Functional and Genomic Characterization of a Pseudomonas aeruginosa Strain Isolated From the Southwestern Gulf of Mexico Reveals an Enhanced Adaptation for Long-Chain Alkane Degradation

Abstract

Indigenous bacterial populations play an important role in the restoration of crude oilpolluted marine environments. The identification and characterization of these bacteria are key in defining bioremediation strategies for the mitigation of possible future oil spills. In this work, we characterized Pseudomonas aeruginosa strain GOM1, which was isolated from the water column in the southwestern Gulf of Mexico. Phylogenetic analysis revealed that GOM1 strain was most closely related to P. aeruginosa WC55, a strain isolated from the northern Gulf of Mexico after the Deepwater Horizon oil spill. The hydrocarbon-degrading capacity of P. aeruginosa GOM1 was investigated using various approaches. This strain degraded 96% of the aliphatic fraction (C12-C38) of crude oil during a 30-day incubation period, exhibiting a high activity on long-chain alkanes, and expressing alkane hydroxylases AlkB1, AlkB2 and AlmA. Addition of nitrogen and phosphate to seawater culture medium enhanced hexadecane degradation by GOM1. Additionally, the strain exhibited high surfactant/rhamnolipid production and emulsifying activity when grown in a complex medium in the presence of hexadecane. Comparisons of growth kinetics, hydrocarbon degradation and gene expression between GOM1 and the closely related P. aeruginosa laboratory strain PAO1 revealed that the marine isolate is better adapted to degrade alkanes. Taken together, our results place P. aeruginosa GOM1 as a potentially effective candidate to be included in a consortium for use in the bioremediation of oil-polluted sites.

Metagenomic Profiling and Microbial Metabolic Potential of Perdido Fold Belt (NW) and Campeche Knolls (SE) in the Gulf of Mexico

“…The diversity of sequences suggests microorganisms have the intrinsic potential to degrade a wide range of hydrocarbon compounds, as might be the case in an oil spill event. alkB genes are associated with the degradation of C10-C28 alkanes ( Van Beilen and Funhoff, 2007 ; Nie et al, 2014 ; Muriel-Millán et al, 2019 ), and we detected the majority of these sequences in water samples. The high diversity of Rieske oxygenases in water samples and in the A04 and E03 sediments, indicates there is potential for degradation of diverse aromatic compounds such as benzoate, benzene, toluene, phthalate, naphthalene or biphenyl ( Duarte et al, 2014 ).…”

Bacteria From the Southern Gulf of Mexico: Baseline, Diversity, Hydrocarbon-Degrading Potential and Future Applications

“…Natural leaks of oil are widely distributed in the GoM (MacDonald et al, 2015), suggesting that it has a basal level of HDB that can grow to address large-scale oil spills. This hypothesis was validated during the oil spill of the DWH and in later studies, in which metagenomic analysis and isolated cultures showed significant enrichment of bacterial populations related to Oceanospirillum, Cycloclasticus, Colwellia, Pseudoalteromonas, Rhodobacterales, methylotrophs, Alcanivorax, Oleiphilus, Oleispira, Thalassolituus, Oceanospirillales, Marinobacter, Acinetobacter, Pseudomonas and Planomicrobium (Hazen et al, 2010;Kostka et al, 2011;Redmond and Valentine, 2012;Mason et al, 2012;Dubansky et al, 2013;Kimes et al, 2013;Mason et al, 2014;Kleindienst et al, 2015;Orcutt et al, 2017;García-Cruz et al, 2018;Muriel-Millán et al, 2019;Uribe-Flores et al, 2019;Cerqueda-García et al, 2020;Rodríguez-Salazar et al, 2020).…”

“…Raggi et al (2020) determined the oxygen concentration in the Perdido Fold Belt zone (7.07 and 3.6 mg/L) and in the Campeche Knolls area (6.9 to 3.5 mg/L), for water column and sediments, respectively. Likewise, in these areas, similar alkB genes sequences related to the aerobic degradation of alkanes (Muriel-Millán et al, 2019) were found mainly in the water column, while in a in Campeche Knolls area sediment sample where anaerobic conditions prevail, shows a high diversity of bssA-like sequences, involved in anaerobic degradation of hydrocarbon (Acosta-González et al, 2013).…”

“…As already mentioned, we established the bacterial baseline in marine sediments from the southwestern GoM with a core of 450 genera, where genera such as Colwellia, Pseudomonas, Oleispira, Marinobacter, Alcanivorax, Shewanella, Pseudoalteromonas, Cycloclasticus and Phaeobacter related to HDB are present at basal levels (Rosano-Hernandez et al, 2009;Godoy-Lozano et al, 2018;Sánchez-Soto Jiménez et al, 2018;Raggi et al, 2020;Ramírez et al, 2020). We also evaluated the natural degradation of oil and oil derivatives using HDB isolated at different depths (water column to sediment) from the northwestern to the southwestern regions of the GoM (García-Cruz et al, 2018;Uribe-Flores et al, 2019;Muriel-Millán et al, 2019;Cerqueda-García et al, 2020;Rodríguez-Salazar et al, 2020), where the largest and most important base of the oil industry in Mexico is concentrated. Cerqueda-García et al (2020) evaluated samples of water and sediment enriched with different types of oil (extra light to extra heavy), finding a higher abundance of Gammaproteobacteria in sediments, where aerobic HDB are mostly found, decreasing the presence of heavy oil.…”

Potential of Biosurfactants’ Production on Degrading Heavy Oil by Bacterial Consortia Obtained from Tsunami-Induced Oil-Spilled Beach Areas in Miyagi, Japan

“…Among the OTUs, the most abundant family of Pseudomonadaceae was OTU_001, which was identified as Pseudomonas aeruginosa. The P. aeruginosa was already known as a player in biodegradation of many substrates such as glycerol [33], diesel oil [34], water column-contaminated oil [35], polluted coastal area [36,37], PAH [38], and more.…”