Community composition and ultrastructure of a Nitrate-dependent anaerobic methane-oxidizing enrichment culture

Lavinia Gambelli, Simon Guerrero-Cruz, Rob J. Mesman, Geert Cremers, Mike S.M. Jetten, Huub J.M. op den Camp, Boran Kartal, Claudia Lueke, Laura van Niftrik (Corresponding author)

Research output: Contribution to journalArticleAcademicpeer-review

22 Citations (Scopus)


Methane is a very potent greenhouse gas and can be oxidized aerobically or anaerobically through microbe-mediated processes, thus decreasing methane emissions in the atmosphere. Using a complementary array of methods, including phylogenetic analysis, physiological experiments, and light and electron microscopy techniques (including electron tomography), we investigated the community composition and ultrastructure of a continuous bioreactor enrichment culture, in which anaerobic oxidation of methane (AOM) was coupled to nitrate reduction. A membrane bioreactor was seeded with AOM biomass and continuously fed with excess methane. After 150 days, the bioreactor reached a daily consumption of 10 mmol nitrate · liter−1 · day−1. The biomass consisted of aggregates that were dominated by nitrate-dependent anaerobic methane-oxidizing “Candidatus Methanoperedens”-like archaea (40%) and nitrite-dependent anaerobic methane-oxidizing “Candidatus Methylomirabilis”-like bacteria (50%). The “Ca. Methanoperedens” spp. were identified by fluorescence in situ hybridization and immunogold localization of the methyl-coenzyme M reductase (Mcr) enzyme, which was located in the cytoplasm. The “Ca. Methanoperedens” sp. aggregates consisted of slightly irregular coccoid cells (∼1.5-μm diameter) which produced extruding tubular structures and putative cell-to-cell contacts among each other. “Ca. Methylomirabilis” sp. bacteria exhibited the polygonal cell shape typical of this genus. In AOM archaea and bacteria, cytochrome c proteins were localized in the cytoplasm and periplasm, respectively, by cytochrome staining. Our results indicate that AOM bacteria and archaea might work closely together in the process of anaerobic methane oxidation, as the bacteria depend on the archaea for nitrite. Future studies will be aimed at elucidating the function of the cell-to-cell interactions in nitrate-dependent AOM.
Original languageEnglish
Article numbere02186-17
Number of pages14
JournalApplied and Environmental Microbiology
Issue number3
Publication statusPublished - 1 Feb 2018


  • 16S analysis
  • AOM
  • electron tomography
  • Candidatus Methanoperedens
  • Candidatus Methylomirabilis
  • ultrastructure
  • Ultrastructure
  • Electron tomography
  • Anaerobiosis
  • Nitrates/metabolism
  • Oxidation-Reduction
  • Electron Microscope Tomography
  • Bacterial Physiological Phenomena
  • Phylogeny
  • Waste Water/microbiology
  • Methane/metabolism
  • Bioreactors/microbiology
  • Archaea/genetics
  • Bacteria/enzymology
  • Oxidoreductases/metabolism
  • Microbial Interactions/genetics
  • Nitrites/metabolism
  • RNA, Ribosomal, 16S


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