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

Anming Xu; Di Wang; Yichen Ding; Yaqian Zheng; Bo Wang; Qing Wei; Shiwei Wang; Liang Yang; Luyan Z Ma

doi:10.3389/fmicb.2020.00519

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

Front Microbiol. 2020 Mar 31:11:519. doi: 10.3389/fmicb.2020.00519. eCollection 2020.

Authors

Anming Xu^{1

2}, Di Wang¹, Yichen Ding³, Yaqian Zheng^{1

2}, Bo Wang^{1

2}, Qing Wei¹, Shiwei Wang¹, Liang Yang⁴, Luyan Z Ma^{1

2}

Affiliations

¹ State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
² University of Chinese Academy of Sciences, Beijing, China.
³ Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Jurong West, Singapore.
⁴ School of Medicine, Southern University of Science and Technology, Shenzhen, China.

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 I-F 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.

Keywords: N-acyl-homoserine lactones; Pseudomonas aeruginosa; alkane hydroxylase; crude oil; rhamnolipids.