The Geoglobus acetivorans Genome: Fe(III) Reduction, Acetate Utilization, Autotrophic Growth, and Degradation of Aromatic Compounds in a Hyperthermophilic Archaeon

ABSTRACTGeoglobus acetivoransis a hyperthermophilic anaerobic euryarchaeon of the orderArchaeoglobalesisolated from deep-sea hydrothermal vents. A unique physiological feature of the members of the genusGeoglobusis their obligate dependence on Fe(III) reduction, which plays an important role in the geochemistry of hydrothermal systems. The features of this organism and its complete 1,860,815-bp genome sequence are described in this report. Genome analysis revealed pathways enabling oxidation of molecular hydrogen, proteinaceous substrates, fatty acids, aromatic compounds,n-alkanes, and organic acids, including acetate, through anaerobic respiration linked to Fe(III) reduction. Consistent with the inability ofG. acetivoransto grow on carbohydrates, the modified Embden-Meyerhof pathway encoded by the genome is incomplete. Autotrophic CO2fixation is enabled by the Wood-Ljungdahl pathway. Reduction of insoluble poorly crystalline Fe(III) oxide depends on the transfer of electrons from the quinone pool to multihemec-type cytochromes exposed on the cell surface. Direct contact of the cells and Fe(III) oxide particles could be facilitated by pilus-like appendages. Genome analysis indicated the presence of metabolic pathways for anaerobic degradation of aromatic compounds andn-alkanes, although an ability ofG. acetivoransto grow on these substrates was not observed in laboratory experiments. Overall, our results suggest thatGeoglobusspecies could play an important role in microbial communities of deep-sea hydrothermal vents as lithoautotrophic producers. An additional role as decomposers would close the biogeochemical cycle of carbon through complete mineralization of various organic compounds via Fe(III) respiration.

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Organic complexation of copper in deep-sea hydrothermal vent systems

Environmental Chemistry ◽

10.1071/en06086 ◽

2007 ◽

Vol 4 (2) ◽

pp. 81 ◽

Cited By ~ 46

Author(s):

Sylvia G. Sander ◽

Andrea Koschinsky ◽

Gary Massoth ◽

Matthew Stott ◽

Keith A. Hunter

Keyword(s):

Deep Sea ◽

Hydrothermal Vent ◽

Hydrothermal Vents ◽

Natural Habitat ◽

Hydrothermal Systems ◽

Conditional Stability ◽

Copper Binding ◽

Medium Temperature ◽

Ambient Seawater ◽

Organic Complexation

Environmental context. Deep-sea hydrothermal vents represent a natural habitat for many extremophile organisms able to cope with extreme physical and chemical conditions, including high loads of heavy metals and reduced gases. To date, no information is available on the level and role of organic complexation of metals in these systems, which will have consequences on the bioavailability and precipitation or mineralisation of metals. In this work, we give evidence for the presence of organic molecules, including thiols, capable of forming complexes with copper strong enough to compete against sulfide present at high levels in hydrothermal systems. Abstract. Here we report, for the first time, that strong organic complexation plays an important role in the chemical speciation of copper in hydrothermal vent systems including medium temperature outlets, diffuse vents with an adjacent hydrothermal biocommunity, and local mixing zone with seawater. Samples from three deep-sea hydrothermal vent areas show a wide concentration range of organic copper-binding ligands, up to 4000 nM, with very high conditional stability constants (log K′Cu′L = 12.48 to 13.46). Measurements were usually made using voltammetric methods after removal of sulfide species under ambient seawater conditions (pH 7.8), but binding still occurs at pH 4.5 and 2.1. The voltammetric behaviour of our hydrothermal samples is compared with that of glutathione (GSH) a known strong Cu-binding ligand, as a representative of an organic thiol. Our results provide compelling evidence for the presence of organic ligands, including thiols, which form complexes strong enough to play an important role in controlling the bioavailability and geochemical behaviour of metal ions around hydrothermal vents.

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Detection of Putatively Thermophilic Anaerobic Methanotrophs in Diffuse Hydrothermal Vent Fluids

Applied and Environmental Microbiology ◽

10.1128/aem.03034-12 ◽

2012 ◽

Vol 79 (3) ◽

pp. 915-923 ◽

Cited By ~ 24

Author(s):

Alexander Y. Merkel ◽

Julie A. Huber ◽

Nikolay A. Chernyh ◽

Elizaveta A. Bonch-Osmolovskaya ◽

Alexander V. Lebedinsky

Keyword(s):

16S Rrna ◽

Deep Sea ◽

Hydrothermal Vents ◽

Optimal Growth ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Anaerobic Oxidation Of Methane ◽

Phylogenetic Groups ◽

Content Type

ABSTRACTThe anaerobic oxidation of methane (AOM) is carried out by a globally distributed group of uncultivatedEuryarchaeota, the anaerobic methanotrophic arachaea (ANME). In this work, we used G+C analysis of 16S rRNA genes to identify a putatively thermophilic ANME group and applied newly designed primers to study its distribution in low-temperature diffuse vent fluids from deep-sea hydrothermal vents. We found that the G+C content of the 16S rRNA genes (PGC) is significantly higher in the ANME-1GBa group than in other ANME groups. Based on the positive correlation between thePGCand optimal growth temperatures (Topt) of archaea, we hypothesize that the ANME-1GBa group is adapted to thrive at high temperatures. We designed specific 16S rRNA gene-targeted primers for the ANME-1 cluster to detect all phylogenetic groups within this cluster, including the deeply branching ANME-1GBa group. The primers were successfully tested bothin silicoand in experiments with sediment samples where ANME-1 phylotypes had previously been detected. The primers were further used to screen for the ANME-1 microorganisms in diffuse vent fluid samples from deep-sea hydrothermal vents in the Pacific Ocean, and sequences belonging to the ANME-1 cluster were detected in four individual vents. Phylotypes belonging to the ANME-1GBa group dominated in clone libraries from three of these vents. Our findings provide evidence of existence of a putatively extremely thermophilic group of methanotrophic archaea that occur in geographically and geologically distinct marine hydrothermal habitats.

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Draft Genome Sequence of Pseudomonas pachastrellae Strain CCUG 46540T, a Deep-Sea Bacterium

Genome Announcements ◽

10.1128/genomea.00136-17 ◽

2017 ◽

Vol 5 (14) ◽

Cited By ~ 1

Author(s):

Margarita Gomila ◽

Magdalena Mulet ◽

Jorge Lalucat ◽

Elena García-Valdés

Keyword(s):

Genome Sequence ◽

Aromatic Compounds ◽

Deep Sea ◽

Draft Genome ◽

Draft Genome Sequence ◽

Content Type ◽

Philippine Sea

ABSTRACT Pseudomonas pachastrellae strain CCUG 46540T (KMM 330T) was isolated from a deep-sea sponge specimen collected in the Philippine Sea at a depth of 750 m. The draft genome has an estimated size of 4.0 Mb, exhibits a G+C content of 61.2 mol%, and is predicted to encode 3,592 proteins, including pathways for the degradation of aromatic compounds.

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Interaction between Microbes, Minerals, and Fluids in Deep-Sea Hydrothermal Systems

Minerals ◽

10.3390/min11121324 ◽

2021 ◽

Vol 11 (12) ◽

pp. 1324

Author(s):

Shamik Dasgupta ◽

Xiaotong Peng ◽

Kaiwen Ta

Keyword(s):

Microbial Communities ◽

Deep Sea ◽

Hydrothermal Vents ◽

Extreme Environments ◽

Past Research ◽

Hydrothermal Systems ◽

Chemical Gradients ◽

Basement Rocks ◽

The Rich ◽

Metabolic Activities

The discovery of deep-sea hydrothermal vents in the late 1970s widened the limits of life and habitability. The mixing of oxidizing seawater and reduction of hydrothermal fluids create a chemical disequilibrium that is exploited by chemosynthetic bacteria and archaea to harness energy by converting inorganic carbon into organic biomass. Due to the rich variety of chemical sources and steep physico-chemical gradients, a large array of microorganisms thrive in these extreme environments, which includes but are not restricted to chemolithoautotrophs, heterotrophs, and mixotrophs. Past research has revealed the underlying relationship of these microbial communities with the subsurface geology and hydrothermal geochemistry. Endolithic microbial communities at the ocean floor catalyze a number of redox reactions through various metabolic activities. Hydrothermal chimneys harbor Fe-reducers, sulfur-reducers, sulfide and H2-oxidizers, methanogens, and heterotrophs that continuously interact with the basaltic, carbonate, or ultramafic basement rocks for energy-yielding reactions. Here, we briefly review the global deep-sea hydrothermal systems, microbial diversity, and microbe–mineral interactions therein to obtain in-depth knowledge of the biogeochemistry in such a unique and geologically critical subseafloor environment.

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Diverse viruses have restricted biogeography in deep-sea hydrothermal vent fluids

10.1101/2020.06.04.125666 ◽

2020 ◽

Author(s):

Elaina Thomas ◽

Rika Anderson ◽

Viola Li ◽

Jenni Rogan ◽

Julie A. Huber

Keyword(s):

Host Range ◽

Deep Sea ◽

Hydrothermal Vents ◽

Hydrothermal Systems ◽

Viral Diversity ◽

Metabolic Potential ◽

Host Interactions ◽

The Pacific ◽

Wide Range ◽

Axial Seamount

AbstractIn the ocean, viruses impact microbial mortality, regulate biogeochemical cycling, and alter the metabolic potential of microbial lineages. At deep-sea hydrothermal vents, abundant viruses infect a wide range of hosts among the archaea and bacteria that inhabit these dynamic habitats. However, little is known about viral diversity, host range, and biogeography across different vent ecosystems, which has important implications for how viruses manipulate microbial function and evolution. Here, we examined viral diversity, viral and host distribution, and viral-host interactions in venting fluids from two geographically distant hydrothermal systems, the Mid-Cayman Rise in the Caribbean Sea and Axial Seamount in the Pacific Ocean. Analysis of viral sequences and CRISPR spacers revealed highly diverse viral assemblages and abundant lysogenic viruses, with 40% of metagenome-assembled genomes encoding a putative prophage. Network analysis revealed that viral host range was relatively narrow, with very few viruses infecting multiple microbial lineages. Viruses were largely endemic to individual vent sites, indicating restricted dispersal, and in some cases viral assemblages persisted over time. Thus, while the viruses at deep-sea hydrothermal systems play an important role in driving the evolution and ecology of resident vent microbial communities, their influence is highly localized to specific regions and taxa.

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Draft Genome Sequence of Streptomyces sp. Strain ventii, Isolated from a Microbial Mat near Hydrothermal Vents within the Axial Seamount in the Pacific Ocean, and Resequencing of the Type Strains Streptomyces lonarensis NCL 716 and Streptomyces bohaiensis 11A07

Microbiology Resource Announcements ◽

10.1128/mra.00607-20 ◽

2020 ◽

Vol 9 (32) ◽

Author(s):

Rachel M. Loughran ◽

Edward A. Mitchell ◽

Oliver B. Vining ◽

David A. Gallegos ◽

Monica C. Deadmond ◽

...

Keyword(s):

Pacific Ocean ◽

Deep Sea ◽

Hydrothermal Vents ◽

Draft Genome ◽

Content Type ◽

Streptomyces Sp ◽

The Pacific ◽

The Pacific Ocean ◽

Axial Seamount ◽

Type Strains

ABSTRACT The draft genome of Streptomyces sp. strain ventii, an environmental isolate recovered from deep-sea hydrothermal vents in the Pacific Ocean, is presented along with the resequenced draft genomes of the type strains Streptomyces bohaiensis 11A07 and Streptomyces lonarensis NCL 716.

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