Article
Multidisciplinary Sciences
Alexandra A. Phillips, Margot E. White, Michael Seidel, Fenfang Wu, Frank F. Pavia, Preston C. Kemeny, Audrey C. Ma, Lihini I. Aluwihare, Thorsten Dittmar, Alex L. Sessions
Summary: Marine dissolved organic matter (DOM) is a major reservoir that connects global carbon, nitrogen, and phosphorus cycles, and it is also the largest water column reservoir of organic sulfur. By analyzing the isotope ratios of different sources of dissolved organic sulfur (DOS), researchers found that DOS in the ocean mainly comes from phytoplankton-derived biomolecules rather than from sulfidic sediments. This study suggests that organic sulfur plays an important role in marine biogeochemistry beyond sulfate.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Environmental Sciences
Wanxuan Yao, Karin F. Kvale, Wolfgang Koeve, Angela Landolfi, Eric Achterberg, Erin M. Bertrand, Andreas Oschlies
Summary: This study used three biogeochemical models to investigate the changes in marine nitrogen cycle under a high CO2 emissions future scenario. The representation of iron had a significant impact on global nitrogen fixation, especially in the Eastern boundary upwelling zones, where bottom-up control of iron limitation played a key role in reducing export production with warming.
GLOBAL BIOGEOCHEMICAL CYCLES
(2022)
Article
Green & Sustainable Science & Technology
Mouna Dammak, Hajer Ben Hlima, Fatma Elleuch, Chantal Pichon, Philippe Michaud, Imen Fendri, Slim Abdelkafi
Summary: Tetraselmis sp. strain MD-01 has been studied for autotrophic lipids production with a two-stage process, showing potential for biodiesel production by effectively increasing lipid content in cells through the two-stage strategy.
Article
Environmental Sciences
Robinson W. Fulweiler
Summary: Nitrogen fixation is a crucial process that links the atmospheric nitrogen pool to the biosphere. Despite the prevailing belief that nitrogen fixation only occurs to meet nitrogen demands, recent research has shown that sediment nitrogen fixation can take place even in nitrogen-rich coastal environments. This challenges the traditional view of nitrogen fixation as solely a relief mechanism for nitrogen limitation. In this article, the author proposes that coastal sediments are actually ideal environments for nitrogen fixation and presents ideas on why this is the case. The goal is to encourage further research on the dynamics and composition of sediment nitrogen fixation.
GLOBAL BIOGEOCHEMICAL CYCLES
(2023)
Review
Microbiology
Shuai Wang, Yu Yang, Jiaojiao Jing
Summary: Nitrogen is a crucial component of cellular macromolecules and plays a significant role in primary production of terrestrial and oceanic ecosystems. While various marine microbes consume nitrogen, only a limited group can replenish it, leading to nitrogen deficiency in the ocean. Viruses contribute to marine nitrogen cycling through host cell lysis, expression of auxiliary metabolic genes, and serving as a reservoir of nitrogen element.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Amy E. Zimmerman, Justin C. Podowski, Gwendolyn E. Gallagher, Maureen L. Coleman, Jacob R. Waldbauer
Summary: Microbial growth is often limited by nitrogen availability, but how complex communities compete for and allocate this resource is not well understood. In this study, a new method was developed to track nitrogen substrates incorporation into microbial community proteomes, enabling quantification of protein turnover and N allocation to specific cellular functions. Application of this method to oligotrophic ocean surface water revealed taxa-specific substrate preferences and a subset of protein functions undergoing active biosynthesis. Prochlorococcus, a cyanobacterium, was found to be the most effective competitor for acquiring ammonium and urea and showed shifts in N allocation over the day/night cycle. This study highlights the importance of infrastructure and protein-turnover functions in the biosynthetic demand for N in Prochlorococcus and other microbial taxa, and provides insights into how nutrient stress affects metabolism in co-existing microbes.
NATURE MICROBIOLOGY
(2023)
Review
Microbiology
Kendra A. Turk-Kubo, Mary R. Gradoville, Shunyan Cheung, Francisco M. Cornejo-Castillo, Katie J. Harding, Michael Morando, Matthew Mills, Jonathan P. Zehr
Summary: This review paper provides a comprehensive understanding of the biology, ecology, and biogeography of marine non-cyanobacterial diazotrophs (NCDs) through the synthesis of multiple datasets. The authors discuss recent advances in studying the diversity, distribution, and ecophysiology of NCDs, as well as their significance to the nitrogen cycle in well-lit oxygenated euphotic waters.
FEMS MICROBIOLOGY REVIEWS
(2023)
Article
Geosciences, Multidisciplinary
Masafumi Saitoh, Manabu Nishizawa, Kazumi Ozaki, Masayuki Ikeda, Yuichiro Ueno, Ken Takai, Yukio Isozaki
Summary: The Capitanian stage is a peculiar stage characterized by marine anoxia and a large extinction. Previous studies have confirmed the occurrence of marine anoxia at least locally in the Capitanian, but the spatial extent and duration of anoxia in the superocean Panthalassa during this stage have been poorly understood. This study provides new insights into the global nitrogen cycle and redox conditions, showing that the nitrogen source was substantially enriched in δ15N via denitrification within subsurface oxygen-deficient zones. Numerical modeling further reveals that reducing water masses prevailed at intermediate water depths in the superocean, contributing to the shelf extinction.
PALEOCEANOGRAPHY AND PALEOCLIMATOLOGY
(2023)
Article
Geochemistry & Geophysics
Qing-Zeng Zhu, Marcus Elvert, Travis B. Meador, Kevin W. Becker, Verena B. Heuer, Kai-Uwe Hinrichs
Summary: Archaea play a crucial role in the global carbon cycle, with their lipids serving as important environmental indicators. This study found that the contributions of different sources to sedimentary lipids can be identified through isotopic analysis, highlighting the importance of in situ lipid production by sedimentary archaea. The significant differences in carbon isotopic values of BPcren and BP0 in samples near the Rhone River delta compared to a marine reference site suggest a substantial terrestrial soil contribution to these sediments, emphasizing the need for caution when using molecular proxies to determine riverine input.
GEOCHIMICA ET COSMOCHIMICA ACTA
(2021)
Article
Environmental Sciences
Paula Bonet-Melia, Jose Miguel Sandoval-Gil, Guillermo Samperio-Ramos, Manuel Vivanco-Bercovich, Sergio R. Canino-Herrera, Reginaldo Durazo, Victor F. Camacho-Ibar, Ana Alexandre
Summary: Marine heatwaves can have detrimental effects on seagrasses, but knowledge about the impacts on their ecosystem services remains scarce. This study found that surfgrasses have high nitrogen uptake rates and biomass, making them effective biofilters for wastewater. However, experimental warming resulted in a significant decline in their ability to incorporate and assimilate nitrogen.
MARINE POLLUTION BULLETIN
(2023)
Article
Ecology
Zoe R. van Kemenade, Laura Villanueva, Ellen C. Hopmans, Peter Kraal, Harry J. Witte, Jaap S. Sinninghe Damste, Darci Rush
Summary: Interpreting lipid biomarkers in sediment archives requires a good understanding of their application and limitations. It has been discovered that marine bacteria performing anaerobic ammonium oxidation (anammox) synthesize a stereoisomer of bacteriohopanetetrol (BHT-x), which can serve as a proxy for water column anoxia. In the water column of the Benguela upwelling system, high BHT-x abundances were found in the oxygen-deficient zone, along with high abundances of Ca. Scalindua genes and ladderane intact polar lipids (IPLs). However, BHT-x ratios were low in oxygenated offshore waters. The BHT-x ratio of >= 0.2 is a robust threshold for oxygen-depleted waters.
Article
Chemistry, Multidisciplinary
Katarzyna Wierzchowska, Bartlomiej Zieniuk, Dorota Nowak, Agata Fabiszewska
Summary: Microbial lipids are considered a sustainable alternative to traditional vegetable oils and have gained attention among researchers. This study investigated the impact of limiting inorganic phosphorus and nitrogen sources on cellular lipid biosynthesis in Y. lipolytica yeast, revealing a significant relationship between phosphorus concentration and lipid accumulation. Simultaneously limiting both phosphorus and nitrogen sources promoted lipid accumulation but hindered biomass growth, highlighting the importance of phosphorus as a factor in cultivating oleaginous microorganisms.
APPLIED SCIENCES-BASEL
(2021)
Article
Engineering, Environmental
Yafei Yang, Cancan Xiao, Qing Yu, Zhiqiang Zhao, Yaobin Zhang
Summary: The study confirmed the occurrence of a novel 'anammox' process in the absence of anammox bacteria, driven by NO-induced Fe(II) oxidation and NH-induced Fe(III) reduction (Feammox) in an anaerobic sludge system. The results showed that Fe(II) was anaerobically oxidized to Fe(III) with the addition of NO2-, leading to significant nitrogen removal. XRD and XPS analysis indicated the production of FeOOH from chemical Fe(II) oxidation with NO2-. Additionally, the isotope experiment confirmed the participation of induced Fe(II) oxidation in Feammox for nitrogen removal.
Article
Geosciences, Multidisciplinary
A. R. Fay, G. A. McKinley
Summary: While global ocean models provide consistent estimates of air-sea CO2 exchange, there is significant variation in regional estimates. By selecting models that align with observational data, the uncertainty of global mean flux can be reduced effectively.
GEOPHYSICAL RESEARCH LETTERS
(2021)
Article
Ecology
Edward B. Rastetter, Bonnie L. Kwiatkowski, David W. Kicklighter, Audrey Barker Plotkin, Helene Genet, Jesse B. Nippert, Kimberly O'Keefe, Steven S. Perakis, Stephen Porder, Sarah S. Roley, Roger W. Ruess, Jonathan R. Thompson, William R. Wieder, Kevin Wilcox, Ruth D. Yanai
Summary: In this study, the Multiple Element Limitation (MEL) model was used to examine the responses of 12 ecosystems to elevated CO2, warming, and changes in precipitation. The results showed that ecosystems responded synergistically to the combined effects of elevated CO2, warming, and decreased precipitation, while the response to the combined effects of elevated CO2, warming, and increased precipitation was additive. The study also analyzed the factors attributing to changes in ecosystem carbon based on nitrogen and phosphorus, and found that different ecosystems exhibit different C-nutrient interactions, which shape their carbon sequestration under simulated global change.
ECOLOGICAL APPLICATIONS
(2022)
Article
Geochemistry & Geophysics
Julie Lattaud, Sergio Balzano, Marcel T. J. van der Meer, Laura Villanueva, Ellen C. Hopmans, Jaap S. Sinninghe Damste, Stefan Schouten
Summary: Long-chain diols (LCDs) show significant seasonal variations in Lake Geneva, possibly produced by multiple producers with eustigmatophytes being the main contributors. LCDs have the potential to trace changes in lake water-column stratification, and the use of C-32 1,15-diol is validated as a proxy for freshwater input in marine sediments.
ORGANIC GEOCHEMISTRY
(2021)
Article
Geography, Physical
T. Fletcher, C. Eble, J. S. Sinninghe Damste, K. J. Brown, N. Rybczynski, J. Gosse, Z. Liu, A. Ballantyne
Summary: Research indicates that Arctic warming may lead to northward migration, changes in fire frequency, intensity, size, and season. During the Pliocene Epoch, there were boreal forests in the Canadian Arctic Archipelago, with frequent wildfires in warm and wet climates.
PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY
(2021)
Article
Microbiology
Nicole J. Bale, Su Ding, Ellen C. Hopmans, Milou G. I. Arts, Laura Villanueva, Christine Boschman, Andreas F. Haas, Stefan Schouten, Jaap S. Sinninghe Damste
Summary: Utilizing ultra-high-pressure liquid chromatography coupled with high-resolution mass spectrometry to conduct untargeted analysis of MS1 spectral data on environmental microbial communities is a valuable approach. By treating each mass spectrum as a component and clustering them based on similarity in abundance depth profiles, this rapid method can visualize component distributions and identify novel lipid biomarkers.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Su Ding, Nicole J. J. Bale, Ellen C. C. Hopmans, Laura Villanueva, Milou G. I. Arts, Stefan Schouten, Jaap Sinninghe S. S. Damste
Summary: By using ultra high-pressure liquid chromatography coupled with high-resolution tandem mass spectrometry (UHPLC-HRMS/MS), a comprehensive profiling of microbial lipids in the water column of a marine euxinic basin (Black Sea) was conducted. An information theory framework combined with molecular networking based on the similarity of the mass spectra of lipids allowed for the capture of lipidomic diversity and specificity in the environment, differentiation of microbial sources within a lipid group, and discovery of potential biomarkers for biogeochemical processes.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Diana X. Sahonero-Canavesi, Laura Villanueva, Nicole J. Bale, Jade Bosviel, Michel Koenen, Ellen C. Hopmans, Jaap S. Sinninghe Damste
Summary: This study reveals that the biosynthesis of membrane-spanning lipids in Thermotogales bacteria is influenced by growth phase rather than temperature. The findings suggest that changes in core lipid levels play a crucial role in the biosynthesis of these lipids.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Geography, Physical
Jaap S. Sinninghe Damste, Yuki Weber, Jakob Zopfi, Moritz F. Lehmann, Helge Niemann
Summary: Isoprenoidal glycerol dialkyl glycerol tetraether (isoGDGT) lipids are mainly derived from archaea in the water column of Lake Lugano, Switzerland. The concentration of isoGDGTs, particularly Crenarchaeol, is higher in deeper waters below the thermocline. The distribution of isoGDGTs in surface sediments indicates downward transport from the water between the thermocline and the anoxic hypolimnion. The composition of isoGDGTs in surface sediments of other (peri-)alpine lakes varies based on lake size.
QUATERNARY SCIENCE REVIEWS
(2022)
Article
Geography, Physical
Carina Hoorn, Tyler Kukla, Giovanni Bogota-Angel, Els van Soelen, Catalina Gonzalez-Arango, Frank P. Wesselingh, Hubert Vonhof, Pedro Val, Gaspar Morcote-Rios, Martin Roddaz, Elton Luiz Dantas, Roberto Ventura Santos, Jaap S. Sinninghe Damste, Jung-Hyun Kim, Robert J. Morley
Summary: During the Miocene period, a large wetland system existed in western Amazonia that had unique sedimentary features and biological communities. The study conducted in Los Chorros site in Colombia revealed a sequence of flood-fill packages with distinct lithological, palynological, malacological and geochemical characteristics that reflect the changing environmental conditions in the wetland. Analysis of sediment sources and biomes indicate the influence of dynamic topography, Andean uplift, eustasy, and orbital forcing on sediment deposition and wetland evolution during the Miocene.
GLOBAL AND PLANETARY CHANGE
(2022)
Correction
Microbiology
Svetlana E. Belova, Nikolai V. Ravin, Timofey A. Pankratov, Andrey L. Rakitin, Anastasia A. Ivanova, Alexey V. Beletsky, Andrey V. Mardanov, Jaap S. Sinninghe Damste, Svetlana N. Dedysh
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Microbiology
Irene Sanchez-Andrea, Charlotte M. van der Graaf, Bastian Hornung, Nicole J. Bale, Monika Jarzembowska, Diana Z. Sousa, W. Irene C. Rijpstra, Jaap S. Sinninghe Damste, Alfons J. M. Stams
Summary: In acid drainage environments, moderately acidophilic sulfate-reducing bacteria (SRB) play a crucial role in attenuating extreme conditions by precipitating metals as sulfides and neutralizing acidity. A new species of moderately acidophilic SRB, Acididesulfobacillus acetoxydans gen. nov. sp. nov. strain INE, is identified with the ability to grow at pH 3.8. Bioreactor studies reveal that strain INE alkalinizes its environment, especially at lower pH, and has the ability to completely oxidize organic acids to CO2. Comparative proteogenomic and membrane lipid analysis suggest that the presence of saturated ether-bound lipids in the membrane serves as a protection mechanism against acid stress.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Irina S. Kulichevskaya, Anastasia A. Ivanova, Nataliya E. Suzina, Jaap S. Sinninghe Damste, Svetlana N. Dedysh
Summary: In this study, a novel freshwater planctomycete of the genus 'Anatilimnocola' was characterized and described. This new species exhibits distinct characteristics in terms of cell morphology, growth conditions, and genomic features compared to known freshwater planctomycetes. The findings of this study are significant in understanding the diversity and ecological functions of planctomycetes in freshwater environments.
ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Dimitry Y. Sorokin, Alexander G. Elcheninov, Tatjana Khizhniak, Michel Koenen, Nicole J. Bale, Jaap S. Sinninghe Damste, Ilya V. Kublanov
Summary: This study isolated and classified several alkaliphilic haloaloarchaea from hypersaline soda lakes in southwestern Siberia. These archaea can grow using various starch-like substrates and exhibit moderate alkaliphilic and low Mg-demanding properties.
SYSTEMATIC AND APPLIED MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Diana X. Sahonero-Canavesi, Melvin F. Siliakus, Alejandro Abdala Asbun, Michel Koenen, F. A. Bastiaan von Meijenfeldt, Sjef Boeren, Nicole J. Bale, Julia C. Engelman, Kerstin Fiege, Lora Strack van Schijndel, Jaap S. Sinninghe Damste, Laura Villanueva
Summary: Bacterial membranes are composed of fatty acids (FAs) ester-linked to glycerol-3-phosphate, while archaea have membranes made of isoprenoid chains ether-linked to glycerol-1-phosphate. Some bacteria can produce ether-bound membrane-spanning lipids (MSLs), which are likely precursors of relevant molecules in paleoclimatology. The enzymes responsible for their production have been discovered, and the building blocks of these lipids are branched fatty acids. Phylogenomic analyses reveal a wider diversity of potential MSL-producing bacteria than previously thought, which has important implications for the evolution of lipid membranes.
Review
Biochemistry & Molecular Biology
Anandi Tamby, Jaap Sinninghe S. Damste, Laura Villanueva
Summary: The deep-sea environment is characterized by extreme conditions, including high hydrostatic pressure and near-freezing temperature. Piezophiles, microorganisms adapted to high pressure, have developed specific membrane lipid strategies to withstand these conditions, such as increased abundance of lipids containing unsaturated and branched-chain fatty acids with increasing hydrostatic pressure. However, not all piezophiles employ this strategy, highlighting the need for further understanding of the effects of hydrostatic pressure on microbial lipid membranes.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Geosciences, Multidisciplinary
Jaap S. Sinninghe Damste, Lisa A. Warden, Carlo Berg, Klaus Juergens, Matthias Moros
Summary: Hydroxylated glycerol dibiphytanyl glycerol tetraethers (OH-GDGTs) are increasingly used for reconstructing past sea surface temperature, but in the Baltic Sea area, a reduced salinity significantly increases the values of the OH-GDGT proxies, which should be considered in other settings.
CLIMATE OF THE PAST
(2022)
Article
Ecology
Zoe R. van Kemenade, Laura Villanueva, Ellen C. Hopmans, Peter Kraal, Harry J. Witte, Jaap S. Sinninghe Damste, Darci Rush
Summary: Interpreting lipid biomarkers in sediment archives requires a good understanding of their application and limitations. It has been discovered that marine bacteria performing anaerobic ammonium oxidation (anammox) synthesize a stereoisomer of bacteriohopanetetrol (BHT-x), which can serve as a proxy for water column anoxia. In the water column of the Benguela upwelling system, high BHT-x abundances were found in the oxygen-deficient zone, along with high abundances of Ca. Scalindua genes and ladderane intact polar lipids (IPLs). However, BHT-x ratios were low in oxygenated offshore waters. The BHT-x ratio of >= 0.2 is a robust threshold for oxygen-depleted waters.