scholarly journals Physiological and Genomic Characterization of a Hyperthermophilic Archaeon Archaeoglobus neptunius sp. nov. Isolated From a Deep-Sea Hydrothermal Vent Warrants the Reclassification of the Genus Archaeoglobus

2021 ◽  
Vol 12 ◽  
Author(s):  
Galina Slobodkina ◽  
Maxime Allioux ◽  
Alexander Merkel ◽  
Marie-Anne Cambon-Bonavita ◽  
Karine Alain ◽  
...  
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
Single Copy ◽  
Amino Acid Identity ◽  
Hyperthermophilic Archaea ◽  
The Novel ◽  
Flagellar Motility ◽  
Isolation And Characterization ◽  
Mid Atlantic Ridge

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.

scholarly journals Identification and Characterization of Carboxyl Esterases of Gill Chamber-Associated Microbiota in the Deep-Sea Shrimp Rimicaris exoculata by Using Functional Metagenomics

2015 ◽  
Vol 81 (6) ◽  
pp. 2125-2136 ◽  
Author(s):  
María Alcaide ◽  
Anatoli Tchigvintsev ◽  
Mónica Martínez-Martínez ◽  
Ana Popovic ◽  
Oleg N. Reva ◽  
...  
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
Metagenomic Library ◽  
Content Type ◽  
Rimicaris Exoculata ◽  
Highly Active ◽  
Gill Chamber ◽  
Unknown Species ◽  
Mid Atlantic Ridge

ABSTRACTThe shrimpRimicaris exoculatadominates the fauna in deep-sea hydrothermal vent sites along the Mid-Atlantic Ridge (depth, 2,320 m). Here, we identified and biochemically characterized three carboxyl esterases from microbial communities inhabiting theR. exoculatagill that were isolated by naive screens of a gill chamber metagenomic library. These proteins exhibit low to moderate identity to known esterase sequences (≤52%) and to each other (11.9 to 63.7%) and appear to have originated from unknown species or from genera ofProteobacteriarelated toThiothrix/Leucothrix(MGS-RG1/RG2) and to theRhodobacteraceaegroup (MGS-RG3). A library of 131 esters and 31 additional esterase/lipase preparations was used to evaluate the activity profiles of these enzymes. All 3 of these enzymes had greater esterase than lipase activity and exhibited specific activities with ester substrates (≤356 U mg−1) in the range of similar enzymes. MGS-RG3 was inhibited by salts and pressure and had a low optimal temperature (30°C), and its substrate profile clustered within a group of low-activity and substrate-restricted marine enzymes. In contrast, MGS-RG1 and MGS-RG2 were most active at 45 to 50°C and were salt activated and barotolerant. They also exhibited wider substrate profiles that were close to those of highly active promiscuous enzymes from a marine hydrothermal vent (MGS-RG2) and from a cold brackish lake (MGS-RG1). The data presented are discussed in the context of promoting the examination of enzyme activities of taxa found in habitats that have been neglected for enzyme prospecting; the enzymes found in these taxa may reflect distinct habitat-specific adaptations and may constitute new sources of rare reaction specificities.

scholarly journals Isolation and Characterization of Salmonella Jumbo-Phage pSal-SNUABM-04

Viruses ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 27
Author(s):  
Jun Kwon ◽  
Sang Guen Kim ◽  
Hyoun Joong Kim ◽  
Sib Sankar Giri ◽  
Sang Wha Kim ◽  
...  
Keyword(s):  
Morphological Traits ◽  
Open Reading Frames ◽  
Genome Comparison ◽  
The Novel ◽  
Promising Alternative ◽  
Isolation And Characterization ◽  
Global Issue ◽  
Reading Frames ◽  
Predicted Function

The increasing emergence of antimicrobial resistance has become a global issue. Therefore, many researchers have attempted to develop alternative antibiotics. One promising alternative is bacteriophage. In this study, we focused on a jumbo-phage infecting Salmonella isolated from exotic pet markets. Using a Salmonella strain isolated from reptiles as a host, we isolated and characterized the novel jumbo-bacteriophage pSal-SNUABM-04. This phage was investigated in terms of its morphology, host infectivity, growth and lysis kinetics, and genome. The phage was classified as Myoviridae based on its morphological traits and showed a comparatively wide host range. The lysis efficacy test showed that the phage can inhibit bacterial growth in the planktonic state. Genetic analysis revealed that the phage possesses a 239,626-base pair genome with 280 putative open reading frames, 76 of which have a predicted function and 195 of which have none. By genome comparison with other jumbo phages, the phage was designated as a novel member of Machinavirus composed of Erwnina phages.

Microbial diversity in deep-sea sediments from the Menez Gwen hydrothermal vent system of the Mid-Atlantic Ridge

2015 ◽  
Vol 24 ◽  
pp. 343-355 ◽  
Author(s):  
Teresa Cerqueira ◽  
Diogo Pinho ◽  
Conceição Egas ◽  
Hugo Froufe ◽  
Bjørn Altermark ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Deep Sea ◽  
Hydrothermal Vent ◽  
Deep Sea Sediments ◽  
Mid Atlantic Ridge ◽  
Menez Gwen

Ultrastructural characteristics of spermatogenesis in three species of deep-sea hydrothermal vent mytilids

1997 ◽  
Vol 75 (2) ◽  
pp. 308-316 ◽  
Author(s):  
Marcel Le Pennec ◽  
Peter G. Beninger
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
The North ◽  
Male Gametes ◽  
Bathymodiolus Thermophilus ◽  
Nutritional Biology ◽  
Protandric Hermaphroditism ◽  
Mid Atlantic Ridge ◽  
Ultrastructural Characteristics ◽  
Species Specific

To enhance our understanding of the reproductive biology of deep-sea hydrothermal vent mytilids, the histology of the male gonad and the ultrastructure of its gametes were studied in Bathymodiolus thermophilus, B. puteoserpentis, and B. elongatus. Specimens of B. thermophilus were collected at the 13°N site on the East Pacific ridge, while B. puteoserpentis were sampled from the Snake Pit site of the mid-Atlantic ridge and B. elongatus were obtained from the North Fiji Basin. Gonad histology conformed to the typical bivalve profile; the differences in the proportions of acinal and interacinal tissue, as well as differences in acinal fullness in B. puteoserpentis, indicate that gametogenesis is discontinuous in these deep-sea mytilids. Evidence of protandric hermaphroditism was observed in B. elongatus, which exhibited acini containing both maturing and residual male gametes and immature oocytes. The ultrastructural characteristics of the male gametes conform to those described for littoral bivalve species, and the spermatozoon is of the primitive type. No species-specific differences in spermatozoon ultrastructure were discerned. No evidence of bacterial inclusions was found in either the gametes or the associated gonad cells in any of the species examined. The male gametes are thus probably not vectors for the endosymbiotic bacteria that characterize the nutritional biology of the adults in this genus.

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

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

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

Viruses ◽  
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.

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