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

• Published in: Microbial ecology 2012-10, Vol.64 (3), p.605-616
• Main Authors: Guibert, Lilian M., Loviso, Claudia L., Marcos, Magalí S., Commendatore, Marta G., Dionisi, Hebe M., Lozada, Mariana
• Format: Article
• Language: English
• Subjects: Actinobacteria; Alkanes; Alkanes - metabolism; Amino acids; Antarctic Regions; Bacteria; Biodegradation; Biodegradation, Environmental; Biological and medical sciences; Biomedical and Life Sciences; Coastal environments; Cold regions; Cytochrome P-450 CYP4A - genetics; DNA, Bacterial - genetics; DNA, Bacterial - metabolism; Ecology; Environmental Pollutants - metabolism; Fundamental and applied biological sciences. Psychology; Gammaproteobacteria - genetics; Gammaproteobacteria - isolation & purification; Gammaproteobacteria - metabolism; Geoecology/Natural Processes; Geologic Sediments - microbiology; Hydrocarbons; Hydrocarbons - metabolism; Libraries; Life Sciences; Marine environment; Marine sediments; Microbial Ecology; Microbiology; MICROBIOLOGY OF AQUATIC SYSTEMS; Microorganisms; Molecular Sequence Data; Nature Conservation; Oil pollution; Petroleum - metabolism; Phylogeny; Polymerase Chain Reaction; Proteobacteria; RNA, Ribosomal, 16S - genetics; Sediment contamination; Sedimentary soils; Sediments; Sequence Analysis, DNA - methods; Slurries; Soil pollution; Water Quality/Water Pollution
• ISSN: 0095-3628; 1432-184X
• DOI: 10.1007/s00248-012-0051-9

Although sediments are the natural hydrocarbon sink in the marine environment, the ecology of hydrocarbondegrading bacteria in sediments is poorly understood, especially in cold regions. We studied the diversity of alkanedegrading 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.