Deferribacter desulfuricans

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Classification

• Domain: Bacteria
• Phylum: Deferribacterota
• Class: Deferribacteres
• Order: Deferribacterales
• Family: Deferribacteraceae
• Genus: Deferribacter
• Species: D. desulfuricans

Species

NCBI: Taxonomy

Deferribacter desulfuricans

Description and Significance

Deferribacter desulfuricans is a bacterium which has been found and isolated from deep-sea hydrothermal vents, much like other members of the Deferribacter genus. This specific species has been confidently isolated from the hydrothermal vents at the Suiyo Seamount of Japan. As one could assume from their preferred habitat, D. desulfuricans is a thermophillic bacteria with its optimal temperature being around 60-65 degrees celsius.

In regard to its appearance, this bacterium is a slightly elongated, oval-like shape with a single long flagellum on one of its shorter ends. They are typically found in the fairly immediate vicinity of the vents, living either in communal mats or freely swimming using the aforementioned flagellum. Both of these lifestyles have benefits to help avoid risks which come with living in the harsh environment of hydrothermal vents. When grouping together in biofilm-like communities, the bacteria have a better chance at avoiding being swept away from their ideal environment by the vents. Alternatively, when more free-floating, the flagellum helps them sense for temperature or chemical environmental stimuli. This helps communicate to them which directions to swim in to get back to optimal temperature or overall environment.

Genome Structure

The genome of D. desulfuricans has two major components. It has a single circular chromosome with base pairs as well as a megaplasmid with base pairs.

The circular chromosome is made up of 2,234,389 base pairs total. Within this sequence, its average G&C content is approximately 31.1%, with two clear points of GC skew transitions which have been assumed to be as a result of origin and termination sites of DNA replication. There have been at least 2,117 protein coding sequence regions found and annotated, with about 66% of them having been functionally assigned as of 2010.

The chromosome contains two ribosomal RNA operons which how 16S-23S-5S rRNA gene alignment. This part of the genome also contains a variety of tRNA genes, adding up to at least 43 total. Researchers have also labeled three distinct genomic islands on D. desulfuricans' circular chromosome. As genomic islands, they have been designated as likely results of horizontal gene transfer event(s), and have been termed DDGI-1, DDGI-2, and DDGI-3. Although they are still being investigated, as with the microbe as a whole, the first two islands seem to have somewhat primary purposes assigned to their coding sequences. DDGI-1 codes for heavy metal transporters, most likely to aid in heavy metal tolerance in the harsh environment of hydrothermal vents. DDGI-2 contains a toxin-antitoxin system, which is most likely also to aid in stress response to the environment as well as act as a phage defense mechanism.

Another interesting feature of D. desulfuricans is the presence of CRISPR/Cas elements. This is a feature which they share with other thermophilic microbes, and most likely aids in phage immunity. Due to this similarity, it is theorized that the CRISPR/Cas systems in this specific species could have been acquired through horizontal transfer via the megaplasmid.

As mentioned, this megaplasmid is the other counterpart of the D. desulfuricans genome. The plasmid, named pDF308, is made up of 308,544 base pairs and has an average G&C content of 24.5%. There have been 257 protein coding sequences mapped, and at least two thirds of them have been labeled as unique to any protein coding sequences currently in the NCBI database.

Cell Structure, Metabolism and Life Cycle

D. desulfuricans is a gram-negative, rod-shaped bacteria. It has a length of approximate length and width of 2 μm and .5 μm respectively. As mentioned, this microbe possesses a single polar flagellum, which it uses to anchor itself to the walls of a hydrothermal vent or propel itself when navigating its environment. The cell membrane of D. desulfuricans possesses a wide variety of digestive enzymes, and energy translocation systems, which aid this microbe in utilizing its diverse metabolism

D. desulfuricans grows heterotrophically using a variety of organic acids available around hydrothermal vents (acetate, formate, pyruvate), and like all other Deferribacter species, is a total anaerobe. It requires nitrate and elemental sulfur to grow, and reduces them to nitrite and sulfide respectively, reducing sulfur through D. desulfuricans reduces sulfur-yielding compounds through polysulfate and thiosulphate reductase. D. desulfuricans can use these as sources of energy, as well as for tricarboxylic acid (TCA) cycling and various anaplerotic pathways.

Ecology and Pathogenesis

D. desulfuricans is only known to inhabit hydrothermal vent environments, and being a thermophilic anaerobe is unlikely to have a presence outside of the hydrothermal vent environment. Hydrothermal vent environments experience extreme fluctuations in both temperature and chemical composition, with temperatures ranging from 140 to 700 degrees Fahrenheit at any given time, and with frequent expulsions of sulfuric compounds from vents, followed by dormant periods of varying length. Due to these frequency changes, Deferribacter species have significantly more chemical and temperature signaling systems than other vent-dwelling species, which is thought to be a contributing factor to its dominant presence on many hydrothermal vents.

Deferribacter species are often the most dominant microbial species on hydrothermal vents, which is thought to be due to their versatile metabolism as well as the multitude of chemical and temperature signaling systems encoded in its genome. While little research has been done on the way Deferribacter species interact with other vent microbes (likely due to the high costs of exploring remote hydrothermal vent ecosystems), the family’s relative dominance in vent ecosystems is one of many factors that has motivated potential future research on species within the family.

References

[BacDive. (n.d.). Deferribacter desulfuricans SSM1: Type strain: DSM 14783, JCM 11476, NBRC 101012: BacDiveID:3841. https://bacdive.dsmz.de/strain/3841]

[Kegg Genome: Deferribacter Desulfuricans. (n.d.-a). https://www.genome.jp/kegg-bin/show_organism?org=ddf]

[Takaki, Y., Shimamura, S., Nakagawa, S., Fukuhara, Y., Horikawa, H., Ankai, A., Harada, T., Hosoyama, A., Oguchi, A., Fukui, S., Fujita, N., Takami, H., & Takai, K. (2010, June). Bacterial lifestyle in a deep-sea hydrothermal vent chimney revealed by the genome sequence of the thermophilic bacterium Deferribacter Desulfuricans SSM1. DNA research : an international journal for rapid publication of reports on genes and genomes. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885270/]

Author

Page authored by Dana Smits and Trent Stocum, students of Prof. Jay Lennon at IndianaUniversity.