Articles | Volume 15, issue 13
https://doi.org/10.5194/bg-15-4047-2018
© Author(s) 2018. 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-15-4047-2018
© Author(s) 2018. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
04 Jul 2018
Research article |
| 04 Jul 2018
| 04 Jul 2018
Benthic archaea as potential sources of tetraether membrane lipids in sediments across an oxygen minimum zone
Marc A. Besseling
CORRESPONDING AUTHOR
NIOZ Royal Netherlands Institute for Sea Research, Department of
Marine Microbiology and Biogeochemistry, and Utrecht University. P.O. Box
59, 1790 AB Den Burg, the Netherlands
Ellen C. Hopmans
NIOZ Royal Netherlands Institute for Sea Research, Department of
Marine Microbiology and Biogeochemistry, and Utrecht University. P.O. Box
59, 1790 AB Den Burg, the Netherlands
R. Christine Boschman
NIOZ Royal Netherlands Institute for Sea Research, Department of
Marine Microbiology and Biogeochemistry, and Utrecht University. P.O. Box
59, 1790 AB Den Burg, the Netherlands
Jaap S. Sinninghe Damsté
NIOZ Royal Netherlands Institute for Sea Research, Department of
Marine Microbiology and Biogeochemistry, and Utrecht University. P.O. Box
59, 1790 AB Den Burg, the Netherlands
Utrecht University, Faculty of Geosciences, Department of Earth
sciences, P.O. Box 80.021, 3508 TA Utrecht, the Netherlands
Laura Villanueva
NIOZ Royal Netherlands Institute for Sea Research, Department of
Marine Microbiology and Biogeochemistry, and Utrecht University. P.O. Box
59, 1790 AB Den Burg, the Netherlands
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Nicole J. Bale, Tracy A. Villareal, Ellen C. Hopmans, Corina P. D. Brussaard, Marc Besseling, Denise Dorhout, Jaap S. Sinninghe Damsté, and Stefan Schouten
Biogeosciences, 15, 1229–1241, https://doi.org/10.5194/bg-15-1229-2018, https://doi.org/10.5194/bg-15-1229-2018, 2018
Short summary
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Associations between diatoms and N-fixing cyanobacteria (diatom–diazotroph associations, DDAs) play an important role in the N cycle of the tropical North Atlantic. Heterocysts are the site of N fixation and contain unique glycolipids. We measured these glycolipids in the water column and surface sediment from the tropical North Atlantic. We found a significant correlation between the concentration of glycolipid and of DDAs, strengthening their application as biomarkers.
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
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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.
Anna Cutmore, Nicole Bale, Rick Hennekam, Bingjie Yang, Darci Rush, Gert-Jan Reichart, Ellen C. Hopmans, and Stefan Schouten
Clim. Past Discuss., https://doi.org/10.5194/cp-2024-59, https://doi.org/10.5194/cp-2024-59, 2024
Revised manuscript accepted for CP
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As human activities lower marine oxygen levels, understanding the impact on the marine nitrogen cycle is vital. The Black Sea, which became oxygen-deprived 9,600 years ago, offers key insights. By studying organic compounds linked to nitrogen cycle processes, we found that 7,200 years ago, the Black Sea's nitrogen cycle significantly altered due to severe deoxygenation. This suggests that continued marine oxygen decline could similarly alter the marine nitrogen cycle, affecting vital ecosystems.
Allix J. Baxter, Francien Peterse, Dirk Verschuren, Aihemaiti Maitituerdi, Nicolas Waldmann, and Jaap S. Sinninghe Damsté
Biogeosciences, 21, 2877–2908, https://doi.org/10.5194/bg-21-2877-2024, https://doi.org/10.5194/bg-21-2877-2024, 2024
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This study investigates the impact of long-term lake-system evolution on the climate signal recorded by glycerol dialkyl glycerol tetraethers (GDGTs), a popular biomarker in paleoclimate research. It compares downcore changes in GDGTs in the 250 000 year sediment sequence of Lake Chala (Kenya/Tanzania) to independent data for lake mixing and water-column chemistry. These factors influence the GDGT proxies in the earliest depositional phases (before ~180 ka), confounding the climate signal.
Zoë Rebecca van Kemenade, Zeynep Erdem, Ellen Christine Hopmans, Jaap Smede Sinninghe Damsté, and Darci Rush
Biogeosciences, 21, 1517–1532, https://doi.org/10.5194/bg-21-1517-2024, https://doi.org/10.5194/bg-21-1517-2024, 2024
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The California Current system (CCS) hosts the eastern subtropical North Pacific oxygen minimum zone (ESTNP OMZ). This study shows anaerobic ammonium oxidizing (anammox) bacteria cause a loss of bioavailable nitrogen (N) in the ESTNP OMZ throughout the late Quaternary. Anammox occurred during both glacial and interglacial periods and was driven by the supply of organic matter and changes in ocean currents. These findings may have important consequences for biogeochemical models of the CCS.
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
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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.
Jaap S. Sinninghe Damsté, Lisa A. Warden, Carlo Berg, Klaus Jürgens, and Matthias Moros
Clim. Past, 18, 2271–2288, https://doi.org/10.5194/cp-18-2271-2022, https://doi.org/10.5194/cp-18-2271-2022, 2022
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Reconstruction of past climate conditions is important for understanding current climate change. These reconstructions are derived from proxies, enabling reconstructions of, e.g., past temperature, precipitation, vegetation, and sea surface temperature (SST). Here we investigate a recently developed SST proxy based on membrane lipids of ammonium-oxidizing archaea in the ocean. We show that low salinities substantially affect the proxy calibration by examining Holocene Baltic Sea sediments.
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
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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.
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
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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.
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
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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.
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
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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.
Elisabeth Dietze, Kai Mangelsdorf, Andrei Andreev, Cornelia Karger, Laura T. Schreuder, Ellen C. Hopmans, Oliver Rach, Dirk Sachse, Volker Wennrich, and Ulrike Herzschuh
Clim. Past, 16, 799–818, https://doi.org/10.5194/cp-16-799-2020, https://doi.org/10.5194/cp-16-799-2020, 2020
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Long-term climate change impacts on fire, vegetation and permafrost in the Arctic are uncertain. Here, we show the high potential of organic compounds from low-temperature biomass burning to serve as proxies for surface fires in lake deposits. During warm periods of the last 430 000 years, surface fires are closely linked to the larch taiga forest with its moss–lichen ground vegetation that isolates the permafrost. They have reduced in warm–wet, spruce–dominated and cool–dry steppe environments.
Emily Dearing Crampton-Flood, Lars J. Noorbergen, Damian Smits, R. Christine Boschman, Timme H. Donders, Dirk K. Munsterman, Johan ten Veen, Francien Peterse, Lucas Lourens, and Jaap S. Sinninghe Damsté
Clim. Past, 16, 523–541, https://doi.org/10.5194/cp-16-523-2020, https://doi.org/10.5194/cp-16-523-2020, 2020
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The mid-Pliocene warm period (mPWP; 3.3–3.0 million years ago) is thought to be the last geological interval with similar atmospheric carbon dioxide concentrations as the present day. Further, the mPWP was 2–3 °C warmer than present, making it a good analogue for estimating the effects of future climate change. Here, we construct a new precise age model for the North Sea during the mPWP, and provide a detailed reconstruction of terrestrial and marine climate using a multi-proxy approach.
Tamara L. Fletcher, Lisa Warden, Jaap S. Sinninghe Damsté, Kendrick J. Brown, Natalia Rybczynski, John C. Gosse, and Ashley P. Ballantyne
Clim. Past, 15, 1063–1081, https://doi.org/10.5194/cp-15-1063-2019, https://doi.org/10.5194/cp-15-1063-2019, 2019
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The last time atmospheric CO2 was similar to the present was 3–4 million years ago. The Arctic was warmer compared to the global average, and the causes are not fully known. To investigate this, we reconstructed summer temperature, forest fire and vegetation at a 3.9 Ma fen peat in Arctic Canada. The summer temperatures averaged 15.4 °C, and charcoal was abundant. Interactions between vegetation and climate were mediated by fire and may contribute to high Arctic temperatures during the Pliocene.
Darci Rush, Helen M. Talbot, Marcel T. J. van der Meer, Ellen C. Hopmans, Ben Douglas, and Jaap S. Sinninghe Damsté
Biogeosciences, 16, 2467–2479, https://doi.org/10.5194/bg-16-2467-2019, https://doi.org/10.5194/bg-16-2467-2019, 2019
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Sapropels are layers of sediment that regularly occur in the Mediterranean. They indicate periods when the Mediterranean Sea water contained no oxygen, a gas vital for most large organisms. This research investigated a key process in the nitrogen cycle (anaerobic ammonium oxidation, anammox), which removes nitrogen – an important nutrient to algae – from the water, during sapropel events. Using lipids to trace this process, we found that anammox was active during the no-oxygen times.
Gabriella M. Weiss, David Chivall, Sebastian Kasper, Hideto Nakamura, Fiz da Costa, Philippe Soudant, Jaap S. Sinninghe Damsté, Stefan Schouten, and Marcel T. J. van der Meer
Biogeosciences Discuss., https://doi.org/10.5194/bg-2019-147, https://doi.org/10.5194/bg-2019-147, 2019
Preprint withdrawn
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In this study, we used four different haptophyte species and six different organic compounds to investigate the relationship between organic matter synthesis and salinity. We showed that creation in different parts of the cell (chloroplast versus cytosol) determined which compounds retain a correlation between their hydrogen isotopes and salinity. This is important for using hydrogen isotopes to reconstruct salinity in the geologic record.
Marijke W. de Bar, Jenny E. Ullgren, Robert C. Thunnell, Stuart G. Wakeham, Geert-Jan A. Brummer, Jan-Berend W. Stuut, Jaap S. Sinninghe Damsté, and Stefan Schouten
Biogeosciences, 16, 1705–1727, https://doi.org/10.5194/bg-16-1705-2019, https://doi.org/10.5194/bg-16-1705-2019, 2019
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We analyzed sediment traps from the Cariaco Basin, the tropical Atlantic and the Mozambique Channel to evaluate seasonal imprints in the concentrations and fluxes of long-chain diols (LDIs), in addition to the long-chain diol index proxy (sea surface temperature proxy) and the diol index (upwelling indicator). Despite significant degradation, LDI-derived temperatures were very similar for the sediment traps and seafloor sediments, and corresponded to annual mean sea surface temperatures.
Marijke W. de Bar, Dave J. Stolwijk, Jerry F. McManus, Jaap S. Sinninghe Damsté, and Stefan Schouten
Clim. Past, 14, 1783–1803, https://doi.org/10.5194/cp-14-1783-2018, https://doi.org/10.5194/cp-14-1783-2018, 2018
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We present a past sea surface temperature and paleoproductivity record over the last 150 000 years for ODP Site 1234 (Chilean margin). We tested the applicability of long-chain diol proxies for the reconstrucion of SST (LDI), past upwelling conditions (diol index), and nutrient concentrations (NDI). The LDI likely reflects past temperature changes, but the diol index and NDI are perhaps more indicative of Proboscia diatom productivity rather than upwelling and/or nutrient conditions.
Sergio Balzano, Julie Lattaud, Laura Villanueva, Sebastiaan W. Rampen, Corina P. D. Brussaard, Judith van Bleijswijk, Nicole Bale, Jaap S. Sinninghe Damsté, and Stefan Schouten
Biogeosciences, 15, 5951–5968, https://doi.org/10.5194/bg-15-5951-2018, https://doi.org/10.5194/bg-15-5951-2018, 2018
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We tried to identify the microbes which biosynthesize a class of lipids widespread in seawater, the long chain alkyl diols (LCDs). We could not find any microorganism likely involved in the production of LCDs. The amounts of LCDs found are too high to be produced by living organisms and are likely to be part of the refractory organic matter persisting for long periods in the water column.
Julie Lattaud, Frédérique Kirkels, Francien Peterse, Chantal V. Freymond, Timothy I. Eglinton, Jens Hefter, Gesine Mollenhauer, Sergio Balzano, Laura Villanueva, Marcel T. J. van der Meer, Ellen C. Hopmans, Jaap S. Sinninghe Damsté, and Stefan Schouten
Biogeosciences, 15, 4147–4161, https://doi.org/10.5194/bg-15-4147-2018, https://doi.org/10.5194/bg-15-4147-2018, 2018
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Long-chain diols (LCDs) are biomarkers that occur widespread in marine environments and also in lakes and rivers. In this study, we looked at the distribution of LCDs in three river systems (Godavari, Danube, and Rhine) in relation to season, precipitation, and temperature. We found out that the LCDs are likely being produced in calm areas of the river systems and that marine LCDs have a different distribution than riverine LCDs.
Timme H. Donders, Niels A. G. M. van Helmond, Roel Verreussel, Dirk Munsterman, Johan ten Veen, Robert P. Speijer, Johan W. H. Weijers, Francesca Sangiorgi, Francien Peterse, Gert-Jan Reichart, Jaap S. Sinninghe Damsté, Lucas Lourens, Gesa Kuhlmann, and Henk Brinkhuis
Clim. Past, 14, 397–411, https://doi.org/10.5194/cp-14-397-2018, https://doi.org/10.5194/cp-14-397-2018, 2018
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The buildup and melting of ice during the early glaciations in the Northern Hemisphere, around 2.5 million years ago, were far shorter in duration than during the last million years. Based on molecular compounds and microfossils from sediments dating back to the early glaciations we show that the temperature on land and in the sea changed simultaneously and was a major factor in the ice buildup in the Northern Hemisphere. These data provide key insights into the dynamics of early glaciations.
Nicole J. Bale, Tracy A. Villareal, Ellen C. Hopmans, Corina P. D. Brussaard, Marc Besseling, Denise Dorhout, Jaap S. Sinninghe Damsté, and Stefan Schouten
Biogeosciences, 15, 1229–1241, https://doi.org/10.5194/bg-15-1229-2018, https://doi.org/10.5194/bg-15-1229-2018, 2018
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Associations between diatoms and N-fixing cyanobacteria (diatom–diazotroph associations, DDAs) play an important role in the N cycle of the tropical North Atlantic. Heterocysts are the site of N fixation and contain unique glycolipids. We measured these glycolipids in the water column and surface sediment from the tropical North Atlantic. We found a significant correlation between the concentration of glycolipid and of DDAs, strengthening their application as biomarkers.
Martina Sollai, Ellen C. Hopmans, Nicole J. Bale, Anchelique Mets, Lisa Warden, Matthias Moros, and Jaap S. Sinninghe Damsté
Biogeosciences, 14, 5789–5804, https://doi.org/10.5194/bg-14-5789-2017, https://doi.org/10.5194/bg-14-5789-2017, 2017
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The Baltic Sea is characterized by recurring summer phytoplankton blooms, dominated by a few cyanobacterial species. These bacteria are able to use dinitrogen gas as the source for nitrogen and produce very specific lipids. We analyzed these lipids in a sediment core to study their presence over the past 7000 years. This reveals that cyanobacterial blooms have not only occurred in the last decades but were common at times when the Baltic was connected to the North Sea.
Gabriella M. Weiss, Eva Y. Pfannerstill, Stefan Schouten, Jaap S. Sinninghe Damsté, and Marcel T. J. van der Meer
Biogeosciences, 14, 5693–5704, https://doi.org/10.5194/bg-14-5693-2017, https://doi.org/10.5194/bg-14-5693-2017, 2017
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Algal-derived compounds allow us to make assumptions about environmental conditions in the past. In order to better understand how organisms record environmental conditions, we grew microscopic marine algae at different light intensities, salinities, and alkalinities in a temperature-controlled environment. We determined how these environmental parameters affected specific algal-derived compounds, especially their relative deuterium content, which seems to be mainly affected by salinity.
Julie Lattaud, Denise Dorhout, Hartmut Schulz, Isla S. Castañeda, Enno Schefuß, Jaap S. Sinninghe Damsté, and Stefan Schouten
Clim. Past, 13, 1049–1061, https://doi.org/10.5194/cp-13-1049-2017, https://doi.org/10.5194/cp-13-1049-2017, 2017
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The study of past sedimentary records from coastal margins allows us to reconstruct variations in terrestrial input into the marine realm and to gain insight into continental climatic variability. The study of two sediment cores close to river mouths allowed us to show the potential of long-chain diols as riverine input proxy.
Lisa Warden, Jung-Hyun Kim, Claudia Zell, Geert-Jan Vis, Henko de Stigter, Jérôme Bonnin, and Jaap S. Sinninghe Damsté
Biogeosciences, 13, 5719–5738, https://doi.org/10.5194/bg-13-5719-2016, https://doi.org/10.5194/bg-13-5719-2016, 2016
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Enhanced analytical techniques were applied to characterize fossilized microbial cell membrane lipids from samples in the Tagus River basin spanning the last 6000 years. Using the novel methods and calibration, the pH estimates were improved upon, and this study reveals new factors that should be considered when using this proxy as well as affirms the importance of examining the provenance of these lipids before applying them for paleoclimate reconstructions.
Sandra Mariam Heinzelmann, Nicole Jane Bale, Laura Villanueva, Danielle Sinke-Schoen, Catharina Johanna Maria Philippart, Jaap Smede Sinninghe Damsté, Stefan Schouten, and Marcel Teunis Jan van der Meer
Biogeosciences, 13, 5527–5539, https://doi.org/10.5194/bg-13-5527-2016, https://doi.org/10.5194/bg-13-5527-2016, 2016
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In order to understand microbial communities in the environment it is necessary to assess their metabolic potential. The hydrogen isotopic composition of fatty acids has been shown to be promising tool to study the general metabolism of microorganisms in pure culture. Here we showed that it is possible to study seasonal changes in the general metabolism of the whole community by studying the hydrogen isotopic composition of fatty acids.
Douwe S. Maat, Nicole J. Bale, Ellen C. Hopmans, Jaap S. Sinninghe Damsté, Stefan Schouten, and Corina P. D. Brussaard
Biogeosciences, 13, 1667–1676, https://doi.org/10.5194/bg-13-1667-2016, https://doi.org/10.5194/bg-13-1667-2016, 2016
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This study shows that the phytoplankter Micromonas pusilla alters its lipid composition when the macronutrient phosphate is in low supply. This reduction in phospholipids is directly dependent on the strength of the limitation. Furthermore we show that, when M. pusilla is infected by viruses, lipid remodeling is lower. The study was carried out to investigate how phytoplankton and its viruses are affected by environmental factors and how this affects food web dynamics.
N. J. Bale, L. Villanueva, E. C. Hopmans, S. Schouten, and J. S. Sinninghe Damsté
Biogeosciences, 10, 7195–7206, https://doi.org/10.5194/bg-10-7195-2013, https://doi.org/10.5194/bg-10-7195-2013, 2013
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This study analysed marine sediment samples from areas with and without minimal hydrocarbon seepage from reservoirs underneath. Depth profiles of dissolved chemical components in the pore water and molecular biological data revealed differences in microbial community composition and activity. These results indicate that even minor hydrocarbon seepage affects sedimentary biogeochemical cycling in marine sediments, potentially providing a new tool for the detection of hydrocarbon reservoirs.
Robin Klomp, Olga M. Żygadłowska, Mike S. M. Jetten, Véronique E. Oldham, Niels A. G. M. van Helmond, Caroline P. Slomp, and Wytze K. Lenstra
Biogeosciences, 22, 751–765, https://doi.org/10.5194/bg-22-751-2025, https://doi.org/10.5194/bg-22-751-2025, 2025
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In marine sediments, dissolved Mn is present as either Mn(III) or Mn(II). We apply a reactive transport model to geochemical data for a seasonally anoxic and sulfidic coastal basin to determine the pathways of formation and removal of dissolved Mn(III) in the sediment. We demonstrate a critical role for reactions with Fe(II) and show evidence for substantial benthic release of dissolved Mn(III). Given the mobility of Mn(III), these findings have important implications for marine Mn cycling.
Amanda C. Semler and Anne E. Dekas
Biogeosciences, 22, 385–403, https://doi.org/10.5194/bg-22-385-2025, https://doi.org/10.5194/bg-22-385-2025, 2025
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Marine hydrocarbon seeps typically host subsurface microorganisms capable of degrading methane before it is emitted to the water column. Here we describe a seep in Monterey Bay which virtually lacks known methanotrophs and where biological consumption of methane at depth is undetected. Our findings suggest that some seeps are missing this critical biofilter and that seeps may be a more significant source of methane to the water column than previously realized.
Thomas W. Garner, J. Andrew G. Cooper, Alan M. Smith, Gavin M. Rishworth, and Matt Forbes
Biogeosciences, 21, 4785–4807, https://doi.org/10.5194/bg-21-4785-2024, https://doi.org/10.5194/bg-21-4785-2024, 2024
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There is a diverse and often conflicting suite of terminologies, classifications, and nomenclature applicable to the study of terrestrial carbonate deposits and microbialites (deposits that wholly or primarily accrete as a result of microbial activity). We review existing schemes, identify duplication and redundancy, and present a new integrated approach applicable to tufa microbialites on rock coasts.
Catherine Brenan, Markus Kienast, Vittorio Maselli, Christopher K. Algar, Benjamin Misiuk, and Craig J. Brown
Biogeosciences, 21, 4569–4586, https://doi.org/10.5194/bg-21-4569-2024, https://doi.org/10.5194/bg-21-4569-2024, 2024
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Quantifying how much organic carbon is stored in seafloor sediments is key to assessing how human activities can accelerate the process of carbon storage at the seabed, an important consideration for climate change. This study uses seafloor sediment maps to model organic carbon content. Carbon estimates were 12 times higher when assuming the absence of detailed sediment maps, demonstrating that high-resolution seafloor mapping is critically important for improved estimates of organic carbon.
Sophie Hage, Megan L. Baker, Nathalie Babonneau, Guillaume Soulet, Bernard Dennielou, Ricardo Silva Jacinto, Robert G. Hilton, Valier Galy, François Baudin, Christophe Rabouille, Clément Vic, Sefa Sahin, Sanem Açikalin, and Peter J. Talling
Biogeosciences, 21, 4251–4272, https://doi.org/10.5194/bg-21-4251-2024, https://doi.org/10.5194/bg-21-4251-2024, 2024
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The land-to-ocean flux of particulate organic carbon (POC) is difficult to measure, inhibiting accurate modeling of the global carbon cycle. Here, we quantify the POC flux between one of the largest rivers on Earth (Congo) and the ocean. POC in the form of vegetation and soil is transported by episodic submarine avalanches in a 1000 km long canyon at up to 5 km water depth. The POC flux induced by avalanches is at least 3 times greater than that induced by the background flow related to tides.
Xuefeng Peng, David J. Yousavich, Annie Bourbonnais, Frank Wenzhöfer, Felix Janssen, Tina Treude, and David L. Valentine
Biogeosciences, 21, 3041–3052, https://doi.org/10.5194/bg-21-3041-2024, https://doi.org/10.5194/bg-21-3041-2024, 2024
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Biologically available (fixed) nitrogen (N) is a limiting nutrient for life in the ocean. Under low-oxygen conditions, fixed N is either removed via denitrification or retained via dissimilatory nitrate reduction to ammonia (DNRA). Using in situ incubations in the Santa Barbara Basin, which undergoes seasonal anoxia, we found that benthic denitrification was the dominant nitrate reduction process, while nitrate availability and organic carbon content control the relative importance of DNRA.
Nicole Burdanowitz, Gerhard Schmiedl, Birgit Gaye, Philipp M. Munz, and Hartmut Schulz
Biogeosciences, 21, 1477–1499, https://doi.org/10.5194/bg-21-1477-2024, https://doi.org/10.5194/bg-21-1477-2024, 2024
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We analyse benthic foraminifera, nitrogen isotopes and lipids in a sediment core from the Gulf of Oman to investigate how the oxygen minimum zone (OMZ) and bottom water (BW) oxygenation have reacted to climatic changes since 43 ka. The OMZ and BW deoxygenation was strong during the Holocene, but the OMZ was well ventilated during the LGM period. We found an unstable mode of oscillating oxygenation states, from moderately oxygenated in cold stadials to deoxygenated in warm interstadials in MIS 3.
Maxime Daviray, Emmanuelle Geslin, Nils Risgaard-Petersen, Vincent V. Scholz, Marie Fouet, and Edouard Metzger
Biogeosciences, 21, 911–928, https://doi.org/10.5194/bg-21-911-2024, https://doi.org/10.5194/bg-21-911-2024, 2024
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Coastal marine sediments are subject to major acidification processes because of climate change and human activities, but these processes can also result from biotic activity. We studied the sediment acidifcation effect on benthic calcareous foraminifera in intertidal mudflats. The strong pH decrease in sediments probably caused by cable bacteria led to calcareous test dissolution of living and dead foraminifera, threatening the test preservation and their robustness as environmental proxies.
Sebastian J. E. Krause, Jiarui Liu, David J. Yousavich, DeMarcus Robinson, David W. Hoyt, Qianhui Qin, Frank Wenzhöfer, Felix Janssen, David L. Valentine, and Tina Treude
Biogeosciences, 20, 4377–4390, https://doi.org/10.5194/bg-20-4377-2023, https://doi.org/10.5194/bg-20-4377-2023, 2023
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Methane is a potent greenhouse gas, and hence it is important to understand its sources and sinks in the environment. Here we present new data from organic-rich surface sediments below an oxygen minimum zone off the coast of California (Santa Barbara Basin) demonstrating the simultaneous microbial production and consumption of methane, which appears to be an important process preventing the build-up of methane in these sediments and the emission into the water column and atmosphere.
Sinan Xu, Bo Liu, Sandra Arndt, Sabine Kasten, and Zijun Wu
Biogeosciences, 20, 2251–2263, https://doi.org/10.5194/bg-20-2251-2023, https://doi.org/10.5194/bg-20-2251-2023, 2023
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We use a reactive continuum model based on a lognormal distribution (l-RCM) to inversely determine model parameters μ and σ at 123 sites across the global ocean. Our results show organic matter (OM) reactivity is more than 3 orders of magnitude higher in shelf than in abyssal regions. In addition, OM reactivity is higher than predicted in some specific regions, yet the l-RCM can still capture OM reactivity features in these regions.
Christiane Schmidt, Emmanuelle Geslin, Joan M. Bernhard, Charlotte LeKieffre, Mette Marianne Svenning, Helene Roberge, Magali Schweizer, and Giuliana Panieri
Biogeosciences, 19, 3897–3909, https://doi.org/10.5194/bg-19-3897-2022, https://doi.org/10.5194/bg-19-3897-2022, 2022
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This study is the first to show non-selective deposit feeding in the foraminifera Nonionella labradorica and the possible uptake of methanotrophic bacteria. We carried out a feeding experiment with a marine methanotroph to examine the ultrastructure of the cell and degradation vacuoles using transmission electron microscopy (TEM). The results revealed three putative methanotrophs at the outside of the cell/test, which could be taken up via non-targeted grazing in seeps or our experiment.
James P. J. Ward, Katharine R. Hendry, Sandra Arndt, Johan C. Faust, Felipe S. Freitas, Sian F. Henley, Jeffrey W. Krause, Christian März, Allyson C. Tessin, and Ruth L. Airs
Biogeosciences, 19, 3445–3467, https://doi.org/10.5194/bg-19-3445-2022, https://doi.org/10.5194/bg-19-3445-2022, 2022
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The seafloor plays an important role in the cycling of silicon (Si), a key nutrient that promotes marine primary productivity. In our model study, we disentangle major controls on the seafloor Si cycle to better anticipate the impacts of continued warming and sea ice melt in the Barents Sea. We uncover a coupling of the iron redox and Si cycles, dissolution of lithogenic silicates, and authigenic clay formation, comprising a Si sink that could have implications for the Arctic Ocean Si budget.
Hanni Vigderovich, Werner Eckert, Michal Elul, Maxim Rubin-Blum, Marcus Elvert, and Orit Sivan
Biogeosciences, 19, 2313–2331, https://doi.org/10.5194/bg-19-2313-2022, https://doi.org/10.5194/bg-19-2313-2022, 2022
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Anaerobic oxidation of methane (AOM) is one of the major processes limiting the release of the greenhouse gas methane from natural environments. Here we show that significant AOM exists in the methane zone of lake sediments in natural conditions and even after long-term (ca. 18 months) anaerobic slurry incubations with two stages. Methanogens were most likely responsible for oxidizing the methane, and humic substances and iron oxides are likely electron acceptors to support this oxidation.
Bjorn Sundby, Pierre Anschutz, Pascal Lecroart, and Alfonso Mucci
Biogeosciences, 19, 1421–1434, https://doi.org/10.5194/bg-19-1421-2022, https://doi.org/10.5194/bg-19-1421-2022, 2022
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A glacial–interglacial methane-fuelled redistribution of reactive phosphorus between the oceanic and sedimentary phosphorus reservoirs can occur in the ocean when falling sea level lowers the pressure on the seafloor, destabilizes methane hydrates, and triggers the dissolution of P-bearing iron oxides. The mass of phosphate potentially mobilizable from the sediment is similar to the size of the current oceanic reservoir. Hence, this process may play a major role in the marine phosphorus cycle.
Florian Lauryssen, Philippe Crombé, Tom Maris, Elliot Van Maldegem, Marijn Van de Broek, Stijn Temmerman, and Erik Smolders
Biogeosciences, 19, 763–776, https://doi.org/10.5194/bg-19-763-2022, https://doi.org/10.5194/bg-19-763-2022, 2022
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Surface waters in lowland regions have a poor surface water quality, mainly due to excess nutrients like phosphate. Therefore, we wanted to know the phosphate levels without humans, also called the pre-industrial background. Phosphate binds strongly to sediment particles, suspended in the river water. In this research we used sediments deposited by a river as an archive for surface water phosphate back to 1800 CE. Pre-industrial phosphate levels were estimated at one-third of the modern levels.
Gerard J. M. Versteegh, Andrea Koschinsky, Thomas Kuhn, Inken Preuss, and Sabine Kasten
Biogeosciences, 18, 4965–4984, https://doi.org/10.5194/bg-18-4965-2021, https://doi.org/10.5194/bg-18-4965-2021, 2021
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Oxygen penetrates sediments not only from the ocean bottom waters but also from the basement. The impact of the latter is poorly understood. We show that this basement oxygen has a clear impact on the nitrogen cycle, the redox state, and the distribution of manganese, nickel cobalt and organic matter in the sediments. This is important for (1) global biogeochemical cycles, (2) understanding sedimentary life and (3) the interpretation of the sediment record to reconstruct the past.
Annika Fiskal, Eva Anthamatten, Longhui Deng, Xingguo Han, Lorenzo Lagostina, Anja Michel, Rong Zhu, Nathalie Dubois, Carsten J. Schubert, Stefano M. Bernasconi, and Mark A. Lever
Biogeosciences, 18, 4369–4388, https://doi.org/10.5194/bg-18-4369-2021, https://doi.org/10.5194/bg-18-4369-2021, 2021
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Microbially produced methane can serve as a carbon source for freshwater macrofauna most likely through grazing on methane-oxidizing bacteria. This study investigates the contributions of different carbon sources to macrofaunal biomass. Our data suggest that the average contribution of methane-derived carbon is similar between different fauna but overall remains low. This is further supported by the low abundance of methane-cycling microorganisms.
Astrid Hylén, Sebastiaan J. van de Velde, Mikhail Kononets, Mingyue Luo, Elin Almroth-Rosell, and Per O. J. Hall
Biogeosciences, 18, 2981–3004, https://doi.org/10.5194/bg-18-2981-2021, https://doi.org/10.5194/bg-18-2981-2021, 2021
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Sediments in oxygen-depleted ocean areas release high amounts of phosphorus, feeding algae that consume oxygen upon degradation, leading to further phosphorus release. Oxygenation is thought to trap phosphorus in the sediment and break this feedback. We studied the sediment phosphorus cycle in a previously anoxic area after an inflow of oxic water. Surprisingly, the sediment phosphorus release increased, showing that feedbacks between phosphorus release and oxygen depletion can be hard to break.
Sebastiaan J. van de Velde, Rebecca K. James, Ine Callebaut, Silvia Hidalgo-Martinez, and Filip J. R. Meysman
Biogeosciences, 18, 1451–1461, https://doi.org/10.5194/bg-18-1451-2021, https://doi.org/10.5194/bg-18-1451-2021, 2021
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Some 540 Myr ago, animal life evolved in the ocean. Previous research suggested that when these early animals started inhabiting the seafloor, they retained phosphorus in the seafloor, thereby limiting photosynthesis in the ocean. We studied salt marsh sediments with and without animals and found that their impact on phosphorus retention is limited, which implies that their impact on the global environment might have been less drastic than previously assumed.
Martijn Hermans, Nils Risgaard-Petersen, Filip J. R. Meysman, and Caroline P. Slomp
Biogeosciences, 17, 5919–5938, https://doi.org/10.5194/bg-17-5919-2020, https://doi.org/10.5194/bg-17-5919-2020, 2020
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This paper demonstrates that the recently discovered cable bacteria are capable of using a mineral, known as siderite, as a source for the formation of iron oxides. This work also demonstrates that the activity of cable bacteria can lead to a distinct subsurface layer in the sediment that can be used as a marker for their activity.
Torben Windirsch, Guido Grosse, Mathias Ulrich, Lutz Schirrmeister, Alexander N. Fedorov, Pavel Y. Konstantinov, Matthias Fuchs, Loeka L. Jongejans, Juliane Wolter, Thomas Opel, and Jens Strauss
Biogeosciences, 17, 3797–3814, https://doi.org/10.5194/bg-17-3797-2020, https://doi.org/10.5194/bg-17-3797-2020, 2020
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To extend the knowledge on circumpolar deep permafrost carbon storage, we examined two deep permafrost deposit types (Yedoma and alas) in central Yakutia. We found little but partially undecomposed organic carbon as a result of largely changing sedimentation processes. The carbon stock of the examined Yedoma deposits is about 50 % lower than the general Yedoma domain mean, implying a very hetererogeneous Yedoma composition, while the alas is approximately 80 % below the thermokarst deposit mean.
Anna Plass, Christian Schlosser, Stefan Sommer, Andrew W. Dale, Eric P. Achterberg, and Florian Scholz
Biogeosciences, 17, 3685–3704, https://doi.org/10.5194/bg-17-3685-2020, https://doi.org/10.5194/bg-17-3685-2020, 2020
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We compare the cycling of Fe and Cd in sulfidic sediments of the Peruvian oxygen minimum zone. Due to the contrasting solubility of their sulfide minerals, the sedimentary Fe release and Cd burial fluxes covary with spatial and temporal distributions of H2S. Depending on the solubility of their sulfide minerals, sedimentary trace metal fluxes will respond differently to ocean deoxygenation/expansion of H2S concentrations, which may change trace metal stoichiometry of upwelling water masses.
Biqing Zhu, Manuel Kübler, Melanie Ridoli, Daniel Breitenstein, and Martin H. Schroth
Biogeosciences, 17, 3613–3630, https://doi.org/10.5194/bg-17-3613-2020, https://doi.org/10.5194/bg-17-3613-2020, 2020
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We provide evidence that the greenhouse gas methane (CH4) is enclosed in calcareous glacier-forefield sediments across Switzerland. Geochemical analyses confirmed that this ancient CH4 has its origin in the calcareous parent bedrock. Our estimate of the total quantity of CH4 enclosed in sediments across Switzerland indicates a large CH4 mass (~105 t CH4). We produced evidence that CH4 is stable in its enclosed state, but additional experiments are needed to elucidate its long-term fate.
Matteo Puglini, Victor Brovkin, Pierre Regnier, and Sandra Arndt
Biogeosciences, 17, 3247–3275, https://doi.org/10.5194/bg-17-3247-2020, https://doi.org/10.5194/bg-17-3247-2020, 2020
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A reaction-transport model to assess the potential non-turbulent methane flux from the East Siberian Arctic sediments to water columns is applied here. We show that anaerobic oxidation of methane (AOM) is an efficient filter except for high values of sedimentation rate and advective flow, which enable considerable non-turbulent steady-state methane fluxes. Significant transient methane fluxes can also occur during the building-up phase of the AOM-performing biomass microbial community.
Kyle Delwiche, Junyao Gu, Harold Hemond, and Sarah P. Preheim
Biogeosciences, 17, 3135–3147, https://doi.org/10.5194/bg-17-3135-2020, https://doi.org/10.5194/bg-17-3135-2020, 2020
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In this study, we investigate whether bubbles transport sediments containing arsenic and cyanobacteria from the bottom to the top of a polluted lake. We measured arsenic and cyanobacteria from bubble traps in the lake and from an experimental bubble column in the laboratory. We found that bubble transport was not an important source of arsenic in the surface waters but that bubbles could transport enough cyanobacteria to the surface to exacerbate harmful algal blooms.
Nathaniel Kemnitz, William M. Berelson, Douglas E. Hammond, Laura Morine, Maria Figueroa, Timothy W. Lyons, Simon Scharf, Nick Rollins, Elizabeth Petsios, Sydnie Lemieux, and Tina Treude
Biogeosciences, 17, 2381–2396, https://doi.org/10.5194/bg-17-2381-2020, https://doi.org/10.5194/bg-17-2381-2020, 2020
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Our paper shows how sedimentation in a very low oxygen setting provides a unique record of environmental change. We look at the past 250 years through the filter of sediment accumulation via radioisotope dating and other physical and chemical analyses of these sediments. We conclude, remarkably, that there has been very little change in net sediment mass accumulation through the past 100–150 years, yet just prior to 1900 CE, sediments were accumulating at 50 %–70 % of today's rate.
Dario Fussmann, Avril Jean Elisabeth von Hoyningen-Huene, Andreas Reimer, Dominik Schneider, Hana Babková, Robert Peticzka, Andreas Maier, Gernot Arp, Rolf Daniel, and Patrick Meister
Biogeosciences, 17, 2085–2106, https://doi.org/10.5194/bg-17-2085-2020, https://doi.org/10.5194/bg-17-2085-2020, 2020
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Dolomite (CaMg(CO3)2) is supersaturated in many aquatic settings (e.g., seawater) on modern Earth but does not precipitate directly from the fluid, a fact known as the dolomite problem. The widely acknowledged concept of dolomite precipitation involves microbial extracellular polymeric substances (EPSs) and anoxic conditions as important drivers. In contrast, results from Lake Neusiedl support an alternative concept of Ca–Mg carbonate precipitation under aerobic and alkaline conditions.
Aurèle Vuillemin, André Friese, Richard Wirth, Jan A. Schuessler, Anja M. Schleicher, Helga Kemnitz, Andreas Lücke, Kohen W. Bauer, Sulung Nomosatryo, Friedhelm von Blanckenburg, Rachel Simister, Luis G. Ordoñez, Daniel Ariztegui, Cynthia Henny, James M. Russell, Satria Bijaksana, Hendrik Vogel, Sean A. Crowe, Jens Kallmeyer, and the Towuti Drilling Project
Science team
Biogeosciences, 17, 1955–1973, https://doi.org/10.5194/bg-17-1955-2020, https://doi.org/10.5194/bg-17-1955-2020, 2020
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Ferruginous lakes experience restricted primary production due to phosphorus trapping by ferric iron oxides under oxic conditions. We report the presence of large crystals of vivianite, a ferrous iron phosphate, in sediments from Lake Towuti, Indonesia. We address processes of P retention linked to diagenesis of iron phases. Vivianite crystals had light Fe2+ isotope signatures and contained mineral inclusions consistent with antecedent processes of microbial sulfate and iron reduction.
Sonja Geilert, Patricia Grasse, Kristin Doering, Klaus Wallmann, Claudia Ehlert, Florian Scholz, Martin Frank, Mark Schmidt, and Christian Hensen
Biogeosciences, 17, 1745–1763, https://doi.org/10.5194/bg-17-1745-2020, https://doi.org/10.5194/bg-17-1745-2020, 2020
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Marine silicate weathering is a key process of the marine silica cycle; however, its controlling processes are not well understood. In the Guaymas Basin, silicate weathering has been studied under markedly differing ambient conditions. Environmental settings like redox conditions or terrigenous input of reactive silicates appear to be major factors controlling marine silicate weathering. These factors need to be taken into account in future oceanic mass balances of Si and in modeling studies.
Jessica B. Volz, Laura Haffert, Matthias Haeckel, Andrea Koschinsky, and Sabine Kasten
Biogeosciences, 17, 1113–1131, https://doi.org/10.5194/bg-17-1113-2020, https://doi.org/10.5194/bg-17-1113-2020, 2020
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Potential future deep-sea mining of polymetallic nodules at the seafloor is expected to severely harm the marine environment. However, the consequences on deep-sea ecosystems are still poorly understood. This study on surface sediments from man-made disturbance tracks in the Pacific Ocean shows that due to the removal of the uppermost sediment layer and thereby the loss of organic matter, the geochemical system in the sediments is disturbed for millennia before reaching a new equilibrium.
Ralf Conrad, Melanie Klose, and Alex Enrich-Prast
Biogeosciences, 17, 1063–1069, https://doi.org/10.5194/bg-17-1063-2020, https://doi.org/10.5194/bg-17-1063-2020, 2020
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Lake sediments release the greenhouse gas CH4. Acetate is an important precursor. Although Amazonian lake sediments all contained acetate-consuming methanogens, measurement of the turnover of labeled acetate showed that some sediments converted acetate not to CH4 plus CO2, as expected, but only to CO2. Our results indicate the operation of acetate-oxidizing microorganisms couples the oxidation process to syntrophic methanogenic partners and/or to the reduction of organic compounds.
Jens Rassmann, Eryn M. Eitel, Bruno Lansard, Cécile Cathalot, Christophe Brandily, Martial Taillefert, and Christophe Rabouille
Biogeosciences, 17, 13–33, https://doi.org/10.5194/bg-17-13-2020, https://doi.org/10.5194/bg-17-13-2020, 2020
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In this paper, we use a large set of measurements made using in situ and lab techniques to elucidate the cause of dissolved inorganic carbon fluxes in sediments from the Rhône delta and its companion compound alkalinity, which carries the absorption capacity of coastal waters with respect to atmospheric CO2. We show that sediment processes (sulfate reduction, FeS precipitation and accumulation) are crucial in generating the alkalinity fluxes observed in this study by in situ incubation chambers.
Sophie A. L. Paul, Matthias Haeckel, Michael Bau, Rajina Bajracharya, and Andrea Koschinsky
Biogeosciences, 16, 4829–4849, https://doi.org/10.5194/bg-16-4829-2019, https://doi.org/10.5194/bg-16-4829-2019, 2019
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We studied the upper 10 m of deep-sea sediments, including pore water, in the Peru Basin to understand small-scale variability of trace metals. Our results show high spatial variability related to topographical variations, which in turn impact organic matter contents, degradation processes, and trace metal cycling. Another interesting finding was the influence of dissolving buried nodules on the surrounding sediment and trace metal cycling.
Sarah Paradis, Antonio Pusceddu, Pere Masqué, Pere Puig, Davide Moccia, Tommaso Russo, and Claudio Lo Iacono
Biogeosciences, 16, 4307–4320, https://doi.org/10.5194/bg-16-4307-2019, https://doi.org/10.5194/bg-16-4307-2019, 2019
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Chronic deep bottom trawling in the Gulf of Castellammare (SW Mediterranean) erodes large volumes of sediment, exposing over-century-old sediment depleted in organic matter. Nevertheless, the arrival of fresh and nutritious sediment recovers superficial organic matter in trawling grounds and leads to high turnover rates, partially and temporarily mitigating the impacts of bottom trawling. However, this deposition is ephemeral and it will be swiftly eroded by the passage of the next trawler.
Zhichao Zhou, Bo Liang, Li-Ying Wang, Jin-Feng Liu, Bo-Zhong Mu, Hojae Shim, and Ji-Dong Gu
Biogeosciences, 16, 4229–4241, https://doi.org/10.5194/bg-16-4229-2019, https://doi.org/10.5194/bg-16-4229-2019, 2019
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This study shows a core bacterial microbiome with a small proportion of shared operational taxonomic units of common sequences among all oil reservoirs. Dominant methanogenesis shifts from the hydrogenotrophic pathway in water phase to the acetoclastic pathway in the oil phase at high temperatures, but the opposite is true at low temperatures. There are also major functional metabolism differences between the two phases for amino acids, hydrocarbons, and carbohydrates.
Annika Fiskal, Longhui Deng, Anja Michel, Philip Eickenbusch, Xingguo Han, Lorenzo Lagostina, Rong Zhu, Michael Sander, Martin H. Schroth, Stefano M. Bernasconi, Nathalie Dubois, and Mark A. Lever
Biogeosciences, 16, 3725–3746, https://doi.org/10.5194/bg-16-3725-2019, https://doi.org/10.5194/bg-16-3725-2019, 2019
Hanni Vigderovich, Lewen Liang, Barak Herut, Fengping Wang, Eyal Wurgaft, Maxim Rubin-Blum, and Orit Sivan
Biogeosciences, 16, 3165–3181, https://doi.org/10.5194/bg-16-3165-2019, https://doi.org/10.5194/bg-16-3165-2019, 2019
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Microbial iron reduction participates in important biogeochemical cycles. In the last decade iron reduction has been observed in many aquatic sediments below its classical zone, in the methane production zone, suggesting a link between the two cycles. Here we present evidence for microbial iron reduction in the methanogenic depth of the oligotrophic SE Mediterranean continental shelf using mainly geochemical and microbial sedimentary profiles and suggest possible mechanisms for this process.
Haoyi Yao, Wei-Li Hong, Giuliana Panieri, Simone Sauer, Marta E. Torres, Moritz F. Lehmann, Friederike Gründger, and Helge Niemann
Biogeosciences, 16, 2221–2232, https://doi.org/10.5194/bg-16-2221-2019, https://doi.org/10.5194/bg-16-2221-2019, 2019
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How methane is transported in the sediment is important for the microbial community living on methane. Here we report an observation of a mini-fracture that facilitates the advective gas transport of methane in the sediment, compared to the diffusive fluid transport without a fracture. We found contrasting bio-geochemical signals in these different transport modes. This finding can help to fill the gap in the fracture network system in modulating methane dynamics in surface sediments.
Laura A. Casella, Sixin He, Erika Griesshaber, Lourdes Fernández-Díaz, Martina Greiner, Elizabeth M. Harper, Daniel J. Jackson, Andreas Ziegler, Vasileios Mavromatis, Martin Dietzel, Anton Eisenhauer, Sabino Veintemillas-Verdaguer, Uwe Brand, and Wolfgang W. Schmahl
Biogeosciences, 15, 7451–7484, https://doi.org/10.5194/bg-15-7451-2018, https://doi.org/10.5194/bg-15-7451-2018, 2018
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Biogenic carbonates record past environmental conditions. Fossil shell chemistry and microstructure change as metastable biogenic carbonates are replaced by inorganic calcite. Simulated diagenetic alteration at 175 °C of different shell microstructures showed that (nacreous) shell aragonite and calcite were partially replaced by coarse inorganic calcite crystals due to dissolution–reprecipitation reactions. EBSD maps allowed for qualitative assessment of the degree of diagenetic overprint.
Wytze K. Lenstra, Matthias Egger, Niels A. G. M. van Helmond, Emma Kritzberg, Daniel J. Conley, and Caroline P. Slomp
Biogeosciences, 15, 6979–6996, https://doi.org/10.5194/bg-15-6979-2018, https://doi.org/10.5194/bg-15-6979-2018, 2018
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We show that burial rates of phosphorus (P) in an estuary in the northern Baltic Sea are very high. We demonstrate that at high sedimentation rates, P retention in the sediment is related to the formation of vivianite. With a reactive transport model, we assess the sensitivity of sedimentary vivianite formation. We suggest that enrichments of iron and P in the sediment are linked to periods of enhanced riverine input of Fe, which subsequently strongly enhances P burial in coastal sediments.
Jiarui Liu, Gareth Izon, Jiasheng Wang, Gilad Antler, Zhou Wang, Jie Zhao, and Matthias Egger
Biogeosciences, 15, 6329–6348, https://doi.org/10.5194/bg-15-6329-2018, https://doi.org/10.5194/bg-15-6329-2018, 2018
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Our work provides new insights into the biogeochemical cycling of iron, methane and phosphorus. We found that vivianite, an iron-phosphate mineral, is pervasive in methane-rich sediments, suggesting that iron reduction at depth is coupled to phosphorus and methane cycling on a much greater spatial scale than previously assumed. Acting as an important burial mechanism for iron and phosphorus, vivianite authigenesis may be an under-considered process in both modern and ancient settings alike.
Georgina Robinson, Thomas MacTavish, Candida Savage, Gary S. Caldwell, Clifford L. W. Jones, Trevor Probyn, Bradley D. Eyre, and Selina M. Stead
Biogeosciences, 15, 1863–1878, https://doi.org/10.5194/bg-15-1863-2018, https://doi.org/10.5194/bg-15-1863-2018, 2018
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This study examined the effect of adding carbon to a sediment-based effluent treatment system to treat nitrogen-rich aquaculture waste. The research was conducted in incubation chambers to measure the exchange of gases and nutrients across the sediment–water interface and examine changes in the sediment microbial community. Adding carbon increased the amount of nitrogen retained in the treatment system, thereby reducing the levels of nitrogen needing to be discharged to the environment.
Daniele Brigolin, Christophe Rabouille, Bruno Bombled, Silvia Colla, Salvatrice Vizzini, Roberto Pastres, and Fabio Pranovi
Biogeosciences, 15, 1347–1366, https://doi.org/10.5194/bg-15-1347-2018, https://doi.org/10.5194/bg-15-1347-2018, 2018
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We present the result of a study carried out in the north-western Adriatic Sea by combining two different types of models with field sampling. A mussel farm was taken as a local source of perturbation to the natural flux of particulate organic carbon to the sediment. Differences in fluxes were primarily associated with mussel physiological conditions. Although restricted, these changes in particulate organic carbon fluxes induced visible effects on sediment biogeochemistry.
Volker Brüchert, Lisa Bröder, Joanna E. Sawicka, Tommaso Tesi, Samantha P. Joye, Xiaole Sun, Igor P. Semiletov, and Vladimir A. Samarkin
Biogeosciences, 15, 471–490, https://doi.org/10.5194/bg-15-471-2018, https://doi.org/10.5194/bg-15-471-2018, 2018
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We determined the aerobic and anaerobic degradation rates of land- and marine-derived organic material in East Siberian shelf sediment. Marine plankton-derived organic carbon was the main source for the oxic dissolved carbon dioxide production, whereas terrestrial organic material significantly contributed to the production of carbon dioxide under anoxic conditions. Our direct degradation rate measurements provide new constraints for the present-day Arctic marine carbon budget.
Jack J. Middelburg
Biogeosciences, 15, 413–427, https://doi.org/10.5194/bg-15-413-2018, https://doi.org/10.5194/bg-15-413-2018, 2018
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Organic carbon processing at the seafloor is studied by geologists to better understand the sedimentary record, by biogeochemists to quantify burial and respiration, by organic geochemists to elucidate compositional changes, and by ecologists to follow carbon transfers within food webs. These disciplinary approaches have their strengths and weaknesses. This award talk provides a synthesis, highlights the role of animals in sediment carbon processing and presents some new concepts.
Craig Smeaton, William E. N. Austin, Althea L. Davies, Agnes Baltzer, John A. Howe, and John M. Baxter
Biogeosciences, 14, 5663–5674, https://doi.org/10.5194/bg-14-5663-2017, https://doi.org/10.5194/bg-14-5663-2017, 2017
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Fjord sediments are recognised as hotspots for the burial and long-term storage of carbon. In this study, we use the Scottish fjords as a natural laboratory. Using geophysical and geochemical analysis in combination with upscaling techniques, we have generated the first full national sedimentary C inventory for a fjordic system. The results indicate that the Scottish fjords on a like-for-like basis are more effective as C stores than their terrestrial counterparts, including Scottish peatlands.
Perran Louis Miall Cook, Adam John Kessler, and Bradley David Eyre
Biogeosciences, 14, 4061–4069, https://doi.org/10.5194/bg-14-4061-2017, https://doi.org/10.5194/bg-14-4061-2017, 2017
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Nitrogen is the key nutrient that typically limits productivity in coastal waters. One of the key controls on the amount of bioavailable nitrogen is the process of denitrification, which converts nitrate (bioavailable) into nitrogen gas. Previous studies suggest high rates of denitrification may take place within carbonate sediments, and one explanation for this is that this process may take place within the sand grains. Here we show evidence to support this hypothesis.
Chris T. Parsons, Fereidoun Rezanezhad, David W. O'Connell, and Philippe Van Cappellen
Biogeosciences, 14, 3585–3602, https://doi.org/10.5194/bg-14-3585-2017, https://doi.org/10.5194/bg-14-3585-2017, 2017
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Phosphorus (P) has accumulated in sediments due to past human activities. The re-release of this P to water contributes to the growth of harmful algal blooms. Our research improves our mechanistic understanding of how P is partitioned between different chemical forms and between sediment and water under dynamic conditions. We demonstrate that P trapped within iron minerals may be less mobile during anoxic conditions than previously thought due to reversible changes to P forms within sediment.
Clint M. Miller, Gerald R. Dickens, Martin Jakobsson, Carina Johansson, Andrey Koshurnikov, Matt O'Regan, Francesco Muschitiello, Christian Stranne, and Carl-Magnus Mörth
Biogeosciences, 14, 2929–2953, https://doi.org/10.5194/bg-14-2929-2017, https://doi.org/10.5194/bg-14-2929-2017, 2017
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Continental slopes north of the East Siberian Sea are assumed to hold large amounts of methane. We present pore water chemistry from the 2014 SWERUS-C3 expedition. These are among the first results generated from this vast climatically sensitive region, and they imply that abundant methane, including gas hydrates, do not characterize the East Siberian Sea slope or rise. This contradicts previous modeling and discussions, which due to the lack of data are almost entirely based assumption.
Cited articles
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J.: Basic
local alignment search tool, J. Mol. Biol., 215, 403–410,
https://doi.org/10.1016/S0022-2836(05)80360-2, 1990.
Besseling, M., Hopmans, E. C., Sinninghe Damsté, J. S., and Villanueva,
L.: Intact polar lipid composition and bottom water and surface sediment
characteristics during R/V Pelagia cruise PASOM to the Arabian Sea in 2009,
PANGAEA, https://doi.org/10.1594/PANGAEA.891253, 2018.
Biddle, J. F., Lipp, J. S., Lever, M. A., Lloyd, K. G., Sørensen, K. B.,
Anderson, R., Fredricks, H. F., Elvert, M., Kelly, T. J., Schrag, D. P.,
Sogin, M. L., Brenchley, J. E., Teske, A., House, C. H., and Hinrichs, K.-U.:
Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru.,
P. Natl. Acad. Sci. USA, 103, 3846–3851,
https://doi.org/10.1073/pnas.0600035103, 2006.
Bligh, E. G. and Dyer, W. J.: A rapid method of total lipid extraction and
Purification, Can. J. Biochem. Phys., 37, 911–917, https://doi.org/10.1139/o59-099,
1959.
Boere, A. C., Rijpstra, W. I. C., de Lange, G. J., Sinninghe Damsté, J.
S., and Coolen, M. J. L.: Preservation potential of ancient plankton DNA in
Pleistocene marine sediments, Geobiology, 9, 377–393,
https://doi.org/10.1111/j.1472-4669.2011.00290.x, 2011.
Buckles, L. K., Villanueva, L., Weijers, J. W. H., Verschuren, D., and
Sinninghe Damsté, J. S.: Linking isoprenoidal GDGT membrane lipid
distributions with gene abundances of ammonia-oxidizing Thaumarchaeota and
uncultured crenarchaeotal groups in the water column of a tropical lake
(Lake Challa, East Africa), Environ. Microbiol., 2, 1–18,
https://doi.org/10.1111/1462-2920.12118, 2013.
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.
D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon,
J. I., Huttley, G. A., Kelley, S. T., Knights, D., Koenig, J. E., Ley, R.
E., Lozupone, C. A., Mcdonald, D., Muegge, B. D., Pirrung, M., Reeder, J.,
Sevinsky, J. R., Turnbaugh, P. J., Walters, W. A., Widmann, J., Yatsunenko,
T., Zaneveld, J., and Knight, R.: correspondEnce QIIME allows analysis of
high- throughput community sequencing data Intensity normalization improves
color calling in SOLiD sequencing, Nat. Publ. Gr., 7, 335–336,
https://doi.org/10.1038/nmeth.f.303, 2010.
Castelle, C. J., Wrighton, K. C., Thomas, B. C., Hug, L. A., Brown, C. T.,
Wilkins, M. J., Frischkorn, K. R., Tringe, S. G., Singh, A., Markillie, L.
M., Taylor, R. C., Williams, K. H., and Banfield, J. F.: Genomic Expansion of
Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic
Carbon Cycling, Curr. Biol., 25, 1–12, https://doi.org/10.1016/j.cub.2015.01.014, 2015.
Coolen, M. J. L., Muyzer, G., Rijpstra, W. I. C., Schouten, S., Volkman, J.
K., and Sinninghe Damsté, J. S.: Combined DNA and lipid analyses of
sediments reveal changes in Holocene haptophyte and diatom populations in an
Antarctic lake, Earth Planet. Sc. Lett., 223, 225–239,
https://doi.org/10.1016/j.epsl.2004.04.014, 2004a.
Coolen, M. J. L., Hopmans, E. C., Rijpstra, W. I. C., Muyzer, G., Schouten,
S., Volkman, J. K., and Sinninghe Damsté, J. S.: Evolution of the methane
cycle in Ace Lake (Antarctica) during the Holocene: response of methanogens
and methanotrophs to environmental change, Org. Geochem., 35,
1151–1167, https://doi.org/10.1016/j.orggeochem.2004.06.009, 2004b.
Cowie, G. L., Calvert, S. E., Pedersen, T. F., Schulz, H., and Von Rad, U.:
Organic content and preservational controls in surficial shelf and slope
sediments from the Arabian Sea (Pakistan margin), Mar. Geol., 161,
23–38, https://doi.org/10.1016/S0025-3227(99)00053-5, 1999.
De La Torre, J. R., Walker, C. B., Ingalls, A. E., Könneke, M., and
Stahl, D. A.: Cultivation of a thermophilic ammonia oxidizing archaeon
synthesizing crenarchaeol, Environ. Microbiol., 10, 810–818,
https://doi.org/10.1111/j.1462-2920.2007.01506.x, 2008.
Delong, E. F. and Pace, N. R.: Environmental Diversity of Bacteria and
Archaea, Soc. Syst. Biol., 50, 470–478, https://doi.org/10.1080/10635150118513,
2001.
DeLong, E. F., Ying Wu, K., Prézelin, B. B., and Jovine, R. V. M.: High
abundance of Archaea in Antarctic marine picoplankton, Nature, 371,
695–697, https://doi.org/10.1038/371695a0, 1994.
De Rosa, M. and Gambacorta, A.: The lipids of archaebacteria, Prog. Lipid Res., 27, 153–175, https://doi.org/10.1016/0163-7827(88)90011-2, 1988.
Durbin, A. M. and Teske, A.: Sediment-associated microdiversity within the
Marine Group I Crenarchaeota, Env. Microbiol. Rep., 2, 693–703,
https://doi.org/10.1111/j.1758-2229.2010.00163.x, 2010.
Edgar, R. C.: MUSCLE: Multiple sequence alignment with high accuracy and
high throughput, Nucleic Acids Res., 32, 1792–1797,
https://doi.org/10.1093/nar/gkh340, 2004.
Elling, F. J., Konneke, M., Lipp, J. S., Becker, K. W., Gagen, E. J., and
Hinrichs, K. U.: Effects of growth phase on the membrane lipid composition
of the thaumarchaeon Nitrosopumilus maritimus and their implications for
archaeal lipid distributions in the marine environment, Geochim. Cosmochim.
Ac., 141, 579–597, https://doi.org/10.1016/j.gca.2014.07.005, 2014.
Elling, F. J., Könneke, M., Mußmann, M., Greve, A., and Hinrichs,
K.-U.: Influence of temperature, pH, and salinity on membrane lipid
composition and TEX86 of marine planktonic thaumarchaeal isolates, Geochim.
Cosmochim. Ac., 171, 238–255, https://doi.org/10.1016/j.gca.2015.09.004, 2015.
Elling, F. J., Könneke, M., Nicol, G. W., Stieglmeier, M., Bayer, B.,
Spieck, E., de la Torre, J. R., Becker, K. W., Thomm, M., Prosser, J. I.,
Herndl, G. J., Schleper, C., and Hinrichs, K. U.: Chemotaxonomic
characterisation of the thaumarchaeal lipidome, Environ. Microbiol., 19,
2681–2700, https://doi.org/10.1111/1462-2920.13759, 2017.
Fillol, M., Auguet, J.-C., Casamayor, E. O., and Borrego, C. M.: Insights in
the ecology and evolutionary history of the Miscellaneous Crenarchaeotic
Group lineage, ISME J., 1–13, https://doi.org/10.1038/ismej.2015.143, 2015.
Francis, C. A., Roberts, K. J., Beman, J. M., Santoro, A. E., and Oakley, B. B.:
Ubiquity and diversity of ammonia-oxidizing archaea in water columns and
sediments of the ocean, P. Natl. Acad. Sci. USA, 102, 14683–14688, https://doi.org/10.1073/pnas.0506625102, 2005.
Harvey, H. R., Fallon, R. D., and Patton, J. S.: The effect of organic matter
and oxygen on the degradation of bacterial membrane lipids in marine
sediments, Geochim. Cosmochim. Ac., 50, 795–804,
https://doi.org/10.1016/0016-7037(86)90355-8, 1986.
Hopmans, E. C., Schouten, S., and Sinninghe, J. S.: The effect of improved
chromatography on GDGT-based palaeoproxies, Org. Geochem., 93, 1–6,
https://doi.org/10.1016/j.orggeochem.2015.12.006, 2016.
Inagaki, F., Suzuki, M., Takai, K., Oida, H., Sakamoto, T., Aoki, K.,
Nealson, K. H., and Horikoshi, K.: Microbial Communities Associated with
Geological Horizons in Coastal Subseafloor Sediments from the Sea of Okhotsk
Microbial Communities Associated with Geological Horizons in Coastal
Subseafloor Sediments from the Sea of Okhotsk, Appl. Environ. Microbiol.,
69, 7224–7235, https://doi.org/10.1128/AEM.69.12.7224-7235.2003, 2003.
Ingalls, A. E., Huguet, C., and Truxal, L. T.: Distribution of intact and
core membrane lipids of archaeal glycerol dialkyl glycerol tetraethers among
size-fractionated particulate organic matter in Hood Canal, Puget Sound,
Appl. Environ. Microbiol., 78, 1480–1490, https://doi.org/10.1128/AEM.07016-11,
2012.
Jahn, U., Summons, R., Sturt, H., Grosjean, E., and Huber, H.: Composition of
the lipids of Nanoarchaeum equitans and their origin from its host
Ignicoccus sp. strain KIN4/I, Arch. Microbiol., 182, 404–413,
https://doi.org/10.1007/s00203-004-0725-x, 2004.
Jorgenson, S. L., Hannisdal, B., Lanzén, A., Baumberger, T., Flesland,
K., Fonseca, R., Øvreås, L., Steen, I. H., Thorseth, I. H., Pedersen,
R. B., and Schleper, C.: Correlating microbial community pro fi les with
geochemical data in highly strati fi ed sediments from the Arctic Mid-Ocean
Ridge, P. Natl. Acad. Sci. USA, 109, E2846–E2855,
https://doi.org/10.1594/PANGAEA.786687, 2012.
Karner, M. B., DeLong, E. F., and Karl, D. M.: Archaeal dominance in the
mesopelagiczone of the Pacific Ocean, Nature, 409, 507–510,
https://doi.org/10.1038/35054051, 2001.
Klindworth, A., Pruesse, E., Schweer, T., Peplies, J., Quast, C., Horn, M.,
and Glockner, F. O.: Evaluation of general 16S ribosomal RNA gene PCR
primers for classical and next-generation sequencing-based diversity
studies, Nucleic Acids Res., 41, 1–11, https://doi.org/10.1093/nar/gks808, 2013.
Koga, Y. and Morii, H.: Biosynthesis of ether-type polar lipids in archaea
and evolutionary considerations, Microbiol. Mol. Biol. R., 71,
97–120, https://doi.org/10.1128/MMBR.00033-06, 2007.
Koho, K. A., Nierop, K. G. J., Moodley, L., Middelburg, J. J., Pozzato, L., Soetaert, K., van der Plicht, J., and Reichart, G.-J.:
Microbial bioavailability regulates organic matter preservation in marine sediments, Biogeosciences, 10, 1131–1141, https://doi.org/10.5194/bg-10-1131-2013, 2013.
Könneke, M., Bernhard, A. E., de la Torre, J. R., Walker, C. B.,
Waterbury, J. B., and Stahl, D. A.: Isolation of an autotrophic
ammonia-oxidizing marine archaeon, Nature, 437, 543–546,
https://doi.org/10.1038/nature03911, 2005.
Kraal, P., Slomp, C. P., Reed, D. C., Reichart, G.-J., and Poulton, S. W.: Sedimentary phosphorus and iron cycling in and below the
oxygen minimum zone of the northern Arabian Sea, Biogeosciences, 9, 2603–2624, https://doi.org/10.5194/bg-9-2603-2012, 2012.
Kubo, K., Lloyd, K. G., Biddle, J. F., Amann, R., Teske, A., and Knittel, K.:
Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and
widespread in marine sediments, ISME J., 6, 1949–1965,
https://doi.org/10.1038/ismej.2012.37, 2012.
Langworthy, T. A., Mayberry, W. R., and Smith, P. F.: Long-chain glycerol
diether and polyol dialkyl glycerol triether lipids of Sulfolobus
acidocaldarius, J. Bacteriol., 119, 106–116, 1974.
Lazar, C. S., Baker, B. J., Seitz, K., Hyde, A. S., Dick, G. J., Hinrichs,
K. U., and Teske, A. P.: Genomic evidence for distinct carbon substrate
preferences and ecological niches of Bathyarchaeota in estuarine sediments,
Environ. Microbiol., 18, 1200–1211, https://doi.org/10.1111/1462-2920.13142, 2016.
Learman, D. R., Henson, M. W., Thrash, J. C., Temperton, B., Brannock, P.
M., Santos, S. R., Mahon, A. R., and Halanych, K. M.: Biogeochemical and
microbial variation across 5500 km of Antarctic surface sediment implicates
organic matter as a driver of benthic community structure, Front. Microbiol., 7, 1–11, https://doi.org/10.3389/fmicb.2016.00284, 2016.
Lengger, S. K., Hopmans, E. C., Reichart, G.-J., Nierop, K. G. J., Sinninghe
Damsté, J. S., and Schouten, S.: Intact polar and core glycerol
dibiphytanyl glycerol tetraether lipids in the Arabian Sea oxygen minimum
zone. Part II: Selective preservation and degradation in sediments and
consequences for the TEX86, Geochim. Cosmochim. Ac., 98, 244–258,
https://doi.org/10.1016/j.gca.2012.05.003, 2012.
Lengger, S. K., Hopmans, E. C., Sinninghe Damsté, J. S., and Schouten,
S.: Impact of sedimentary degradation and deep water column production on
GDGT abundance and distribution in surface sediments in the Arabian Sea:
Implications for the TEX86 paleothermometer, Geochim. Cosmochim. Ac., 142,
386–399, https://doi.org/10.1016/j.gca.2014.07.013, 2014.
Lincoln, S. A., Wai, B., Eppley, J. M., Church, M. J., Summons, R. E., and
DeLong, E. F.: Planktonic Euryarchaeota are a significant source of archaeal
tetraether lipids in the ocean, P. Natl. Acad. Sci. USA, 111,
9858–9863, https://doi.org/10.1073/pnas.1409439111, 2014a.
Lincoln, S. A., Wai, B., Eppley, J. M., Curch, M. J., Summons, R. E., and
Delong, E. F.: Reply to Schouten et al.: Marine Group II planktonic
Euryarchaeota are significant contributors to tetraether lipids in the
ocean, P. Natl. Acad. Sci. USA, 111, 4286, https://doi.org/10.1073/pnas.1416736111,
2014b.
Lipp, J. S. and Hinrichs, K.-U.: Structural diversity and fate of intact
polar lipids in marine sediments, Geochim. Cosmochim. Ac., 73,
6816–6833, https://doi.org/10.1016/j.gca.2009.08.003, 2009.
Lipp, J. S., Morono, Y., Inagaki, F., and Hinrichs, K.-U.: Significant
contribution of Archaea to extant biomass in marine subsurface sediments,
Nature, 454, 991–994, https://doi.org/10.1038/nature07174, 2008.
Lloyd, K. G., Schreiber, L., Petersen, D. G., Kjeldsen, K. U., Lever, M. A.,
Steen, A. D., Stepanauskas, R., Richter, M., Kleindienst, S., Lenk, S.,
Schramm, A., and Jørgensen, B. B.: Predominant archaea in marine sediments
degrade detrital proteins, Nature, 496, 215–218,
https://doi.org/10.1038/nature12033, 2013.
Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar,
Buchner, A., Lai, T., Steppi, S., Jobb, G., Förster, W., Brettske, I.,
Gerber, S., Ginhart, A. W., Gross, O., Grumann, S., Hermann, S., Jost, R.,
König, A., Liss, T., Lüssmann, R., May, M., Nonhoff, B., Reichel,
B., Strehlow, R., Stamatakis, A., Stuckmann, N., Vilbig, A., Lenke, M.,
Ludwig, T., Bode, A., and Schleifer, K.-H.: ARB: a software environment for
sequence data, Nucleic Acids Res., 32, 1363–1371, https://doi.org/10.1093/nar/gkh293,
2004.
Massana, R., Castresana, J., Balague, V., Guillou, L., Romari, K.,
Groisillier, A., Valentin, K., and Pedros-Alio, C.: Phylogenetic and
Ecological Analysis of Novel Marine Stramenopiles, Appl. Environ.
Microbiol., 70, 3528–3534, https://doi.org/10.1128/AEM.70.6.3528-3534.2004, 2004.
Meador, T. B., Bowles, M., Lazar, C. S., Zhu, C., Teske, A., and Hinrichs,
K.-U.: The archaeal lipidome in estuarine sediment dominated by members of
the Miscellaneous Crenarchaeotal Group, Environ. Microbiol., 17,
2441–2458, https://doi.org/10.1111/1462-2920.12716, 2015.
Meng, J., Xu, J., Qin, D., He, Y., Xiao, X., and Wang, F.: Genetic and
functional properties of uncultivated MCG archaea assessed by metagenome and
gene expression analyses, ISME J., 8, 650–659,
https://doi.org/10.1038/ismej.2013.174, 2014.
Moore, E. K., Villanueva, L., Hopmans, E. C., Rijpstra, W. I. C., Mets, A.,
Dedysh, S. N., and Sinninghe Damsté, J. S.: Abundant trimethylornithine
lipids and specific gene sequences are indicative of planctomycete
importance at the oxic/anoxic interface in sphagnum-dominated northern
wetlands, Appl. Environ. Microbiol., 81, 6333–6344,
https://doi.org/10.1128/AEM.00324-15, 2015.
Nierop, K. G. J., Reichart, G., Veld, H., and Sinninghe Damsté, J. S.:
The influence of oxygen exposure time on the composition of macromolecular
organic matter as revealed by surface sediments on the Murray Ridge (Arabian
Sea), Geochim. Cosmochim. Ac., 206, 40–56, 2017.
Offre, P., Spang, A., and Schleper, C.: Archaea in Biogeochemical Cycles,
Annu. Rev. Microbiol., 437–457, https://doi.org/10.1146/annurev-micro-092412-155614,
2013.
Oni, O. E., Schmidt, F., Miyatake, T., Kasten, S., Witt, M., Hinrichs, K.-U.,
and Friedrich, M. W.: Microbial Communities and Organic Matter Composition
in Surface and Subsurface Sediments of the Helgoland Mud Area, North Sea,
Front. Microbiol., 6, 1–16, https://doi.org/10.3389/fmicb.2015.01290, 2015.
Park, S.-J., Park, B.-J., and Rhee, S.-K.: Comparative analysis of archaeal
16S rRNA and amoA genes to estimate the abundance and diversity of
ammonia-oxidizing archaea in marine sediments, Extremophiles, 12,
605–615, https://doi.org/10.1007/s00792-008-0165-7, 2008.
Pitcher, A., Rychlik, N., Hopmans, E. C., Spieck, E., Rijpstra, W. I. C.,
Ossebaar, J., Schouten, S., Wagner, M., and Sinninghe Damsté, J. S.:
Crenarchaeol dominates the membrane lipids of Candidatus Nitrososphaera
gargensis, a thermophilic group I.1b Archaeon, ISME J., 4, 542–552,
https://doi.org/10.1038/ismej.2009.138, 2010.
Pitcher, A., Villanueva, L., Hopmans, E. C., Schouten, S., Reichart, G.-J.,
and Sinninghe Damsté, J. S.: Niche segregation of ammonia-oxidizing
archaea and anammox bacteria in the Arabian Sea oxygen minimum zone, ISME
J., 5, 1896–904, https://doi.org/10.1038/ismej.2011.60, 2011.
Podar, M., Makarova, K. S., Graham, D. E., Wolf, Y. I., Koonin, E. V., and
Reysenbach, A.-L.: Insights into archaeal evolution and symbiosis from the
genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian
Pool, Yellowstone National Park, Biol. Direct, 8, 1–20,
https://doi.org/10.1186/1745-6150-8-9, 2013.
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P.,
Peplies, J., and Glockner, F. O.: The SILVA ribosomal RNA gene database
project: improved data processing and web-based tools, Nucleic Acids Res.,
41, D590–D596, https://doi.org/10.1093/nar/gks1219, 2013.
Rinke, C., Schwientek, P., Sczyrba, A., Ivanova, N. N., Anderson, I. J.,
Cheng, J.-F., Darling, A. E., Malfatti, S., Swan, B. K., Gies, E. A.,
Dodsworth, J. A., Hedlund, B. P., Tsiamis, G., Sievert, S. M., Liu, W.-T.,
Eisen, J. A., Hallam, S. J., Kyrpides, N. C., Stepanauskas, R., Rubin, E. M.,
Hugenholtz, P., and Woyke, T.: Insights into the phylogeny and coding
potential of microbial dark matter, Nature, 499, 431–437,
https://doi.org/10.1038/nature12352, 2013.
Rossel, P. E., Lipp, J. S., Fredricks, H. F., Arnds, J., Boetius, A.,
Elvert, M., and Hinrichs, K. U.: Intact polar lipids of anaerobic
methanotrophic archaea and associated bacteria, Org. Geochem., 39,
992–999, https://doi.org/10.1016/j.orggeochem.2008.02.021, 2008.
Saitou, N. and Nei, M.: The Neighbor-joining Method: A New Method for
Reconstructing Phylogenetic Trees, Mol. Biol. Evol., 4, 406–425,
1987.
Schleper, C., Jurgens, G., and Jonuscheit, M.: Genomic studies of
uncultivated archaea, Nat. Rev. Microbiol., 3, 479–488,
https://doi.org/10.1038/nrmicro1159, 2005.
Schouten, S., Hopmans, E. C., Baas, M., Boumann, H., Standfest, S.,
Könneke, M., Stahl, D. A., and Sinninghe Damsté, J. S.: Intact
membrane lipids of “Candidatus Nitrosopumilus maritimus,” a cultivated
representative of the cosmopolitan mesophilic group I crenarchaeota, Appl.
Environ. Microbiol., 74, 2433–2440, https://doi.org/10.1128/AEM.01709-07, 2008.
Schouten, S., Middelburg, J. J., Hopmans, E. C., and Sinninghe Damsté, J.
S.: Fossilization and degradation of intact polar lipids in deep subsurface
sediments: A theoretical approach, Geochim. Cosmochim. Ac., 74,
3806–3814, https://doi.org/10.1016/j.gca.2010.03.029, 2010.
Schouten, S., Pitcher, A., Hopmans, E. C., Villanueva, L., van Bleijswijk,
J., and Sinninghe Damsté, J. S.: Intact polar and core glycerol
dibiphytanyl glycerol tetraether lipids in the Arabian Sea oxygen minimum
zone: I. Selective preservation and degradation in the water column and
consequences for the TEX86, Geochim. Cosmochim. Ac., 98, 228–243,
https://doi.org/10.1016/j.gca.2012.05.002, 2012.
Schouten, S., Hopmans, E. C., and Sinninghe Damsté, J. S.: The organic
geochemistry of glycerol dialkyl glycerol tetraether lipids: A review, Org.
Geochem., 54, 19–61, https://doi.org/10.1016/j.orggeochem.2012.09.006, 2013.
Schouten, S., Villanueva, L., Hopmans, E. C., van der Meer, M. T. J., and
Sinninghe Damsté, J. S.: Are Marine Group II Euryarchaeota significant
contributors to tetraether lipids in the ocean?, P. Natl. Acad. Sci. USA, 111, E4285, https://doi.org/10.1073/pnas.1416176111, 2014.
Schubotz, F., Wakeham, S. G., Lipp, J. S., Fredricks, H. F., and Hinrichs,
K.-U.: Detection of microbial biomass by intact polar membrane lipid
analysis in the water column and surface sediments of the Black Sea,
Environ. Microbiol., 11, 2720–2734,
https://doi.org/10.1111/j.1462-2920.2009.01999.x, 2009.
Sinninghe Damsté, J. S., Schouten, S., Hopmans, E. C., van Duin, A. C.
T., and Geenevasen, J. A. J.: Crenarchaeol: the characteristic core glycerol
dibiphytanyl glycerol tetraether membrane lipid of cosmopolitan pelagic
crenarchaeota, J. Lipid Res., 43, 1641–1651,
https://doi.org/10.1194/jlr.M200148-JLR200, 2002.
Sinninghe Damsté, J. S., Rijpstra, W. I. C., Hopmans, E. C., Jung,
M.-Y., Kim, J.-G., Rhee, S.-K., Stieglmeier, M., and Schleper, C.: Intact
Polar and Core Glycerol Dibiphytanyl Glycerol Tetraether Lipids of Group
I.1a and I.1b Thaumarchaeota in Soil, Appl. Environ. Microbiol., 78,
6866–6874, https://doi.org/10.1128/AEM.01681-12, 2012.
Spang, A., Caceres, E. F., and Ettema, T. J. G.: Genomic exploration of the
diversity, ecology, and evolution of the archaeal domain of life, Science, 357, 1–10,
https://doi.org/10.1126/science.aaf3883, 2017.
Stetter, K. O., Fiala, G., Huber, G., Huber, R., and Segerer,
A.: Hyperthermophilic microorganisms, FEMS
Microbiol. Rev., 75, 117–124, https://doi.org/10.1111/j.1574-6968.1990.tb04089.x,
1990.
Sturt, H. F., Summons, R. E., Smith, K., Elvert, M., and Hinrichs, K.-U.:
Intact polar membrane lipids in prokaryotes and sediments deciphered by
high-performance liquid chromatography/electrospray ionization multistage
mass spectrometry – new biomarkers for biogeochemistry and microbial
ecology, Rapid Commun. Mass Spectrom., 18, 617–628,
https://doi.org/10.1002/rcm.1378, 2004.
Sugai, A., Sakuma, R., Fukuda, I., Kurosawa, N., and Itoh, Y. H.: The
Structure of the Core Polyol of the Ether Lipids from Sulfolobus
acidocaldarius, Lipids, 30, 339–344, https://doi.org/10.1007/BF02536042, 1995.
Teske, A.: Marine deep sediment microbial communities, in: The Prokaryotes, edited by: Rosenberg, E., DeLong, E. F., Lory, S., Stackebrandt, E., and Thompson, F., Springer, Berlin, Heidelberg, 2013.
Teske, A. and Sørensen, K. B.: Uncultured archaea in deep marine
subsurface sediments: have we caught them all?, ISME J., 2, 3–18,
https://doi.org/10.1038/ismej.2007.90, 2008.
Villanueva, L., Schouten, S., and Sinninghe Damsté, J. S.: Depth-related
distribution of a key gene of the tetraether lipid biosynthetic pathway in
marine Thaumarchaeota, Environ. Microbiol., 17, 3527–3539,
https://doi.org/10.1111/1462-2920.12508, 2014.
Villanueva, L., Schouten, S., and Sinninghe Damsté, J. S.: Phylogenomic
analysis of lipid biosynthetic genes of Archaea shed light on the “lipid
divide”, Environ. Microbiol., 19, 54–69, https://doi.org/10.1111/1462-2920.13361,
2017.
Waters, E., Hohn, M. J., Ahel, I., Graham, D. E., Adams, M. D., Barnstead,
M., Beeson, K. Y., Bibbs, L., Bolanos, R., Keller, M., Kretz, K., Lin, X.,
Mathur, E., Ni, J., Podar, M., Richardson, T., Sutton, G. G., Simon, M.,
Soll, D., Stetter, K. O., Short, J. M., and Noordewier, M.: The genome of
Nanoarchaeum equitans: insights into early archaeal evolution and derived
parasitism, P. Natl. Acad. Sci. USA, 100, 12984–12988,
https://doi.org/10.1073/pnas.1735403100, 2003.
Wörmer, L., Lipp, J. S., Schröder, J. M., and Hinrichs, K. U.:
Application of two new LC-ESI-MS methods for improved detection of intact
polar lipids (IPLs) in environmental samples, Org. Geochem., 59, 10–21,
https://doi.org/10.1016/j.orggeochem.2013.03.004, 2013.
Xie, S., Lipp, J. S., Wegener, G., Ferdelman, T. G., and Hinrichs, K.-U.:
Turnover of microbial lipids in the deep biosphere and growth of benthic
archaeal populations, P. Natl. Acad. Sci. USA, 110, 6010–6014,
https://doi.org/10.1073/pnas.1218569110, 2013.
Yakimov, M. M., Cono, V. La, Smedile, F., DeLuca, T. H., Juárez, S.,
Ciordia, S., Fernández, M., Albar, J. P., Ferrer, M., Golyshin, P. N.,
and Giuliano, L.: Contribution of crenarchaeal autotrophic ammonia oxidizers
to the dark primary production in Tyrrhenian deep waters (Central
Mediterranean Sea), ISME J., 5, 945–961, https://doi.org/10.1038/ismej.2010.197,
2011.
Yu, T., Wu, W., Liang, W., Lever, M. A., Hinrichs, K., and Wang, F.: Growth
of sedimentary Bathyarchaeota on lignin as an energy source, P. Natl.
Acad. Sci. USA, 1–6, https://doi.org/10.1073/pnas.1718854115, 2018.
Short summary
Benthic archaea comprise a significant part of the total prokaryotic biomass in marine sediments. Here, we compared the archaeal diversity and intact polar lipid (IPL) composition in both surface and subsurface sediments with different oxygen regimes in the Arabian Sea oxygen minimum zone. The oxygenated sediments were dominated by Thaumarchaeota and IPL-GDGT-0. The anoxic sediment contained highly diverse archaeal communities and high relative abundances of IPL-GDGT-1 to -4.
Benthic archaea comprise a significant part of the total prokaryotic biomass in marine...
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