Publications

2025

[43] Spiegel, T., Dale, A.D., Lenz, N., Schmidt, M., Sommer, S., Becker, K., Elling, F.J., Porz, L., Daewel, U., Fuhr, M., Kalapurakkal, H.T., Wallmann, K.  Benthic POC cycling in the Skagerrak basin: The role of lateral POC input. Continental Shelf Research 293, 105536.

[42] Harris C.M., Kopf S., Rhim J.H., Cobban A., Elling F.J., Feng X., McFarlin J., Weber Y., Zhang Y., Zhou A., Batther H., Pearson A., Leavitt W.D. 2025. Lipid hydrogen isotope compositions primarily reflect growth water in the model archaeon Sulfolobus acidocaldarius. Applied and Environmental Microbiolology 91, e01983-24.

[41] Elling, F.J., Pierrel,F., Chobert, S.-C., Abby, S.S., Evans, T.W., Reveillard, A., Pelosi, L., Schnoebelen, J., Hemingway, J.D., Boumendjel, A. Becker, K.W., Blom, P., Cordes, J., Nathan, V., Baymann, F., Lücker, S., Spieck,E., Leadbetter, J.R., Hinrichs, K.-U., Summons, R.E., Pearson, A. A novel quinone biosynthetic pathway illuminates the evolution of aerobic metabolism. Proceedings of the National Academy of Sciences of the United States of America 122, e2421994122.

[40] Hoogakker, B.A.A., Davis, C., Wang, Y., Kusch, S., Nilsson-Kerr, K., Hardisty, D.S., Jacobel, A., Reyes Macaya, D., Glock, N., Ni, S., Sepúlveda, J., Ren, A., Auderset, A., Hess, A., Meissner, K., Cardich, J., Anderson, R., Castillo, A., Costa, K., Barras, C., Basak, C., Bradbury, H.J., Brinkmann, I., Cook, M., Choquel, C., Diz, P., Donnenfield, J., Elling, F.J., Erdem, Z., Filipsson, H.L., Garrido, S., Gottschalk, J., Govindankutty Menon, A., Groeneveld, J., Hallmann, C., Hendy, I., Hennekam, R., Lu, W., Lynch-Stieglitz, J., Matos, L., Martínez- García, A., Molina, G., Muñoz, P., Moretti, S., Morford, J., Nuber, S., Radionovskaya, S., Raven, M.R., Somes, C., Studer, A.S., Sweere, T., Tachikawa, K., Tapia, R., Tetard, M., Vollmer, T., Wu, S., Zhang, Y., Zheng, X., Zhou, Y. Review of proxies for low-oxygen paleoceanographic reconstructions. Biogeosciences 22, 863-957.

2024

 [39] De Jonge, C., Peterse, F., Nierop, K.G.J., Blattmann, T.M., Alexandre, M., Ansanay-Alex, S., Austin, T., Babin, M., Bard, E., Bauersachs, T., Blewett, J., Boehman, B., Castañeda, I.S., Chen, J., Conti, M.L.G., Contreras, S., Cordes, J., Davtian, N., van Dongen, B., Duncan, B., Elling, F.J., Galy, V., Gao, S., Hefter, J., Hinrichs, K.-U., Helling, M., Hoorweg, M., Hopmans, E., Hou, J., Huang, Y., Huguet, A., Jia, G., Karger, C., Keely, B.J., Kusch, S., Li, H., Liang, J., Lipp, J.S., Liu, W., Lu, H., Mangelsdorf, K., Manners, H., Martinez-Garcia, A., Ménot, G., Mollenhauer, G., Naafs, B.D.A., Naeher, S., O’Connor, L.K., Pearce, E.M., Pearson, A., Rao, Z., Rodrigo-Gámiz, M., Rosendahl, C., Rostek, F., Rui, B., Sanyal, P., Schubotz, F., Scott, W., Sen, R., Sluijs, A., Smittenberg, R., Stefanescu, I., Sun, J., Sutton, P., Tierney, J., Tejos, E., Villanueva, J., Wang, H., Werne, J., Yamamoto, M., Yang, H., Zhou, A. (2024). Interlaboratory comparison of branched GDGT temperature and pH proxies using soils and lipid extracts. Geochemistry, Geophysics, Geosystems 25,e2024GC011583.

[38] Zhu, Q.-Z., Elvert, M., Meador, T.B., Schröder, J.M., Doeana, K.D., Becker, K.W., Elling, F.J., Lipp, J.S., Heuer, V.B., Zabel, M., Hinrichs, K.-U. (2024). Comprehensive molecular-isotopic characterization of archaeal lipids in the Black Sea water column and underlying sediments. Geobiology 22, e1258.

[37] Hollingsworth, E.H., Elling, F.J., Badger, M.P.S., Pancost, R.D., Dickson, A.J., Rees-Owen, R.L., Papadomanolaki, N.M., Pearson, A., Sluijs, A., Freeman, K.H., Baczynski, A.A., Foster, G.L., Whiteside, J.H., Inglis, G.N. (2024). Spatial and Temporal Patterns in Petrogenic Organic Carbon Mobilization during the Paleocene-Eocene Thermal Maximum. Paleoceanography and Paleoclimatology 39, e2023PA004773.

2023

[36] Rhim, J.H., Zhou, A., Amenabar, M.J., Elling, F.J., Weber, Y., Pearson, A., Boyd, E.S., Leavitt, W.D. Mode of carbon and energy metabolism shifts lipid composition in the thermoacidophile Acidianus. Applied and Environmental Microbiology.

[35] Chiu, B. K., Waldbauer, J., Elling, F.J., Mete, Ö.Z., Pearson, A., Eggleston, E., Leavitt, W.D. (2023). Membrane lipid and expression responses of Saccharolobus islandicus REY15A to acid and cold stress. Frontiers in Microbiology 14.

[34] Leavitt, W.D., Kopf, S.H., Weber, Y., Chiu, B., McFarlin, J.M., Elling, F.J., Hoeft-McCann, S., Pearson, A. (2023). Controls on the hydrogen isotope composition of tetraether lipids in a marine thaumarchaeon. Geochimica et Cosmochimica Acta 352, 194-210.

2022

[33] Elling, F.J.*, Kattein, L.*, Naafs, B.D., Lauretano, V., Pearson, A. (2023). Heterotrophic origin and diverse sources of branched glycerol monoalkyl glycerol tetraethers (brGMGTs) in peats and lignites. Organic Geochemistry 178, 104558.

[32] Elling, F.J., Evans, T.W., Hemingway, J.D., Kharbush, J.J., Spieck, E., Summons, R.E., Pearson, A. (2022). Marine and terrestrial nitrifying bacteria are sources of diverse bacteriohopanepolyols. Geobiology 20, 399-420.

[31] Evans, T.W., Elling, F.J., Li, Y., Pearson, A., Summons, R.E. (2022). A new and improved protocol for extraction of intact polar membrane lipids from archaea. Organic Geochemistry 165, 104353.

[30] Blewett, J., Elling, F.J., Naafs, B.D.A., Kattein, L., Evans, T.W., Lauretano, V., Gallego-Sala, A.V., Pancost, R.D., Pearson, A. (2022). Metabolic and ecological controls on the stable carbon isotopic composition of archaeal (isoGDGT and BDGT) and bacterial (brGDGT) lipids in wetlands and lignites. Geochimica et Cosmochimica Acta 320, 1-25.

2021

[29] Elling, F.J.*, Hemingway, J.D.*, Kharbush, J.J., Becker, K.W., Polik, C.A., Pearson, A.  (2021) Linking diatom-diazotroph symbioses to nitrogen cycle perturbations and deep-water anoxia: Insights from Mediterranean sapropel events. Earth and Planetary Science Letters 2021;571:117110.

[28] Lattaud, J., De Jonge, C., Pearson, Elling, F.J., A., Eglinton, T.I. Microbial lipid signatures in Arctic deltaic sediments – insights into methane cycling and climate variability. Organic Geochemistry 2021;157:104242.

[27] Santoro, A.E., Bayer, B., Elling, F.J., Pearson, A. Candidatus Nitrosopelagicus. In Bergey’s Manual of Systematics of Archaea and Bacteria 2021 (eds M.E. Trujillo, S. Dedysh, P. DeVos, B. Hedlund, P. Kämpfer, F.A. Rainey and W.B. Whitman).

2020

[26] Elling, F.J., Hemingway, J.D., Evans, T.W., Kharbush, J.J., Spieck, E., Summons, R.E., Pearson, A. Vitamin B₁₂-dependent biosynthesis ties amplified 2-methylhopanoid production during oceanic anoxic events to nitrification. Proceedings of the National Academy of Sciences of the United States of America 2020;117:32996-33004.

[25] Cobban, A., Zhang, Y., Zhou, A., Weber, Y., Elling, F.J., Pearson, A, Leavitt, W.D. Multiple environmental parameters impact lipid cyclization in Sulfolobus acidocaldarius. Environmental Microbiology 2020;22:4046-4056.

[24] Nigro, L., Elling, F.J., Hinrichs, K.-U., Joye, S.B., Teske, A. Microbial diversity and biogeochemistry of hypersaline sediments in Orca Basin. Plos One 2020;15(4):e0231676.

[23] Probst, A.J.*, Elling, F.J.*, Castelle, C., Zhu, Q., Elvert, M., Birarda, G., Holman, H.-Y.N., Lane, K.R., Ladd, B., Ryan, M.C., Woyke, T., Hinrichs, K.-U., Banfield, J.F. Lipid analysis of CO₂-rich subsurface aquifers suggests an autotrophy-based deep biosphere with lysolipids enriched in CPR bacteria. ISME Journal 2020;14:1547-1560.

[22] Zhou, A., Weber, Y., Chiu, B.K., Elling, F.J., Cobban, A.B., Pearson, A., Leavitt, W.D. Energy flux controls tetraether lipid cyclization in Sulfolobus acidocaldarius. Environmental Microbiology 2020;22(1):343-353.

2019

[21] Elling, F.J., Gottschalk, J., Doeana, K., Kusch, S., Hurley, S.J., Pearson, A. Archaeal lipid biomarker constraints on the Paleocene-Eocene carbon isotope excursion. Nature Communications 2019;10:4519.

[20] Pearson, A., Hurley, S.J., Elling, F.J., Wilkes, E.B. CO₂-dependent carbon isotope fractionation in Archaea, Part I: Modeling the 3HP/4HB pathway. Geochimica et Cosmochimica Acta 2019;261(368):382.

[19] Hurley, S.J., Close, H.G., Elling, F.J., Jasper, C.E., Gospodinova, K., McNichol, A.P., Pearson, A. CO₂-dependent carbon isotope fractionation in Archaea, Part II: The marine water column. Geochimica et Cosmochimica Acta 2019;261:383-395.

2018

[18] Polik, C.A., Elling, F.J., Pearson, A. Impacts of Paleoecology on the TEX₈₆ Sea Surface Temperature Proxy in the Pliocene-Pleistocene Mediterranean Sea. Paleoceanography and Paleoclimatology 2018;33:1472-1489.

[17] Becker, K.W.*, Elling, F.J.*, Schröder, J.M., Lipp, J.S., Goldhammer, T., Zabel, M., Elvert, M., Overmann, J., Hinrichs, K.-U. Isoprenoid quinones resolve the stratification of microbial redox processes in a biogeochemical continuum from the photic zone to deep anoxic sediments of the Black Sea. Applied and Environmental Microbiology 2018;84:e02736-17.

[16] Hemingway, J.D., Kusch, S., Shah Walter, S.R., Polik, C.A., Elling, F.J., Pearson, A. A novel method to measure the ¹³C composition of intact bacteriohopanepolyols. Organic Geochemistry 2018;123:144-147.

2017

[15] Elling, F.J., Könneke, M., Nicol, G.W., Stieglmeier, M., Bayer, B., Spieck, E., de la Torre, J.R., Becker, K.W., Thomm, M., Prosser, J.I., Herndl, G.J., Schleper, C., Hinrichs, K.-U. Chemotaxonomic characterisation of the thaumarchaeal lipidome. Environmental Microbiology 2017;19:2681–2700.

2016

[14] Hurley, S.J.*, Elling, F.J.*, Könneke, M., Buchwald, C., Wankel, S.D., Santoro, A.E., Lipp, J.S., Hinrichs, K.-U., Pearson, A. Influence of ammonia oxidation rate on thaumarchaeal lipid composition and the TEX₈₆ temperature proxy. Proceedings of the National Academy of Sciences of the United States of America 2016;113(28):7762-7767.

[13] Elling, F.J., Spiegel, C., Estrada, S., Davis, D.W., Reinhardt, L., Henjes-Kunst, F., Allroggen, N., Dohrmann, R., Piepjohn, K., Lisker, F. Origin of bentonites and detrital zircons of the Paleocene Basilika Formation, Svalbard. Frontiers in Earth Science 2016;4:73.

[12] Zhuang, G.-C.*, Elling, F.J.*, Nigro, L.M., Samarkin, V., Joye, S.B., Teske, A., Hinrichs, K.-U. Multiple evidence for methylotrophic methanogenesis as the dominant methanogenic pathway in deep-sea hypersaline sediments. Geochimica et Cosmochimica Acta 2016;187:1-20.

[11] Becker, K.W., Elling, F.J., Yoshinaga, M.Y., Söllinger, A., Urich, T., Hinrichs, K.-U. Unusual butane- and pentanetriol-based tetraether lipids in Methanomassiliicoccus luminyensis, a representative of the seventh order of methanogens. Applied and Environmental Microbiology 2016;82:4505-4516.

[10] Liu, X.-L., Birgel, D., Elling, F.J., Sutton, P.A., Lipp, J.S., Zhu, R., Zhang, C., Könneke, M., Peckmann, J., Rowland, S.J., Summons, R.E., Hinrichs, K.-U. From ether to acid: A plausible degradation pathway of glycerol dialkyl glycerol tetraethers. Geochimica et Cosmochimica Acta 2016;183:138-152.

[9] Zhu, C., Wakeham, S.G., Elling, F.J., Basse, A., Mollenhauer, G., Versteegh, G.J.M., Könneke, M., Hinrichs, K.-U. Stratification of archaeal membrane lipids in the ocean and implications for adaptation and chemotaxonomy of planktonic archaea. Environmental Microbiology 2016;18:4324-4336.

[8] Yao, M., Elling, F.J., Jones, C.A., Nomosatryo, S., Long, C.P., Crowe, S.A., Antoniewicz, M.R., Hinrichs, K.-U., Maresca, J.A. Heterotrophic bacteria from an extremely phosphate-poor lake have conditionally reduced phosphorus demand and utilize diverse sources of phosphorus. Environmental Microbiology 2016;18(2): 656–667.

[7] Elling FJ*, Becker KW*, Könneke M, Schröder JM, Kellermann MY, Thomm M, Hinrichs K-U. Respiratory quinones in Archaea: phylogenetic distribution and application as biomarkers in the marine environment. Environmental Microbiology 2016;18(2):692–707.

2015

[6] Coban, H., Miltner, A., Elling, F.J., Hinrichs, K.-U., Kästner, M. The contribution of biogas residues to soil organic matter formation and CO₂ emissions in an arable soil. Soil Biology and Biochemistry 2015;86:108–115.

[5] Lü, X., Liu, X.-L., Elling, F.J., Yang, H., Xie, S., Song, J., Li, X., Yuan, H., Li, N., Hinrichs K.-U. Hydroxylated isoprenoid GDGTs in Chinese coastal seas and their potential as a paleotemperature proxy for mid-to-low latitude marginal seas. Organic Geochemistry 2015;89-90:31–43.

[4] Elling, F.J., Könneke, M., Mußmann, M., Greve, A., Hinrichs, K.-U. Influence of temperature, pH, and salinity on membrane lipid composition and TEX₈₆ of marine planktonic thaumarchaeal isolates. Geochimica et Cosmochimica Acta 2015;171:238–255.

[3] Widderich, N., Czech, L., Elling FJ, Könneke, M., Stöveken, N., Pittelkow, M., Riclea, R., Dickschat, J.S., Heider, J., Bremer, E. Strangers in the archaeal world: osmostress-responsive biosynthesis of ectoine and hydroxyectoine by the marine thaumarchaeon Nitrosopumilus maritimus. Environmental Microbiology 2015;18:1227 – 1248.

2014

[2] Elling, F.J., Könneke, M., Lipp, J.S., Becker, K.W., Gagen, E.J., Hinrichs, K.-U. Effects of growth phase on the membrane lipid composition of the thaumarchaeon Nitrosopumilus maritimus and their implications for archaeal lipid distributions in the marine environment. Geochimica et Cosmochimica Acta 2014;141:579–597.

[1] Meador, T.B., Zhu, C., Elling, F.J., Könneke, M., Hinrichs, K.-U. Identification of isoprenoid glycosidic glycerol dibiphytanol diethers and indications for their biosynthetic origin. Organic Geochemistry 2014;69:70–75.

Theses

2015

Elling, F.J. Factors controlling the lipid composition of marine planktonic Thaumarchaeota. PhD Thesis. Department of Geosciences, University of Bremen.