The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology

Current Opinion in Microbiology, Journal Year: 2011, Volume and Issue: 14(3), P. 300 - 306

Published: May 7, 2011

Thaumarchaeota range among the most abundant archaea on Earth. Initially classified as 'mesophilic Crenarchaeota', comparative genomics has recently revealed that they form a separate and deep-branching phylum within Archaea. This novel comprises in 16S rRNA gene trees not only all known archaeal ammonia oxidizers but also several clusters of environmental sequences representing microorganisms with unknown energy metabolism. Ecophysiological studies ammonia-oxidizing suggest adaptation to low concentrations an autotrophic or possibly mixotrophic lifestyle. Extrapolating from wide substrate copper-containing membrane-bound monooxygenases, which thaumarchaeal monooxygenases belong, use substrates other than for generating by some members seems likely.

Language: Английский

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Archaea catalyze iron-dependent anaerobic oxidation of methane

Proceedings of the National Academy of Sciences, Journal Year: 2016, Volume and Issue: 113(45), P. 12792 - 12796

Published: Oct. 24, 2016

Anaerobic oxidation of methane (AOM) is crucial for controlling the emission this potent greenhouse gas to atmosphere. Nitrite-, nitrate-, and sulfate-dependent well-documented, but AOM coupled reduction oxidized metals has so far been demonstrated only in environmental samples. Here, using a freshwater enrichment culture, we show that archaea order Methanosarcinales, related "Candidatus Methanoperedens nitroreducens," couple environmentally relevant forms Fe3+ Mn4+ methane. We obtained an culture these under anaerobic, nitrate-reducing conditions with continuous supply Via batch incubations [13C]methane, soluble ferric iron (Fe3+, as Fe-citrate) nanoparticulate supported methane-oxidizing activity. CO2 ferrous (Fe2+) were produced stoichiometric amounts. Our study connects previous finding iron-dependent microorganisms detected numerous habitats worldwide. Consequently, it enables better understanding interaction between biogeochemical cycles

Language: Английский

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Methane Feedbacks to the Global Climate System in a Warmer World

Reviews of Geophysics, Journal Year: 2018, Volume and Issue: 56(1), P. 207 - 250

Published: Feb. 16, 2018

Abstract Methane (CH 4 ) is produced in many natural systems that are vulnerable to change under a warming climate, yet current CH budgets, as well future shifts emissions, have high uncertainties. Climate has the potential increase emissions from critical such wetlands, marine and freshwater systems, permafrost, methane hydrates, through temperature, hydrology, vegetation, landscape disturbance, sea level rise. Increased these would turn induce further climate change, resulting positive feedback. Here we synthesize biological, geochemical, physically focused feedback literature, bringing together key findings of disciplines. We discuss environment‐specific processes, including microbial, physical, geochemical interlinkages timescales on which they operate, present state knowledge feedbacks immediate distant future. The important linkages between microbial activity discussed with aim better constrain sensitivity cycle predictions. determine wetlands will form majority up 2100. Beyond this timescale, permafrost environments could become more important. Significant atmosphere dissociation hydrates not expected near Our highlight importance quantifying whether consumption can counterbalance production scenarios.

Language: Английский

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Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker

Frontiers in Microbiology, Journal Year: 2015, Volume and Issue: 6

Published: Dec. 15, 2015

Methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. Cultivation-dependent –independent methods have revealed that this functional guild comprises a substantial diversity organisms. In particular the use cultivation-independent targeting subunit particulate monooxygenase (pmoA) marker for detection aerobic methanotrophs has resulted in thousands sequences representing "unknown methanotrophic bacteria". This limits data interpretation due restricted information about these uncultured methanotrophs. A few groups uncultivated assumed play important roles oxidation specific habitats, while biology behind other sequence clusters remains still largely unknown. The discovery evolutionary related monooxygenases non-methanotrophic pmoA paralogs requires organisms be interpreted with care. review article describes present cultivated based gene diversity. It summarizes current knowledge major evaluates habitat specificity at different levels taxonomic resolution. Habitat exists diverse lineages levels. Methanotrophic genera such Methylocystis Methylocaldum identified generalists, but they harbor species level. finding implies future studies should consider diverging preferences when analyzing communities.

Language: Английский

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Seafloor oxygen consumption fuelled by methane from cold seeps

Nature Geoscience, Journal Year: 2013, Volume and Issue: 6(9), P. 725 - 734

Published: Aug. 29, 2013

Language: Английский

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Intergenomic Comparisons Highlight Modularity of the Denitrification Pathway and Underpin the Importance of Community Structure for N2O Emissions

PLoS ONE, Journal Year: 2014, Volume and Issue: 9(12), P. e114118 - e114118

Published: Dec. 1, 2014

Nitrous oxide (N2O) is a potent greenhouse gas and the predominant ozone depleting substance. The only enzyme known to reduce N2O nitrous reductase, encoded by nosZ gene, which present among bacteria archaea capable of either complete denitrification or reduction di-nitrogen gas. To determine whether occurrence nosZ, being proxy for trait reduction, differed taxonomic groups, preferred habitats organisms having NirK NirS nitrite reductases nirK nirS genes, respectively, 652 microbial genomes across 18 phyla were compared. Furthermore, association different co-occurrence patterns with enzymes reducing nitric nor genes was examined. We observed that not randomly distributed taxa, as specific found be more dominant absent than expected within groups. gene had significantly higher frequency presence absence largely explained this pattern, almost always co-occurred nor. This suggests type denitrifiers are likely thus contribute less emissions under favorable environmental conditions. Comparative phylogenetic analysis indicated greater degree shared evolutionary history between nirS. However 30% did possess nir several these also lacking nor, suggesting potentially important role in reduction. Co-occurrence non-randomly amongst habitat categories, showing significant differences frequencies denitrifiers. These results demonstrate pathway highly modular, underpinning importance community structure emissions.

Language: Английский

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The nitrogen cycle

Current Biology, Journal Year: 2016, Volume and Issue: 26(3), P. R94 - R98

Published: Feb. 1, 2016

Language: Английский

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Rare earth metals are essential for methanotrophic life in volcanic mudpots

Environmental Microbiology, Journal Year: 2013, Volume and Issue: 16(1), P. 255 - 264

Published: Aug. 19, 2013

Growth of Methylacidiphilum fumariolicum SolV, an extremely acidophilic methanotrophic microbe isolated from Italian volcanic mudpot, is shown to be strictly dependent on the presence lanthanides, a group rare earth elements (REEs) such as lanthanum (Ln), cerium (Ce), praseodymium (Pr) and neodymium (Nd). After fractionation bacterial cells crystallization methanol dehydrogenase (MDH), it was that lanthanides were essential cofactor in homodimeric MDH comparable with one MDHs Methylobacterium extorquens AM1. We hypothesize provide superior catalytic properties pyrroloquinoline quinone (PQQ)-dependent MDH, which key enzyme for both methanotrophs methylotrophs. Thus far, all MxaF-type contain calcium cofactor. The gene encoding strain SolV identified xoxF-ortholog, phylogenetically closely related mxaF. Analysis protein structure alignment amino acids showed potential REE-binding motifs XoxF enzymes many methylotrophs, suggesting these may also lanthanide-dependent MDHs. Our findings will have major environmental implications metagenome studies (lanthanide-containing) XoxF-type much more prominent nature than enzymes.

Language: Английский

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Archaea in Biogeochemical Cycles

Annual Review of Microbiology, Journal Year: 2013, Volume and Issue: 67(1), P. 437 - 457

Published: June 29, 2013

Archaea constitute a considerable fraction of the microbial biomass on Earth. Like Bacteria they have evolved variety energy metabolisms using organic and/or inorganic electron donors and acceptors, many them are able to fix carbon from sources. thus play crucial roles in Earth's global geochemical cycles influence greenhouse gas emissions. Methanogenesis anaerobic methane oxidation important steps cycle; both performed exclusively by archaea. Oxidation ammonia nitrite is Thaumarchaeota. They represent only archaeal group that resides large numbers aerobic terrestrial marine environments Sulfur-dependent archaea confined mostly hot environments, but metal leaching acidophiles reduction sulfate anaerobic, nonthermophilic oxidizers potential impact environment. The number archaea, particular those dominating subsurface, remain be explored.

Language: Английский

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A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways

Scientific Reports, Journal Year: 2018, Volume and Issue: 8(1)

Published: March 8, 2018

In this study, we report transcription of genes involved in aerobic and anaerobic benzene degradation pathways a benzene-degrading denitrifying continuous culture. Transcripts associated with the family Peptococcaceae dominated all samples (21-36% relative abundance) indicating their key role community. We found highly transcribed gene cluster encoding presumed carboxylase (AbcA AbcD) benzoate-coenzyme A ligase (BzlA). Predicted products showed >96% amino acid identity similar order to corresponding described previously, providing further evidence for activation via carboxylation. For subsequent benzoyl-CoA dearomatization, bam-like analogous ones other strict anaerobes were transcribed, whereas transcripts downstream mostly facultative anaerobes. The concurrent enzymes oxygenase-mediated suggested oxygen presence culture, possibly formed recently identified nitric oxide dismutase (Nod). Although unable detect Nod-encoding genes, addition nitrite formate culture indication production. Such an production would enable microbes thrive oxygen-depleted nitrate-containing subsurface environments contaminated hydrocarbons.

Language: Английский

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