Articles | Volume 18, issue 4
https://doi.org/10.5194/bg-18-1463-2021
© 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-18-1463-2021
© Author(s) 2021. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
01 Mar 2021
Research article |
| 01 Mar 2021
Novel hydrocarbon-utilizing soil mycobacteria synthesize unique mycocerosic acids at a Sicilian everlasting fire
Nadine T. Smit
CORRESPONDING AUTHOR
NIOZ Royal Netherlands Institute for Sea Research, Department of
Marine Microbiology and Biogeochemistry, P.O. Box 59, 1790 AB Den Burg, Texel, the Netherlands
Laura Villanueva
NIOZ Royal Netherlands Institute for Sea Research, Department of
Marine Microbiology and Biogeochemistry, P.O. Box 59, 1790 AB Den Burg, Texel, the Netherlands
Department of Earth Sciences, Faculty of Geosciences, Utrecht
University, P.O. Box 80.121, 3508 TA Utrecht, the Netherlands
Darci Rush
NIOZ Royal Netherlands Institute for Sea Research, Department of
Marine Microbiology and Biogeochemistry, P.O. Box 59, 1790 AB Den Burg, Texel, the Netherlands
Fausto Grassa
Istituto Nazionale di Geofisica e Vulcanologia, Sezione di Palermo,
Via Ugo La Malfa, 153, 90146, Palermo, Italy
Caitlyn R. Witkowski
NIOZ Royal Netherlands Institute for Sea Research, Department of
Marine Microbiology and Biogeochemistry, P.O. Box 59, 1790 AB Den Burg, Texel, the Netherlands
Mira Holzheimer
Stratingh Institute for Chemistry, University of Groningen, 9747 AG
Groningen, the Netherlands
Adriaan J. Minnaard
Stratingh Institute for Chemistry, University of Groningen, 9747 AG
Groningen, the Netherlands
Jaap S. Sinninghe Damsté
NIOZ Royal Netherlands Institute for Sea Research, Department of
Marine Microbiology and Biogeochemistry, P.O. Box 59, 1790 AB Den Burg, Texel, the Netherlands
Department of Earth Sciences, Faculty of Geosciences, Utrecht
University, P.O. Box 80.121, 3508 TA Utrecht, the Netherlands
Stefan Schouten
NIOZ Royal Netherlands Institute for Sea Research, Department of
Marine Microbiology and Biogeochemistry, P.O. Box 59, 1790 AB Den Burg, Texel, the Netherlands
Department of Earth Sciences, Faculty of Geosciences, Utrecht
University, P.O. Box 80.121, 3508 TA Utrecht, the Netherlands
Related authors
No articles found.
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 Discuss., https://doi.org/10.5194/bg-2023-29, https://doi.org/10.5194/bg-2023-29, 2023
Preprint under review for BG
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 from 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.
Kasia K. Śliwińska, Helen K. Coxall, David K. Hutchinson, Diederik Liebrand, Stefan Schouten, and Agatha M. de Boer
Clim. Past, 19, 123–140, https://doi.org/10.5194/cp-19-123-2023, https://doi.org/10.5194/cp-19-123-2023, 2023
Short summary
Short summary
We provide a sea surface temperature record from the Labrador Sea (ODP Site 647) based on organic geochemical proxies across the late Eocene and early Oligocene. Our study reveals heterogenic cooling of the Atlantic. The cooling of the North Atlantic is difficult to reconcile with the active Atlantic Meridional Overturning Circulation (AMOC). We discuss possible explanations like uncertainty in the data, paleogeography and atmospheric CO2 boundary conditions, model weaknesses, and AMOC activity.
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
Short summary
Short summary
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.
Carolien M. H. van der Weijst, Koen J. van der Laan, Francien Peterse, Gert-Jan Reichart, Francesca Sangiorgi, Stefan Schouten, Tjerk J. T. Veenstra, and Appy Sluijs
Clim. Past, 18, 1947–1962, https://doi.org/10.5194/cp-18-1947-2022, https://doi.org/10.5194/cp-18-1947-2022, 2022
Short summary
Short summary
The TEX86 proxy is often used by paleoceanographers to reconstruct past sea-surface temperatures. However, the origin of the TEX86 signal in marine sediments has been debated since the proxy was first proposed. In our paper, we show that TEX86 carries a mixed sea-surface and subsurface temperature signal and should be calibrated accordingly. Using our 15-million-year record, we subsequently show how a TEX86 subsurface temperature record can be used to inform us on past sea-surface temperatures.
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.
Alessandro Gattuso, Francesco Italiano, Giorgio Capasso, Antonino D'Alessandro, Fausto Grassa, Antonino Fabio Pisciotta, and Davide Romano
Nat. Hazards Earth Syst. Sci., 21, 3407–3419, https://doi.org/10.5194/nhess-21-3407-2021, https://doi.org/10.5194/nhess-21-3407-2021, 2021
Short summary
Short summary
Santa Barbara and Aragona are affected by mud volcanism with episodic hazardous paroxysm events. Two potentially hazardous paroxysm exposed surfaces of 0.12 and 0.20 km2 were elaborated with DSMs and with historical information on the paroxysms that occurred in the past. This paper, in the end, could be a useful tool for civil protection authorities in order to take appropriate risk mitigation measurements for exposed people and for monitoring activities.
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.
Cécile L. Blanchet, Rik Tjallingii, Anja M. Schleicher, Stefan Schouten, Martin Frank, and Achim Brauer
Clim. Past, 17, 1025–1050, https://doi.org/10.5194/cp-17-1025-2021, https://doi.org/10.5194/cp-17-1025-2021, 2021
Short summary
Short summary
The Mediterranean Sea turned repeatedly into an oxygen-deprived basin during the geological past, as evidenced by distinct sediment layers called sapropels. We use here records of the last sapropel S1 retrieved in front of the Nile River to explore the relationships between riverine input and seawater oxygenation. We decipher the seasonal cycle of fluvial input and seawater chemistry as well as the decisive influence of primary productivity on deoxygenation at millennial timescales.
Appy Sluijs, Joost Frieling, Gordon N. Inglis, Klaas G. J. Nierop, Francien Peterse, Francesca Sangiorgi, and Stefan Schouten
Clim. Past, 16, 2381–2400, https://doi.org/10.5194/cp-16-2381-2020, https://doi.org/10.5194/cp-16-2381-2020, 2020
Short summary
Short summary
We revisit 15-year-old reconstructions of sea surface temperatures in the Arctic Ocean for the late Paleocene and early Eocene epochs (∼ 57–53 million years ago) based on the distribution of fossil membrane lipids of archaea preserved in Arctic Ocean sediments. We find that improvements in the methods over the past 15 years do not lead to different results. However, data quality is now higher and potential biases better characterized. Results confirm remarkable Arctic warmth during this time.
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.
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
Short summary
Short summary
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.
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.
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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.
Julian D. Hartman, Francesca Sangiorgi, Ariadna Salabarnada, Francien Peterse, Alexander J. P. Houben, Stefan Schouten, Henk Brinkhuis, Carlota Escutia, and Peter K. Bijl
Clim. Past, 14, 1275–1297, https://doi.org/10.5194/cp-14-1275-2018, https://doi.org/10.5194/cp-14-1275-2018, 2018
Short summary
Short summary
We reconstructed sea surface temperatures for the Oligocene and Miocene periods (34–11 Ma) based on archaeal lipids from a site close to the Wilkes Land coast, Antarctica. Our record suggests generally warm to temperate surface waters: on average 17 °C. Based on the lithology, glacial and interglacial temperatures could be distinguished, showing an average 3 °C offset. The long-term temperature trend resembles the benthic δ18O stack, which may have implications for ice volume reconstructions.
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
Short summary
Short summary
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.
Marc A. Besseling, Ellen C. Hopmans, R. Christine Boschman, Jaap S. Sinninghe Damsté, and Laura Villanueva
Biogeosciences, 15, 4047–4064, https://doi.org/10.5194/bg-15-4047-2018, https://doi.org/10.5194/bg-15-4047-2018, 2018
Short summary
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.
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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.
Laura F. Korte, Geert-Jan A. Brummer, Michèlle van der Does, Catarina V. Guerreiro, Rick Hennekam, Johannes A. van Hateren, Dirk Jong, Chris I. Munday, Stefan Schouten, and Jan-Berend W. Stuut
Atmos. Chem. Phys., 17, 6023–6040, https://doi.org/10.5194/acp-17-6023-2017, https://doi.org/10.5194/acp-17-6023-2017, 2017
Short summary
Short summary
We collected Saharan dust at the Mauritanian coast as well as in the deep the North Atlantic Ocean, along a transect at 12 °N, using an array of moored sediment traps. We demonstrated that the lithogenic particles collected in the ocean are from the same source as dust collected on the African coast. With increasing distance from the source, lithogenic elements associated with clay minerals become more important relative to quartz which is settling out faster. Seasonality is prominent, but weak.
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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.
M. Rodrigo-Gámiz, S. W. Rampen, H. de Haas, M. Baas, S. Schouten, and J. S. Sinninghe Damsté
Biogeosciences, 12, 6573–6590, https://doi.org/10.5194/bg-12-6573-2015, https://doi.org/10.5194/bg-12-6573-2015, 2015
Short summary
Short summary
This research reports a test of the applicability of three organic-derived temperature proxies (UK'37, TEX86 and LDI) at high latitudes around Iceland. A range of samples including suspended particular material (SPM), trapped descending particles and surface sediments were collected to test the different proxies in the water column and the sediment.The combination of three independent SST organic proxies provided important information about seasonality and differences in habitat depth.
M. Sollai, E. C. Hopmans, S. Schouten, R. G. Keil, and J. S. Sinninghe Damsté
Biogeosciences, 12, 4725–4737, https://doi.org/10.5194/bg-12-4725-2015, https://doi.org/10.5194/bg-12-4725-2015, 2015
Short summary
Short summary
The distribution of Thaumarchaeota and anammox bacteria in the water column of the eastern tropical North Pacific (ETNP) oxygen-deficient zone (ODZ) was investigated by collecting suspended particulate matter (SPM) and analyzing it for the content of specific intact polar lipids (IPLs) produced by the two microbial groups. We found a clear niche segregation in the distribution of the two groups in the coastal waters of the ETNP but a partial overlap of their niches in the open-water setting.
C. Bottini, E. Erba, D. Tiraboschi, H. C. Jenkyns, S. Schouten, and J. S. Sinninghe Damsté
Clim. Past, 11, 383–402, https://doi.org/10.5194/cp-11-383-2015, https://doi.org/10.5194/cp-11-383-2015, 2015
A. de Kluijver, P. L. Schoon, J. A. Downing, S. Schouten, and J. J. Middelburg
Biogeosciences, 11, 6265–6276, https://doi.org/10.5194/bg-11-6265-2014, https://doi.org/10.5194/bg-11-6265-2014, 2014
A. Sluijs, L. van Roij, G. J. Harrington, S. Schouten, J. A. Sessa, L. J. LeVay, G.-J. Reichart, and C. P. Slomp
Clim. Past, 10, 1421–1439, https://doi.org/10.5194/cp-10-1421-2014, https://doi.org/10.5194/cp-10-1421-2014, 2014
S. K. Lengger, Y. A. Lipsewers, H. de Haas, J. S. Sinninghe Damsté, and S. Schouten
Biogeosciences, 11, 201–216, https://doi.org/10.5194/bg-11-201-2014, https://doi.org/10.5194/bg-11-201-2014, 2014
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
Related subject area
Biogeochemistry: Organic Biogeochemistry
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
Reviews and syntheses: Heterotrophic fixation of inorganic carbon – significant but invisible flux in environmental carbon cycling
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
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
Spatiotemporal transformation of dissolved organic matter along an alpine stream flow path on the Qinghai–Tibet Plateau: importance of source and permafrost degradation
A quest for the biological sources of long chain alkyl diols in the western tropical North Atlantic Ocean
Long-chain diols in rivers: distribution and potential biological sources
Leaf wax n-alkanes in modern plants and topsoils from eastern Georgia (Caucasus) – implications for reconstructing regional paleovegetation
The role of diatom resting spores in pelagic–benthic coupling in the Southern Ocean
Calcium content and high calcium adaptation of plants in karst areas of southwestern Hunan, China
Substrate potential of last interglacial to Holocene permafrost organic matter for future microbial greenhouse gas production
Variation pattern of particulate organic carbon and nitrogen in oceans and inland waters
C5 glycolipids of heterocystous cyanobacteria track symbiont abundance in the diatom Hemiaulus hauckii across the tropical North Atlantic
Molecular fingerprinting of particulate organic matter as a new tool for its source apportionment: changes along a headwater drainage in coarse, medium and fine particles as a function of rainfalls
Variations and determinants of carbon content in plants: a global synthesis
The Holocene sedimentary record of cyanobacterial glycolipids in the Baltic Sea: an evaluation of their application as tracers of past nitrogen fixation
Technical note: An inverse method to relate organic carbon reactivity to isotope composition from serial oxidation
A mechanistic model of an upper bound on oceanic carbon export as a function of mixed layer depth and temperature
New molecular evidence for surface and sub-surface soil erosion controls on the composition of stream DOM during storm events
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.
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.
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.
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.
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.
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.
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.
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).
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.
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.
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.
Alexander Braun, Marina Spona-Friedl, Maria Avramov, Martin Elsner, Federico Baltar, Thomas Reinthaler, Gerhard J. Herndl, and Christian Griebler
Biogeosciences, 18, 3689–3700, https://doi.org/10.5194/bg-18-3689-2021, https://doi.org/10.5194/bg-18-3689-2021, 2021
Short summary
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Yinghui Wang, Robert G. M. Spencer, David C. Podgorski, Anne M. Kellerman, Harunur Rashid, Phoebe Zito, Wenjie Xiao, Dandan Wei, Yuanhe Yang, and Yunping Xu
Biogeosciences, 15, 6637–6648, https://doi.org/10.5194/bg-15-6637-2018, https://doi.org/10.5194/bg-15-6637-2018, 2018
Short summary
Short summary
With global warming, thawing of permafrost releases dissolved organic matter (DOM) into streams. By analyzing DOM along an alpine stream on the Qinghai–Tibet Plateau, we found DOM was mainly from the active layer, but with deepening of the active layer, the contribution of the deep permafrost layer increased, causing a change in the chemical composition of DOM. From the head- to downstream, DOM is undergoing rapid degradation, but some components are persistent and can be transported downstream.
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
Short summary
Short summary
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
Short summary
Short summary
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.
Marcel Bliedtner, Imke K. Schäfer, Roland Zech, and Hans von Suchodoletz
Biogeosciences, 15, 3927–3936, https://doi.org/10.5194/bg-15-3927-2018, https://doi.org/10.5194/bg-15-3927-2018, 2018
Short summary
Short summary
In this study, we systematically analyze leaf wax derived n-alkane patterns in eastern Georgia to test their potential for paleoenvironmental reconstructions in the semi-humid to semi-arid central southern Caucasus region. We investigated the influence of vegetation types on the leaf wax signal in modern plants and topsoil material. Our results show distinct and systematic differences in the n-alkane patterns between vegetation types and prove their potential for vegetation reconstructions.
Mathieu Rembauville, Stéphane Blain, Clara Manno, Geraint Tarling, Anu Thompson, George Wolff, and Ian Salter
Biogeosciences, 15, 3071–3084, https://doi.org/10.5194/bg-15-3071-2018, https://doi.org/10.5194/bg-15-3071-2018, 2018
Short summary
Short summary
Sinking phytoplankton from the surface ocean provide the principal energy source to deep-ocean ecosystems. Our aim was to understand how different phytoplankton communities impact the chemical nature of this sinking material. We show certain types of phytoplankton can preferentially export energy-rich storage compounds to the seafloor. Any climate-driven effects on phytoplankton community structure could thus impact remote deep-ocean ecosystems thousands of kilometres beneath the surface.
Xiaocong Wei, Xiangwen Deng, Wenhua Xiang, Pifeng Lei, Shuai Ouyang, Hongfang Wen, and Liang Chen
Biogeosciences, 15, 2991–3002, https://doi.org/10.5194/bg-15-2991-2018, https://doi.org/10.5194/bg-15-2991-2018, 2018
Short summary
Short summary
Karst is a kind of typical calcium-rich environment, which is widely distributed. We measured the Ca2+ content of 41 plant species, as well as soil total Ca2+ and exchange Ca2+. We found out that different plants have different ways to high Ca2+ adaptation. According to the different high Ca2+ adaptation of the 17 dominant species, we divided them into 3 categories: Ca-indifferent plants, high-Ca plants and low-Ca plants. Our results can provide a theoretical basis for vegetation restoration.
Janina G. Stapel, Georg Schwamborn, Lutz Schirrmeister, Brian Horsfield, and Kai Mangelsdorf
Biogeosciences, 15, 1969–1985, https://doi.org/10.5194/bg-15-1969-2018, https://doi.org/10.5194/bg-15-1969-2018, 2018
Short summary
Short summary
Climate warming in the Arctic results in thawing of permafrost deposits. This promotes the accessibility of freeze-locked old organic matter (OM) accumulated during the past. Characterizing OM of different depositional ages, we were able to show that OM from last glacial Yedoma deposits possess the highest potential to provide organic substrates such as acetate for microbial greenhouse gas production and therefore to accelerate the carbon–climate feedback cycle during ongoing global warming.
Changchun Huang, Quanliang Jiang, Ling Yao, Hao Yang, Chen Lin, Tao Huang, A-Xing Zhu, and Yimin Zhang
Biogeosciences, 15, 1827–1841, https://doi.org/10.5194/bg-15-1827-2018, https://doi.org/10.5194/bg-15-1827-2018, 2018
Short summary
Short summary
The latitudinal dependency of POC / PON in ocean and inland water is significant, regulated by trophic state and climate, etc. factors. POC / PON significantly increased from coastal water (6.89 ± 2.38) to open ocean (7.59 ± 4.22) with the increasing rate of 0.0024 / km. The re-examination of the global relationship between, and variations in, POC and PON could be important for the global and regional coupling between the carbon and nitrogen cycles in the ocean and freshwater.
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
Short summary
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.
Laurent Jeanneau, Richard Rowland, and Shreeram Inamdar
Biogeosciences, 15, 973–985, https://doi.org/10.5194/bg-15-973-2018, https://doi.org/10.5194/bg-15-973-2018, 2018
Short summary
Short summary
The source of particulate organic matter in headwaters during storm events remains an open question. We use the molecular composition of organic matter sampled during four spring–summer storms and compare it to potential sources. We identify litter, streambed and vicinal soils as the main sources of particulate organic matter. Their proportions depend on (i) the size of the catchment and (ii) the rain event.
Suhui Ma, Feng He, Di Tian, Dongting Zou, Zhengbing Yan, Yulong Yang, Tiancheng Zhou, Kaiyue Huang, Haihua Shen, and Jingyun Fang
Biogeosciences, 15, 693–702, https://doi.org/10.5194/bg-15-693-2018, https://doi.org/10.5194/bg-15-693-2018, 2018
Short summary
Short summary
Plant carbon (C) content is critical to the assessment of the global C cycle. Our results showed that the global average C contents in organs were significantly lower than a canonical value of 50 %. Plant C content tended to decrease with increasing latitude, and life form explained more variation than climate. Our findings suggest that specific C content values of different organs and life forms should be incorporated into the estimations of regional and global vegetation biomass C stocks.
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
Short summary
Short summary
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.
Jordon D. Hemingway, Daniel H. Rothman, Sarah Z. Rosengard, and Valier V. Galy
Biogeosciences, 14, 5099–5114, https://doi.org/10.5194/bg-14-5099-2017, https://doi.org/10.5194/bg-14-5099-2017, 2017
Short summary
Short summary
The balance between organic matter (OM) fixation and decay is a major control on atmospheric CO2 concentrations. Understanding the environmental, chemical, and physical mechanisms that control the distribution of OM decay rates is therefore critical for constraining the global carbon cycle. In this manuscript, we derive a method to relate OM reactivity to its isotope composition using a kinetic model and provide a novel framework to discern the controls on OM decay rates.
Zuchuan Li and Nicolas Cassar
Biogeosciences, 14, 5015–5027, https://doi.org/10.5194/bg-14-5015-2017, https://doi.org/10.5194/bg-14-5015-2017, 2017
Marie Denis, Laurent Jeanneau, Patrice Petitjean, Anaëlle Murzeau, Marine Liotaud, Louison Yonnet, and Gérard Gruau
Biogeosciences, 14, 5039–5051, https://doi.org/10.5194/bg-14-5039-2017, https://doi.org/10.5194/bg-14-5039-2017, 2017
Short summary
Short summary
The results of this study highlight the changes of DOM composition in soil solutions and surface runoff, probably controlled by water-table dynamics and pre-event hydrological conditions. These changes should be taken into account for a better understanding of micropollutant mobility. Moreover, this work has implications for modeling DOM export in headwater catchments, as many studies assume that DOM transfer during storm events consists of the flushing of pre-existing soil solution DOM.
Cited articles
Abdala Asbun, A., Besseling, M. A., Balzano, S., van Bleijswijk, J. D. L.,
Witte, H. J., Villanueva, L., and Engelmann, J. C.: Cascabel: A Scalable and Versatile Amplicon Sequence Data Analysis Pipeline Delivering Reproducible and Documented Results, Frontiers in Genetics, 11, 1329,
https://doi.org/10.3389/fgene.2020.489357, 2020.
Ahmed, M., Schouten, S., Baas, M., and De Leeuw, J.: Bound lipids in
kerogens from the Monterey Formation, Naples Beach, California, The Monterey
Formation: From Rock to Molecules, Columbia University Press, New York,
189–205, 2001.
Alugupalli, S., Sikka, M. K., Larsson, L., and White, D. C.: Gas
chromatography–mass spectrometry methods for the analysis of mycocerosic
acids present in Mycobacterium tuberculosis, J. Microbiol. Meth., 31, 143–150, 1998.
Andrews, S.: FastQC: a quality control tool for high throughput sequence
data, available at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc (last access: 5 August 2018), 2010.
Bale, N. J., Villanueva, L., Hopmans, E. C., Schouten, S., and Sinninghe Damsté, J. S.: Different seasonality of pelagic and benthic Thaumarchaeota in the North Sea, Biogeosciences, 10, 7195–7206, https://doi.org/10.5194/bg-10-7195-2013, 2013.
Balesdent, J., Mariotti, A., and Guillet, B.: Natural 13C abundance as
a tracer for studies of soil organic matter dynamics, Soil Biol. Biochem., 19, 25–30, 1987.
Bardgett, R. D. and van der Putten, W. H.: Belowground biodiversity and
ecosystem functioning, Nature, 515, 505–511, 2014.
Basilone, L.: Litostratigrafia della Sicilia, Dipartimento di scienze della
terra e del mare, Università degli studi, Arti Grafiche Palermitane s.r.l, Palermo, Italy, ISBN: 978-88-97559-09-2, 2012.
Berndmeyer, C., Thiel, V., Schmale, O., and Blumenberg, M.: Biomarkers for
aerobic methanotrophy in the water column of the stratified Gotland Deep
(Baltic Sea), Org. Geochem., 55, 103–111, 2013.
Besseling, M. A., Hopmans, E. C., Boschman, R. C., Sinninghe Damsté, J. S., and Villanueva, L.: Benthic archaea as potential sources of tetraether membrane lipids in sediments across an oxygen minimum zone, Biogeosciences, 15, 4047–4064, https://doi.org/10.5194/bg-15-4047-2018, 2018.
Birgel, D. and Peckmann, J.: Aerobic methanotrophy at ancient marine
methane seeps: a synthesis, Org. Geochem., 39, 1659–1667, 2008.
Blumenberg, M., Seifert, R., and Michaelis, W.: Aerobic methanotrophy in the
oxic–anoxic transition zone of the Black Sea water column, Org. Geochem., 38, 84–91, 2007.
Bodelier, P. L., Gillisen, M.-J. B., Hordijk, K., Sinninghe Damsté, J.
S., Rijpstra, W. I. C., Geenevasen, J. A., and Dunfield, P. F.: A reanalysis
of phospholipid fatty acids as ecological biomarkers for methanotrophic
bacteria, The ISME journal, 3, 606–617, 2009.
Bouam, A., Armstrong, N., Levasseur, A., and Drancourt, M.: Mycobacterium
terramassiliense, Mycobacterium rhizamassiliense and Mycobacterium
numidiamassiliense sp. nov., three new Mycobacterium simiae complex species
cultured from plant roots, Scientific Reports, 8, 1–13, 2018.
Bowman, J.: The methanotrophs – the families Methylococcaceae and
Methylocystaceae, The Prokaryotes, 5, 266–289, 2006.
Bowman, J. P., Sly, L. I., Nichols, P. D., and Hayward, A.: Revised taxonomy
of the methanotrophs: description of Methylobacter gen. nov., emendation of
Methylococcus, validation of Methylosinus and Methylocystis species, and a
proposal that the family Methylococcaceae includes only the group I
methanotrophs, Int. J. Syst. Evol. Micr., 43, 735–753, 1993.
Brennan, P. J.: Structure, function, and biogenesis of the cell wall of
Mycobacterium tuberculosis, Tuberculosis, 83, 91–97, 2003.
Brennan, P. J. and Nikaido, H.: The envelope of mycobacteria, Annu. Rev. Biochem., 64, 29–63, 1995.
Bull, I. D., Parekh, N. R., Hall, G. H., Ineson, P., and Evershed, R. P.:
Detection and classification of atmospheric methane oxidizing bacteria in
soil, Nature, 405, 175–1778, 2000.
Camacho-Ibar, V. F., Aveytua-Alcázar, L., and Carriquiry, J. D.: Fatty acid reactivities in sediment cores from the northern Gulf of California, Org. Geochem., 34, 425–439, 2003.
Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Huntley, J.,
Fierer, N., Owens, S. M., Betley, J., Fraser, L., and Bauer, M.:
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and
MiSeq platforms, The ISME journal, 6, 1621–1624, 2012.
Chou, S., Chedore, P., Haddad, A., Paul, N., and Kasatiya, S.: Direct
identification of Mycobacterium species in Bactec 7H12B medium by gas-liquid
chromatography, J. Clin. Microbiol., 34, 1317–1320, 1996.
Chou, S., Chedore, P., and Kasatiya, S.: Use of gas chromatographic fatty
acid and mycolic acid cleavage product determination to differentiate among
Mycobacterium genavense, Mycobacterium fortuitum, Mycobacterium simiae, and
Mycobacterium tuberculosis, J. Clin. Microbiol., 36, 577–579, 1998.
Christie, W. W.: Gas chromatography-mass spectrometry methods for structural
analysis of fatty acids, Lipids, 33, 343–353, 1998.
Coleman, N. V., Yau, S., Wilson, N. L., Nolan, L. M., Migocki, M. D., Ly, M.
a., Crossett, B., and Holmes, A. J.: Untangling the multiple monooxygenases
of Mycobacterium chubuense strain NBB4, a versatile hydrocarbon degrader,
Env. Microbiol. Rep., 3, 297–307, 2011.
Coleman, N. V., Le, N. B., Ly, M. A., Ogawa, H. E., Mc Carl, V., Wilson, N.
L., and Holmes, A. J.: Hydrocarbon monooxygenase in Mycobacterium:
recombinant expression of a member of the ammonia monooxygenase superfamily,
The ISME journal, 6, 171–182, 2012.
Crossman, Z., Ineson, P., and Evershed, R.: The use of 13C labelling of bacterial lipids in the characterisation of ambient methane-oxidising bacteria in soils, Org. Geochem., 36, 769–778, 2005.
Daffé, M. and Laneelle, M.: Distribution of phthiocerol diester,
phenolic mycosides and related compounds in mycobacteria, Microbiology, 134,
2049–2055, 1988.
Daffé, M., Quémard, A., and Marrakchi, H.: Mycolic Acids: From Chemistry to Biology, in: Biogenesis of Fatty Acids, Lipids and Membranes, Springer International Publishing, 181–216, https://doi.org/10.1007/978-3-319-50430-8_18, 2019.
Davis, J., Chase, H., and Raymond, R.: Mycobacterium paraffinicum n. sp., a
bacterium isolated from soil, Appl. Microbiol., 4, 310–315, 1956.
Davis, J., Raymond, R., and Stanley, J.: Areal contrasts in the abundance of
hydrocarbon oxidizing microbes in soils, Appl. Microbiol., 7, 156–165, 1959.
Dedysh, S. N., Belova, S. E., Bodelier, P. L., Smirnova, K. V., Khmelenina,
V. N., Chidthaisong, A., Trotsenko, Y. A., Liesack, W., and Dunfield, P. F.:
Methylocystis heyeri sp. nov., a novel type II methanotrophic bacterium
possessing “signature” fatty acids of type I methanotrophs, Int. J. Syst. Evol. Micr., 57, 472–479, 2007.
Delgado-Baquerizo, M., Oliverio, A. M., Brewer, T. E.,
Benavent-González, A., Eldridge, D. J., Bardgett, R. D., Maestre, F. T.,
Singh, B. K., and Fierer, N.: A global atlas of the dominant bacteria found
in soil, Science, 359, 320–325, 2018.
Donoghue, H., Taylor, G., Stewart, G., Lee, O., Wu, H., Besra, G., and
Minnikin, D.: Positive diagnosis of ancient leprosy and tuberculosis using
ancient DNA and lipid biomarkers, Diversity, 9, 46, https://doi.org/10.3390/d9040046, 2017.
Dworkin, M. and Foster, J.: Experiments with some microorganisms which
utilize ethane and hydrogen, J. Bacteriol., 75, 592–603, 1958.
Edgar, R. C.: MUSCLE: multiple sequence alignment with high accuracy and
high throughput, Nucleic Acids Res., 32, 1792–1797, 2004.
Edgar, R. C.: Search and clustering orders of magnitude faster than BLAST,
Bioinformatics, 26, 2460–2461, 2010.
Etiope, G., Caracausi, A., Favara, R., Italiano, F., and Baciu, C.: Methane
emission from the mud volcanoes of Sicily (Italy), Geophys. Res. Lett., 29, 56-51–56-54, 2002.
Etiope, G., Martinelli, G., Caracausi, A., and Italiano, F.: Methane seeps
and mud volcanoes in Italy: gas origin, fractionation and emission to the
atmosphere, Geophys. Res. Lett., 34, L14303, https://doi.org/10.1029/2007GL030341, 2007.
Falkinham, J. O.: The biology of environmental mycobacteria, Env. Microbiol. Rep., 1, 477–487, 2009.
Falkinham, J. O.: Environmental sources of nontuberculous mycobacteria,
Clin. Chest Med., 36, 35–41, 2015.
Farrimond, P., Griffiths, T., and Evdokiadis, E.: Hopanoic acids in Mesozoic
sedimentary rocks: their origin and relationship with hopanes, Org.
Geochem., 33, 965–977, 2002.
Fernandes, N. D. and Kolattukudy, P. E.: Methylmalonyl coenzyme A
selectivity of cloned and expressed acyltransferase and beta-ketoacyl
synthase domains of mycocerosic acid synthase from Mycobacterium bovis BCG,
J. Bacteriol., 179, 7538–7543, 1997.
Fierer, N., Leff, J. W., Adams, B. J., Nielsen, U. N., Bates, S. T., Lauber,
C. L., Owens, S., Gilbert, J. A., Wall, D. H., and Caporaso, J. G.:
Cross-biome metagenomic analyses of soil microbial communities and their
functional attributes, P. Natl. Acad. Sci. USA, 109, 21390–21395, 2012.
Francis, G. W.: Alkylthiolation for the determination of double-bond
position in unsaturated fatty acid esters, Chem. Phys. Lipids, 29, 369–374, 1981.
Frostegård, Å., Tunlid, A., and Bååth, E.: Use and misuse of
PLFA measurements in soils, Soil Biol. Biochem., 43, 1621–1625, 2011.
Gago, G., Diacovich, L., Parabolize, A., Tsai, S.-C., and Gramajo, H.: Fatty
acid biosynthesis in actinomycetes, FEMS Microbiol. Rev., 35, 475–497, 2011.
Grassa, F., Capasso, G., Favara, R., Inguaggiato, S., Faber, E., and
Valenza, M.: Molecular and isotopic composition of free hydrocarbon gases
from Sicily, Italy, Geophys. Res. Lett., 31, L06607, https://doi.org/10.1029/2003GL019362, 2004.
Hamieh, A., Tayyar, R., Tabaja, H., EL Zein, S., Bou Khalil, P., Kara, N.,
Kanafani, Z. A., Kanj, N., Bou Akl, I., and Araj, G.: Emergence of
Mycobacterium simiae: A retrospective study from a tertiary care center in
Lebanon, PloS One, 13, e0195390, https://doi.org/10.1371/journal.pone.0195390, 2018.
Harvey, D. J.: Picolinyl esters for the structural determination of fatty
acids by GC/MS, Mol. Biotechnol., 10, 251–260, 1998.
Heap, B.: Mycobacterium simiae as a cause of intra-abdominal disease: a case
report, Tubercle, 70, 217–221, 1989.
Hennessee, C. T., Seo, J.-S., Alvarez, A. M., and Li, Q. X.: Polycyclic
aromatic hydrocarbon-degrading species isolated from Hawaiian soils:
Mycobacterium crocinum sp. nov., Mycobacterium pallens sp. nov.,
Mycobacterium rutilum sp. nov., Mycobacterium rufum sp. nov. and
Mycobacterium aromaticivorans sp. nov, Int. J. Syst. Evol. Micr., 59, 378–387, 2009.
Holzheimer, M., Reijneveld, J. F., Ramnarine, A. K., Misiakos, G., Young, D.
C., Ishikawa, E., Cheng, T.-Y., Yamasaki, S., Moody, D. B., Van Rhijn, I.
and Minnaard A. J.: Asymmetric Total Synthesis of Mycobacterial Diacyl
Trehaloses Demonstrates a Role for Lipid Structure in Immunogenicity, ACS
Chem. Biol., 7, 1835–1841, 2020.
Huang, Y., Bol, R., Harkness, D. D., Ineson, P., and Eglinton, G.:
Post-glacial variations in distributions, 13C and 14C contents of
aliphatic hydrocarbons and bulk organic matter in three types of British
acid upland soils, Org. Geochem., 24, 273–287, 1996.
Inglis, G. N., Naafs, B. D. A., Zheng, Y., Mc Clymont, E. L., Evershed, R.
P., and Pancost, R. D.: Distributions of geohopanoids in peat: Implications
for the use of hopanoid-based proxies in natural archives, Geochim. Cosmochim. Ac., 224, 249–261, 2018.
Inglis, G. N., Naafs, B. D. A., Zheng, Y., Schellekens, J., and Pancost, R.
D.: δ13C values of bacterial hopanoids and leaf waxes as
tracers for methanotrophy in peatlands, Geochim. Cosmochim. Ac., 260, 244–256, 2019.
Jackson, M., Stadthagen, G., and Gicquel, B.: Long-chain multiple
methyl-branched fatty acid-containing lipids of Mycobacterium tuberculosis:
biosynthesis, transport, regulation and biological activities, Tuberculosis,
87, 78–86, 2007.
Jahnke, L. L., Summons, R. E., Hope, J. M., and Des Marais, D. J.: Carbon
isotopic fractionation in lipids from methanotrophic bacteria II: The
effects of physiology and environmental parameters on the biosynthesis and
isotopic signatures of biomarkers, Geochim. Cosmochim. Ac., 63, 79–93, 1999.
Kweon, O., Kim, S.-J., Blom, J., Kim, S.-K., Kim, B.-S., Baek, D.-H., Park,
S. I., Sutherland, J. B., and Cerniglia, C. E.: Comparative functional
pan-genome analyses to build connections between genomic dynamics and
phenotypic evolution in polycyclic aromatic hydrocarbon metabolism in the
genus Mycobacterium,
BMC Evol. Biol., 15, 21, https://doi.org/10.1186/s12862-015-0302-8, 2015.
Lamb, D. C., Kelly, D. E., Manning, N. J., and Kelly, S. L.: A sterol
biosynthetic pathway in Mycobacterium, FEBS Lett., 437, 142–144, 1998.
Lee, O. Y., Wu, H. H., Donoghue, H. D., Spigelman, M., Greenblatt, C. L.,
Bull, I. D., Rothschild, B. M., Martin, L. D., Minnikin, D. E., and Besra,
G. S.: Mycobacterium tuberculosis complex lipid virulence factors preserved
in the 17,000-year-old skeleton of an extinct bison, Bison antiquus, PLoS ONE, 7, e41923, https://doi.org/10.1371/journal.pone.0041923, 2012.
Lévy-Frébault, V., Pangon, B., Buré, A., Katlama, C., Marche,
C., and David, H.: Mycobacterium simiae and Mycobacterium avium-M.
intracellulare mixed infection in acquired immune deficiency syndrome,
J. Clin. Microbiol., 25, 154–157, 1987.
Lough, A.: The chemistry and biochemistry of phytanic, pristanic and related
acids, Progress in the Chemistry of Fats and other Lipids, 14, 1–48, 1975.
Martin, K. E., Ozsvar, J., and Coleman, N. V.: SmoXYB1C1Z of Mycobacterium
sp. strain NBB4: a soluble methane monooxygenase (sMMO)-like enzyme, active
on C2 to C4 alkanes and alkenes, Appl. Environ. Microbiol., 80,
5801–5806, 2014.
Miller, C., Child, R., Hughes, J., Benscai, M., Der, J., Sims, R., and
Anderson, A.: Diversity of soil mycobacterium isolates from three sites that
degrade polycyclic aromatic hydrocarbons, J. Appl. Microbiol., 102, 1612–1624, 2007.
Minnikin, D., Dobson, G., Goodfellow, M., Magnusson, M., and Ridell, M.:
Distribution of some mycobacterial waxes based on the phthiocerol family,
Microbiology, 131, 1375–1381, 1985.
Minnikin, D., Besra, G., Bolton, R., Datta, A., Mallet, A., Sharif, A.,
Stanford, J., Ridell, M., and Magnusson, M.: Identification of the leprosy
bacillus and related mycobacteria by analysis of mycocerosate profiles, Ann. Soc. Belg. Med. Tr., 73, 25–34, 1993a.
Minnikin, D., Bolton, R., Hartmann, S., Besra, G., Jenkins, P., Mallet, A.,
Wilkins, E., Lawson, A., and Ridell, M.: An integrated procedure for the
direct detection of characteristic lipids in tuberculous patients, Ann. Soc. Belg. Med. Tr., 73, 13–24, 1993b.
Minnikin, D. E., Kremer, L., Dover, L. G., and Besra, G. S.: The
methyl-branched fortifications of Mycobacterium tuberculosis, Chem. Biol., 9, 545–553, 2002.
Nechaeva, N: Two species of methane oxidizing mycobacteria.
Mikrobiologiya, 18, 310–317, 1949 (English Translation: Associated
Technical Service, East Orange, NJ).
Nei, M. and Kumar, S.: Molecular evolution and phylogenetics, Oxford
University Press, ISBN: 0-19-513584-9, 2000.
Nichols, P. D., Guckert, J. B., and White, D. C.: Determination of
monosaturated fatty acid double-bond position and geometry for microbial
monocultures and complex consortia by capillary GC-MS of their dimethyl
disulphide adducts, J. Microbiol. Meth., 5, 49–55, 1986.
Nicoara, S. C., Minnikin, D. E., Lee, O. C., O'Sullivan, D. M., McNerney,
R., Pillinger, C. T., Wright, I. P., and Morgan, G. H.: Development and
optimization of a gas chromatography/mass spectrometry method for the
analysis of thermochemolytic degradation products of phthiocerol
dimycocerosate waxes found in Mycobacterium tuberculosis, Rapid
Commun. Mass Sp., 27, 2374–2382, 2013.
Ourisson, G., Albrecht, P., and Rohmer, M.: The hopanoids: palaeochemistry
and biochemistry of a group of natural products, Pure Appl. Chem., 51, 709–729, 1979.
Park, H., Lee, H., Ro, Y. T., and Kim, Y. M.: Identification and functional
characterization of a gene for the methanol: N, N′-dimethyl-4-nitrosoaniline oxidoreductase from Mycobacterium sp. strain JC1 (DSM 3803), Microbiology, 156, 463–471, 2010.
Park, S. W., Hwang, E. H., Park, H., Kim, J. A., Heo, J., Lee, K. H., Song,
T., Kim, E., Ro, Y. T., and Kim, S. W.: Growth of mycobacteria on carbon
monoxide and methanol, J. Bacteriol., 185, 142–147, 2003.
Peterse, F., Nicol, G. W., Schouten, S., and Damsté, J. S. S.: Influence
of soil pH on the abundance and distribution of core and intact polar
lipid-derived branched GDGTs in soil, Org. Geochem., 41, 1171–1175, 2010.
Podust, L. M., Poulos, T. L., and Waterman, M. R.: Crystal structure of
cytochrome P450 14α-sterol demethylase (CYP51) from Mycobacterium
tuberculosis in complex with azole inhibitors, P. Natl. Acad. Sci. USA, 98, 3068–3073, 2001.
Ran-Ressler, R. R., Lawrence, P., and Brenna, J. T.: Structural
characterization of saturated branched chain fatty acid methyl esters by
collisional dissociation of molecular ions generated by electron ionization,
J. Lipid Res., 53, 195–203, 2012.
Redman, J. E., Shaw, M. J., Mallet, A. I., Santos, A. L., Roberts, C. A.,
Gernaey, A. M., and Minnikin, D. E.: Mycocerosic acid biomarkers for the
diagnosis of tuberculosis in the Coimbra Skeletal Collection, Tuberculosis,
89, 267–277, 2009.
Reed, W. M. and Dugan, P. R.: Isolation and characterization of the
facultative methylotroph Mycobacterium ID-Y, Microbiology, 133, 1389–1395,
1987.
Řezanka, T. and Sigler, K.: Odd-numbered very-long-chain fatty acids
from the microbial, animal and plant kingdoms, Prog. Lipid Res., 48, 206–238, 2009.
Ries-Kautt, M. and Albrecht, P.: Hopane-derived triterpenoids in soils,
Chem. Geol., 76, 143–151, 1989.
Rohmer, M., Bouvier-Nave, P., and Ourisson, G.: Distribution of hopanoid
triterpenes in prokaryotes, Microbiology, 130, 1137–1150, 1984.
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. Microb., 74, 2433–2440, 2008.
Sinninghe Damsté, J. S., Rijpstra, W. I. C., Schouten, S., Fuerst, J.
A., Jetten, M. S., and Strous, M.: The occurrence of hopanoids in
planctomycetes: implications for the sedimentary biomarker record, Org.
Geochem., 35, 561–566, 2004.
Sinninghe Damsté, J. S., Rijpstra, W. I. C., Dedysh, S. N., Foesel, B.
U., and Villanueva, L.: Pheno-and genotyping of hopanoid production in
Acidobacteria, Front. Microbiol., 8, 968, https://doi.org/10.3389/fmicb.2017.00968, 2017.
Sinninghe Damsté, J. S., Rijpstra, W. I. C., Foesel, B. U., Huber, K.
J., Overmann, J., Nakagawa, S., Kim, J. J., Dunfield, P. F., Dedysh, S. N.,
and Villanueva, L.: An overview of the occurrence of ether-and ester-linked
iso-diabolic acid membrane lipids in microbial cultures of the
Acidobacteria: Implications for brGDGT paleoproxies for temperature and pH,
Org. Geochem., 124, 63–76, 2018.
Staccioli, G., McMillan, N., Meli, A., and Bartolini, G.: Chemical
characterisation of a 45-million-year bark from Geodetic Hills fossil
forest, Axel Heiberg Island, Canada, Wood Sci. Technol., 36, 419–427, 2002.
Talbot, H. M., Mc Clymont, E. L., Inglis, G. N., Evershed, R. P., and
Pancost, R. D.: Origin and preservation of bacteriohopanepolyol signatures
in Sphagnum peat from Bissendorfer Moor (Germany), Org. Geochem., 97, 95–110, 2016.
Tamura, K., Stecher, G., Peterson, D., Filipski, A., and Kumar, S.: MEGA6:
molecular evolutionary genetics analysis version 6.0, Mol. Biol. Evol., 30, 2725–2729, 2013.
Thiel, V., Blumenberg, M., Pape, T., Seifert, R., and Michaelis, W.:
Unexpected occurrence of hopanoids at gas seeps in the Black Sea, Org.
Geochem., 34, 81–87, 2003.
Tiedje, J. M., Asuming-Brempong, S., Nüsslein, K., Marsh, T. L., and
Flynn, S. J.: Opening the black box of soil microbial diversity, Appl. Soil Ecol., 13, 109–122, 1999.
Torkko, P., Suomalainen, S., Iivanainen, E., Suutari, M., Paulin, L.,
Rudbäck, E., Tortoli, E., Vincent, V., Mattila, R., and Katila, M.-L.:
Characterization of Mycobacterium bohemicum isolated from human, veterinary,
and environmental sources, J. Clin. Microbiol., 39, 207–211, 2001.
Torkko, P., Suomalainen, S., Iivanainen, E., Tortoli, E., Suutari, M.,
Seppänen, J., Paulin, L., and Katila, M.-L.: Mycobacterium palustre sp.
nov., a potentially pathogenic, slowly growing mycobacterium isolated from
clinical and veterinary specimens and from Finnish stream waters,
Int. J. Syst. Evol. Micr., 52, 1519–1525, 2002.
Torkko, P., Katila, M.-L., and Kontro, M.: Gas-chromatographic lipid
profiles in identification of currently known slowly growing environmental
mycobacteria, J. Med. Microbiol., 52, 315–323, 2003.
Tortoli, E.: Microbiological features and clinical relevance of new species
of the genus Mycobacterium, Clin. Microbiol. Rev., 27, 727–752, 2014.
Trincianti, E., Frixa, A., and Sartorio, D.: Palynology and stratigraphic
characterization of subsurface sedimentary successions in the Sicanian and
Imerese Domains–Central Western Sicily, Rev. Palaeobot. Palyno., 218, 48–66, 2015.
Valero-Guillén, P., Martín-Luengo, F., Larsson, L., Jimenez, J.,
Juhlin, I., and Portaels, F.: Fatty and mycolic acids of Mycobacterium
malmoense, J. Clin. Microbiol., 26, 153–154, 1988.
van Winden, J. F., Talbot, H. M., Kip, N., Reichart, G.-J., Pol, A.,
McNamara, N. P., Jetten, M. S., Op den Camp, H. J., and Sinninghe
Damsté, J. S.: Bacteriohopanepolyol signatures as markers for
methanotrophic bacteria in peat moss, Geochim. Cosmochim. Ac., 77, 52–61, 2012.
van Winden, J. F., Talbot, H. M., Reichart, G.-J., McNamara, N. P.,
Benthien, A., and Sinninghe Damsté, J. S.: Influence of temperature on
the δ13C values and distribution of methanotroph-related hopanoids in Sphagnum-dominated peat bogs, Geobiology, 18, 497–507,
https://doi.org/10.1111/gbi.12389, 2020.
Walsh, C. M., Gebert, M. J., Delgado-Baquerizo, M., Maestre, F., and Fierer,
N.: A global survey of mycobacterial diversity in soil, Appl. Environ. Microb., 85, e01180-19, https://doi.org/10.1128/AEM.01180-19, 2019.
Weijers, J. W., Panoto, E., van Bleijswijk, J., Schouten, S., Rijpstra, W.
I. C., Balk, M., Stams, A. J., and Damste, J. S. S.: Constraints on the
biological source(s) of the orphan branched tetraether membrane lipids,
Geomicrobiol. J., 26, 402–414, 2009.
Wenger, L. M., Davis, C. L., and Isaksen, G. H.: Multiple controls on
petroleum biodegradation and impact on oil quality, SPE Reserv. Eval. Eng., 5, 375–383, 2002.
World Health Organization: World health statistics 2019: monitoring health
for the SDGs, sustainable development goals, World Health Organization, 120 pp., ISBN: 9241565705, 2019.
Zhang, J., Kobert, K., Flouri, T., and Stamatakis, A.: PEAR: a fast and
accurate Illumina Paired-End reAd mergeR, Bioinformatics, 30, 614–620, 2013.
Zundel, M. and Rohmer, M.: Prokaryotic triterpenoids: 1. 3β-Methylhopanoids from Acetobacter species and Methylococcus capsulatus, Eur. J. Biochem., 150, 23–27, 1985.
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.
Soils from an everlasting fire (gas seep) in Sicily, Italy, reveal high relative abundances of...
Altmetrics
Final-revised paper
Preprint