Alam K, Zhao Y, Lu X, Gong K, Zhong L, Hao J, Islam MM, Islam S, Li G, Zhang Y (2022) Isolation, complete genome sequencing and in silico genome mining of Burkholderia for secondary metabolites. BMC Microbiol 22:323

Article  CAS  PubMed  PubMed Central  Google Scholar 

Alvarez F, Simonetti E, Draghi WO, Vinacour M, Palumbo MC, Do Porto DF, Montecchia MS, Roberts IN, Ruiz JA (2022) Genome mining of Burkholderia ambifaria strain T16, a rhizobacterium able to produce antimicrobial compounds and degrade the mycotoxin fusaric acid. World J Microb Biot 38:114

Article  CAS  Google Scholar 

Ankenbauer RG, Toyokuni T, Staley A, Rinehart KL, Cox CD (1988) Synthesis and biological activity of pyochelin, a siderophore of Pseudomonas aeruginosa. J Bacteriol 170:5344–5351

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bertelli C, Brinkman FSL, Valencia A (2018) Improved genomic island predictions with IslandPath-DIMOB. Bioinformatics 34:2161–2167

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P (2007) CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinform 8:209

Article  Google Scholar 

Chan PP, Lowe TM (2019) tRNAscan-SE: searching for tRNA genes in genomic sequences. Gene Prediction 1962:1–14

CAS  Google Scholar 

Chaudhari NM, Gupta VK, Dutta C (2016) BPGA- an ultra-fast pan-genome analysis pipeline. Sci Rep 6:24373

Article  CAS  PubMed  PubMed Central  Google Scholar 

Deng P, Foxfire A, Xu J, Baird SM, Jia J, Delgado KH, Shin R, Smith L, Lu S-E, Drake HL (2017) The siderophore product ornibactin is required for the bactericidal activity of Burkholderia contaminans MS14. Appl Environ Microb 83:e00051-e117

Article  CAS  Google Scholar 

Deng J, Guan R, Liang T, Su L, Ge F, Cui X, Liu D (2022) Dirigent gene family is involved in the molecular interaction between Panax notoginseng and root rot pathogen Fusarium solani. Ind Crop Prod 178:114544

Article  CAS  Google Scholar 

Dong H, Gao R, Dong Y, Yao Q, Zhu H (2023a) Whole-genome sequencing of a biocontrol Myxococcus xanthus R31 isolate and comparative genomic analysis. Gene 863:147286

Article  CAS  PubMed  Google Scholar 

Dong Q, Liu Q, Goodwin PH, Deng X, Xu W, Xia M, Zhang J, Sun R, Wu C, Wang Q (2023b) Isolation and genome-based characterization of biocontrol potential of Bacillus siamensis YB-1631 against wheat crown rot caused by Fusarium pseudograminearum. J Fungi (basel) 9:547

Article  CAS  PubMed  Google Scholar 

Elshafie HS, Racioppi R, Bufo SA, Camele I (2017) In vitro study of biological activity of four strains of Burkholderia gladioli pv. agaricicola and identification of their bioactive metabolites using GC–MS. Saudi J Biol Sci 24:295–301

Article  CAS  PubMed  Google Scholar 

Guo Y, Zeng C, Ma C, Cai H, Jiang X, Zhai S, Xu X, Lin M (2022) Comparative genomics analysis of the multidrug-resistant Aeromonas hydrophila MX16A providing insights into antibiotic resistance genes. Front Cell Infect Microbiol 12:1042350

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hwang J, Chilton WS, Benson DM (2002) Pyrrolnitrin production by Burkholderia cepacia and biocontrol of Rhizoctonia stem rot of poinsettia. Biol Control 25:56–63

Article  CAS  Google Scholar 

Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform 11:119

Article  Google Scholar 

Jung BK, Hong SJ, Park GS, Kim MC, Shin JH (2018) Isolation of Burkholderia cepacia JBK9 with plant growth-promoting activity while producing pyrrolnitrin antagonistic to plant fungal diseases. Appl Biol Chem 61:173–180

Article  CAS  Google Scholar 

Keum YS, Lee HR, Kim J-H (2010) Effects of pesticides on the bacterial production of pyrrolnitrin. J Agric Food Chem 58:5531–5537

Article  CAS  PubMed  Google Scholar 

Kumar H, Dubey RC, Maheshwari DK (2017) Seed-coating fenugreek with Burkholderia rhizobacteria enhances yield in field trials and can combat Fusarium wilt. Rhizosphere 3:92–99

Article  Google Scholar 

Kunakom S, Eustáquio AS (2019) Burkholderia as a source of natural products. J Nat Prod 82:2018–2037

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li C, Cheng P, Zheng L, Li Y, Chen Y, Wen S, Yu G (2021) Comparative genomics analysis of two banana Fusarium wilt biocontrol endophytes Bacillus subtilis R31 and TR21 provides insights into their differences on phytobeneficial trait. Genomics 113:900–909

Article  CAS  PubMed  Google Scholar 

Li Y, Liu Y, Zhang Z, Li J, Zhu S, Yang M, Luo L (2022) Application of plant survival-promoting and pathogen-suppressing Trichoderma species for crop biofertilization and biocontrol of root rot in Panax notoginseng. J Plant Pathol 104:1361–1369

Article  Google Scholar 

Liu X, Yu X, Yang Y, Heeb S, Gao S, Chan KG, Camara M, Gao K (2018) Functional identification of the prnABCD operon and its regulation in Serratia plymuthica. Appl Microbiol Biotechnol 102:3711–3721

Article  CAS  PubMed  Google Scholar 

Luo Y, Cheng Y, Yi J, Zhang Z, Luo Q, Zhang D, Li Y (2018) Complete genome sequence of industrial biocontrol strain Paenibacillus polymyxa HY96-2 and further analysis of its biocontrol mechanism. Front Microbiol 9:1520

Article  PubMed  PubMed Central  Google Scholar 

Ma YN, Chen CJ, Li QQ, Xu FR, Cheng YX, Dong X (2019) Monitoring Antifungal Agents of Artemisia annua against Fusarium oxysporum and Fusarium solani, Associated with Panax notoginseng Root-Rot Disease. Molecules 24:213

Article  PubMed  PubMed Central  Google Scholar 

Mališová L, Španělová P, Sedláček I, Pajer P, Musílek M, Puchálková B, Jakubů V, Žemličková H, Šafránková R (2021) The first case of Planococcus glaciei found in blood, a report from the Czech Republic. Folia Microbiol 67:121–127

Article  Google Scholar 

Nawrocki EP, Eddy SR (2013) Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29:2933–2935

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ong KS, Cheow YL, Lee SM (2017) The role of reactive oxygen species in the antimicrobial activity of pyochelin. J Adv Res 8:393–398

Article  CAS  PubMed  PubMed Central  Google Scholar 

Petrova YD, Zhao J, Webster G, Mullins AJ, Williams K, Alswat AS, Challis GL, Bailey AM, Mahenthiralingam E (2022) Cloning and expression of Burkholderia polyyne biosynthetic gene clusters in Paraburkholderia hosts provides a strategy for biopesticide development. Microb Biotechnol 15:2547–2561

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sandani HBP, Ranathunge NP, Lakshman PLN, Weerakoon WMW (2019) Biocontrol potential of five Burkholderia and Pseudomonasstrains against Colletotrichum truncatum infecting chilli pepper. Biocontrol Sci Techn 29:727–745

Article  Google Scholar 

Sansinenea E, Malik MS, Rehman A, Khan IU, Khan TA, Jamil M, Rha ES, Anees M (2023) Thermo-neutrophilic cellulases and chitinases characterized from a novel putative antifungal biocontrol agent: Bacillus subtilis TD11. PLoS ONE 18:e0281102

Article  Google Scholar 

Singh TB, Sahai V, Goyal D, Prasad M, Yadav A, Shrivastav P, Ali A, Dantu PK (2020) Identification, characterization and evaluation of multifaceted traits of plant growth promoting rhizobacteria from soil for sustainable approach to agriculture. Curr Microbiol 77:3633–3642

Article  CAS  PubMed  Google Scholar 

Svetlicic E, Jaen-Luchoro D, Klobucar RS, Jers C, Kazazic S, Franjevic D, Klobucar G, Shelton BG, Mijakovic I (2022) Genomic characterization and assessment of pathogenic potential of Legionella spp isolates from environmental monitoring. Front Microbiol 13:1091964

Article  PubMed  Google Scholar 

Tang C, Fan C, Guo DB, Ma XJ, Cai QT, Chen XX, Zhang M, Li JY, An QY, Zhao R (2021) Identification of Boseongicola sediminum sp. nov., a novel decabromodiphenyl ether (BDE-209)-tolerant strain isolated from coastal sediment in Xiamen, China. Biomed Environ Sci 34:656–661

CAS  PubMed  Google Scholar 

Tarailo-Graovac M, Chen N (2009) Using repeat masker to identify repetitive elements in genomic sequences. Current Protocols in Bioinformatics 25:4.10.11–14.10.14

Wang X, Zhang M, Loh B, Leptihn S, Ahmed T, Li B (2021) A novel NRPS cluster, acquired by horizontal gene transfer from algae, regulates siderophore iron metabolism in Burkholderia seminalis R456. Int J Biol Macromol 182:838–848

Article  CAS  PubMed  Google Scholar 

Wang C, Zhao X, Wu K, Liang C, Liu J, Yang H, Wang C, Yang B, Yin F, Zhang W (2023) Isolation and characterization of Bacillus velezensis strain B19 for biocontrol of Panax notoginseng root rot. Biol Control 185:105311

Article  CAS  Google Scholar 

Wei J, Zhao J, Suo M, Wu H, Zhao M, Yang H (2023) Biocontrol mechanisms of Bacillus velezensis against Fusarium oxysporum from Panax ginseng. Biol Control 182:105222

Article  CAS  Google Scholar 

Wemheuer F, Taylor JA, Daniel R, Johnston E, Meinicke P, Thomas T, Wemheuer B (2020) Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences. Environ Microbiome 15:11

Article  CAS  PubMed  PubMed Central