Integrated Comparative Genomic Analysis and Phenotypic Profiling of Pseudomonas aeruginosa Isolates From Crude Oil

Abstract

Pseudomonas aeruginosa is an environmental microorganism that can thrive in diverse ecological niches including plants, animals, water, soil, and crude oil. It also one of the microorganism widely used in tertiary recovery of crude oil and bioremediation. However, the genomic information regarding the mechanisms of survival and adapation of this bacterium in crude oil is still limited. In this study, three Pseudomonads strains (named as IMP66, IMP67, and IMP68) isolated from crude oil were taken for whole-genome sequencing by using a hybridized PacBio and Illumina approach. The phylogeny analysis showed that the three strains were all P. aeruginosa species and clustered in clade 1, the group with PAO1 as a representitive. Subsequent comparative genomic analysis revealed a high degree of individual genomic plasticity, with a probable alkane degradation genomic island, one type IF CRISPR-Cas system and several prophages integrated into their genomes. Nine genes encoding alkane hydroxylases (AHs) homologs were found in each strain, which might enable these strains to degrade alkane in crude oil. P. aeruginosa can produce rhamnolipids (RLs) biosurfactant to emulsify oil, which enables their survival in crude oil enviroments. Our previous report showed that IMP67 and IMP68 were high RLs producers, while IMP66 produced little RLs. Genomic analysis suggested that their RLs yield was not likely due to differences at genetic level. We then further analyzed the quorum sensing (QS) signal molecules that regulate RLs synthesis. IMP67 and IMP68 produced more N-acyl-homoserine lactones (AHLs) signal molecules than that of PAO1 and IMP66, which could explain their high RLs yield. This study provides evidence for adaptation of P. aeruginosa in crude oil and proposes the potential application of IMP67 and IMP68 in microbial-enhanced oil recovery and bioremediation.

Comparative Genomic Analysis of Antarctic Pseudomonas Isolates with 2,4,6-Trinitrotoluene Transformation Capabilities Reveals Their Unique Features for Xenobiotics Degradation

“…The high GI content in KT2440 evidences its high genomic plasticity, compared with the other species analyzed. It is worth mentioning that the vast majority of genes within the GIs in the genome of TNT-transforming species encode hypothetical proteins and phage-related proteins, which is consistent with other pseudomonad genomes [ 83 , 84 , 85 ]. Interestingly, a GI sequence containing a prophage region and a putative gene cluster encoding three TNT-degrading enzymes (two xenobiotic reductases and one nitroreductase) was found in JLR11 ( Figure S9d ) and KT2440 ( Figure S9e ) (this finding is addressed in more detail in Section 3.7 ), suggesting that these catabolic genes could have been acquired via horizontal gene transfer in both strains.…”

Dual functions: A coumarin–chalcone conjugate inhibits cyclic‐di‐GMP and quorum‐sensing signaling to reduce biofilm formation and virulence of pathogens

“…The three QS signaling molecules of 3‐oxo‐C 12 ‐HSL, C 4 ‐HSL, and PQS were quantified using LC‐MS/MS as described 70 . Briefly, P. aeruginosa strains with 5 mM C9 treatment or DMSO as a control were grown in LB media at 37°C for 24 h. One milliliter of bacterial cultures was spun down and supernatants were collected for LC‐MS/MS analysis using a mass spectrometer (QTRAP 6500 System; AB SCIEX) for further determination.…”

A Review on Biotechnological Approaches Applied for Marine Hydrocarbon Spills Remediation

“…The combination of alkanes with fumarate and secondary carbon triggers hydrocarbon hydrolysis at aerobic conditions. Alkane hydroxylases are a prominent investigated aerobic enzyme encoded by the almA and alkB genes, as well as p450 cytochrome [ 123 , 124 ]. In anaerobic conditions, however, the addition of fumarate to alkanes, leads to the synthesis of alkyl succinates, which is an important enzyme in anaerobic biodegradation [ 16 ].…”