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


Subgroup Ia: Open ocean, crown group — includes Pelagibacter unique HTCC1062
Subgroup Ia: HTCC1062, HTCC1002, HTCC9565, HTCC7211, HIMB5


Subgroup Ib, open ocean, sister clade to Ia
Subgroup Ib: SAR193, SAR11


Subgroup II, coastal, basal to Ia + Ib
Subgroup II: Artic95B-1, SAR11


Subgroup III, brackish, basal to I + II along with its sister clade IV
Subgroup IIIa: HIMB114, OM155


Subgroup IV, also known as LD12 clade, freshwater[13]
Subgroup IIIb: S9D-28, LD12


Subgroup V, which includes alphaproteobacterium HIMB59, basal to the remainder
Subgroup IV: DQ009255


[[Image:SAR11Phylo.jpg|thumb|500px|FIGURE 3: 16S phylogenetic tree of the SAR11 clade (blue)]
Subgroup V: HIMB59, DQ009262
 
SAR11 has three divergent phylogenetic lineages of the proposed family “Pelagibacteraceae” (Figure 2).
 
Five SAR11 strains HTCC1062, HTCC1002, HTCC9565, HTCC7211, and HIMB5) form a group of closely related lineages (16S identity ≥ 98%; ANI [average nucleotide identity] ≥ 75%) within SAR11 subclade Ia, which is ubiquitous in geographic distribution (1, 2). Strain HIMB114 is more distantly related (88% 16S identity with HTCC1062) and is part of the subclade IIIa, which is a sister group to the freshwater SAR11 subclade IIIb/LD12 lineage (Vergin et al., submitted). The subclade Va strain HIMB59 is very distantly related (82% 16S identity with HTCC1062) but has been classified as a SAR11 strain based on monophyletic grouping with the other SAR11 strains using both 16S (Vergin et al., submitted) (Fig. 1) and concatenated protein phylogenies (6). Here we present a detailed comparative analysis of these seven SAR11 genomes that provides new insight into the genome features and genetic content of this diverse group of globally abundant organisms.
 
General genome features.The strains in this study were isolated from surface seawater of disparate origin: HTCC1062 and HTCC1002 from the temperate coastal Northeast Pacific (4), HTCC9565 from the temperate open ocean of the Northeast Pacific, HTCC7211 from the Sargasso Sea in the subtropical Atlantic (21), and HIMB5, HIMB114, and HIMB59 from the coastal tropical North Pacific (Table 1; see also Table S8 at http://giovannonilab.science.oregonstate.edu/publications). The genomes of HTCC1062, HTCC1002, HTCC7211, HIMB5 and HIMB59 are closed, while the genomes of HIMB114 and HTCC9565 consist of scaffolds with one and three contigs, respectively. Based on synteny with the other genomes of subclade Ia, the amount of missing information for the HTCC9565 genome is estimated to be from <1 to ca. 5.5 kbp. While the degree of completion of the HIMB114 genome is more difficult to estimate, a second recently sequenced subclade IIIa genome is complete at 1.285 Mbp (22), which is less than 50 kbp larger than the current HIMB114 sequence. The presence of a compact (mean genome size of 1.337 ± 0.08 Mbp), low G+C (28.6 to 32.3%) genome is a unifying characteristic of the SAR11 clade (Table 1). The genomes code for between 1,357 and 1,576 genes, one copy of the 5S, 16S, and 23S ribosomal RNA genes, and 30 to 35 tRNAs (see Table S1 at the above URL). No pseudogenes were identified in any of the strains.
 
==Cell Structure, Metabolism and Life Cycle==
''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).
 
 
 
==Ecology==
''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).


[[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==
Line 71: Line 55:
(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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