Pelagibacter ubique

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A Microbial Biorealm page on the genus Pelagibacter ubique

Pelagibacter ubique. Image courtesy of Office of Biological & Environmental Research
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Contents

Classification

Higher order taxa

Bacteria; Proteobacteria; Alphaproteobacteria; Rickettsiales; SAR11 cluster; Candidatus Pelagibacter; Candidatus Pelagibacter ubique

Species

NCBI: Candidatus Pelagibacter ubique HTCC1062 Taxonomy

Pelagibacter ubique

Equivalent Names:

    Pelagibacter ubique HTCC1062 
    Candidatus Pelagibacter ubique strain HTCC1062 
    SAR11

Description and significance

Pelagibacter ubique, strain HTCC1062, is significantly known to be one of smallest and simplest, self-replicating, and free living cell. It is part of the SAR11 clade, which are small, heterotrophic alphaproteobacteria, equaling to ~25% of all microbial plankton cells. During the summer time, it can increase to ~50% of the cells in the temperate ocean (12). P. ubique has a coastal, ocean surface ecotype (6), living in a low nutrient habitat. As the first cultivated member of SAR11 clade (the most successful clade of organisms), P. ubique is completely sequenced and has the smallest genome (1,308,759 bp) for any free living organism, as well as the smallest number of predicted open reading frames (ORF) (3). Differing from bacteria and archaea, which have small genomes as well, P. ubique has complete biosynthetic pathways for all 20 amino acids and all but a few cofactors. Also, it has no pseudogenes, introns, transposons, extrachromosomal elements, or inteins (9). In other words, P. ubique has no duplicate gene copies, no viral genes, and no junk DNA (14). The genome is about the size of intracellular parasites R. conorii and W. pipientis, however, its metabolic features are very simple (10). With a shorter DNA length to be copied for each generation, then the less work is to be done (14). Although there are numerous P. ubique microbes present in the ocean, mutation has not been a problem, mostly due to the fact that it is self-sufficient. Ongoing research is occurring to explain this phenomenon.

With a small genome size of 1,308,759 base pairs, whose DNA is completely sequenced, the “simplicity” of the P. ubique is more understood. It is a simple microbe, and with a refined understanding, we can identify what is needed for self cellular replication. (8)

P. ubique was first isolated in 2002 from the Sargasso Sea, from which SAR11 obtained its name, and the Oregon coastal surface waters, by a team from Oregon State University. The first cultivated strains of P. ubique were by high throughput dilution-to-extinction culturing (HTC), using a natural seawater media for dilution. The cultures were regularly reproduced in autoclaved seawater, where they reached their typical cell densities as in their natural populations, which is about 10^6 cells/ml (12). In collaboration with Diversa Corporation, liquid chromatography and tandem mass spectrometry was used to find proteorhodopsin genes were present in the culture (12), from which the genes were abundant in the Oregon coast. The proteorhodopsin genes are light dependent proton pumps, supplying energy for microbial metabolism (6).

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Genome structure

The genome of P. ubique has 1,308,759 bp, constituting 30% of the cell volume (9), and is completely sequenced. It encodes the smallest number of predicted open reading frames (3) and has complete biosynthetic pathways for all 20 amino acids and all but a few cofactors. With a small genome size, almost all the basic functions are encoded, which is attributed to the absence of nonfunctional or repeating DNA. There has been no evidence of DNA originating from any gene transfers. (9) Although the number of P. ubique is vast in the ocean and there are many opportunities for random mutations, the microbe has been able to streamline its genes - simplify and organize its genes to be self-sufficient (14).

In addition, P. ubique has a circular shaped chromosome with 1354 protein genes, and 35 RNA genes (11). According to the Comprehensive Microbial Resource website, from the total size of the DNA molecules, 26.68% (388480 bp) is the amount of G+C bases and 95.46% (1249346 bp) is the amount of primary annotation coding bases (2). P. ubique has 1354 protein coding genes, with 85.89% (1163 genes) which are assigned a role category, 2.51% (34 genes) which are not assigned a role category, 2.88% (39 genes) which are conserved hypothetical genes, and 8.71% (118 genes) which are hypothetical genes (11).

The pattern of genome reduction observed is adherent with the hypothesis of genome streamlining, from a large population which originates in a low nutrient environment. This simply suggests that P. ubique is one of the most abundant organisms in the ocean because of its simple life form. (3)

Proteorhodopsins, which was active in the ocean, have been found to be first expressed in the SAR11 strain HTCC1062 – P. ubique, when cultured in both autoclaved seawater and in its natural environment. Proteorhodopsins are light dependent proton pumps which give energy for microbial metabolism. Some structural features of P. ubique proteorhodopsin genes had an affect on its absorbance. At position 105, if a leucine residue is present, then green light is absorbed, which is common of the shallow water proteorhodopsins. However, from the proteorhodopsin genes taken from the Sargasso Sea, glutamine residues were located at position 105, therefore, absorbing blue light. Through research, the gene is still expressed when cells are grown in both light and dark environments, showing not difference in growth rates or cell yields. (6)

Cell structure and metabolism

P. ubique is rod or crescent shaped, with a length of 0.37-0.89 μm and an average cell diameter of 0.12-0.20 μm (8). The size range is due to natural variation associated with cell division. Also, the cells were measured after fixation in glutaraldehyde, which may have decreased the size. An average cell size after cell division is about 0.4 × 0.2μm^2, with the cell volume of 0.01 μm^3. (8)

It is stated many times that P. ubique is one of the most abundant and smallest organisms in the ocean. This is true because the combined weight of the SAR11 clade outweighs the total weight of all the fish present in the sea. (1, 3)

P. ubique is a self-sufficient organism. It is a small microbe, consisting of only 1,354 genes, which encodes for the bare essentials for life (14), compared to the 30,000 human genes. It gains energy from consuming dead organic carbon in its natural habitat, which is a low nutrient environment. From this process, the microbe releases nutrients needed by the ocean algae to convert carbon dioxide into oxygen, which is a photosynthetic process. Because nitrogen, which is a difficult element to attain, P. ubique favors base pairing, which requires less nitrogen.

Ecology

P. ubique is an efficient microbe. It is a heterotrophic alphaproteobacteria, and therefore is dependent on organic matter. It consumes the dead organic matter which is dissolved in the ocean water. Because the ocean is a vast area, there is no drawback of overabundance or under abundance; therefore, there is no need for a special metabolic cycle. Furthermore, adding nutrients to the ocean would not affect the microbe’s feeding tendencies. By feeding off the dissolved organic carbon, P. ubique produced nutrients needed by the algae to grow, from which the algae is needed to convert carbon dioxide to oxygen. It is known that ocean algae are credited for most of photosynthetic oxygen. (1)

In addition, P. ubique uses less nitrogen, which is sometimes a difficult nutrient for organisms to attain. This is possible because P. ubique uses base pairs, which require less nitrogen. (1)

Pathology

P. ubique has a completely coded genome, which does not consist of any junk DNA, duplicate entries, or viral genes (1). It is one of the simplest microbes found in the ocean, which simply eats to survive. As stated in the Ecology section, it feeds off dead organic matter and even uses base pairing to use less nitrogen. Therefore, currently, there is no research stating this organism causes or contributes to any disease.

Application to Biotechnology

P. ubique produces nutrients which are essential for the growth of ocean algae, by feeding off of dead organic carbon. In turn, the ocean algae convert carbon dioxide to oxygen by photosynthesis. Oxygen is necessary for most life forms on Earth to exist, and since algae constitutes more than half of the oxygen produced, P. ubique plays a crucial part in the production of oxygen.

Current Research

Giovannoni Lab

Dr. Stephen Giovannoni, from Oregon State University, is head of a lab which cultured SAR11, that was renamed P. ubique. On-going experiements are trying to understand how SAR 11 contributes to geochemical cycles and the basic architecture of cells and genomes. Currently, they are understanding the role of the proterohodopsin gene as part of the metabolism of P. ubique. (4)

Artificial ‘’Pelagibacter ubique’’

Craig Venter, a bio-entrepreneur, is attempting to create an artificial version of P. ubique with about 300 genes. His purpose is to discover how few genes are needed for a living organism to survive. (14)

Metabolic reconstruction

There is current research to predict the organic carbon sources used by P. ubique by metabolic reconstruction. Also, the proteome state of the microbe is studied, to be used as a means of finding information of the biological state of the system. (3)

Improvement of techniques

In the Spring of 2007, Ulrich Sting, Harry James Tripp and Stephen Giovannoni, of Oregon State University, published a journal article in The ISME Journal, entitled Improvements of high-throughput culturing yielded novel SAR 11 strains and other abundant marine bacteria from the Oregon coast and the Bermuda Atlantic Time Series study site. In their research, they improved the high-throughput dilution-to-extinction culturing (HTC), leading to the isolation of 17 new SAR11 strains from the Oregon coast and the Sargasso Sea. Sterilized natural sea water was used as a medium. With phylogenetic analysis of the internal transcribed spacer (ITS) region, the new strains found in the Oregon coast were divided into three subclusters of SAR11, while the strains from the Sargasso Sea represented one ITS cluster. Using a PCR assay, proteorhodopsin (PR) was present in all the strains. By analyzing the PR amino acid sequences of the isolates, those from the Oregon coast were tuned to either blue or green light and those from the Sargasso Sea were tuned to only blue light. However, the phylogenies of the strains, according to the ITS and PR, did not correlate, therefore indicating some kind of lateral gene transfer. The new information about the SAR11 clade could possibly lead to more information of P. ubique and its minimal macromolecular machinery needed for self-replication. (15)

Recombination

In 2007, a group of biologists contributed to an article in Environmental Microbiology, entitled High intraspecific recombination rate in a native population of Candidatus Pelagibacter ubique (SAR 11). The groups studied the recombination, which is an important progression in microbial evolution. Having low rates of recombination is enough to have lateral gene transfers, which will not disturb the clonal pattern of inheritance for other genes. However, a high rate of recombination can obscure clonal patterns, which can lead to sexually interbreeding eukaryotic populations. In the research, recombination between eight loci from nine strains of Candidatus P. ubique (SAR11), which was isolated from a 2L niskin sample of seawater. Using a test called the Shimodaira-Hasegawa test, it was found that there were phylogenetic differences in seven of the genes, showing that “frequent recombination obscures phylogenetic signals from the linear inheritance of genes in this population.” At this point, the methods of genetic transfer is unknown. However, tests have shown that the recombination rates are higher than the point mutation rates, which is the source of genetic diversity within the SAR11 clade. (16)

References

(1) Cascio, Jamais. World Changing. Genetic Efficiency and the Carbon Cycle. 19 August 2005. Accessed 26 August 2007.

(2) Comprehensive Microbial Resource. Candidatus Pelagibacter ubique HTCC1062 Genome Page. Last updated 27 September 2006. Accessed 26 August 2007.

(3) European Bioinformatics Institute. Bacteria Genomes - CANDIDATUS PELAGIBACTER UBIQUE. Accessed 26 August 2007.

(4) Giovannoni, Stephen. Oregon State University. Giovannoni Lab: SAR 11. Accessed 26 August 2007.

(5) Giovannoni, Stephen, and Douglas Barofsky, comps. U.S. Department of Energy. Biological and Environmental Research - PNNL Proteomics. Biological Applications - Organisms: Pelagibacter ubique. Last updated May 2007. Accessed 26 August 2007.

(6) Giovannoni, S.J., Bibbs, L., Cho, J.-C., Stapels, M.D., Desiderio, R., Vergin, K.L., Rappe, M.S., Laney, S., Wilhelm, L.J., Tripp, H.J., Mathur, E.J., and Barofsky, D.F. Proteorhodopsin in the ubiquitous marine bacterium SAR11. Nature 438 (3 November 2005): 82-85.

(7) Giovannoni S.J., Morris, R. M., Rappe, M. S., Connon, S. A., Vergin, K. L., Siebold, W. A., and Carlson, C. A. SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420 (December 2002): 806-810.

(8) Giovannoni, S.J., Rappe, M. S., Connan, S. A., and Vergin, K. L. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418 (8 August 2002): 630-631.

(9) Giovannoni, S.J., Tripp, H.J., Givan, S., Podar, M., Vergin, K.L., Baptista, D., Bibbs, L., Eads, J., Richardson, T.H., Noordewier, M., Rappe, M.S., Short, J., Carrington, J.C., and Mathur, E.J. Genome Streamlining in a Cosmopolitan Oceanic Bacterium. Science 309 (19 August 2005): 1242-1245.

(10) Genomics: GTL. U.S. Department of Energy Office of Science. Systems for Biology for Energy and Environment: Genomes to Life Contractor-Grantee Workschop 2005. Microbial Genomics - Pelagibacter ubique: A Post-Genomic Investigation of Carbon Metabolism and Photochemistry in an Extraordinarily Abundant Oceanic Bacterium. February 2005. Accessed 26 August 2007.

(11) Kyoto Encyclopedia of Genes and Genomes. Candidatus Pelagibacter ubique. Accessed 26 August 2007.

(12) Monterey Bay Aquarium Research Institute (MBARI). Giovannoni, Stephen. Pelagibacter ubique: A Perfect engineering solution? Seminar: Pacific Forum. 15 April 2005. Accessed 26 August 2007.

(13) National Library of Medicine (NLM) and National Institutes of Health (NIH). National Center for Biotechnology Information (NCBI): Pelagibacter ubique. Accessed 26 August 2007.

(14) Pease, Roland. BBC News. Ocean bug has 'smallest genome'. Last updated 19 August 2005. Accessed 26 August 2007.

(15) Sting, U., Tripp, H. J., and Giovannoni S. J. ISME Journal. Improvements of high-throughput culturing yielded novel SAR11 strains and other abundant marine bacteria from the Oregon coast and the Bermuda Atlantic Time Series study site. Oregon State University. 5 July 2007. Accessed 28 August 2007.

(16) Vergin, K.L., Tripp, H.J., Wilhelm, L.J., Denver, D.R., Rappe, M.S., and Giovannoni, S.J. Environmental Microbiology (OnlineEarly Articles). High intraspecific recombination rate in a native population of ‘’Candidatus Pelagibacter ubique’’ (SAR11). 2007. Accessed 28 August 2007.

(17) National Aeronautics and Space Administration (NASA). When Sun’s Too Strong, Plankton Make Clouds. 2 July 2004. Accessed 28 August 2007.

Edited by Liza Dizon, student of Rachel Larsen

Edited by KLB

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