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). S. pomeroyi has a linear chromosome while its DSS-3 strain 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.” It has both heterotrophic and lithoheterotrophic characteristics, which means that it relies on inorganic compounds such as carbon monoxide and sulfphide for energy. S. pomeroyi has genes that are specialized in the uptake of compounds derived from algae, allow for fast growth, and facilitate the use of metabolites by the bacterium to reduce microzones. The Silicibacter genus is also known to possess numerous peptide transporters, which indicate the importance of proteins as carbon source for these species7. Another distinctive feature of this bacterium is its six ABC-type transporter systems since “no other sequenced genome has more than three”7. These transporter systems are primarily used by S. pomeroyi for the purpose of cell growth regulation. S. pomeroyi also has five tranport sysems for DMSP transport, “four transporters for ammonium and one for urea”7. Its genome also houses genes that facilitate integration of ammonium and urea, which are useful sources of nitrogen7.

The S. pomeroyi genome contains two operans that encode aerobic carbon monoxide dehydrogenases. These dehydrogenases are used to oxidize carbon monoxide to carbone dioxide. There are also three rRNA operons present in its genome, which explains the organism’s ability to quickly respond to modifications in the availability of resources. When there is plenty of carbon and energy available, S. pomeroyi stores it via the polyhydroxyalkanoic acid synthesis pathway. This organism does not display any evidence of pathways for autotrophy, which implies that it obtains its energy through carboxidotrophy. The genome of S. pomeryi contains “31 genes that encode elements for motility,” which the organism achieves by rotating its complex flagellum7.

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 membrane4. These blebs may be responsible for the “degradation of insoluble substrates”5. 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, which allow it to survive in environments with low nutrient salt and high oxygen concentrations4. This organism uses organic acids, amino acids, and other compounds such as ethanol, glycerol, acetate, DMSP, glucose, pyruvate, succinate, etc. to grow at 10-40°C temperature range. It requires NaCl for growth. Although vitamins are not required, enhanced growth was observed in their presence. S. pomeroyi is not able to either ferment glucose or reduce nitrate4, but it can degrade aromatic compounds1,2. It hydrolyzes gelatin but not cellulose or starch. In the presence of arginine, S. pomeroyi can also oxidize thiosulfate. It has the capacity to produce both oxidase and catalse. It forms cream-colored, circular colonies on marine agar. A noteworthy characteristic of this bacterium is its ability to separate its outer membrane from the cytoplasm4.

Ecology

Silicibacter pomeroyi contributes to the environment by degrading DMSP in order to produce dimethylsulfide (DMS). DMS is a sulfur compound that makes a major contribution to the sulfur supply in the atmosphere. It also plays an important role in the regulation of the climate by forming clouds and scattering the radiation coming from the sun3. The sulfur obtained from DMSP is integrated into proteins of bacteria; as a result, DMSP acts as a major source of sulfur for marine bacterioplankton This organism is also known to carry out the DMSP-demethylation/demethiolation pathway. This pathway produces methanethiol (MeSH), which expedites the incorporation of sulfur obtained from the degradation of DMSP into bacterial proteins6.

Pathology

S. pomeroyi is not known to cause any diseases in humans, plants, or animals. It is an environmental microbe.

Application to Biotechnology

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

Current Research

Enter summaries of the most recent research here--at least three required

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