Genomic Characterization and Environmental Distribution of a Thermophilic Anaerobe Dissulfurirhabdus thermomarina SH388T Involved in Disproportionation of Sulfur Compounds in Shallow Sea Hydrothermal Vents
Abstract
:1. Introduction
2. Materials and Methods
2.1. Genome Sequencing and Assembly
2.2. Genome Annotation
2.3. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) and Genomic Islands
2.4. Geographical Distribution
2.5. Taxonomical Analyses and Comparative Genomics
3. Results and Discussions
3.1. General Genome Properties and Genomic Islands
3.2. Central Carbon Metabolism
3.3. Hydrogen Metabolism
3.4. Nitrogen Metabolism
3.5. Sulfur Metabolism
3.6. Comparative Genomics
3.7. Geographical and Environmental Distribution
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
ANI | Average nucleotide identity |
CDS | Coding DNA sequences |
COGs | Clusters of orthologous groups |
CRISPR | Clustered regularly interspaced short palindromic repeats |
DNRA | Dissimilatory nitrate reduction to ammonium |
ENA | European Nucleotide Archive |
G6P | Glucose-6-phosphate |
INSDC | International Nucleotide Sequence Database Collaboration |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
MIGS | Minimum information about a genome sequence |
NCBI | National Center for Biotechnology Information |
PAHs | Polycyclic aromatic hydrocarbons |
PGAP | Prokaryotic genome annotation pipeline |
bp | Base pair |
SOR | Sulfur oxygenase reductase |
TCA | Tricarboxylic acid cycle |
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Item | Description |
---|---|
Investigation | |
Strain | Dissulfurirhabdus thermomarina strain SH388T |
Submitted to INSDC | GenBank |
Investigation type | Bacteria |
Project name | JAATWC000000000 |
Geographic location (latitude and longitude) | 44°29.469′ N, 146°06.247′ E |
Geographic location (country and/or sea, region) | Sea of Okhotsk, 250 m from the Kunashir Island shore (Sakhalin oblast, Russia) |
Collection date | June 2013 |
Environment (biome) | marine hydrothermal vent biome ENVO:01000030 |
Environment (feature) | marine hydrothermal vent ENVO:01000122 |
Environment (material) | marine hydrothermal vent chimney ENVO:01000129 |
Depth | −12 m |
General features | |
Classification | Domain Bacteria |
Phylum Proteobacteria | |
Class Deltaproteobacteria | |
Not assigned to an Order | |
Not assigned to a Family | |
Genus Dissulfurirhabdus | |
Species Dissulfurirhabdus thermomarina | |
Gram stain | Negative |
Cell shape | short rods |
Motility | Motile |
Growth temperature | Thermophilic, optimum at 50 °C |
Relationship to oxygen | Anaerobic |
Trophic level | Chemolithoautotrophic |
Biotic relationship | free-living |
Isolation and growth conditions | DOI 10.1099/ijsem.0.001083 |
Sequencing | |
Sequencing technology | Illumina MiSeq 2 × 150 bp |
Sequencing platform | Molecular Research, MrDNA (Shallowater, TX, USA) |
Assembler | Unicycler (version: 0.4.8-beta) |
Contig number | 36 |
N50 | 240,491 |
Genome coverage | 1384.362× |
Genome assembly NCBI | ASM1297923v1 |
Assembly level | Contigs |
Genomic features: | |
Genome size (bp) | 2,461,642 |
GC content (mol%) | 71.1 |
Protein coding genes | 2267 |
Number of RNAs | 50 |
tRNAs | 47 |
16S-23S-5S rRNAs | 1-1-1 |
Genus | Class | Occurrence | Georeferenced Records | ||
---|---|---|---|---|---|
Genus | Species | Genus | Species | ||
Dissulfurirhabdus | Deltaproteobacteria | 200 | 35 a | 114 | 25 a |
Dissulfuribacter | Deltaproteobacteria | 230 | 27 b | 130 | 14 b |
Caldimicrobium | Thermodesulfobacteria | 85 | 2 c | 39 | 1 c |
Thermosulfurimonas | Thermodesulfobacteria | 27 | 17 d | 5 | 3 d |
Thermosulfuriphilus | Thermodesulfobacteria | 0 | NA | 0 | NA |
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Share and Cite
Allioux, M.; Yvenou, S.; Slobodkina, G.; Slobodkin, A.; Shao, Z.; Jebbar, M.; Alain, K. Genomic Characterization and Environmental Distribution of a Thermophilic Anaerobe Dissulfurirhabdus thermomarina SH388T Involved in Disproportionation of Sulfur Compounds in Shallow Sea Hydrothermal Vents. Microorganisms 2020, 8, 1132. https://doi.org/10.3390/microorganisms8081132
Allioux M, Yvenou S, Slobodkina G, Slobodkin A, Shao Z, Jebbar M, Alain K. Genomic Characterization and Environmental Distribution of a Thermophilic Anaerobe Dissulfurirhabdus thermomarina SH388T Involved in Disproportionation of Sulfur Compounds in Shallow Sea Hydrothermal Vents. Microorganisms. 2020; 8(8):1132. https://doi.org/10.3390/microorganisms8081132
Chicago/Turabian StyleAllioux, Maxime, Stéven Yvenou, Galina Slobodkina, Alexander Slobodkin, Zongze Shao, Mohamed Jebbar, and Karine Alain. 2020. "Genomic Characterization and Environmental Distribution of a Thermophilic Anaerobe Dissulfurirhabdus thermomarina SH388T Involved in Disproportionation of Sulfur Compounds in Shallow Sea Hydrothermal Vents" Microorganisms 8, no. 8: 1132. https://doi.org/10.3390/microorganisms8081132