Genome Sequence Resource of a Quorum-Quenching Biocontrol Agent, Pseudomonas nitroreducens HS-18

HomeMolecular Plant-Microbe Interactions®Vol. 35, No. 4Genome Sequence Resource of a Quorum-Quenching Biocontrol Agent, Pseudomonas nitroreducens HS-18 Previous RESOURCE ANNOUNCEMENT OPENOpen Access licenseGenome Sequence Resource of a Quorum-Quenching Biocontrol Agent, Pseudomonas nitroreducens HS-18Huishan Wang, Lisheng Liao, Xiaofan Zhou, Lingling Dong, Xin Lin, and Lianhui ZhangHuishan Wanghttps://orcid.org/0000-0001-5378-3385Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, ChinaGuangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, ChinaSearch for more papers by this author, Lisheng LiaoGuangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, ChinaGuangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, ChinaSearch for more papers by this author, Xiaofan ZhouGuangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, ChinaGuangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, ChinaSearch for more papers by this author, Lingling DongGuangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, ChinaGuangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, ChinaSearch for more papers by this author, Xin LinInstitute of Microbiology, Meizhou Academy of Agricultural and Forestry Sciences, Meizhou, Guangdong Province 514071, ChinaSearch for more papers by this author, and Lianhui Zhang†Corresponding author: L. Zhang; E-mail Address: lhzhang01@scau.edu.cnGuangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, ChinaGuangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, ChinaSearch for more papers by this author AffiliationsAuthors and Affiliations Huishan Wang1 3 Lisheng Liao1 3 Xiaofan Zhou1 3 Lingling Dong1 3 Xin Lin2 Lianhui Zhang1 3 † 1Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China 2Institute of Microbiology, Meizhou Academy of Agricultural and Forestry Sciences, Meizhou, Guangdong Province 514071, China 3Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China Published Online:14 Mar 2022https://doi.org/10.1094/MPMI-12-21-0310-AAboutSectionsPDF ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat Genome AnnouncementPseudomonas nitroreducens HS-18 isolated from oil contaminated-soil samples in Guangzhou, China was shown to produce multiple substrate-inducible quorum-quenching (QQ) enzymes for effective degradation of N-acyl-homoserine lactones (AHL) and diffusible signal factor (DSF) molecules, which represent two families of widely conserved bacterial quorum sensing (QS) signals. HS-18 showed a promising potential in biocontrol of the DSF or AHL-dependent phytopathogens due to its remarkable QQ ability. Here, we report the whole-genome sequence of strain HS-18. Genomic analysis revealed that strain HS-18 contains one circular chromosome of 6,493,503 bp in length and one circle plasmid of 101,450 bp. The confirmed DSF QQ genes digA, digB, digC, digD encoding fatty acyl-CoA ligases and confirmed AHL QQ genes aigA, aigB, aigC encoding AHL acylases were all found located in the chromosome. The findings from this study will provide valuable information for further exploitation of this useful biocontrol agent and for unveiling the detailed QQ regulatory mechanisms.QS is a cell-to-cell communication mechanism utilized by microorganism to regulate their adaptability to changing environmental conditions and pathogenicity on various host organisms (Mukherjee and Bassler 2019). Bacterial cells produce, release, and perceive QS signals to coordinate community activities through modulation of the transcriptional expression of a large set of target genes. AHL and DSF represent two families of widely conserved QS signals (Zhang and Dong 2004; Zhou et al. 2017). Given its important role in regulation of bacterial virulence, a strategy known as QQ aimed at blocking bacterial QS communications was proposed and shown to be an efficient therapy to control QS-dependent bacterial infections (Ahator and Zhang 2019; Zhang 2003). Pseudomonas nitroreducens HS-18 was recently identified with a highly efficient DSF degradation capacity (Wang et al. 2020), which has also been found to have AHL signal-degrading properties. The complete genome analysis confirmed the multi-QQ properties of this strain. To uncover the regulatory mechanisms that govern AHL- or DSF-inducible QQ and to further explore the application potential of this useful biocontrol agent, the genome sequence information of strain HS-18 would be of critical importance.Here, we report the complete genome sequence information of strain HS-18. Strain HS-18 was cultured overnight at 30°C in 50 ml of Luria Bertani broth, with shaking at 200 rpm. The cells were harvested by centrifugation and genomic DNA of strain HS-18 was extracted, using the EasyPure bacteria genomic DNA kit (Transgene Biotech). A Qubit 2.0 fluorometer (Life Technologies) and NanoDrop 2000 UV-Vis spectrophotometer (Thermo Scientific) were applied to determine the quantity and quality of the extracted genomic DNA sample. Then, the DNA sample was subjected to complete genome sequencing at Beijing Novogene Bioinformatic Technology Co., Ltd., using Illumina PE150 platform sequencing technologies with 350-bp small-fragment library of strain HS-18 genomic DNA and using PacBio sequencing technologies with a 10 Kb single molecule real-time (SMRT) Bell library of strain HS-18 genome DNA. The short reads from Illumina PE150 were obtained to counter the error-prone long reads produced by PacBio.Sequencing yielded 1,362,105,628 bp of high-quality long-read sequence (clean data) (sequence depth ≥200×) comprising 190,859 reads with a mean read length of 7,137 bp. The genome was assembled using SMRT Link v5.0.1 and was optimized, using arrow software of SMRT Link v5.0.1, to gain a high-quality contig without gaps (Ardui et al. 2018). The optimized assembly was taken as the reference genome, and Illumina sequencing reads were used to align to the reference genome, using bwa-0.7.8 for further correction. Illumina sequencing reads were quality-filtered (quality score ≥20, 4 ≤ read depth ≤1,000). Circularization corrections were performed by searching the overlap of the beginning and the end sequences of the corrected assembly results. The coding genes were predicted using GeneMarkS (version 4.17) (Besemer et al. 2001). Repeat sequences were analyzed by RepeatMasker (version open 4.0.5) and Tandem Repeats Finder (version 4.07b) (Benson 1999; Saha et al. 2008). For noncoding RNA genes, transfer RNA (tRNA) genes were analyzed by tRNAscan-SE (version 1.3.1), ribosome RNA (rRNA) genes were predicted by rRNAmmer (version 1.2), small RNA (sRNA) were predicted by blasting against the Rfam database and cmsearch (version 1.1rc4) (Gardner et al. 2009; Lagesen et al. 2007; Lowe and Eddy 1997). Genomic islands were predicted by IslandPath-DIOMB (version 0.2), and the CRISPR recognition tool was analyzed by CRISPRdigger (version 1.0) (Grissa et al. 2007; Hsiao et al. 2003). The prophage genes were predicted by phiSpy (version 2.3) (Zhou et al. 2011). The protein functional analysis was conducted by comparing the peptide sequences of strain HS-18 with bacterial protein sequences in the Gene Ontology, Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups of proteins, Non-Redundant Protein databases, Pfam, the Transporter Classification and Carbohydrate-Active Enzymes databases, and Swiss-Prot. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain HS-18 and its closely related strains were calculated on ANI Calculator (Yoon et al. 2017) and Genome-to-Genome Distance Calculator 2.1 (Meier-Kolthoff et al. 2013), respectively.Genome assembly showed that strain HS-18 contains a single circular DNA chromosome with a length of 6,493,503 bp with G+C content of 64.74% and one single circular plasmid of 101,450 bp with G+C content of 55.01% (Table 1). The overall genome features are presented in Table 1. Strain HS-18 consists of 6,090 genes accounting for 87.81% of the whole genome, which includes 67 tRNA genes, 16 rRNA genes, and 16 sRNA genes (Table 1). HS-18 resulted in one contig and one scaffold, and the contig N50 was 6,493,503 bp and L50 was 1 (Table 2). The genome assembly statistics of strain HS-18 were compared with a number of sequenced genomes of P. nitroreducens from the National Center for Biotechnology Information database with ANI and dDDH. The ANI values between strain HS-18 and these type strains ranged from 98.63 to 98.93%, and the dDDH values ranged from 87.30 to 91.60%. These values are above the threshold ANI value of 95% and dDDH value of 70%, respectively, suggesting that strain HS-18 and the P. nitroreducens strains occupied the same taxonomic position.Table 1. Genome statistics of Pseudomonas nitroreducens HS-18FeatureChromosomeGenome size (bp)6,594,953G+C content (%)65.47Total genes6090Plasmid1Transfer RNAs67Ribosome RNAs16Small RNAs16Prophage5Genomic islands14CRISPRs1GenBank accessionCP084413-CP084414Table 1. Genome statistics of Pseudomonas nitroreducens HS-18View as image HTML Table 2. Overview of the genome assembly statistics of HS-18 and other Pseudomonas nitroreducens strainsaGenomic featuresHS-18DSM 14399NBRC 12694PSA00705WZBFD3-5A2Aramco JHBP1ANI value (%)10098.935598.913998.849198.812898.808198.7566dDDH (%)10090.3090.1091.6087.3088.4089.20GenBank assembly accessionGCA_ 020401845.1GCA_ 012986245.1GCA_ 002091755.1GCA_ 015763095.1GCA_ 010994165.1GCA_ 000807755.1GCA_ 011044415.1Genome size (bp)6,594,9536,171,3166,105,1376,787,0546,397,9367,333,6757,427,551Scaffolds number1NANANANANANAContigs number150402061291NAContig N50 (bp)6,493,503855,214537,64356,451932,199322,424NAContig L501NA43737NAAssembly methodSMRT Link v. v5.1.0SPAdes v. 2.5.1newbler v. 3.0SPAdes v. 3.14.1Newbler v. 2.3Newbler v. 2.8HGAP v. 3Genome coverage200×138×80×43×12×72×83×Sequencing technologyPacBio; IlluminaIllumina MiSeqIllumina HiSeq 1000; 454 GS-FLX TitaniumIllumina NextSeqIllumina HiSeqIonTorrentPacBioaANI = average nucleotide identity; dDDH = digital DNA-DNA hybridization; NA = not available or not applicable.Table 2. Overview of the genome assembly statistics of HS-18 and other Pseudomonas nitroreducens strainsaView as image HTML The genome assembly statistics of strain HS-18 showed high completeness (>98%) without contamination, indicating the higher-quality of the complete genome sequences of strain HS-18 than other P. nitroreducens strains. It might provide better resources for comparative genomic studies and for analyzing the function mechanisms presented in P. nitroreducens species.Multiple genes were identified that may contribute to the QQ activity of P. nitroreducens HS-18 against other bacteria. Besides digA, digB, digC, and digD (Wang et al. 2020), at least another four homologous DSF QQ genes (locus_tags LDJ84_10985, LDJ84_14290, LDJ84_18380, and LDJ84_19965) were found in the strain HS-18 genome. Furthermore, we also found multiple genes, aigA, aigB, and aigC (GenBank accession numbers MW619635, MW619636, and MW619637, respectively), encoding putative AHL acylases, based on KEGG annotation and function BLAST. In the metabolism category, 115 genes in strain HS-18 were predicted to be involved in lipid metabolism, which might be related to the metabolism of fatty acid derivative DSF. The QQ capacity and potentials of strain HS-18 deserve further investigation. 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Nucleic Acids Res. 39:W347-W352. https://doi.org/10.1093/nar/gkr485 Crossref, Medline, ISI, Google ScholarHuishan Wang and Lisheng Liao contributed equally.Funding: This work was supported by the grants from the Key Realm R&D Program of Guangdong Province (2020B0202090001; 2018B020205003), Guangdong Forestry Science and Technology Innovation Project (2018KJCX009; 2020KJCX009), Key Projects of Guangzhou Science and Technology Plan (201804020066), National Natural Science Foundation of China (31900076) and Basic Research and Applied Basic Research Program of Guangdong Province (2020A1515110111).The author(s) declare no conflict of interest. Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.DetailsFiguresLiterature CitedRelated Vol. 35, No. 4 April 2022ISSN:0894-0282e-ISSN:1943-7706 Download Metrics Downloaded 674 times Article History Issue Date: 12 Apr 2022Published: 14 Mar 2022Accepted: 23 Jan 2022 Pages: 364-367 InformationCopyright © 2022 The Author(s).This is an open access article distributed under the CC BY-NC-ND 4.0 International license.FundingKey Realm R&D Program of Guangdong ProvinceGrant/Award Number: 2020B0202090001Grant/Award Number: 2018B020205003Guangdong Forestry Science and Technology Innovation ProjectGrant/Award Number: 2018KJCX009Grant/Award Number: 2020KJCX009Key Projects of Guangzhou Science and Technology PlanGrant/Award Number: 201804020066National Natural Science Foundation of ChinaGrant/Award Number: 31900076Basic Research and Applied Basic Research Program of Guangdong ProvinceGrant/Award Number: 2020A1515110111KeywordsAHLDSFgenome sequence resourcequorum quenchingThe author(s) declare no conflict of interest.PDF download