Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Methane-dependent selenate reduction by a bacterial consortium

Abstract

Methanotrophic microorganisms play a critical role in controlling the flux of methane from natural sediments into the atmosphere. Methanotrophs have been shown to couple the oxidation of methane to the reduction of diverse electron acceptors (e.g., oxygen, sulfate, nitrate, and metal oxides), either independently or in consortia with other microbial partners. Although several studies have reported the phenomenon of methane oxidation linked to selenate reduction, neither the microorganisms involved nor the underlying trophic interaction has been clearly identified. Here, we provide the first detailed evidence for interspecies electron transfer between bacterial populations in a bioreactor community where the reduction of selenate is linked to methane oxidation. Metagenomic and metaproteomic analyses of the community revealed a novel species of Methylocystis as the most abundant methanotroph, which actively expressed proteins for oxygen-dependent methane oxidation and fermentation pathways, but lacked the genetic potential for selenate reduction. Pseudoxanthomonas, Piscinibacter, and Rhodocyclaceae populations appeared to be responsible for the observed selenate reduction using proteins initially annotated as periplasmic nitrate reductases, with fermentation by-products released by the methanotrophs as electron donors. The ability for the annotated nitrate reductases to reduce selenate was confirmed by gene knockout studies in an isolate of Pseudoxanthomonas. Overall, this study provides novel insights into the metabolic flexibility of the aerobic methanotrophs that likely allows them to thrive across natural oxygen gradients, and highlights the potential role for similar microbial consortia in linking methane and other biogeochemical cycles in environments where oxygen is limited.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Fig. 1: Kinetics of methane oxidation linked to selenate reduction.
Fig. 2: Phylogeny of the DMSO reductase superfamily.
Fig. 3: Physiology comparison of the wild-type and mutant strains of Pseudoxanthomonas.
Fig. 4: Selenate reduction in the presence of different electron donors.
Fig. 5: Metabolic pathway linking methane oxidation to selenate reduction by bacterial consortia.

Data availability

All raw Illumina metagenomic sequence data were submitted to the Sequence Read Archive under accession numbers SRP136677, SRP136696, SRP136790, and SRP136859. The 16S rRNA gene sequences generated from the wetland inoculum were submitted under the accession number SRR14328346. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [82] partner repository with the dataset identifier PXD011889. Public release of the PRIDE projects will be requested as soon as a citable pre-print is online. The username and password of temporary reviewer account are: reviewer66716@ebi.ac.uk and Y5JAcO59, respectively.

References

  1. 1.

    Trotsenko YA, Murrell JC. Metabolic aspects of aerobic obligate methanotrophy. Adv Appl Microbiol. 2008;63:183–229.

    CAS  PubMed  Article  Google Scholar 

  2. 2.

    Knittel K, Boetius A. Anaerobic oxidation of methane: progress with an unknown process. Annu Rev Microbiol. 2009;63:311–34.

    CAS  PubMed  Article  Google Scholar 

  3. 3.

    Khmelenina VN, Murrell JC, Smith TJ, Trotsenko YA. Physiology and Biochemistry of the Aerobic Methanotrophs. In: Rojo F (editor) Aerobic Utilization of Hydrocarbons, Oils and Lipids. Handbook of Hydrocarbon and Lipid Microbiology. Springer; Cham; 2018;1–25. https://doi.org/10.1007/978-3-319-39782-5_4-1.

  4. 4.

    Kalyuzhnaya MG, Yang S, Rozova ON, Smalley NE, Clubb J, Lamb A, et al. Highly efficient methane biocatalysis revealed in a methanotrophic bacterium. Nat Commun. 2013;4:2785.

    CAS  PubMed  Article  Google Scholar 

  5. 5.

    Kits KD, Klotz MG, Stein LY. Methane oxidation coupled to nitrate reduction under hypoxia by the Gammaproteobacterium Methylomonas denitrificans, sp. nov type strain FJG1. Environ Microbiol. 2015;17:3219–32.

    CAS  PubMed  Article  Google Scholar 

  6. 6.

    Kits KD, Campbell DJ, Rosana AR, Stein LY. Diverse electron sources support denitrification under hypoxia in the obligate methanotroph Methylomicrobium album strain BG8. Front Microbiol. 2015;6:1072.

    PubMed  PubMed Central  Article  Google Scholar 

  7. 7.

    Gilman A, Fu Y, Hendershott M, Chu F, Puri AW, Smith AL, et al. Oxygen-limited metabolism in the methanotroph Methylomicrobium buryatense 5GB1C. PeerJ. 2017;5:5.

    Article  CAS  Google Scholar 

  8. 8.

    Ettwig KF, Butler MK, Le Paslier D, Pelletier E, Mangenot S, Kuypers MM, et al. Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature. 2010;464:543–8.

    CAS  PubMed  Article  Google Scholar 

  9. 9.

    Devol AH, Ahmed SI. Are high-rates of sulfate reduction associated with anaerobic oxidation of methane. Nature. 1981;291:407–8.

    CAS  Article  Google Scholar 

  10. 10.

    Boetius A, Ravenschlag K, Schubert CJ, Rickert D, Widdel F, Gieseke A, et al. A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 2000;407:623–6.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  11. 11.

    Orphan VJ, House CH, Hinrichs KU, McKeegan KD, DeLong EF. Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis. Science. 2001;293:484–7.

    CAS  PubMed  Article  Google Scholar 

  12. 12.

    Ettwig KF, Zhu BL, Speth D, Keltjens JT, Jetten MSM, Kartal B. Archaea catalyze iron-dependent anaerobic oxidation of methane. Proc Natl Acad Sci USA. 2016;113:12792–6.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  13. 13.

    Cai C, Leu AO, Xie GJ, Guo J, Feng Y, Zhao JX, et al. A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction. ISME J. 2018;12:1929–39.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  14. 14.

    Leu AO, Cai C, McIlroy SJ, Southam G, Orphan VJ, Yuan Z, et al. Anaerobic methane oxidation coupled to manganese reduction by members of the Methanoperedenaceae. ISME J. 2020;14:1030–41.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  15. 15.

    Haroon MF, Hu S, Shi Y, Imelfort M, Keller J, Hugenholtz P, et al. Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature. 2013;500:567–70.

    CAS  PubMed  Article  Google Scholar 

  16. 16.

    Shi LD, Guo T, Lv PL, Niu ZF, Zhou YJ, Tang XJ, et al. Coupled anaerobic methane oxidation and reductive arsenic mobilization in wetland soils. Nat Geosci. 2020;13:799–805. -+

    Article  CAS  Google Scholar 

  17. 17.

    Leu AO, McIlroy SJ, Ye J, Parks DH, Orphan VJ, Tyson GW. Lateral gene transfer drives metabolic flexibility in the anaerobic methane-oxidizing archaeal family Methanoperedenaceae. Mbio 2020;11:11.

    Article  Google Scholar 

  18. 18.

    Lemly AD. Aquatic selenium pollution is a global environmental safety issue. Ecotox Environ Safe. 2004;59:44–56.

    CAS  Article  Google Scholar 

  19. 19.

    Simmons DBD, Wallschlager D. A critical review of the biogeochemistry and ecotoxicology of selenium in lotic and lentic environments. Environ Toxicol Chem. 2005;24:1331–43.

    CAS  PubMed  Article  Google Scholar 

  20. 20.

    Reim A, Luke C, Krause S, Pratscher J, Frenzel P. One millimetre makes the difference: high-resolution analysis of methane-oxidizing bacteria and their specific activity at the oxic-anoxic interface in a flooded paddy soil. ISME J. 2012;6:2128–39.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  21. 21.

    Danilova OV, Suzina NE, Van De Kamp J, Svenning MM, Bodrossy L, Dedysh SN. A new cell morphotype among methane oxidizers: a spiral-shaped obligately microaerophilic methanotroph from northern low-oxygen environments. ISME J. 2016;10:2734–43.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  22. 22.

    Smith GJ, Angle JC, Solden LM, Borton MA, Morin TH, Daly RA, et al. Members of the genus methylobacter are inferred to account for the majority of aerobic methane oxidation in oxic soils from a freshwater wetland. Mbio 2018;9:9.

    Google Scholar 

  23. 23.

    Fernández-Martínez A, Charlet L. Selenium environmental cycling and bioavailability: a structural chemist point of view. Rev Environ Sci Biotechnol. 2009;8:81–110.

    Article  CAS  Google Scholar 

  24. 24.

    Chung J, Nerenberg R, Rittmann BE. Bioreduction of selenate using a hydrogen-based membrane biofilm reactor. Environ Sci Technol. 2006;40:1664–71.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  25. 25.

    Lai CY, Wen LL, Shi LD, Zhao KK, Wang YQ, Yang X, et al. Selenate and nitrate bioreductions using methane as the electron donor in a membrane biofilm reactor. Environ Sci Technol. 2016;50:10179–86.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  26. 26.

    Luo JH, Chen H, Hu S, Cai C, Yuan Z, Guo J. Microbial selenate reduction driven by a denitrifying anaerobic methane oxidation biofilm. Environ Sci Technol. 2018;52:4006–12.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  27. 27.

    Shi LD, Lv PL, Wang M, Lai CY, Zhao HP. A mixed consortium of methanotrophic archaea and bacteria boosts methane-dependent selenate reduction. Sci Total Environ. 2020;732:139310.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  28. 28.

    Parks DH, Chuvochina M, Chaumeil PA, Rinke C, Mussig AJ, Hugenholtz P. A complete domain-to-species taxonomy for bacteria and archaea. Nat Biotechnol. 2020;38:1079–86.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  29. 29.

    Jakobs G, Labrenz M, Rehder G, Hietanen S, Kießlich K, Vogts A, et al. A bioreactor approach to investigate the linkage between methane oxidation and nitrate/nitrite reduction in the pelagic oxic-anoxic transition zone of the central baltic sea. Front Mar Sci. 2016;3:3.

    Article  Google Scholar 

  30. 30.

    Naqvi SWA, Lam P, Narvenkar G, Sarkar A, Naik H, Pratihary A, et al. Methane stimulates massive nitrogen loss from freshwater reservoirs in India. Nat Commun. 2018;9:9.

    Article  CAS  Google Scholar 

  31. 31.

    Martinez-Cruz K, Leewis MC, Herriott IC, Sepulveda-Jauregui A, Anthony KW, Thalasso F, et al. Anaerobic oxidation of methane by aerobic methanotrophs in sub-arctic lake sediments. Sci Total Environ. 2017;607:23–31.

    PubMed  Article  CAS  Google Scholar 

  32. 32.

    Zheng Y, Wang H, Liu Y, Zhu B, Li J, Yang Y, et al. Methane-dependent mineral reduction by aerobic methanotrophs under hypoxia. Environ Sci Tech Lett. 2020;7:606–12.

  33. 33.

    Oswald K, Milucka J, Brand A, Hach P, Littmann S, Wehrli B, et al. Aerobic gammaproteobacterial methanotrophs mitigate methane emissions from oxic and anoxic lake waters. Limnol Oceanogr. 2016;61:S101–S118.

    Article  Google Scholar 

  34. 34.

    Schroder I, Rech S, Krafft T, Macy JM. Purification and characterization of the selenate reductase from Thauera selenatis. J Biol Chem. 1997;272:23765–8.

    CAS  PubMed  Article  Google Scholar 

  35. 35.

    Ridley H, Watts CA, Richardson DJ, Butler CS. Resolution of distinct membrane-bound enzymes from Enterobacter cloacae SLD1a-1 that are responsible for selective reduction of nitrate and selenate oxyanions. Appl Environ Microbiol. 2006;72:5173–80.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  36. 36.

    Sabaty M, Avazeri C, Pignol D, Vermeglio A. Characterization of the reduction of selenate and tellurite by nitrate reductases. Appl Environ Microbiol 2001;67:5122–6.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  37. 37.

    Turner RJ, Weiner JH, Taylor DE. Selenium metabolism in Escherichia coli. Biometals 1998;11:223–7.

    CAS  PubMed  Article  Google Scholar 

  38. 38.

    Hunter WJ. An Azospira oryzae (syn Dechlorosoma suillum) strain that reduces selenate and selenite to elemental red selenium. Curr Microbiol. 2007;54:376–81.

    CAS  PubMed  Article  Google Scholar 

  39. 39.

    Li D, Pang HC, Sun LC, Fan JP, Li YY, Zhang JL. Pseudoxanthomonas wuyuanensis sp. nov., isolated from saline-alkali soil. Int J Syst Evol Microbiol. 2014;64:799–804.

    CAS  PubMed  Article  Google Scholar 

  40. 40.

    Harrison G, Curle C, Laishley EJ. Purification and characterization of an inducible dissimilatory type sulfite reductase from Clostridium pasteurianum. Arch Microbiol. 1984;138:72–8.

    CAS  PubMed  Article  Google Scholar 

  41. 41.

    Basaglia M, Toffanin A, Baldan E, Bottegal M, Shapleigh JP, Casella S. Selenite-reducing capacity of the copper-containing nitrite reductase of Rhizobium sullae. FEMS Microbiol Lett. 2007;269:124–30.

    CAS  PubMed  Article  Google Scholar 

  42. 42.

    Li DB, Cheng YY, Wu C, Li WW, Li N, Yang ZC, et al. Selenite reduction by Shewanella oneidensis MR-1 is mediated by fumarate reductase in periplasm. Sci Rep. 2014;4:3735.

  43. 43.

    Song DG, Li XX, Cheng YZ, Xiao X, Lu ZQ, Wang YZ, et al. Aerobic biogenesis of selenium nanoparticles by Enterobacter cloacae Z0206 as a consequence of fumarate reductase mediated selenite reduction. Sci Rep. 2017;7:3239.

  44. 44.

    Hunter WJ. A rhizobium selenitireducens protein showing selenite reductase activity. Curr Microbiol. 2014;68:311–6.

    CAS  PubMed  Article  Google Scholar 

  45. 45.

    Nancharaiah YV, Lens PNL. Selenium biomineralization for biotechnological applications. Trends Biotechnol. 2015;33:323–30.

    CAS  PubMed  Article  Google Scholar 

  46. 46.

    McGlynn SE, Chadwick GL, Kempes CP, Orphan VJ. Single cell activity reveals direct electron transfer in methanotrophic consortia. Nature. 2015;526:531–U146.

    CAS  PubMed  Article  Google Scholar 

  47. 47.

    Wegener G, Krukenberg V, Riedel D, Tegetmeyer HE, Boetius A. Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria. Nature. 2015;526:587–U315.

    CAS  PubMed  Article  Google Scholar 

  48. 48.

    Kleiner M, Dong X, Hinzke T, Wippler J, Thorson E, Mayer B, et al. Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities. Proc Natl Acad Sci USA. 2018;115:E5576–84.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  49. 49.

    Anthony C. How half a century of research was required to understand bacterial growth on C1 and C2 compounds; the story of the serine cycle and the ethylmalonyl-CoA pathway. Sci Prog. 2011;94:109–37.

    CAS  PubMed  Article  Google Scholar 

  50. 50.

    Salem AR, Hacking AJ, Quayle JR. Cleavage of malyl-coenzyme-A into acetyl-coenzyme-A and glyoxylate by Pseudomonas AM1 and other C1-unit utilizing bacteria. Biochem J. 1973;136:89–96.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  51. 51.

    Large PJ, Peel D, Quayle JR. Microbial growth on C1 compounds. 3. Distribution of radioactivity in metabolites of methanol-grown Pseudomonas AM1 after incubation with 14C-methanol and 14C-bicarbonate. Biochem J 1962;82:483–8.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  52. 52.

    Shi LD, Wang Z, Liu T, Wu M, Lai CY, Rittmann BE, et al. Making good use of methane to remove oxidized contaminants from wastewater. Water Res. 2021;197:117082.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  53. 53.

    Chistoserdova L, Kalyuzhnaya MG. Current trends in methylotrophy. Trends Microbiol. 2018;26:703–14.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  54. 54.

    Karwautz C, Kus G, Stockl M, Neu TR, Lueders T. Microbial megacities fueled by methane oxidation in a mineral spring cave. ISME J. 2018;12:87–100.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  55. 55.

    Hernandez ME, Beck DAC, Lidstrom ME, Chistoserdova L. Oxygen availability is a major factor in determining the composition of microbial communities involved in methane oxidation. PeerJ. 2015;3:3.

    Article  Google Scholar 

  56. 56.

    Oshkin IY, Beck DA, Lamb AE, Tchesnokova V, Benuska G, McTaggart TL, et al. Methane-fed microbial microcosms show differential community dynamics and pinpoint taxa involved in communal response. ISME J. 2015;9:1119–29.

    CAS  PubMed  Article  Google Scholar 

  57. 57.

    Hoehler TM, Alperin MJ, Albert DB, Martens CS. Field and laboratory studies of methane oxidation in an anoxic marine sediment—evidence for a methanogen-sulfate reducer consortium. Glob Biogeochem Cycles. 1994;8:451–63.

    CAS  Article  Google Scholar 

  58. 58.

    Nauhaus K, Treude T, Boetius A, Kruger M. Environmental regulation of the anaerobic oxidation of methane: a comparison of ANME-I and ANME-II communities. Environ Microbiol. 2005;7:98–106.

    CAS  PubMed  Article  Google Scholar 

  59. 59.

    Meulepas RJW, Jagersma CG, Khadem AF, Stams AJM, Lens PNL. Effect of methanogenic substrates on anaerobic oxidation of methane and sulfate reduction by an anaerobic methanotrophic enrichment. Appl Microbiol Biotechnol 2010;87:1499–506.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  60. 60.

    Sorensen KB, Finster K, Ramsing NB. Thermodynamic and kinetic requirements in anaerobic methane oxidizing consortia exclude hydrogen, acetate, and methanol as possible electron shuttles. Micro Ecol. 2001;42:1–10.

    CAS  Article  Google Scholar 

  61. 61.

    Krukenberg V, Riedel D, Gruber-Vodicka HR, Buttigieg PL, Tegetmeyer HE, Boetius A, et al. Gene expression and ultrastructure of meso- and thermophilic methanotrophic consortia. Environ Microbiol. 2018;20:1651–66.

  62. 62.

    Kaneko M, Poulson SR. Rate of oxygen isotope exchange between selenate and water. Environ Sci Technol. 2012;46:4539–45.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  63. 63.

    Volant S, Lechat P, Woringer P, Motreff L, Campagne P, Malabat C, et al. Shaman: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis. BMC Bioinform. 2020;21:345.

  64. 64.

    Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. Metaspades: a new versatile metagenomic assembler. Genome Res. 2017;27:824–34.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  65. 65.

    Li D, Luo R, Liu CM, Leung CM, Ting HF, Sadakane K, et al. Megahit v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods. 2016;102:3–11.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  66. 66.

    Dong XL, Strous M. An integrated pipeline for annotation and visualization of metagenomic contigs. Front Genet. 2019;10:999.

  67. 67.

    Kang DD, Li F, Kirton E, Thomas A, Egan R, An H, et al. Metabat 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ. 2019;7:e7359.

    PubMed  PubMed Central  Article  Google Scholar 

  68. 68.

    Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  69. 69.

    Olm MR, Brown CT, Brooks B, Banfield JF. Drep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 2017;11:2864–8.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  70. 70.

    Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics. 2020;36:1925–7.

    CAS  Google Scholar 

  71. 71.

    Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. Mega6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30:2725–9.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  72. 72.

    Huang WL, Wilks A. A rapid seamless method for gene knockout in Pseudomonas aeruginosa. BMC Microbiol. 2017;17:199.

  73. 73.

    Bru D, Sarr A, Philippot L. Relative abundances of proteobacterial membrane-bound and periplasmic nitrate reductases in selected environments. Appl Environ Microbiol 2007;73:5971–4.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  74. 74.

    Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(t)(-delta delta c) method. Methods. 2001;25:402–8.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  75. 75.

    Maeda H, Fujimoto C, Haruki Y, Maeda T, Kokeguchi S, Petelin M, et al. Quantitative real-time PCR using Taqman and SYBR green for Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, tetQ gene and total bacteria. FEMS Immunol Med Microbiol. 2003;39:81–6.

    CAS  PubMed  Article  Google Scholar 

  76. 76.

    Tyanova S, Temu T, Cox J. The maxquant computational platform for mass spectrometry-based shotgun proteomics. Nat Protoc. 2016;11:2301–19.

    CAS  PubMed  Article  Google Scholar 

  77. 77.

    Daims H, Stoecker K, Wagner M. “Fluorescence in situ hybridization for the detection of prokaryotes,”. In: Osborn AM, Smith cJ, editors. Molecular microbial ecology. New york: Taylor & francis; 2005. p. 213–39.

  78. 78.

    Wallner G, Amann R, Beisker W. Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry. 1993;14:136–43.

    CAS  PubMed  Article  Google Scholar 

  79. 79.

    Eller G, Stubner S, Frenzel P. Group-specific 16S rRNA targeted probes for the detection of Type I and Type II methanotrophs by fluorescence in situ hybridisation. FEMS Microbiol Lett. 2001;198:91–7.

    CAS  PubMed  Article  Google Scholar 

  80. 80.

    Lagkouvardos I, Joseph D, Kapfhammer M, Giritli S, Horn M, Haller D, et al. Imngs: a comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies. Sci Rep. 2016;6:33721.

  81. 81.

    Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W, Schleifer KH, et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol. 2014;12:635–45.

    CAS  PubMed  Article  Google Scholar 

  82. 82.

    Vizcaíno JA, Csordas A, del-Toro N, Dianes JA, Griss J, Lavidas I, et al. 2016 update of the pride database and its related tools. Nucleic Acids Res. 2016;44:D447–D456.

    PubMed  Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors greatly thank the “National Natural Science Foundation of China (Grant No. 51878596, 21577123)”, the “Natural Science Funds for Distinguished Young Scholar of Zhejiang Province (LR17B070001)”, and the National Key Technology R&D Program (2018YFC1802203)” for their financial support. A.K. and M.S. are supported by NSERC, CFI, CFREF and the Government of Alberta. GWT and S.M are supported by Australian Research Council (ARC) Future Fellowships (FT170100070 and FT190100211, respectively). The authors also thank Dr. Erica M. Hartmann for her assistance in manuscript preparation.

Author information

Affiliations

Authors

Contributions

LDS designed the study, performed the experiments, collected and analyzed the data, evaluated and arranged the results, and drafted the manuscript; LPL, ZW, and CYL characterized the reduction product and collected the data; SJM performed FISH, analyzed the results, and contributed to the manuscript preparation; XLD helped to analyze the metagenomic data; AK performed proteomics and analyzed the data; GWT and MS helped to analyze and discuss the results, and contributed to the manuscript preparation; HPZ initiated and supervised the project, conceived the experiments, and wrote the manuscript; all authors contributed to revising the manuscript.

Corresponding author

Correspondence to He-Ping Zhao.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Shi, LD., Lv, PL., McIlroy, S.J. et al. Methane-dependent selenate reduction by a bacterial consortium. ISME J (2021). https://doi.org/10.1038/s41396-021-01044-3

Download citation

Search

Quick links