Microbial community analysis of Deepwater Horizon oil-spill impacted sites along the Gulf Coast using functional and phylogenetic markers

Abstract

We investigated the impact of the Deepwater Horizon oil spill on microbial assemblages in sediment, soil and seawater samples collected from sites along the Gulf Shore. Based on a GC/MS analysis only one sample from Bay Jimmy, LA, had detectable signs of hydrocarbon contamination, identified as n-alkanes similar to the GC/MS pattern of the Deepwater Horizon source oil (MC – 252). To identify changes in microbial assemblage structure and functional diversity in response to hydrocarbon contamination five genes were selected (bacterial 16S rRNA, Pseudomonas-specific 16S rRNA, alkB, P450, and PAH-RHDα) to determine phylogenetic affiliation and specific enzymes encoded by bacteria to degrade alkanes and polycyclic aromatic hydrocarbons (PAHs). A qPCR analysis revealed the presence of alkane and PAH-degrading genes in contaminated and non-contaminated samples, with no significant difference in gene content between the different samples. However, the ribotype analysis identified 17 bacteria genera known for their capacity to degrade hydrocarbons, including Mycobacterium, Novosphingobium, Parvibaculum, Pseudomonas, and Sphingomonas, with the highest relative abundance of these potential hydrocarbon degraders found within the contaminated soil sample. Furthermore, the contaminated sample had a very high relative abundance of 16S rRNA gene sequences affiliated with the genus Parvibaculum, members of which have been characterized for their degradative abilities. These data suggest that specific bacterial taxa within the genus Parvibaculum have the capacity for hydrocarbon degradation and can use the hydrocarbons as a carbon and energy source, resulting in a dominant population within a hydrocarbon-contaminated soil.