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. 2022 May 6;12(1):51.
doi: 10.1186/s13568-022-01392-z.

Whole genome sequencing and analysis of fenvalerate degrading bacteria Citrobacter freundii CD-9

Xuerui Zhou  1 , Dan Lei  1 , Jie Tang  2 , Min Wu  1 , Hong Ye  1 , Qing Zhang  1
Affiliations

Whole genome sequencing and analysis of fenvalerate degrading bacteria Citrobacter freundii CD-9

Xuerui Zhou et al. AMB Express. .

Abstract

Citrobacter freundii CD-9 is a Gram-negative bacteria sourced from factory sludge that can use fenvalerate as its sole carbon source and has a broad degradation spectrum for pyrethroid pesticides. The whole genome of CD-9 sequenced using Illumina HiSeq PE150 was reported in this study. The CD-9 genome size was 5.33 Mb and the G + C content was 51.55%. A total of 5291 coding genes, 9 5s-rRNA, and 79 tRNA were predicted bioinformatically. 3586 genes annotated to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database that can be involved in 173 metabolic pathways, including various microbial metabolic pathways that degrade exogenous chemicals, especially those that degrade aromatic compounds, and also produce a variety of bioactive substances. Fifty genes related to pyrethroid degradation were identified in the C. freundii CD-9 genome, including 9 dioxygenase, 25 hydrolase, and 16 esterase genes. Notably, RT-qPCR results showed that from the predicted 13 genes related to fenvalerate degradation, the expression of six genes, including esterase, HAD family hydrolase, lipolytic enzyme, and gentisic acid dioxygenase, was induced in the presence of fenvalerate. In this study, the key genes and degradation mechanism of C. freundii CD-9 were analyzed and the results provide scientific evidence to support its application in environmental bioremediation. It can establish application models for different environmental pollution management by constructing genetically engineered bacteria for efficient fenvalerate or developing enzyme formulations that can be industrially produced.

Keywords: Bioremediation; Genomics; Pyrethroids; RT-qPCR.

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Conflict of interest statement

All authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
C. freundii CD-9 degradation of pyrethroids
Fig. 2
Fig. 2
Draft genome C. freundii CGMCC 20106. The first circle is contigs and corresponding length information, the second circle is GC content information, the third circle is the corresponding base sequencing depth, the fourth circle and the fifth circle are CDS, rRNA, tRNA distribution information, and the sixth circle and the seventh circle are the corresponding COG function classification. (From outmost to innermost)
Fig. 3
Fig. 3
a The map of GOclassification annotation. b The map of COG classification annotation. c KEGG pathway classification histogram
Fig. 4
Fig. 4
a Degradation pathway of benzoate. b Biosynthetic pathway of streptomycin. The red boxes represent the key genes contained in strain CD-9
Fig. 4
Fig. 4
a Degradation pathway of benzoate. b Biosynthetic pathway of streptomycin. The red boxes represent the key genes contained in strain CD-9
Fig. 5
Fig. 5
The evolutionary relationship between nine predicted proteins in the strain CD-9 genome and the reported proteins that degrade pyrethroids
Fig. 6
Fig. 6
Relative expression of genes in C. freundii CD-9 under the presence of fenvalerate. All data are expressed as means ± standard deviation (SD)
Fig. 7
Fig. 7
Proposed pathway of fenvalerate degradation by C. freundii CD-9
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