Articles | Volume 18, issue 12
https://doi.org/10.5194/bg-18-3689-2021
© Author(s) 2021. 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-18-3689-2021
© Author(s) 2021. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Reviews and syntheses
| 
21 Jun 2021
Reviews and syntheses |
| 21 Jun 2021
| 21 Jun 2021
Reviews and syntheses: Heterotrophic fixation of inorganic carbon – significant but invisible flux in environmental carbon cycling
Alexander Braun
Institute of Groundwater Ecology, Helmholtz Zentrum München,
Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
Marina Spona-Friedl
Institute of Groundwater Ecology, Helmholtz Zentrum München,
Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
Maria Avramov
Institute of Groundwater Ecology, Helmholtz Zentrum München,
Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
Martin Elsner
Institute of Groundwater Ecology, Helmholtz Zentrum München,
Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
Department of Analytical Chemistry
and Water Chemistry, Technical University of Munich, Munich, Germany
Federico Baltar
Department of Functional and Evolutionary
Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
Thomas Reinthaler
Department of Functional and Evolutionary
Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
Gerhard J. Herndl
Department of Functional and Evolutionary
Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
Department of Marine Microbiology and Biogeochemistry, Royal
Netherlands Institute for Sea Research, Utrecht University, P.O. Box 59, 1790
AB Den Burg, the Netherlands
Christian Griebler
CORRESPONDING AUTHOR
Institute of Groundwater Ecology, Helmholtz Zentrum München,
Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
Department of Functional and Evolutionary
Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
Related authors
No articles found.
Mak A. Saito, Jaclyn K. Saunders, Matthew R. McIlvin, Erin M. Bertrand, John A. Breier, Margaret Mars Brisbin, Sophie M. Colston, Jaimee R. Compton, Tim J. Griffin, W. Judson Hervey, Robert L. Hettich, Pratik D. Jagtap, Michael Janech, Rod Johnson, Rick Keil, Hugo Kleikamp, Dagmar Leary, Lennart Martens, J. Scott P. McCain, Eli Moore, Subina Mehta, Dawn M. Moran, Jaqui Neibauer, Benjamin A. Neely, Michael V. Jakuba, Jim Johnson, Megan Duffy, Gerhard J. Herndl, Richard Giannone, Ryan Mueller, Brook L. Nunn, Martin Pabst, Samantha Peters, Andrew Rajczewski, Elden Rowland, Brian Searle, Tim Van Den Bossche, Gary J. Vora, Jacob R. Waldbauer, Haiyan Zheng, and Zihao Zhao
Biogeosciences, 21, 4889–4908, https://doi.org/10.5194/bg-21-4889-2024, https://doi.org/10.5194/bg-21-4889-2024, 2024
Short summary
Short summary
The ability to assess the functional capabilities of microbes in the environment is of increasing interest. Metaproteomics, the ability to measure proteins across microbial populations, has been increasing in capability and popularity in recent years. Here, an international team of scientists conducted an intercomparison study using samples collected from the North Atlantic Ocean and observed consistency in the peptides and proteins identified, their functions, and their taxonomic origins.
This article is included in the Encyclopedia of Geosciences
Weiyi Tang, Bess B. Ward, Michael Beman, Laura Bristow, Darren Clark, Sarah Fawcett, Claudia Frey, François Fripiat, Gerhard J. Herndl, Mhlangabezi Mdutyana, Fabien Paulot, Xuefeng Peng, Alyson E. Santoro, Takuhei Shiozaki, Eva Sintes, Charles Stock, Xin Sun, Xianhui S. Wan, Min N. Xu, and Yao Zhang
Earth Syst. Sci. Data, 15, 5039–5077, https://doi.org/10.5194/essd-15-5039-2023, https://doi.org/10.5194/essd-15-5039-2023, 2023
Short summary
Short summary
Nitrification and nitrifiers play an important role in marine nitrogen and carbon cycles by converting ammonium to nitrite and nitrate. Nitrification could affect microbial community structure, marine productivity, and the production of nitrous oxide – a powerful greenhouse gas. We introduce the newly constructed database of nitrification and nitrifiers in the marine water column and guide future research efforts in field observations and model development of nitrification.
This article is included in the Encyclopedia of Geosciences
Mirjana Najdek, Marino Korlević, Paolo Paliaga, Marsej Markovski, Ingrid Ivančić, Ljiljana Iveša, Igor Felja, and Gerhard J. Herndl
Biogeosciences, 17, 3299–3315, https://doi.org/10.5194/bg-17-3299-2020, https://doi.org/10.5194/bg-17-3299-2020, 2020
Short summary
Short summary
The response of Cymodocea nodosa to environmental changes was reported during a 15-month period. The meadow decline was triggered in spring by the simultaneous reduction of available light in the water column and the creation of anoxic conditions in the rooted area. This disturbance was critical for the plant since it took place during its recruitment phase when metabolic needs are maximal and stored reserves minimal. The loss of such habitat-forming seagrass is a major environmental concern.
This article is included in the Encyclopedia of Geosciences
Federico Baltar and Gerhard J. Herndl
Biogeosciences, 16, 3793–3799, https://doi.org/10.5194/bg-16-3793-2019, https://doi.org/10.5194/bg-16-3793-2019, 2019
Short summary
Short summary
Around half of the global primary production (PP) is produced in the ocean. Here we quantified how much oceanic PP estimates would increase if we included the dark DIC fixation rates (which are usually excluded in the carbon-14 method) into the PP estimation. We found that the inclusion of dark DIC fixation would increase PP estimates by 5–22 %. This represents ca. 1.2 to 11 Pg C yr−1 of newly synthesized organic carbon available for the marine food web.
This article is included in the Encyclopedia of Geosciences
Related subject area
Biogeochemistry: Organic Biogeochemistry
Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures
Controls on the composition of hydroxylated isoprenoidal glycerol dialkyl glycerol tetraethers (isoGDGTs) in cultivated ammonia-oxidizing Thaumarchaeota
Reviews and syntheses: Opportunities for robust use of peak intensities from high-resolution mass spectrometry in organic matter studies
Elemental stoichiometry of particulate organic matter across the Atlantic Ocean
Lipid remodeling in phytoplankton exposed to multi-environmental drivers in a mesocosm experiment
Molecular-level carbon traits of fine roots: unveiling adaptation and decomposition under flooded conditions
Environmental controls on the distribution of brGDGTs and brGMGTs across the Seine River basin (NW France): implications for bacterial tetraethers as a proxy for riverine runoff
Ocean liming effects on dissolved organic matter dynamics
Latitudinal distribution of biomarkers across the western Arctic Ocean and the Bering Sea: an approach to assess sympagic and pelagic algal production
Sinking fate and carbon export of zooplankton fecal pellets: insights from time-series sediment trap observations in the northern South China Sea
Microbial strong organic ligand production is tightly coupled to iron in hydrothermal plumes
Low cobalt inventories in the Amundsen and Ross seas driven by high demand for labile cobalt uptake among native phytoplankton communities
Methods to characterize type, relevance, and interactions of organic matter and microorganisms in fluids along the flow path of a geothermal facility
Potential bioavailability of representative pyrogenic organic matter compounds in comparison to natural dissolved organic matter pools
Distributions of bacteriohopanepolyols in lakes and coastal lagoons of the Azores Archipelago
Recently fixed carbon fuels microbial activity several meters below the soil surface
Environmental and hydrologic controls on sediment and organic carbon export from a subalpine catchment: insights from a time series
Climate and geology overwrite land use effects on soil organic nitrogen cycling on a continental scale
Compositions of dissolved organic matter in the ice-covered waters above the Aurora hydrothermal vent system, Gakkel Ridge, Arctic Ocean
Organic matter characteristics of a rapidly eroding permafrost cliff in NE Siberia (Lena Delta, Laptev Sea region)
Microbial labilization and diversification of pyrogenic dissolved organic matter
Bacterial and eukaryotic intact polar lipids point to in situ production as a key source of labile organic matter in hadal surface sediment of the Atacama Trench
What can we learn from amino acids about oceanic organic matter cycling and degradation?
Bacteriohopanetetrol-x: constraining its application as a lipid biomarker for marine anammox using the water column oxygen gradient of the Benguela upwelling system
Active and passive fluxes of carbon, nitrogen, and phosphorus in the northern South China Sea
Cyanobacteria net community production in the Baltic Sea as inferred from profiling pCO2 measurements
Revised fractional abundances and warm-season temperatures substantially improve brGDGT calibrations in lake sediments
Archaeal intact polar lipids in polar waters: a comparison between the Amundsen and Scotia seas
Reproducible determination of dissolved organic matter photosensitivity
Technical note: Uncovering the influence of methodological variations on the extractability of iron-bound organic carbon
Anthropocene climate warming enhances autochthonous carbon cycling in an upland Arctic lake, Disko Island, West Greenland
Novel hydrocarbon-utilizing soil mycobacteria synthesize unique mycocerosic acids at a Sicilian everlasting fire
Alkenone isotopes show evidence of active carbon concentrating mechanisms in coccolithophores as aqueous carbon dioxide concentrations fall below 7 µmol L−1
Seasonal variability and sources of in situ brGDGT production in a permanently stratified African crater lake
Sediment release of dissolved organic matter to the oxygen minimum zone off Peru
Better molecular preservation of organic matter in an oxic than in a sulfidic depositional environment: evidence from Thalassiphora pelagica (Dinoflagellata, Eocene) cysts
Assessing branched tetraether lipids as tracers of soil organic carbon transport through the Carminowe Creek catchment (southwest England)
The nonconservative distribution pattern of organic matter in the Rajang, a tropical river with peatland in its estuary
Predominance of hexamethylated 6-methyl branched glycerol dialkyl glycerol tetraethers in the Mariana Trench: source and environmental implication
High-pH and anoxic conditions during soil organic matter extraction increases its electron-exchange capacity and ability to stimulate microbial Fe(III) reduction by electron shuttling
Sterol preservation in hypersaline microbial mats
Structural elucidation and environmental distributions of butanetriol and pentanetriol dialkyl glycerol tetraethers (BDGTs and PDGTs)
Distribution and degradation of terrestrial organic matter in the sediments of peat-draining rivers, Sarawak, Malaysian Borneo
Validation of carbon isotope fractionation in algal lipids as a pCO2 proxy using a natural CO2 seep (Shikine Island, Japan)
Composition and cycling of dissolved organic matter from tropical peatlands of coastal Sarawak, Borneo, revealed by fluorescence spectroscopy and parallel factor analysis
Latitudinal variations in δ30Si and δ15N signatures along the Peruvian shelf: quantifying the effects of nutrient utilization versus denitrification over the past 600 years
Diapycnal dissolved organic matter supply into the upper Peruvian oxycline
Composition and vertical flux of particulate organic matter to the oxygen minimum zone of the central Baltic Sea: impact of a sporadic North Sea inflow
Main drivers of transparent exopolymer particle distribution across the surface Atlantic Ocean
Biochemical and structural controls on the decomposition dynamics of boreal upland forest moss tissues
Mak A. Saito, Jaclyn K. Saunders, Matthew R. McIlvin, Erin M. Bertrand, John A. Breier, Margaret Mars Brisbin, Sophie M. Colston, Jaimee R. Compton, Tim J. Griffin, W. Judson Hervey, Robert L. Hettich, Pratik D. Jagtap, Michael Janech, Rod Johnson, Rick Keil, Hugo Kleikamp, Dagmar Leary, Lennart Martens, J. Scott P. McCain, Eli Moore, Subina Mehta, Dawn M. Moran, Jaqui Neibauer, Benjamin A. Neely, Michael V. Jakuba, Jim Johnson, Megan Duffy, Gerhard J. Herndl, Richard Giannone, Ryan Mueller, Brook L. Nunn, Martin Pabst, Samantha Peters, Andrew Rajczewski, Elden Rowland, Brian Searle, Tim Van Den Bossche, Gary J. Vora, Jacob R. Waldbauer, Haiyan Zheng, and Zihao Zhao
Biogeosciences, 21, 4889–4908, https://doi.org/10.5194/bg-21-4889-2024, https://doi.org/10.5194/bg-21-4889-2024, 2024
Short summary
Short summary
The ability to assess the functional capabilities of microbes in the environment is of increasing interest. Metaproteomics, the ability to measure proteins across microbial populations, has been increasing in capability and popularity in recent years. Here, an international team of scientists conducted an intercomparison study using samples collected from the North Atlantic Ocean and observed consistency in the peptides and proteins identified, their functions, and their taxonomic origins.
This article is included in the Encyclopedia of Geosciences
Devika Varma, Laura Villanueva, Nicole J. Bale, Pierre Offre, Gert-Jan Reichart, and Stefan Schouten
Biogeosciences, 21, 4875–4888, https://doi.org/10.5194/bg-21-4875-2024, https://doi.org/10.5194/bg-21-4875-2024, 2024
Short summary
Short summary
Archaeal hydroxylated tetraether lipids are increasingly used as temperature indicators in marine settings, but the factors influencing their distribution are still unclear. Analyzing membrane lipids of two thaumarchaeotal strains showed that the growth phase of the cultures does not affect the lipid distribution, but growth temperature profoundly affects the degree of cyclization of these lipids. Also, the abundance of these lipids is species-specific and is not influenced by temperature.
This article is included in the Encyclopedia of Geosciences
William Kew, Allison Myers-Pigg, Christine H. Chang, Sean M. Colby, Josie Eder, Malak M. Tfaily, Jeffrey Hawkes, Rosalie K. Chu, and James C. Stegen
Biogeosciences, 21, 4665–4679, https://doi.org/10.5194/bg-21-4665-2024, https://doi.org/10.5194/bg-21-4665-2024, 2024
Short summary
Short summary
Natural organic matter (NOM) is often studied via Fourier transform mass spectrometry (FTMS), which identifies organic molecules as mass spectra peaks. The intensity of peaks is data that is often discarded due to technical concerns. We review the theory behind these concerns and show they are supported empirically. However, simulations show that ecological analyses of NOM data that include FTMS peak intensities are often valid. This opens a path for robust use of FTMS peak intensities for NOM.
This article is included in the Encyclopedia of Geosciences
Adam J. Fagan, Tatsuro Tanioka, Alyse A. Larkin, Jenna A. Lee, Nathan S. Garcia, and Adam C. Martiny
Biogeosciences, 21, 4239–4250, https://doi.org/10.5194/bg-21-4239-2024, https://doi.org/10.5194/bg-21-4239-2024, 2024
Short summary
Short summary
Climate change is anticipated to influence the biological pump by altering phytoplankton nutrient distribution. In our research, we collected measurements of particulate matter concentrations during two oceanographic field studies. We observed systematic variations in organic matter concentrations and ratios across the Atlantic Ocean. From statistical modeling, we determined that these variations are associated with differences in the availability of essential nutrients for phytoplankton growth.
This article is included in the Encyclopedia of Geosciences
Sebastian I. Cantarero, Edgart Flores, Harry Allbrook, Paulina Aguayo, Cristian A. Vargas, John E. Tamanaha, J. Bentley C. Scholz, Lennart T. Bach, Carolin R. Löscher, Ulf Riebesell, Balaji Rajagopalan, Nadia Dildar, and Julio Sepúlveda
Biogeosciences, 21, 3927–3958, https://doi.org/10.5194/bg-21-3927-2024, https://doi.org/10.5194/bg-21-3927-2024, 2024
Short summary
Short summary
Our study explores lipid remodeling in response to environmental stress, specifically how cell membrane chemistry changes. We focus on intact polar lipids in a phytoplankton community exposed to diverse stressors in a mesocosm experiment. The observed remodeling indicates acyl chain recycling for energy storage in intact polar lipids during stress, reallocating resources based on varying growth conditions. This understanding is essential to grasp the system's impact on cellular pools.
This article is included in the Encyclopedia of Geosciences
Mengke Wang, Peng Zhang, Huishan Li, Guisen Deng, Deliang Kong, Sifang Kong, and Junjian Wang
Biogeosciences, 21, 2691–2704, https://doi.org/10.5194/bg-21-2691-2024, https://doi.org/10.5194/bg-21-2691-2024, 2024
Short summary
Short summary
We developed and applied complementary analyses to characterize molecular-level carbon traits for water-grown and soil-grown fine roots. The adaptive strategy of developing more labile carbon in water-grown roots accelerated root decomposition and counteracted the decelerated effects of anoxia on decomposition, highlighting an indirect effect of environmental change on belowground carbon cycling.
This article is included in the Encyclopedia of Geosciences
Zhe-Xuan Zhang, Edith Parlanti, Christelle Anquetil, Jérôme Morelle, Anniet M. Laverman, Alexandre Thibault, Elisa Bou, and Arnaud Huguet
Biogeosciences, 21, 2227–2252, https://doi.org/10.5194/bg-21-2227-2024, https://doi.org/10.5194/bg-21-2227-2024, 2024
Short summary
Short summary
Bacterial tetraethers have important implications for palaeoclimate reconstruction. However, fundamental understanding of how these lipids are transformed from land to sea and which environmental factors influence their distributions is lacking. Here, we investigate the sources of brGDGTs and brGMGTs and the factors controlling their distributions in a large dataset (n=237). We propose a novel proxy (RIX) to trace riverine runoff, which is applicable in modern systems and in paleorecord.
This article is included in the Encyclopedia of Geosciences
Chiara Santinelli, Silvia Valsecchi, Simona Retelletti Brogi, Giancarlo Bachi, Giovanni Checcucci, Mirco Guerrazzi, Elisa Camatti, Stefano Caserini, Arianna Azzellino, and Daniela Basso
EGUsphere, https://doi.org/10.5194/egusphere-2024-625, https://doi.org/10.5194/egusphere-2024-625, 2024
Short summary
Short summary
To the best of our knowledge, there is no study investigating the impact of ocean liming on dissolved organic matter (DOM) dynamics. Given the central role played by DOM in the microbial loop, a change in its concentration and/or quality has a cascading effect the entire marine ecosystem. Our data clearly show that the addition of hydrated lime cause a reduction in DOM concentration and a change in its quality. The observed effects, detectable at pH 9, becomes significant at pH 10.
This article is included in the Encyclopedia of Geosciences
Youcheng Bai, Marie-Alexandrine Sicre, Jian Ren, Vincent Klein, Haiyan Jin, and Jianfang Chen
Biogeosciences, 21, 689–709, https://doi.org/10.5194/bg-21-689-2024, https://doi.org/10.5194/bg-21-689-2024, 2024
Short summary
Short summary
Algal biomarkers were used to assess sea ice and pelagic algal production across the western Arctic Ocean with changing sea-ice conditions. They show three distinct areas along with a marked latitudinal gradient of sea ice over pelagic algal production in surface sediments that are reflected by the H-Print index. Our data also show that efficient grazing consumption accounted for the dramatic decrease of diatom-derived biomarkers in sediments compared to that of particulate matter.
This article is included in the Encyclopedia of Geosciences
Hanxiao Wang, Zhifei Liu, Jiaying Li, Baozhi Lin, Yulong Zhao, Xiaodong Zhang, Junyuan Cao, Jingwen Zhang, Hongzhe Song, and Wenzhuo Wang
Biogeosciences, 20, 5109–5123, https://doi.org/10.5194/bg-20-5109-2023, https://doi.org/10.5194/bg-20-5109-2023, 2023
Short summary
Short summary
The sinking of zooplankton fecal pellets is a key process in the marine biological carbon pump. This study presents carbon export of four shapes of fecal pellets from two time-series sediment traps in the South China Sea. The results show that the sinking fate of fecal pellets is regulated by marine primary productivity, deep-dwelling zooplankton community, and deep-sea currents in the tropical marginal sea, thus providing a new perspective for exploring the carbon cycle in the world ocean.
This article is included in the Encyclopedia of Geosciences
Colleen L. Hoffman, Patrick J. Monreal, Justine B. Albers, Alastair J. M. Lough, Alyson E. Santoro, Travis Mellett, Kristen N. Buck, Alessandro Tagliabue, Maeve C. Lohan, Joseph A. Resing, and Randelle M. Bundy
EGUsphere, https://doi.org/10.1101/2023.01.05.522639, https://doi.org/10.1101/2023.01.05.522639, 2023
Short summary
Short summary
Hydrothermally-derived iron can be transported thousands of kilometers away from deep-sea vents, representing a significant flux of vital micronutrients to the ocean. However, the mechanisms that support the stabilization and transport of dissolved iron remain elusive. Using electrochemical methods, advanced mass spectrometry techniques, and genomic tools we demonstrate that strong microbially-produced ligands appear to exert an important control on plume iron biogeochemistry and dissemination.
This article is included in the Encyclopedia of Geosciences
Rebecca J. Chmiel, Riss M. Kell, Deepa Rao, Dawn M. Moran, Giacomo R. DiTullio, and Mak A. Saito
Biogeosciences, 20, 3997–4027, https://doi.org/10.5194/bg-20-3997-2023, https://doi.org/10.5194/bg-20-3997-2023, 2023
Short summary
Short summary
Cobalt is an important micronutrient for plankton, yet it is often scarce throughout the oceans. A 2017/2018 expedition to coastal Antarctica, including regions of the Amundsen Sea and the Ross Sea, discovered lower concentrations of cobalt compared to two past expeditions in 2005 and 2006, particularly for the type of cobalt preferred as a nutrient by phytoplankton. This loss may be due to changing inputs of other nutrients, causing higher uptake of cobalt by plankton over the last decade.
This article is included in the Encyclopedia of Geosciences
Alessio Leins, Danaé Bregnard, Andrea Vieth-Hillebrand, Stefanie Poetz, Florian Eichinger, Guillaume Cailleau, Pilar Junier, and Simona Regenspurg
Biogeosciences Discuss., https://doi.org/10.5194/bg-2023-159, https://doi.org/10.5194/bg-2023-159, 2023
Revised manuscript accepted for BG
Short summary
Short summary
Organic matter and microbial fluid analyses are rarely taken into account in the geothermal industry and research. However, they can have a significant effect on the efficiency of geothermal power production. We discovered a high variety in organic compound composition in our samples and were able to differentiate it with regard to various sources (e.g. artificial and biogenic). Furthermore, the microbial diversity undergoes significant changes within the flow path of a geothermal power plant.
This article is included in the Encyclopedia of Geosciences
Emily B. Graham, Hyun-Seob Song, Samantha Grieger, Vanessa A. Garayburu-Caruso, James C. Stegen, Kevin D. Bladon, and Allison N. Myers-Pigg
Biogeosciences, 20, 3449–3457, https://doi.org/10.5194/bg-20-3449-2023, https://doi.org/10.5194/bg-20-3449-2023, 2023
Short summary
Short summary
Intensifying wildfires are increasing pyrogenic organic matter (PyOM) production and its impact on water quality. Recent work indicates that PyOM may have a greater impact on aquatic biogeochemistry than previously assumed, driven by higher bioavailability. We provide a full assessment of the potential bioavailability of PyOM across its chemical spectrum. We indicate that PyOM can be actively transformed within the river corridor and, therefore, may be a growing source of riverine C emissions.
This article is included in the Encyclopedia of Geosciences
Nora Richter, Ellen C. Hopmans, Danica Mitrović, Pedro M. Raposeiro, Vítor Gonçalves, Ana C. Costa, Linda A. Amaral-Zettler, Laura Villanueva, and Darci Rush
Biogeosciences, 20, 2065–2098, https://doi.org/10.5194/bg-20-2065-2023, https://doi.org/10.5194/bg-20-2065-2023, 2023
Short summary
Short summary
Bacteriohopanepolyols (BHPs) are a diverse class of lipids produced by bacteria across a wide range of environments. This study characterizes the diversity of BHPs in lakes and coastal lagoons in the Azores Archipelago, as well as a co-culture enriched for methanotrophs. We highlight the potential of BHPs as taxonomic markers for bacteria associated with certain ecological niches, which can be preserved in sedimentary records.
This article is included in the Encyclopedia of Geosciences
Andrea Scheibe, Carlos A. Sierra, and Marie Spohn
Biogeosciences, 20, 827–838, https://doi.org/10.5194/bg-20-827-2023, https://doi.org/10.5194/bg-20-827-2023, 2023
Short summary
Short summary
We explored carbon cycling in soils in three climate zones in Chile down to a depth of 6 m, using carbon isotopes. Our results show that microbial activity several meters below the soil surface is mostly fueled by recently fixed carbon and that strong decomposition of soil organic matter only occurs in the upper decimeters of the soils. The study shows that different layers of the critical zone are tightly connected and that processes in the deep soil depend on recently fixed carbon.
This article is included in the Encyclopedia of Geosciences
Melissa Sophia Schwab, Hannah Gies, Chantal Valérie Freymond, Maarten Lupker, Negar Haghipour, and Timothy Ian Eglinton
Biogeosciences, 19, 5591–5616, https://doi.org/10.5194/bg-19-5591-2022, https://doi.org/10.5194/bg-19-5591-2022, 2022
Short summary
Short summary
The majority of river studies focus on headwater or floodplain systems, while often neglecting intermediate river segments. Our study on the subalpine Sihl River bridges the gap between streams and lowlands and demonstrates that moderately steep river segments are areas of significant instream alterations, modulating the export of organic carbon over short distances.
This article is included in the Encyclopedia of Geosciences
Lisa Noll, Shasha Zhang, Qing Zheng, Yuntao Hu, Florian Hofhansl, and Wolfgang Wanek
Biogeosciences, 19, 5419–5433, https://doi.org/10.5194/bg-19-5419-2022, https://doi.org/10.5194/bg-19-5419-2022, 2022
Short summary
Short summary
Cleavage of proteins to smaller nitrogen compounds allows microorganisms and plants to exploit the largest nitrogen reservoir in soils and is considered the bottleneck in soil organic nitrogen cycling. Results from soils covering a European transect show that protein turnover is constrained by soil geochemistry, shifts in climate and associated alterations in soil weathering and should be considered as a driver of soil nitrogen availability with repercussions on carbon cycle processes.
This article is included in the Encyclopedia of Geosciences
Muhammed Fatih Sert, Helge Niemann, Eoghan P. Reeves, Mats A. Granskog, Kevin P. Hand, Timo Kekäläinen, Janne Jänis, Pamela E. Rossel, Bénédicte Ferré, Anna Silyakova, and Friederike Gründger
Biogeosciences, 19, 2101–2120, https://doi.org/10.5194/bg-19-2101-2022, https://doi.org/10.5194/bg-19-2101-2022, 2022
Short summary
Short summary
We investigate organic matter composition in the Arctic Ocean water column. We collected seawater samples from sea ice to deep waters at six vertical profiles near an active hydrothermal vent and its plume. In comparison to seawater, we found that the organic matter in waters directly affected by the hydrothermal plume had different chemical composition. We suggest that hydrothermal processes may influence the organic matter distribution in the deep ocean.
This article is included in the Encyclopedia of Geosciences
Charlotte Haugk, Loeka L. Jongejans, Kai Mangelsdorf, Matthias Fuchs, Olga Ogneva, Juri Palmtag, Gesine Mollenhauer, Paul J. Mann, P. Paul Overduin, Guido Grosse, Tina Sanders, Robyn E. Tuerena, Lutz Schirrmeister, Sebastian Wetterich, Alexander Kizyakov, Cornelia Karger, and Jens Strauss
Biogeosciences, 19, 2079–2094, https://doi.org/10.5194/bg-19-2079-2022, https://doi.org/10.5194/bg-19-2079-2022, 2022
Short summary
Short summary
Buried animal and plant remains (carbon) from the last ice age were freeze-locked in permafrost. At an extremely fast eroding permafrost cliff in the Lena Delta (Siberia), we found this formerly frozen carbon well preserved. Our results show that ongoing degradation releases substantial amounts of this carbon, making it available for future carbon emissions. This mobilisation at the studied cliff and also similarly eroding sites bear the potential to affect rivers and oceans negatively.
This article is included in the Encyclopedia of Geosciences
Aleksandar I. Goranov, Andrew S. Wozniak, Kyle W. Bostick, Andrew R. Zimmerman, Siddhartha Mitra, and Patrick G. Hatcher
Biogeosciences, 19, 1491–1514, https://doi.org/10.5194/bg-19-1491-2022, https://doi.org/10.5194/bg-19-1491-2022, 2022
Short summary
Short summary
Wildfire-derived molecules are ubiquitous in the aquatic environment, but their biological fate remains understudied. We have evaluated the compositional changes that occur to wildfire-derived molecules after incubation with soil microbes. We observe a significant degradation but also a production of numerous new labile molecules. Our results indicate that wildfire-derived molecules can be broken down and the carbon and nitrogen therein can be incorporated into microbial food webs.
This article is included in the Encyclopedia of Geosciences
Edgart Flores, Sebastian I. Cantarero, Paula Ruiz-Fernández, Nadia Dildar, Matthias Zabel, Osvaldo Ulloa, and Julio Sepúlveda
Biogeosciences, 19, 1395–1420, https://doi.org/10.5194/bg-19-1395-2022, https://doi.org/10.5194/bg-19-1395-2022, 2022
Short summary
Short summary
In this study, we investigate the chemical diversity and abundance of microbial lipids as markers of organic matter sources in the deepest points of the Atacama Trench sediments and compare them to similar lipid stocks in shallower surface sediments and in the overlying water column. We evaluate possible organic matter provenance and some potential chemical adaptations of the in situ microbial community to the extreme conditions of high hydrostatic pressure in hadal realm.
This article is included in the Encyclopedia of Geosciences
Birgit Gaye, Niko Lahajnar, Natalie Harms, Sophie Anna Luise Paul, Tim Rixen, and Kay-Christian Emeis
Biogeosciences, 19, 807–830, https://doi.org/10.5194/bg-19-807-2022, https://doi.org/10.5194/bg-19-807-2022, 2022
Short summary
Short summary
Amino acids were analyzed in a large number of samples of particulate and dissolved organic matter from coastal regions and the open ocean. A statistical analysis produced two new biogeochemical indicators. An indicator of sinking particle and sediment degradation (SDI) traces the degradation of organic matter from the surface waters into the sediments. A second indicator shows the residence time of suspended matter in the ocean (RTI).
This article is included in the Encyclopedia of Geosciences
Zoë R. van Kemenade, Laura Villanueva, Ellen C. Hopmans, Peter Kraal, Harry J. Witte, Jaap S. Sinninghe Damsté, and Darci Rush
Biogeosciences, 19, 201–221, https://doi.org/10.5194/bg-19-201-2022, https://doi.org/10.5194/bg-19-201-2022, 2022
Short summary
Short summary
Anaerobic ammonium oxidation (anammox) is an important nitrogen-removal process in the ocean. We assess the distribution of bacteriohopanetetrol-x (BHT-x), used to trace past anammox, along a redox gradient in the water column of the Benguela upwelling system. BHT-x / BHT ratios of >0.18 correspond to the presence of living anammox bacteria and oxygen levels <50 μmol L−1. This allows for a more robust application of BHT-x to trace past marine anammox and deoxygenation in dynamic marine systems.
This article is included in the Encyclopedia of Geosciences
Jia-Jang Hung, Ching-Han Tung, Zong-Ying Lin, Yuh-ling Lee Chen, Shao-Hung Peng, Yen-Huei Lin, and Li-Shan Tsai
Biogeosciences, 18, 5141–5162, https://doi.org/10.5194/bg-18-5141-2021, https://doi.org/10.5194/bg-18-5141-2021, 2021
Short summary
Short summary
We report measured active and passive fluxes and their controlling mechanisms in the northern South China Sea (NSCS). The total fluxes were higher than most reports in open oceans, indicating the significance of NSCS in atmospheric CO2 uptake and in storing that CO2 in the ocean’s interior. Winter cooling and extreme events enhanced nutrient availability and elevated fluxes. Global warming may have profound impacts on reducing ocean’s uptake and storage of CO2 in subtropical–tropical oceans.
This article is included in the Encyclopedia of Geosciences
Jens Daniel Müller, Bernd Schneider, Ulf Gräwe, Peer Fietzek, Marcus Bo Wallin, Anna Rutgersson, Norbert Wasmund, Siegfried Krüger, and Gregor Rehder
Biogeosciences, 18, 4889–4917, https://doi.org/10.5194/bg-18-4889-2021, https://doi.org/10.5194/bg-18-4889-2021, 2021
Short summary
Short summary
Based on profiling pCO2 measurements from a field campaign, we quantify the biomass production of a cyanobacteria bloom in the Baltic Sea, the export of which would foster deep water deoxygenation. We further demonstrate how this biomass production can be accurately reconstructed from long-term surface measurements made on cargo vessels in combination with modelled temperature profiles. This approach enables a better understanding of a severe concern for the Baltic’s good environmental status.
This article is included in the Encyclopedia of Geosciences
Jonathan H. Raberg, David J. Harning, Sarah E. Crump, Greg de Wet, Aria Blumm, Sebastian Kopf, Áslaug Geirsdóttir, Gifford H. Miller, and Julio Sepúlveda
Biogeosciences, 18, 3579–3603, https://doi.org/10.5194/bg-18-3579-2021, https://doi.org/10.5194/bg-18-3579-2021, 2021
Short summary
Short summary
BrGDGT lipids are a proxy for temperature in lake sediments, but other parameters like pH can influence them, and seasonality can affect the temperatures they record. We find a warm-season bias at 43 new high-latitude sites. We also present a new method that deconvolves the effects of temperature, pH, and conductivity and generate global calibrations for these variables. Our study provides new paleoclimate tools, insight into brGDGTs at the biochemical level, and a new method for future study.
This article is included in the Encyclopedia of Geosciences
Charlotte L. Spencer-Jones, Erin L. McClymont, Nicole J. Bale, Ellen C. Hopmans, Stefan Schouten, Juliane Müller, E. Povl Abrahamsen, Claire Allen, Torsten Bickert, Claus-Dieter Hillenbrand, Elaine Mawbey, Victoria Peck, Aleksandra Svalova, and James A. Smith
Biogeosciences, 18, 3485–3504, https://doi.org/10.5194/bg-18-3485-2021, https://doi.org/10.5194/bg-18-3485-2021, 2021
Short summary
Short summary
Long-term ocean temperature records are needed to fully understand the impact of West Antarctic Ice Sheet collapse. Glycerol dialkyl glycerol tetraethers (GDGTs) are powerful tools for reconstructing ocean temperature but can be difficult to apply to the Southern Ocean. Our results show active GDGT synthesis in relatively warm depths of the ocean. This research improves the application of GDGT palaeoceanographic proxies in the Southern Ocean.
This article is included in the Encyclopedia of Geosciences
Alec W. Armstrong, Leanne Powers, and Michael Gonsior
Biogeosciences, 18, 3367–3390, https://doi.org/10.5194/bg-18-3367-2021, https://doi.org/10.5194/bg-18-3367-2021, 2021
Short summary
Short summary
Living things decay into organic matter, which can dissolve into water (like tea brewing). Tea receives its color by absorbing light. Similarly, this material absorbs light, which can then cause chemical reactions that change it. By measuring changes in these optical properties, we found that materials from some places are more sensitive to light than others. Comparing sensitivity to light helps us understand where these materials come from and what happens as they move through water.
This article is included in the Encyclopedia of Geosciences
Ben J. Fisher, Johan C. Faust, Oliver W. Moore, Caroline L. Peacock, and Christian März
Biogeosciences, 18, 3409–3419, https://doi.org/10.5194/bg-18-3409-2021, https://doi.org/10.5194/bg-18-3409-2021, 2021
Short summary
Short summary
Organic carbon can be protected from microbial degradation in marine sediments through association with iron minerals on 1000-year timescales. Despite the importance of this carbon sink, our spatial and temporal understanding of iron-bound organic carbon interactions globally is poor. Here we show that caution must be applied when comparing quantification of iron-bound organic carbon extracted by different methods as the extraction strength and method specificity can be highly variable.
This article is included in the Encyclopedia of Geosciences
Mark A. Stevenson, Suzanne McGowan, Emma J. Pearson, George E. A. Swann, Melanie J. Leng, Vivienne J. Jones, Joseph J. Bailey, Xianyu Huang, and Erika Whiteford
Biogeosciences, 18, 2465–2485, https://doi.org/10.5194/bg-18-2465-2021, https://doi.org/10.5194/bg-18-2465-2021, 2021
Short summary
Short summary
We link detailed stable isotope and biomarker analyses from the catchments of three Arctic upland lakes on Disko Island (West Greenland) to a recent dated sediment core to understand how carbon cycling has changed over the past ~500 years. We find that the carbon deposited in sediments in these upland lakes is predominately sourced from in-lake production due to the catchment's limited terrestrial vegetation and elevation and that recent increases in algal production link with climate change.
This article is included in the Encyclopedia of Geosciences
Nadine T. Smit, Laura Villanueva, Darci Rush, Fausto Grassa, Caitlyn R. Witkowski, Mira Holzheimer, Adriaan J. Minnaard, Jaap S. Sinninghe Damsté, and Stefan Schouten
Biogeosciences, 18, 1463–1479, https://doi.org/10.5194/bg-18-1463-2021, https://doi.org/10.5194/bg-18-1463-2021, 2021
Short summary
Short summary
Soils from an everlasting fire (gas seep) in Sicily, Italy, reveal high relative abundances of novel uncultivated mycobacteria and unique 13C-depleted mycocerosic acids (multi-methyl branched fatty acids) close to the main gas seep. Our results imply that mycocerosic acids in combination with their depleted δ13C values offer a new biomarker tool to study the role of soil mycobacteria as hydrocarbon consumers in the modern and past global carbon cycle.
This article is included in the Encyclopedia of Geosciences
Marcus P. S. Badger
Biogeosciences, 18, 1149–1160, https://doi.org/10.5194/bg-18-1149-2021, https://doi.org/10.5194/bg-18-1149-2021, 2021
Short summary
Short summary
Reconstructing ancient atmospheric CO2 is an important aim of palaeoclimate science in order to understand the Earth's climate system. One method, the alkenone proxy based on molecular fossils of coccolithophores, has been recently shown to be ineffective at low-to-moderate CO2 levels. In this paper I show that this is likely due to changes in the biogeochemistry of the coccolithophores when there is low carbon availability, but for much of the Cenozoic the alkenone proxy should have utility.
This article is included in the Encyclopedia of Geosciences
Loes G. J. van Bree, Francien Peterse, Allix J. Baxter, Wannes De Crop, Sigrid van Grinsven, Laura Villanueva, Dirk Verschuren, and Jaap S. Sinninghe Damsté
Biogeosciences, 17, 5443–5463, https://doi.org/10.5194/bg-17-5443-2020, https://doi.org/10.5194/bg-17-5443-2020, 2020
Short summary
Short summary
Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are used as a paleothermometer based on their temperature dependence in global soils, but aquatic production complicates their use in lakes. BrGDGTs in the water column of Lake Chala, East Africa, respond to oxygen conditions and mixing. Changes in their signal can be linked to bacterial community composition rather than membrane adaptation to changing conditions. Their integrated signal in the sediment reflects mean air temperature.
This article is included in the Encyclopedia of Geosciences
Alexandra N. Loginova, Andrew W. Dale, Frédéric A. C. Le Moigne, Sören Thomsen, Stefan Sommer, David Clemens, Klaus Wallmann, and Anja Engel
Biogeosciences, 17, 4663–4679, https://doi.org/10.5194/bg-17-4663-2020, https://doi.org/10.5194/bg-17-4663-2020, 2020
Short summary
Short summary
We measured dissolved organic carbon (DOC), nitrogen (DON) and matter (DOM) optical properties in pore waters and near-bottom waters of the eastern tropical South Pacific off Peru. The difference between diffusion-driven and net fluxes of DOC and DON and qualitative changes in DOM optical properties suggested active microbial utilisation of the released DOM at the sediment–water interface. Our results suggest that the sediment release of DOM contributes to microbial processes in the area.
This article is included in the Encyclopedia of Geosciences
Gerard J. M. Versteegh, Alexander J. P. Houben, and Karin A. F. Zonneveld
Biogeosciences, 17, 3545–3561, https://doi.org/10.5194/bg-17-3545-2020, https://doi.org/10.5194/bg-17-3545-2020, 2020
Short summary
Short summary
Anoxic sediments mostly contain much more organic matter than oxic ones, and therefore organic matter in anoxic settings is often considered to be preserved better than in oxic settings. However, through the analysis of the same fossil dinoflagellate cyst species from both oxic and anoxic settings, we show that at a molecular level the preservation in the oxic sediments may be better since in the anoxic setting the cyst macromolecule has been altered by postdepositional modification.
This article is included in the Encyclopedia of Geosciences
Jingjing Guo, Miriam Glendell, Jeroen Meersmans, Frédérique Kirkels, Jack J. Middelburg, and Francien Peterse
Biogeosciences, 17, 3183–3201, https://doi.org/10.5194/bg-17-3183-2020, https://doi.org/10.5194/bg-17-3183-2020, 2020
Short summary
Short summary
The fluxes of soil organic carbon (OC) transport from land to sea are poorly constrained, mostly due to the lack of a specific tracer for soil OC. Here we evaluate the use of specific molecules derived from soil bacteria as a tracer for soil OC in a small river catchment. We find that the initial soil signal is lost upon entering the aquatic environment. However, the local environmental history of the catchment is reflected by these molecules in the lake sediments that act as their sink.
This article is included in the Encyclopedia of Geosciences
Zhuo-Yi Zhu, Joanne Oakes, Bradley Eyre, Youyou Hao, Edwin Sien Aun Sia, Shan Jiang, Moritz Müller, and Jing Zhang
Biogeosciences, 17, 2473–2485, https://doi.org/10.5194/bg-17-2473-2020, https://doi.org/10.5194/bg-17-2473-2020, 2020
Short summary
Short summary
Samples were collected in August 2016 in the Rajang River and its estuary, with tropical forest in the river basin and peatland in the estuary. Organic matter composition was influenced by transportation in the river basin, whereas peatland added clear biodegraded parts to the fluvial organic matter, which implies modification of the initial lability and/or starting points in the subsequent degradation and alternation processes after the organic matter enters the sea.
This article is included in the Encyclopedia of Geosciences
Wenjie Xiao, Yasong Wang, Yongsheng Liu, Xi Zhang, Linlin Shi, and Yunping Xu
Biogeosciences, 17, 2135–2148, https://doi.org/10.5194/bg-17-2135-2020, https://doi.org/10.5194/bg-17-2135-2020, 2020
Short summary
Short summary
The hadal zone (6–11 km depth) is the least explored habitat on Earth. We studied microbial branched glycerol dialkyl glycerol tetraethers (brGDGTs) in the Challenger Deep, Mariana Trench. One unique feature is the strong predominance of 6-methyl brGDGT, which likely reflects an adaption of brGDGT-producing bacteria to alkaline seawater and low temperature. BrGDGTs, with elemental and isotopic data, suggest an autochthonous product for brGDGT. A new approach is proposed for brGDGT sourcing.
This article is included in the Encyclopedia of Geosciences
Yuge Bai, Edisson Subdiaga, Stefan B. Haderlein, Heike Knicker, and Andreas Kappler
Biogeosciences, 17, 683–698, https://doi.org/10.5194/bg-17-683-2020, https://doi.org/10.5194/bg-17-683-2020, 2020
Short summary
Short summary
Biogeochemical processes of SOM are key for greenhouse gas emission and water quality. We extracted SOM by water or by NaOH–HCl under oxic–anoxic conditions. Chemical and anoxic extractions lead to higher SOM electron exchange capacities, resulting in stimulation of microbial Fe(III) reduction. Therefore, aqueous pH-neutral SOM extracts should be used to reflect environmental SOM redox processes, and artifacts of chemical extractions need to be considered when evaluating SOM redox processes.
This article is included in the Encyclopedia of Geosciences
Yan Shen, Volker Thiel, Pablo Suarez-Gonzalez, Sebastiaan W. Rampen, and Joachim Reitner
Biogeosciences, 17, 649–666, https://doi.org/10.5194/bg-17-649-2020, https://doi.org/10.5194/bg-17-649-2020, 2020
Short summary
Short summary
Today, sterols are widespread in plants, animals, and fungi but are almost absent in the oldest rocks. Microbial mats, representing the earliest complex ecosystems on Earth, were omnipresent in Precambrian marine environments and may have degraded the sterols at that time. Here we analyze the distribution of sterols through a microbial mat. This provides insight into how variations in biological and nonbiological factors affect the preservation of sterols in modern and ancient microbial mats.
This article is included in the Encyclopedia of Geosciences
Sarah Coffinet, Travis B. Meador, Lukas Mühlena, Kevin W. Becker, Jan Schröder, Qing-Zeng Zhu, Julius S. Lipp, Verena B. Heuer, Matthew P. Crump, and Kai-Uwe Hinrichs
Biogeosciences, 17, 317–330, https://doi.org/10.5194/bg-17-317-2020, https://doi.org/10.5194/bg-17-317-2020, 2020
Short summary
Short summary
This study deals with two membrane lipids called BDGTs and PDGTs. Membrane lipids are molecules forming the cell envelope of all organisms. Different organisms produce different lipids thus they can be used to detect the presence of specific organisms in the environment. We analyzed the structure of these new lipids and looked for potential producers. We found that they are likely made by microbes emitting methane below the sediment surface and could be used to track these specific microbes.
This article is included in the Encyclopedia of Geosciences
Ying Wu, Kun Zhu, Jing Zhang, Moritz Müller, Shan Jiang, Aazani Mujahid, Mohd Fakharuddin Muhamad, and Edwin Sien Aun Sia
Biogeosciences, 16, 4517–4533, https://doi.org/10.5194/bg-16-4517-2019, https://doi.org/10.5194/bg-16-4517-2019, 2019
Short summary
Short summary
Our understanding of terrestrial organic matter (TOM) in tropical peat-draining rivers remains limited, especially in Southeast Asia. We explored the characteristics of TOM via bulk parameters and lignin phenols of sediment in Malaysia. This showed that the most important plant source of the organic matter in these rivers is woody angiosperm C3 plants with limited diagenetic alteration. This slower degradation of TOM may be a link to higher total nitrogen content, especially for the small river.
This article is included in the Encyclopedia of Geosciences
Caitlyn R. Witkowski, Sylvain Agostini, Ben P. Harvey, Marcel T. J. van der Meer, Jaap S. Sinninghe Damsté, and Stefan Schouten
Biogeosciences, 16, 4451–4461, https://doi.org/10.5194/bg-16-4451-2019, https://doi.org/10.5194/bg-16-4451-2019, 2019
Short summary
Short summary
Carbon dioxide concentrations (pCO2) in the atmosphere play an integral role in Earth system dynamics, especially climate. Past climates help us understand future ones, but reconstructing pCO2 over the geologic record remains a challenge. This research demonstrates new approaches for exploring past pCO2 via the carbon isotope fractionation in general algal lipids, which we test over a high CO2 gradient from a naturally occurring CO2 seep.
This article is included in the Encyclopedia of Geosciences
Yongli Zhou, Patrick Martin, and Moritz Müller
Biogeosciences, 16, 2733–2749, https://doi.org/10.5194/bg-16-2733-2019, https://doi.org/10.5194/bg-16-2733-2019, 2019
Short summary
Short summary
We found that peatlands in coastal Sarawak, Borneo, export extremely humified organic matter, which dominates the riverine organic matter pool and conservatively mixes with seawater, while the freshly produced fraction is low and stable in concentration at all salinities. We estimated that terrigenous fractions, which showed high photolability, still account for 20 % of the coastal dissolved organic carbon pool, implying the importance of peat-derived organic matter in the coastal carbon cycle.
This article is included in the Encyclopedia of Geosciences
Kristin Doering, Claudia Ehlert, Philippe Martinez, Martin Frank, and Ralph Schneider
Biogeosciences, 16, 2163–2180, https://doi.org/10.5194/bg-16-2163-2019, https://doi.org/10.5194/bg-16-2163-2019, 2019
Alexandra N. Loginova, Sören Thomsen, Marcus Dengler, Jan Lüdke, and Anja Engel
Biogeosciences, 16, 2033–2047, https://doi.org/10.5194/bg-16-2033-2019, https://doi.org/10.5194/bg-16-2033-2019, 2019
Short summary
Short summary
High primary production in the Peruvian upwelling system is followed by rapid heterotrophic utilization of organic matter and supports the formation of one of the most intense oxygen minimum zones (OMZs) in the world. Here, we estimated vertical fluxes of oxygen and dissolved organic matter (DOM) from the surface to the OMZ. Our results suggest that DOM remineralization substantially reduces oxygen concentration in the upper water column and controls the shape of the upper oxycline.
This article is included in the Encyclopedia of Geosciences
Carolina Cisternas-Novoa, Frédéric A. C. Le Moigne, and Anja Engel
Biogeosciences, 16, 927–947, https://doi.org/10.5194/bg-16-927-2019, https://doi.org/10.5194/bg-16-927-2019, 2019
Short summary
Short summary
We investigate the composition and vertical fluxes of POM in two deep basins of the Baltic Sea (GB: Gotland Basin and LD: Landsort Deep). The two basins showed different O2 regimes resulting from the intrusion of oxygen-rich water from the North Sea that ventilated the deep waters in GB, but not in LD.
In GB, O2 intrusions lead to a high abundance of manganese oxides that aggregate with POM, altering its composition and vertical flux and contributing to a higher POC transfer efficiency in GB.
This article is included in the Encyclopedia of Geosciences
Marina Zamanillo, Eva Ortega-Retuerta, Sdena Nunes, Pablo Rodríguez-Ros, Manuel Dall'Osto, Marta Estrada, Maria Montserrat Sala, and Rafel Simó
Biogeosciences, 16, 733–749, https://doi.org/10.5194/bg-16-733-2019, https://doi.org/10.5194/bg-16-733-2019, 2019
Short summary
Short summary
Many marine microorganisms produce polysaccharide-rich transparent exopolymer particles (TEPs) for rather unknown reasons but with important consequences for the ocean carbon cycle, sea–air gas exchange and formation of organic aerosols. Here we compare surface–ocean distributions of TEPs and physical, chemical and biological variables along a N–S transect in the Atlantic Ocean. Our data suggest that phytoplankton and not bacteria are the main TEP producers, and solar radiation acts as a sink.
This article is included in the Encyclopedia of Geosciences
Michael Philben, Sara Butler, Sharon A. Billings, Ronald Benner, Kate A. Edwards, and Susan E. Ziegler
Biogeosciences, 15, 6731–6746, https://doi.org/10.5194/bg-15-6731-2018, https://doi.org/10.5194/bg-15-6731-2018, 2018
Short summary
Short summary
We explored the relationship between chemical composition and the temperature sensitivity of moss decomposition using 959-day lab incubations. Mass loss was low despite the predominance of carbohydrates, indicating the persistence of labile C. Scanning electron microscopy revealed little change in the moss cell-wall structure. These results suggest that the moss cell-wall matrix protects labile C from decomposition, contributing to the globally important stocks of moss-derived C.
This article is included in the Encyclopedia of Geosciences
Cited articles
Akinyede, R., Taubert, M., Schrumpf, M., Trumbore, S., and Küsel, K.:
Rates of dark CO2 fixation are driven by microbial biomass in a
temperate forest soil, Soil Biol. Biochem., 150, 107950, https://doi.org/10.1016/j.soilbio.2020.107950, 2020.
Alonso-Sáez, L., Galand, P. E., Casamayor, E. O., Pedrós-Alió,
C., and Bertilsson, S.: High bicarbonate assimilation in the dark by Arctic
bacteria, ISME J., 4, 1581–1590, 2010.
Arístegui, J., Gasol, J. M., Duarte, C. M., and Herndl, G. J.: Microbial
oceanography of the dark ocean's pelagic realm, Limnol. Oceanogr., 54,
1501–1529, 2009.
Attwood, P. V.: The structure and the mechanism of action of
pyruvate-carboxylase, Int. J. Biochem. Cell B, 27, 231–249, 1995.
Baltar, F. and Herndl, G. J.: Ideas and perspectives: Is dark carbon fixation relevant for oceanic primary production estimates?, Biogeosciences, 16, 3793–3799, https://doi.org/10.5194/bg-16-3793-2019, 2019.
Baltar, F., Arístegui, J., Sintes, E., Gasol, J. M., Reinthaler, T.,
and Herndl, G. J.: Significance of non-sinking particulate organic carbon and
dark CO2 fixation to heterotrophic carbon demand in the mesopelagic
northeast Atlantic, Geophys. Res. Lett., 37, 1–6, 2010.
Baltar, F., Lundin, D., Palovaara, J., Lekunberri, I., Reinthaler, T.,
Herndl, G. J., and Pinhassi, J.: Prokaryotic responses to ammonium and
organic carbon reveal alternative CO2 fixation pathways and importance
of alkaline phosphatase in the mesopelagic North Atlantic, Front.
Microbiol., 7, 1670, https://doi.org/10.3389/fmicb.2016.01670, 2016.
Baltar, F., Bayer, B., Bednarsek, N., Deppeler, S., Escribano, R., Gonzalez, C. E., Hansman, R. L., Mishra, R. K., Moran, M. A., Repeta, D. J., Robinson, C., Sintes, E., Tamburini, C., Valentin, L. E., and Herndl, G. J.: Towards integrating evolution, metabolism, and
climate change studies of marine ecosystems, Trends Ecol. Evol., 34,
1022–1033, 2019.
Bar-Even, A., Noor, E., and Milo, R.: A survey of carbon fixation pathways
through a quantitative lens, J. Exp. Bot., 63, 2325–2342, 2012.
Bar-On, Y. M., Phillips, R., and Milo, R.: The biomass distribution on Earth,
P. Natl. Acad. Sci. USA, 115, 6506–6511, 2018.
Battley, E. H.: A theoretical study of the thermodynamics of microbial growth
using Saccharomyces cerevisiae and a different free energy equation, Q. Rev. Biol., 88, 69–96,
2013.
Beer, C., Reichstein, M., Tomelleri, E., Ciais, P., Jung, M., Carvalhais,
N., Rödenbeck, C., Arain, M. A., Baldocchi, D., Bonan, G. B., Bondeau,
A., Cescatti, A., Lasslop, G., Lindroth, A., Lomas, M., Luyssaert, S.,
Margolis, H., Oleson, K. W., Roupsard, O., Veenendaal, E., Viovy, N.,
Williams, C., Woodward, F. I., and Papale, D.: Terrestrial gross carbon
dioxide uptake: global distribution and covariation with climate, Science,
329, 834–838, 2010.
Berg, I. A.: Ecological aspects of the distribution of different autotrophic
CO2 fixation pathways, Appl. Environ. Microbiol., 77, 1925–1936, 2011.
Berg, I. A., Kockelkorn, D., Buckel, W., and Fuchs, G.: A
3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide
assimilation pathway in Archaea, Science, 318, 1782–1786, 2007.
Beulig, F., Heuer, V. B., Akob, D. M., Viehweger, B., Elvert, M., Herrmann,
M., Hinrichs, K.-U., and Küsel, K.: Carbon flow from volcanic CO2
into soil microbial communities of a wetland mofette, ISME J., 9, 746–759,
2015.
Bräuer, S. L., Kranzler, K., Goodson, N., Murphy, D., Simon, H. M.,
Baptista, A. M., and Tebo, B. M.: Dark carbon fixation in the Columbia River's
estuarine turbidity maxima: molecular characterization of red-type cbbl genes
and measurement of DIC uptake rates in response to added electron donors,
Estuar. Coast. Shelf S., 36, 1073–1083, 2013.
Burd, A. B., Hansell, D. A., Steinberg, D. K., Anderson, T. R.,
Arístegui, J., Baltar, F., Beaupre, S. R., Buesseler, K. O., De- Hairs,
F., Jackson, G. A., Kadko, D. C., Koppelmann, R., Lampitt, R. S., Nagata,
T., Reinthaler, T., Robinson, C., Robison, B. H., Tamburini, C., and Tanaka,
T.: Assessing the apparent imbalance between geochemical and biochemical
indicators of meso-and bathypelagic biological activity: What the @$#! is
wrong with present calculations of carbon budgets?, Deep-Sea Res. Pt. II,
57, 1557–1571, 2010.
Casamayor, E. O., García-Cantizano, J., Mas, J., and
Pedrós-Alió, C.: Primary production in estuarine oxic/anoxic
interfaces: contribution of microbial dark CO2 fixation in the Ebro
River Salt Wedge Estuary, Mar. Ecol.-Prog. Ser., 215, 49–56, 2001.
Ciais, P., Sabine, C., Bala, G., Bopp, L., Brovkin, V., Canadell, J., Chhabra, A.,
DeFries, R., Galloway, J., Heimann, M., Jones, C., Le Quéré, C.,
Myneni, R. B., Piao, S., and Thornton, P.: Carbon and other biogeochemical cycles, in:
Climate change 2013: The physical science basis. Contribution of working
group I to the fifth assessment report of the Intergovernmental Panel on
Climate Change, edited by: Stocker, T. F., Qin, D., Plattner, G.-K., Tignor, M.,
Allen, S. K., Boschung, J., Nauels, A., Xia, Y., Bex, V., and Midgley, P. M., 465–570,
Cambridge, United Kingdom and New York, NY, USA, Cambridge University Press,
2013.
Cochrane, V. W.: Physiology of fungi, John Wiley, New York, 1958.
Cole, J. J., Findlay, S. E. G., and Pace, M. L.: Bacterial production in
fresh and saltwater ecosystems: a cross-system overview, Mar. Ecol.-Prog.
Ser., 43, 1–10, 1988.
DeLorenzo, S., Bräuer, S. L., Edgmont, C. A., Herfort, L., Tebo, B. M.,
and Zuber, P.: Ubiquitous dissolved inorganic carbon assimilation by marine
bacteria in the Pacific Northwest Coastal Ocean as determined by stable
isotope probing, PLoS ONE, 7, e46695, https://doi.org/10.1371/journal.pone.0046695, 2012.
Detmer, A. E., Giesenhagen, H. C., Trenkel, V. M., Auf dem Venne, H., and
Jochem, F. J.: Phototrophic and heterotrophic pico- and nanoplankton in
anoxic depths of the central Baltic Sea, Mar. Ecol.-Prog. Ser., 99,
197–203, 1993.
Dijkhuizen, L. and Harder, W.: Current views on the regulation of
autotrophic carbon dioxide fixation via the Calvin cycle in bacteria,
Antonie van Leeuwenhoek, 50, 473–487, 1984.
Doronina, N. V. and Trotsenko, Y. A.: The levels of carbon dioxide
assimilation in bacteria with different pathways of 1-carbon metabolism,
Mikrobiologiya, 53, 885–889, 1984.
Ehleringer, J. R., Buchmann, N., and Flanagan, L. B.: Carbon isotope ratios in belowground carbon cycle processes, Ecol. Appl., 10, 412–422, 2000.
Ekendahl, S. and Pedersen, K.: Carbon transformations by attached bacterial populations in granitic ground water from deep crystalline bed-rock of the Stripa research mine, Microbiology, 140, 1565–1573, 1994.
Ensign, S. A., Small, F. J., Allen, J. R., and Sluis, M. K.: New roles for
CO2 in the metabolism of aliphatic epoxides and ketones, Arch.
Microbiol., 169, 179–187, 1998.
Erb, T. J.: Carboxylases in natural and synthetic microbial pathways, Appl.
Environ. Microb., 77, 8466–8477, 2011.
Erb, T. J., Brecht, V., Fuchs, G., Muller, M., and Alber, B. E.: Carboxylation
mechanism and stereochemistry of crotonyl-CoA carboxylase/reductase, a
carboxylating enoyl-thioester reductase, P. Natl. Acad. Sci. USA, 106, 8871–8876, 2009.
Evans Jr., E. A. and Slotin, L.: The utilization of carbon dioxide in the
synthesis of α-ketoglutaric acid, J. Biol. Chem., 136, 301–302, 1940.
Faber, K., Fessner, W. D., and Turner, N. J.: Science of synthesis:
biocatalysis in organic synthesis Vol. 2, 672 pp., Georg Thieme, Stuttgart, 2015.
Feisthauer, S., Wick, L. Y., Kastner, M., Kaschabek, S. R., Schlomann, M., and
Richnow, H. H.: Differences of heterotrophic 13CO2 assimilation by
Pseudomonas knackmussii strain B13 and Rhodococcus opacus 1CP and potential impact on biomarker stable isotope
probing, Environ. Microbiol., 10, 1641–1651, 2008.
Fraga, F., Rios, A., Perez, F., and Figueras, F.: Theoretical limits of
oxygen:carbon and oxygen : nitrogen ratios during photosynthesis and
mineralisation of organic matter in the sea, Mar. Chem., 62, 161–168, 1998.
Fuchs, G.: Biosynthesis of building blocks, in: Biology of the prokaryotes,
edited by: Lengeler, J. W., Drews, G., and Schlegel, H. G., 110–160, Thieme, Stuttgart,
New York, 1999.
Giovannoni, S. J. and Stingl, U.: Molecular diversity and ecology of microbial plankton, Nature, 437, 343–348, https://doi.org/10.1038/nature04158, 2005.
González, J. M., Fernández-Gómez, B., Fernández-Guerra, A.,
Gómez-Consarnau, L., Sánchez, O., Coll-Lladó, M., del Campo, J.,
Escudero, L., Rodríguez-Martínez, R., Alonso-Sáez, L., Latasa,
M., Paulsen, I., Nedashkovskaya, O., Lekumberri, I., Pinhassi, J., and
Pedrós-Alió, C.: Genome analysis of the proteorhodopsin-containing
marine bacterium Polaribacter sp. MED152 (Flavobacteria), P. Natl. Acad.
Sci. USA, 105, 8724–8729, 2008.
Gruber, N., Friedlingstein, P., Field, C., Valentini, R., Heimann, M.,
Richey, J. E., Romero-Lankao, P., Schulze, E. D., and Chen, C.-T. A.: The
vulnerability of the carbon cycle in the 21st century: an assessment of
carbon-climate-human interactions, in: The global carbon cycle: integrating
humans, climate, and the natural world, edited by: Field, C. B. and Raupach, M.
R., 45–76, Island Press, Washington D.C., London, 2004.
Han, L., Yang, K., Kulowski, K., Wendt-Plienkowski, E., Hutchinson, C. R.,
and Vining, L. C.: An acyl-coenzyme A carboxylase encoding gene associated
with jadomycin biosynthesis in Streptomyces venezuelae ISP5230, Microbiol. UK, 146, 903–910, 2000.
Hartman, R. E. and Keen, N. T.: Enzymes catalysing anaplerotic carbon
dioxide fixation in Verticillium albo-atrum, Phytopathol., 63, 947–953, 1973.
Hartman, R. E., Keen, N. T., and Long, M.: Carbon dioxide fixation by
Verticillium albo-atrum, J. Gen. Microbiol., 73, 29–34, 1972.
Heijnen, J. J. and Roels, J. A.: A macroscopic model describing yield and
maintenance relationship in aerobic fermentation processes, Biotechnol.
Bioeng., 23, 739–763, 1981.
Herndl, G. J. and Reinthaler, T.: Microbial control of the dark end of the
biological pump, Nat. Geosci., 6, 718–724, 2013.
Hesselsoe, M., Nielsen, J. L., Roslev, P., and Nielsen, P. H.: Isotope
labeling and microautoradiography of active heterotrophic bacteria on the
basis of assimilation of 14CO2, Appl. Environ. Microb., 71,
646–655, 2005.
Hoppe, H. G., Gocke, K., Koppe, R., and Begler, C.: Bacterial growth and
primary production along a north-south transect of the Atlantic Ocean,
Nature, 416, 168–171, 2002.
Houghton, R. A.: Balancing the global carbon budget, Annu. Rev. Earth Planet.
Sc., 35, 313–347, 2007.
Ingalls, A. E., Shah, S. R., Hansman, R. L., Aluwihare, L. I., Santos, G.
M., Druffel, E. R., and Pearson, A.: Quantifying archaeal community
autotrophy in the mesopelagic ocean using natural radiocarbon, P. Natl. Acad. Sci. USA, 103,
6442–6447, 2006.
Jitrapakdee, S. and Wallace, J. C.: Structure, function and regulation of
pyruvate carboxylase, Biochem. J., 340, 1–16, 1999.
Jitrapakdee, S., St. Maurice, M., Rayment, I., Cleland, W. W., Wallace, J. C.,
and Attwood, P. V.: Structure, mechanism and regulation of pyruvate
carboxylase, Biochem. J., 413, 369–387, 2008.
Kellermann, C., Selesi, D., Lee, N., Hügler, M., Esperschütz, J.,
Hartmann, A., and Griebler, C.: Microbial CO2 fixation potential in a
tar-oil-contaminated porous aquifer, FEMS Microbiol. Ecol., 81, 172–187,
2012.
Kleiber, M., Smith, A. H., and Black, A. L.: Carbonate as precursor of milk
constituents in the intact dairy cow, J. Biol. Chem., 195, 707–714, 1952.
Kornberg, H. L.: Anaplerotic sequences in microbial metabolism, Angew. Chem.
Int. Edit., 4, 558–565, 1965.
Kornberg, H. L. and Krebs, E. H.: Synthesis of cell constituents from
C2-units by a modified tricarboxylic acid cycle, Nature, 179, 988–991,
1957.
Kotelnikova, S. and Pedersen, K.: Distribution and activity of methanogens
and homoacetogens in deep granitic aquifers at Äspö Hard Rock
Laboratory, Sweden, FEMS Microbiol. Ecol., 26, 121–134, 1998.
Krebs, H. A.: Carbon dioxide assimilation in heterotrophic organisms, Nature,
147, 560–563, 1941.
Lazar, C. S., Stoll, W., Lehmann, R., Herrmann, M., Schwab, V. F., Akob, D. M.,
Nawaz, A., Wubet, T., Buscot, F., Totsche, K.-U., and Küsel, K.: Archaeal
diversity and CO2 fixers in carbonate-/siliciclastic-rock groundwater
ecosystems, Archaea, 2136287, 1–13, 2017.
Le Quéré, C., Raupach, M. R., Canadell, J. G., Marland, G., Bopp, L.,
Ciais, P., Conway, T. J., Doney, S. C., Feely, R. A., Foster, P., Friedlingstein, P.,
Gurney, K., Houghton, R. A., House, J. I., Huntingford, C., Levy, P. E.,
Lomas, M. R., Majkut, J., Metzl, N., Ometto, J. P., Peters, G. P., Prentice, I. C., Randerson, J.
T., Running, S. W., Sarmiento, J. L., Schuster, U., Sitch, S.,
Takahashi, T., Viovy, N., van der Werf, G. R., and Woodward, F. I.: Trends in the
sources and sinks of carbon dioxide, Nat. Geosci., 2, 831–836, 2009.
Le Quéré, C., Andrew, R. M., Canadell, J. G., Sitch, S., Korsbakken, J. I., Peters, G. P., Manning, A. C., Boden, T. A., Tans, P. P., Houghton, R. A., Keeling, R. F., Alin, S., Andrews, O. D., Anthoni, P., Barbero, L., Bopp, L., Chevallier, F., Chini, L. P., Ciais, P., Currie, K., Delire, C., Doney, S. C., Friedlingstein, P., Gkritzalis, T., Harris, I., Hauck, J., Haverd, V., Hoppema, M., Klein Goldewijk, K., Jain, A. K., Kato, E., Körtzinger, A., Landschützer, P., Lefèvre, N., Lenton, A., Lienert, S., Lombardozzi, D., Melton, J. R., Metzl, N., Millero, F., Monteiro, P. M. S., Munro, D. R., Nabel, J. E. M. S., Nakaoka, S., O'Brien, K., Olsen, A., Omar, A. M., Ono, T., Pierrot, D., Poulter, B., Rödenbeck, C., Salisbury, J., Schuster, U., Schwinger, J., Séférian, R., Skjelvan, I., Stocker, B. D., Sutton, A. J., Takahashi, T., Tian, H., Tilbrook, B., van der Laan-Luijkx, I. T., van der Werf, G. R., Viovy, N., Walker, A. P., Wiltshire, A. J., and Zaehle, S.: Global Carbon Budget 2016, Earth Syst. Sci. Data, 8, 605–649, https://doi.org/10.5194/essd-8-605-2016, 2016.
Lengger, S. K., Rush, D., Mayser, J. P., Blewett, J., Schwartz-Narbonne, R.,
Talbot, H. B., Middelburg, J. J., Jetten, M. S. M., Schouten, S., Sinninghe
Damsté, J. S., and Pancost, R. D.: Dark carbon fixation in the Arabian Sea
oxygen minimum zone contributes to sedimentary organic carbon (SOM), Global
Biogeochem. Cy., 33, 1715–1732, 2019.
Lliros, M., Alonso-Saéz, L., Gich, F., Plasencia, A., Auguet, O.,
Casamayor, E. O., and Borrego, C. M.: Active bacteria and archaea cells fixing
bicarbonate in the dark along the water column of a stratified eutrophic
lagoon, FEMS Microbiol. Ecol., 77, 370–384, 2011.
Magnabosco, C., Lin, L. H., Dong, H., Bomberg, M., Ghiorse, W., Stan-Lotter,
H., Pedersen, K., Kieft, T. L., van Heerden, E., and Onstott, T. C.: The
biomass and biodiversity of the continental subsurface, Nat. Geosci.,
11, 707–717, 2018.
McMahon, S. and Parnell, J.: Weighing the deep continental biosphere, FEMS
Microbiol. Ecol., 87, 113–120, 2014.
Melzer, E. and O'Leary M. H.: Anapleurotic CO2 fixation by
phosphoenolpyruvate carboxylase in C3 plants, Plant Physiol., 84, 58–60,
1987.
Merlin, C., Masters, M., McAteer, S., and Coulson, A.: Why is carbonic
anhydrase essential to Escherichia coli?, J. Bacteriol., 185, 6415–6424, 2003.
Middelburg, J. J.: Chemoautotrophy in the ocean, Geophy. Res. Lett., 38, 1–4,
2011.
Miltner, A., Richnow, H.-H., Kopinke, F.-D., and Kästner, M.: Assimilation
of CO2 by soil microorganisms and transformation into soil organic
matter, Org. Geochem., 35, 1015–1024, 2004.
Miltner, A., Kopinke, F.-D., Kindler, R., Selesi, D., Hartmann, A., and
Kästner, M.: Non-phototrophic CO2 fixation by soil microorganisms,
Plant Soil, 269, 193–203, 2005.
Molari, M., Manini, E., and Dell'Anno, A.: Dark inorganic carbon fixation
sustains the functioning of benthic deep-sea ecosystems, Global Biogeochem.
Cy., 27, 212–221, 2013.
Morán, X. A. G., Pérez, V., and Fernández, E.: Mismatch between
community respiration and the contribution of heterotrophic bacteria in the
NE Atlantic open ocean: What causes high respiration in oligotrophic waters?,
J. Mar. Res., 65, 545–560, 2007.
Nel, J. A. and Cramer, M. D.: Soil microbial anaplerotic CO2 fixation in
temperate soils, Geoderma, 335, 170–178, 2019.
Noguerola, I., Picazo, A., Lliros, M., Camacho, A., and Borrego, C. M.:
Diversity of freshwater Epsilonproteobacteria and dark inorganic carbon
fixation in the sulphidic redoxcline of a meromictic karstic lake, FEMS
Microbiol. Ecol., 91, fiv086, https://doi.org/10.1093/femsec/fiv086, 2015.
Overbeck, J.: Dark CO2 uptake – biochemical background and its relevance
to in situ bacterial production, Arch. Hydrobiol. Beiheft, 12, 38–47, 1979.
Palovaara, J., Akram, N., Baltar, F., Bunse, C., Forsberg, J., Pedrós-
Alió, C., González, J. M., and Pinhassi, J.: Stimulation of growth
by proteorhodopsin phototrophy involves regulation of central metabolic
pathways in marine planktonic bacteria, P. Natl. Acad. Sci. USA, 111,
E3650–E3658, 2014.
Parkinson, S. M., Killham, K., and Wainwright, M.: Assimilation of
14CO2 by Fusarium oxysporum grown under oligotrophic conditions, Mycol. Res., 94,
959–964, 1990.
Parkinson, S. M., Jones, R., Meharg, A. A., Wainwright, M., and Killham, K.:
The quantity and fate of carbon assimilated from 14CO2 by
Fusarium oxysporum grown under oligotrophic and near oligotrophic conditions, Mycol. Res., 95,
1345–1349, 1991.
Paulmier, A., Kriest, I., and Oschlies, A.: Stoichiometries of remineralisation and denitrification in global biogeochemical ocean models, Biogeosciences, 6, 923–935, https://doi.org/10.5194/bg-6-923-2009, 2009.
Pedersen, K. and Ekendahl, S.: Assimilation of CO2 and introduced
organic compounds by bacterial communities in groundwater from southeastern
Sweden deep crystalline bedrock, Microb. Ecol., 23, 1–14, 1992a.
Pedersen, K. and Ekendahl, S.: Incorporation of CO2 and introduced
organic compounds by bacterial populations in groundwater from deep
crystalline bedrock of Stripa mine, J. Gen. Microbiol., 138, 369–376, 1992b.
Perez, R. C. and Matin, A.: Carbon dioxide assimilation by Thiobacillus novellus under
nutrient-limited mixotrophic conditions, J. Bacteriol., 150, 46–51, 1982.
Reinthaler, T., Van Aken, H. M., and Herndl, G. J.: Major contribution of
autotrophy to microbial carbon cycling in the deep North Atlantic,
Äôs interior, Deep-Sea Res. Pt. II, 57, 1572–1580, 2010.
Robinson, C.: Microbial respiration, the engine of ocean deoxygenation,
Front. Mar. Sci., 5, 533, https://doi.org/10.3389/fmars.2018.00533, 2019.
Robinson, C. and Williams, P. J.: Respiration and its measurement in surface
marine waters, in: Respiration in aquatic ecosystems, edited by: del Giorgio, P. A.
and Williams, P. J., Oxford University Press, Oxford, 2005.
Romanenko, V. I.: Heterotrophic CO2 assimilation by water bacterial
flora, Mikrobiologiya, 33, 679–683, 1964.
Romanenko, V. I., Overbeck, J., and Sorokin, Y. I.: Estimation of production
of heterotrophic bacteria using I4C, in: Techniques for the assessment of microbial production and
decomposition in fresh waters, edited by: Sorokin, Y. I. and Kadota, H., IBP Handbook No. 23, Blackwell, Oxford,
82–85, 1972.
Roslev, P., Larsen, M. B., Jørgensen, D., and Hesselsoe, M.: Use of
heterotrophic CO2 assimilation as a measure of metabolic activity in
planktonic and sessile bacteria, J. Microbiol. Meth., 59, 381–393, 2004.
Santoro, A. L., Bastviken, D., Gudasz, C., Tranvik, L., and Enrich-Prast, A.: Dark
carbon fixation: an important process in lake sediments, PLoS ONE, 8, e65813, https://doi.org/10.1371/journal.pone.0065813,
2013.
Šantrůčková, H., Bird, M. I., Elhottova, D., Novak, J.,
Picek, T., Simek, M., and Tykva, R.: Heterotrophic fixation of CO2 in
soil, Microb. Ecol., 49, 218–225, 2005.
Šantrůčková, H., Kotas, P., Bárta, J., Urich, T.,
Čapek P., Palmtag J., Eloy Alves, R. J., Biasi, C., Diáková, K.,
Gentsch, N., Gittel, A., Guggenberger, G., Hugelius, G., Lashchinsky, N.,
Martikainen, P. J., Mikutta, R., Schleper, C., Schnecker, J., Schwab, C.,
Shibistova, O., Wild, B., and Richter, A.: Significance of dark CO2
fixation in arctic soils, Soil Biol. Biochem., 119, 11–21, 2018.
Sauer, U. and Eikmanns, B. J.: The PEP–pyruvate–oxaloacetate node as the
switch point for carbon flux distribution in bacteria, FEMS Microbiol. Rev.,
29, 765–794, 2005.
Schink, B.: An alternative to the glyoxylate shunt, Mol. Microbiol., 73,
975–977, 2009.
Schinner, F., Concin, R., and Binder, H.: Heterotrophic CO2-fixation
by fungi in dependence on the concentration of the carbon source, Phyton, 22,
81–85, 1982.
Scrutton, M. C.: Assay of enzymes of CO2 metabolism, Method.
Microbiol., 6, Part A, 479–541, 1971.
Signori, C. N., Valentin, J. L., Pollery, R. C. G., and Enrich-Prast, A.:
Temporal variability of dark carbon fixation and bacterial production and
their relation with environmental factors in a tropical estuarine system,
Estuar. Coast., 41, 1089–1101, 2017.
Smith, A. R., Kieft, B., Mueller, R., Fisk, M. R., Mason, O. U., Popa, R.,
and Colwell, F. S.: Carbon fixation and energy metabolisms of a subseafloor
olivine biofilm, ISME J., 13, 1737–1749, 2019.
Spohn, M., Müller, K., Höschen, C., Mueller, C. W., and Marhan, S.:
Dark microbial CO2 fixation in temperate forest soils increases with
CO2 concentrations, Glob. Change Biol., 26, 1926–1935, 2019.
Spona-Friedl, M., Braun, A., Huber, C., Eisenreich, W., Griebler, C.,
Kappler, A., and Elsner, M.: Substrate-dependent CO2-fixation in heterotrophic
bacteria revealed by stable isotope labelling, FEMS Microbiol. Ecol., 96,
fiaa080, https://doi.org/10.1093/femsec/fiaa080, 2020.
Strong, P. J., Xie, S., and Clarke, W. P. Methane as a resource: can the
methanotrophs add value?, Environ. Sci. Technol., 49, 4001–4018, 2015.
Swan, B. K., Martinez-Garcia, M., Preston, C. M., Sczyrba, A., Woyke, T., Lamy, D., Reinthaler, T., Poulton, N. J., Masland, E. D. P., Lluesma Gomez, M., Sieracki, M. E., DeLong, E. F., Herndl, G. J., and Stepanauskas, R.: Potential for chemolithoautotrophy among ubiquitous bacteria
lineages in the dark ocean, Science, 333, 1296–1300, 2011.
Tait, L. W. and Schiel, D. R.: Impacts of temperature on primary productivity
and respiration in naturally structured macroalgal assemblages, PLoS ONE, 8,
e74413, https://doi.org/10.1371/journal.pone.0074413, 2013.
Teiro, E., Fernández, A., Álvarez-Salgado, X. A.,
García-Martín, E. E., Serret, P., and Sobrino, C.: Response of two
marine bacterial isolates to high CO2 concentration, Mar. Ecol.-Prog.
Ser., 453, 27–36, 2012.
Tempest, D. W. and Neijssel, O. M.: Physiological and energetic aspects of
bacterial metabolite overproduction, FEMS Microbiol. Lett., 100, 169–176,
1992.
Tuttle, J. H. and Jannasch, H. W.: Microbial dark assimilation of CO2 in
the Cariaco Trench, Limnol. Oceanogr., 24, 746–753, 1979.
Vasquez-Cardenas, D., Meysman, F. J. R., and Boschker, H. T. S.: A
cross-system comparison of dark carbon fixation in coastal sediments, Global
Biogeochem. Cy., 34, 1–14, 2020.
Vick-Majors, T. J. and Priscu, J. C.: Inorganic carbon fixation in
ice-covered lakes of the McMurdo Dry Valleys, Antarctic Sci., 1–10, https://doi.org/10.1017/S0954102019000075, 2019.
von Stockar, U., Maskow, T., Liu, J., Marison, I. W., and Patiño, R.:
Thermodynamics of microbial growth and metabolism: An analysis of the
current situation, J. Biotechnol., 121, 517–533, 2006.
Wegener, G., Bausch, M., Holler, T., Thang, N. M., Mollar, X. P.,
Kellermann, M. Y., Hinrichs, K. U., and Boetius, A.: Assessing sub-seafloor
microbial activity by combined stable isotope probing with deuterated water
and 13C-bicarbonate, Environ. Microbiol., 14, 1517–1527, 2012.
Werkman, C. H. and Wood, H. G.: Heterotrophic assimilation of carbon dioxide,
in: Advances in Enzymology and Related Areas of Molecular Biology, edited by: Nord,
F. F., 2, 135–182, Interscience Publishers, Inc., 1942.
Whitman, W. B., Coleman, D. C., and Wiebe, W. J.: Prokaryotes: The unseen
majority, P. Natl. Acad. Sci., 95, 6578–6583, 1998.
Wood, H. G. and Stjernholm, R. L.: Assimilation of carbon dioxid by
heterotrophic organisms, in: The Bacteria: A
Treatise on Structure and Function, Vol. 3, edited by: Gunsalus, I. C. and Stanier, R. Y., Biosynthesis Academic Press, New
York, 41–117, 1962.
Wood, H. G. and Werkman, C. H.: The utilisation of CO2 in the
dissimilation of glycerol by the propionic acid bacteria, Biochem. J., 30,
48–53, 1936.
Wood, H. G. and Werkman, C. H.: The utilization of CO2 by the propionic
acid bacteria, Biochem. J., 32, 1262–1271, 1938.
Wood, H. G. and Werkman, C. H.: The position of carbon dioxide-carbon in
succinic acid synthesized by heterotrophic bacteria, J. Biol. Chem., 139,
377–381, 1941.
Wuchter, C., Schouten, S., Boschker, H. T. S., and Sinninghe Damsté, J.
S.: Bicarbonate uptake by marine Crenarchaeota, FEMS Microbiol. Lett., 219,
203–207, 2003.
Yakimov, M. M., La Cono, V., Smedile, F., Crisafi, F., Arcadi, E., Leonardi,
M., Decembrini, F., Catalfamo, M., Bargiela, R., Ferrer, M., Golyshin, P.
N., and Giuliano, L.: Heterotrophic bicarbonate assimilation is the main
process of de novoorganic carbon synthesis in hadal zone of the Hellenic
Trench, the deepest part of Mediterranean Sea, Environ. Microbiol. Rep., 6,
709–722, 2014.
Zhang, Y., Qin, W., Hou, L., Zakem, E. J., Wan, X., Zhao, Z., Liu, L., Hunt,
K. A., Jiao, N., Kao, S.-J., Tang, K., Xie, X., Shen, J., Li, Y., Chen, M.,
Dai, X., Liu, C., Deng, W., Dai, M., Ingalls, A. E., Stahl, D. A., and Herndl,
G. J.: Nitrifier adaptation to low energy flux controls inventory of reduced
nitrogen in the dark ocean, P. Natl. Acad. Sci. USA, 117, 4823–4830, 2020.
Zhao, Y., Liu, P., Rui, J., Cheng, L., Wang, Q., Liu, X., and Yuan, Q.: Dark
carbon fixation and chemolithotrophic microbial community in surface
sediments of the cascade reservoirs, Southwest China, Sci. Total Environ., 698,
134316, https://doi.org/10.1016/j.scitotenv.2019.134316, 2020.
Zhou, W., Liao, J., Guo, Y., Yuan, X., Huang, H., Yuan, T., and Liu, S.:
High dark carbon fixation in the tropical South China Sea, Cont. Shelf Res.,
146, 82–88, 2017.
Zopfi, J., Ferdelman, T. G., Jørgensen, B. B., Teske, A., and Thamdrup,
B.: Influence of water column dynamics on sulfide oxidation and other major
biogeochemical process in the chemocline of Mariager Fjord (Denmark), Mar.
Chem., 74, 29–51, 2001.
Download
- Article
(1789 KB) - Full-text XML
Short summary
It is known that CO2 fixation by photoautotrophic organisms is the major sink from the atmosphere. While biologists are aware that CO2 fixation also occurs in heterotrophic organisms, this route of inorganic carbon, and its quantitative role, is hardly recognized in biogeochemistry. We demonstrate that a considerable amount of CO2 is fixed annually through anaplerotic reactions in heterotrophic organisms, and a significant quantity of inorganic carbon is temporally sequestered in biomass.
It is known that CO2 fixation by photoautotrophic organisms is the major sink from the...
Altmetrics
Final-revised paper
Preprint