Molecular analysis of high-affinity methane-oxidizing enrichment cultures isolated from a forest biocenosis and agrocenoses

Кравченко, И. К.; Kizilova, A. K.; Bykova, S. A.; Men’ko, E. V.; Гальченко, В. Ф.

doi:10.1134/s0026261710010145

Cited by 24 publications

(25 citation statements)

References 23 publications

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“…In conclusion, a new strain (84), "Ca. Methanoperedens nitroreducens Verserenetto" was enriched and sequenced.…”

Section: Discussionmentioning

confidence: 91%

“…Furthermore, the competition in anoxic environments between MOB and N-AOM microorganisms for methane when traces of oxygen become available might be driven by their abilities to consume methane at different rates. ANME archaea carrying out sulfate-dependent AOM exhibit an affinity constant for methane in the millimolar range (83), whereas some MOB have extremely low affinity constants, in the nanomolar range (84). Another factor that drives the shift from aerobic to anaerobic methanotrophy may be the oscillating anoxic conditions in environments such as paddy fields, where the agricultural runoff provides nitrogen-based electron acceptors, which become more abundant than oxygen.…”

Section: Discussionmentioning

confidence: 99%

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Response of the Anaerobic Methanotroph “ Candidatus Methanoperedens nitroreducens” to Oxygen Stress

Guerrero-Cruz

Cremers

Alen

et al. 2018

Appl Environ Microbiol

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ABSTRACT“CandidatusMethanoperedens nitroreducens” is an archaeon that couples the anaerobic oxidation of methane to nitrate reduction. In natural and man-made ecosystems, this archaeon is often found at oxic-anoxic interfaces where nitrate, the product of aerobic nitrification, cooccurs with methane produced by methanogens. As such, populations of “Ca. Methanoperedens nitroreducens” could be prone to regular oxygen exposure. Here, we investigated the effect of 5% (vol/vol) oxygen exposure in batch activity assays on a “Ca. Methanoperedens nitroreducens” culture, enriched from an Italian paddy field. Metagenome sequencing of the DNA extracted from the enrichment culture revealed that 83% of 16S rRNA gene reads were assigned to a novel strain, “CandidatusMethanoperedens nitroreducens Verserenetto.” RNA was extracted, and metatranscriptome sequencing upon oxygen exposure revealed that the active community changed, most notably in the appearance of aerobic methanotrophs. The gene expression of “Ca. Methanoperedens nitroreducens” revealed that the key genes encoding enzymes of the methane oxidation and nitrate reduction pathways were downregulated. In contrast to this, we identified upregulation of glutaredoxin, thioredoxin family/like proteins, rubrerythrins, peroxiredoxins, peroxidase, alkyl hydroperoxidase, type A flavoproteins, FeS cluster assembly protein, and cysteine desulfurases, indicating the genomic potential of “Ca. Methanoperedens nitroreducens Verserenetto” to counteract the oxidative damage and adapt in environments where they might be exposed to regular oxygen intrusion.IMPORTANCE“CandidatusMethanoperedens nitroreducens” is an anaerobic archaeon which couples the reduction of nitrate to the oxidation of methane. This microorganism is present in a wide range of aquatic environments and man-made ecosystems, such as paddy fields and wastewater treatment systems. In such environments, these archaea may experience regular oxygen exposure. However, “Ca. Methanoperedens nitroreducens” is able to thrive under such conditions and could be applied for the simultaneous removal of dissolved methane and nitrogenous pollutants in oxygen-limited systems. To understand what machinery “Ca. Methanoperedens nitroreducens” possesses to counteract the oxidative stress and survive, we characterized the response to oxygen exposure using a multi-omics approach.

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“…In conclusion, a new strain (84), "Ca. Methanoperedens nitroreducens Verserenetto" was enriched and sequenced.…”

Section: Discussionmentioning

confidence: 91%

Section: Discussionmentioning

confidence: 99%

Response of the Anaerobic Methanotroph “ Candidatus Methanoperedens nitroreducens” to Oxygen Stress

Guerrero-Cruz

Cremers

Alen

et al. 2018

Appl Environ Microbiol

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“…However, in our previous studies, we have successfully amplified pmoA2 from methane-oxidizing enrichments [44], where the amount of this gene was high enough. We assume that the contribution of pmoA2 to methane oxidation during our experiments was rather low.…”

Section: Diversity Of Methanotrophs In Unmanaged and Managed Soilsmentioning

confidence: 98%

Aerobic Methanotrophs in Natural and Agricultural Soils of European Russia

2013

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Human activities such as land management and global warming have great impact on the environment. Among changes associated with the global warming, rising methane emission is a serious concern. Therefore, we assessed methane oxidation activity and diversity of aerobic methanotrophic bacteria in eight soil types (both unmanaged and agricultural) distributed across the European part of Russia. Using a culture-independent approach targeting pmoA gene, we provide the first baseline data on the diversity of methanotrophs inhabiting most typical soil types. The analysis of pmoA clone libraries showed that methanotrophic populations in unmanaged soils are less diverse than in agricultural areas. These clone sequences were placed in three groups of, so far, uncultured methanotrophs: USC-gamma, cluster I, and pmoA/amoA cluster, which are believed to be responsible for atmospheric methane oxidation in upland soils. Agricultural soils harbored methanotrophs related to genera Methylosinus, Methylocystis, Methylomicrobium, Methylobacter, and Methylocaldum. Despite higher numbers of detected molecular operational taxonomic units (MOTUs), managed soils showed decreased methane oxidation rates as observed in both in situ and laboratory experiments. Our results also suggest that soil restoration may have a positive effect on methane consumption by terrestrial ecosystems.

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“…Almost all extant methanotrophs cannot grow on the low CH 4 concentrations in the atmosphere. Several Methylocystis and Methylosinus species contain a second monooxygenase that catalyses oxidation of CH 4 at atmospheric levels (Dunfield et al, 2002;Baani and Liesack, 2008;Kravchenko et al, 2010) but they also cannot sustain activity and growth at those low concentrations of methane (Baani and Liesack, 2008;Dunfield et al, 2010;Belova et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Unravelling the Identity, Metabolic Potential and Global Biogeography of the Atmospheric Methane‐Oxidizing Upland Soil Cluster α

Pratscher

Vollmers

Wiegand

et al. 2018

Environmental Microbiology

109

102

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Summary Understanding of global methane sources and sinks is a prerequisite for the design of strategies to counteract global warming. Microbial methane oxidation in soils represents the largest biological sink for atmospheric methane. However, still very little is known about the identity, metabolic properties and distribution of the microbial group proposed to be responsible for most of this uptake, the uncultivated upland soil cluster α (USCα). Here, we reconstructed a draft genome of USCα from a combination of targeted cell sorting and metagenomes from forest soil, providing the first insights into its metabolic potential and environmental adaptation strategies. The 16S rRNA gene sequence recovered was distinctive and suggests this crucial group as a new genus within the Beijerinckiaceae, close to Methylocapsa. Application of a fluorescently labelled suicide substrate for the particulate methane monooxygenase enzyme (pMMO) coupled to 16S rRNA fluorescence in situ hybridisation (FISH) allowed for the first time a direct link of the high‐affinity activity of methane oxidation to USCα cells in situ. Analysis of the global biogeography of this group further revealed its presence in previously unrecognized habitats, such as subterranean and volcanic biofilm environments, indicating a potential role of these environments in the biological sink for atmospheric methane.

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Molecular analysis of high-affinity methane-oxidizing enrichment cultures isolated from a forest biocenosis and agrocenoses

Cited by 24 publications

References 23 publications

Response of the Anaerobic Methanotroph “ Candidatus Methanoperedens nitroreducens” to Oxygen Stress

Response of the Anaerobic Methanotroph “ Candidatus Methanoperedens nitroreducens” to Oxygen Stress

Aerobic Methanotrophs in Natural and Agricultural Soils of European Russia

Unravelling the Identity, Metabolic Potential and Global Biogeography of the Atmospheric Methane‐Oxidizing Upland Soil Cluster α

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