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von Arx JN, Kidane AT, Philippi M, Mohr W, Lavik G, Schorn S, Kuypers MMM, Milucka J. Methylphosphonate-driven methane formation and its link to primary production in the oligotrophic North Atlantic. Nat Commun 2023; 14:6529. [PMID: 37845220 PMCID: PMC10579326 DOI: 10.1038/s41467-023-42304-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 10/06/2023] [Indexed: 10/18/2023] Open
Abstract
Methylphosphonate is an organic phosphorus compound used by microorganisms when phosphate, a key nutrient limiting growth in most marine surface waters, becomes unavailable. Microbial methylphosphonate use can result in the formation of methane, a potent greenhouse gas, in oxic waters where methane production is traditionally unexpected. The extent and controlling factors of such aerobic methane formation remain underexplored. Here, we show high potential net rates of methylphosphonate-driven methane formation (median 0.4 nmol methane L-1 d-1) in the upper water column of the western tropical North Atlantic. The rates are repressed but still quantifiable in the presence of in-situ or added phosphate, suggesting that some methylphosphonate-driven methane formation persists in phosphate-replete waters. The genetic potential for methylphosphonate utilisation is present in and transcribed by key photo- and heterotrophic microbial taxa, such as Pelagibacterales, SAR116, and Trichodesmium. While the large cyanobacterial nitrogen-fixers dominate in the surface layer, phosphonate utilisation by Alphaproteobacteria appears to become more important in deeper depths. We estimate that at our study site, a substantial part (median 11%) of the measured surface carbon fixation can be sustained by phosphorus liberated from phosphonate utilisation, highlighting the ecological importance of phosphonates in the carbon cycle of the oligotrophic ocean.
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Affiliation(s)
- Jan N von Arx
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Abiel T Kidane
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Miriam Philippi
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Wiebke Mohr
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Gaute Lavik
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sina Schorn
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Jana Milucka
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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Philippi M, Kitzinger K, Berg JS, Tschitschko B, Kidane AT, Littmann S, Marchant HK, Storelli N, Winkel LHE, Schubert CJ, Mohr W, Kuypers MMM. Purple sulfur bacteria fix N 2 via molybdenum-nitrogenase in a low molybdenum Proterozoic ocean analogue. Nat Commun 2021; 12:4774. [PMID: 34362886 PMCID: PMC8346585 DOI: 10.1038/s41467-021-25000-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/15/2021] [Indexed: 01/04/2023] Open
Abstract
Biological N2 fixation was key to the expansion of life on early Earth. The N2-fixing microorganisms and the nitrogenase type used in the Proterozoic are unknown, although it has been proposed that the canonical molybdenum-nitrogenase was not used due to low molybdenum availability. We investigate N2 fixation in Lake Cadagno, an analogue system to the sulfidic Proterozoic continental margins, using a combination of biogeochemical, molecular and single cell techniques. In Lake Cadagno, purple sulfur bacteria (PSB) are responsible for high N2 fixation rates, to our knowledge providing the first direct evidence for PSB in situ N2 fixation. Surprisingly, no alternative nitrogenases are detectable, and N2 fixation is exclusively catalyzed by molybdenum-nitrogenase. Our results show that molybdenum-nitrogenase is functional at low molybdenum conditions in situ and that in contrast to previous beliefs, PSB may have driven N2 fixation in the Proterozoic ocean.
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Affiliation(s)
- Miriam Philippi
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Katharina Kitzinger
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Jasmine S Berg
- Department of Environmental Systems Science, ETH-Zurich, Zurich, Switzerland
| | - Bernhard Tschitschko
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Abiel T Kidane
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sten Littmann
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Hannah K Marchant
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Nicola Storelli
- Laboratory of Applied Microbiology, Department of Environment, Constructions and Design, University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
| | - Lenny H E Winkel
- Department of Environmental Systems Science, ETH-Zurich, Zurich, Switzerland.,Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Carsten J Schubert
- Department of Environmental Systems Science, ETH-Zurich, Zurich, Switzerland.,Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Wiebke Mohr
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Marcel M M Kuypers
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
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Kitzinger K, Padilla CC, Marchant HK, Hach PF, Herbold CW, Kidane AT, Könneke M, Littmann S, Mooshammer M, Niggemann J, Petrov S, Richter A, Stewart FJ, Wagner M, Kuypers MMM, Bristow LA. Cyanate and urea are substrates for nitrification by Thaumarchaeota in the marine environment. Nat Microbiol 2018; 4:234-243. [PMID: 30531977 DOI: 10.1038/s41564-018-0316-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 10/30/2018] [Indexed: 02/01/2023]
Abstract
Ammonia-oxidizing archaea of the phylum Thaumarchaeota are among the most abundant marine microorganisms1. These organisms thrive in the oceans despite ammonium being present at low nanomolar concentrations2,3. Some Thaumarchaeota isolates have been shown to utilize urea and cyanate as energy and N sources through intracellular conversion to ammonium4-6. Yet, it is unclear whether patterns observed in culture extend to marine Thaumarchaeota, and whether Thaumarchaeota in the ocean directly utilize urea and cyanate or rely on co-occurring microorganisms to break these substrates down to ammonium. Urea utilization has been reported for marine ammonia-oxidizing communities7-10, but no evidence of cyanate utilization exists for marine ammonia oxidizers. Here, we demonstrate that in the Gulf of Mexico, Thaumarchaeota use urea and cyanate both directly and indirectly as energy and N sources. We observed substantial and linear rates of nitrite production from urea and cyanate additions, which often persisted even when ammonium was added to micromolar concentrations. Furthermore, single-cell analysis revealed that the Thaumarchaeota incorporated ammonium-, urea- and cyanate-derived N at significantly higher rates than most other microorganisms. Yet, no cyanases were detected in thaumarchaeal genomic data from the Gulf of Mexico. Therefore, we tested cyanate utilization in Nitrosopumilus maritimus, which also lacks a canonical cyanase, and showed that cyanate was oxidized to nitrite. Our findings demonstrate that marine Thaumarchaeota can use urea and cyanate as both an energy and N source. On the basis of these results, we hypothesize that urea and cyanate are substrates for ammonia-oxidizing Thaumarchaeota throughout the ocean.
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Affiliation(s)
- Katharina Kitzinger
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Cory C Padilla
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | | | - Philipp F Hach
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Craig W Herbold
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Abiel T Kidane
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Martin Könneke
- Marine Archaea Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, Germany
| | - Sten Littmann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Maria Mooshammer
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Jutta Niggemann
- Research Group for Marine Geochemistry (ICBM-MPI Bridging Group), Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Sandra Petrov
- Marine Archaea Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, Germany
| | - Andreas Richter
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | | | - Laura A Bristow
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Department of Biology and Nordic Center for Earth Evolution (NordCEE), University of Southern Denmark, Odense, Denmark
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