scholarly journals Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi

2018 ◽  
Author(s):  
Joel A. Boyd ◽  
Sean P. Jungbluth ◽  
Andy O. Leu ◽  
Paul N. Evans ◽  
Ben J. Woodcroft ◽  
...  
Keyword(s):  
Juan De Fuca Ridge ◽  
Coenzyme M ◽  
Methane Generation ◽  
Transport Chain ◽  
Juan De Fuca ◽  
Key Enzyme ◽  
History Of ◽  
Ridge Flank ◽  
Methyl Coenzyme M Reductase ◽  
Deep Subseafloor

AbstractThe methyl-coenzyme M reductase (MCR) complex is a key enzyme in archaeal methane generation and has recently been proposed to also be involved in the oxidation of short-chain hydrocarbons including methane, butane and potentially propane. The number of archaeal clades encoding the MCR complex continues to grow, suggesting that this complex was inherited from an ancient ancestor, or has undergone extensive horizontal gene transfer. Expanding the representation of MCR-encoding lineages through metagenomic approaches will help resolve the evolutionary history of this complex. Here, a near-complete Archaeoglobi metagenome-assembled genome (MAG; rG16) was recovered from the deep subseafloor along the Juan de Fuca Ridge flank that encodes two divergent McrABG operons similar to those found inCandidatusBathyarchaeota andCandidatusSyntrophoarchaeum MAGs. rG16 is basal to members of the class Archaeoglobi, and encodes the genes for β-oxidation, potentially allowing an alkanotrophic metabolism similar to that proposed forCa.Syntrophoarchaeum. rG16 also encodes a respiratory electron transport chain that can potentially utilize nitrate, iron, and sulfur compounds as electron acceptors. As the first Archaeoglobi with the MCR complex, rG16 extends our understanding of the evolution and distribution of novel MCR encoding lineages among the Archaea.

Acetogenesis in Deep Subseafloor Sediments of The Juan de Fuca Ridge Flank: A Synthesis of Geochemical, Thermodynamic, and Gene-based Evidence

2010 ◽  
Vol 27 (2) ◽  
pp. 183-211 ◽  
Author(s):  
Mark A. Lever ◽  
Verena B. Heuer ◽  
Yuki Morono ◽  
Noriaki Masui ◽  
Frauke Schmidt ◽  
...  
Keyword(s):  
Juan De Fuca Ridge ◽  
Fuca Ridge ◽  
Juan De Fuca ◽  
Ridge Flank ◽  
Deep Subseafloor

scholarly journals Phylogenomic Analysis of Viral Genomes Assembled from Juan de Fuca Ridge Flank Basalt-Hosted Crustal Fluids

2020 ◽  
Author(s):  
Cherise Spotkaeff ◽  
Michael Rappe ◽  
Sean Jungbluth ◽  
Grieg Steward ◽  
Olivia Nigro
Keyword(s):  
Juan De Fuca Ridge ◽  
Phylogenomic Analysis ◽  
Viral Genomes ◽  
Fuca Ridge ◽  
Crustal Fluids ◽  
Juan De Fuca ◽  
Ridge Flank

scholarly journals Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids

2016 ◽  
Author(s):  
Sean P Jungbluth ◽  
Jan P Amend ◽  
Michael S Rappé
Keyword(s):  
Juan De Fuca Ridge ◽  
Phylogenomic Analysis ◽  
Data Set ◽  
Microbial Life ◽  
Fuca Ridge ◽  
Juan De Fuca ◽  
Metagenome Sequencing ◽  
The Many ◽  
Ridge Flank ◽  
Informatics Tools

The global deep subsurface biosphere is thought to be one of the largest reservoirs for microbial life on our planet. This study takes advantage of new sampling technologies and couples them with improvements to DNA sequencing and associated informatics tools to reconstruct the genomes of uncultivated Bacteria and Archaea from fluids collected deep within the subseafloor of the Juan de Fuca Ridge. Here, we generated two metagenomes from borehole observatories located 311 meters apart and, using binning tools, retrieved 98 genomes from metagenomes (GFMs) with completeness > 10%. Of the GFMs, 31 were estimated to be > 90% complete, while an additional 17 were > 70% complete. In most instances, estimated redundancy in the GFMs was < 10%. Phylogenomic analysis revealed 53 bacterial and 45 archaeal GFMs and nearly all were distantly related to known cultivates. In the GFMs, abundant bacteria included Chloroflexi, Nitrospirae, Acetothermia (OP1), EM3, Aminicenantes (OP8), Gammaproteobacteria, and Deltaproteobacteria and abundant archaea included Archaeoglobi, Bathyarchaeota (MCG), and Marine Benthic Group E (MBG-E). In this study, we identified the first near-complete genomes from archaeal and bacterial lineages THSCG, MBG-E, and EM3 and, based on the warm, subsurface and hydrothermally-associated from which these groups tend to be found, propose the names, Geothermarchaeota, Hydrothermarchaeota, and Hydrothermae, respectively. The data set presented here are the first description of Juan de Fuca igneous basement microbial GFMs reported and will provide a platform by which one can perform a higher level interrogation of the many uncultivated lineages presented herein.

Hydrothermal scavenging on the Juan de Fuca Ridge: 23OThxs, 10Be, and REEs in ridge-flank sediments

1997 ◽  
Vol 61 (19) ◽  
pp. 4067-4078 ◽  
Author(s):  
C.R. German ◽  
D.L. Bourlés ◽  
E.T. Brown ◽  
J. Hergt ◽  
S. Colley ◽  
...  
Keyword(s):  
Juan De Fuca Ridge ◽  
Fuca Ridge ◽  
Juan De Fuca ◽  
Ridge Flank

scholarly journals Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids

2017 ◽  
Vol 4 (1) ◽  
Author(s):  
Sean P. Jungbluth ◽  
Jan P. Amend ◽  
Michael S. Rappé
Keyword(s):  
Juan De Fuca Ridge ◽  
Phylogenomic Analysis ◽  
Microbial Genomes ◽  
Microbial Life ◽  
Fuca Ridge ◽  
Juan De Fuca ◽  
Metagenome Sequencing ◽  
Ridge Flank ◽  
Informatics Tools ◽  
Uncultivated Bacteria

Abstract The global deep subsurface biosphere is one of the largest reservoirs for microbial life on our planet. This study takes advantage of new sampling technologies and couples them with improvements to DNA sequencing and associated informatics tools to reconstruct the genomes of uncultivated Bacteria and Archaea from fluids collected deep within the Juan de Fuca Ridge subseafloor. Here, we generated two metagenomes from borehole observatories located 311 meters apart and, using binning tools, retrieved 98 genomes from metagenomes (GFMs). Of the GFMs, 31 were estimated to be >90% complete, while an additional 17 were >70% complete. Phylogenomic analysis revealed 53 bacterial and 45 archaeal GFMs, of which nearly all were distantly related to known cultivated isolates. In the GFMs, abundant Bacteria included Chloroflexi, Nitrospirae, Acetothermia (OP1), EM3, Aminicenantes (OP8), Gammaproteobacteria, and Deltaproteobacteria, while abundant Archaea included Archaeoglobi, Bathyarchaeota (MCG), and Marine Benthic Group E (MBG-E). These data are the first GFMs reconstructed from the deep basaltic subseafloor biosphere, and provide a dataset available for further interrogation.

Energy yields from chemolithotrophic metabolisms in igneous basement of the Juan de Fuca ridge flank system

2013 ◽  
Vol 337-338 ◽  
pp. 11-19 ◽  
Author(s):  
Jason Boettger ◽  
Huei-Ting Lin ◽  
James P. Cowen ◽  
Michael Hentscher ◽  
Jan P. Amend
Keyword(s):  
Juan De Fuca Ridge ◽  
Fuca Ridge ◽  
Juan De Fuca ◽  
Ridge Flank

scholarly journals Temporal and spatial history of the 1999-2000 Endeavour Segment seismic series, Juan de Fuca Ridge

2004 ◽  
Vol 5 (9) ◽  
pp. n/a-n/a ◽  
Author(s):  
DelWayne R. Bohnenstiehl ◽  
Robert P. Dziak ◽  
Maya Tolstoy ◽  
Christopher G. Fox ◽  
Mathew Fowler
Keyword(s):  
Juan De Fuca Ridge ◽  
Fuca Ridge ◽  
Spatial History ◽  
Juan De Fuca ◽  
History Of ◽  
Temporal And Spatial ◽  
Endeavour Segment

scholarly journals Post-translational thioamidation of methyl-coenzyme M reductase, a key enzyme in methanogenic and methanotrophic Archaea

2017 ◽  
Author(s):  
Dipti D. Nayak ◽  
Nilkamal Mahanta ◽  
Douglas A. Mitchell ◽  
William W. Metcalf
Keyword(s):  
Strictly Anaerobic ◽  
Methanosarcina Acetivorans ◽  
Coenzyme M ◽  
Α Subunit ◽  
Post Translational Modifications ◽  
Physiological Characterization ◽  
Key Enzyme ◽  
Catalytic Role ◽  
Methyl Coenzyme M Reductase

AbstractThe enzyme methyl-coenzyme M reductase (MCR), found in strictly anaerobic methanogenic and methanotrophic archaea, catalyzes a reversible reaction involved in the production and consumption of the potent greenhouse gas methane. The α subunit of this enzyme (McrA) contains several unusual post-translational modifications, including an exceptionally rare thioamidation of glycine. Based on the presumed function of homologous genes involved in the biosynthesis of thioamide-containing natural products, we hypothesized that the archaealtfuAandycaOgenes would be responsible for post-translational installation of thioglycine into McrA. Mass spectrometric characterization of McrA in a ΔycaO-tfuAmutant of the methanogenic archaeonMethanosarcina acetivoransrevealed the presence of glycine, rather than thioglycine, supporting this hypothesis. Physiological characterization of this mutant suggested a new role for the thioglycine modification in enhancing protein stability, as opposed to playing a direct catalytic role. The universal conservation of this modification suggests that MCR arose in a thermophilic ancestor.

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