Diverse Bacterial Groups Contribute to the Alkane Degradation Potential of Chronically Polluted Subantarctic Coastal Sediments

• Published in: Microbial ecology Vol. 71; no. 1; pp. 100 - 112
• Main Authors: Guibert, Lilian M, Loviso, Claudia L, Borglin, Sharon, Jansson, Janet K, Dionisi, Hebe M, Lozada, Mariana
• Format: Journal Article
• Language: English
• Published: New York Springer US 01.01.2016; Springer Science + Business Media; Springer Nature B.V; Springer
• Subjects: alkanes; Alkanes - metabolism; Bacteria - classification; Bacteria - genetics; Bacteria - isolation & purification; Bacteria - metabolism; BASIC BIOLOGICAL SCIENCES; Biodegradation; Biodegradation, Environmental; Biodiversity; Biomedical and Life Sciences; Coastal environments; data collection; Ecology; ENVIRONMENTAL MICROBIOLOGY; Environmental stress; functional diversity; genes; genomic libraries; Geoecology/Natural Processes; Geologic Sediments - analysis; Geologic Sediments - microbiology; Hydrogen-Ion Concentration; latitude; Life Sciences; lipid metabolism; littoral zone; metagenomics; Microbial activity; microbial communities; Microbial Ecology; Microbiology; Molecular Sequence Data; Nature Conservation; nucleotide sequences; Phylogeny; Planctomycetes; Proteobacteria; ribosomal RNA; salinity; screening; Seawater - analysis; Seawater - microbiology; Sediment pollution; sediments; Water Pollutants, Chemical - analysis; Water Pollutants, Chemical - metabolism; Water Quality/Water Pollution; Metagenomics; Actinomycetes; Bacteroidetes; Planctomycetes; Alkane monooxygenase; Coastal sediments
• ISSN: 0095-3628; 1432-184X
• DOI: 10.1007/s00248-015-0698-0

We aimed to gain insight into the alkane degradation potential of microbial communities from chronically polluted sediments of a subantarctic coastal environment using a combination of metagenomic approaches. A total of 6178 sequences annotated as alkane-1-monooxygenases (EC 1.14.15.3) were retrieved from a shotgun metagenomic dataset that included two sites analyzed in triplicate. The majority of the sequences binned with AlkB described in Bacteroidetes (32 ± 13 %) or Proteobacteria (29 ± 7 %), although a large proportion remained unclassified at the phylum level. Operational taxonomic unit (OTU)-based analyses showed small differences in AlkB distribution among samples that could be correlated with alkane concentrations, as well as with site-specific variations in pH and salinity. A number of low-abundance OTUs, mostly affiliated with Actinobacterial sequences, were found to be only present in the most contaminated samples. On the other hand, the molecular screening of a large-insert metagenomic library of intertidal sediments from one of the sampling sites identified two genomic fragments containing novel alkB gene sequences, as well as various contiguous genes related to lipid metabolism. Both genomic fragments were affiliated with the phylum Planctomycetes, and one could be further assigned to the genus Rhodopirellula due to the presence of a partial sequence of the 23S ribosomal RNA (rRNA) gene. This work highlights the diversity of bacterial groups contributing to the alkane degradation potential and reveals patterns of functional diversity in relation with environmental stressors in a chronically polluted, high-latitude coastal environment. In addition, alkane biodegradation genes are described for the first time in members of Planctomycetes.