Silicibacter pomeroyi

A Microbial Biorealm page on the genus Silicibacter pomeroyi

Classification

Higher order taxa

cellular organisms; Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales; Rhodobacteraceae; Silicibacter

This bacterium belongs to the phylum bacteria and the genus is silicibacter (Global). Evidence suggests silicibacter pomeroyi belongs to the Roseobacter lineage (Gonzalez).

Species

NCBI: Taxonomy

Genus species

Description and significance

Silicibacter pomeroyi is among organisms that are capable of degrading sulfur compounds found in marine environments. In fact, this bacteria has the ability not only to degrade but also to demehtylate and cleave dimethylsulfoniopropionate (DMSP). It is a rod-shaped, Gram-negative bacterium that lives in marine environments and uses oxygen for its metabolic activities, such as to obtain energy. Silicibacter pomeroyi has a single but complex flagellum that rotates in the clockwise direction4, which accounts for its motility (Moran). This important characteristic enables the organism to place itself in favorable environments (Moran). Its surface is covered with blebs and its interior contains poly-β-hydroxybutyrate inclusions. It was isolated in Georgia from coastal sea water. This organism should be given a lot of attention because it plays an important role in climate regulation and greatly contributes to the “global atmospheric sulfur pool”4. By degrading DMSP, Silicibacter pomeroyi causes the formation of dimethylsulfide (DMS), which is a volatile sulfur compound that greatly adds to the sulfur supply in the atmosphere. DMS also influences climate regulation by forming clouds and backscattering solar radiation3,8. In addition, this bacterium also metabolizes DMSP through the demethylation/ demethiolation pathway to produce methanethiol (MeSH). The significance of MeSH lies in its critical role in the incorporation of DMSP sulfur into bacterial proteins. In the presence of MeSH, DMSP is quickly integraded into the bacterial proteins6.

Figure 1: Degradation of organic sulfur compounds by marine bacteria via various pathways (Gonzalez).

Figure 2: (a) Phase-contrast microphraph, (d) transmission electron micrgraph, (h) scanning electron micrograph of silicibacter pomeroyi.

Genome structure

The genomic sequence of silicibacter pomeroyi is 4,109,442 base pairs long. It contains a megaplasmid that is 491,611 base pairs long. The genome sequence also has 4,283 coding sequences (CDS). The DSS-3 strain of Silicibacter pomeroyi has a circular chromosome. A unique and noteworthy characteristic of S. pomeroyi is that it has “the highest proportion of genes coding for signal transduction,” which gives the organism an “enhanced ability to sense and respond to conditions outside the cell” (citation). This is a lithoheterotrophic and heterotrophic organism that uses inorganic compounds such as carbon monoxide and sulfide.

Cell structure and metabolism

Figure 2 shows the phase-contrast micrograph, tramission electron micrograph, and scanning electron micrograph of silicibacter pomeroyi. Analysis of this organism using these different micrographs has allowed scientists to detect blebs that are present in the outer membrane. These blebs may be responsible for the “degradation of insoluble substrates.” The bacterium also is seen to contain poly-β-hydroxybutyrate (PHB) inclusion bodies. The importance of the blebs and PHB bodies lies in the fact that they help silicibacter pomeroyi to pick up and store nutrients allowing it to survive in environments with low nutrient salt and high oxygen concentrations (Gonz). It uses organic acids and amino acids for growth and grows at 10-40°C temperature range. However, silicibacter pomeroyi does not have the ability to ferment glucose or reduce nitrate (Gonzalez), but it can degrade aromatic compounds (Buchan). Silicibacter pomeroyi has a polar flagellum, which rotates in the clockwise direction.

Ecology

Describe any interactions with other organisms (included eukaryotes), contributions to the environment, effect on environment, etc.

Pathology

How does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.

Application to Biotechnology

Does this organism produce any useful compounds or enzymes? What are they and how are they used?

Current Research

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References

Prototype data portal. Global Biodiversity Information Facility.

http://www.asia.gbif.net/portal/ecat_browser.jsp?termsAccepted=true 

Charlson, R. J., Lovelock, J. E., Andreae, M. O. & Warren, S. G. (1987). Oceanic phytoplankton, atmospheric sulfur, cloud albedo and climate. Nature 326, 655–661

Simó, R. (2001). Production of atmospheric sulfur by oceanic plankton: biogeochemical, ecological and evolutionary links. Trends Ecol Evol 16, 287–294

Gonzalez JM, Covert JS, Whitman WB, Henriksen JR, Mayer F, Scharf B, Schmitt R, Buchan A, Fuhrman JA, Kiene RP, Moran MA. “Silicibacter pomeroyi sp. Nov. and Roseovarius nubinhibens sp. Nov., dimethylsulfonioproprionate-demethylating bacteria from marine environments.” Int J Syst Evol Microbiol. 2003 Sep;53(Pt 5):1261-9.

Buchan, A., Collier, L. S., Neidle, E. L. & Moran, M. A. (2000). Key aromatic-ring-cleaving enzyme, protocatechuate 3,4-dioxygenase, in the ecologically important marine Roseobacter lineage. Appl Environ Microbiol 66, 4662–4672

Buchan, A., Neidle, E. L. & Moran, M. A. (2001). Diversity of the ring-cleaving dioxygenase gene pcaH in a salt marsh bacterial community. Appl Environ Microbiol 67, 5801–5809.

Moran MA, Buchan A, Gonzalez JM, Heidelberg JF, Whitman WB, Kiene RP, Henriksen JR, King GM, Belas R, Fuqua C, Brinkac L, Lewis M, Johri S, Weaver B, Pai G, Eisen JA, Rahe E, Sheldon WM, Ye W, Miller TR, Carlton J, Rasko DA, Paulsen IT, Ren Q, Daugherty SC, Deboy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Rosovitz MJ, Haft DH, Selengut J, Ward N. “Genome sequence of silicibacter pomeroyi reveals adaptions to the marine environment.” Nature 2004 Dec 16;432(7019):910-3.

Edited by Lusine Khachatryan, student of Rachel Larsen and Kit Pogliano