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Mills J, Gebhard LJ, Schubotz F, Shevchenko A, Speth DR, Liao Y, Duggin IG, Marchfelder A, Erdmann S. Extracellular vesicle formation in Euryarchaeota is driven by a small GTPase. Proc Natl Acad Sci U S A 2024; 121:e2311321121. [PMID: 38408251 DOI: 10.1073/pnas.2311321121] [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: 07/14/2023] [Accepted: 01/14/2024] [Indexed: 02/28/2024] Open
Abstract
Since their discovery, extracellular vesicles (EVs) have changed our view on how organisms interact with their extracellular world. EVs are able to traffic a diverse array of molecules across different species and even domains, facilitating numerous functions. In this study, we investigate EV production in Euryarchaeota, using the model organism Haloferax volcanii. We uncover that EVs enclose RNA, with specific transcripts preferentially enriched, including those with regulatory potential, and conclude that EVs can act as an RNA communication system between haloarchaea. We demonstrate the key role of an EV-associated small GTPase for EV formation in H. volcanii that is also present across other diverse evolutionary branches of Archaea. We propose the name, ArvA, for the identified family of archaeal vesiculating GTPases. Additionally, we show that two genes in the same operon with arvA (arvB and arvC) are also involved in EV formation. Both, arvB and arvC, are closely associated with arvA in the majority of other archaea encoding ArvA. Our work demonstrates that small GTPases involved in membrane deformation and vesiculation, ubiquitous in Eukaryotes, are also present in Archaea and are widely distributed across diverse archaeal phyla.
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Affiliation(s)
- Joshua Mills
- Archaeal Virology, Max Planck Institute for Marine Microbiology, Bremen 28359, Germany
| | - L Johanna Gebhard
- Archaeal Virology, Max Planck Institute for Marine Microbiology, Bremen 28359, Germany
| | - Florence Schubotz
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen 28359, Germany
| | - Anna Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Daan R Speth
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen 28359, Germany
| | - Yan Liao
- The Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Iain G Duggin
- The Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW 2007, Australia
| | | | - Susanne Erdmann
- Archaeal Virology, Max Planck Institute for Marine Microbiology, Bremen 28359, Germany
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2
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Garrido-Amador P, Stortenbeker N, Wessels HJCT, Speth DR, Garcia-Heredia I, Kartal B. Publisher Correction: Enrichment and characterization of a nitric oxide-reducing microbial community in a continuous bioreactor. Nat Microbiol 2024:10.1038/s41564-024-01602-3. [PMID: 38308099 DOI: 10.1038/s41564-024-01602-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
Affiliation(s)
| | | | - Hans J C T Wessels
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Daan R Speth
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Boran Kartal
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- School of Science, Constructor University, Bremen, Germany.
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3
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Murali R, Yu H, Speth DR, Wu F, Metcalfe KS, Crémière A, Laso-Pèrez R, Malmstrom RR, Goudeau D, Woyke T, Hatzenpichler R, Chadwick GL, Connon SA, Orphan VJ. Physiological potential and evolutionary trajectories of syntrophic sulfate-reducing bacterial partners of anaerobic methanotrophic archaea. PLoS Biol 2023; 21:e3002292. [PMID: 37747940 PMCID: PMC10553843 DOI: 10.1371/journal.pbio.3002292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 10/05/2023] [Accepted: 08/08/2023] [Indexed: 09/27/2023] Open
Abstract
Sulfate-coupled anaerobic oxidation of methane (AOM) is performed by multicellular consortia of anaerobic methanotrophic archaea (ANME) in obligate syntrophic partnership with sulfate-reducing bacteria (SRB). Diverse ANME and SRB clades co-associate but the physiological basis for their adaptation and diversification is not well understood. In this work, we used comparative metagenomics and phylogenetics to investigate the metabolic adaptation among the 4 main syntrophic SRB clades (HotSeep-1, Seep-SRB2, Seep-SRB1a, and Seep-SRB1g) and identified features associated with their syntrophic lifestyle that distinguish them from their non-syntrophic evolutionary neighbors in the phylum Desulfobacterota. We show that the protein complexes involved in direct interspecies electron transfer (DIET) from ANME to the SRB outer membrane are conserved between the syntrophic lineages. In contrast, the proteins involved in electron transfer within the SRB inner membrane differ between clades, indicative of convergent evolution in the adaptation to a syntrophic lifestyle. Our analysis suggests that in most cases, this adaptation likely occurred after the acquisition of the DIET complexes in an ancestral clade and involve horizontal gene transfers within pathways for electron transfer (CbcBA) and biofilm formation (Pel). We also provide evidence for unique adaptations within syntrophic SRB clades, which vary depending on the archaeal partner. Among the most widespread syntrophic SRB, Seep-SRB1a, subclades that specifically partner ANME-2a are missing the cobalamin synthesis pathway, suggestive of nutritional dependency on its partner, while closely related Seep-SRB1a partners of ANME-2c lack nutritional auxotrophies. Our work provides insight into the features associated with DIET-based syntrophy and the adaptation of SRB towards it.
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Affiliation(s)
- Ranjani Murali
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Hang Yu
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, Unites Stated of America
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, United States of America
| | - Daan R. Speth
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Fabai Wu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Kyle S. Metcalfe
- Department of Plant and Molecular Biology, University of California, Berkeley. Berkeley, California, United States of America
| | - Antoine Crémière
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, Unites Stated of America
| | - Rafael Laso-Pèrez
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Rex R. Malmstrom
- DOE Joint Genome Institute, Department of Energy, Berkeley, California, United States of America
| | - Danielle Goudeau
- DOE Joint Genome Institute, Department of Energy, Berkeley, California, United States of America
| | - Tanja Woyke
- DOE Joint Genome Institute, Department of Energy, Berkeley, California, United States of America
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
| | - Grayson L. Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, Unites Stated of America
- Department of Plant and Molecular Biology, University of California, Berkeley. Berkeley, California, United States of America
| | - Stephanie A. Connon
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, Unites Stated of America
| | - Victoria J. Orphan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, Unites Stated of America
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4
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Garrido-Amador P, Stortenbeker N, Wessels HJCT, Speth DR, Garcia-Heredia I, Kartal B. Enrichment and characterization of a nitric oxide-reducing microbial community in a continuous bioreactor. Nat Microbiol 2023; 8:1574-1586. [PMID: 37429908 PMCID: PMC10390337 DOI: 10.1038/s41564-023-01425-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 02/09/2023] [Accepted: 06/14/2023] [Indexed: 07/12/2023]
Abstract
Nitric oxide (NO) is a highly reactive and climate-active molecule and a key intermediate in the microbial nitrogen cycle. Despite its role in the evolution of denitrification and aerobic respiration, high redox potential and capacity to sustain microbial growth, our understanding of NO-reducing microorganisms remains limited due to the absence of NO-reducing microbial cultures obtained directly from the environment using NO as a substrate. Here, using a continuous bioreactor and a constant supply of NO as the sole electron acceptor, we enriched and characterized a microbial community dominated by two previously unknown microorganisms that grow at nanomolar NO concentrations and survive high amounts (>6 µM) of this toxic gas, reducing it to N2 with little to non-detectable production of the greenhouse gas nitrous oxide. These results provide insight into the physiology of NO-reducing microorganisms, which have pivotal roles in the control of climate-active gases, waste removal, and evolution of nitrate and oxygen respiration.
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Affiliation(s)
| | | | - Hans J C T Wessels
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Daan R Speth
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Boran Kartal
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- School of Science, Constructor University, Bremen, Germany.
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5
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Laso-Pérez R, Wu F, Crémière A, Speth DR, Magyar JS, Zhao K, Krupovic M, Orphan VJ. Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome. Nat Microbiol 2023; 8:231-245. [PMID: 36658397 PMCID: PMC9894754 DOI: 10.1038/s41564-022-01297-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/29/2022] [Indexed: 01/21/2023]
Abstract
'Candidatus Methanophagales' (ANME-1) is an order-level clade of archaea responsible for anaerobic methane oxidation in deep-sea sediments. The diversity, ecology and evolution of ANME-1 remain poorly understood. In this study, we use metagenomics on deep-sea hydrothermal samples to expand ANME-1 diversity and uncover the effect of virus-host dynamics. Phylogenetic analyses reveal a deep-branching, thermophilic family, 'Candidatus Methanospirareceae', closely related to short-chain alkane oxidizers. Global phylogeny and near-complete genomes show that hydrogen metabolism within ANME-1 is an ancient trait that was vertically inherited but differentially lost during lineage diversification. Metagenomics also uncovered 16 undescribed virus families so far exclusively targeting ANME-1 archaea, showing unique structural and replicative signatures. The expansive ANME-1 virome contains a metabolic gene repertoire that can influence host ecology and evolution through virus-mediated gene displacement. Our results suggest an evolutionary continuum between anaerobic methane and short-chain alkane oxidizers and underscore the effects of viruses on the dynamics and evolution of methane-driven ecosystems.
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Affiliation(s)
- Rafael Laso-Pérez
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany.
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
| | - Fabai Wu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China.
- Ocean College, Zhejiang University, Zhoushan, China.
- Donghai Laboratory, Zhoushan, China.
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
| | - Antoine Crémière
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Daan R Speth
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
| | - John S Magyar
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Kehan Zhao
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France.
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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6
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Aronson HS, Monteverde DR, Barnes BD, Johnson BR, Zawaski MJ, Speth DR, Wang XT, Wu F, Webb SM, Trower EJ, Magyar JS, Sessions AL, Orphan VJ, Fischer WW. Sulfur cycling at natural hydrocarbon and sulfur seeps in Santa Paula Creek, CA. Geobiology 2022; 20:707-725. [PMID: 35894090 DOI: 10.1111/gbi.12512] [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] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 05/31/2022] [Accepted: 06/26/2022] [Indexed: 06/15/2023]
Abstract
Biogeochemical cycling of sulfur is relatively understudied in terrestrial environments compared to marine environments. However, the comparative ease of access, observation, and sampling of terrestrial settings can expand our understanding of organisms and processes important in the modern sulfur cycle. Furthermore, these sites may allow for the discovery of useful process analogs for ancient sulfur-metabolizing microbial communities at times in Earth's past when atmospheric O2 concentrations were lower and sulfide was more prevalent in Earth surface environments. We identified a new site at Santa Paula Creek (SPC) in Ventura County, CA-a remarkable freshwater, gravel-bedded mountain stream charged with a range of oxidized and reduced sulfur species and heavy hydrocarbons from the emergence of subsurface fluids within the underlying sulfur- and organic-rich Miocene-age Monterey Formation. SPC hosts a suite of morphologically distinct microbial biofacies that form in association with the naturally occurring hydrocarbon seeps and sulfur springs. We characterized the geology, stream geochemistry, and microbial facies and diversity of the Santa Paula Creek ecosystem. Using geochemical analyses and 16S rRNA gene sequencing, we found that SPC supports a dynamic sulfur cycle that is largely driven by sulfide-oxidizing microbial taxa, with contributions from smaller populations of sulfate-reducing and sulfur-disproportionating taxa. This preliminary characterization of SPC revealed an intriguing site in which to study geological and geochemical controls on microbial community composition and to expand our understanding of sulfur cycling in terrestrial environments.
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Affiliation(s)
- Heidi S Aronson
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Danielle R Monteverde
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
| | - Ben Davis Barnes
- Department of Geosciences, Pennsylvania State University, Pennsylvania, USA
| | - Brooke R Johnson
- Early Life Traces & Evolution-Astrobiology, University of Liège, Liège, Belgium
- Department of Earth Sciences, Oxford University, Oxford, UK
| | - Mike J Zawaski
- Department of Geological Sciences, University of Colorado Boulder, Boulder, Colorado, USA
| | - Daan R Speth
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Xingchen Tony Wang
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
- Department of Earth and Environmental Sciences, Boston College, Chestnut Hill, Massachusetts, USA
| | - Fenfang Wu
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
| | - Samuel M Webb
- SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, Menlo Park, California, USA
| | | | - John S Magyar
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
| | - Alex L Sessions
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Woodward W Fischer
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
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7
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Chadwick GL, Skennerton CT, Laso-Pérez R, Leu AO, Speth DR, Yu H, Morgan-Lang C, Hatzenpichler R, Goudeau D, Malmstrom R, Brazelton WJ, Woyke T, Hallam SJ, Tyson GW, Wegener G, Boetius A, Orphan VJ. Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea. PLoS Biol 2022; 20:e3001508. [PMID: 34986141 PMCID: PMC9012536 DOI: 10.1371/journal.pbio.3001508] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 04/15/2022] [Accepted: 12/08/2021] [Indexed: 11/25/2022] Open
Abstract
The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota, none of which have been isolated in pure culture. Here, we reconstruct 28 ANME genomes from environmental metagenomes and flow sorted syntrophic consortia. Together with a reanalysis of previously published datasets, these genomes enable a comparative analysis of all marine ANME clades. We review the genomic features that separate ANME from their methanogenic relatives and identify what differentiates ANME clades. Large multiheme cytochromes and bioenergetic complexes predicted to be involved in novel electron bifurcation reactions are well distributed and conserved in the ANME archaea, while significant variations in the anabolic C1 pathways exists between clades. Our analysis raises the possibility that methylotrophic methanogenesis may have evolved from a methanotrophic ancestor. A comparative genomics study of anaerobic methanotrophic (ANME) archaea reveals the genetic "parts list" associated with the repeated evolutionary transition between methanogenic and methanotrophic metabolism in the archaeal domain of life.
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Affiliation(s)
- Grayson L. Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (GLC); (VJO)
| | - Connor T. Skennerton
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Rafael Laso-Pérez
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Andy O. Leu
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Daan R. Speth
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Hang Yu
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Connor Morgan-Lang
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Roland Hatzenpichler
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Danielle Goudeau
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - Rex Malmstrom
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - William J. Brazelton
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Tanja Woyke
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - Steven J. Hallam
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia, Canada
- Department of Microbiology & Immunology, University of British Columbia, British Columbia, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada
- Life Sciences Institute, University of British Columbia, British Columbia, Canada
| | - Gene W. Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Gunter Wegener
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Antje Boetius
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
- Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Victoria J. Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (GLC); (VJO)
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8
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Phillips AA, Speth DR, Miller LG, Wang XT, Wu F, Medeiros PM, Monteverde DR, Osburn MR, Berelson WM, Betts HL, Wijker RS, Mullin SW, Johnson HA, Orphan VJ, Fischer WW, Sessions AL. Microbial succession and dynamics in meromictic Mono Lake, California. Geobiology 2021; 19:376-393. [PMID: 33629529 PMCID: PMC8359280 DOI: 10.1111/gbi.12437] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 11/18/2020] [Accepted: 02/08/2021] [Indexed: 05/30/2023]
Abstract
Mono Lake is a closed-basin, hypersaline, alkaline lake located in Eastern Sierra Nevada, California, that is dominated by microbial life. This unique ecosystem offers a natural laboratory for probing microbial community responses to environmental change. In 2017, a heavy snowpack and subsequent runoff led Mono Lake to transition from annually mixed (monomictic) to indefinitely stratified (meromictic). We followed microbial succession during this limnological shift, establishing a two-year (2017-2018) water-column time series of geochemical and microbiological data. Following meromictic conditions, anoxia persisted below the chemocline and reduced compounds such as sulfide and ammonium increased in concentration from near 0 to ~400 and ~150 µM, respectively, throughout 2018. We observed significant microbial succession, with trends varying by water depth. In the epilimnion (above the chemocline), aerobic heterotrophs were displaced by phototrophic genera when a large bloom of cyanobacteria appeared in fall 2018. Bacteria in the hypolimnion (below the chemocline) had a delayed, but systematic, response reflecting colonization by sediment "seed bank" communities. Phototrophic sulfide-oxidizing bacteria appeared first in summer 2017, followed by microbes associated with anaerobic fermentation in spring 2018, and eventually sulfate-reducing taxa by fall 2018. This slow shift indicated that multi-year meromixis was required to establish a sulfate-reducing community in Mono Lake, although sulfide oxidizers thrive throughout mixing regimes. The abundant green alga Picocystis remained the dominant primary producer during the meromixis event, abundant throughout the water column including in the hypolimnion despite the absence of light and prevalence of sulfide. Our study adds to the growing literature describing microbial resistance and resilience during lake mixing events related to climatic events and environmental change.
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Affiliation(s)
- Alexandra A. Phillips
- Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
| | - Daan R. Speth
- Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
| | - Laurence G. Miller
- United States Geological Survey, Earth Systems Process DivisionMenlo ParkCAUSA
| | - Xingchen T. Wang
- Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
- Department of Earth and Environmental SciencesBoston CollegeChestnut HillMAUSA
| | - Fenfang Wu
- Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
| | | | - Danielle R. Monteverde
- Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
| | - Magdalena R. Osburn
- Department of Earth and Planetary SciencesNorthwestern UniversityEvanstonILUSA
| | - William M. Berelson
- Department of Earth SciencesUniversity of Southern CaliforniaLos AngelesCAUSA
| | | | - Reto S. Wijker
- Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
| | - Sean W. Mullin
- Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
| | - Hope A. Johnson
- Department of Biological ScienceCalifornia State University FullertonFullertonCAUSA
| | - Victoria J. Orphan
- Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
| | - Woodward W. Fischer
- Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
| | - Geobiology Course 2017
- Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
| | - Geobiology Course 2018
- Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
| | - Alex L. Sessions
- Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
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9
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Kox MAR, Smolders AJP, Speth DR, Lamers LPM, Op den Camp HJM, Jetten MSM, van Kessel MAHJ. A Novel Laboratory-Scale Mesocosm Setup to Study Methane Emission Mitigation by Sphagnum Mosses and Associated Methanotrophs. Front Microbiol 2021; 12:652486. [PMID: 33981290 PMCID: PMC8108401 DOI: 10.3389/fmicb.2021.651103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/26/2021] [Indexed: 11/13/2022] Open
Abstract
Degraded peatlands are often rewetted to prevent oxidation of the peat, which reduces CO2 emission. However, the created anoxic conditions will boost methane (CH4) production and thus emission. Here, we show that submerged Sphagnum peat mosses in rewetted-submerged peatlands can reduce CH4 emission from peatlands with 93%. We were able to mimic the field situation in the laboratory by using a novel mesocosm set-up. By combining these with 16S rRNA gene amplicon sequencing and qPCR analysis of the pmoA and mmoX genes, we showed that submerged Sphagnum mosses act as a niche for CH4 oxidizing bacteria. The tight association between Sphagnum peat mosses and methane oxidizing bacteria (MOB) significantly reduces CH4 emissions by peatlands and can be studied in more detail in the mesocosm setup developed in this study.
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Affiliation(s)
- Martine A R Kox
- Department of Microbiology, IWWR, Radboud University, Nijmegen, Netherlands.,Department of Aquatic Ecology and Environmental Biology, IWWR, Radboud University, Nijmegen, Netherlands
| | - Alfons J P Smolders
- Department of Aquatic Ecology and Environmental Biology, IWWR, Radboud University, Nijmegen, Netherlands.,B-WARE Research Centre, Nijmegen, Netherlands
| | - Daan R Speth
- Department of Microbiology, IWWR, Radboud University, Nijmegen, Netherlands
| | - Leon P M Lamers
- Department of Aquatic Ecology and Environmental Biology, IWWR, Radboud University, Nijmegen, Netherlands
| | | | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University, Nijmegen, Netherlands
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10
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Speth DR, Orphan VJ. Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales. PeerJ 2018; 6:e5614. [PMID: 30245936 PMCID: PMC6147122 DOI: 10.7717/peerj.5614] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 08/21/2018] [Indexed: 01/24/2023] Open
Abstract
Over the past years, metagenomics has revolutionized our view of microbial diversity. Moreover, extracting near-complete genomes from metagenomes has led to the discovery of known metabolic traits in unsuspected lineages. Genome-resolved metagenomics relies on assembly of the sequencing reads and subsequent binning of assembled contigs, which might be hampered by strain heterogeneity or low abundance of a target organism. Here we present a complementary approach, metagenome marker gene mining, and use it to assess the global diversity of archaeal methane metabolism through the mcrA gene. To this end, we have screened 18,465 metagenomes for the presence of reads matching a database representative of all known mcrA proteins and reconstructed gene sequences from the matching reads. We use our mcrA dataset to assess the environmental distribution of the Methanomassiliicoccales and reconstruct and analyze a draft genome belonging to the ‘Lake Pavin cluster’, an uncultivated environmental clade of the Methanomassiliicoccales. Analysis of the ‘Lake Pavin cluster’ draft genome suggests that this organism has a more restricted capacity for hydrogenotrophic methylotrophic methanogenesis than previously studied Methanomassiliicoccales, with only genes for growth on methanol present. However, the presence of the soluble subunits of methyltetrahydromethanopterin:CoM methyltransferase (mtrAH) provide hypothetical pathways for methanol fermentation, and aceticlastic methanogenesis that await experimental verification. Thus, we show that marker gene mining can enhance the discovery power of metagenomics, by identifying novel lineages and aiding selection of targets for in-depth analyses. Marker gene mining is less sensitive to strain heterogeneity and has a lower abundance threshold than genome-resolved metagenomics, as it only requires short contigs and there is no binning step. Additionally, it is computationally cheaper than genome resolved metagenomics, since only a small subset of reads needs to be assembled. It is therefore a suitable approach to extract knowledge from the many publicly available sequencing projects.
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Affiliation(s)
- Daan R Speth
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States of America
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States of America
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11
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Versantvoort W, Guerrero-Cruz S, Speth DR, Frank J, Gambelli L, Cremers G, van Alen T, Jetten MSM, Kartal B, Op den Camp HJM, Reimann J. Comparative Genomics of Candidatus Methylomirabilis Species and Description of Ca. Methylomirabilis Lanthanidiphila. Front Microbiol 2018; 9:1672. [PMID: 30140258 PMCID: PMC6094997 DOI: 10.3389/fmicb.2018.01672] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 07/04/2018] [Indexed: 11/18/2022] Open
Abstract
Methane is a potent greenhouse gas, which can be converted by microorganism at the expense of oxygen, nitrate, nitrite, metal-oxides or sulfate. The bacterium ‘Candidatus Methylomirabilis oxyfera,’ a member of the NC10 phylum, is capable of nitrite-dependent anaerobic methane oxidation. Prolonged enrichment of ‘Ca. M. oxyfera’ with cerium added as trace element and without nitrate resulted in the shift of the dominant species. Here, we present a high quality draft genome of the new species ‘Candidatus Methylomirabilis lanthanidiphila’ and use comparative genomics to analyze its metabolic potential in both nitrogen and carbon cycling. To distinguish between gene content specific for the ‘Ca. Methylomirabilis’ genus and the NC10 phylum, the genome of a distantly related NC10 phylum member, CSP1-5, an aerobic methylotroph, is included in the analysis. All genes for the conversion of nitrite to N2 identified in ‘Ca. M. oxyfera’ are conserved in ‘Ca. M. lanthanidiphila,’ including the two putative genes for NO dismutase. In addition both species have several heme-copper oxidases potentially involved in NO and O2 respiration. For the oxidation of methane ‘Ca. Methylomirabilis’ species encode a membrane bound methane monooxygenase. CSP1-5 can act as a methylotroph, but lacks the ability to activate methane. In contrast to ‘Ca. M. oxyfera,’ which harbors three methanol dehydrogenases (MDH), both CSP1-5 and ‘Ca. M. lanthanidiphila’ only encode a lanthanide-dependent XoxF-type MDH, once more underlining the importance of rare earth elements for methylotrophic bacteria. The pathways for the subsequent oxidation of formaldehyde to carbon dioxide and for the Calvin–Benson–Bassham cycle are conserved in all species. Furthermore, CSP1-5 can only interconvert nitrate and nitrite, but lacks subsequent nitrite or NO reductases. Thus, it appears that although the conversion of methanol to carbon dioxide is present in several NC10 phylum bacteria, the coupling of nitrite reduction to the oxidation of methane is a trait so far unique to the genus ‘Ca. Methylomirabilis.’
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Affiliation(s)
- Wouter Versantvoort
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Simon Guerrero-Cruz
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Daan R Speth
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Jeroen Frank
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Lavinia Gambelli
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Geert Cremers
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Theo van Alen
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands.,Soehngen Institute of Anaerobic Microbiology, Nijmegen, Netherlands
| | - Boran Kartal
- Microbial Physiology Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Huub J M Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Joachim Reimann
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
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12
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Speth DR, Lagkouvardos I, Wang Y, Qian PY, Dutilh BE, Jetten MSM. Draft Genome of Scalindua rubra, Obtained from the Interface Above the Discovery Deep Brine in the Red Sea, Sheds Light on Potential Salt Adaptation Strategies in Anammox Bacteria. Microb Ecol 2017; 74:1-5. [PMID: 28074246 PMCID: PMC5486813 DOI: 10.1007/s00248-017-0929-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 01/01/2017] [Indexed: 05/21/2023]
Abstract
Several recent studies have indicated that members of the phylum Planctomycetes are abundantly present at the brine-seawater interface (BSI) above multiple brine pools in the Red Sea. Planctomycetes include bacteria capable of anaerobic ammonium oxidation (anammox). Here, we investigated the possibility of anammox at BSI sites using metagenomic shotgun sequencing of DNA obtained from the BSI above the Discovery Deep brine pool. Analysis of sequencing reads matching the 16S rRNA and hzsA genes confirmed presence of anammox bacteria of the genus Scalindua. Phylogenetic analysis of the 16S rRNA gene indicated that this Scalindua sp. belongs to a distinct group, separate from the anammox bacteria in the seawater column, that contains mostly sequences retrieved from high-salt environments. Using coverage- and composition-based binning, we extracted and assembled the draft genome of the dominant anammox bacterium. Comparative genomic analysis indicated that this Scalindua species uses compatible solutes for osmoadaptation, in contrast to other marine anammox bacteria that likely use a salt-in strategy. We propose the name Candidatus Scalindua rubra for this novel species, alluding to its discovery in the Red Sea.
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Affiliation(s)
- Daan R Speth
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands.
- Division for Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
| | - Ilias Lagkouvardos
- ZIEL Institute for Food and Health, Technische Universität München, Freising, Germany
| | - Yong Wang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Pei-Yuan Qian
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
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13
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Lüke C, Speth DR, Kox MAR, Villanueva L, Jetten MSM. Metagenomic analysis of nitrogen and methane cycling in the Arabian Sea oxygen minimum zone. PeerJ 2016; 4:e1924. [PMID: 27077014 PMCID: PMC4830246 DOI: 10.7717/peerj.1924] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Accepted: 03/21/2016] [Indexed: 01/24/2023] Open
Abstract
Oxygen minimum zones (OMZ) are areas in the global ocean where oxygen concentrations drop to below one percent. Low oxygen concentrations allow alternative respiration with nitrate and nitrite as electron acceptor to become prevalent in these areas, making them main contributors to oceanic nitrogen loss. The contribution of anammox and denitrification to nitrogen loss seems to vary in different OMZs. In the Arabian Sea, both processes were reported. Here, we performed a metagenomics study of the upper and core zone of the Arabian Sea OMZ, to provide a comprehensive overview of the genetic potential for nitrogen and methane cycling. We propose that aerobic ammonium oxidation is carried out by a diverse community of Thaumarchaeota in the upper zone of the OMZ, whereas a low diversity of Scalindua-like anammox bacteria contribute significantly to nitrogen loss in the core zone. Aerobic nitrite oxidation in the OMZ seems to be performed by Nitrospina spp. and a novel lineage of nitrite oxidizing organisms that is present in roughly equal abundance as Nitrospina. Dissimilatory nitrate reduction to ammonia (DNRA) can be carried out by yet unknown microorganisms harbouring a divergent nrfA gene. The metagenomes do not provide conclusive evidence for active methane cycling; however, a low abundance of novel alkane monooxygenase diversity was detected. Taken together, our approach confirmed the genomic potential for an active nitrogen cycle in the Arabian Sea and allowed detection of hitherto overlooked lineages of carbon and nitrogen cycle bacteria.
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Affiliation(s)
- Claudia Lüke
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Daan R Speth
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Martine A R Kox
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Laura Villanueva
- Department of Marine Organic Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), 't Horntje (Texel), Netherlands
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, Netherlands.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands.,Soehngen Institute of Anaerobic Microbiology, Nijmegen, Netherlands
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14
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Arshad A, Speth DR, de Graaf RM, Op den Camp HJM, Jetten MSM, Welte CU. A Metagenomics-Based Metabolic Model of Nitrate-Dependent Anaerobic Oxidation of Methane by Methanoperedens-Like Archaea. Front Microbiol 2015; 6:1423. [PMID: 26733968 PMCID: PMC4683180 DOI: 10.3389/fmicb.2015.01423] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 11/30/2015] [Indexed: 11/22/2022] Open
Abstract
Methane oxidation is an important process to mitigate the emission of the greenhouse gas methane and further exacerbating of climate forcing. Both aerobic and anaerobic microorganisms have been reported to catalyze methane oxidation with only a few possible electron acceptors. Recently, new microorganisms were identified that could couple the oxidation of methane to nitrate or nitrite reduction. Here we investigated such an enrichment culture at the (meta) genomic level to establish a metabolic model of nitrate-driven anaerobic oxidation of methane (nitrate-AOM). Nitrate-AOM is catalyzed by an archaeon closely related to (reverse) methanogens that belongs to the ANME-2d clade, tentatively named Methanoperedens nitroreducens. Methane may be activated by methyl-CoM reductase and subsequently undergo full oxidation to carbon dioxide via reverse methanogenesis. All enzymes of this pathway were present and expressed in the investigated culture. The genome of the archaeal enrichment culture encoded a variety of enzymes involved in an electron transport chain similar to those found in Methanosarcina species with additional features not previously found in methane-converting archaea. Nitrate reduction to nitrite seems to be located in the pseudoperiplasm and may be catalyzed by an unusual Nar-like protein complex. A small part of the resulting nitrite is reduced to ammonium which may be catalyzed by a Nrf-type nitrite reductase. One of the key questions is how electrons from cytoplasmically located reverse methanogenesis reach the nitrate reductase in the pseudoperiplasm. Electron transport in M. nitroreducens probably involves cofactor F420 in the cytoplasm, quinones in the cytoplasmic membrane and cytochrome c in the pseudoperiplasm. The membrane-bound electron transport chain includes F420H2 dehydrogenase and an unusual Rieske/cytochrome b complex. Based on genome and transcriptome studies a tentative model of how central energy metabolism of nitrate-AOM could work is presented and discussed.
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Affiliation(s)
- Arslan Arshad
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Netherlands
| | - Daan R Speth
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Netherlands
| | - Rob M de Graaf
- 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
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Netherlands
| | - Cornelia U Welte
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Netherlands
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15
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Dutilh BE, Cassman N, McNair K, Sanchez SE, Silva GGZ, Boling L, Barr JJ, Speth DR, Seguritan V, Aziz RK, Felts B, Dinsdale EA, Mokili JL, Edwards RA. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat Commun 2014; 5:4498. [PMID: 25058116 PMCID: PMC4111155 DOI: 10.1038/ncomms5498] [Citation(s) in RCA: 483] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 06/25/2014] [Indexed: 01/20/2023] Open
Abstract
Metagenomics, or sequencing of the genetic material from a complete microbial community, is a
promising tool to discover novel microbes and viruses. Viral metagenomes typically contain many
unknown sequences. Here we describe the discovery of a previously unidentified bacteriophage present
in the majority of published human faecal metagenomes, which we refer to as crAssphage. Its
~97 kbp genome is six times more abundant in publicly available metagenomes than all other
known phages together; it comprises up to 90% and 22% of all reads in virus-like particle
(VLP)-derived metagenomes and total community metagenomes, respectively; and it totals 1.68% of all
human faecal metagenomic sequencing reads in the public databases. The majority of
crAssphage-encoded proteins match no known sequences in the database, which is why it was not
detected before. Using a new co-occurrence profiling approach, we predict a Bacteroides host
for this phage, consistent with Bacteroides-related protein homologues and a unique
carbohydrate-binding domain encoded in the phage genome. Metagenomic studies of microbial communities often report DNA sequences from
unidentified viruses. Here, Dutilh et al. analyse metagenomic data to reveal the complete
genome of an abundant, ubiquitous virus from human faeces, and predict that the virus infects
bacteria of the Bacteroides group.
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Affiliation(s)
- Bas E Dutilh
- 1] Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical centre, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands [2] Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [3] Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [4] Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo. 373, Prédio Anexo ao Bloco A do Centro de Ciências da Saúde, Ilha do Fundão, CEP 21941-902 Rio de Janeiro, Brazil
| | - Noriko Cassman
- 1] Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [2]
| | - Katelyn McNair
- Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Savannah E Sanchez
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Genivaldo G Z Silva
- Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Lance Boling
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Jeremy J Barr
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Daan R Speth
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Victor Seguritan
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Ramy K Aziz
- 1] Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [2] Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo 11562, Egypt
| | - Ben Felts
- Department of Mathematics, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Elizabeth A Dinsdale
- 1] Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [2] Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - John L Mokili
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Robert A Edwards
- 1] Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [2] Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo. 373, Prédio Anexo ao Bloco A do Centro de Ciências da Saúde, Ilha do Fundão, CEP 21941-902 Rio de Janeiro, Brazil [3] Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [4] Division of Mathematics and Computer Science, Argonne National Laboratory, 9700 S Cass Ave B109, Argonne, Illinois 60439, USA
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16
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Russ L, Speth DR, Jetten MSM, Op den Camp HJM, Kartal B. Interactions between anaerobic ammonium and sulfur-oxidizing bacteria in a laboratory scale model system. Environ Microbiol 2014; 16:3487-98. [DOI: 10.1111/1462-2920.12487] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 04/12/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Lina Russ
- Department of Microbiology; IWWR; Radboud University Nijmegen; Nijmegen The Netherlands
| | - Daan R. Speth
- Department of Microbiology; IWWR; Radboud University Nijmegen; Nijmegen The Netherlands
| | - Mike S. M. Jetten
- Department of Microbiology; IWWR; Radboud University Nijmegen; Nijmegen The Netherlands
| | | | - Boran Kartal
- Department of Microbiology; IWWR; Radboud University Nijmegen; Nijmegen The Netherlands
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17
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Villanueva L, Speth DR, van Alen T, Hoischen A, Jetten MSM. Shotgun metagenomic data reveals significant abundance but low diversity of "Candidatus Scalindua" marine anammox bacteria in the Arabian Sea oxygen minimum zone. Front Microbiol 2014; 5:31. [PMID: 24550902 PMCID: PMC3913995 DOI: 10.3389/fmicb.2014.00031] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 01/17/2014] [Indexed: 12/02/2022] Open
Abstract
Anaerobic ammonium oxidizing (anammox) bacteria are responsible for a significant portion of the loss of fixed nitrogen from the oceans, making them important players in the global nitrogen cycle. To date, marine anammox bacteria found in both water columns and sediments worldwide belong almost exclusively to “Candidatus Scalindua” species. Recently the genome assembly of a marine anammox enrichment culture dominated by “Candidatus Scalindua profunda” became available and can now be used as a template to study metagenome data obtained from various oxygen minimum zones (OMZs). Here, we sequenced genomic DNA from suspended particulate matter recovered at the upper (170 m deep) and center (600 m) area of the OMZ in the Arabian Sea by SOLiD and Ion Torrent technology. The genome of “Candidatus Scalindua profunda” served as a template to collect reads. Based on the mapped reads marine anammox Abundance was estimated to be at least 0.4% in the upper and 1.7% in the center area. Single nucleotide variation (SNV) analysis was performed to assess diversity of the “Candidatus Scalindua” populations. Most highly covered were the two diagnostic anammox genes hydrazine synthase (scal_01318c, hzsA) and hydrazine dehydrogenase (scal_03295, hdh), while other genes involved in anammox metabolism (narGH, nirS, amtB, focA, and ACS) had a lower coverage but could still be assembled and analyzed. The results show that “Candidatus Scalindua” is abundantly present in the Arabian Sea OMZ, but that the diversity within the ecosystem is relatively low.
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Affiliation(s)
- Laura Villanueva
- Department of Marine Organic Biogeochemistry, Royal Netherlands Institute for Sea Research Den Burg, Netherlands
| | - Daan R Speth
- Department of Microbiology, IWWR, Radboud University Nijmegen Nijmegen, Netherlands
| | - Theo van Alen
- Department of Microbiology, IWWR, Radboud University Nijmegen Nijmegen, Netherlands
| | | | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University Nijmegen Nijmegen, Netherlands ; Department of Biotechnology, Delft University of Technology Delft, Netherlands
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18
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van Teeseling MCF, de Almeida NM, Klingl A, Speth DR, Op den Camp HJM, Rachel R, Jetten MSM, van Niftrik L. A new addition to the cell plan of anammox bacteria: "Candidatus Kuenenia stuttgartiensis" has a protein surface layer as the outermost layer of the cell. J Bacteriol 2014; 196:80-9. [PMID: 24142254 PMCID: PMC3911120 DOI: 10.1128/jb.00988-13] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 10/11/2013] [Indexed: 01/24/2023] Open
Abstract
Anammox bacteria perform anaerobic ammonium oxidation (anammox) and have a unique compartmentalized cell consisting of three membrane-bound compartments (from inside outwards): the anammoxosome, riboplasm, and paryphoplasm. The cell envelope of anammox bacteria has been proposed to deviate from typical bacterial cell envelopes by lacking both peptidoglycan and a typical outer membrane. However, the composition of the anammox cell envelope is presently unknown. Here, we investigated the outermost layer of the anammox cell and identified a proteinaceous surface layer (S-layer) (a crystalline array of protein subunits) as the outermost component of the cell envelope of the anammox bacterium "Candidatus Kuenenia stuttgartiensis." This is the first description of an S-layer in the phylum of the Planctomycetes and a new addition to the cell plan of anammox bacteria. This S-layer showed hexagonal symmetry with a unit cell consisting of six protein subunits. The enrichment of the S-layer from the cell led to a 160-kDa candidate protein, Kustd1514, which has no homology to any known protein. This protein is present in a glycosylated form. Antibodies were generated against the glycoprotein and used for immunogold localization. The antiserum localized Kustd1514 to the S-layer and thus verified that this protein forms the "Ca. Kuenenia stuttgartiensis" S-layer.
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Affiliation(s)
- Muriel C. F. van Teeseling
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Naomi M. de Almeida
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Andreas Klingl
- Centre for Electron Microscopy, Institute for Anatomy, University of Regensburg, Regensburg, Germany
| | - Daan R. Speth
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Huub J. M. Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Reinhard Rachel
- Centre for Electron Microscopy, Institute for Anatomy, University of Regensburg, Regensburg, Germany
| | - Mike S. M. Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Laura van Niftrik
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University Nijmegen, Nijmegen, the Netherlands
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19
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Ferousi C, Speth DR, Reimann J, Op den Camp HJM, Allen JWA, Keltjens JTM, Jetten MSM. Identification of the type II cytochrome c maturation pathway in anammox bacteria by comparative genomics. BMC Microbiol 2013; 13:265. [PMID: 24267221 PMCID: PMC4222556 DOI: 10.1186/1471-2180-13-265] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [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: 06/26/2013] [Accepted: 11/18/2013] [Indexed: 11/10/2022] Open
Abstract
Background Anaerobic ammonium oxidizing (anammox) bacteria may contribute up to 50% to the global nitrogen production, and are, thus, key players of the global nitrogen cycle. The molecular mechanism of anammox was recently elucidated and is suggested to proceed through a branched respiratory chain. This chain involves an exceptionally high number of c-type cytochrome proteins which are localized within the anammoxosome, a unique subcellular organelle. During transport into the organelle the c-type cytochrome apoproteins need to be post-translationally processed so that heme groups become covalently attached to them, resulting in mature c-type cytochrome proteins. Results In this study, a comparative genome analysis was performed to identify the cytochrome c maturation system employed by anammox bacteria. Our results show that all available anammox genome assemblies contain a complete type II cytochrome c maturation system. Conclusions Our working model suggests that this machinery is localized at the anammoxosome membrane which is assumed to be the locus of anammox catabolism. These findings will stimulate further studies in dissecting the molecular and cellular basis of cytochrome c biogenesis in anammox bacteria.
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Affiliation(s)
- Christina Ferousi
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Heyendaalseweg 135, 6525, AJ, Nijmegen, the Netherlands.
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Hu Z, Speth DR, Francoijs KJ, Quan ZX, Jetten MSM. Metagenome Analysis of a Complex Community Reveals the Metabolic Blueprint of Anammox Bacterium "Candidatus Jettenia asiatica". Front Microbiol 2012; 3:366. [PMID: 23112795 PMCID: PMC3482989 DOI: 10.3389/fmicb.2012.00366] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 09/27/2012] [Indexed: 11/30/2022] Open
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria are key players in the global nitrogen cycle and responsible for significant global nitrogen loss. Moreover, the anammox process is widely implemented for nitrogen removal from wastewaters as a cost-effective and environment-friendly alternative to conventional nitrification-denitrification systems. Currently, five genera of anammox bacteria have been identified, together forming a deep-branching order in the Planctomycetes-Verrucomicrobium-Chlamydiae superphylum. Members of all genera have been detected in wastewater treatment plants and have been enriched in lab-scale bioreactors, but genome information is not yet available for all genera. Here we report the metagenomic analysis of a granular sludge anammox reactor dominated (∼50%) by “Candidatus Jettenia asiatica.” The metagenome was sequenced using both Illumina and 454 pyrosequencing. After de novo assembly 37,432 contigs with an average length of 571 nt were obtained. The contigs were then analyzed by BLASTx searches against the protein sequences of “Candidatus Kuenenia stuttgartiensis” and a set of 25 genes essential in anammox metabolism were detected. Additionally all reads were mapped to the genome of an anammox strain KSU-1 and de novo assembly was performed again using the reads that could be mapped on KSU-1. Using this approach, a gene encoding copper-containing nitrite reductase NirK was identified in the genome, instead of cytochrome cd1-type nitrite reductase (NirS, present in “Ca. Kuenenia stuttgartiensis” and “Ca. Scalindua profunda”). Finally, the community composition was investigated through MetaCluster analysis, 16S rRNA gene analysis and read mapping, which showed the presence of other important community members such as aerobic ammonia-oxidizing bacteria, methanogens, and the denitrifying methanotroph “Ca. Methylomirabilis oxyfera”, indicating a possible active methane and nitrogen cycle in the bioreactor under the prevailing operational conditions.
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Affiliation(s)
- Ziye Hu
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen Nijmegen, Netherlands
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Speth DR, Hu B, Bosch N, Keltjens JT, Stunnenberg HG, Jetten MSM. Comparative genomics of two independently enriched "candidatus kuenenia stuttgartiensis" anammox bacteria. Front Microbiol 2012; 3:307. [PMID: 22934093 PMCID: PMC3423927 DOI: 10.3389/fmicb.2012.00307] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 08/02/2012] [Indexed: 11/13/2022] Open
Abstract
Bacteria capable of anaerobic oxidation of ammonium (anammox) form a deep branching clade within the Planctomycetes. Although the core metabolic pathway of anammox bacteria is largely resolved, many questions still remain. Data mining of the (meta) genomes of anammox bacteria is a powerful method to address these questions or identify targets for further study. The availability of high quality reference data greatly aids such analysis. Currently, only a single “near complete” (∼98%) reference genome of an anammox bacterium is available; that of model organism “Candidatus Kuenenia stuttgartiensis.” Here we present a comparative genomic analysis of two “Ca. K. stuttgartiensis” anammox bacteria that were independently enriched. The two anammox bacteria used are “Ca. K. stuttgartiensis” RU1, which was originally sequenced for the reference genome in 2002 and “Ca. K. stuttgartiensis” CH1, independently enriched from a Chinese wastewater treatment plant. The two different “Ca. Kuenenia” bacteria have a very high sequence identity (>99% at nucleotide level) over the entire genome, but 31 genomic regions (average size 11 kb) were absent from strain CH1 and 220 kb of sequence was unique to the CH1 assembly. The high sequence homology between these two bacteria indicates that mobile genetic elements are the main source of variation between these geographically widely separated strains. Comparative analysis of the RU1 and CH1 assemblies led to the identification of 49 genes absent from the reference genome. These include a leucyl-tRNA-synthase, the absence of which led to the estimation of the 98% completeness of the reference genome. Finally, a set of 244 genes was present in the reference genome, but absent in the RU1 and CH1 assemblies. These could represent either identical gene duplicates or assembly errors in the published genome. We are confident that this analysis has further improved the most complete available high quality reference genome of an anammox bacterium and will aid further studies on this globally important group of organisms.
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Affiliation(s)
- Daan R Speth
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen Nijmegen, Netherlands
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Speth DR, van Teeseling MCF, Jetten MSM. Genomic analysis indicates the presence of an asymmetric bilayer outer membrane in planctomycetes and verrucomicrobia. Front Microbiol 2012; 3:304. [PMID: 22934092 PMCID: PMC3422733 DOI: 10.3389/fmicb.2012.00304] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Accepted: 07/31/2012] [Indexed: 11/13/2022] Open
Abstract
Bacteria of the phylum Planctomycetes are of special interest for the study of compartmental cellular organization. Members of this phylum share a very unusual prokaryotic cell plan, featuring several membrane-bound compartments. Recently, it was shown that this cellular organization might extend to certain members of the phylum Verrucomicrobia. The Planctomycete cell plan has been defined as featuring a proteinaceous cell wall, a cytoplasmic membrane surrounding the paryphoplasm, and an intracytoplasmic membrane defining the riboplasm. So far it was presumed that Planctomycetes did not have an asymmetric bilayer outer membrane as observed in Gram-negative bacteria. However, recent work on outer membrane biogenesis has provided several marker genes in the outer membrane protein (OMP) assembly and the lipopolysaccharide (LPS) insertion complexes. Additionally, advances in computational prediction of OMPs provided new tools to perform more accurate genomic screening for such proteins. Here we searched all 22 Planctomycetes and Verrucomicrobia genomes available in GenBank, plus the recently published genome of "Candidatus Scalindua profunda," for markers of outer membrane biogenesis and OMPs. We were able to identify the key components of LPS insertion, OMP assembly and at least eight OMPs in all genomes tested. Additionally, we have analyzed the transcriptome and proteome data of the Planctomycetes "Candidatus Kuenenia stuttgartiensis" and "Ca. S. profunda" and could confirm high expression of several predicted OMPs, including the biomarkers of outer membrane biogenesis. These analyses provide a strong indication that an asymmetrical outer membrane may be present in bacteria of both phyla. However, previous experiments have made obvious that the cell envelope of Planctomycetes is clearly divergent from both the Gram-negative and Gram-positive cell types. Thus, the functional implications of the presence of an outer membrane for the Planctomycete cell plan and compartmentalization are discussed and a revised model including an outer membrane is proposed. Although this model agrees with most experimental data, we do note that the presence, location, and role of an outer membrane within the Planctomycetes and Verrucomicrobia awaits further experimental validation.
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Affiliation(s)
- Daan R. Speth
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University NijmegenNijmegen, Netherlands
| | - Muriel C. F. van Teeseling
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University NijmegenNijmegen, Netherlands
| | - Mike S. M. Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University NijmegenNijmegen, Netherlands
- Department of Biotechnology, Delft University of TechnologyDelft, Netherlands
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Abstract
Nitric oxide (NO) and nitrous oxide (N(2)O) are among nature's most powerful electron acceptors. In recent years it became clear that microorganisms can take advantage of the oxidizing power of these compounds to degrade aliphatic and aromatic hydrocarbons. For two unrelated bacterial species, the "NC10" phylum bacterium "Candidatus Methylomirabilis oxyfera" and the γ-proteobacterial strain HdN1 it has been suggested that under anoxic conditions with nitrate and/or nitrite, monooxygenases are used for methane and hexadecane oxidation, respectively. No degradation was observed with nitrous oxide only. Similarly, "aerobic" pathways for hydrocarbon degradation are employed by (per)chlorate-reducing bacteria, which are known to produce oxygen from chlorite [Formula: see text]. In the anaerobic methanotroph M. oxyfera, which lacks identifiable enzymes for nitrogen formation, substrate activation in the presence of nitrite was directly associated with both oxygen and nitrogen formation. These findings strongly argue for the role of NO, or an oxygen species derived from it, in the activation reaction of methane. Although oxygen generation elegantly explains the utilization of "aerobic" pathways under anoxic conditions, the underlying mechanism is still elusive. In this perspective, we review the current knowledge about intra-aerobic pathways, their potential presence in other organisms, and identify candidate enzymes related to quinol-dependent NO reductases (qNORs) that might be involved in the formation of oxygen.
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Affiliation(s)
- Katharina F Ettwig
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
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