Oil type and temperature dependent biodegradation dynamics - Combining chemical and microbial community data through multivariate analysis
Ribicic D, McFarlin KM, Netzer R, Brakstad OG, Winkler A, Throne-Holst M, Storseth TR (2018)
BMC MICROBIOLOGY 18(1): 83.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Autor*in
Ribicic, Deni;
McFarlin, Kelly Marie;
Netzer, Roman;
Brakstad, Odd Gunnar;
Winkler, AnikaUniBi;
Throne-Holst, Mimmi;
Storseth, Trond Rovik
Abstract / Bemerkung
Background: This study investigates a comparative multivariate approach for studying the biodegradation of chemically dispersed oil. The rationale for this approach lies in the inherent complexity of the data and challenges associated with comparing multiple experiments with inconsistent sampling points, with respect to inferring correlations and visualizing multiple datasets with numerous variables. We aim to identify novel correlations among microbial community composition, the chemical change of individual petroleum hydrocarbons, oil type and temperature by creating modelled datasets from inconsistent sampling time points. Four different incubation experiments were conducted with freshly collected Norwegian seawater and either Grane and Troll oil dispersed with Corexit 9500. Incubations were conducted at two different temperatures (5 degrees C and 13 degrees C) over a period of 64 days. Results: PCA analysis of modelled chemical datasets and calculated half-lives revealed differences in the biodegradation of individual hydrocarbons among temperatures and oil types. At 5 degrees C, most n-alkanes biodegraded faster in heavy Grane oil compared to light Troll oil. PCA analysis of modelled microbial community datasets reveal differences between temperature and oil type, especially at low temperature. For both oils, Colwelliaceae and Oceanospirillaceae were more prominent in the colder incubation (5 degrees C) than the warmer (13 degrees C). Overall, Colwelliaceae, Oceanospirillaceae, Flavobacteriaceae, Rhodobacteraceae, Alteromonadaceae and Piscirickettsiaceae consistently dominated the microbial community at both temperatures and in both oil types. Other families known to include oil-degrading bacteria were also identified, such as Alcanivoracaceae, Methylophilaceae, Sphingomonadaceae and Erythrobacteraceae, but they were all present in dispersed oil incubations at a low abundance (< 1%). Conclusions: In the current study, our goal was to introduce a comparative multivariate approach for studying the biodegradation of dispersed oil, including curve-fitted models of datasets for a greater data resolution and comparability. By applying these approaches, we have shown how different temperatures and oil types influence the biodegradation of oil in incubations with inconsistent sampling points. Clustering analysis revealed further how temperature and oil type influence single compound depletion and microbial community composition. Finally, correlation analysis of degraders community, with single compound data, revealed complexity beneath usual abundance cut-offs used for microbial community data in biodegradation studies.
Erscheinungsjahr
2018
Zeitschriftentitel
BMC MICROBIOLOGY
Band
18
Ausgabe
1
Art.-Nr.
83
ISSN
1471-2180
Page URI
https://pub.uni-bielefeld.de/record/2930633
Zitieren
Ribicic D, McFarlin KM, Netzer R, et al. Oil type and temperature dependent biodegradation dynamics - Combining chemical and microbial community data through multivariate analysis. BMC MICROBIOLOGY. 2018;18(1): 83.
Ribicic, D., McFarlin, K. M., Netzer, R., Brakstad, O. G., Winkler, A., Throne-Holst, M., & Storseth, T. R. (2018). Oil type and temperature dependent biodegradation dynamics - Combining chemical and microbial community data through multivariate analysis. BMC MICROBIOLOGY, 18(1), 83. doi:10.1186/s12866-018-1221-9
Ribicic, Deni, McFarlin, Kelly Marie, Netzer, Roman, Brakstad, Odd Gunnar, Winkler, Anika, Throne-Holst, Mimmi, and Storseth, Trond Rovik. 2018. “Oil type and temperature dependent biodegradation dynamics - Combining chemical and microbial community data through multivariate analysis”. BMC MICROBIOLOGY 18 (1): 83.
Ribicic, D., McFarlin, K. M., Netzer, R., Brakstad, O. G., Winkler, A., Throne-Holst, M., and Storseth, T. R. (2018). Oil type and temperature dependent biodegradation dynamics - Combining chemical and microbial community data through multivariate analysis. BMC MICROBIOLOGY 18:83.
Ribicic, D., et al., 2018. Oil type and temperature dependent biodegradation dynamics - Combining chemical and microbial community data through multivariate analysis. BMC MICROBIOLOGY, 18(1): 83.
D. Ribicic, et al., “Oil type and temperature dependent biodegradation dynamics - Combining chemical and microbial community data through multivariate analysis”, BMC MICROBIOLOGY, vol. 18, 2018, : 83.
Ribicic, D., McFarlin, K.M., Netzer, R., Brakstad, O.G., Winkler, A., Throne-Holst, M., Storseth, T.R.: Oil type and temperature dependent biodegradation dynamics - Combining chemical and microbial community data through multivariate analysis. BMC MICROBIOLOGY. 18, : 83 (2018).
Ribicic, Deni, McFarlin, Kelly Marie, Netzer, Roman, Brakstad, Odd Gunnar, Winkler, Anika, Throne-Holst, Mimmi, and Storseth, Trond Rovik. “Oil type and temperature dependent biodegradation dynamics - Combining chemical and microbial community data through multivariate analysis”. BMC MICROBIOLOGY 18.1 (2018): 83.
Daten bereitgestellt von European Bioinformatics Institute (EBI)
2 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
A Simple Microbiome in the European Common Cuttlefish, Sepia officinalis.
Lutz HL, Ramírez-Puebla ST, Abbo L, Durand A, Schlundt C, Gottel NR, Sjaarda AK, Hanlon RT, Gilbert JA, Mark Welch JL., mSystems 4(4), 2019
PMID: 31098396
Lutz HL, Ramírez-Puebla ST, Abbo L, Durand A, Schlundt C, Gottel NR, Sjaarda AK, Hanlon RT, Gilbert JA, Mark Welch JL., mSystems 4(4), 2019
PMID: 31098396
A Simple Microbiome in the European Common Cuttlefish, Sepia officinalis.
Lutz HL, Ramírez-Puebla ST, Abbo L, Durand A, Schlundt C, Gottel NR, Sjaarda AK, Hanlon RT, Gilbert JA, Mark Welch JL., mSystems 4(4), 2019
PMID: 31120031
Lutz HL, Ramírez-Puebla ST, Abbo L, Durand A, Schlundt C, Gottel NR, Sjaarda AK, Hanlon RT, Gilbert JA, Mark Welch JL., mSystems 4(4), 2019
PMID: 31120031
45 References
Daten bereitgestellt von Europe PubMed Central.
AUTHOR UNKNOWN, 0
Effects of temperature and crude oil composition on petroleum biodegradation.
Atlas RM., Appl Microbiol 30(3), 1975
PMID: 1180548
Atlas RM., Appl Microbiol 30(3), 1975
PMID: 1180548
Microbial degradation of hydrocarbons in the environment.
Leahy JG, Colwell RR., Microbiol. Rev. 54(3), 1990
PMID: 2215423
Leahy JG, Colwell RR., Microbiol. Rev. 54(3), 1990
PMID: 2215423
Psychrophilic microorganisms: challenges for life.
D'Amico S, Collins T, Marx JC, Feller G, Gerday C., EMBO Rep. 7(4), 2006
PMID: 16585939
D'Amico S, Collins T, Marx JC, Feller G, Gerday C., EMBO Rep. 7(4), 2006
PMID: 16585939
Structural, kinetic, and calorimetric characterization of the cold-active phosphoglycerate kinase from the antarctic Pseudomonas sp. TACII18.
Bentahir M, Feller G, Aittaleb M, Lamotte-Brasseur J, Himri T, Chessa JP, Gerday C., J. Biol. Chem. 275(15), 2000
PMID: 10753921
Bentahir M, Feller G, Aittaleb M, Lamotte-Brasseur J, Himri T, Chessa JP, Gerday C., J. Biol. Chem. 275(15), 2000
PMID: 10753921
Natural gas and temperature structured a microbial community response to the Deepwater Horizon oil spill.
Redmond MC, Valentine DL., Proc. Natl. Acad. Sci. U.S.A. 109(50), 2011
PMID: 21969552
Redmond MC, Valentine DL., Proc. Natl. Acad. Sci. U.S.A. 109(50), 2011
PMID: 21969552
KM, Cont Shelf Res 136(), 2017
Deep-sea oil plume enriches indigenous oil-degrading bacteria.
Hazen TC, Dubinsky EA, DeSantis TZ, Andersen GL, Piceno YM, Singh N, Jansson JK, Probst A, Borglin SE, Fortney JL, Stringfellow WT, Bill M, Conrad ME, Tom LM, Chavarria KL, Alusi TR, Lamendella R, Joyner DC, Spier C, Baelum J, Auer M, Zemla ML, Chakraborty R, Sonnenthal EL, D'haeseleer P, Holman HY, Osman S, Lu Z, Van Nostrand JD, Deng Y, Zhou J, Mason OU., Science 330(6001), 2010
PMID: 20736401
Hazen TC, Dubinsky EA, DeSantis TZ, Andersen GL, Piceno YM, Singh N, Jansson JK, Probst A, Borglin SE, Fortney JL, Stringfellow WT, Bill M, Conrad ME, Tom LM, Chavarria KL, Alusi TR, Lamendella R, Joyner DC, Spier C, Baelum J, Auer M, Zemla ML, Chakraborty R, Sonnenthal EL, D'haeseleer P, Holman HY, Osman S, Lu Z, Van Nostrand JD, Deng Y, Zhou J, Mason OU., Science 330(6001), 2010
PMID: 20736401
Composition of the water accommodated fractions as a function of exposure times and temperatures.
Faksness LG, Brandvik PJ, Sydnes LK., Mar. Pollut. Bull. 56(10), 2008
PMID: 18715599
Faksness LG, Brandvik PJ, Sydnes LK., Mar. Pollut. Bull. 56(10), 2008
PMID: 18715599
R, J Eng Educ 92(1), 2003
M, Spill Science & Technology Bulletin 2(1), 1995
JE, 2010
OG, 2017
Biodegradation of dispersed Macondo oil in seawater at low temperature and different oil droplet sizes.
Brakstad OG, Nordtug T, Throne-Holst M., Mar. Pollut. Bull. 93(1-2), 2015
PMID: 25746198
Brakstad OG, Nordtug T, Throne-Holst M., Mar. Pollut. Bull. 93(1-2), 2015
PMID: 25746198
The primary biodegradation of dispersed crude oil in the sea.
Prince RC, McFarlin KM, Butler JD, Febbo EJ, Wang FC, Nedwed TJ., Chemosphere 90(2), 2012
PMID: 22967931
Prince RC, McFarlin KM, Butler JD, Febbo EJ, Wang FC, Nedwed TJ., Chemosphere 90(2), 2012
PMID: 22967931
Depletion and biodegradation of hydrocarbons in dispersions and emulsions of the Macondo 252 oil generated in an oil-on-seawater mesocosm flume basin.
Brakstad OG, Daling PS, Faksness LG, Almas IK, Vang SH, Syslak L, Leirvik F., Mar. Pollut. Bull. 84(1-2), 2014
PMID: 24928454
Brakstad OG, Daling PS, Faksness LG, Almas IK, Vang SH, Syslak L, Leirvik F., Mar. Pollut. Bull. 84(1-2), 2014
PMID: 24928454
17.alpha.(H)-21.beta.(H)-hopane as a conserved internal marker for estimating the biodegradation of crude oil.
Prince RC, Elmendorf DL, Lute JR, Hsu CS, Haith CE, Senius JD, Dechert GJ, Douglas GS, Butler EL., Environ. Sci. Technol. 28(1), 1994
PMID: 22175843
Prince RC, Elmendorf DL, Lute JR, Hsu CS, Haith CE, Senius JD, Dechert GJ, Douglas GS, Butler EL., Environ. Sci. Technol. 28(1), 1994
PMID: 22175843
Comparison of oil composition changes due to biodegradation and physical weathering in different oils.
Wang Z, Fingas M, Blenkinsopp S, Sergy G, Landriault M, Sigouin L, Foght J, Semple K, Westlake DW., J Chromatogr A 809(1-2), 1998
PMID: 9677713
Wang Z, Fingas M, Blenkinsopp S, Sergy G, Landriault M, Sigouin L, Foght J, Semple K, Westlake DW., J Chromatogr A 809(1-2), 1998
PMID: 9677713
Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies.
Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glockner FO., Nucleic Acids Res. 41(1), 2012
PMID: 22933715
Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glockner FO., Nucleic Acids Res. 41(1), 2012
PMID: 22933715
QIIME allows analysis of high-throughput community sequencing data.
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R., Nat. Methods 7(5), 2010
PMID: 20383131
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R., Nat. Methods 7(5), 2010
PMID: 20383131
UCHIME improves sensitivity and speed of chimera detection.
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R., Bioinformatics 27(16), 2011
PMID: 21700674
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R., Bioinformatics 27(16), 2011
PMID: 21700674
Search and clustering orders of magnitude faster than BLAST.
Edgar RC., Bioinformatics 26(19), 2010
PMID: 20709691
Edgar RC., Bioinformatics 26(19), 2010
PMID: 20709691
PyNAST: a flexible tool for aligning sequences to a template alignment.
Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R., Bioinformatics 26(2), 2009
PMID: 19914921
Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R., Bioinformatics 26(2), 2009
PMID: 19914921
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.
Wang Q, Garrity GM, Tiedje JM, Cole JR., Appl. Environ. Microbiol. 73(16), 2007
PMID: 17586664
Wang Q, Garrity GM, Tiedje JM, Cole JR., Appl. Environ. Microbiol. 73(16), 2007
PMID: 17586664
phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data.
McMurdie PJ, Holmes S., PLoS ONE 8(4), 2013
PMID: 23630581
McMurdie PJ, Holmes S., PLoS ONE 8(4), 2013
PMID: 23630581
MixMC: A Multivariate Statistical Framework to Gain Insight into Microbial Communities.
Le Cao KA, Costello ME, Lakis VA, Bartolo F, Chua XY, Brazeilles R, Rondeau P., PLoS ONE 11(8), 2016
PMID: 27513472
Le Cao KA, Costello ME, Lakis VA, Bartolo F, Chua XY, Brazeilles R, Rondeau P., PLoS ONE 11(8), 2016
PMID: 27513472
Uptake and trans-membrane transport of petroleum hydrocarbons by microorganisms.
Hua F, Wang HQ., Biotechnol. Biotechnol. Equip. 28(2), 2014
PMID: 26740752
Hua F, Wang HQ., Biotechnol. Biotechnol. Equip. 28(2), 2014
PMID: 26740752
Does bioavailability limit biodegradation? A comparison of hydrocarbon biodegradation and desorption rates in aged soils.
Huesemann MH, Hausmann TS, Fortman TJ., Biodegradation 15(4), 2004
PMID: 15473555
Huesemann MH, Hausmann TS, Fortman TJ., Biodegradation 15(4), 2004
PMID: 15473555
OG, 2009
Estimation of hydrocarbon biodegradation rates in marine environments: a critical review of the Q10 approach.
Bagi A, Pampanin DM, Brakstad OG, Kommedal R., Mar. Environ. Res. 89(), 2013
PMID: 23756048
Bagi A, Pampanin DM, Brakstad OG, Kommedal R., Mar. Environ. Res. 89(), 2013
PMID: 23756048
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
Succession of hydrocarbon-degrading bacteria in the aftermath of the deepwater horizon oil spill in the gulf of Mexico.
Dubinsky EA, Conrad ME, Chakraborty R, Bill M, Borglin SE, Hollibaugh JT, Mason OU, M Piceno Y, Reid FC, Stringfellow WT, Tom LM, Hazen TC, Andersen GL., Environ. Sci. Technol. 47(19), 2013
PMID: 23937111
Dubinsky EA, Conrad ME, Chakraborty R, Bill M, Borglin SE, Hollibaugh JT, Mason OU, M Piceno Y, Reid FC, Stringfellow WT, Tom LM, Hazen TC, Andersen GL., Environ. Sci. Technol. 47(19), 2013
PMID: 23937111
Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill.
Mason OU, Hazen TC, Borglin S, Chain PS, Dubinsky EA, Fortney JL, Han J, Holman HY, Hultman J, Lamendella R, Mackelprang R, Malfatti S, Tom LM, Tringe SG, Woyke T, Zhou J, Rubin EM, Jansson JK., ISME J 6(9), 2012
PMID: 22717885
Mason OU, Hazen TC, Borglin S, Chain PS, Dubinsky EA, Fortney JL, Han J, Holman HY, Hultman J, Lamendella R, Mackelprang R, Malfatti S, Tom LM, Tringe SG, Woyke T, Zhou J, Rubin EM, Jansson JK., ISME J 6(9), 2012
PMID: 22717885
Single-cell genomics reveals features of a Colwellia species that was dominant during the Deepwater Horizon oil spill.
Mason OU, Han J, Woyke T, Jansson JK., Front Microbiol 5(), 2014
PMID: 25071745
Mason OU, Han J, Woyke T, Jansson JK., Front Microbiol 5(), 2014
PMID: 25071745
Degradation of crude oil by an arctic microbial consortium.
Deppe U, Richnow HH, Michaelis W, Antranikian G., Extremophiles 9(6), 2005
PMID: 15999222
Deppe U, Richnow HH, Michaelis W, Antranikian G., Extremophiles 9(6), 2005
PMID: 15999222
Obligate oil-degrading marine bacteria.
Yakimov MM, Timmis KN, Golyshin PN., Curr. Opin. Biotechnol. 18(3), 2007
PMID: 17493798
Yakimov MM, Timmis KN, Golyshin PN., Curr. Opin. Biotechnol. 18(3), 2007
PMID: 17493798
Deep-sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill.
Baelum J, Borglin S, Chakraborty R, Fortney JL, Lamendella R, Mason OU, Auer M, Zemla M, Bill M, Conrad ME, Malfatti SA, Tringe SG, Holman HY, Hazen TC, Jansson JK., Environ. Microbiol. 14(9), 2012
PMID: 22616650
Baelum J, Borglin S, Chakraborty R, Fortney JL, Lamendella R, Mason OU, Auer M, Zemla M, Bill M, Conrad ME, Malfatti SA, Tringe SG, Holman HY, Hazen TC, Jansson JK., Environ. Microbiol. 14(9), 2012
PMID: 22616650
AUTHOR UNKNOWN, 0
Microbial population structures in the deep marine biosphere.
Huber JA, Mark Welch DB, Morrison HG, Huse SM, Neal PR, Butterfield DA, Sogin ML., Science 318(5847), 2007
PMID: 17916733
Huber JA, Mark Welch DB, Morrison HG, Huse SM, Neal PR, Butterfield DA, Sogin ML., Science 318(5847), 2007
PMID: 17916733
Co-acclimation of bacterial communities under stresses of hydrocarbons with different structures.
Wang H, Wang B, Dong W, Hu X., Sci Rep 6(), 2016
PMID: 27698451
Wang H, Wang B, Dong W, Hu X., Sci Rep 6(), 2016
PMID: 27698451
Identification of novel methane-, ethane-, and propane-oxidizing bacteria at marine hydrocarbon seeps by stable isotope probing.
Redmond MC, Valentine DL, Sessions AL., Appl. Environ. Microbiol. 76(19), 2010
PMID: 20675448
Redmond MC, Valentine DL, Sessions AL., Appl. Environ. Microbiol. 76(19), 2010
PMID: 20675448
Current State of Knowledge in Microbial Degradation of Polycyclic Aromatic Hydrocarbons (PAHs): A Review.
Ghosal D, Ghosh S, Dutta TK, Ahn Y., Front Microbiol 7(), 2016
PMID: 27630626
Ghosal D, Ghosh S, Dutta TK, Ahn Y., Front Microbiol 7(), 2016
PMID: 27630626
Alcanivorax borkumensis gen. nov., sp. nov., a new, hydrocarbon-degrading and surfactant-producing marine bacterium.
Yakimov MM, Golyshin PN, Lang S, Moore ER, Abraham WR, Lunsdorf H, Timmis KN., Int. J. Syst. Bacteriol. 48 Pt 2(), 1998
PMID: 9731272
Yakimov MM, Golyshin PN, Lang S, Moore ER, Abraham WR, Lunsdorf H, Timmis KN., Int. J. Syst. Bacteriol. 48 Pt 2(), 1998
PMID: 9731272
Metagenomics meets time series analysis: unraveling microbial community dynamics.
Faust K, Lahti L, Gonze D, de Vos WM, Raes J., Curr. Opin. Microbiol. 25(), 2015
PMID: 26005845
Faust K, Lahti L, Gonze D, de Vos WM, Raes J., Curr. Opin. Microbiol. 25(), 2015
PMID: 26005845
Export
Markieren/ Markierung löschen
Markierte Publikationen
Web of Science
Dieser Datensatz im Web of Science®Quellen
PMID: 30086723
PubMed | Europe PMC
Suchen in