Enrichment of anaerobic nitrate-dependent methanotrophic ‘Candidatus Methanoperedens nitroreducens’ archaea from an Italian paddy field soil

Enrichment of anaerobic nitrate-dependent methanotrophic ‘Candidatus Methanoperedens nitroreducens’ archaea from an Italian paddy field soil

Vaksmaa, Annika (Radboud Universiteit Nijmegen)
Guerrero-Cruz, Simon (Radboud Universiteit Nijmegen)
van Alen, Theo A. (Radboud Universiteit Nijmegen)
Cremers, Geert (Radboud Universiteit Nijmegen)
Ettwig, Katharina F. (Radboud Universiteit Nijmegen)
Lüke, Claudia (Radboud Universiteit Nijmegen)
Jetten, M.S.M. (TU Delft BT/Environmental Biotechnology; Radboud Universiteit Nijmegen; Soehngen Institute of Anaerobic Microbiology)

2017

Paddy fields are a significant source of methane and contribute up to 20% of total methane emissions from wetland ecosystems. These inundated, anoxic soils featuring abundant nitrogen compounds and methane are an ideal niche for nitrate-dependent anaerobic methanotrophs. After 2 years of enrichment with a continuous supply of methane and nitrate as the sole electron donor and acceptor, a stable enrichment dominated by ‘Candidatus Methanoperedens nitroreducens’ archaea and ‘Candidatus Methylomirabilis oxyfera’ NC10 phylum bacteria was achieved. In this community, the methanotrophic archaea supplied the NC10 phylum bacteria with the necessary nitrite through nitrate reduction coupled to methane oxidation. The results of qPCR quantification of 16S ribosomal RNA (rRNA) gene copies, analysis of metagenomic 16S rRNA reads, and fluorescence in situ hybridization (FISH) correlated well and showed that after 2 years, ‘Candidatus Methanoperedens nitroreducens’ had the highest abundance of (2.2 ± 0.4 × 10⁸) 16S rRNA copies per milliliter and constituted approximately 22% of the total microbial community. Phylogenetic analysis showed that the 16S rRNA genes of the dominant microorganisms clustered with previously described ‘Candidatus Methanoperedens nitroreducens ANME2D’ (96% identity) and ‘Candidatus Methylomirabilis oxyfera’ (99% identity) strains. The pooled metagenomic sequences resulted in a high-quality draft genome assembly of ‘Candidatus Methanoperedens nitroreducens Vercelli’ that contained all key functional genes for the reverse methanogenesis pathway and nitrate reduction. The diagnostic mcrA gene was 96% similar to ‘Candidatus Methanoperedens nitroreducens ANME2D’ (WP_048089615.1) at the protein level. The ‘Candidatus Methylomirabilis oxyfera’ draft genome contained the marker genes pmoCAB, mdh, and nirS and putative NO dismutase genes. Whole-reactor anaerobic activity measurements with methane and nitrate revealed an average methane oxidation rate of 0.012 mmol/h/L, with cell-specific methane oxidation rates up to 0.57 fmol/cell/day for ‘Candidatus Methanoperedens nitroreducens’. In summary, this study describes the first enrichment and draft genome of methanotrophic archaea from paddy field soil, where these organisms can contribute significantly to the mitigation of methane emissions.

Anaerobic oxidation of methane
NC10 phylum bacteria
‘Candidatus Methanoperedens nitroreducens’

http://resolver.tudelft.nl/uuid:74b08e15-7994-4b15-a55a-744a27b3f0a7

https://doi.org/10.1007/s00253-017-8416-0

0175-7598

Applied Microbiology and Biotechnology, 101 (18), 7075-7084

Institutional Repository

journal article

© 2017 Annika Vaksmaa, Simon Guerrero-Cruz, Theo A. van Alen, Geert Cremers, Katharina F. Ettwig, Claudia Lüke, M.S.M. Jetten