A Microbial Biorealm page on the genus Salinibacter ruber
Higher order taxa
cellular organisms; Bacteria; Bacteroidetes/Chlorobi group; Bacteroidetes; Sphingobacteria; Sphingobacteriales; Sphingobacteriales genera incertae sedis; Salinibacter
Description and Significance
Salinibacter ruber is an extremely halophilic red bacteria and was found in saltern crystallizer ponds in Alicante and Mallorca, Spain in 2002 by Anton et al.. This environment has very high salt concentrations, and Salinibacter ruber itself cannot grow below 15% salt concentration, with an ideal concentration between 20-30%. Salinibacter ruber survives in this harsh environment because of its adaptations in order to cope with the high salt concentrations. These adaptations are: modifying the sequences of its proteins, recruiting proteins from different sources with different functions, as well as lateral gene transfer from other halophilic organisms.
This bacteria is very interesting because of it extremophile tendencies as a bacteria, when this is common mostly in the domain Archaea. Bacteria do not, in general, play a large role in microbial communities of hypersaline brines at or approaching NaCl saturation. However, with the discovery of S. ruber, this belief was weakened. It was found that S. ruber made up from 5% to 25% of the total prokaryotic community of the Spanish saltern ponds! (2)
Salinibacter ruber is most closely related to the genus Rhodothermus which is a thermophilic, slightly halophilic bacteria. Though genetically it is considered to be closest to the Rhodothermus genus, it is most comparable to the family Halobacteriaceae, because of similarity in protein structure.
S. ruber is comprised of a 3,551,823-bp chromosome of high G+C content (66.29%) and a 35,505-bp plasmid (57.9% G+C content). The chromosome contains 2,934 ORFs and the plasmid contains 33. Similar to the Archaea, S. ruber also has regions of low G+C content.
The first of these so-called islands is located 250 kb from the origin of replication. It contains 15 transposases and 5 prophage components, including 3 glycosyl-transferases. The second island is over 55 kb, with 12 transposases and multiple prophage-related ORFs. Additionally, there are some ORFs involved in capsular polysaccharide synthesis. The final G+C island is 39 kb and contains the sole restriction-modification system.
The plasmid codes for 19 hypothetical and conserved hypothetical genes and contains several ORFs involved in DNA metabolism, replication, recombination, as well as a gene involved in UV protection. It also encodes an IS5 family transposon element that is not found in the chromosome.
Within the genome of S. ruber, there is a hypersalinity island, which is extremely crucial for survival in a halophilic environment. This cluster of 19 genes includes a K+ uptake/efflux systems and cationic amino acid transporters. This island is mosaic in nature and is formed by various bacterial and archaeal sources. Many of the genes are similar to those of haloarchaea. Especially important genes in this island are the trkH gene and trkA gene. The Trk system is responsible for the uptake of K+. TrkH is a membrane bound translocating subunit and TrkA is a cytoplasmic membrane surface protein that binds NAD+. There are multiple trkA genes, thus suggesting the complex regulation of this trk system. The overlapping between Salinibacter ruber and members of Archaea suggest lateral gene transfer.
Also within the genome, S. ruber contains 4 rhodopsin genes. 2 are sensory rhodopsin genes, 83 kb apart on the genome. These 2 genes interact in order to produce a color-sensitive photoactive behavior. Also, a sensory rhodopsin is linked to signal transduction genes, which further solidifies the belief that Salinibacter ruber has photosensory function. The final rhodopsin gene identified not only the proton pumping activity of S. ruber, but also a new light-harvesting complex that allows the rhodopsin to have great absorbency (4).
Cell structure and metabolism
Salinibacter ruber is red, rod-shaped, gram-negative and aerobic with flagella for motility (2)
In order to survive in hypersaline environments, Salinibacter ruber had to adapt to its protein structures, which id different from other bacteria which use proton pumps. There is a high level of acidic amino acids, low levels of basic amino acids (especially lysine) as well as a low level of hydrophobic amino acids and finally, a high serine content. This allows for a pI value of 5.2, which allows this organism to thrive in high salt concentrations (4).
Salinibacter ruber has shown to maintain a high intracellular K-concentration and to posses enzymes that are functional at high salt concentrations. These enzymes are very similar to those of archaeal halophiles. The enzymes are as follows:
1. NAD-dependent isocitrate dehydrogenase (IDH)- functions optimally at 0.5-2.0 M KCl, with about 60% of optimum value at 3.3 M. This enzyme reacted less with NaCl, with about 70% of the activity of KCl. The max rate was at 0.2-1.2 M NaCl and above 3.0 M NaCl activity was very low. 2. NADP-dependent isocitrate dehydrogenase (IDH)- functions at a constant rate over a NaCl concentration of 1-3.2 M. However, varying levels of KCl provide stimulation. 3. NAD-dependent malate dehydrogenase (MDH)- functions optimally with the absence of salt and activity decreased with increased KCl and NaCl concentrations. 4. NAD-dependent glutamate dehydrogenase (GDH)- functions at a low activity rate in the absence of salt, and decreases with an increase in KCl concentration. However, this enzyme shoes an increase in activity with an increase in NaCl concentration. Optimum levels of activity are achieved at 3.0-3.5 M NaCl (1)
In addition to these enzymatic activities in S. ruber metabolism, S. ruber also metabolizes glucose, mannose, starch and glycerol. However, metabolism of sugars is not preferred, and only occurs once all other substrates have been depleted. S. ruber uses a modified Entner–Doudoroff pathway during which the phosphorylation step is delayed. However, glycerol is abundantly used for growth, as it is one of the most common substrates in saltern lakes. Glycerol metabolism starts with the phosphorylation of glycerol by glycerol kinase, followed by dehydrogenation of glycerol 3-phosphate (7, 8).
S. ruber is found in high salt concentration ponds in Spain. This bacteria has an extremely high salt requirement, which makes it unique among bacteria. Optimum levels of growth are achieved between 2.5 and 3.9 M NaCl, with a minimum of 1.7 M NaCl for any growth at all. This organism is a major component of the microbial community, and as stated before, can be up to 25% of the microbial population. S. ruber requires chloride for growth. This was tested by substituting only 20% of NaCl with gluconate, which ceased growth (6).
This organism is not a pathogen. There are no known diseases that are caused by this organism.
Application to Biotechnology
Since Salinibacter ruber was only discovered 5 years ago, in 2002, research has just begun and hasn’t progressed far enough in order to apply this organism to biotechnology. Research on the genome and protein structures has only just finished, and still more is being done. Researchers are going more into depth about certain functions of S. ruber (see current research), and have not yet learned enough to effectively use it as a tool in biotechnology.
8.1 Light modulation of respiration
Researchers have found that S. rubercells that contain Xanthorhodopsin display a light-induced reversible decrease of O2 uptake rate. Typically, the photoinhibition of respiration in ‘’S. ruber’’ saturates at light intensities of ≥ 2 mW cm− 2 in the spectral range 400–600 nm with a max depression of O2 uptake rate at 40–50%. They measured cells with different contents of xanthorhodopsin (caused by variations in the culture growth conditions or strain features) which showed that the light-saturated level of photoinhibition is not very variable. The expression of xanthorhodopsin was stimulated by illumination and low aeration of the culture (9).
8.2 Contribution to red-coloration to saltern ponds
Since it has been discovered that prokaryotes make up a large percentage of the microbial community in saltern pools, questions have arisen about the red-coloration of the water. There has been a belief that the red color is caused by red halophilic Archaea of the family Halobacteriaceae, in combination with β-carotene-rich ‘’Dunaliella’’ cells. However, researchers are trying to prove that s. ruber” also helps with coloration. Researchers used HPLC which showed a single pigment peak, eluting after 17.3±0.2 min. This suggests the presence of C-40 carotenoids. This is distinctly different from halophilic archaea (10).
8.3 Phylogeny specific for Bacteroidetes and Chlorobi
Researchers performed blast searches to find proteins found in Bacteroidetes, Chlorobi, or both. They found many specific proteins found at various taxonomic levels. The patterns of these signature proteins and conserved indels suggest that they or the genes for them have evolved at various stages in the evolution. However, subsequent to their evolution or introduction in these genes, the characteristics of the genome are retained in various descendents of these lineages with minimal gene loss or lateral gene transfer. This research helps with finding evolutionar paths for ‘’S. ruber’’ and will help identify why it has the characteristics it does.(11).
1. Oren A and Mana L. “Amino acid composition of bulk protein and salt relationships of selected enzymes of Salinibacter ruber, an extremely halophilic bacterium.” Extremophiles. 2002 Jun; 6(3):217-23. Epub 2002 Feb 1.
2. Anton J, Oren A, Benlloch S, Rodriguez-Valera F, Amann R, and Rossello-Mora R. “Salinibacter ruber gen. nov., sp. nov., a novel, extremely halophilic member of the Bacteria from saltern crystallizer ponds.” Int J Syst Evol Microbiol. 2002 Mar;52(Pt 2): 485-91.
3. Oren A and Rodríguez-Valera F. “The contribution of halophilic Bacteria to the red coloration of saltern crystallizer ponds” FEMS Microbiology Ecology, Volume 36, Issues 2-3, July 2001. p 123-130
4. Mongodin EF, Nelson KE, Daugherty S, Deboy RT, Wister J, Khouri H, Weidman J, Walsh DA, Papke RT, Sanchez Perez G, Sharma AK, Nesbo CL, MacLeod D, Bapteste E, Doolittle WF, Charlebois RL, Legault B, and Rodriguez-Valera F. “The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea.” Proc Natl Acad Sci U S A. 2005 Dec 13;102(50):18147-52. Epub 2005 Dec 5.
5. Bonete MJ, Perez-Pomares F, Diaz S, Ferrer J, and Oren A. “Occurrence of two different glutamate dehydrogenase activities in the halophilic bacterium Salinibacter ruber.” FEMS Microbiol Lett. 2003 Sep 12;226(1):181-6.
6. Muller V, and Oren A. “Metabolism of chloride in halophilic prokaryotes.” Extremophiles. 2003 Aug;7(4):261-6. Epub 2003 May 1. Review.
7. Elevi R, Mana L, Oren A, Sher J. The Institute of Life Sciences, and the Moshe Shilo Minerva Center for Marine Biogeochemistry, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
8. A. Oren and L. Mana. “Sugar metabolism in the extremely halophilic bacterium Salinibacter ruber.” FEMS Microbiol. Lett. 223 (2003), pp. 83–87.
9. Anton J, Balashov S, Boichenko V, Lanyi J, Wang J. “Functions of carotenoids in xanthorhodopsin and archaerhodopsin, from action spectra of photoinhibition of cell respiration.” Biochimica et Biophysica Acta (BBA) - Bioenergetics, Volume 1757, Issue 12, December 2006, Pages 1649-1656
10. Lutnaes BF, Oren A, and Liaaen-Jensen S. “New C(40)-carotenoid acyl glycoside as principal carotenoid in Salinibacter ruber, an extremely halophilic eubacterium.” J Nat Prod. 2002 Sep;65(9):1340-3.
11. Amann R, Anton J, Castresana J, Pena A, Rossello-Mora R, Soria-Carrasco V, Valens-Vadell M. “Phylogenetic position of Salinibacter ruber based on concatenated protein alignments.” Systematic and Applied Microbiology, Volume 30, Issue 3, 19 April 2007, p 171-179