Oleispira antarctica: Difference between revisions
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= ''Oleispira antarctica'' = |
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{{Taxobox |
{{Taxobox |
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| domain = [[Bacteria]] |
| domain = [[Bacteria]] |
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| binomial = ''Oleispira antarctica'' |
| binomial = ''Oleispira antarctica'' |
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| binomial_authority = Yakimov et al. 2003 |
| binomial_authority = Yakimov et al. 2003 |
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}}'''''Oleispira antarctica''''' is a [https://www.ncbi.nlm.nih.gov/pubmed/17493798 hydrocarbonoclastic] marine [[Bacteria|bacterium]], the type species in its genus. It is [[psychrophilic]], [[Cellular respiration|aerobic]] and [[Gram-negative]], with polar [[flagellum]].<ref name="Yakimov2003">{{cite journal|last1=Yakimov|first1=M. M.|title=Oleispira antarctica gen. nov., sp. nov., a novel hydrocarbonoclastic marine bacterium isolated from Antarctic coastal sea water|journal=International Journal of Systematic and Evolutionary Microbiology|volume=53|issue=3|year=2003|pages=779–785|issn=1466-5026|doi=10.1099/ijs.0.02366-0}}</ref> Its genome has been sequenced and from this information, it has been recognized as a potentially important organism capable of oil degradation in the deep sea.<ref name=":1">{{Cite journal|last=Mason|first=Olivia U.|last2=Hazen|first2=Terry C.|last3=Borglin|first3=Sharon|last4=Chain|first4=Patrick S. G.|last5=Dubinsky|first5=Eric A.|last6=Fortney|first6=Julian L.|last7=Han|first7=James|last8=Holman|first8=Hoi-Ying N.|last9=Hultman|first9=Jenni|date=2012-09-01|year=|title=Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill|url=http://www.nature.com/ismej/journal/v6/n9/full/ismej201259a.html|journal=The ISME Journal|language=en|volume=6|issue=9|pages=1715–1727|doi=10.1038/ismej.2012.59|issn=1751-7362|pmc=3498917|pmid=22717885|via=}}</ref> |
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}} |
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==== Etymology ==== |
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''Oleispira antarctica'', "oleum" meaning oil, "spira" meaning a spire (in other words, coiled or twisted) for a combined meaning of a spiral-shaped, oil-degrading organism from [[Antarctica]].<ref name="Yakimov2003" /> |
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==== Phylogeny ==== |
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Based on sequencing of [[16S ribosomal RNA|16S ribosomal RNA genes]] conducted by Yakimov et al., [[Phylogenetics|phylogenetically]], this organism is related most closely to species of ''Oceanobacter, [[Marinobacterium]],'' and ''Marinomonas''.<ref name="Yakimov2003" /> It belongs to the phylum [[Gammaproteobacteria]] and had its own phyletic line within the phylum.<ref name="Yakimov2003" /> Its 16S rRNA gene sequences were no more than 90% similar to any other Gammaproteobacteria 16S rRNA gene sequence, and thus represented a novel species within a new genus.<ref name="Yakimov2003" /> ''O. antarctica'' was the first species in the new genus, but another new species, ''[https://www.ncbi.nlm.nih.gov/pubmed/22228140 Oleispira lenta]'', was characterized 9 years later.<ref name=":0">{{Cite journal|last=Wang|first=Yan|last2=Yu|first2=Min|last3=Austin|first3=Brian|last4=Zhang|first4=Xiao-Hua|date=2012-05-01|title=Oleispiralenta sp. nov., a novel marine bacterium isolated from Yellow sea coastal seawater in Qingdao, China|url=https://link.springer.com/article/10.1007/s10482-011-9693-8|journal=Antonie van Leeuwenhoek|language=en|volume=101|issue=4|pages=787–794|doi=10.1007/s10482-011-9693-8|issn=0003-6072}}</ref> Sequencing of ''O. lenta''<nowiki/>'s 16S ribosomal RNA genes revealed sequence similarity of about 97.2% to ''O. antarctica.''<ref name=":0" /> |
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== Isolation == |
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''Oleispira antarctica'' was isolated and characterized from shallow samples of sea water collected from the inlet portion of [[Ross Sea|Rod Bay in the Ross Sea]] (74°41.753'S, 164°07.188'E) during an expedition from the summer season in Antarctica of 1999 to the same time in the year 2000 by Yakimov ''et al''.<ref name="Yakimov2003" /> The investigators performed [[Enrichment culture|enrichment]] and [[Incubator (culture)|incubation]] of collected samples in 20 ml volumes of crude oil and additional nutrients.<ref name="Yakimov2003" /> After 2 months of enrichment at 4°C, cultures were [[Dilution cloning|diluted]] in tubes containing solutions of mineral medium of type ONR7a that were additionally supplemented with more crude light oil.<ref name="Yakimov2003" /> These tube cultures were then incubated in darkness until [[turbidity]] (which was used to indicate bacterial growth changes over some period of time) became high enough to indicate saturated growth samples (which took approximately 2 months).<ref name="Yakimov2003" /> These cultures were then diluted and the most diluted cultures (10<sup>-4</sup>) with positive growth were plated on solid form ONR7a mineral medium that also contained [[tetradecane]] (a 14 carbon hydrocarbon).<ref name="Yakimov2003" /> After 15 days and further incubation at 4°C, the investigators retrieved individual colonies.<ref name="Yakimov2003" /> |
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== Morphology == |
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The species has a [[Gram-negative bacteria|Gram-negative]] cell wall.<ref name="Yakimov2003" /> It exists as a curved rod to spiraled [[Bacterial cellular morphologies|cell shape]] with dimensions 2-5μm by 0.4-0.8μm.<ref name="Yakimov2003" /> It is mobile with a long, helical-structured polar [[flagellum]] >5μm in length.<ref name="Yakimov2003" /> One morphologically distinct characteristic is a unique drumstick-like enlargement and congealing of one or both ends of the cell where the cell wall is more electron-dense.<ref name="Yakimov2003" /> |
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== Growth, Genomics, and Metabolism == |
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====== Growth and Genomics ====== |
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| ⚫ | Colonies appeared uncolored, a little translucent and opaque, or a little bit yellow, on ONR7a plates additionally containing [[tetradecane]].<ref name="Yakimov2003" /> The organism grows best at 1-25°C with optimal growth temperature at 2-4°C, making it a [[psychrophile]].<ref name="Yakimov2003" /> It is a [[stenohaline]] organism, meaning it grows in only a narrow range of salinity, requires sodium ions for growth, and grows best in presence of 3-5% sodium chloride.<ref name="Yakimov2003" /> Oxidase and catalase enzymes were present.<ref name="Yakimov2003" /> Its principle [[Fatty acid|fatty acids]] are [[Monounsaturated fat|monounsaturated]], with principle fatty acids being [[Oleic acid|C18:1]], [[Palmitoleic acid|C16:1]], and [[Palmitic acid|C16:0]].<ref name="Yakimov2003" /> Strains of the species could synthesize [[Polyunsaturated fatty acid|polyunsaturated]] [[eicosapentaenoic acid]] at low temperatures.<ref name="Yakimov2003" /> It has a [[GC-content]] of 41-42% and the size of its [[genome]] is about 2 Mbp.<ref name="Yakimov2003" /><ref name="KubeChernikova2013">{{cite journal|last2=Chernikova|first2=Tatyana N.|last3=Al-Ramahi|first3=Yamal|last4=Beloqui|first4=Ana|last5=Lopez-Cortez|first5=Nieves|last6=Guazzaroni|first6=María-Eugenia|last7=Heipieper|first7=Hermann J.|last8=Klages|first8=Sven|last9=Kotsyurbenko|first9=Oleg R.|year=2013|title=Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica|journal=Nature Communications|volume=4|doi=10.1038/ncomms3156|issn=2041-1723|pmc=3759055|pmid=23877221|last1=Kube|first1=Michael|last10=Langer|first10=Ines|last11=Nechitaylo|first11=Taras Y.|last12=Lünsdorf|first12=Heinrich|last13=Fernández|first13=Marisol|last14=Juárez|first14=Silvia|last15=Ciordia|first15=Sergio|last16=Singer|first16=Alexander|last17=Kagan|first17=Olga|last18=Egorova|first18=Olga|last19=Alain Petit|first19=Pierre|last20=Stogios|first20=Peter|last21=Kim|first21=Youngchang|last22=Tchigvintsev|first22=Anatoli|last23=Flick|first23=Robert|last24=Denaro|first24=Renata|last25=Genovese|first25=Maria|last26=Albar|first26=Juan P.|last27=Reva|first27=Oleg N.|last28=Martínez-Gomariz|first28=Montserrat|last29=Tran|first29=Hai|last30=Ferrer|first30=Manuel|last31=Savchenko|first31=Alexei|last32=Yakunin|first32=Alexander F.|last33=Yakimov|first33=Michail M.|last34=Golyshina|first34=Olga V.|last35=Reinhardt|first35=Richard|last36=Golyshin|first36=Peter N.}}</ref> There are 3919 protein coding genes present.<ref name="KubeChernikova2013" /> There were no [[Plasmid|plasmids]] found.<ref name="Yakimov2003" /> |
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====== Metabolism ====== |
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''Oleispira antarctica'' performs [[aerobic respiration]], but can also grow under [[Anaerobic respiration|anaerobic]] conditions by performing [[Redox|reduction]] of [[nitrate]].<ref name="Yakimov2003" /> [[Ammonia]] and nitrate may serve as nitrogen sources in this case.<ref name="Yakimov2003" /> It is a [[Chemoorganoheterotrophy|chemoorganoheterotroph]] with a small range of substrates that facilitate its growth.<ref name="Yakimov2003" /> This small range includes primarily [[Aliphatic compound|aliphatic carbon molecules]], Tweens (derivatives of [[Fatty acid ester|fatty acid esters]] of [[sorbitan]]), and [[Volatile organic compound|volatilized]] fatty acids.<ref name="Yakimov2003" /> This species also lacks the ability to [[Hydrolysis|hydrolyze]] or [[Metabolism|metabolize]] [[starch]], [[casein]], [[lecithin]], [[Alginic acid|alginate]] or [[agar]].<ref name="Yakimov2003" /> Rarely did this species take up or use either commonly-utilized [[Carbohydrate|carbohydrates]] (e.g. [[glucose]]) or [[Amino acid|amino acids]] (e.g. [[glutamine]]) for its metabolism.<ref name="Yakimov2003" /> |
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== Importance and Application == |
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''Oleispira antarctica'', in addition to a few other species, has recently received increasing consideration and attention for potential application in microbe-based [[bioremediation]].<ref name=":2" /> Specifically, ''O. antarctica'' could potentially be used in the [[Environmental remediation|clean up]] of [[Marine pollution|marine environments]] damaged or contaminated by [[hydrocarbon]] [[pollution]], especially in the context of [[Oil spill|oil spills]].<ref name=":2">{{Cite journal|last=Yakimov|first=Michail M|last2=Timmis|first2=Kenneth N|last3=Golyshin|first3=Peter N|title=Obligate oil-degrading marine bacteria|url=http://linkinghub.elsevier.com/retrieve/pii/S0958166907000559|journal=Current Opinion in Biotechnology|volume=18|issue=3|pages=257–266|doi=10.1016/j.copbio.2007.04.006}}</ref><ref>{{Cite journal|last=Joye|first=Samantha B.|last2=Teske|first2=Andreas P.|last3=Kostka|first3=Joel E.|date=2014-09-01|title=Microbial Dynamics Following the Macondo Oil Well Blowout across Gulf of Mexico Environments|url=https://academic.oup.com/bioscience/article/64/9/766/269545/Microbial-Dynamics-Following-the-Macondo-Oil-Well|journal=BioScience|volume=64|issue=9|pages=766–777|doi=10.1093/biosci/biu121|issn=0006-3568}}</ref> |
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[[16S ribosomal RNA]] gene clones identified as belonging to the genus ''Oleispira'' were found to be very commonly occurring in samples obtained from deep underwater depths at the [[Deepwater Horizon oil spill]] in 2010.<ref name=":1" /><ref>{{Cite journal|last=Hazen|first=Terry C.|last2=Dubinsky|first2=Eric A.|last3=DeSantis|first3=Todd Z.|last4=Andersen|first4=Gary L.|last5=Piceno|first5=Yvette M.|last6=Singh|first6=Navjeet|last7=Jansson|first7=Janet K.|last8=Probst|first8=Alexander|last9=Borglin|first9=Sharon E.|date=2010-10-08|title=Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria|url=http://science.sciencemag.org/content/330/6001/204|journal=Science|language=en|volume=330|issue=6001|pages=204–208|doi=10.1126/science.1195979|issn=0036-8075|pmid=20736401}}</ref> ''Oleispira antarctica'' in particular is a cold marine dwelling species so this species could be applied as part of a bioremediation toolbox of organisms that can work to degrade petroleum hydrocarbons pollutants at, for example, different temperature ranges in different environments.<ref name="KubeChernikova2013" /><ref>{{Cite journal|last=Gentile|first=G.|last2=Bonsignore|first2=M.|last3=Santisi|first3=S.|last4=Catalfamo|first4=M.|last5=Giuliano|first5=L.|last6=Genovese|first6=L.|last7=Yakimov|first7=M. M.|last8=Denaro|first8=R.|last9=Genovese|first9=M.|date=2016-04-15|title=Biodegradation potentiality of psychrophilic bacterial strain Oleispira antarctica RB-8T|url=http://www.sciencedirect.com/science/article/pii/S0025326X16300972|journal=Marine Pollution Bulletin|volume=105|issue=1|pages=125–130|doi=10.1016/j.marpolbul.2016.02.041}}</ref> |
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==References== |
==References== |
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[[Category:Proteobacteria]] |
[[Category:Proteobacteria]] |
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[[Category:Bacteria described in 2003]] |
[[Category:Bacteria described in 2003]] |
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{{Gammaproteobacteria-stub}} |
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Revision as of 23:21, 26 April 2017
Oleispira antarctica
| Oleispira antarctica | |
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| Species: | O. antarctica
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| Oleispira antarctica Yakimov et al. 2003
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Oleispira antarctica is a hydrocarbonoclastic marine bacterium, the type species in its genus. It is psychrophilic, aerobic and Gram-negative, with polar flagellum.[1] Its genome has been sequenced and from this information, it has been recognized as a potentially important organism capable of oil degradation in the deep sea.[2]
Etymology
Oleispira antarctica, "oleum" meaning oil, "spira" meaning a spire (in other words, coiled or twisted) for a combined meaning of a spiral-shaped, oil-degrading organism from Antarctica.[1]
Phylogeny
Based on sequencing of 16S ribosomal RNA genes conducted by Yakimov et al., phylogenetically, this organism is related most closely to species of Oceanobacter, Marinobacterium, and Marinomonas.[1] It belongs to the phylum Gammaproteobacteria and had its own phyletic line within the phylum.[1] Its 16S rRNA gene sequences were no more than 90% similar to any other Gammaproteobacteria 16S rRNA gene sequence, and thus represented a novel species within a new genus.[1] O. antarctica was the first species in the new genus, but another new species, Oleispira lenta, was characterized 9 years later.[3] Sequencing of O. lenta's 16S ribosomal RNA genes revealed sequence similarity of about 97.2% to O. antarctica.[3]
Isolation
Oleispira antarctica was isolated and characterized from shallow samples of sea water collected from the inlet portion of Rod Bay in the Ross Sea (74°41.753'S, 164°07.188'E) during an expedition from the summer season in Antarctica of 1999 to the same time in the year 2000 by Yakimov et al.[1] The investigators performed enrichment and incubation of collected samples in 20 ml volumes of crude oil and additional nutrients.[1] After 2 months of enrichment at 4°C, cultures were diluted in tubes containing solutions of mineral medium of type ONR7a that were additionally supplemented with more crude light oil.[1] These tube cultures were then incubated in darkness until turbidity (which was used to indicate bacterial growth changes over some period of time) became high enough to indicate saturated growth samples (which took approximately 2 months).[1] These cultures were then diluted and the most diluted cultures (10-4) with positive growth were plated on solid form ONR7a mineral medium that also contained tetradecane (a 14 carbon hydrocarbon).[1] After 15 days and further incubation at 4°C, the investigators retrieved individual colonies.[1]
Morphology
The species has a Gram-negative cell wall.[1] It exists as a curved rod to spiraled cell shape with dimensions 2-5μm by 0.4-0.8μm.[1] It is mobile with a long, helical-structured polar flagellum >5μm in length.[1] One morphologically distinct characteristic is a unique drumstick-like enlargement and congealing of one or both ends of the cell where the cell wall is more electron-dense.[1]
Growth, Genomics, and Metabolism
Growth and Genomics
Colonies appeared uncolored, a little translucent and opaque, or a little bit yellow, on ONR7a plates additionally containing tetradecane.[1] The organism grows best at 1-25°C with optimal growth temperature at 2-4°C, making it a psychrophile.[1] It is a stenohaline organism, meaning it grows in only a narrow range of salinity, requires sodium ions for growth, and grows best in presence of 3-5% sodium chloride.[1] Oxidase and catalase enzymes were present.[1] Its principle fatty acids are monounsaturated, with principle fatty acids being C18:1, C16:1, and C16:0.[1] Strains of the species could synthesize polyunsaturated eicosapentaenoic acid at low temperatures.[1] It has a GC-content of 41-42% and the size of its genome is about 2 Mbp.[1][4] There are 3919 protein coding genes present.[4] There were no plasmids found.[1]
Metabolism
Oleispira antarctica performs aerobic respiration, but can also grow under anaerobic conditions by performing reduction of nitrate.[1] Ammonia and nitrate may serve as nitrogen sources in this case.[1] It is a chemoorganoheterotroph with a small range of substrates that facilitate its growth.[1] This small range includes primarily aliphatic carbon molecules, Tweens (derivatives of fatty acid esters of sorbitan), and volatilized fatty acids.[1] This species also lacks the ability to hydrolyze or metabolize starch, casein, lecithin, alginate or agar.[1] Rarely did this species take up or use either commonly-utilized carbohydrates (e.g. glucose) or amino acids (e.g. glutamine) for its metabolism.[1]
Importance and Application
Oleispira antarctica, in addition to a few other species, has recently received increasing consideration and attention for potential application in microbe-based bioremediation.[5] Specifically, O. antarctica could potentially be used in the clean up of marine environments damaged or contaminated by hydrocarbon pollution, especially in the context of oil spills.[5][6]
16S ribosomal RNA gene clones identified as belonging to the genus Oleispira were found to be very commonly occurring in samples obtained from deep underwater depths at the Deepwater Horizon oil spill in 2010.[2][7] Oleispira antarctica in particular is a cold marine dwelling species so this species could be applied as part of a bioremediation toolbox of organisms that can work to degrade petroleum hydrocarbons pollutants at, for example, different temperature ranges in different environments.[4][8]
References
- ^ a b c d e f g h i j k l m n o p q r s t u v w x y z aa ab ac Yakimov, M. M. (2003). "Oleispira antarctica gen. nov., sp. nov., a novel hydrocarbonoclastic marine bacterium isolated from Antarctic coastal sea water". International Journal of Systematic and Evolutionary Microbiology. 53 (3): 779–785. doi:10.1099/ijs.0.02366-0. ISSN 1466-5026.
- ^ a b Mason, Olivia U.; Hazen, Terry C.; Borglin, Sharon; Chain, Patrick S. G.; Dubinsky, Eric A.; Fortney, Julian L.; Han, James; Holman, Hoi-Ying N.; Hultman, Jenni (2012-09-01). "Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill". The ISME Journal. 6 (9): 1715–1727. doi:10.1038/ismej.2012.59. ISSN 1751-7362. PMC 3498917. PMID 22717885.
- ^ a b Wang, Yan; Yu, Min; Austin, Brian; Zhang, Xiao-Hua (2012-05-01). "Oleispiralenta sp. nov., a novel marine bacterium isolated from Yellow sea coastal seawater in Qingdao, China". Antonie van Leeuwenhoek. 101 (4): 787–794. doi:10.1007/s10482-011-9693-8. ISSN 0003-6072.
- ^ a b c Kube, Michael; Chernikova, Tatyana N.; Al-Ramahi, Yamal; Beloqui, Ana; Lopez-Cortez, Nieves; Guazzaroni, María-Eugenia; Heipieper, Hermann J.; Klages, Sven; Kotsyurbenko, Oleg R.; Langer, Ines; Nechitaylo, Taras Y.; Lünsdorf, Heinrich; Fernández, Marisol; Juárez, Silvia; Ciordia, Sergio; Singer, Alexander; Kagan, Olga; Egorova, Olga; Alain Petit, Pierre; Stogios, Peter; Kim, Youngchang; Tchigvintsev, Anatoli; Flick, Robert; Denaro, Renata; Genovese, Maria; Albar, Juan P.; Reva, Oleg N.; Martínez-Gomariz, Montserrat; Tran, Hai; Ferrer, Manuel; Savchenko, Alexei; Yakunin, Alexander F.; Yakimov, Michail M.; Golyshina, Olga V.; Reinhardt, Richard; Golyshin, Peter N. (2013). "Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica". Nature Communications. 4. doi:10.1038/ncomms3156. ISSN 2041-1723. PMC 3759055. PMID 23877221.
- ^ a b Yakimov, Michail M; Timmis, Kenneth N; Golyshin, Peter N. "Obligate oil-degrading marine bacteria". Current Opinion in Biotechnology. 18 (3): 257–266. doi:10.1016/j.copbio.2007.04.006.
- ^ Joye, Samantha B.; Teske, Andreas P.; Kostka, Joel E. (2014-09-01). "Microbial Dynamics Following the Macondo Oil Well Blowout across Gulf of Mexico Environments". BioScience. 64 (9): 766–777. doi:10.1093/biosci/biu121. ISSN 0006-3568.
- ^ Hazen, Terry C.; Dubinsky, Eric A.; DeSantis, Todd Z.; Andersen, Gary L.; Piceno, Yvette M.; Singh, Navjeet; Jansson, Janet K.; Probst, Alexander; Borglin, Sharon E. (2010-10-08). "Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria". Science. 330 (6001): 204–208. doi:10.1126/science.1195979. ISSN 0036-8075. PMID 20736401.
- ^ Gentile, G.; Bonsignore, M.; Santisi, S.; Catalfamo, M.; Giuliano, L.; Genovese, L.; Yakimov, M. M.; Denaro, R.; Genovese, M. (2016-04-15). "Biodegradation potentiality of psychrophilic bacterial strain Oleispira antarctica RB-8T". Marine Pollution Bulletin. 105 (1): 125–130. doi:10.1016/j.marpolbul.2016.02.041.
Further reading
- Goral, Anna M.; Tkaczuk, Karolina L.; Chruszcz, Maksymilian; Kagan, Olga; Savchenko, Alexei; Minor, Wladek (2012). "Crystal structure of a putative isochorismatase hydrolase from Oleispira antarctica". Journal of Structural and Functional Genomics. 13 (1): 27–36. doi:10.1007/s10969-012-9127-5. ISSN 1345-711X.