scholarly journals Dehalogenation Activities and Distribution of Reductive Dehalogenase Homologous Genes in Marine Subsurface Sediments

2009 ◽  
Vol 75 (21) ◽  
pp. 6905-6909 ◽  
Author(s):  
Taiki Futagami ◽  
Yuki Morono ◽  
Takeshi Terada ◽  
Anna H. Kaksonen ◽  
Fumio Inagaki
Keyword(s):  
Anaerobic Respiration ◽  
Northwest Pacific ◽  
Diverse Range ◽  
Reductive Dehalogenase ◽  
Homologous Genes ◽  
Eastern Equatorial Pacific ◽  
Sediment Slurry ◽  
Subsurface Sediments ◽  
Juan De Fuca ◽  
Ridge Flank

ABSTRACT Halogenated organic compounds serve as terminal electron acceptors for anaerobic respiration in a diverse range of microorganisms. Here, we report on the widespread distribution and diversity of reductive dehalogenase homologous (rdhA) genes in marine subsurface sediments. A total of 32 putative rdhA phylotypes were detected in sediments from the southeast Pacific off Peru, the eastern equatorial Pacific, the Juan de Fuca Ridge flank off Oregon, and the northwest Pacific off Japan, collected at a maximum depth of 358 m below the seafloor. In addition, significant dehalogenation activity involving 2,4,6-tribromophenol and trichloroethene was observed in sediment slurry from the Nankai Trough Forearc Basin. These results suggest that dehalorespiration is an important energy-yielding pathway in the subseafloor microbial ecosystem.

scholarly journals Distribution of dehalogenation activity in subseafloor sediments of the Nankai Trough subduction zone

2013 ◽  
Vol 368 (1616) ◽  
pp. 20120249 ◽  
Author(s):  
Taiki Futagami ◽  
Yuki Morono ◽  
Takeshi Terada ◽  
Anna H. Kaksonen ◽  
Fumio Inagaki
Keyword(s):  
Subduction Zone ◽  
Nankai Trough ◽  
Anaerobic Respiration ◽  
Northwest Pacific ◽  
Kii Peninsula ◽  
Expression Screening ◽  
Reductive Dehalogenase ◽  
Enrichment Cultures ◽  
Incubation Experiments ◽  
Plate Subduction

Halogenated organic matter buried in marine subsurface sediment may serve as a source of electron acceptors for anaerobic respiration of subseafloor microbes. Detection of a diverse array of reductive dehalogenase-homologous ( rdhA ) genes suggests that subseafloor organohalide-respiring microbial communities may play significant ecological roles in the biogeochemical carbon and halogen cycle in the subseafloor biosphere. We report here the spatial distribution of dehalogenation activity in the Nankai Trough plate-subduction zone of the northwest Pacific off the Kii Peninsula of Japan. Incubation experiments with slurries of sediment collected at various depths and locations showed that degradation of several organohalides tested only occurred in the shallow sedimentary basin, down to 4.7 metres below the seafloor, despite detection of rdhA in the deeper sediments. We studied the phylogenetic diversity of the metabolically active microbes in positive enrichment cultures by extracting RNA, and found that Desulfuromonadales bacteria predominate. In addition, for the isolation of genes involved in the dehalogenation reaction, we performed a substrate-induced gene expression screening on DNA extracted from the enrichment cultures. Diverse DNA fragments were obtained and some of them showed best BLAST hit to known organohalide respirers such as Dehalococcoides , whereas no functionally known dehalogenation-related genes such as rdhA were found, indicating the need to improve the molecular approach to assess functional genes for organohalide respiration.

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

Investigating carbon metabolisms in the marine subsurface environment of the Juan de Fuca Ridge Flank

2020 ◽  
Vol 34 (S1) ◽  
pp. 1-1
Author(s):  
Tylisha Gourdine ◽  
Kelle Freel ◽  
Jessica Choi ◽  
Andrian Gajigan ◽  
Cherise Spotkaeff ◽  
...  
Keyword(s):  
Juan De Fuca Ridge ◽  
Fuca Ridge ◽  
Subsurface Environment ◽  
Juan De Fuca ◽  
Ridge Flank

scholarly journals High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes

2014 ◽  
Vol 5 ◽  
Author(s):  
Mikihiko Kawai ◽  
Taiki Futagami ◽  
Atsushi Toyoda ◽  
Yoshihiro Takaki ◽  
Shinro Nishi ◽  
...  
Keyword(s):  
High Frequency ◽  
Reductive Dehalogenase ◽  
Homologous Genes ◽  
Deep Subseafloor
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