Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage

Abstract

Anaerobic oxidation of methane (AOM) is critical for controlling the flux of methane from anoxic environments. AOM coupled to iron, manganese and sulphate reduction have been demonstrated in consortia containing anaerobic methanotrophic (ANME) archaea. More recently it has been shown that the bacterium Candidatus 'Methylomirabilis oxyfera' can couple AOM to nitrite reduction through an intra-aerobic methane oxidation pathway. Bioreactors capable of AOM coupled to denitrification have resulted in the enrichment of 'M. oxyfera' and a novel ANME lineage, ANME-2d. However, as 'M. oxyfera' can independently couple AOM to denitrification, the role of ANME-2d in the process is unresolved. Here, a bioreactor fed with nitrate, ammonium and methane was dominated by a single ANME-2d population performing nitrate-driven AOM. Metagenomic, single-cell genomic and metatranscriptomic analyses combined with bioreactor performance and (13)C- and (15)N-labelling experiments show that ANME-2d is capable of independent AOM through reverse methanogenesis using nitrate as the terminal electron acceptor. Comparative analyses reveal that the genes for nitrate reduction were transferred laterally from a bacterial donor, suggesting selection for this novel process within ANME-2d. Nitrite produced by ANME-2d is reduced to dinitrogen gas through a syntrophic relationship with an anaerobic ammonium-oxidizing bacterium, effectively outcompeting 'M. oxyfera' in the system. We propose the name Candidatus 'Methanoperedens nitroreducens' for the ANME-2d population and the family Candidatus 'Methanoperedenaceae' for the ANME-2d lineage. We predict that 'M. nitroreducens' and other members of the 'Methanoperedenaceae' have an important role in linking the global carbon and nitrogen cycles in anoxic environments.

High rates of anaerobic methane oxidation in freshwater wetlands reduce potential atmospheric methane emissions

“…In contrast, a dominant electron acceptor for freshwater AOM has not been identified. Experimental evidence suggest sulphate is not the sole electron acceptor for AOM in freshwater sediments and peat 2,9,15,20 , and AOM in low-sulphate environments has been linked to the reduction of nitrate, nitrite, iron and manganese 4,5,12,13,16,33 . The geochemical and rate profiles in the wetlands studied here support a linkage between SR and AOM.…”

“…Thus, while AOM in Maine and Florida may be coupled to SR, at least some fraction of AOM activity in Georgia must be supported by alternative electron acceptor(s). Such alternative electron acceptors (for example, nitrate, nitrite, iron oxides or manganese oxides) were readily available in these sediments (Table 1; Supplementary Table 2) and may support AOM in FWW 5,9,13 . The production of reduced iron at depth in Georgia ( Supplementary Fig.…”

“…In addition to quantifying rates of AOM and SR, we evaluated the impact of AOM on microbial carbon flow in these wetlands by measuring the stable carbon isotopic composition (d 13 C) of methane, dissolved inorganic carbon (DIC) and intact microbial lipids. Biological consumption results in 13 C enrichment of residual methane through the preferential consumption of isotopically light methane 40 . The zone of maximum AOM activity (0-3 cm) corresponded to the lowest d 13 C-DIC values and the highest d 13 C-CH 4 , a clear geochemical signature of AOM (Fig.…”

“…In the marine environment, lipid biomarkers are robust indicators of metabolic coupling between methane-oxidizing archaea and their sulphate-reducing bacterial partners: both groups of microorganisms exhibit lipids that are highly depleted in 13 C relative to methane, indicating assimilation of methanederived carbon through AOM 7,41 . However, results from freshwaters are inconsistent: some evidence of extreme depletion of 13 C in microbial lipids 14 has been noted while others report little to no depletion in lipid isotopic signatures 11,16 .…”

“…Yet, despite low sulphate concentrations, FWW support a dynamic sulphur cycle and high rates of sulphate reduction 9 (SR) are maintained by rapid recycling of reduced sulphur species 10 . Moreover, studies of freshwater AOM have indicated several electron acceptors for methane oxidation, including sulphate 11 , nitrate/nitrite 5,[12][13][14][15] , iron 16 and manganese 17 . Geochemical profiles 4,18,19 , stable isotope geochemistry 16,18,19 , potential methane oxidation assays 2,4,5,20 and long-term enrichments 4 have provided tantalizing evidence of AOM in FWW, but environmentally relevant, in vitro, rate measurements are rare 9 .…”