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Murali R, Pace LA, Sanford RA, Ward LM, Lynes MM, Hatzenpichler R, Lingappa UF, Fischer WW, Gennis RB, Hemp J. Diversity and evolution of nitric oxide reduction in bacteria and archaea. Proc Natl Acad Sci U S A 2024; 121:e2316422121. [PMID: 38900790 DOI: 10.1073/pnas.2316422121] [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: 09/27/2023] [Accepted: 04/24/2024] [Indexed: 06/22/2024] Open
Abstract
Nitrous oxide is a potent greenhouse gas whose production is catalyzed by nitric oxide reductase (NOR) members of the heme-copper oxidoreductase (HCO) enzyme superfamily. We identified several previously uncharacterized HCO families, four of which (eNOR, sNOR, gNOR, and nNOR) appear to perform NO reduction. These families have novel active-site structures and several have conserved proton channels, suggesting that they might be able to couple NO reduction to energy conservation. We isolated and biochemically characterized a member of the eNOR family from the bacterium Rhodothermus marinus and found that it performs NO reduction. These recently identified NORs exhibited broad phylogenetic and environmental distributions, greatly expanding the diversity of microbes in nature capable of NO reduction. Phylogenetic analyses further demonstrated that NORs evolved multiple times independently from oxygen reductases, supporting the view that complete denitrification evolved after aerobic respiration.
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Affiliation(s)
- Ranjani Murali
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL 61801
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89154
| | - Laura A Pace
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL 61801
- meliora.bio, Salt Lake City, UT 84103
| | - Robert A Sanford
- Department of Earth Science and Environmental Change, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - L M Ward
- Department of Geosciences, Smith College, Northampton, MA 01063
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125
| | - Mackenzie M Lynes
- Department of Chemistry and Biochemistry, Thermal Biology Institute, Montana State University, Bozeman, MT 59717
- Center for Biofilm Enginering, Montana State University, Bozeman, MT 59717
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Thermal Biology Institute, Montana State University, Bozeman, MT 59717
- Center for Biofilm Enginering, Montana State University, Bozeman, MT 59717
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717
| | - Usha F Lingappa
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Woodward W Fischer
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125
| | - Robert B Gennis
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL 61801
| | - James Hemp
- meliora.bio, Salt Lake City, UT 84103
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125
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2
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Sarkar J, Mondal M, Bhattacharya S, Dutta S, Chatterjee S, Mondal N, N S, Peketi A, Mazumdar A, Ghosh W. Extremely oligotrophic and complex-carbon-degrading microaerobic bacteria from Arabian Sea oxygen minimum zone sediments. Arch Microbiol 2024; 206:179. [PMID: 38498215 DOI: 10.1007/s00203-024-03875-y] [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: 10/30/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 03/20/2024]
Abstract
Sediments underlying marine hypoxic zones are huge sinks of unreacted complex organic matter, where despite acute O2 limitation, obligately aerobic bacteria thrive, and steady depletion of organic carbon takes place within a few meters below the seafloor. However, little knowledge exists about the sustenance and complex carbon degradation potentials of aerobic chemoorganotrophs in these sulfidic ecosystems. We isolated and characterized a number of aerobic bacterial chemoorganoheterotrophs from across a ~ 3 m sediment horizon underlying the perennial hypoxic zone of the eastern Arabian Sea. High levels of sequence correspondence between the isolates' genomes and the habitat's metagenomes and metatranscriptomes illustrated that the strains were widespread and active across the sediment cores explored. The isolates catabolized several complex organic compounds of marine and terrestrial origins in the presence of high or low, but not zero, O2. Some of them could also grow anaerobically on yeast extract or acetate by reducing nitrate and/or nitrite. Fermentation did not support growth, but enabled all the strains to maintain a fraction of their cell populations over prolonged anoxia. Under extreme oligotrophy, limited growth followed by protracted stationary phase was observed for all the isolates at low cell density, amid high or low, but not zero, O2 concentration. While population control and maintenance could be particularly useful for the strains' survival in the critically carbon-depleted layers below the explored sediment depths (core-bottom organic carbon: 0.5-1.0% w/w), metagenomic data suggested that in situ anoxia could be surmounted via potential supplies of cryptic O2 from previously reported sources such as Nitrosopumilus species.
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Affiliation(s)
- Jagannath Sarkar
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, West Bengal, India.
| | - Mahamadul Mondal
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, West Bengal, India
| | - Sabyasachi Bhattacharya
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, West Bengal, India
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Subhajit Dutta
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, West Bengal, India
| | - Sumit Chatterjee
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, West Bengal, India
| | - Nibendu Mondal
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, West Bengal, India
- International Institute of Innovation and Technology, Kolkata, West Bengal, India
| | - Saran N
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, West Bengal, India
| | - Aditya Peketi
- Geological Oceanography, CSIR National Institute of Oceanography, Dona Paula, Goa, 403004, India
| | - Aninda Mazumdar
- Geological Oceanography, CSIR National Institute of Oceanography, Dona Paula, Goa, 403004, India
| | - Wriddhiman Ghosh
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, West Bengal, India.
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Saghaï A, Pold G, Jones CM, Hallin S. Phyloecology of nitrate ammonifiers and their importance relative to denitrifiers in global terrestrial biomes. Nat Commun 2023; 14:8249. [PMID: 38086813 PMCID: PMC10716430 DOI: 10.1038/s41467-023-44022-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Nitrate ammonification is important for soil nitrogen retention. However, the ecology of ammonifiers and their prevalence compared with denitrifiers, being competitors for nitrate, are overlooked. Here, we screen 1 million genomes for nrfA and onr, encoding ammonifier nitrite reductases. About 40% of ammonifier assemblies carry at least one denitrification gene and show higher potential for nitrous oxide production than consumption. We then use a phylogeny-based approach to recruit gene fragments of nrfA, onr and denitrification nitrite reductase genes (nirK, nirS) in 1861 global terrestrial metagenomes. nrfA outnumbers the nearly negligible onr counts in all biomes, but denitrification genes dominate, except in tundra. Random forest modelling teases apart the influence of the soil C/N on nrfA-ammonifier vs denitrifier abundance, showing an effect of nitrate rather than carbon content. This study demonstrates the multiple roles nitrate ammonifiers play in nitrogen cycling and identifies factors ultimately controlling the fate of soil nitrate.
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Affiliation(s)
- Aurélien Saghaï
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden
| | - Grace Pold
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden
| | - Christopher M Jones
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden
| | - Sara Hallin
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden.
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Khalfaoui-Hassani B, Blaby-Haas CE, Verissimo A, Daldal F. The Escherichia coli MFS-type transporter genes yhjE, ydiM, and yfcJ are required to produce an active bo3 quinol oxidase. PLoS One 2023; 18:e0293015. [PMID: 37862358 PMCID: PMC10588857 DOI: 10.1371/journal.pone.0293015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/04/2023] [Indexed: 10/22/2023] Open
Abstract
Heme-copper oxygen reductases are membrane-bound oligomeric complexes that are integral to prokaryotic and eukaryotic aerobic respiratory chains. Biogenesis of these enzymes is complex and requires coordinated assembly of the subunits and their cofactors. Some of the components are involved in the acquisition and integration of different heme and copper (Cu) cofactors into these terminal oxygen reductases. As such, MFS-type transporters of the CalT family (e.g., CcoA) are required for Cu import and heme-CuB center biogenesis of the cbb3-type cytochrome c oxidases (cbb3-Cox). However, functionally homologous Cu transporters for similar heme-Cu containing bo3-type quinol oxidases (bo3-Qox) are unknown. Despite the occurrence of multiple MFS-type transporters, orthologs of CcoA are absent in bacteria like Escherichia coli that contain bo3-Qox. In this work, we identified a subset of uncharacterized MFS transporters, based on the presence of putative metal-binding residues, as likely candidates for the missing Cu transporter. Using a genetic approach, we tested whether these transporters are involved in the biogenesis of E. coli bo3-Qox. When respiratory growth is dependent on bo3-Qox, because of deletion of the bd-type Qox enzymes, three candidate genes, yhjE, ydiM, and yfcJ, were found to be critical for E. coli growth. Radioactive metal uptake assays showed that ΔydiM has a slower 64Cu uptake, whereas ΔyhjE accumulates reduced 55Fe in the cell, while no similar uptake defect is associated with ΔycfJ. Phylogenomic analyses suggest plausible roles for the YhjE, YdiM, and YfcJ transporters, and overall findings illustrate the diverse roles that the MFS-type transporters play in cellular metal homeostasis and production of active heme-Cu oxygen reductases.
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Affiliation(s)
- Bahia Khalfaoui-Hassani
- Université de Pau et des Pays de l’Adour, E2S UPPA, IPREM, UMR CNRS, Pau, France
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Crysten E. Blaby-Haas
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
- Lawrence Berkeley National Laboratory, The Molecular Foundry, Berkeley, CA, United States of America
| | - Andreia Verissimo
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States of America
- bioMT-Institute for Biomolecular Targeting, Geisel School of Medicine at Dartmouth, Hanover, NH, United States of America
| | - Fevzi Daldal
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States of America
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5
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Zhang IH, Sun X, Jayakumar A, Fortin SG, Ward BB, Babbin AR. Partitioning of the denitrification pathway and other nitrite metabolisms within global oxygen deficient zones. ISME COMMUNICATIONS 2023; 3:76. [PMID: 37474642 PMCID: PMC10359470 DOI: 10.1038/s43705-023-00284-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 07/22/2023]
Abstract
Oxygen deficient zones (ODZs) account for about 30% of total oceanic fixed nitrogen loss via processes including denitrification, a microbially mediated pathway proceeding stepwise from NO3- to N2. This process may be performed entirely by complete denitrifiers capable of all four enzymatic steps, but many organisms possess only partial denitrification pathways, either producing or consuming key intermediates such as the greenhouse gas N2O. Metagenomics and marker gene surveys have revealed a diversity of denitrification genes within ODZs, but whether these genes co-occur within complete or partial denitrifiers and the identities of denitrifying taxa remain open questions. We assemble genomes from metagenomes spanning the ETNP and Arabian Sea, and map these metagenome-assembled genomes (MAGs) to 56 metagenomes from all three major ODZs to reveal the predominance of partial denitrifiers, particularly single-step denitrifiers. We find niche differentiation among nitrogen-cycling organisms, with communities performing each nitrogen transformation distinct in taxonomic identity and motility traits. Our collection of 962 MAGs presents the largest collection of pelagic ODZ microorganisms and reveals a clearer picture of the nitrogen cycling community within this environment.
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Affiliation(s)
- Irene H Zhang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Program in Microbiology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Xin Sun
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Amal Jayakumar
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | | | - Bess B Ward
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Andrew R Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
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6
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Ruff SE, Humez P, de Angelis IH, Diao M, Nightingale M, Cho S, Connors L, Kuloyo OO, Seltzer A, Bowman S, Wankel SD, McClain CN, Mayer B, Strous M. Hydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems. Nat Commun 2023; 14:3194. [PMID: 37311764 DOI: 10.1038/s41467-023-38523-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 05/05/2023] [Indexed: 06/15/2023] Open
Abstract
Around 50% of humankind relies on groundwater as a source of drinking water. Here we investigate the age, geochemistry, and microbiology of 138 groundwater samples from 95 monitoring wells (<250 m depth) located in 14 aquifers in Canada. The geochemistry and microbiology show consistent trends suggesting large-scale aerobic and anaerobic hydrogen, methane, nitrogen, and sulfur cycling carried out by diverse microbial communities. Older groundwaters, especially in aquifers with organic carbon-rich strata, contain on average more cells (up to 1.4 × 107 mL-1) than younger groundwaters, challenging current estimates of subsurface cell abundances. We observe substantial concentrations of dissolved oxygen (0.52 ± 0.12 mg L-1 [mean ± SE]; n = 57) in older groundwaters that seem to support aerobic metabolisms in subsurface ecosystems at an unprecedented scale. Metagenomics, oxygen isotope analyses and mixing models indicate that dark oxygen is produced in situ via microbial dismutation. We show that ancient groundwaters sustain productive communities and highlight an overlooked oxygen source in present and past subsurface ecosystems of Earth.
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Affiliation(s)
- S Emil Ruff
- Department of Geoscience, University of Calgary, Calgary, Canada.
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA.
- Ecosystems Center, Marine Biological Laboratory, Woods Hole, MA, USA.
| | - Pauline Humez
- Department of Geoscience, University of Calgary, Calgary, Canada
| | - Isabella Hrabe de Angelis
- Department of Geoscience, University of Calgary, Calgary, Canada
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
| | - Muhe Diao
- Department of Geoscience, University of Calgary, Calgary, Canada
| | | | - Sara Cho
- Department of Geoscience, University of Calgary, Calgary, Canada
| | - Liam Connors
- Department of Geoscience, University of Calgary, Calgary, Canada
| | | | - Alan Seltzer
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Samuel Bowman
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Scott D Wankel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Cynthia N McClain
- Department of Geoscience, University of Calgary, Calgary, Canada
- Alberta Environment and Protected Areas, Calgary, Canada
- Alberta Biodiversity Monitoring Institute, Edmonton, Canada
| | - Bernhard Mayer
- Department of Geoscience, University of Calgary, Calgary, Canada
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, Canada
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7
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Flynn AJ, Antonyuk SV, Eady RR, Muench SP, Hasnain SS. A 2.2 Å cryoEM structure of a quinol-dependent NO Reductase shows close similarity to respiratory oxidases. Nat Commun 2023; 14:3416. [PMID: 37296134 PMCID: PMC10256718 DOI: 10.1038/s41467-023-39140-x] [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: 11/25/2022] [Accepted: 05/31/2023] [Indexed: 06/12/2023] Open
Abstract
Quinol-dependent nitric oxide reductases (qNORs) are considered members of the respiratory heme-copper oxidase superfamily, are unique to bacteria, and are commonly found in pathogenic bacteria where they play a role in combating the host immune response. qNORs are also essential enzymes in the denitrification pathway, catalysing the reduction of nitric oxide to nitrous oxide. Here, we determine a 2.2 Å cryoEM structure of qNOR from Alcaligenes xylosoxidans, an opportunistic pathogen and a denitrifying bacterium of importance in the nitrogen cycle. This high-resolution structure provides insight into electron, substrate, and proton pathways, and provides evidence that the quinol binding site not only contains the conserved His and Asp residues but also possesses a critical Arg (Arg720) observed in cytochrome bo3, a respiratory quinol oxidase.
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Affiliation(s)
- Alex J Flynn
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Svetlana V Antonyuk
- Molecular Biophysics Group, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, England
| | - Robert R Eady
- Molecular Biophysics Group, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, England
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - S Samar Hasnain
- Molecular Biophysics Group, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, England.
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8
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Structures of the intermediates in the catalytic cycle of mitochondrial cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148933. [PMID: 36403794 DOI: 10.1016/j.bbabio.2022.148933] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/30/2022] [Accepted: 11/07/2022] [Indexed: 11/18/2022]
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