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Microbial Ecology

, Volume 64, Issue 3, pp 605–616 | Cite as

Alkane Biodegradation Genes from Chronically Polluted Subantarctic Coastal Sediments and Their Shifts in Response to Oil Exposure

  • Lilian M. Guibert
  • Claudia L. Loviso
  • Magalí S. Marcos
  • Marta G. Commendatore
  • Hebe M. Dionisi
  • Mariana Lozada
Microbiology of Aquatic Systems

Abstract

Although sediments are the natural hydrocarbon sink in the marine environment, the ecology of hydrocarbon-degrading bacteria in sediments is poorly understood, especially in cold regions. We studied the diversity of alkane-degrading bacterial populations and their response to oil exposure in sediments of a chronically polluted Subantarctic coastal environment, by analyzing alkane monooxygenase (alkB) gene libraries. Sequences from the sediment clone libraries were affiliated with genes described in Proteobacteria and Actinobacteria, with 67 % amino acid identity in average to sequences from isolated microorganisms. The majority of the sequences were most closely related to uncultured microorganisms from cold marine sediments or soils from high latitude regions, highlighting the role of temperature in the structuring of this bacterial guild. The distribution of alkB sequences among samples of different sites and years, and selection after experimental oil exposure allowed us to identify ecologically relevant alkB genes in Subantarctic sediments, which could be used as biomarkers for alkane biodegradation in this environment. 16 S rRNA amplicon pyrosequencing indicated the abundance of several genera for which no alkB genes have yet been described (Oleispira, Thalassospira) or that have not been previously associated with oil biodegradation (Spongiibacter—formerly Melitea—, Maribius, Robiginitomaculum, Bizionia and Gillisia). These genera constitute candidates for future work involving identification of hydrocarbon biodegradation pathway genes.

Keywords

Rhodococcus Marinobacter Unresolved Complex Mixture Nocardioides Hydrocarbon Biodegradation 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

LMG, CLL and MSM are recipients of graduate student fellowships from the National Research Council of Argentina (CONICET). ML, HMD and MGC are staff members from CONICET. Grants from CONICET, National Agency for the Promotion of Science and Technology (ANPCyT, Argentina) and Secretary of Science, Technology and Innovation of the Chubut Province (Argentina) supported this research.

We would like to thank M. Gil, J. L. Esteves, H. Ocariz, A. Torres and R. Vera for their help during sample collection.

Supplementary material

248_2012_51_MOESM1_ESM.pdf (225 kb)
Online Resource 1 Hydrocarbon content and alkB PCR clone library information of coastal sediment samples from Ushuaia Bay. (PDF 225 kb)
248_2012_51_MOESM2_ESM.pdf (103 kb)
Online Resource 2 Alignment of deduced AlkB sequences from clones obtained in this study and related sequences from public databases. Only one representative sequence per OTU is shown. The conserved histidine box II [72, 73] is indicated. The beginning of histidine box II in the sequences from this study is not included, as it was included in the forward primer [54]. Residues ≥50% identical and similar are shaded in black and gray, respectively. CLUSTAL, MEGA5 and BioEdit softwares were used to build and shade the alignment. (PDF 102 kb)
248_2012_51_MOESM3_ESM.pdf (68 kb)
Online Resource 3 BLAST results of the alkB gene OTUs identified in this study. OTUs are ordered by relative abundances. For each OTU, the first BLAST match and the sequence from the closest isolated microorganism is indicated, with GenBank accession numbers in parentheses. Percent identity at the amino acid level is shown. N: number of sequences in the OTU; n: number of samples where the OTU was detected; samples correspond to: S (sediment), O (oil-exposed slurry), ON (oil-plus-nutrient amended slurry). (PDF 67 kb)
248_2012_51_MOESM4_ESM.pdf (90 kb)
Online Resource 4 Profiles obtained by high resolution gas chromatography of the aliphatic hydrocarbon fraction of sediments and experimental systems. a. OR08 sediment sample from Ushuaia Bay. b. crude oil added to the experimental systems. c. oil-exposed slurry (expOR08-O) after twenty days of exposure. d. oil-plus-nutrient amended slurry (expOR08-ON) after twenty days of exposure. e. control slurry (expOR08-c, neither oil nor nutrients added) after twenty days. Representative compound abbreviations are indicated above the corresponding peaks. UCM: unresolved complex mixture. (PDF 90 kb)

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Lilian M. Guibert
    • 1
  • Claudia L. Loviso
    • 1
  • Magalí S. Marcos
    • 1
  • Marta G. Commendatore
    • 1
  • Hebe M. Dionisi
    • 1
  • Mariana Lozada
    • 1
  1. 1.Centro Nacional Patagónico (CENPAT - CONICET)Puerto MadrynArgentina

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