increase cellular contents of carbohydrate and POC and the allocation of POC to carbohydrate. These regulation mechanisms in Emiliania huxleyi could provide vital information for evaluating carbon cycle in marine ecosystems under global change.
Beatriz Gill-Olivas, Jon Telling, Mark Skidmore, and Martyn Tranter
Biogeosciences, 20, 929–943, https://doi.org/10.5194/bg-20-929-2023, https://doi.org/10.5194/bg-20-929-2023, 2023
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Microbial ecosystems have been found in all subglacial environments sampled to date. Yet, little is known of the sources of energy and nutrients that sustain these microbial populations. This study shows that crushing of sedimentary rocks, which contain organic carbon, carbonate and sulfide minerals, along with previously weathered silicate minerals, produces a range of compounds and nutrients which can be utilised by the diverse suite of microbes that inhabit glacier beds.
Federico Fabisik, Benoit Guieysse, Jonathan Procter, and Maxence Plouviez
Biogeosciences, 20, 687–693, https://doi.org/10.5194/bg-20-687-2023, https://doi.org/10.5194/bg-20-687-2023, 2023
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We show, for the first time, that pure cultures of the cyanobacterium Microcystis aeruginosa can synthesize the potent greenhouse gas N2O using nitrite as substrate. Our findings have broad environmental implications because M. aeruginosa is globally found in freshwater ecosystems and is often the dominant species found in algae blooms. Further research is now needed to determine the occurrence and significance of N2O emissions from ecosystems rich with M. aeruginosa.
Fanny Noirmain, Jean-Luc Baray, Frédéric Tridon, Philippe Cacault, Hermine Billard, Guillaume Voyard, Joël Van Baelen, and Delphine Latour
Biogeosciences, 19, 5729–5749, https://doi.org/10.5194/bg-19-5729-2022, https://doi.org/10.5194/bg-19-5729-2022, 2022
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We present a study linking rain, meteorology, and mountain lake phytoplankton dynamics on the basis of a case study at Aydat (France) in September 2020. The air mass origin mainly influences the rain chemical composition, which depends on the type of rain, convective or stratiform. Our results also highlighted a non-negligible presence of photosynthetic cells in rainwater. The impact of the atmospheric forcing on the lake could play a key role in phytoplankton dynamics in the temperate zone.
Sarah A. Brown, John Paul Balmonte, Adrienne Hoarfrost, Sherif Ghobrial, and Carol Arnosti
Biogeosciences, 19, 5617–5631, https://doi.org/10.5194/bg-19-5617-2022, https://doi.org/10.5194/bg-19-5617-2022, 2022
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Bacteria use extracellular enzymes to cut large organic matter to sizes small enough for uptake. We compared the enzymatic response of surface, mid-water, and deep-ocean bacteria to complex natural substrates. Bacteria in surface and mid-depth waters produced a much wider range of enzymes than those in the deep ocean and may therefore consume a broader range of organic matter. The extent to which organic matter is recycled by bacteria depends in part on its residence time at different depths.
Aaron Ferderer, Zanna Chase, Fraser Kennedy, Kai G. Schulz, and Lennart T. Bach
Biogeosciences, 19, 5375–5399, https://doi.org/10.5194/bg-19-5375-2022, https://doi.org/10.5194/bg-19-5375-2022, 2022
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Ocean alkalinity enhancement has the capacity to remove vast quantities of carbon from the atmosphere, but its effect on marine ecosystems is largely unknown. We assessed the effect of increased alkalinity on a coastal phytoplankton community when seawater was equilibrated and not equilibrated with atmospheric CO2. We found that the phytoplankton community was moderately affected by increased alkalinity and equilibration with atmospheric CO2 had little influence on this effect.
Quentin Devresse, Kevin W. Becker, Arne Bendinger, Johannes Hahn, and Anja Engel
Biogeosciences, 19, 5199–5219, https://doi.org/10.5194/bg-19-5199-2022, https://doi.org/10.5194/bg-19-5199-2022, 2022
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Eddies are ubiquitous in the ocean and alter physical, chemical, and biological processes. However, how they affect organic carbon production and consumption is largely unknown. Here we show how an eddy triggers a cascade effect on biomass production and metabolic activities of phyto- and bacterioplankton. Our results may contribute to the improvement of biogeochemical models used to estimate carbon fluxes in the ocean.
Sania Arif, Heiko Nacke, Elias Schliekmann, Andreas Reimer, Gernot Arp, and Michael Hoppert
Biogeosciences, 19, 4883–4902, https://doi.org/10.5194/bg-19-4883-2022, https://doi.org/10.5194/bg-19-4883-2022, 2022
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The natural enrichment of Chloroflexi (Ktedonobacteria) at the Kilianstollen Marsberg copper mine rocks being exposed to the acidic sulfate-rich leachate led to an investigation of eight metagenomically assembled genomes (MAGs) involved in copper and other transition heavy metal resistance in addition to low pH resistance and aromatic compounds degradation. The present study offers functional insights about a novel cold-adapted Ktedonobacteria MAG extremophily along with other phyla MAGs.
Chunmei Zhang, Huirong Li, Yinxin Zeng, Haitao Ding, Bin Wang, Yangjie Li, Zhongqiang Ji, Yonghong Bi, and Wei Luo
Biogeosciences, 19, 4639–4654, https://doi.org/10.5194/bg-19-4639-2022, https://doi.org/10.5194/bg-19-4639-2022, 2022
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The unique microbial eukaryotic community structure and lower diversity have been demonstrated in five freshwater lakes of the Fildes Peninsula, Antarctica. Stochastic processes and biotic co-occurrence patterns were shown to be important in shaping microbial eukaryotic communities in the area. Our study provides a better understanding of the dynamic patterns and ecological assembly processes of microbial eukaryotic communities in Antarctic oligotrophic lakes (Fildes Peninsula).
Juan Pablo Almeida, Nicholas P. Rosenstock, Susanne K. Woche, Georg Guggenberger, and Håkan Wallander
Biogeosciences, 19, 3713–3726, https://doi.org/10.5194/bg-19-3713-2022, https://doi.org/10.5194/bg-19-3713-2022, 2022
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Fungi living in symbiosis with tree roots can accumulate belowground, forming special tissues than can repel water. We measured the water repellency of organic material incubated belowground and correlated it with fungal growth. We found a positive association between water repellency and root symbiotic fungi. These results are important because an increase in soil water repellency can reduce the release of CO2 from soils into the atmosphere and mitigate the effects of greenhouse gasses.
Karen M. Brandenburg, Björn Rost, Dedmer B. Van de Waal, Mirja Hoins, and Appy Sluijs
Biogeosciences, 19, 3305–3315, https://doi.org/10.5194/bg-19-3305-2022, https://doi.org/10.5194/bg-19-3305-2022, 2022
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Reconstructions of past CO2 concentrations rely on proxy estimates, with one line of proxies relying on the CO2-dependence of stable carbon isotope fractionation in marine phytoplankton. Culturing experiments provide insights into which processes may impact this. We found, however, that the methods with which these culturing experiments are performed also influence 13C fractionation. Caution should therefore be taken when extrapolating results from these experiments to proxy applications.
Weilin Huang, Peter M. van Bodegom, Toni Viskari, Jari Liski, and Nadejda A. Soudzilovskaia
Biogeosciences, 19, 1469–1490, https://doi.org/10.5194/bg-19-1469-2022, https://doi.org/10.5194/bg-19-1469-2022, 2022
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This work focuses on one of the essential pathways of mycorrhizal impact on C cycles: the mediation of plant litter decomposition. We present a model based on litter chemical quality which precludes a conclusive examination of mycorrhizal impacts on soil C. It improves long-term decomposition predictions and advances our understanding of litter decomposition dynamics. It creates a benchmark in quantitatively examining the impacts of plant–microbe interactions on soil C dynamics.
Julie Dinasquet, Estelle Bigeard, Frédéric Gazeau, Farooq Azam, Cécile Guieu, Emilio Marañón, Céline Ridame, France Van Wambeke, Ingrid Obernosterer, and Anne-Claire Baudoux
Biogeosciences, 19, 1303–1319, https://doi.org/10.5194/bg-19-1303-2022, https://doi.org/10.5194/bg-19-1303-2022, 2022
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Saharan dust deposition of nutrients and trace metals is crucial to microbes in the Mediterranean Sea. Here, we tested the response of microbial and viral communities to simulated dust deposition under present and future conditions of temperature and pH. Overall, the effect of the deposition was dependent on the initial microbial assemblage, and future conditions will intensify microbial responses. We observed effects on trophic interactions, cascading all the way down to viral processes.
Ralf Conrad, Pengfei Liu, and Peter Claus
Biogeosciences, 18, 6533–6546, https://doi.org/10.5194/bg-18-6533-2021, https://doi.org/10.5194/bg-18-6533-2021, 2021
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Acetate is an important intermediate during the anaerobic degradation of organic matter. It is consumed by methanogenic and sulfidogenic microorganisms accompanied by stable carbon isotope fractionation. We determined isotope fractionation under different conditions in two paddy soils and two lake sediments and also determined the composition of the microbial communities. Despite a relatively wide range of experimental conditions, the range of fractionation factors was quite moderate.
Natalie R. Cohen, Abigail E. Noble, Dawn M. Moran, Matthew R. McIlvin, Tyler J. Goepfert, Nicholas J. Hawco, Christopher R. German, Tristan J. Horner, Carl H. Lamborg, John P. McCrow, Andrew E. Allen, and Mak A. Saito
Biogeosciences, 18, 5397–5422, https://doi.org/10.5194/bg-18-5397-2021, https://doi.org/10.5194/bg-18-5397-2021, 2021
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A previous study documented an intense hydrothermal plume in the South Pacific Ocean; however, the iron release associated with this plume and the impact on microbiology were unclear. We describe metal concentrations associated with multiple hydrothermal plumes in this region and protein signatures of plume-influenced microbes. Our findings demonstrate that resources released from these systems can be transported away from their source and may alter the physiology of surrounding microbes.
Sabyasachi Bhattacharya, Tarunendu Mapder, Svetlana Fernandes, Chayan Roy, Jagannath Sarkar, Moidu Jameela Rameez, Subhrangshu Mandal, Abhijit Sar, Amit Kumar Chakraborty, Nibendu Mondal, Sumit Chatterjee, Bomba Dam, Aditya Peketi, Ranadhir Chakraborty, Aninda Mazumdar, and Wriddhiman Ghosh
Biogeosciences, 18, 5203–5222, https://doi.org/10.5194/bg-18-5203-2021, https://doi.org/10.5194/bg-18-5203-2021, 2021
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Physicochemical determinants of microbiome architecture across continental shelves–slopes are unknown, so we explored the geomicrobiology along 3 m sediment horizons of seasonal (shallow coastal) and perennial (deep sea) hypoxic zones of the Arabian Sea. Nature, concentration, and fate of the organic matter delivered to the sea floor were found to shape the microbiome across the western Indian margin, under direct–indirect influence of sedimentation rate and water column O2 level.
Aditi Sengupta, Sarah J. Fansler, Rosalie K. Chu, Robert E. Danczak, Vanessa A. Garayburu-Caruso, Lupita Renteria, Hyun-Seob Song, Jason Toyoda, Jacqueline Hager, and James C. Stegen
Biogeosciences, 18, 4773–4789, https://doi.org/10.5194/bg-18-4773-2021, https://doi.org/10.5194/bg-18-4773-2021, 2021
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Conceptual models link microbes with the environment but are untested. We test a recent model using riverbed sediments. We exposed sediments to disturbances, going dry and becoming wet again. As the length of dry conditions got longer, there was a sudden shift in the ecology of microbes, chemistry of organic matter, and rates of microbial metabolism. We propose a new model based on feedbacks initiated by disturbance that cascade across biological, chemical, and functional aspects of the system.
Cora Hörstmann, Eric J. Raes, Pier Luigi Buttigieg, Claire Lo Monaco, Uwe John, and Anya M. Waite
Biogeosciences, 18, 3733–3749, https://doi.org/10.5194/bg-18-3733-2021, https://doi.org/10.5194/bg-18-3733-2021, 2021
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Microbes are the main drivers of productivity and nutrient cycling in the ocean. We present a combined approach assessing C and N uptake and microbial community diversity across ecological provinces in the Southern Ocean and southern Indian Ocean. Provinces showed distinct genetic fingerprints, but microbial activity varied gradually across regions, correlating with nutrient concentrations. Our study advances the biogeographic understanding of microbial diversity across C and N uptake regimes.
Nimrod Wieler, Tali Erickson Gini, Osnat Gillor, and Roey Angel
Biogeosciences, 18, 3331–3342, https://doi.org/10.5194/bg-18-3331-2021, https://doi.org/10.5194/bg-18-3331-2021, 2021
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Biological rock crusts (BRCs) are common microbial-based assemblages covering rocks in drylands. BRCs play a crucial role in arid environments because of the limited activity of plants and soil. Nevertheless, BRC development rates have never been dated. Here we integrated archaeological, microbiological and geological methods to provide a first estimation of the growth rate of BRCs under natural conditions. This can serve as an affordable dating tool in archaeological sites in arid regions.
Michal Elul, Maxim Rubin-Blum, Zeev Ronen, Itay Bar-Or, Werner Eckert, and Orit Sivan
Biogeosciences, 18, 2091–2106, https://doi.org/10.5194/bg-18-2091-2021, https://doi.org/10.5194/bg-18-2091-2021, 2021
Mindaugas Zilius, Irma Vybernaite-Lubiene, Diana Vaiciute, Donata Overlingė, Evelina Grinienė, Anastasija Zaiko, Stefano Bonaglia, Iris Liskow, Maren Voss, Agneta Andersson, Sonia Brugel, Tobia Politi, and Paul A. Bukaveckas
Biogeosciences, 18, 1857–1871, https://doi.org/10.5194/bg-18-1857-2021, https://doi.org/10.5194/bg-18-1857-2021, 2021
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In fresh and brackish waters, algal blooms are often dominated by cyanobacteria, which have the ability to utilize atmospheric nitrogen. Cyanobacteria are also unusual in that they float to the surface and are dispersed by wind-driven currents. Their patchy and dynamic distribution makes it difficult to track their abundance and quantify their effects on nutrient cycling. We used remote sensing to map the distribution of cyanobacteria in a large Baltic lagoon and quantify their contributions.
Saly Jaber, Muriel Joly, Maxence Brissy, Martin Leremboure, Amina Khaled, Barbara Ervens, and Anne-Marie Delort
Biogeosciences, 18, 1067–1080, https://doi.org/10.5194/bg-18-1067-2021, https://doi.org/10.5194/bg-18-1067-2021, 2021
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Our study is of interest to atmospheric scientists and environmental microbiologists, as we show that clouds can be considered a medium where bacteria efficiently degrade and transform amino acids, in competition with chemical processes. As current atmospheric multiphase models are restricted to chemical degradation of organic compounds, our conclusions motivate further model development.
Kahina Djaoudi, France Van Wambeke, Aude Barani, Nagib Bhairy, Servanne Chevaillier, Karine Desboeufs, Sandra Nunige, Mohamed Labiadh, Thierry Henry des Tureaux, Dominique Lefèvre, Amel Nouara, Christos Panagiotopoulos, Marc Tedetti, and Elvira Pulido-Villena
Biogeosciences, 17, 6271–6285, https://doi.org/10.5194/bg-17-6271-2020, https://doi.org/10.5194/bg-17-6271-2020, 2020
Romie Tignat-Perrier, Aurélien Dommergue, Alban Thollot, Olivier Magand, Timothy M. Vogel, and Catherine Larose
Biogeosciences, 17, 6081–6095, https://doi.org/10.5194/bg-17-6081-2020, https://doi.org/10.5194/bg-17-6081-2020, 2020
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The adverse atmospheric environmental conditions do not appear suited for microbial life. We conducted the first global comparative metagenomic analysis to find out if airborne microbial communities might be selected by their ability to resist these adverse conditions. The relatively higher concentration of fungi led to the observation of higher proportions of stress-related functions in air. Fungi might likely resist and survive atmospheric physical stress better than bacteria.
Yanhong Lu, Shunyan Cheung, Ling Chen, Shuh-Ji Kao, Xiaomin Xia, Jianping Gan, Minhan Dai, and Hongbin Liu
Biogeosciences, 17, 6017–6032, https://doi.org/10.5194/bg-17-6017-2020, https://doi.org/10.5194/bg-17-6017-2020, 2020
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Through a comprehensive investigation, we observed differential niche partitioning among diverse ammonia-oxidizing archaea (AOA) sublineages in a typical subtropical estuary. Distinct AOA communities observed at DNA and RNA levels suggested that a strong divergence in ammonia-oxidizing activity among different AOA groups occurs. Our result highlights the importance of identifying major ammonia oxidizers at RNA level in future studies.
Anna-Neva Visser, Scott D. Wankel, Pascal A. Niklaus, James M. Byrne, Andreas A. Kappler, and Moritz F. Lehmann
Biogeosciences, 17, 4355–4374, https://doi.org/10.5194/bg-17-4355-2020, https://doi.org/10.5194/bg-17-4355-2020, 2020
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This study focuses on the chemical reaction between Fe(II) and nitrite, which has been reported to produce high levels of the greenhouse gas N2O. We investigated the extent to which dead biomass and Fe(II) minerals might enhance this reaction. Here, nitrite reduction was highest when both additives were present but less pronounced if only Fe(II) minerals were added. Both reaction systems show distinct differences, rather low N2O levels, and indicated the abiotic production of N2.
Lisa Tanet, Séverine Martini, Laurie Casalot, and Christian Tamburini
Biogeosciences, 17, 3757–3778, https://doi.org/10.5194/bg-17-3757-2020, https://doi.org/10.5194/bg-17-3757-2020, 2020
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Bioluminescent bacteria, the most abundant light-emitting organisms in the ocean, can be free-living, be symbiotic or colonize organic particles. This review suggests that they act as a visual target and may indirectly influence the sequestration of biogenic carbon in oceans by increasing the attraction rate for consumers. We summarize the instrumentation available to quantify this impact in future studies and propose synthetic figures integrating these ecological and biogeochemical concepts.
Michael Lintner, Bianca Biedrawa, Julia Wukovits, Wolfgang Wanek, and Petra Heinz
Biogeosciences, 17, 3723–3732, https://doi.org/10.5194/bg-17-3723-2020, https://doi.org/10.5194/bg-17-3723-2020, 2020
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Foraminifera are unicellular marine organisms that play an important role in the marine element cycle. Changes of environmental parameters such as salinity or temperature have a significant impact on the faunal assemblages. Our experiments show that changing salinity in the German Wadden Sea immediately influences the foraminiferal community. It seems that A. tepida is better adapted to salinity fluctuations than H. germanica.
Kathrin Busch, Ulrike Hanz, Furu Mienis, Benjamin Mueller, Andre Franke, Emyr Martyn Roberts, Hans Tore Rapp, and Ute Hentschel
Biogeosciences, 17, 3471–3486, https://doi.org/10.5194/bg-17-3471-2020, https://doi.org/10.5194/bg-17-3471-2020, 2020
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Seamounts are globally abundant submarine structures that offer great potential to study the impacts and interactions of environmental gradients at a single geographic location. In an exemplary way, we describe potential mechanisms by which a seamount can affect the structure of pelagic and benthic (sponge-)associated microbial communities. We conclude that the geology, physical oceanography, biogeochemistry, and microbiology of seamounts are even more closely linked than currently appreciated.
Alexander Bratek, Justus E. E. van
Beusekom, Andreas Neumann, Tina Sanders, Jana Friedrich, Kay-Christian Emeis, and Kirstin Dähnke
Biogeosciences, 17, 2839–2851, https://doi.org/10.5194/bg-17-2839-2020, https://doi.org/10.5194/bg-17-2839-2020, 2020
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The following paper highlights the importance of benthic N-transformation rates in different sediment types in the southern North Sea as a source of fixed nitrogen for primary producers and also as a sink of fixed nitrogen. Sedimentary fluxes of dissolved inorganic nitrogen support ∼7 to 59 % of the average annual primary production. Semi-permeable and permeable sediments contribute ∼68 % of the total benthic N2 production rates, counteracting eutrophication in the southern North Sea.
Sabine Haalboom, David M. Price, Furu Mienis, Judith D. L. van Bleijswijk, Henko C. de Stigter, Harry J. Witte, Gert-Jan Reichart, and Gerard C. A. Duineveld
Biogeosciences, 17, 2499–2519, https://doi.org/10.5194/bg-17-2499-2020, https://doi.org/10.5194/bg-17-2499-2020, 2020
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Mineral mining in deep-sea hydrothermal settings will lead to the formation of plumes of fine-grained, chemically reactive, suspended matter. Understanding how natural hydrothermal plumes evolve as they disperse from their source, and how they affect their surrounding environment, may help in characterising the behaviour of the diluted part of mining plumes. The natural plume provided a heterogeneous, geochemically enriched habitat conducive to the development of a distinct microbial ecology.
Noelle A. Held, Eric A. Webb, Matthew M. McIlvin, David A. Hutchins, Natalie R. Cohen, Dawn M. Moran, Korinna Kunde, Maeve C. Lohan, Claire Mahaffey, E. Malcolm S. Woodward, and Mak A. Saito
Biogeosciences, 17, 2537–2551, https://doi.org/10.5194/bg-17-2537-2020, https://doi.org/10.5194/bg-17-2537-2020, 2020
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Trichodesmium is a globally important marine nitrogen fixer that stimulates primary production in the surface ocean. We surveyed metaproteomes of Trichodesmium populations across the North Atlantic and other oceans, and we found that they experience simultaneous phosphate and iron stress because of the biophysical limits of nutrient uptake. Importantly, nitrogenase was most abundant during co-stress, indicating the potential importance of this phenotype to global nitrogen and carbon cycling.
Helmke Hepach, Claire Hughes, Karen Hogg, Susannah Collings, and Rosie Chance
Biogeosciences, 17, 2453–2471, https://doi.org/10.5194/bg-17-2453-2020, https://doi.org/10.5194/bg-17-2453-2020, 2020
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Tropospheric iodine takes part in numerous atmospheric chemical cycles, including tropospheric ozone destruction and aerosol formation. Due to its significance for atmospheric processes, it is crucial to constrain its sources and sinks. This paper aims at investigating and understanding features of biogenic iodate-to-iodide reduction in microalgal monocultures. We find that phytoplankton senescence may play a crucial role in the release of iodide to the marine environment.
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.
Cited articles
Ahmed, E. and Holmström, S. J. M.: Siderophores in
environmental research: roles and applications, Microb. Biotechnol., 7,
196–208, 2014.
Ahmed, E. and Holmstrom, S. J. M.: Microbe-mineral interactions: The impact
of surface attachment on mineral weathering and element selectivity by
microorganisms, Chem. Geol., 403, 13–23, 2015.
Ahonen-Jonnarth, U., Van Hees, P. A. W., Lundstrom, U. S., and Finlay, R.
D.: Organic acids produced by mycorrhizal Pinus sylvestris exposed to elevated aluminium and
heavy metal concentrations, New Phytol., 146, 557–567, 2000.
Akselsson, C., Westling, O., Sverdrup, H., and Gundersen, P.: Nutrient and
carbon budgets in forest soils as decision support in sustainable forest
management, Forest Ecol. Manag., 238, 167–174, 2007.
Akselsson, C., Olsson, J., Belyazid, S., and Capell, R.: Can increased
weathering rates due to future warming compensate for base cation losses
following whole-tree harvesting in spruce forests?, Biogeochemistry, 128,
89–105, 2016.
Akselsson, C., Belyazid, S., Stendahl, J., Finlay, R., Olsson, B. A., Erlandsson Lampa, M., Wallander, H., Gustafsson, J. P., and Bishop, K.: Weathering rates in Swedish forest soils, Biogeosciences, 16, 4429–4450, https://doi.org/10.5194/bg-16-4429-2019, 2019.
Allen, J. F.: A proposal for formation of Archaean stromatolites before the
advent of oxygenic photosynthesis, Front. Microbiol., 7, 1784, https://doi.org/10.3389/fmicb.2016.01784, 2016.
Almeida, J. P., Rosenstock, N. P., Forsmark, B., Bergh, J., and Wallander, H.:
Ectomycorrhizal community composition and function in a spruce forest
transitioning between nitrogen and phosphorus limitation, Fungal. Ecol.,
40, 20–31, 2019.
Andrews, J. A. and Schlesinger, W. H.: Soil CO2 dynamics,
acidification, and chemical weathering in a temperate forest with
experimental CO2 enrichment, Global Biogeochem. Cy., 15, 149–162, 2001.
Archibald, J. M.: Genomic perspectives on the birth and spread of plastids,
P. Natl. Acad. Sci. USA, 112, 10147–10153, 2015.
Averill, C., Dietze, M. C., and Bhatnagar, J. M.: Continental-scale nitrogen
pollution is shifting forest mycorrhizal associations and soil carbon
stocks, Glob. Change Biol., 24, 4544–4553, 2018.
Bahr, A., Ellstrom, M., Bergh, J., and Wallander, H.: Nitrogen leaching and
ectomycorrhizal nitrogen retention capacity in a Norway spruce forest
fertilized with nitrogen and phosphorus, Plant Soil, 390, 323–335, 2015.
Balogh-Brunstad, Z., Kent Keller, C., Thomas Dickinson, J., Stevens, F., Li,
C. Y., and Bormann, B. T.: Biotite weathering and nutrient uptake by
ectomycorrhizal fungus, Suillus tomentosus, in liquid-culture experiments,
Geochim. Cosmochim. Ac., 72, 2601–2618, 2008.
Banfield, J. F., Barker, W. W., Welch, S. A., and Taunton, A.: Biological
impact on mineral dissolution: application of the lichen model to
understanding mineral weathering in the rhizosphere, P. Natl. Acad. Sci.
USA, 96, 3404–3411, 1999.
Banwart, S. A., Berg, A., and Beerling, D. J.: Process-based modeling of
silicate mineral weathering responses to increasing atmospheric CO2 and
climate change, Global Biogeochem. Cy., 23, GB4013,
https://doi.org/10.1029/2008GB003243, 2009.
Beerling, D. J., Taylor, L. L., Bradshaw, C. D. C., Lunt, D. J., Valdes, P.
J., Banwart, S. A., Pagani, M., and Leake, J. R.: Ecosystem CO2
starvation and terrestrial silicate weathering: mechanisms and global-scale
quantification during the late Miocene, J. Ecol., 100, 31–41, 2012.
Beerling, D. J., Leake, J. R., Long, S. P., Scholes, J. D., Ton, J., Nelson,
P. N., Bird, M., Kantzas, E., Taylor, L. L., Sarkar, B., Kelland, M.,
DeLucia, E., Kantola, I., Muller, C., Rau, G. H., and Hansen, J.: Farming
with crops and rocks to address global climate, food and soil security, Nat.
Plants, 4, 138–147, 2018.
Bell, E. A., Boehnke, P., Harrison, T. M., and Mao, W. L.: Potentially
biogenic carbon preserved in a 4.1 billion-year-old zircon, P. Natl.
Acad. Sci. USA, 112, 14518–14521, 2015.
Belyazid, S., Akselsson, C., and Zanchi, G.: Water limitation may restrict the positive effect of higher temperatures on weathering rates in forest soils, Biogeosciences Discuss., https://doi.org/10.5194/bg-2019-44, in review, 2019.
Berner, R. A.: Paleoclimate – The rise of plants and their effect on
weathering and atmospheric CO2, Science, 276, 544–546, 1997.
Blum, J. D., Klaue, A., Nezat, C. A., Driscoll, C. T., Johnson, C. E.,
Siccama, T. G., Eagar, C., Fahey, T. J., and Likens, G. E.: Mycorrhizal
weathering of apatite as an important calcium source in base-poor forest
ecosystems, Nature, 417, 729–731, 2002.
Bolou-Bi, E. B., Vigier, N., Brenot, A., and Poszwa, A.: Magnesium isotope
compositions of natural reference materials, Geostand. Geoanal. Res., 33,
95–109, 2009.
Bolou-Bi, E. B., Vigier, N., Poszwa, A., Boudot, J. P., and Dambrine, E.:
Effects of biogeochemical processes on magnesium isotope variations in a
forested catchment in the Vosges Mountains (France), Geochim. Cosmochim. Ac., 87, 341–355, 2012.
Bonneville, S., Smits, M. M., Brown, A., Harrington, J., Leake, J. R.,
Brydson, R., and Benning, L. G.: Plant-driven fungal weathering: Early
stages of mineral alteration at the nanometer scale, Geology, 37, 615–618,
2009.
Bonneville, S., Morgan, D. J., Schmalenberger, A., Bray, A., Brown, A.,
Banwart, S. A., and Benning, L. G.: Tree-mycorrhiza symbiosis accelerate
mineral weathering: Evidences from nanometer-scale elemental fluxes at the
hypha–mineral interface, Geochim. Cosmochim. Ac., 75, 6988–7005, 2011.
Bonneville, S., Bray, A. W., and Benning, L. G.: Structural Fe(II) oxidation
in biotite by an ectomycorrhizal fungi drives mechanical forcing, Environ.
Sci. Technol., 50, 5589–5596, 2016.
Borgeaud, S., Metzger, L. C., Scrignari, T., and Blokesch, M.: The type VI
secretion system of Vibrio cholerae fosters horizontal gene transfer, Science, 347, 63–67,
2015.
Brantley, S. L., Megonigal, J. P., Scatena, F. N., Balogh-Brunstad, Z.,
Barnes, R. T., Bruns, M. A., Van Cappellen, P., Dontsova, K., Hartnett, H.
E., Hartshorn, A. S., Heimsath, A., Herndon, E., Jin, L., Keller, C. K.,
Leake, J. R., McDowell, W. H., Meinzer, F. C., Mozdzer, T. J., Petsch, S.,
Pett-Ridge, J., Pregitzer, K. S., Raymond, P. A., Riebe, C. S., Shumaker,
K., Sutton-Grier, A., Walter, R., and Yoo, K.: Twelve testable hypotheses on
the geobiology of weathering, Geobiology, 9, 140–165, 2011.
Brocks, J. J., Logan, G. A., Buick, R., and Summons, R. E.: Archean
molecular fossils and the early rise of eukaryotes, Science, 285, 1033–1036,
1999.
Brown, G., Mitchell, D. T., and Stock, W. D.: Deposition of phosphorus in a
coastal Fynbos ecosystem of the south-western Cape, South Africa, J. Ecol.,
72, 547–551, 1984.
Cailleau, G., Braissant, O., and Verrecchia, E. P.: Turning sunlight into stone: the oxalate-carbonate pathway in a tropical tree ecosystem, Biogeosciences, 8, 1755–1767, https://doi.org/10.5194/bg-8-1755-2011, 2011.
Cailleau, G., Mota, M., Bindschedler, S., Junier, P., and Verrecchia, E. P.:
Detection of active oxalate-carbonate pathway ecosystems in the Amazon
Basin: Global implications of a natural potential C sink, Catena, 116,
132–141, 2014.
Callot, G., Maurette, M., Pottier, L., and Dubois, A.: Biogenic Etching of
Microfractures in Amorphous and Crystalline Silicates, Nature, 328, 147–149,
1987.
Calvaruso, C., Turpault, M-. P., Frey-Klett, P., Uroz, S., Pierret, M.-C.
Tosheva, Z., and Antoine, K.: Increase of apatite dissolution rate by Scots
pine roots associated or not with Burkholderia glathei PML1(12)Rp in open-system flow microcosms,
Geochim. Cosmochim. Ac., 106, 287–306, 2013.
Chizhikova, N. P., Lessovaia, S. N., and Gorbushina, A. A.: Biogenic
Weathering of Mineral Substrates (Review), in: Biogenic-Abiogenic
Interactions in Natural and Anthropogenic Systems, edited by:
Frank-Kamenetskaya, O. V., Panova, E. G., and Vlasov, D. Y., Springer, Cham,
7–14, https://doi.org/10.1007/978-3-319-24987-2_2, 2016.
Clemmensen, K. E., Bahr, A., Ovaskainen, O., Dahlberg, A., Ekblad, A.,
Wallander, H., Stenlid, J., Finlay, R. D., Wardle, D. A., and Lindahl, B.
D.: Roots and associated fungi drive long-term carbon sequestration in
boreal forest, Science, 339, 1615–1618, 2013.
Cobert, F., Schmitt, A. D., Bourgeade, P., Labolle, F., Badot, P. M.,
Chabaux, F., and Stille, P.: Experimental identification of Ca isotopic
fractionations in higher plants, Geochim. Cosmochim. Ac., 75, 5467–5482,
2011.
DasSarma, S. and Schwieterman, E. W.: Early evolution of purple retinal
pigments on Earth and implications for exoplanet biosignatures, Int. J.
Astrobiol., 1–10, https://doi.org/10.1017/S1473550418000423, 2018.
Deveau, A., Bonito, G., Uehling, J., Paoletti, M., Becker, M., Bindschedler,
S., Hacquard, S., Herve, V., Labbe, J., Lastovetsky, O. A., Mieszkin, S.,
Millet, L. J., Vajna, B., Junier, P., Bonfante, P., Krom, B. P., Olsson, S.,
van Elsas, J. D., and Wick, L. Y.: Bacterial-fungal interactions: ecology,
mechanisms and challenges, FEMS Microbiol. Rev., 42, 335–352, 2018.
Dijkstra, F. A. and Smits, M. M.: Tree species effects on calcium cycling:
the role of calcium uptake in deep soils, Ecosystems, 5, 385–398, 2002.
Drever, J. I. and Stillings, L. L.: The role of organic acids in mineral
weathering, Coll. Surf. A, 120, 167–181, https://doi.org/10.1016/S0927-7757(96)03720-X,
1997.
Erlandsson, M., Oelkers, E. H., Bishop, K., Sverdrup, H., Belyazid, S.,
Ledesma, J. L. J., and Kohler, S. J.: Spatial and temporal variations of
base cation release from chemical weathering on a hillslope scale, Chem.
Geol., 441, 1–13, 2016.
Fahad, Z. A., Bolou-Bi, E. B., Kohler, S. J., Finlay, R. D., and Mahmood,
S.: Fractionation and assimilation of Mg isotopes by fungi is species
dependent, Env. Microbiol. Rep., 8, 956–965, https://doi.org/10.1111/1758-2229.12459, 2016.
Ferris, F. G., Wiese, R. G., and Fyfe, W. S.: Precipitation of carbonate
minerals by microorganisms – Implications for silicate weathering and the
global carbon-dioxide budget, Geomicrobiol. J., 12, 1–13, 1994.
Field, K. J., Cameron, D. D., Leake, J. R., Tille, S., Bidartondo, M. I.,
and Beerling, D. J.: Contrasting arbuscular mycorrhizal responses of vascular and non-vascular plants to a simulated Palaeozoic CO2 decline, 3, 835, https://doi.org/10.1038/ncomms1831, 2012.
Field, K. J., Davidson, S. J., Alghamadi, S. A., and Cameron, D. D.:
Magnitude, dynamics and control of carbon flow to mycorrhizas, in:
Mycorrhizal Mediation of Soil Fertility, Structure, and Carbon Storage,
edited by: Johnson, N. C., Gehring, C., and Jansa, J., Elsevier, Amsterdam,
375–393, ISBN 978-0-12-8043127, 2017.
Finlay, R. D. and Clemmensen, K. E.: Immobilization of carbon in
mycorrhizal mycelial biomass and secretions, in: Mycorrhizal Mediation of
Soil Fertility, Structure, and Carbon Storage, edited by: Johnson, N. C.,
Gehring, C., and Jansa, J.: Elsevier, Amsterdam, 413–440,
ISBN 978-0-12-8043127, 2017.
Finlay, R. D., Wallander, H., Smits, M., Holmstrom, S., Hees, P. V., Lian,
B., and Rosling, A.: The role of fungi in biogenic weathering in boreal forest
soils, Fung. Biol. Rev., 4, 101–106, 2009.
Flemming, H. C. and Wingender, J.: The biofilm matrix, Nat. Rev.
Microbiol., 8, 623–633, 2010.
Flemming, H. C., Wingender, J., Szewzyk, U., Steinberg, P., Rice, S. A., and
Kjelleberg, S.: Biofilms: an emergent form of bacterial life, Nat. Rev.
Microbiol., 14, 563–575, 2016.
Fomina, M., Burford, E. P., Hillier, S., Kierans, M., and Gadd, G. M.:
Rock-building fungi, Geomicrobiol. J., 27, 624–629, 2010.
Futter, M. N., Klaminder, J., Lucas, R. W., Laudon, H., and Kohler, S. J.:
Uncertainty in silicate mineral weathering rate estimates: source
partitioning and policy implications, Environ. Res. Lett., 7, 024025, https://doi.org/10.1088/1748-9326/7/2/024025,
2012.
Gadd, G. M.: Metals, minerals and microbes: geomicrobiology and
bioremediation, Microbiology, 156, 609–643, 2010.
Gadd, G. M.: Microbial roles in mineral transformations and metal cycling in the Earth's critical zone, in: Molecular Environmental Soil Science. Progress in Soil Science, edited by: Xu J. and Sparks D.: Springer, Dordrecht, 115–165, ISBN 978-94-007-4176-8, 2013a.
Gadd, G. M.: Geomycology: Fungi as agents of biogeochemical change, Biology
and Environment, P. Roy. Irish Acad., 113b, 139–153, 2013b.
Gadd, G. M.: Fungi, rocks, and minerals, Elements, 13, 171–176, 2017.
Gazzè, S. A., Saccone, L., Ragnarsdottir, K. V., Smits, M. M., Duran, A.
L., Leake, J. R., Banwart, S. A., and McMaster, T. J.: Nanoscale channels on
ectomycorrhizal-colonized chlorite: Evidence for plant-driven fungal
dissolution, J. Geophys. Res.-Biogeo., 117, G00n09, https://doi.org/10.1029/2012JG002016, 2012.
Gazzè, S. A., Saccone, L., Smits, M. M., Duran, A. L., Leake, J. R.,
Banwart, S. A., Ragnarsdottir, K. V., and McMaster, T. J.: Nanoscale
observations of extracellular polymeric substances deposition on
phyllosilicates by an ectomycorrhizal fungus, Geomicrobiol. J., 30, 721–730,
2013.
Gazze, S. A., Stack, A. G., Ragnarsdottir, K. V., and McMaster, T. J.:
Chlorite topography and dissolution of the interlayer studied with atomic
force microscopy, Am. Mineral., 99, 128–138, 2014.
Gleeson, D. B., Clipson, N., Melville, K., Gadd, G. M., and McDermott, F. P.:
Mineralogical control of fungal community structure in a weathered
pegmatitic granite, Microb. Ecol., 50, 360–368, 2005.
Gorbushina, A. A.: Life on the rocks, Env. Microbiol., 9, 1613–1631, 2007.
Goudie, A. S. and Viles, H. A.: Weathering and the global carbon cycle:
Geomorphological perspectives, Earth-Sci. Rev., 113, 59–71, 2012.
Griffiths, R. P., Baham, J. E., and Caldwell, B. A.: Soil solution chemistry of
ectomycorrhizal mats in forest soil, Soil Biol. Biochem., 26, 331–337, 1994.
Grube, M., Cernava, T., Soh, J., Fuchs, S., Aschenbrenner, I., Lassek, C.,
Wegner, U., Becher, D., Riedel, K., Sensen, C. W., and Berg, G.: Exploring
functional contexts of symbiotic sustain within lichen-associated bacteria
by comparative omics, ISME J., 9, 412–424, 2015.
Guennoc, C. M., Rose, C., Labbe, J., and Deveau, A.: Bacterial biofilm
formation on the hyphae of ectomycorrhizal fungi: a widespread ability under
controls?, FEMS Microbiol. Ecol., 94, fiy093, https://doi.org/10.1093/femsec/fiy093,
2018.
Hartmann, J. and Moosdorf, N.: Chemical weathering rates of
silicate-dominated lithological classes and associated liberation rates of
phosphorus on the Japanese Archipelago – Implications for global scale
analysis, Chem. Geol., 287, 125–157, 2011.
Hazen, R. M., Papineau, D., Leeker, W. B., Downs, R. T., Ferry, J. M.,
McCoy, T. J., Sverjensky, D. A., and Yang, H. X.: Mineral evolution, Am.
Mineral., 93, 1693–1720, 2008.
Hibbett, D., Gilbert, L., and Donoghue, M.: Evolutionary instability of
ectomycorrhizal symbiosis in basidiomycetes, Nature, 407, 506–508, 2000.
Hindshaw, R. S., Reynolds, B. C., Wiederhold, J. G., Kretzschmar, R., and
Bourdon, B.: Calcium isotopes in a proglacial weathering environment: Damma
glacier, Switzerland, Geochim. Cosmochim. Ac., 75, 106–118, 2011.
Hodkinson, B. P., Gottel, N. R., Schadt, C. W., and Lutzoni, F.:
Photoautotrophic symbiont and geography are major factors affecting highly
structured and diverse bacterial communities in the lichen microbiome,
Environ. Microbiol., 14, 147–161, 2012.
Hoffland, E., Giesler, R., Jongmans, T., and van Breemen, N.: Increasing
feldspar tunneling by fungi across a north Sweden podzol chronosequence,
Ecosystems, 5, 11–22, 2002.
Hoffland, E., Giesler, R., Jongmans, A. G., and van Breemen, N.: Feldspar
tunneling by fungi along natural productivity gradients, Ecosystems, 6,
739–746, 2003.
Hoffland, E., Kuyper, T. W., Wallander, H., Plassard, C., Gorbushina, A. A.,
Haselwandter, K., Holmstrom, S., Landeweert, R., Lundstrom, U. S., Rosling,
A., Sen, R., Smits, M. M., van Hees, P. A., and van Breemen, N.: The role of
fungi in weathering, Front. Ecol. Environ., 2, 258–264, 2004.
Högberg, M. N. and Högberg, P.: Extramatrical ectomycorrhizal
mycelium contributes one-third of microbial biomass and produces, together
with associated roots, half the dissolved organic carbon in a forest soil,
New Phytol., 154, 791–795, 2002.
Högberg, P., Nordgren, A., Buchmann, N., Taylor, A. F. S., Ekblad, A.,
Högberg, M. N., Nyberg, G., Ottosson-Lofvenius, M., and Read, D. J.:
Large-scale forest girdling shows that current photosynthesis drives soil
respiration, Nature, 411, 789–792, 2001.
Holmden, C. and Belanger, N.: Ca isotope cycling in a forested ecosystem,
Geochim. Cosmochim. Ac., 74, 995–1015, 2010.
Holmstrom, S. J. M., Lundstrom, U. S., Finlay, R. D., and Van Hees, P. A.
W.: Siderophores in forest soil solution, Biogeochemistry, 71, 247–258,
2004.
Howard, R. J., Ferrari, M. A., Roach, D. H., and Money, N. P.: Penetration of
hard substrates by a fungus employing enormous turgor pressures, P. Natl.
Acad. Sci. USA, 88, 11281–11284, 1991.
Huang, K. J., Teng, F. Z., Wei, G. J., Ma, J. L., and Bao, Z. Y.:
Adsorption- and desorption-controlled magnesium isotope fractionation during
extreme weathering of basalt in Hainan Island, China, Earth Planet. Sc.
Lett., 359, 73–83, 2012.
Hutchens, E.: Microbial selectivity on mineral surfaces: possible
implications for weathering processes, Fung. Biol. Rev., 23, 115–121, 2010.
Johansson, E. M., Fransson, P. M. A., Finlay, R. D., and van Hees, P. A. W.:
Quantitative analysis of soluble exudates produced by ectomycorrhizal roots
as a response to ambient and elevated CO2, Soil Biol. Biochem., 41,
1111–1116, 2009.
Jones, D. L., Nguyen, C., and Finlay, R. D.: Carbon flow in the rhizosphere:
carbon trading at the soil-root interface, Plant Soil, 321, 5–33, 2009.
Jongmans, A. G., van Breemen, N., Lundstrom, U., van Hees, P. A. W., Finlay,
R. D., Srinivasan, M., Unestam, T., Giesler, R., Melkerud, P. A., and
Olsson, M.: Rock-eating fungi, Nature, 389, 682–683, 1997.
Kalinowski, B. E., Liermann, L. J., Brantley, S. L., Barnes, A., and
Pantano, C. G.: X-ray photoelectron evidence for bacteria-enhanced
dissolution of hornblende, Geochim. Cosmochim. Ac., 64, 1331–1343, 2000.
Klaminder, J., Lucas, R. W., Futter, M. N., Bishop, K. H., Kohler, S. J.,
Egnell, G., and Laudon, H.: Silicate mineral weathering rate estimates: Are
they precise enough to be useful when predicting the recovery of nutrient
pools after harvesting?, Forest Ecol. Manag., 261, 1–9, 2011.
Koele, N., Dickie, I. A., Oleksyn, J., Richardson, S. J., and Reich, P. B.:
No globally consistent effect of ectomycorrhizal status on foliar traits,
New Phytol., 196, 845–852, 2012.
Koele, N., Dickie, I. A., Blum, J. D., Gleason, J. D., and de Graaf, L.:
Ecological significance of mineral weathering in ectomycorrhizal and
arbuscular mycorrhizal ecosystems from a field-based comparison, Soil Biol.
Biochem., 69, 63–70, 2014.
Kohler, A., Kuo, A., Nagy, L. G., Morin, E., Barry, K. W., Buscot, F., Canback, B., Choi, C., Cichocki, N., Clum, A., Colpaert, J., Copeland, A., Costa, M. D., Dore, J., Floudas, D., Gay, G., Girlanda, M., Henrissat, B., Herrmann, S., Hess, J., Hogberg, N., Johansson, T., Khouja, H. R., LaButti, K., Lahrmann, U., Levasseur, A., Lindquist, E. A., Lipzen, A., Marmeisse, R., Martino, E., Murat, C., Ngan, C. Y., Nehls, U., Plett, J. M., Pringle, A., Ohm, R. A., Perotto, S., Peter, M., Riley, R., Rineau, F., Ruytinx, J., Salamov, A., Shah, F., Sun, H., Tarkka, M., Tritt, A., Veneault-Fourrey, C., Zuccaro, A., Tunlid, A., Grigoriev, I. V., Hibbett, D. S., Martin, F., and Mycorrhizal Genomics Initiative: Convergent
losses of decay mechanisms and rapid turnover of symbiosis genes in
mycorrhizal mutualists, Nat. Genet., 47, 410–415, 2015.
Kohler, P., Hartmann, J., and Wolf-Gladrow, D. A.: Geoengineering potential
of artificially enhanced silicate weathering of olivine, P. Natl. Acad.
Sci. USA, 107, 20228–20233, 2010.
Kraemer, S. M., Duckworth, O. W., Harrington, J. M., and Schenkeveld, W. D.
C.: Metallophores and trace metal bio-geochemistry, Aquat. Geochem., 21,
159–195, 2014.
Kronnäs, V., Akselsson, C., and Belyazid, S.: Dynamic
modelling of weathering rates – the benefit over steady-state modelling,
Soil, 5, 33–47, 2019.
Kump, L. R.: The rise of atmospheric oxygen, Nature, 451, 277–278, 2008.
Lambers, H., Raven, J. A., Shaver, G. R., and Smith, S. E.: Plant
nutrient-acquisition strategies change with soil age, Trends Ecol. Evol.,
23, 95–103, 2008.
Lambers, H., Mougel, C., Jaillard, B., and Hinsinger, P.: Plant-microbe-soil
interactions in the rhizosphere: an evolutionary perspective, Plant Soil,
321, 83–115, 2009.
Landeweert, R., Hofflund, E., Finlay, R. D., and van Breemen, N.: Linking
plants to rocks: Ectomycorrhizal fungi mobilize nutrients from minerals,
Trends Ecol. Evol., 16, 248–254, 2001.
Lawrence, C., Harden, J., and Maher, K.: Modeling the influence of organic
acids on soil weathering, Geochim. Cosmochim. Ac., 139, 487–507, 2014.
Leake, J. R. and Read, D. J.: Mycorrhizal symbioses and pedogenesis
throughout Earth's history, in: Mycorrhizal Mediation of Soil Fertility,
Structure, and Carbon Storage, edited by: Johnson, N. C., Gehring, C., and
Jansa, J.: Elsevier, Amsterdam, 9–33, ISBN 978-0-12-8043127, 2017.
Leake, J. R., Duran, A. L., Hardy, K. E., Johnson, I., Beerling, D. J.,
Banwart, S. A., and Smits, M. M.: Biological weathering in soil: the role of
symbiotic root-associated fungi biosensing minerals and directing
photosynthate-energy into grain-scale mineral weathering, Min. Mag., 72,
85–89, 2008.
Li, Z. B., Liu, L. W., Chen, J., and Teng, H. H.: Cellular dissolution at
hypha- and spore- mineral interfaces revealing unrecognized mechanisms and
scales of fungal weathering, Geology, 44, 319–322, 2016.
Lian, B., Wang, B., Pan, M., Liu, C. Q., and Teng, H. H.: Microbial release
of potassium from K-bearing minerals by thermophilic fungus Aspergillus fumigatus, Geochim.
Cosmochim. Ac., 72, 87–98, 2008.
Lian, B., Chen, Y., and Tang, Y. A.: Microbes on Carbonate Rocks and
Pedogenesis in Karst Regions, J. Earth Sci.-China, 21, 293–296, 2010.
Lian, B., Yuan, D. X., and Liu, Z. H.: Effect of microbes on karstification
in karst ecosystems, Chinese Sci. Bull., 56, 3743–3747, 2011.
Lindahl, B. D. and Tunlid, A.: Ectomycorrhizal fungi – potential organic
matter decomposers, yet not saprotrophs, New Phytol., 205, 1443–1447, 2015.
Lindahl, B. D., Ihrmark, K., Boberg, J., Trumbore, S. E., Hogberg, P.,
Stenlid, J., and Finlay, R. D.: Spatial separation of litter decomposition
and mycorrhizal nitrogen uptake in a boreal forest, New Phytol., 173,
611–620, 2007.
Liu, H. L. and Lian, B.: Quantitative evaluation of different fractions of
extracellular polymeric substances derived from Paenibacillus mucilaginosus against the toxicity of
gold ions, Coll. Surf. B, 175, 195–201, 2019.
Liu, Y. P., Sun, Q. B., Li, J., and Lian, B.: Bacterial diversity among the
fruit bodies of ectomycorrhizal and saprophytic fungi and their
corresponding hyphosphere soils, Sci. Rep., 8, 11672, https://doi.org/10.1038/s41598-018-30120-6, 2018.
Luo, G. M., Ono, S. H., Beukes, N. J., Wang, D. T., Xie, S. C., and Summons,
R. E.: Rapid oxygenation of Earth's atmosphere 2.33 billion years ago, Sci.
Adv., 2, e1600134, https://doi.org/10.1126/sciadv.1600134, 2016.
Ma, J. F., Ryan, P. R., and Delhaize, E.: Aluminium tolerance in plants and
the complexing role of organic acids, Trends Plant Sci., 6, 273–278, 2001.
Maher, K.: The dependence of chemical weathering rates on fluid residence
time, Earth Planet. Sc. Lett., 294, 101–110, 2010.
Martin, F., Kohler, A., Murat, C., Veneault-Fourrey, C., and Hibbett, D. S.:
Unearthing the roots of ectomycorrhizal symbioses, Nat. Rev. Microbiol., 14, 760–773, 2016.
Martino, E., Perotto, S., Parsons, R., and Gadd, G. M.: Solubilization of
insoluble inorganic zinc compounds by ericoid mycorrhizal fungi derived from
heavy metal polluted sites, Soil Biol. Biochem., 35, 133–141, 2003.
Marupakula, S., Mahmood, S., and Finlay, R. D.: Analysis of single root tip
microbiomes suggests that distinctive bacterial communities are selected by
Pinus sylvestris roots colonized by different ectomycorrhizal fungi, Env. Microbiol., 18,
1470–1483, 2016.
Marupakula, S., Mahmood, S., Jernberg, J., Nallanchakravarthula, S., Fahad,
Z. A., and Finlay, R. D.: Bacterial microbiomes of individual
ectomycorrhizal Pinus sylvestris roots are shaped by soil horizon and differentially
sensitive to nitrogen addition, Env. Microbiol., 19, 4736–4753, 2017.
Mavromatis, V., Prokushkin, A. S., Pokrovsky, O. S., Viers, J., and Korets,
M. A.: Magnesium isotopes in permafrost-dominated Central Siberian larch
forest watersheds, Geochim. Cosmochim. Ac., 147, 76–89, 2014.
McLoughlin, N., Staudigel, H., Furnes, H., Eickmann, B., and Ivarsson, M.:
Mechanisms of microtunneling in rock substrates: distinguishing endolithic
biosignatures from abiotic microtunnels, Geobiology, 8, 245–255, 2010.
McMaster, T. J.: Atomic Force Microscopy of the fungi-mineral interface:
applications in mineral dissolution, weathering and biogeochemistry, Curr.
Opin. Biotech., 23, 562–569, 2012.
Mitchell, A. C., Lafreniere, M. J., Skidmore, M. L., and Boyd, E. S.:
Influence of bedrock mineral composition on microbial diversity in a
subglacial environment, Geology, 41, 855–858, 2013.
Moldan, F., Stadmark, J., Fölster, J., Jutterström, S., Futter, M.
N., Cosby, B. J., and Wright, R. F.: Consequences of intensive forest
harvesting on the recovery of Swedish lakes from acidification and on
critical load exceedances, Sci. Total Environ., 603, 562–569, 2017.
Montross, S. N., Skidmore, M., Tranter, M., Kivimaki, A. L., and Parkes, R. J.:
A microbial driver of chemical weathering in glaciated systems, Geology, 41,
215–218, 2013.
Moreau, D., Bardgett, R. D., Finlay, R. D., Jones, D. L., and Philippot, L.:
A plant perspective on nitrogen cycling in the rhizosphere, Funct. Ecol.,
33, 540–552, 2019.
Morris, J. L., Leake, J. R., Stein, W. E., Berry, C. M., Marshall, J. E. A.,
Wellman, C. H., Milton, A., Hillier, S., Mannolini, F., Quirk, J., and
Beerling, D. J.: Investigating Devonian trees as geoengineers of past
climates: linking palaeosols to palaeobotany and experimental geobiology,
Palaeontology, 58, 787–801, 2015.
Neaman, A., Chorover, J., and Brantley, S. L.: Effects of organic ligands on
granite dissolution in batch experiments at pH 6, Amer. J. Sci., 306, 451–473, 2006.
Nicolás, C., Martin-Bertelsen, T., Floudas, D., Bentzer, J., Smits, M.,
Johansson, T., Troein, C., Persson, P., and Tunlid, A.: The soil organic
matter decomposition mechanisms in ectomycorrhizal fungi are tuned for
liberating soil organic nitrogen, ISME J., 13, 977–988, 2019.
Ochs, M.: Influence of humified and non-humified natural organic compounds
on mineral dissolution, Chem. Geol., 132, 119–124, 1996.
Opfergelt, S., Burton, K. W., Georg, R. B., West, A. J., Guicharnaud, R. A.,
Sigfusson, B., Siebert, C., Gislason, S. R., and Halliday, A. N.: Magnesium
retention on the soil exchange complex controlling Mg isotope variations in
soils, soil solutions and vegetation in volcanic soils, Iceland, Geochim. Cosmochim. Ac., 125, 110–130, 2014.
Pagani, M., Caldeira, K., Berner, R., and Beerling, D. J.: The role of
terrestrial plants in limiting atmospheric CO2 decline over the past 24
million years, Nature, 460, 85–94, 2009.
Page, B. D., Bullen, T. D., and Mitchell, M. J.: Influences of calcium
availability and tree species on Ca isotope fractionation in soil and
vegetation, Biogeochemistry, 88, 1–13, 2008.
Paris, F., Bonnaud, P., Ranger, J., and Lapeyrie F.: In vitro weathering of
phlogopite by ectomycorrhizal fungi. I. Effect of K+ and Mg2+
deficiency on phyllosilicate evolution, Plant Soil, 177, 191–201, 1995.
Paris, F., Botton, B., and Lapeyrie, F.: In vitro weathering of phlogopite by
ectomycorrhizal fungi. 2. Effect of K+ and Mg2+ deficiency and N
sources on accumulation of oxalate and H+, Plant Soil, 179, 141–50,
1996.
Perakis, S. S. and Pett-Ridge, J. C.: Nitrogen-fixing red alder trees tap
rock-derived nutrients, P. Natl. Acad. Sci. USA, 116, 5009–5014, 2019.
Phelan, J., Belyazid, S., Kurz, D., Guthrie, S., Cajka, J., Sverdrup, H.,
and Waite, R.: Estimation of soil base cation weathering rates with the
PROFILE model to determine critical loads of acidity for forested ecosystems
in Pennsylvania, USA: Pilot application of a potential national
methodology, Water Air Soil Poll., 225, 2109,
https://doi.org/10.1007/s11270-014-2109-4, 2014.
Philippot, L., Raaijmakers, J. M., Lemanceau, P., and van der Putten, W. H.:
Going back to the roots: the microbial ecology of the rhizosphere, Nat. Rev.
Microbiol., 11, 789–799, 2013.
Pogge von Strandmann, P. A. E., Burton, K. W., James, R. H., van Calsteren,
P., Gislason, S. R., and Sigfusson, B.: The influence of weathering
processes on riverine magnesium isotopes in a basaltic terrain, Earth
Planet. Sc. Lett., 276, 187–197, 2008.
Povak, N. A., Hessburg, P. F., McDonnell, T. C., Reynolds, K. M., Sullivan,
T. J., Salter, R. B., and Cosby, B. J.: Machine learning and linear regression
models to predict catchment-level base cation weathering rates across the
southern Appalachian Mountain region, USA, Water Resour. Res., 50,
2798–2814, 2014.
Price, J. R., Peresolak, K., Brice, R. L., and Tefend, K. S.: Temporal
variability in the chemical weathering of Ca2+-bearing phases in the
Loch Vale watershed, Colorado, USA: A mass-balance approach, Chem. Geol.,
342, 151–166, 2013.
Querejeta, J. I., Egerton-Warburton, L. M., and Allen, M. F.: Direct
nocturnal water transfer from oaks to their mycorrhizal symbionts during
severe soil drying, Oecologia, 134, 55–64, 2003.
Quirk, J., Beerling, D. J., Banwart, S. A., Kakonyi, G., Romero-Gonzalez, M.
E., and Leake, J. R.: Evolution of trees and mycorrhizal fungi intensifies
silicate mineral weathering, Biol. Lett., 8, 1006–1011, 2012.
Quirk, J., Andrews, M. Y., Leake, J. R., Banwart, S. A., and Beerling, D.
J.: Ectomycorrhizal fungi and past high CO2 atmospheres enhance mineral
weathering through increased below-ground carbon-energy fluxes, Biol. Lett.,
10, 20140375, https://doi.org/10.1098/rsbl.2014.0375, 2014a.
Quirk, J., Leake, J. R., Banwart, S. A., Taylor, L. L., and Beerling, D. J.: Weathering by tree-root-associating fungi diminishes under simulated Cenozoic atmospheric CO2 decline, Biogeosciences, 11, 321–331, https://doi.org/10.5194/bg-11-321-2014, 2014b.
Quirk, J., Leake, J. R., Johnson, D. A., Taylor, L. L., Saccone, L., and
Beerling, D. J.: Constraining the role of early land plants in Palaeozoic
weathering and global cooling, P. Roy. Soc. B, 282,
20151115, https://doi.org/10.1098/rspb.2015.1115, 2015.
Redfield, G. W.: Atmospheric deposition of phosphorus to the everglades:
concepts, constraints and published deposition rates for ecosystem
management, Sci. World J., 2, 1843–1873, 2002.
Reichard, P. U., Kraemer, S. M., Frazier, S. W., and Kretzschmar, R.:
Goethite dissolution in the presence of phytosiderophores: Rates,
mechanisms, and the synergistic effect of oxalate, Plant Soil, 276, 115–132,
2005.
Remiszewski, K. A., Bryce, J. G., Fahnestock, M. F, Pettitt, E. A.,
Blichert-Toft, J., Vadeboncoeur, M. A., and Bailey, S. W.: Elemental and
isotopic perspectives on the impact of arbuscular mycorrhizal and
ectomycorrhizal fungi on mineral weathering across imposed geologic
gradients, Chem. Geol., 445, 164–171, 2016.
Retallack, G. J.: Early forest soils and their role in Devonian global
change, Science, 276, 583–585, 1997.
Roelandt, C., Goddéris, Y., and Bonnet, M.: Coupled modeling of
biospheric and chemical weathering processes at the continental scale, Global
Biogeochem. Cy., 24, GB2004, https://doi.org/10.1029/2008GB003420, 2010.
Rosenstock, N. P., Berner, C., Smits, M. M., Kram, P., and Wallander, H.:
The role of phosphorus, magnesium and potassium availability in soil fungal
exploration of mineral nutrient sources in Norway spruce forests, New
Phytol., 211, 542–553, 2016.
Rosling, A., Lindahl, B. D., and Finlay, R. D.: Carbon allocation to
ectomycorrhizal roots and mycelium colonising different mineral substrates,
New Phytol., 162, 795–802, 2004.
Rosling, A., Roose, T., Herrmann, A. M., Davidson, F. A., Finlay, R. D., and
Gadd, G. M.: Approaches to modelling mineral weathering by fungi, Fung.
Biol. Rev., 23, 138–144, 2009.
Ryan, M. H., Tibbett, M., Edmonds-Tibbett, T., Suriyagoda, L. D. B.,
Lambers, H., Cawthray, G. R., and Pang, J.: Carbon trading for phosphorus
gain: the balance between rhizosphere carboxylates and arbuscular
mycorrhizal symbiosis in plant phosphorus acquisition, Plant Cell Environ.,
35, 2170–2180, 2012.
Ryu, J. S., Jacobson, A. D., Holmden, C., Lundstrom, C., and Zhang, Z. F.:
The major ion, delta Ca-44/40, delta Ca-44/42, and delta Mg-26/24
geochemistry of granite weathering at pH =1 and T =25 degrees C: power-law
processes and the relative reactivity of minerals, Geochim. Cosmochim. Ac.,
75, 6004–6026, 2011.
Saccone, L., Gazze, S. A., Duran, A. L., Leake, J. R., Banwart, S. A.,
Ragnarsdottir, K. V., Smits, M. M., and McMaster, T. J.: High resolution
characterization of ectomycorrhizal fungal-mineral interactions in axenic
microcosm experiments, Biogeochemistry, 111, 411–425, 2012.
Savage, V. J., Chopra, I., and O'Neill, A. J.: Staphylococcus aureus biofilms promote horizontal
transfer of antibiotic resistance, Antimicrob. Agents Ch., 57,
1968–1970, 2013.
Schmalenberger, A., Duran, A. L., Bray, A. W., Bridge, J., Bonneville, S.,
Benning, L. G., Romero-Gonzalez, M. E., Leake, J. R., and Banwart, S. A.:
Oxalate secretion by ectomycorrhizal Paxillus involutus is mineral-specific and controls
calcium weathering from minerals, Sci. Rep., 5, 12187, https://doi.org/10.1038/srep12187, 2015.
Seiffert, F., Bandow, N., Bouehez, J., von Blanekenburg, F., and Gorbushina,
A. A.: Microbial colonization of bare rocks: laboratory biofilm enhances
mineral weathering, Proced. Earth Plan. Sc., 10, 123–129, 2014.
Shen, B., Jacobsen, B., Lee, C. T. A., Yin, Q. Z., and Morton, D. M.: The Mg
isotopic systematics of granitoids in continental arcs and implications for
the role of chemical weathering in crust formation, P. Natl. Acad. Sci.
USA, 106, 20652–20657, 2009.
Sigurbjornsdottir, M. A., Andresson, O. S., and Vilhelmsson, O.: Analysis of
the Peltigera membranacea metagenome indicates that lichen-associated bacteria are involved in
phosphate solubilization, Microbiol.-SGM, 161, 989–996, 2015.
Simonsson, M., Bergholm, J., Olsson, B., von Brömssen, C., and
Öborn, I.: Estimating weathering rates using base cation budgets in a
Norway spruce stand on podzolised soil: Analysis of fluxes and
uncertainties, Forest Ecol. Manag., 340, 135–152, 2015.
Smith, S. E. and Read, D. J.: Mycorrhizal Symbiosis, 3rd ed.,
Academic Press, Amsterdam, London, 2008.
Smits, M. M.: Scale matters? Exploring the effect of scale on fungal-mineral
interactions, Fung. Biol. Rev., 23, 132–137, 2009.
Smits, M. M. and Wallander, H.: Role of mycorrhizal symbiosis in mineral
weathering and nutrient mining from soil parent material, in: Mycorrhizal
Mediation of Soil Fertility, Structure, and Carbon Storage, edited by:
Johnson, N. C., Gehring, C., and Jansa, J., Elsevier, Amsterdam, 35–46,
ISBN 978-0-12-8043127, 2017.
Smits, M. M., Hoffland, E., Jongmans, A. G., and van Breemen, N.:
Contribution of mineral tunneling to total feldspar weathering, Geoderma,
125, 59–69, 2005.
Smits, M. M., Bonneville, S., Haward, S., and Leake, J. R.: Ectomycorrhizal
weathering, a matter of scale?, Mineral. Mag., 72, 131–134, 2008.
Smits, M. M., Bonneville, S., Benning, L. G., Banwart, S. A., and Leake, J.
R.: Plant-driven weathering of apatite – the role of an ectomycorrhizal
fungus, Geobiology, 10, 445–456, 2012.
Smits, M. M., Johansson, L., and Wallander, H.: Soil fungi appear to have a
retarding rather than a stimulating role on soil apatite weathering, Plant
Soil., 385, 217–228, 2014.
Söderström, B. E.: Seasonal fluctuations of active fungal biomass in
horizons of a podzolized pine-forest soil in central Sweden, Soil Biol.
Biochem., 11, 149–154, 1979.
Sokolova, T. A., Tolpeshta, I. I., and Topunova, I. V.: Biotite weathering
in podzolic soil under conditions of a model field experiment, Euras. Soil
Sci., 43, 1150–1158, 2010.
Stendahl, J., Akselsson, C., Melkerud, P. A., and Belyazid, S.: Pedon-scale
silicate weathering: comparison of the PROFILE model and the depletion
method at 16 forest sites in Sweden, Geoderma, 211, 65–74, 2013.
Sterkenburg, E., Clemmensen, K. E., Ekblad, A., Finlay, R. D., and Lindahl,
B. D.: Contrasting effects of ectomycorrhizal fungi on early and late stage
decomposition in a boreal forest, ISME J., 12, 2187–2197, 2018.
Sun, Q., Li, J., Finlay, R. D., and Lian, B.: Oxalotrophic bacteria
assemblages in the ectomycorrhizosphere and their effects on oxalate
degradation and carbon fixation potential, Chem. Geol., 514, 54–65, 2019a.
Sun, Q., Ziyu, F., Finlay, R. D., and Lian, B.: Transcriptome analysis
provides novel insights into the response of the ectomycorrhizal fungus
Amanita pantherina to weather K-containing feldspar and apatite, Appl. Environ. Microb.,
85, e00719-19, https://doi.org/10.1128/AEM.00719-19, 2019b.
Sun, Q. B. and Lian, B.: The different roles of Aspergillus nidulans carbonic anhydrases in
wollastonite weathering accompanied by carbonation, Geochim. Cosmochim. Ac., 244, 437–450, 2019.
Sun, Y. P., Unestam, T., Lucas, S. D., Johanson, K. J., Kenne, L., and
Finlay, R.: Exudation-reabsorption in a mycorrhizal fungus, the dynamic
interface for interaction with soil and soil microorganisms, Mycorrhiza, 9,
137–144, 1999.
Sverdrup, H.: Chemical weathering of soil minerals and the role of
biological processes, Fung. Biol. Rev., 23, 94–100, 2009.
Taylor, L., Banwart, S., Leake, J., and Beerling, D. J.: Modeling the
evolutionary rise of ectomycorrhiza on sub-surface weathering environments
and the geochemical carbon cycle, Am. J. Sci., 311, 369–403, 2011.
Taylor, L. L., Banwart, S. A., Valdes, P. J., Leake, J. R., and Beerling, D.
J.: Evaluating the effects of terrestrial ecosystems, climate and carbon
dioxide on weathering over geological time: a global-scale process-based
approach, Philos. T. R. Soc. B, 367, 565–582, 2012.
Taylor, L. L., Quirk, J., Thorley, R. M. S., Kharecha, P. A., Hansen, J.,
Ridgwell, A., Lomas, M. R., Banwart, S. A., and Beerling, D. J.: Enhanced
weathering strategies for stabilizing climate and averting ocean
acidification, Nat. Clim. Change, 6, 402–406, 2016.
Thorley, R. M. S., Taylor, L. L., Banwart, S. A., Leake, J. R., and
Beerling, D. J.: The role of forest trees and their mycorrhizal fungi in
carbonate rock weathering and its significance for global carbon cycling,
Plant Cell Environ., 38, 1947–1961, 2015.
Tipper, E. T., Gaillardet, J., Louvat, P., Capmas, F., and White, A. F.: Mg
isotope constraints on soil pore-fluid chemistry: Evidence from Santa Cruz,
California, Geochim. Cosmochim. Ac., 74, 3883–3896, 2010.
Toljander, J., Lindahl, B., Paul, L., Elfstrand, M., and Finlay, R. D..:
Influence of arbuscular mycorrhizal mycelial exudates on soil bacterial
growth and community structure, FEMS Microbiol. Ecol., 61, 295–304, 2007.
Tuason, M. M. S. and Arocena, J. M.: Calcium oxalate biomineralization by
Piloderma fallax in response to various levels of calcium and phosphorus, Appl. Environ.
Microb., 75, 7079–7085, 2009.
Turpault, M.-P., Nys, C., and Calvaruso, C.: Rhizosphere impact on the
dissolution of test minerals in a forest ecosystem, Geoderma, 153, 147–154,
2009.
Uhlig, D., Schuessler, J. A., Bouchez, J., Dixon, J. L., and von Blanckenburg, F.: Quantifying nutrient uptake as driver of rock weathering in forest ecosystems by magnesium stable isotopes, Biogeosciences, 14, 3111–3128, https://doi.org/10.5194/bg-14-3111-2017, 2017.
Uroz, S., Oger, P., Lepleux, C., Collignon, C., Frey-Klett, P., and
Turpault, M. P.: Bacterial weathering and its contribution to nutrient
cycling in temperate forest ecosystems, Res. Microbiol., 162, 820–831, 2011.
Uroz, S., Turpault, M. P., Delaruelle, C., Mareschal, L., Pierrat, J. C.,
and Frey-Klett, P.: Minerals affect the specific diversity of forest soil
bacterial communities, Geomicrobiol. J., 29, 88–98, 2012.
Uroz, S., Kelly, L. C., Turpault, M. P., Lepleux, C., and Frey-Klett, P.:
The mineralosphere concept: Mineralogical control of the distribution and
function of mineral-associated bacterial communities, Trends Microbiol., 23,
751–762, 2015.
Vaario, L. M., Pennanen, T., Lu, J. R., Palmen, J., Stenman, J., Leveinen,
J., Kilpelainen, P., and Kitunen, V.: Tricholoma matsutake can absorb and accumulate trace
elements directly from rock fragments in the shiro, Mycorrhiza, 25, 325–334,
2015.
van Breemen, N., Finlay, R., Lundstrom, U., Jongmans, A. G., Giesler, R.,
and Olsson, M.: Mycorrhizal weathering: A true case of mineral plant
nutrition?, Biogeochemistry, 49, 53–67, 2000.
Vandenkoornhuyse, P., Quaiser, A., Duhamel, M., Le Van, A., and Dufresne,
A.: The importance of the microbiome of the plant holobiont, New Phytol.,
206, 1196–1206, 2015.
van der Heijden, G., Bel, J., Craig, C. A., Midwood, A. J., Mareschal, L.,
Ranger, J., Dambrine, E., and Legout, A.: Measuring plant-available Mg, Ca,
and K pools in the soil-an isotopic dilution assay, ACS Earth Space Chem.,
2, 292–313, 2018.
van Hees, P. A. W., Vinogradoff, S. I., Edwards, A. C., Godbold, D. L., and
Jones, D. L.: Low molecular weight organic acid adsorption in forest soils:
effects on soil solution concentrations and biodegradation rates, Soil Biol.
Biochem., 35, 1015–1026, 2003.
van Hees, P. A. W., Jones, D. L., Finlay, R., Godbold, D. L., and
Lundström, U. S.: The carbon we do not see – the impact of low
molecular weight compounds on carbon dynamics and respiration in forest
soils: a review, Soil Biol. Biochem., 37, 1–13, 2005.
van Hees, P. A. W., Rosling, A., Essen, S., Godbold, D. L., Jones, D. L.,
and Finlay, R. D.: Oxalate and ferricrocin exudation by the extramatrical
mycelium of an ectomycorrhizal fungus in symbiosis with Pinus sylvestris, New Phytol., 169,
367–377, 2006.
van Schöll, L., Hoffland, E., and van Breemen, N.:
Organic anion exudation by ectomycorrhizal fungi and Pinus sylvestris in response to
nutrient deficiencies, New Phytol., 170, 153–163, 2006a.
van Schöll, L., Smits, M. M., and Hoffland, E.:
Ectomycorrhizal weathering of the soil minerals muscovite and hornblende,
New Phytol., 171, 805–814, 2006b.
Verrecchia, E. P, Braissant, O., and Cailleau, G.: The oxalate-carbonate
pathway in soil carbon storage: the role of fungi and oxalotrophic bacteria,
in: Fungi in Biogeochemical Cycles, edited by: Gadd, G. M., Cambridge
University Press, Cambridge, 289–310, 2006.
Wallander, H., Johansson, L., and Pallon, J.: PIXE analysis to estimate the
elemental composition of ectomycorrhizal rhizomorphs grown in contact with
different minerals in forest soil, FEMS Microbiol. Ecol., 39, 147–156, 2002.
Wallander, H., Hagerberg, D., and Aberg, G.: Uptake of Sr-87 from microcline
and biotite by ectomycorrhizal fungi in a Norway spruce forest, Soil Biol.
Biochem., 38, 2487–2490, 2006.
Wang, W. Y., Lian, B., and Pan, L.: An RNA-sequencing study of the genes and
metabolic pathways involved in Aspergillus niger weathering of potassium feldspar,
Geomicrobiol. J., 32, 689–700, 2015.
Watmough, S. A. and Dillon, P. J.: Mycorrhizal weathering in base-poor
forests, Nature, 423, 823–824, 2003.
Wilcke, W., Velescu, A., Leimer, S., Bigalke, M., Boy, J., and Valarezo, C.:
Biological versus geochemical control and environmental change drivers of
the base metal budgets of a tropical montane forest in Ecuador during 15
years, Biogeochemistry, 136, 167–189, 2017.
Wild, B., Imfeld, G., Guyot, F., and Daval, D.: Early stages of bacterial
community adaptation to silicate aging, Geology, 46, 555–558, 2018.
Wild, B., Daval, D., Beaulieu, E., Pierret, M.-C., Viville, D., and Imfeld,
G.: In-situ dissolution rates of silicate minerals and associated bacterial
communities in the critical zone (Strengbach catchment, France), Geochim. Cosmochim. Ac., 249, 95–120, 2019.
Wimpenny, J., Gislason, S. R., James, R. H., Gannoun, A., Pogge Von
Strandmann, P. A. E., and Burton, K. W.: The behaviour of Li and Mg isotopes
during primary phase dissolution and secondary mineral formation in basalt,
Geochim. Cosmochim. Ac., 74, 5259–5279, 2010.
Winnick, M. J. and Maher, K.: Relationships between CO2, thermodynamic
limits on silicate weathering, and the strength of the silicate weathering
feedback, Earth Planet. Sc. Lett., 485, 111–120, 2018.
Xiao, B., Lian, B., Sun, L. L., and Shao, W. L.: Gene transcription response
to weathering of K-bearing minerals by Aspergillus fumigatus, Chem. Geol., 306–307, 1–9, https://doi.org/10.1080/01490451.2014.884195, 2012.
Xiao, L. L., Hao, J. C, Wang, W. Y., Lian, B., Shang, G. D., Yang, Y. W,
Liu, C. Q., and Wang, S. J.: The up-regulation of carbonic anhydrase genes of
Bacillus mucilaginosus under soluble Ca2+ deficiency and the heterologously expressed enzyme
promotes calcite dissolution, Geomicrobiol. J., 31, 632–641, 2014.
Xiao, L. L., Lian, B., Hao, J. C., Liu, C. Q., and Wang, S. J.: Effect of
carbonic anhydrase on silicate weathering and carbonate formation at present
day CO2 concentrations compared to primordial values, Sci. Rep., 5,
7733, https://doi.org/10.1038/srep07733, 2015.
Xiao, L. L., Sun, Q. B., Yuan, H. T., and Lian, B.: A practical soil
management to improve soil quality by applying mineral organic fertilizer,
Acta Geochim., 36, 198–204, 2017.
Zetterberg, T., Olsson, B.A., Löfgren, S., Hyvönen, R., and
Brandtberg, P. O.: Long-term soil calcium depletion after conventional and
whole-tree harvest, Forest Ecol. Manag., 369, 102–115, 2016.
Zhang, L., Fan, J., Ding, X., He, X., Zhang, F., and Feng, G.: Hyphosphere
interactions between an arbuscular mycorrhizal fungus and a phosphate
solubilizing bacterium promote phytate mineralization in soil, Soil Biol.
Biochem., 74, 177–183, 2014.
Zhang, L., Xu, M., Liu, Y., Zhang, F., Hodge, A., and Feng. G.: Carbon and
phosphorus exchange may enable cooperation between an arbuscular mycorrhizal
fungus and a phosphate-solubilizing bacterium, New Phytol., 210, 1022–1032,
2016.
Zimorski, V., Ku, C., Martin, W. F., and Gould, S.B.: Endosymbiotic theory
for organelle origins, Curr. Opin. Microbiol., 22, 38–48, 2014.
Short summary
Effects of biological activity on mineral weathering operate at scales ranging from short-term, microscopic interactions to global, evolutionary timescale processes. Microorganisms have had well-documented effects at large spatio-temporal scales, but to establish the quantitative significance of microscopic measurements for field-scale processes, higher-resolution studies of liquid chemistry at local weathering sites and improved upscaling to soil-scale dissolution rates are still required.
Effects of biological activity on mineral weathering operate at scales ranging from short-term,...
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