Isolation and characterization of Thiobacillus hydrothermalis sp. nov., a mesophilic obligately chemolithotrophic bacterium isolated from a deep-sea hydrothermal vent in Fiji Basin

Hyperthermophilic archaea of the genus Archaeoglobus are the subject of many fundamental and biotechnological researches. Despite their significance, the class Archaeoglobi is currently represented by only eight species obtained as axenic cultures and taxonomically characterized. Here, we report the isolation and characterization of a new species of Archaeoglobus from a deep-sea hydrothermal vent (Mid-Atlantic Ridge, TAG) for which the name Archaeoglobus neptunius sp. nov. is proposed. The type strain is SE56T (=DSM 110954T = VKM B-3474T). The cells of the novel isolate are motile irregular cocci growing at 50–85°C, pH 5.5–7.5, and NaCl concentrations of 1.5–4.5% (w/v). Strain SE56T grows lithoautotrophically with H2 as an electron donor, sulfite or thiosulfate as an electron acceptor, and CO2/HCO3− as a carbon source. It is also capable of chemoorganotrophic growth by reduction of sulfate, sulfite, or thiosulfate. The genome of the new isolate consists of a 2,115,826 bp chromosome with an overall G + C content of 46.0 mol%. The whole-genome annotation confirms the key metabolic features of the novel isolate demonstrated experimentally. Genome contains a complete set of genes involved in CO2 fixation via reductive acetyl-CoA pathway, gluconeogenesis, hydrogen and fatty acids oxidation, sulfate reduction, and flagellar motility. The phylogenomic reconstruction based on 122 conserved single-copy archaeal proteins supported by average nucleotide identity (ANI), average amino acid identity (AAI), and alignment fraction (AF) values, indicates a polyphyletic origin of the species currently included into the genus Archaeoglobus, warranting its reclassification.

Download Full-text

Isolation and characterization of nine polymorphic microsatellite markers for the deep-sea shrimp Nematocarcinus lanceopes (Crustacea: Decapoda: Caridea)

BMC Research Notes ◽

10.1186/1756-0500-6-75 ◽

2013 ◽

Vol 6 (1) ◽

Cited By ~ 3

Author(s):

Johannes Dambach ◽

Michael J Raupach ◽

Christoph Mayer ◽

Julia Schwarzer ◽

Florian Leese

Keyword(s):

Microsatellite Markers ◽

Deep Sea ◽

Isolation And Characterization ◽

Polymorphic Microsatellite

Download Full-text

Characterization of DNA polymerase δ from deep-sea hydrothermal vent shrimp Rimicaris exoculata

Acta Oceanologica Sinica ◽

10.1007/s13131-021-1823-1 ◽

2021 ◽

Vol 40 (8) ◽

pp. 168-175

Author(s):

Wenlin Wu ◽

Hongyun Li ◽

Tiantian Ma ◽

Xiaobo Zhang

Keyword(s):

Dna Polymerase ◽

Deep Sea ◽

Hydrothermal Vent ◽

Dna Polymerase Δ ◽

Rimicaris Exoculata

Download Full-text

Isolation and Characterization of the First Temperate Virus Infecting Psychrobacillus from Marine Sediments

Viruses ◽

10.3390/v14010108 ◽

2022 ◽

Vol 14 (1) ◽

pp. 108

Author(s):

Wang Liu ◽

Xiaowei Zheng ◽

Xin Dai ◽

Zhenfeng Zhang ◽

Wenyan Zhang ◽

...

Keyword(s):

Marine Sediments ◽

Hydrothermal Vent ◽

Okinawa Trough ◽

Marine Ecosystem ◽

Genome Replication ◽

Gene Encoding ◽

Significant Similarity ◽

Host Chromosome ◽

Isolation And Characterization

Viruses are far more abundant than cellular microorganisms in the marine ecosystem. However, very few viruses have so far been isolated from marine sediments, especially hydrothermal vent sediments, hindering the understanding of the biology and ecological functions of these tiny organisms. Here, we report the isolation and characterization of a temperate bacteriophage, named PVJ1, which infects Psychrobacillus from a hydrothermal vent field in Okinawa Trough. PVJ1 belongs to the Myoviridae family of the order Caudovirales. The tailed phage possesses a 53,187 bp linear dsDNA genome, with 84 ORFs encoding structural proteins, genome replication, host lysis, etc. in a modular pattern. The phage genome is integrated into the host chromosome near the 3′-end of deoD, a gene encoding purine nucleoside phosphorylase (PNP). The phage integration does not appear to disrupt the function of PNP. The phage DNA is packaged by the headful mechanism. Release of PVJ1 from the host cell was drastically enhanced by treatment with mitomycin C. Phages encoding an MCP sharing significant similarity (≥70% identical amino acids) with that of PVJ1 are widespread in diverse environments, including marine and freshwater sediments, soils, artificial ecosystems, and animal intestines, and primarily infect Firmicutes. These results are valuable to the understanding of the lifestyle and host interactions of bacterial viruses at the bottom of the ocean.

Download Full-text

A g-Type Lysozyme from Deep-Sea Hydrothermal Vent Shrimp Kills Selectively Gram-Negative Bacteria

Molecules ◽

10.3390/molecules26247624 ◽

2021 ◽

Vol 26 (24) ◽

pp. 7624

Author(s):

Jing-Chang Luo ◽

Jian Zhang ◽

Li Sun

Keyword(s):

Deep Sea ◽

Hydrothermal Vent ◽

Binding Capacity ◽

Cellular Membrane ◽

Structural Features ◽

Gram Negative Bacteria ◽

Gram Negative ◽

Bacterial Binding ◽

Muramidase Activity

Lysozyme is a key effector molecule of the innate immune system in both vertebrate and invertebrate. It is classified into six types, one of which is the goose-type (g-type). To date, no study on g-type lysozyme in crustacean has been documented. Here, we report the identification and characterization of a g-type lysozyme (named LysG1) from the shrimp inhabiting a deep-sea hydrothermal vent in Manus Basin. LysG1 possesses conserved structural features of g-type lysozymes. The recombinant LysG1 (rLysG1) exhibited no muramidase activity and killed selectively Gram-negative bacteria in a manner that depended on temperature, pH, and metal ions. rLysG1 bound target bacteria via interaction with bacterial cell wall components, notably lipopolysaccharide (LPS), and induced cellular membrane permeabilization, which eventually caused cell lysis. The endotoxin-binding capacity enabled rLysG1 to alleviate the inflammatory response induced by LPS. Mutation analysis showed that the bacterial binding and killing activities of rLysG1 required the integrity of the conserved α3 and 4 helixes of the protein. Together, these results provide the first insight into the activity and working mechanism of g-type lysozyme in crustacean and deep-sea organisms.

Download Full-text

Isolation and Characterization of Novel Psychrophilic, Neutrophilic, Fe-Oxidizing, Chemolithoautotrophic α- and γ-Proteobacteria from the Deep Sea

Applied and Environmental Microbiology ◽

10.1128/aem.69.5.2906-2913.2003 ◽

2003 ◽

Vol 69 (5) ◽

pp. 2906-2913 ◽

Cited By ~ 239

Author(s):

K. J. Edwards ◽

D. R. Rogers ◽

C. O. Wirsen ◽

T. M. McCollom

Keyword(s):

Deep Sea ◽

Sequence Similarity ◽

Heterotrophic Bacterium ◽

Physiological Characterization ◽

Metalliferous Sediments ◽

Basalt Glass ◽

Isolation And Characterization ◽

Iron Oxidizing Bacteria ◽

Microaerobic Conditions

ABSTRACT We report the isolation and physiological characterization of novel, psychrophilic, iron-oxidizing bacteria (FeOB) from low-temperature weathering habitats in the vicinity of the Juan de Fuca deep-sea hydrothermal area. The FeOB were cultured from the surfaces of weathered rock and metalliferous sediments. They are capable of growth on a variety of natural and synthetic solid rock and mineral substrates, such as pyrite (FeS2), basalt glass (∼10 wt% FeO), and siderite (FeCO3), as their sole energy source, as well as numerous aqueous Fe substrates. Growth temperature characteristics correspond to the in situ environmental conditions of sample origin; the FeOB grow optimally at 3 to 10°C and at generation times ranging from 57 to 74 h. They are obligate chemolithoautotrophs and grow optimally under microaerobic conditions in the presence of an oxygen gradient or anaerobically in the presence of nitrate. None of the strains are capable of using any organic or alternate inorganic substrates tested. The bacteria are phylogenetically diverse and have no close Fe-oxidizing or autotrophic relatives represented in pure culture. One group of isolates are γ-Proteobacteria most closely related to the heterotrophic bacterium Marinobacter aquaeolei (87 to 94% sequence similarity). A second group of isolates are α-Proteobacteria most closely related to the deep-sea heterotrophic bacterium Hyphomonas jannaschiana (81 to 89% sequence similarity). This study provides further evidence for the evolutionarily widespread capacity for Fe oxidation among bacteria and suggests that FeOB may play an unrecognized geomicrobiological role in rock weathering in the deep sea.

Download Full-text