Dataset Information

Nitrate-dependent anaerobic methane oxidation (N-DAMO) as a bioremediation strategy for waters affected by agricultural runoff.

ABSTRACT: Agricultural drainage ditches are subjected to high anthropogenic nitrogen input, leading to eutrophication and greenhouse gas emissions. Nitrate-dependent anaerobic methane oxidation (N-DAMO) could be a promising remediation strategy to remove methane (CH4) and nitrate (NO3-) simultaneously. Therefore, we aimed to evaluate the potential of N-DAMO to remove excess NO3- and decrease CH4 release from agricultural drainage ditches. Microcosm experiments were conducted using sediment and surface water collected from three different sites: a sandy-clay ditch (SCD), a freshwater-fed peatland ditch (FPD), and a brackish peatland ditch (BPD). The microcosms were inoculated with an N-DAMO enrichment culture dominated by Candidatus Methanoperedens and Candidatus Methylomirabilis and supplemented with 13CH4 and 15NO3-. A significant decrease in CH4 and NO3- concentration was only observed in the BPD sediment. In freshwater sediments (FPD and SCD), the effect of N-DAMO inoculation on CH4 and NO3- removal was negligible, likely because N-DAMO microorganisms were outcompeted by heterotrophic denitrifiers consuming NO3- much faster. Overall, our results suggest that bioaugmentation with N-DAMO might be a potential strategy for decreasing NO3- concentrations and CH4 emission in brackish ecosystems with increasing agricultural activities where the native microbial community is incapable of efficient denitrification.

SUBMITTER: Legierse A

PROVIDER: S-EPMC10214460 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature

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Nitrate-dependent anaerobic methane oxidation (N-DAMO) as a bioremediation strategy for waters affected by agricultural runoff.

Legierse Annabel A Struik Quinten Q Smith Garrett G Echeveste Medrano Maider J MJ Weideveld Stefan S van Dijk Gijs G Smolders Alfons J P AJP Jetten Mike M Veraart Annelies J AJ Welte Cornelia U CU Glodowska Martyna M

FEMS microbiology letters 20230101

Agricultural drainage ditches are subjected to high anthropogenic nitrogen input, leading to eutrophication and greenhouse gas emissions. Nitrate-dependent anaerobic methane oxidation (N-DAMO) could be a promising remediation strategy to remove methane (CH4) and nitrate (NO3-) simultaneously. Therefore, we aimed to evaluate the potential of N-DAMO to remove excess NO3- and decrease CH4 release from agricultural drainage ditches. Microcosm experiments were conducted using sediment and surface wat ...[more]

PMID: 37170064

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Project description:Diverse associations between methanotrophic archaea (ANME) and sulfate-reducing bacterial groups (SRB) often co-occur in marine methane seeps; however, the ecophysiology of these different symbiotic associations has not been examined. Here, we applied a combination of molecular, geochemical and Fluorescence in situ hybridization (FISH) coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS) analyses of in situ seep sediments and methane-amended sediment incubations from diverse locations (Eel River Basin, Hydrate Ridge and Costa Rican Margin seeps) to investigate the distribution and physiology of a newly identified subgroup of the Desulfobulbaceae (seepDBB) found in consortia with ANME-2c archaea, and compared these with the more commonly observed associations between the same ANME partner and the Desulfobacteraceae (DSS). FISH analyses revealed aggregates of seepDBB cells in association with ANME-2 from both environmental samples and laboratory incubations that are distinct in their structure relative to co-occurring ANME/DSS consortia. ANME/seepDBB aggregates were most abundant in shallow sediment depths below sulfide-oxidizing microbial mats. Depth profiles of ANME/seepDBB aggregate abundance revealed a positive correlation with elevated porewater nitrate relative to ANME/DSS aggregates in all seep sites examined. This relationship with nitrate was supported by sediment microcosm experiments, in which the abundance of ANME/seepDBB was greater in nitrate-amended incubations relative to the unamended control. FISH-NanoSIMS additionally revealed significantly higher (15)N-nitrate incorporation levels in individual aggregates of ANME/seepDBB relative to ANME/DSS aggregates from the same incubation. These combined results suggest that nitrate is a geochemical effector of ANME/seepDBB aggregate distribution, and provides a unique niche for these consortia through their utilization of a greater range of nitrogen substrates than the ANME/DSS.

Project description: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.

Dataset Information

Nitrate-dependent anaerobic methane oxidation (N-DAMO) as a bioremediation strategy for waters affected by agricultural runoff.

Publications

Nitrate-dependent anaerobic methane oxidation (N-DAMO) as a bioremediation strategy for waters affected by agricultural runoff.

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