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Microbiol Resour Announc
Microbiol Resour Announc
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mra00668-24
10.1128/mra.00668-24
mra.00668-24
Genome Sequences
applied-and-industrial-microbiologyApplied and Industrial MicrobiologyComplete genome sequence of Pseudomonas aeruginosa Y010, a taro rhizosphere strain producing potent antimicrobial agents
Wen Yongqi 1 2 Data curation Investigation Validation Writing – original draft
Cao Huiluo 3 Conceptualization Data curation Formal analysis Funding acquisition Writing – review and editing
Mo Zhifeng 1 2 Investigation
Fang Hanshu 3 Investigation
https://orcid.org/0000-0003-4662-8111
Xu Zeling 1 2 Conceptualization Funding acquisition Supervision Writing – review and editing zelingxu@scau.edu.cn

1 Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University , Guangzhou, China
2 State Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University , Guangzhou, China
3 Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong , Hong Kong SAR, China
Editor Baltrus David A. The University of Arizona , Tucson, Arizona, USA

Address correspondence to Zeling Xu, zelingxu@scau.edu.cn
Yongqi Wen and Huiluo Cao contributed equally to this article. Author order was determined by who drafted the manuscript.

The authors declare no conflict of interest.

9 2024
20 8 2024
20 8 2024
13 9 e00668-2418 6 2024
12 7 2024
Copyright © 2024 Wen et al.
2024
Wen et al.
https://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

ABSTRACT

Pseudomonas aeruginosa Y010, isolated from the taro rhizosphere, exhibits great antagonistic abilities against Dickeya strains that cause soft-rot and blackleg diseases of plants by producing potent antimicrobial agents. The complete genome of Y010 was sequenced and annotated, which is 6,415,628 bp in length with 66.39% GC content.

KEYWORDS

P. aeruginosa
Dickeya
biocontrol
antimicrobial agents
MOST | National Natural Science Foundation of China (NSFC) 32100020 Xu Zeling Health and Medical Research Fund (HMRF) 19201901 Cao Huiluo cover-dateSeptember 2024
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pmcANNOUNCEMENT

The Dickeya genus is one of the most destructive phytopathogens (1). To screen biocontrol bacterial strains against plant diseases caused by Dickeya strains, we collected soil samples at the taro rhizosphere (23°09'38.6"N and 113°21'31.9"E) in Guangzhou, Guangdong, People’s Republic of China. Ten grams of the soil sample was added in 90 mL of sterilized Milli-Q water and shaken for 30 minutes. Next, 100 µL of the suspension was serially diluted and spread on lysogeny broth (LB) agar plates. Bacterial strains with single colonies were obtained after the plates were incubated at 28°C for 48 hours. The antagonistic ability of isolated strains against Dickeya strains was determined using the spot-on-lawn assay (2). Y010 was obtained owing to its great antagonistic effect and its production of potent antimicrobial agents against various Dickeya strains, including D. fangzhongdai CL3, D. zeae MS2, and D. oryzae EC1 (Fig. 1). According to the comparison of the 16S rRNA sequences, the strain Y010 showed a 100% similarity to members within the species Pseudomonas aeruginosa.

Fig 1 (A) Antagonistic activities of P. aeruginosa Y010 against Dickeya pathogens (D. fangzhongdai CL3, D. zeae MS2, and D. oryzae EC1) determined using spot-on-lawn assay. Diameters of inhibition zones as shown in the left panel were measured and are presented in the right panel. (B) Growth of the Dickeya pathogens in the presence or absence of the Y010 culture supernatant (Sup).

A single colony of P. aeruginosa Y010 was inoculated in 10 mL of the LB broth at 28°C with 220 rpm agitation for 20 hours. Genomic DNA was extracted from the bacterial culture using the EasyPure Genomic DNA Kit (TransGen, China) to prepare both short-read and long-read libraries. A short-read library was prepared with the Nextera XT DNA Library Preparation Kit (Illumina, USA) and sequenced using an Illumina NovaSeq 6000 platform with 150-bp paired-end reads (Novogene, China), which contained 7,519,498 pairs of reads with a total length of 2.26 gigabase (Gb). A long-read library was prepared with Ligation Sequencing Kit V14 (SQK-LSK114) without size selection and shearing and sequenced using a flow cell (R10.4.1) and Nanopore MinION sequencer Mk1B (Oxford Nanopore Technologies, UK), which generated 56,049 reads with a total length of 676.39 million bp (Mb) (N50, 18,737 bp and mean length, 12,067.8 bp) using Guppy v4.2.2 for base-calling. Quality-based filtering and adapter trimming were performed using Trimmomatic v0.39 (3) and NanoFilt v2.8.0 (4), respectively. The genome was hybrid-assembled using Unicycler v0.50 (5). The quality of the assembled genome was evaluated using QUAST v5.0.2 (6). Circulator v1.5.5 was used to circularize and rotate the genome with the dnaA gene of P. aeruginosa PAO1 (GenBank: AE004091) as the reference (7). The NCBI Prokaryotic Genome Annotation Pipeline (Version 6.7 March 2024) was used for gene annotation. rRNA, non-coding RNAs, and tRNAs were annotated by Rfam (v.14.4) (8), Infernal (v.1.1.5) (9), and tRNAscan-SE (v2.0.12), respectively (10). Default parameters were used for all the abovementioned software.

Collectively, the assembly yielded a single genome. The circular genome size of Y010 is 6,415,628 bp in length with 66.39% GC content and 367 x average coverage depth. A total of 5,885 genes were predicted in the Y010 genome, including 5,775 coding gene sequences (CDS), 31 pseudogenes, 12 rRNAs, 63 tRNAs, and four ncRNAs (Table 1). Two prophages were identified using PHASTEST (11), and three CRISPR arrays were revealed using CRISPRCasFinder (12). Based on PubMLST (13), multiple locus sequence type (MLST) of Y010 was assigned to MLST633.

TABLE 1 Genomic information for P. aeruginosa Y010

Bacterial strain	P. aeruginosa Y010	
Total length (bp)	6,415,628	
% GC content	66.39	
Genes	5,885	
Proteins	5,775	
rRNA	12	
tRNA	63	
ncRNA	4	
Pseudogenes	31	
CRISPR arrays	3	
Prophages	2	

ACKNOWLEDGMENTS

This work was supported by the National Natural Science Foundation of China (No. 32100020) and the Health and Medical Research Fund (No. 19201901).

DATA AVAILABILITY

The genomic data of P. aeruginosa Y010 were deposited in the NCBI under the BioProject accession number PRJNA1116115, the BioSample accession number SAMN41523228, and the GenBank accession number CP158050. Sequence Read Archive (SRA) accession numbers for Illumina and Nanopore reads are SRX24924469 and SRX24924471, respectively.
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