Pelagibacterales (SAR11): Difference between revisions

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==Description and Significance==
==Description and Significance==
Pelagibacterales (SAR11) is an order in the Alphaproteobacteria composed of free-living planktonic oligotrophic facultative photochemotroph bacteria. (4)(5) They are most abundant group of planktonic cells in marine systems and possibly the most numerous bacterium in the world. Typically accounting for ~25% of prokaryotic cells in seawater worldwide.(3)  
Pelagibacterales (SAR11) is an order in the Alphaproteobacteria composed of free-living planktonic oligotrophic facultative photochemotroph bacteria. (4)(5) They are most abundant group of planktonic cells in marine systems and possibly the most numerous bacterium in the world. Typically accounting for ~25% of prokaryotic cells in seawater worldwide, SAR11 bacteria play an important role in the global carbon cycle.(3) SAR11 bacteria oxidize organic compounds from primary production into CO2.  
The order was originally named SAR11 following its discovery in the Sargasso Sea in 1990 by Professor Stephen Giovannoni and colleagues, from Oregon State University.(2)(5) It was first placed in the order of Rickettsiales, but after rRNA gene-based phyogenetic analysis, in 2013 it was raised to the rank of order, and then placed as sister order to the Rickettsiales in the subclass Rickettsidae.(5)


These gram negative, rod shaped bacteria are one of the smallest free cell living organisms, with a cell volume less than 1/500th the volume of E.coli. They have a high surface to volume ratio to better absorb nutrients from its oligotrophic environment. Unsurprisingly, it is also known to have one of the smallest genomes of free living cells.(7) Pelagibacterales have the complete biosynthetic pathway for all 20 amino acids and all but a few cofactors. There are also  no pseudogenes, introns, transposons, or extrachromosomal elements yet observed for any cell. (7)
The order was originally named SAR11 following its discovery in the Sargasso Sea in 1990 by Professor Stephen Giovannoni and colleagues, from Oregon State University.(2)(5) It was first placed in the order of Rickettsiales, but after rRNA gene-based phyogenetic analysis, in 2013 it was raised to the rank of order, and then placed as sister order to the Rickettsiales in the subclass Rickettsidae. They are most closely related to the their sister order, the Rickettsiales. (5)


==Genome Structure==
These gram negative, rod shaped bacteria are one of the smallest free cell living organisms (<0.7 um), with a cell volume less than 1/500th the volume of E.coli. They have a high surface to volume ratio to better absorb nutrients from its oligotrophic environment. These organisms are difficult to grow in pure culture due to their environmental adaptation to such low nutrients and slow growth. Unsurprisingly, it is also known to have one of the smallest genomes of free living cells.(7) The genome of the SAR11 clade has been generated by the DOE Joint Genome Institute. It was found that the isolates formed three micro clusters, closely related groupings within the clade. They were surprised to find that unlike marine SAR11 bacteria, the freshwater bacteria were much less genetically diverse, when measured based on the ratio of recombination to mutation in their genes.(9) It was also found that the bacteria have the complete biosynthetic pathway for all 20 amino acids and all but a few cofactors. There are also no pseudogenes, introns, transposons, or extrachromosomal elements yet observed for any cell. It is the most genetically efficient order of bacteria.
An industrial standard strain of ''O. oeni,'' PSU-1, has a circular genome of 1780517 basepair nucleotides, 1691 protein-coding genes, and 51 RNA genes (7). 43 tRNA sequences that represent 20 amino acids and 14 different insertion sequence transposase genes are present. Comparing different strains of ''O. oeni'' genomes, the general number of nucleotides tends to be very similar across the specie (7). The critical malolactic fermentation operates from the mleA gene, coding for the malolactic enzyme that breaks down the malic acid in the environment. Morphological and genomic evidence established the grounds to reclassify this bacteria as ''Oenococcus oeni''.  


[[Image:Oenococcus_genome.jpg|thumb|800px|FIGURE 3. Genome of ''Oenococcus oeni'' PSU-1. Inner most circle shows ORF classification: (1) Information storage, (2) cellular processes, (3) metabolism, (4) poorly characterized, (5) uncharacterized. The next circle outwards shows ORF orientation. Next circle next shows tRNA (green) and rRNA (blue). The red dots are transposase genes. The green (low) and orange (high) bands show deviation in GC content. (8).]]
==Subgroups==
Currently the SAR11 clade is divided into five subgroups (8):


==Cell Structure, Metabolism and Life Cycle==
Subgroup Ia: HTCC1062, HTCC1002, HTCC9565, HTCC7211, HIMB5
''Oenococcus oeni'' is a facultative anaerobe. It is able to use oxygen for cellular respiration but can also gain energy through fermentation. It characteristically grows well in the environments of wine, being able to survive in acidic conditions below pH 3.0 and tolerant of ethanol levels above 10% (2). Optimal growth occurs on sugar and protein rich media, like grape or tomato juice. The cocci are ellipsoidal to spherical in shape, usually grow in chains or pairs, and are typically non-sporulating.
Lactic acid bacteria, like ''Oenococcus oeni'', perform malolactic fermentation (also known as malolatic conversion). It occurs after (or sometimes during) primary fermentation. The main function of malolatic fermentation is converting glucose and malic acid to lactic acid. This is occurs by the uptake of malate, decarboxylation of malate to L-lactic acid and carbon dioxide, and the export of end products. ''O. oeni'' is heterofermentative, meaning it can create multiple end products from fermenting the sugars. In O. ''oeni''’s case, it produces carbon dioxide, ethanol, and acetate, as well as characteristic flavor molecules like diacetyl.  Strain variation of ''Oenoccocus oeni'' cellular processes can have significant effects on the community dynamics, fermentation, and overall quality of wine. Strain variation exists in sugar utilization pathways, phosphototransferase enzyme II systems, bacteriophage integration, and cell wall exopolysaccharides (3).


Subgroup Ib: SAR193, SAR11


Subgroup II: Artic95B-1, SAR11


==Ecology==
Subgroup IIIa: HIMB114, OM155
''Oenococcus oeni'' stabilizes wine communities by consuming available nutrients and lowering potential growth of other microbes, but its malolactic fermentation can be beneficial or detrimental to the production of wine depending on grapes, climate, and style of wine. Variations between strains and fermentation conditions have the potential to impact general quality and production of wine. Industrial winemakers use a standardized strain of ''O. oeni'', but the many external and environmental variables will dictate the success of the wine. ''O. oeni'' is not the only lactic acid bacteria that can perform secondary fermentation. There are a variety of lactic acid bacteria that can dominate bacterial community in response to temperature, nutrients, sulfur dioxide content, pH, ethanol levels, and inoculation densities. ''O. oeni'' commonly dominates secondary fermentation from its extreme tolerance to pH and ethanol levels.
The molecule diacetyl is produced as a byproduct of lactic acid bacteria in secondary fermentation. In wine, the levels of diacetyl create buttery and caramel flavor notes. It is generated when there is little or no malic acid to be consumed so citric acid is used. This byproduct is sought out by some winemakers while it is avoided by others. Rarely do the diacetyl levels reach a point of spoiling the wine (10).


Because of its heterofermentive properties, ''Oenoccocus'' may be viewed as an ecosystem engineer. ''O. oeni'' plays a major role in establishing the environment for which other microbes will interact. Its end products and life strategies positively feedback into creating a more harsh environment for other microbes like yeasts and fungi while making the conditions more ideal for other lactic acid bacteria (5).
Subgroup IIIb: S9D-28, LD12


Subgroup IV: DQ009255


Subgroup V: HIMB59, DQ009262
[[Image:SAR11Phylo.jpg|thumb|500px|FIGURE 3: 16S phylogenetic tree of the SAR11 clade (blue). SAR11 has three divergent phylogenetic lineages of the proposed family “Pelagibacteraceae”. Within the SAR11 clade there are 5 subgroups (8).]]
SAR11 clade possesses many unusual features for a free-living organism, including an extremely small, streamlined genome with few paralogs, no pseudogenes, and many missing genes and pathways that are otherwise common in bacteria(8). However, the SAR11 clade is phylogenetically diverse, spanning 18% 16S rRNA gene divergence. They have greater genomic rearrangement at operon boundaries than within operons, as well as hyper variable regions, possibly allowing these organisms to acquire new genetic material with adaptive significance (8).


==References==
==References==
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(6) [http://oregonstate.edu/ua/ncs/archives/2013/feb/war-without-end-earth’s-carbon-cycle-held-balance A war without end - with Earth’s carbon cycle held in the balance]
(6) [http://oregonstate.edu/ua/ncs/archives/2013/feb/war-without-end-earth’s-carbon-cycle-held-balance A war without end - with Earth’s carbon cycle held in the balance]


(7) [http://www.sciencemag.org.ezproxy.library.wisc.edu/content/309/5738/1242.long Kakarova, K., et al. “Genome Streamlining in a Cosmopolitan Oceanic Bacterium. Stephen J. Giovannoni1,*, H. James Tripp1, Scott Givan2, Mircea Podar3, Kevin L. Vergin1, Damon Baptista3, Lisa Bibbs3, Jonathan Eads3, Toby H. Richardson3, Michiel Noordewier3, Michael S. Rappé4, Jay M. Short3, James C. Carrington2, Eric J. Mathur3. Science 19 August 2005: Vol. 309 no. 5738 pp. 1242-1245 DOI: 10.1126/science.1114057] 
(7) [http://www.sciencemag.org.ezproxy.library.wisc.edu/content/309/5738/1242.long Kakarova, K., et al. “Genome Streamlining in a Cosmopolitan Oceanic Bacterium. Stephen J. Giovannoni1,*, H. James Tripp1, Scott Givan2, Mircea Podar3, Kevin L. Vergin1, Damon Baptista3, Lisa Bibbs3, Jonathan Eads3, Toby H. Richardson3, Michiel Noordewier3, Michael S. Rappé4, Jay M. Short3, James C. Carrington2, Eric J. Mathur3. Science 19 August 2005: Vol. 309 no. 5738 pp. 1242-1245 DOI: 10.1126/science.1114057]
 
 
 
(8) [http://www.sciencedirect.com/science/article/pii/S0168644505000355 Mills, D. A., Rawsthorne, H., Parker, C., Tamir, D., Makarova, K. “Genomic analysis of Oenococcus oeni PSU-1 and its relevance to winemaking”. “FEMS Microbiology Reviews”. 2005. Volume 29. P. 465-475]


(9) [http://phys.org/news/2014-02-glass-oenococcus-oeni-real-wine.html  phys.org “Raise your glass to Oenococcus oeni, a real wine bug”. “Science X Network”. 2014.]
(8) [http://mbio.asm.org/content/3/5/e00252-12.full Grote J, et al. 2012. Streamlining and core genome conservation among highly divergent members of the SAR11 clade. mBio 3(5):e00252-12. doi:10.1128/mBio.00252-12.]


(10) [http://www.bcawa.ca/winemaking/flaws.htm “Gibson, G., Farkas, M. “Flaws and Faults in wine”. ”British Columbia Amateur Winemakers Association”. Accessed 28 April 2014]
(9) [http://jgi.doe.gov/fresh-water-marine-sar11-bacteria-distant-relatives-different-lives Zaremba-Niedzwiedzka K et al. Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade. Genome Biology 2013, 14:R130
doi: 10.1186/gb-2013-14-11-r130]


==Author==
==Author==
Page authored by Digvinder Singh Mavi student of Prof. Katherine Mcmahon at University of Wisconsin-Madison.
Page authored by Digvinder Singh Mavi student of Prof. Katherine Mcmahon at University of Wisconsin-Madison.


<!-- Do not remove this line-->[[Category:Pages edited by students of Katherine Mcmahon at University of Wisconsin-Madison]]
<!-- Do not remove this line-->[[Category:Pages edited by students of Katherine McMahon at University of Wisconsin-Madison]]

Latest revision as of 19:54, 15 October 2015

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Classification

Domain: Bacteria

FIGURE 1. Scanning electron microscope image of SAR11 (1).

Phylum: Proteobacteria

Class: Alphaproteobacteria

Subclass: Rickettsidae

Order: Pelagibacterales


Description and Significance

Pelagibacterales (SAR11) is an order in the Alphaproteobacteria composed of free-living planktonic oligotrophic facultative photochemotroph bacteria. (4)(5) They are most abundant group of planktonic cells in marine systems and possibly the most numerous bacterium in the world. Typically accounting for ~25% of prokaryotic cells in seawater worldwide, SAR11 bacteria play an important role in the global carbon cycle.(3) SAR11 bacteria oxidize organic compounds from primary production into CO2.

The order was originally named SAR11 following its discovery in the Sargasso Sea in 1990 by Professor Stephen Giovannoni and colleagues, from Oregon State University.(2)(5) It was first placed in the order of Rickettsiales, but after rRNA gene-based phyogenetic analysis, in 2013 it was raised to the rank of order, and then placed as sister order to the Rickettsiales in the subclass Rickettsidae. They are most closely related to the their sister order, the Rickettsiales. (5)

These gram negative, rod shaped bacteria are one of the smallest free cell living organisms (<0.7 um), with a cell volume less than 1/500th the volume of E.coli. They have a high surface to volume ratio to better absorb nutrients from its oligotrophic environment. These organisms are difficult to grow in pure culture due to their environmental adaptation to such low nutrients and slow growth. Unsurprisingly, it is also known to have one of the smallest genomes of free living cells.(7) The genome of the SAR11 clade has been generated by the DOE Joint Genome Institute. It was found that the isolates formed three micro clusters, closely related groupings within the clade. They were surprised to find that unlike marine SAR11 bacteria, the freshwater bacteria were much less genetically diverse, when measured based on the ratio of recombination to mutation in their genes.(9) It was also found that the bacteria have the complete biosynthetic pathway for all 20 amino acids and all but a few cofactors. There are also no pseudogenes, introns, transposons, or extrachromosomal elements yet observed for any cell. It is the most genetically efficient order of bacteria.

Subgroups

Currently the SAR11 clade is divided into five subgroups (8):

Subgroup Ia: HTCC1062, HTCC1002, HTCC9565, HTCC7211, HIMB5

Subgroup Ib: SAR193, SAR11

Subgroup II: Artic95B-1, SAR11

Subgroup IIIa: HIMB114, OM155

Subgroup IIIb: S9D-28, LD12

Subgroup IV: DQ009255

Subgroup V: HIMB59, DQ009262

FIGURE 3: 16S phylogenetic tree of the SAR11 clade (blue). SAR11 has three divergent phylogenetic lineages of the proposed family “Pelagibacteraceae”. Within the SAR11 clade there are 5 subgroups (8).

SAR11 clade possesses many unusual features for a free-living organism, including an extremely small, streamlined genome with few paralogs, no pseudogenes, and many missing genes and pathways that are otherwise common in bacteria(8). However, the SAR11 clade is phylogenetically diverse, spanning 18% 16S rRNA gene divergence. They have greater genomic rearrangement at operon boundaries than within operons, as well as hyper variable regions, possibly allowing these organisms to acquire new genetic material with adaptive significance (8).

References

(1) "Rebounding bacteria". 2013

(2) “SAR11 bacteria thrive — despite viruses”.“Nature”

(3) "Why Sequence SAR11 Genome Evolution?". "Joint Genome Institute" Stephen Giovannoni, Oregon State University and Michael Rappé, Hawaii Institute of Marine Biology

(4) Grote J, et al. 2012. Streamlining and core genome conservation among highly divergent members of the SAR11 clade. mBio 3(5):e00252-12. doi:10.1128/mBio.00252-12.

(5) Ferla MP, Thrash JC, Giovannoni SJ, Patrick WM (2013) New rRNA gene-based phylogenies of the Alphaproteobacteria provide perspective on major groups, mitochondrial ancestry and phylogenetic instability. PLoS ONE 8: e83383 doi:

(6) A war without end - with Earth’s carbon cycle held in the balance

(7) Kakarova, K., et al. “Genome Streamlining in a Cosmopolitan Oceanic Bacterium. Stephen J. Giovannoni1,*, H. James Tripp1, Scott Givan2, Mircea Podar3, Kevin L. Vergin1, Damon Baptista3, Lisa Bibbs3, Jonathan Eads3, Toby H. Richardson3, Michiel Noordewier3, Michael S. Rappé4, Jay M. Short3, James C. Carrington2, Eric J. Mathur3. Science 19 August 2005: Vol. 309 no. 5738 pp. 1242-1245 DOI: 10.1126/science.1114057

(8) Grote J, et al. 2012. Streamlining and core genome conservation among highly divergent members of the SAR11 clade. mBio 3(5):e00252-12. doi:10.1128/mBio.00252-12.

(9) [http://jgi.doe.gov/fresh-water-marine-sar11-bacteria-distant-relatives-different-lives Zaremba-Niedzwiedzka K et al. Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade. Genome Biology 2013, 14:R130 doi: 10.1186/gb-2013-14-11-r130]

Author

Page authored by Digvinder Singh Mavi student of Prof. Katherine Mcmahon at University of Wisconsin-Madison.

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