Dynamic Response of Mycobacterium vanbaalenii PYR-1 to BP Deepwater Horizon Crude Oil

Abstract

We investigated the response of the hydrocarbon-degrading Mycobacterium vanbaalenii PYR-1 to crude oil from the BP Deepwater Horizon (DWH) spill, using substrate depletion, genomic, and proteome analyses. M. vanbaalenii PYR-1 cultures were incubated with BP DWH crude oil, and proteomes and degradation of alkanes and polycyclic aromatic hydrocarbons (PAHs) were analyzed at four time points over 30 days. Gas chromatography-mass spectrometry (GC-MS) analysis showed a chain length-dependent pattern of alkane degradation, with C 12 and C 13 being degraded at the highest rate, although alkanes up to C 28 were degraded. Whereas phenanthrene and pyrene were completely degraded, a significantly smaller amount of fluoranthene was degraded. Proteome analysis identified 3,948 proteins, with 876 and 1,859 proteins up-and downregulated, respectively. We observed dynamic changes in protein expression during BP crude oil incubation, including transcriptional factors and transporters potentially involved in adaptation to crude oil. The proteome also provided a molecular basis for the metabolism of the aliphatic and aromatic hydrocarbon components in the BP DWH crude oil, which included upregulation of AlkB alkane hydroxylase and an expression pattern of PAH-metabolizing enzymes different from those in previous proteome expression studies of strain PYR-1 incubated with pure or mixed PAHs, particularly the ring-hydroxylating oxygenase (RHO) responsible for the initial oxidation of aromatic hydrocarbons. Based on these results, a comprehensive cellular response of M. vanbaalenii PYR-1 to BP crude oil was proposed. This study increases our fundamental understanding of the impact of crude oil on the cellular response of bacteria and provides data needed for development of practical bioremediation applications.

Aerobic bacteria degrading both n-alkanes and aromatic hydrocarbons: an undervalued strategy for metabolic diversity and flexibility

“…In addition to the four-ring pyrene, it was able to transform other compounds such as two-, three-, and four-ring PAHs as well as their alkyl derivatives (more details are given in Table 1). Moreover, the strain also biodegraded nC 13 -nC 23 (Kim et al 2015). Further Fig.…”

“…The proven n-alkaneutilizing capabilities of some strains include not only linear n-alkanes but also branched pristane (Table 1). Interestingly, Kim et al (2015) demonstrated preferential n-alkane utilization by M. vanbaalenii PYR-1 (the highest removal yields obtained for nC 12 and nC 13 ) suggesting narrow substrate specificity of nalkane metabolic routes. However, to reliably evaluate n-alkane utilization preferences (broad or narrow) within this taxon, more detailed studies are required.…”

“…Among wealth of reports related to bacteria with enhanced hydrocarbon preferences, their degradative pathways were investigated less often. In particular, the synchronous functioning of n-alkane and PAHs/ BTEX metabolic pathways was studied rarely (Kim et al 2015). In most cases the researchers mainly focused on catabolism of selected aromatic compounds, while additionally indicating a concomitant nalkane removal, growth in the presence of an aliphatic substrate or the presence of alkB gene.…”

“…It should be also stressed that the observed coexistence of metabolic degradation pathways of n-alkane and aromatic hydrocarbons does not directly imply a capacity to induce the two biochemical systems simultaneously. There is only a limited evidence regarding concomitant functioning of both catabolic routes (Vila and Grifoll 2009;Kim et al 2015). While demonstrating removal of n-alkanes during biodegradation of the Prestige fuel oil with Mycobacterium sp.…”

Effects of Polycyclic Aromatic Hydrocarbon Mixtures on Degradation, Gene Expression, and Metabolite Production in Four Mycobacterium Species

“…As Mycobacterium is one of the few bacterial genera able to degrade HMW PAHs, and one that is being used in developing remediation strategies for real-world spill mixtures (49,50), understanding the intricacies of PAH mixture degradation by Mycobacterium species is an area of importance in bioremediation research. The aim of this study was to investigate the degradation of PAH substrates by Mycobacterium species and characterize the metabolic changes associated with mixed-substrate antagonism.…”