Crude oil induced microbial communities in seawater

Abstract

Abstract Background: The Menai Strait comprises unique and diverse habitats and is a site of a great biodiversity and natural beauty. It is also, however, an important route for commercial fishing and recreational traffic, which both have a potential to adversely affect the biodiversity in that environment. This unique ecosystem was the focus of this study into the biodiversity of the marine obligate hydrocarbon-degrading bacteria, as it is hoped, that such understanding may help to address the environmental problems in that area by designing the bioremediation programmes specific for the local microbial communities. Aims: Due to the majority of the bacterial strains being uncultivated, the diversity of the microbial life in marine environments remains poorly understood. Thus, the aim this study, was to assess and compare the taxonomic diversity of the microbial communities in the seawater and the marine sediment samples collected from the Menai Strait, and to attempt to culture and isolate the hydrocarbon-degrading bacteria from that ecosystem through culture dependent analyses of the collected samples. Methods: The combined approach to the isolation and identification of the seawater and marine sediment microbial taxa was used. Environmental samples collected from Menai Strait were cultured in the laboratory conditions simulating the environmental oil-spill event, and the bacterial strains present in the enrichment cultures thus prepared were isolated and identified. In the culture-based approach, the attempt to cultivate and isolate the OHCB bacteria from the collected samples was made, based on their ability to degrade alkanes, polyaromatic hydrocarbons or crude oil. The 16S rRNA gene sequence analysis was performed, to identify the isolated bacterial strains, and the phylogenetic trees were constructed, using the BioEdit and MEGA sequence-analysis tools, to explore the evolutionary relationships between the identified taxa. Results: In the first experimental phase, the overall biodiversity of the Menai Strait was assessed to be broad, with diverse phylla identified in the control samples, including Gammaproteobacteria, Alphaproteobacteria, Opitutae and Flavobacteria. The taxonomic assignment of the bacterial strains isolated from the oil-spill simulation cultures revealed a dramatic decrease of biodiversity and a presence of species previously described as the obligate hydrocarbon-degraders (Alcanivorax borkumensis, Alcanivorax jadensis, Thalassolituus marinus, Thalassolituus oleivorans, Thalassospira tepidiphila, and others) and the sulphate-degrading strains, such as Thioalkalivibrio sulfidiphilus. In the culture-based substrate-specific analysis of the hydrocarbon-degrading taxa, the marked decrease in biodiversity was observed in the samples, and the strains showing close homology to the xi several known hydrocarbon-degrading species were isolated and identified, including Alcanivorax borkumensis, Alcanivorax jadensis, Alcanivorax dieselolei, Thalassolituus marinus and others. Conclusions: Identification of OHCB and sulphate-degrading species in the Menai Strait suggests the presence of anthropogenic contaminants in that ecosystem. The genomic and taxonomic data generated in this study through diverse approaches to the analysis of microbial communities, will help to understand the biodiversity and the biology of the OHCB taxa. The better understanding of the diversity of the niches that the hydrocarbon-degrading microbes occupy in the marine ecosystems could help to assess how the marine ecosystems may be threatened by anthropogenic activities, and could be used to design the bioremediation strategies that help to avoid and remedy those threats, to preserve the essential biodiversity of those ecosystems