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Schmider T, Hestnes AG, Brzykcy J, Schmidt H, Schintlmeister A, Roller BRK, Teran EJ, Söllinger A, Schmidt O, Polz MF, Richter A, Svenning MM, Tveit AT. Physiological basis for atmospheric methane oxidation and methanotrophic growth on air. Nat Commun 2024; 15:4151. [PMID: 38755154 DOI: 10.1038/s41467-024-48197-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 04/22/2024] [Indexed: 05/18/2024] Open
Abstract
Atmospheric methane oxidizing bacteria (atmMOB) constitute the sole biological sink for atmospheric methane. Still, the physiological basis allowing atmMOB to grow on air is not well understood. Here we assess the ability and strategies of seven methanotrophic species to grow with air as sole energy, carbon, and nitrogen source. Four species, including three outside the canonical atmMOB group USCα, enduringly oxidized atmospheric methane, carbon monoxide, and hydrogen during 12 months of growth on air. These four species exhibited distinct substrate preferences implying the existence of multiple metabolic strategies to grow on air. The estimated energy yields of the atmMOB were substantially lower than previously assumed necessary for cellular maintenance in atmMOB and other aerobic microorganisms. Moreover, the atmMOB also covered their nitrogen requirements from air. During growth on air, the atmMOB decreased investments in biosynthesis while increasing investments in trace gas oxidation. Furthermore, we confirm that a high apparent specific affinity for methane is a key characteristic of atmMOB. Our work shows that atmMOB grow on the trace concentrations of methane, carbon monoxide, and hydrogen present in air and outlines the metabolic strategies that enable atmMOB to mitigate greenhouse gases.
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Affiliation(s)
- Tilman Schmider
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT-The Arctic University of Norway, 9037, Tromsø, Norway.
| | - Anne Grethe Hestnes
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT-The Arctic University of Norway, 9037, Tromsø, Norway
| | - Julia Brzykcy
- Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096, Warsaw, Poland
| | - Hannes Schmidt
- Department of Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem Research, University of Vienna, 1030, Vienna, Austria
| | - Arno Schintlmeister
- Department of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, 1030, Vienna, Austria
| | - Benjamin R K Roller
- Department of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, 1030, Vienna, Austria
| | - Ezequiel Jesús Teran
- Centro de Investigaciones en Física e Ingeniería del Centro de la Provincia de Buenos Aires (CIFICEN-UNCPBA-CONICET-CICPBA), Pinto, 399, Tandil (7000), Argentina
- Universidad Nacional del Centro de la Provincia de Buenos Aires, Facultad de Ciencias Exactas, Instituto de Física Arroyo Seco (IFAS), Pinto, 399, Tandil (7000), Argentina
| | - Andrea Söllinger
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT-The Arctic University of Norway, 9037, Tromsø, Norway
| | - Oliver Schmidt
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT-The Arctic University of Norway, 9037, Tromsø, Norway
| | - Martin F Polz
- Department of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, 1030, Vienna, Austria
| | - Andreas Richter
- Department of Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem Research, University of Vienna, 1030, Vienna, Austria
| | - Mette M Svenning
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT-The Arctic University of Norway, 9037, Tromsø, Norway
| | - Alexander T Tveit
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT-The Arctic University of Norway, 9037, Tromsø, Norway.
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2
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Leung PM, Grinter R, Tudor-Matthew E, Lingford JP, Jimenez L, Lee HC, Milton M, Hanchapola I, Tanuwidjaya E, Kropp A, Peach HA, Carere CR, Stott MB, Schittenhelm RB, Greening C. Trace gas oxidation sustains energy needs of a thermophilic archaeon at suboptimal temperatures. Nat Commun 2024; 15:3219. [PMID: 38622143 PMCID: PMC11018855 DOI: 10.1038/s41467-024-47324-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/22/2024] [Indexed: 04/17/2024] Open
Abstract
Diverse aerobic bacteria use atmospheric hydrogen (H2) and carbon monoxide (CO) as energy sources to support growth and survival. Such trace gas oxidation is recognised as a globally significant process that serves as the main sink in the biogeochemical H2 cycle and sustains microbial biodiversity in oligotrophic ecosystems. However, it is unclear whether archaea can also use atmospheric H2. Here we show that a thermoacidophilic archaeon, Acidianus brierleyi (Thermoproteota), constitutively consumes H2 and CO to sub-atmospheric levels. Oxidation occurs across a wide range of temperatures (10 to 70 °C) and enhances ATP production during starvation-induced persistence under temperate conditions. The genome of A. brierleyi encodes a canonical CO dehydrogenase and four distinct [NiFe]-hydrogenases, which are differentially produced in response to electron donor and acceptor availability. Another archaeon, Metallosphaera sedula, can also oxidize atmospheric H2. Our results suggest that trace gas oxidation is a common trait of Sulfolobales archaea and may play a role in their survival and niche expansion, including during dispersal through temperate environments.
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Affiliation(s)
- Pok Man Leung
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.
| | - Rhys Grinter
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Eve Tudor-Matthew
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - James P Lingford
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Luis Jimenez
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Han-Chung Lee
- Monash Proteomics and Metabolomics Platform and Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Michael Milton
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Iresha Hanchapola
- Monash Proteomics and Metabolomics Platform and Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Erwin Tanuwidjaya
- Monash Proteomics and Metabolomics Platform and Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Ashleigh Kropp
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Hanna A Peach
- Geomicrobiology Research Group, Department of Geothermal Sciences, Te Pū Ao | GNS Science, Wairakei, Taupō, 3377, Aotearoa New Zealand
| | - Carlo R Carere
- Geomicrobiology Research Group, Department of Geothermal Sciences, Te Pū Ao | GNS Science, Wairakei, Taupō, 3377, Aotearoa New Zealand
- Te Tari Pūhanga Tukanga Matū | Department of Chemical and Process Engineering, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, 8140, Aotearoa New Zealand
| | - Matthew B Stott
- Geomicrobiology Research Group, Department of Geothermal Sciences, Te Pū Ao | GNS Science, Wairakei, Taupō, 3377, Aotearoa New Zealand
- Te Kura Pūtaiao Koiora | School of Biological Sciences, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, 8140, Aotearoa New Zealand
| | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Platform and Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.
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3
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Ray AE, Tribbia DZ, Cowan DA, Ferrari BC. Clearing the air: unraveling past and guiding future research in atmospheric chemosynthesis. Microbiol Mol Biol Rev 2023; 87:e0004823. [PMID: 37914532 PMCID: PMC10732025 DOI: 10.1128/mmbr.00048-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
SUMMARY Atmospheric chemosynthesis is a recently proposed form of chemoautotrophic microbial primary production. The proposed process relies on the oxidation of trace concentrations of hydrogen (≤530 ppbv), carbon monoxide (≤90 ppbv), and methane (≤1,870 ppbv) gases using high-affinity enzymes. Atmospheric hydrogen and carbon monoxide oxidation have been primarily linked to microbial growth in desert surface soils scarce in liquid water and organic nutrients, and low in photosynthetic communities. It is well established that the oxidation of trace hydrogen and carbon monoxide gases widely supports the persistence of microbial communities in a diminished metabolic state, with the former potentially providing a reliable source of metabolic water. Microbial atmospheric methane oxidation also occurs in oligotrophic desert soils and is widespread throughout copiotrophic environments, with established links to microbial growth. Despite these findings, the direct link between trace gas oxidation and carbon fixation remains disputable. Here, we review the supporting evidence, outlining major gaps in our understanding of this phenomenon, and propose approaches to validate atmospheric chemosynthesis as a primary production process. We also explore the implications of this minimalistic survival strategy in terms of nutrient cycling, climate change, aerobiology, and astrobiology.
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Affiliation(s)
- Angelique E. Ray
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, Australia
| | - Dana Z. Tribbia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, Australia
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Belinda C. Ferrari
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, Australia
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4
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Alexander LT, Durairaj J, Kryshtafovych A, Abriata LA, Bayo Y, Bhabha G, Breyton C, Caulton SG, Chen J, Degroux S, Ekiert DC, Erlandsen BS, Freddolino PL, Gilzer D, Greening C, Grimes JM, Grinter R, Gurusaran M, Hartmann MD, Hitchman CJ, Keown JR, Kropp A, Kursula P, Lovering AL, Lemaitre B, Lia A, Liu S, Logotheti M, Lu S, Markússon S, Miller MD, Minasov G, Niemann HH, Opazo F, Phillips GN, Davies OR, Rommelaere S, Rosas‐Lemus M, Roversi P, Satchell K, Smith N, Wilson MA, Wu K, Xia X, Xiao H, Zhang W, Zhou ZH, Fidelis K, Topf M, Moult J, Schwede T. Protein target highlights in CASP15: Analysis of models by structure providers. Proteins 2023; 91:1571-1599. [PMID: 37493353 PMCID: PMC10792529 DOI: 10.1002/prot.26545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 07/27/2023]
Abstract
We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the submitted predictions. While the overall ability to predict three-dimensional protein structures continues to impress, reproducing uncommon features not previously observed in experimental structures is still a challenge. Furthermore, instances with conformational flexibility and large multimeric complexes highlight the need for novel scoring strategies to better emphasize biologically relevant structural regions. Looking ahead, closer integration of computational and experimental techniques will play a key role in determining the next challenges to be unraveled in the field of structural molecular biology.
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Affiliation(s)
- Leila T. Alexander
- BiozentrumUniversity of BaselBaselSwitzerland
- Computational Structural BiologySIB Swiss Institute of BioinformaticsBaselSwitzerland
| | - Janani Durairaj
- BiozentrumUniversity of BaselBaselSwitzerland
- Computational Structural BiologySIB Swiss Institute of BioinformaticsBaselSwitzerland
| | | | - Luciano A. Abriata
- School of Life SciencesÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Yusupha Bayo
- Department of BiosciencesUniversity of MilanoMilanItaly
- IBBA‐CNR Unit of MilanoInstitute of Agricultural Biology and BiotechnologyMilanItaly
| | - Gira Bhabha
- Department of Cell BiologyNew York University School of MedicineNew YorkNew YorkUSA
| | | | | | - James Chen
- Department of Cell BiologyNew York University School of MedicineNew YorkNew YorkUSA
| | | | - Damian C. Ekiert
- Department of Cell BiologyNew York University School of MedicineNew YorkNew YorkUSA
- Department of MicrobiologyNew York University School of MedicineNew YorkNew YorkUSA
| | - Benedikte S. Erlandsen
- Wellcome Centre for Cell BiologyInstitute of Cell Biology, University of EdinburghEdinburghUK
| | - Peter L. Freddolino
- Department of Biological Chemistry, Computational Medicine and BioinformaticsUniversity of MichiganAnn ArborMichiganUSA
| | - Dominic Gilzer
- Department of ChemistryBielefeld UniversityBielefeldGermany
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
- Securing Antarctica's Environmental FutureMonash UniversityClaytonVictoriaAustralia
- Centre to Impact AMRMonash UniversityClaytonVictoriaAustralia
- ARC Research Hub for Carbon Utilisation and RecyclingMonash UniversityClaytonVictoriaAustralia
| | - Jonathan M. Grimes
- Division of Structural Biology, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Rhys Grinter
- Department of Microbiology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
- Centre for Electron Microscopy of Membrane ProteinsMonash Institute of Pharmaceutical SciencesParkvilleVictoriaAustralia
| | - Manickam Gurusaran
- Wellcome Centre for Cell BiologyInstitute of Cell Biology, University of EdinburghEdinburghUK
| | - Marcus D. Hartmann
- Max Planck Institute for BiologyTübingenGermany
- Interfaculty Institute of Biochemistry, University of TübingenTübingenGermany
| | - Charlie J. Hitchman
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLeicesterUK
| | - Jeremy R. Keown
- Division of Structural Biology, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Ashleigh Kropp
- Department of Microbiology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| | - Petri Kursula
- Department of BiomedicineUniversity of BergenBergenNorway
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuluUniversity of OuluOuluFinland
| | | | - Bruno Lemaitre
- School of Life SciencesÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Andrea Lia
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLeicesterUK
- ISPA‐CNR Unit of LecceInstitute of Sciences of Food ProductionLecceItaly
| | - Shiheng Liu
- Department of Microbiology, Immunology, and Molecular GeneticsUniversity of CaliforniaLos AngelesCaliforniaUSA
- California NanoSystems InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Maria Logotheti
- Max Planck Institute for BiologyTübingenGermany
- Interfaculty Institute of Biochemistry, University of TübingenTübingenGermany
- Present address:
Institute of BiochemistryUniversity of GreifswaldGreifswaldGermany
| | - Shuze Lu
- Lanzhou University School of Life SciencesLanzhouChina
| | | | | | - George Minasov
- Department of Microbiology‐ImmunologyNorthwestern Feinberg School of MedicineChicagoIllinoisUSA
| | | | - Felipe Opazo
- NanoTag Biotechnologies GmbHGöttingenGermany
- Institute of Neuro‐ and Sensory PhysiologyUniversity of Göttingen Medical CenterGöttingenGermany
- Center for Biostructural Imaging of Neurodegeneration (BIN)University of Göttingen Medical CenterGöttingenGermany
| | - George N. Phillips
- Department of BiosciencesRice UniversityHoustonTexasUSA
- Department of ChemistryRice UniversityHoustonTexasUSA
| | - Owen R. Davies
- Wellcome Centre for Cell BiologyInstitute of Cell Biology, University of EdinburghEdinburghUK
| | - Samuel Rommelaere
- School of Life SciencesÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Monica Rosas‐Lemus
- Department of Microbiology‐ImmunologyNorthwestern Feinberg School of MedicineChicagoIllinoisUSA
- Present address:
Department of Molecular Genetics and MicrobiologyUniversity of New MexicoAlbuquerqueNew MexicoUSA
| | - Pietro Roversi
- IBBA‐CNR Unit of MilanoInstitute of Agricultural Biology and BiotechnologyMilanItaly
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLeicesterUK
| | - Karla Satchell
- Department of Microbiology‐ImmunologyNorthwestern Feinberg School of MedicineChicagoIllinoisUSA
| | - Nathan Smith
- Department of Biochemistry and the Redox Biology CenterUniversity of NebraskaLincolnNebraskaUSA
| | - Mark A. Wilson
- Department of Biochemistry and the Redox Biology CenterUniversity of NebraskaLincolnNebraskaUSA
| | - Kuan‐Lin Wu
- Department of ChemistryRice UniversityHoustonTexasUSA
| | - Xian Xia
- Department of Microbiology, Immunology, and Molecular GeneticsUniversity of CaliforniaLos AngelesCaliforniaUSA
- California NanoSystems InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Han Xiao
- Department of BiosciencesRice UniversityHoustonTexasUSA
- Department of ChemistryRice UniversityHoustonTexasUSA
- Department of BioengineeringRice UniversityHoustonTexasUSA
| | - Wenhua Zhang
- Lanzhou University School of Life SciencesLanzhouChina
| | - Z. Hong Zhou
- Department of Microbiology, Immunology, and Molecular GeneticsUniversity of CaliforniaLos AngelesCaliforniaUSA
- California NanoSystems InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA
| | | | - Maya Topf
- University Medical Center Hamburg‐Eppendorf (UKE)HamburgGermany
- Centre for Structural Systems BiologyLeibniz‐Institut für Virologie (LIV)HamburgGermany
| | - John Moult
- Department of Cell Biology and Molecular Genetics, Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMarylandUSA
| | - Torsten Schwede
- BiozentrumUniversity of BaselBaselSwitzerland
- Computational Structural BiologySIB Swiss Institute of BioinformaticsBaselSwitzerland
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5
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Greening C, Kropp A, Vincent K, Grinter R. Developing high-affinity, oxygen-insensitive [NiFe]-hydrogenases as biocatalysts for energy conversion. Biochem Soc Trans 2023; 51:1921-1933. [PMID: 37743798 PMCID: PMC10657181 DOI: 10.1042/bst20230120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/26/2023]
Abstract
The splitting of hydrogen (H2) is an energy-yielding process, which is important for both biological systems and as a means of providing green energy. In biology, this reaction is mediated by enzymes called hydrogenases, which utilise complex nickel and iron cofactors to split H2 and transfer the resulting electrons to an electron-acceptor. These [NiFe]-hydrogenases have received considerable attention as catalysts in fuel cells, which utilise H2 to produce electrical current. [NiFe]-hydrogenases are a promising alternative to the platinum-based catalysts that currently predominate in fuel cells due to the abundance of nickel and iron, and the resistance of some family members to inhibition by gases, including carbon monoxide, which rapidly poison platinum-based catalysts. However, the majority of characterised [NiFe]-hydrogenases are inhibited by oxygen (O2), limiting their activity and stability. We recently reported the isolation and characterisation of the [NiFe]-hydrogenase Huc from Mycobacterium smegmatis, which is insensitive to inhibition by O2 and has an extremely high affinity, making it capable of oxidising H2 in air to below atmospheric concentrations. These properties make Huc a promising candidate for the development of enzyme-based fuel cells (EBFCs), which utilise H2 at low concentrations and in impure gas mixtures. In this review, we aim to provide context for the use of Huc for this purpose by discussing the advantages of [NiFe]-hydrogenases as catalysts and their deployment in fuel cells. We also address the challenges associated with using [NiFe]-hydrogenases for this purpose, and how these might be overcome to develop EBFCs that can be deployed at scale.
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Affiliation(s)
- Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Securing Antarctica's Environmental Future, Monash University, Clayton, VIC 3800, Australia
- Centre to Impact AMR, Monash University, Clayton, VIC 3800, Australia
- ARC Research Hub for Carbon Utilisation and Recycling, Monash University, Clayton, VIC 3800, Australia
| | - Ashleigh Kropp
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Kylie Vincent
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, Oxford OX1 3QR, U.K
| | - Rhys Grinter
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Centre for Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria 3052, Australia
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6
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Grinter R, Kropp A, Venugopal H, Senger M, Badley J, Cabotaje PR, Jia R, Duan Z, Huang P, Stripp ST, Barlow CK, Belousoff M, Shafaat HS, Cook GM, Schittenhelm RB, Vincent KA, Khalid S, Berggren G, Greening C. Structural basis for bacterial energy extraction from atmospheric hydrogen. Nature 2023; 615:541-547. [PMID: 36890228 PMCID: PMC10017518 DOI: 10.1038/s41586-023-05781-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 02/02/2023] [Indexed: 03/10/2023]
Abstract
Diverse aerobic bacteria use atmospheric H2 as an energy source for growth and survival1. This globally significant process regulates the composition of the atmosphere, enhances soil biodiversity and drives primary production in extreme environments2,3. Atmospheric H2 oxidation is attributed to uncharacterized members of the [NiFe] hydrogenase superfamily4,5. However, it remains unresolved how these enzymes overcome the extraordinary catalytic challenge of oxidizing picomolar levels of H2 amid ambient levels of the catalytic poison O2 and how the derived electrons are transferred to the respiratory chain1. Here we determined the cryo-electron microscopy structure of the Mycobacterium smegmatis hydrogenase Huc and investigated its mechanism. Huc is a highly efficient oxygen-insensitive enzyme that couples oxidation of atmospheric H2 to the hydrogenation of the respiratory electron carrier menaquinone. Huc uses narrow hydrophobic gas channels to selectively bind atmospheric H2 at the expense of O2, and 3 [3Fe-4S] clusters modulate the properties of the enzyme so that atmospheric H2 oxidation is energetically feasible. The Huc catalytic subunits form an octameric 833 kDa complex around a membrane-associated stalk, which transports and reduces menaquinone 94 Å from the membrane. These findings provide a mechanistic basis for the biogeochemically and ecologically important process of atmospheric H2 oxidation, uncover a mode of energy coupling dependent on long-range quinone transport, and pave the way for the development of catalysts that oxidize H2 in ambient air.
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Affiliation(s)
- Rhys Grinter
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
| | - Ashleigh Kropp
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Hari Venugopal
- Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, Victoria, Australia
| | - Moritz Senger
- Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Jack Badley
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Princess R Cabotaje
- Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Ruyu Jia
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Zehui Duan
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, Oxford, UK
| | - Ping Huang
- Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Sven T Stripp
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Christopher K Barlow
- Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Monash Proteomics and Metabolomics Facility, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Matthew Belousoff
- Centre for Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria, Australia
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Ralf B Schittenhelm
- Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Monash Proteomics and Metabolomics Facility, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Kylie A Vincent
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, Oxford, UK
| | - Syma Khalid
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Gustav Berggren
- Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
- Securing Antarctica's Environmental Future, Monash University, Clayton, Victoria, Australia.
- Centre to Impact AMR, Monash University, Clayton, Victoria, Australia.
- ARC Research Hub for Carbon Utilisation and Recycling, Monash University, Clayton, Victoria, Australia.
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7
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Leung PM, Daebeler A, Chiri E, Hanchapola I, Gillett DL, Schittenhelm RB, Daims H, Greening C. A nitrite-oxidising bacterium constitutively consumes atmospheric hydrogen. THE ISME JOURNAL 2022; 16:2213-2219. [PMID: 35752717 PMCID: PMC9381531 DOI: 10.1038/s41396-022-01265-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 05/27/2022] [Accepted: 06/07/2022] [Indexed: 11/08/2022]
Abstract
Chemolithoautotrophic nitrite-oxidising bacteria (NOB) of the genus Nitrospira contribute to nitrification in diverse natural environments and engineered systems. Nitrospira are thought to be well-adapted to substrate limitation owing to their high affinity for nitrite and capacity to use alternative energy sources. Here, we demonstrate that the canonical nitrite oxidiser Nitrospira moscoviensis oxidises hydrogen (H2) below atmospheric levels using a high-affinity group 2a nickel-iron hydrogenase [Km(app) = 32 nM]. Atmospheric H2 oxidation occurred under both nitrite-replete and nitrite-deplete conditions, suggesting low-potential electrons derived from H2 oxidation promote nitrite-dependent growth and enable survival during nitrite limitation. Proteomic analyses confirmed the hydrogenase was abundant under both conditions and indicated extensive metabolic changes occur to reduce energy expenditure and growth under nitrite-deplete conditions. Thermodynamic modelling revealed that H2 oxidation theoretically generates higher power yield than nitrite oxidation at low substrate concentrations and significantly contributes to growth at elevated nitrite concentrations. Collectively, this study suggests atmospheric H2 oxidation enhances the growth and survival of NOB amid variability of nitrite supply, extends the phenomenon of atmospheric H2 oxidation to an eighth phylum (Nitrospirota), and reveals unexpected new links between the global hydrogen and nitrogen cycles. Long classified as obligate nitrite oxidisers, our findings suggest H2 may primarily support growth and survival of certain NOB in natural environments.
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Affiliation(s)
- Pok Man Leung
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Anne Daebeler
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Soil and Water Research Infrastructure, Biology Centre CAS, Budweis, Czechia.
| | - Eleonora Chiri
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Iresha Hanchapola
- Monash Proteomics and Metabolomics Facility and Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - David L Gillett
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Facility and Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Holger Daims
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- University of Vienna, The Comammox Research Platform, Vienna, Austria.
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.
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8
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Greening C, Grinter R. Microbial oxidation of atmospheric trace gases. Nat Rev Microbiol 2022; 20:513-528. [PMID: 35414013 DOI: 10.1038/s41579-022-00724-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2022] [Indexed: 02/06/2023]
Abstract
The atmosphere has recently been recognized as a major source of energy sustaining life. Diverse aerobic bacteria oxidize the three most abundant reduced trace gases in the atmosphere, namely hydrogen (H2), carbon monoxide (CO) and methane (CH4). This Review describes the taxonomic distribution, physiological role and biochemical basis of microbial oxidation of these atmospheric trace gases, as well as the ecological, environmental, medical and astrobiological importance of this process. Most soil bacteria and some archaea can survive by using atmospheric H2 and CO as alternative energy sources, as illustrated through genetic studies on Mycobacterium cells and Streptomyces spores. Certain specialist bacteria can also grow on air alone, as confirmed by the landmark characterization of Methylocapsa gorgona, which grows by simultaneously consuming atmospheric CH4, H2 and CO. Bacteria use high-affinity lineages of metalloenzymes, namely hydrogenases, CO dehydrogenases and methane monooxygenases, to utilize atmospheric trace gases for aerobic respiration and carbon fixation. More broadly, trace gas oxidizers enhance the biodiversity and resilience of soil and marine ecosystems, drive primary productivity in extreme environments such as Antarctic desert soils and perform critical regulatory services by mitigating anthropogenic emissions of greenhouse gases and toxic pollutants.
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Affiliation(s)
- Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. .,Securing Antarctica's Environmental Future, Monash University, Clayton, Victoria, Australia. .,Centre to Impact AMR, Monash University, Clayton, Victoria, Australia.
| | - Rhys Grinter
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
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9
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Ortiz M, Leung PM, Shelley G, Jirapanjawat T, Nauer PA, Van Goethem MW, Bay SK, Islam ZF, Jordaan K, Vikram S, Chown SL, Hogg ID, Makhalanyane TP, Grinter R, Cowan DA, Greening C. Multiple energy sources and metabolic strategies sustain microbial diversity in Antarctic desert soils. Proc Natl Acad Sci U S A 2021; 118:e2025322118. [PMID: 34732568 PMCID: PMC8609440 DOI: 10.1073/pnas.2025322118] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2021] [Indexed: 12/11/2022] Open
Abstract
Numerous diverse microorganisms reside in the cold desert soils of continental Antarctica, though we lack a holistic understanding of the metabolic processes that sustain them. Here, we profile the composition, capabilities, and activities of the microbial communities in 16 physicochemically diverse mountainous and glacial soils. We assembled 451 metagenome-assembled genomes from 18 microbial phyla and inferred through Bayesian divergence analysis that the dominant lineages present are likely native to Antarctica. In support of earlier findings, metagenomic analysis revealed that the most abundant and prevalent microorganisms are metabolically versatile aerobes that use atmospheric hydrogen to support aerobic respiration and sometimes carbon fixation. Surprisingly, however, hydrogen oxidation in this region was catalyzed primarily by a phylogenetically and structurally distinct enzyme, the group 1l [NiFe]-hydrogenase, encoded by nine bacterial phyla. Through gas chromatography, we provide evidence that both Antarctic soil communities and an axenic Bacteroidota isolate (Hymenobacter roseosalivarius) oxidize atmospheric hydrogen using this enzyme. Based on ex situ rates at environmentally representative temperatures, hydrogen oxidation is theoretically sufficient for soil communities to meet energy requirements and, through metabolic water production, sustain hydration. Diverse carbon monoxide oxidizers and abundant methanotrophs were also active in the soils. We also recovered genomes of microorganisms capable of oxidizing edaphic inorganic nitrogen, sulfur, and iron compounds and harvesting solar energy via microbial rhodopsins and conventional photosystems. Obligately symbiotic bacteria, including Patescibacteria, Chlamydiae, and predatory Bdellovibrionota, were also present. We conclude that microbial diversity in Antarctic soils reflects the coexistence of metabolically flexible mixotrophs with metabolically constrained specialists.
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Affiliation(s)
- Maximiliano Ortiz
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
| | - Pok Man Leung
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton VIC 3800, Australia;
| | - Guy Shelley
- School of Biological Sciences, Monash University, Clayton VIC 3800, Australia
| | - Thanavit Jirapanjawat
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton VIC 3800, Australia
| | - Philipp A Nauer
- School of Chemistry, Monash University, Clayton VIC 3800, Australia
| | - Marc W Van Goethem
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Sean K Bay
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton VIC 3800, Australia
- School of Biological Sciences, Monash University, Clayton VIC 3800, Australia
| | - Zahra F Islam
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton VIC 3800, Australia
- School of Biological Sciences, Monash University, Clayton VIC 3800, Australia
| | - Karen Jordaan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Surendra Vikram
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
| | - Steven L Chown
- Securing Antarctica's Environmental Future, School of Biological Sciences, Monash University, Clayton VIC 3800, Australia
| | - Ian D Hogg
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
- School of Science, University of Waikato, Hamilton 3240, New Zealand
- Polar Knowledge Canada, Canadian High Arctic Research Station, Cambridge Bay NU X0B 0C0, Canada
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
| | - Rhys Grinter
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton VIC 3800, Australia
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa;
| | - Chris Greening
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton VIC 3800, Australia;
- School of Biological Sciences, Monash University, Clayton VIC 3800, Australia
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10
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Bay SK, Waite DW, Dong X, Gillor O, Chown SL, Hugenholtz P, Greening C. Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradient. THE ISME JOURNAL 2021; 15:3339-3356. [PMID: 34035443 PMCID: PMC8528921 DOI: 10.1038/s41396-021-01001-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 04/16/2021] [Accepted: 04/28/2021] [Indexed: 02/04/2023]
Abstract
Desert soils harbour diverse communities of aerobic bacteria despite lacking substantial organic carbon inputs from vegetation. A major question is therefore how these communities maintain their biodiversity and biomass in these resource-limiting ecosystems. Here, we investigated desert topsoils and biological soil crusts collected along an aridity gradient traversing four climatic regions (sub-humid, semi-arid, arid, and hyper-arid). Metagenomic analysis indicated these communities vary in their capacity to use sunlight, organic compounds, and inorganic compounds as energy sources. Thermoleophilia, Actinobacteria, and Acidimicrobiia were the most abundant and prevalent bacterial classes across the aridity gradient in both topsoils and biocrusts. Contrary to the classical view that these taxa are obligate organoheterotrophs, genome-resolved analysis suggested they are metabolically flexible, with the capacity to also use atmospheric H2 to support aerobic respiration and often carbon fixation. In contrast, Cyanobacteria were patchily distributed and only abundant in certain biocrusts. Activity measurements profiled how aerobic H2 oxidation, chemosynthetic CO2 fixation, and photosynthesis varied with aridity. Cell-specific rates of atmospheric H2 consumption increased 143-fold along the aridity gradient, correlating with increased abundance of high-affinity hydrogenases. Photosynthetic and chemosynthetic primary production co-occurred throughout the gradient, with photosynthesis dominant in biocrusts and chemosynthesis dominant in arid and hyper-arid soils. Altogether, these findings suggest that the major bacterial lineages inhabiting hot deserts use different strategies for energy and carbon acquisition depending on resource availability. Moreover, they highlight the previously overlooked roles of Actinobacteriota as abundant primary producers and trace gases as critical energy sources supporting productivity and resilience of desert ecosystems.
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Affiliation(s)
- Sean K Bay
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
- School of Biological Sciences, Monash University, Clayton, VIC, Australia.
| | - David W Waite
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Xiyang Dong
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sde Boker, Israel
| | - Steven L Chown
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
- School of Biological Sciences, Monash University, Clayton, VIC, Australia.
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11
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Greening C, Islam ZF, Bay SK. Hydrogen is a major lifeline for aerobic bacteria. Trends Microbiol 2021; 30:330-337. [PMID: 34462186 DOI: 10.1016/j.tim.2021.08.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 12/31/2022]
Abstract
Molecular hydrogen (H2) is available in trace amounts in most ecosystems through atmospheric, biological, geochemical, and anthropogenic sources. Aerobic bacteria use this energy-dense gas, including at atmospheric concentrations, to support respiration and carbon fixation. While it was thought that aerobic H2 consumers are rare community members, here we summarize evidence suggesting that they are dominant throughout soils and other aerated ecosystems. Bacterial cultures from at least eight major phyla can consume atmospheric H2. At the ecosystem scale, H2 consumers are abundant, diverse, and active across diverse soils and are key primary producers in extreme environments such as hyper-arid deserts. On this basis, we propose that H2 is a universally available energy source for the survival of aerobic bacteria.
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Affiliation(s)
- Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Securing Antarctica's Environmental Future, Monash University, Clayton, VIC 3800, Australia; Centre to Impact AMR, Monash University, Clayton, VIC 3800, Australia.
| | - Zahra F Islam
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; STEM College, RMIT University, Bundoora, VIC 3083, Australia
| | - Sean K Bay
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Securing Antarctica's Environmental Future, Monash University, Clayton, VIC 3800, Australia; School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
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12
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Abstract
Carbon monoxide has an infamous reputation as a toxic gas, and it has been suggested that it has potential as an antibacterial agent. Despite this, how bacteria resist its toxic effects is not well understood. Carbon monoxide (CO) gas is infamous for its acute toxicity. This toxicity predominantly stems from its tendency to form carbonyl complexes with transition metals, thus inhibiting the heme-prosthetic groups of proteins, including respiratory terminal oxidases. While CO has been proposed as an antibacterial agent, the evidence supporting its toxicity toward bacteria is equivocal, and its cellular targets remain poorly defined. In this work, we investigate the physiological response of mycobacteria to CO. We show that Mycobacterium smegmatis is highly resistant to the toxic effects of CO, exhibiting only minor inhibition of growth when cultured in its presence. We profiled the proteome of M. smegmatis during growth in CO, identifying strong induction of cytochrome bd oxidase and members of the dos regulon, but relatively few other changes. We show that the activity of cytochrome bd oxidase is resistant to CO, whereas cytochrome bcc-aa3 oxidase is strongly inhibited by this gas. Consistent with these findings, growth analysis shows that M. smegmatis lacking cytochrome bd oxidase displays a significant growth defect in the presence of CO, while induction of the dos regulon appears to be unimportant for adaptation to CO. Altogether, our findings indicate that M. smegmatis has considerable resistance to CO and benefits from respiratory flexibility to withstand its inhibitory effects. IMPORTANCE Carbon monoxide has an infamous reputation as a toxic gas, and it has been suggested that it has potential as an antibacterial agent. Despite this, how bacteria resist its toxic effects is not well understood. In this study, we investigated how CO influences growth, proteome, and aerobic respiration of wild-type and mutant strains of Mycobacterium smegmatis. We show that this bacterium produces the CO-resistant cytochrome bd oxidase to tolerate poisoning of its CO-sensitive complex IV homolog. Further, we show that aside from this remodeling of its respiratory chain, M. smegmatis makes few other functional changes to its proteome, suggesting it has a high level of inherent resistance to CO.
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13
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A widely distributed hydrogenase oxidises atmospheric H 2 during bacterial growth. ISME JOURNAL 2020; 14:2649-2658. [PMID: 32647310 PMCID: PMC7784904 DOI: 10.1038/s41396-020-0713-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/25/2020] [Accepted: 06/30/2020] [Indexed: 11/09/2022]
Abstract
Diverse aerobic bacteria persist by consuming atmospheric hydrogen (H2) using group 1h [NiFe]-hydrogenases. However, other hydrogenase classes are also distributed in aerobes, including the group 2a [NiFe]-hydrogenase. Based on studies focused on Cyanobacteria, the reported physiological role of the group 2a [NiFe]-hydrogenase is to recycle H2 produced by nitrogenase. However, given this hydrogenase is also present in various heterotrophs and lithoautotrophs lacking nitrogenases, it may play a wider role in bacterial metabolism. Here we investigated the role of this enzyme in three species from different phylogenetic lineages and ecological niches: Acidithiobacillus ferrooxidans (phylum Proteobacteria), Chloroflexus aggregans (phylum Chloroflexota), and Gemmatimonas aurantiaca (phylum Gemmatimonadota). qRT-PCR analysis revealed that the group 2a [NiFe]-hydrogenase of all three species is significantly upregulated during exponential growth compared to stationary phase, in contrast to the profile of the persistence-linked group 1h [NiFe]-hydrogenase. Whole-cell biochemical assays confirmed that all three strains aerobically respire H2 to sub-atmospheric levels, and oxidation rates were much higher during growth. Moreover, the oxidation of H2 supported mixotrophic growth of the carbon-fixing strains C. aggregans and A. ferrooxidans. Finally, we used phylogenomic analyses to show that this hydrogenase is widely distributed and is encoded by 13 bacterial phyla. These findings challenge the current persistence-centric model of the physiological role of atmospheric H2 oxidation and extend this process to two more phyla, Proteobacteria and Gemmatimonadota. In turn, these findings have broader relevance for understanding how bacteria conserve energy in different environments and control the biogeochemical cycling of atmospheric trace gases.
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14
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Benoit SL, Maier RJ, Sawers RG, Greening C. Molecular Hydrogen Metabolism: a Widespread Trait of Pathogenic Bacteria and Protists. Microbiol Mol Biol Rev 2020; 84:e00092-19. [PMID: 31996394 PMCID: PMC7167206 DOI: 10.1128/mmbr.00092-19] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Pathogenic microorganisms use various mechanisms to conserve energy in host tissues and environmental reservoirs. One widespread but often overlooked means of energy conservation is through the consumption or production of molecular hydrogen (H2). Here, we comprehensively review the distribution, biochemistry, and physiology of H2 metabolism in pathogens. Over 200 pathogens and pathobionts carry genes for hydrogenases, the enzymes responsible for H2 oxidation and/or production. Furthermore, at least 46 of these species have been experimentally shown to consume or produce H2 Several major human pathogens use the large amounts of H2 produced by colonic microbiota as an energy source for aerobic or anaerobic respiration. This process has been shown to be critical for growth and virulence of the gastrointestinal bacteria Salmonella enterica serovar Typhimurium, Campylobacter jejuni, Campylobacter concisus, and Helicobacter pylori (including carcinogenic strains). H2 oxidation is generally a facultative trait controlled by central regulators in response to energy and oxidant availability. Other bacterial and protist pathogens produce H2 as a diffusible end product of fermentation processes. These include facultative anaerobes such as Escherichia coli, S Typhimurium, and Giardia intestinalis, which persist by fermentation when limited for respiratory electron acceptors, as well as obligate anaerobes, such as Clostridium perfringens, Clostridioides difficile, and Trichomonas vaginalis, that produce large amounts of H2 during growth. Overall, there is a rich literature on hydrogenases in growth, survival, and virulence in some pathogens. However, we lack a detailed understanding of H2 metabolism in most pathogens, especially obligately anaerobic bacteria, as well as a holistic understanding of gastrointestinal H2 transactions overall. Based on these findings, we also evaluate H2 metabolism as a possible target for drug development or other therapies.
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Affiliation(s)
- Stéphane L Benoit
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Robert J Maier
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - R Gary Sawers
- Institute of Microbiology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia
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15
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Schmitz RA, Pol A, Mohammadi SS, Hogendoorn C, van Gelder AH, Jetten MSM, Daumann LJ, Op den Camp HJM. The thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV oxidizes subatmospheric H 2 with a high-affinity, membrane-associated [NiFe] hydrogenase. ISME JOURNAL 2020; 14:1223-1232. [PMID: 32042101 PMCID: PMC7174314 DOI: 10.1038/s41396-020-0609-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/28/2020] [Accepted: 01/30/2020] [Indexed: 12/23/2022]
Abstract
The trace amounts (0.53 ppmv) of atmospheric hydrogen gas (H2) can be utilized by microorganisms to persist during dormancy. This process is catalyzed by certain Actinobacteria, Acidobacteria, and Chloroflexi, and is estimated to convert 75 × 1012 g H2 annually, which is half of the total atmospheric H2. This rapid atmospheric H2 turnover is hypothesized to be catalyzed by high-affinity [NiFe] hydrogenases. However, apparent high-affinity H2 oxidation has only been shown in whole cells, rather than for the purified enzyme. Here, we show that the membrane-associated hydrogenase from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV possesses a high apparent affinity (Km(app) = 140 nM) for H2 and that methanotrophs can oxidize subatmospheric H2. Our findings add to the evidence that the group 1h [NiFe] hydrogenase is accountable for atmospheric H2 oxidation and that it therefore could be a strong controlling factor in the global H2 cycle. We show that the isolated enzyme possesses a lower affinity (Km = 300 nM) for H2 than the membrane-associated enzyme. Hence, the membrane association seems essential for a high affinity for H2. The enzyme is extremely thermostable and remains folded up to 95 °C. Strain SolV is the only known organism in which the group 1h [NiFe] hydrogenase is responsible for rapid growth on H2 as sole energy source as well as oxidation of subatmospheric H2. The ability to conserve energy from H2 could increase fitness of verrucomicrobial methanotrophs in geothermal ecosystems with varying CH4 fluxes. We propose that H2 oxidation can enhance growth of methanotrophs in aerated methane-driven ecosystems. Group 1h [NiFe] hydrogenases could therefore contribute to mitigation of global warming, since CH4 is an important and extremely potent greenhouse gas.
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Affiliation(s)
- Rob A Schmitz
- Department of Microbiology, Radboud University, Heyendaalseweg 135, NL-6525 AJ, Nijmegen, The Netherlands
| | - Arjan Pol
- Department of Microbiology, Radboud University, Heyendaalseweg 135, NL-6525 AJ, Nijmegen, The Netherlands
| | - Sepehr S Mohammadi
- Department of Microbiology, Radboud University, Heyendaalseweg 135, NL-6525 AJ, Nijmegen, The Netherlands
| | - Carmen Hogendoorn
- Department of Microbiology, Radboud University, Heyendaalseweg 135, NL-6525 AJ, Nijmegen, The Netherlands
| | - Antonie H van Gelder
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud University, Heyendaalseweg 135, NL-6525 AJ, Nijmegen, The Netherlands
| | - Lena J Daumann
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstraβe 5-13, D-81377, München, Germany
| | - Huub J M Op den Camp
- Department of Microbiology, Radboud University, Heyendaalseweg 135, NL-6525 AJ, Nijmegen, The Netherlands.
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16
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Greening C, Boyd E. Editorial: Microbial Hydrogen Metabolism. Front Microbiol 2020; 11:56. [PMID: 32082284 PMCID: PMC7002543 DOI: 10.3389/fmicb.2020.00056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 01/13/2020] [Indexed: 11/14/2022] Open
Affiliation(s)
- Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Eric Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
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17
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Islam ZF, Cordero PRF, Greening C. Putative Iron-Sulfur Proteins Are Required for Hydrogen Consumption and Enhance Survival of Mycobacteria. Front Microbiol 2019; 10:2749. [PMID: 31824474 PMCID: PMC6883350 DOI: 10.3389/fmicb.2019.02749] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 11/12/2019] [Indexed: 01/01/2023] Open
Abstract
Aerobic soil bacteria persist by scavenging molecular hydrogen (H2) from the atmosphere. This key process is the primary sink in the biogeochemical hydrogen cycle and supports the productivity of oligotrophic ecosystems. In Mycobacterium smegmatis, atmospheric H2 oxidation is catalyzed by two phylogenetically distinct [NiFe]-hydrogenases, Huc (group 2a) and Hhy (group 1h). However, it is currently unresolved how these enzymes transfer electrons derived from H2 oxidation into the aerobic respiratory chain. In this work, we used genetic approaches to confirm that two putative iron-sulfur cluster proteins encoded on the hydrogenase structural operons, HucE and HhyE, are required for H2 consumption in M. smegmatis. Sequence analysis show that these proteins, while homologous, fall into distinct phylogenetic clades and have distinct metal-binding motifs. H2 oxidation was reduced when the genes encoding these proteins were deleted individually and was eliminated when they were deleted in combination. In turn, the growth yield and long-term survival of these deletion strains was modestly but significantly reduced compared to the parent strain. In both biochemical and phenotypic assays, the mutant strains lacking the putative iron-sulfur proteins phenocopied those of hydrogenase structural subunit mutants. We hypothesize that these proteins mediate electron transfer between the catalytic subunits of the hydrogenases and the menaquinone pool of the M. smegmatis respiratory chain; however, other roles (e.g., in maturation) are also plausible and further work is required to resolve their role. The conserved nature of these proteins within most Hhy- or Huc-encoding organisms suggests that these proteins are important determinants of atmospheric H2 oxidation.
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Affiliation(s)
| | | | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
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18
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Mohammadi SS, Schmitz RA, Pol A, Berben T, Jetten MSM, Op den Camp HJM. The Acidophilic Methanotroph Methylacidimicrobium tartarophylax 4AC Grows as Autotroph on H 2 Under Microoxic Conditions. Front Microbiol 2019; 10:2352. [PMID: 31681216 PMCID: PMC6813726 DOI: 10.3389/fmicb.2019.02352] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 09/27/2019] [Indexed: 12/17/2022] Open
Abstract
Emissions of the strong greenhouse gas methane (CH4) to the atmosphere are mitigated by methanotrophic microorganisms. Methanotrophs found in extremely acidic geothermal systems belong to the phylum Verrucomicrobia. Thermophilic verrucomicrobial methanotrophs from the genus Methylacidiphilum can grow autotrophically on hydrogen gas (H2), but it is unknown whether this also holds for their mesophilic counterparts from the genus Methylacidimicrobium. To determine this, we examined H2 consumption and CO2 fixation by the mesophilic verrucomicrobial methanotroph Methylacidimicrobium tartarophylax 4AC. We found that strain 4AC grows autotrophically on H2 with a maximum growth rate of 0.0048 h–1 and a yield of 2.1 g dry weight⋅mol H2–1, which is about 12 and 41% compared to the growth rate and yield on methane, respectively. The genome of strain 4AC only encodes for an oxygen-sensitive group 1b [NiFe] hydrogenase and H2 is respired only when oxygen concentrations are below 40 μM. Phylogenetic analysis and genomic comparison of methanotrophs revealed diverse [NiFe] hydrogenases, presumably with varying oxygen sensitivity and affinity for H2, which could drive niche differentiation. Our results show that both thermophilic and mesophilic verrucomicrobial methanotrophs can grow as autotrophs on H2 as a sole energy source. Our results suggest that verrucomicrobial methanotrophs are particularly well-equipped to thrive in hostile volcanic ecosystems, since they can consume H2 as additional energy source.
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Affiliation(s)
- Sepehr S Mohammadi
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Rob A Schmitz
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Arjan Pol
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Tom Berben
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
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