组学技术在生防芽胞杆菌的应用进展

doi:10.13560/j.cnki.biotech.bull.1985.2024-0498

摘要/Abstract

摘要：

芽胞杆菌（Bacillus spp.）是全世界应用最广泛的生防微生物菌种资源之一，在基因组学成为普遍性基础学科的时代，转录组、蛋白质组、代谢组等多组学技术的联用成为深入揭示芽胞杆菌生物学特性和生防机制研究的重要手段。目前NCBI数据库共计发布了10 813个芽胞杆菌全基因组序列，其中装配注释完整的共1 842个，占总数量的17.04%。对芽胞杆菌基因组与比较基因组的分析发现，次级代谢产物基因簇是芽胞杆菌基因组中最具有保守性，又具有特异性的部分，它们既是天然产物的重要来源，也在细菌间以及细菌与环境的相互作用和生命周期中扮演着重要角色。截至目前，对于芽胞杆菌的相关研究，多采取整合组学模式和生物信息学计算方法，聚焦于芽胞杆菌的抗性形成、生物膜形成、定殖、促生、诱导植物抗逆性等机制。随着研究的不断深入，芽胞杆菌生防过程中的基因调控机制、蛋白质表达和代谢途径将进一步解析，这将有助于发现新的生防活性物质和优化生防策略。本文综述了转录组、蛋白质组、代谢组等多组学技术在芽胞杆菌上的研究进展，以期为芽胞杆菌生防作用机制的解析以及生防菌株改良的深入研究提供参考。

关键词: 芽胞杆菌, 基因组学, 转录组学, 蛋白质组学, 代谢组学

Abstract:

Bacillus is one of the most widely used biocontrol microbial resources in the world. In the era when genomics has become a universal basic discipline, the combined application of transcriptomics, proteomics, metabonomics and other multi-omics technologies have become an important means to deeply reveal the biological characteristics and biocontrol mechanisms of Bacillus. Currently, the NCBI database has published a total of 10 813 genome sequences of Bacillus, of which 1 842 have complete assembly annotations, accounting for 17.04% of the total number. The secondary metabolite gene clusters are the most conserved and specific part of the Bacillus genome. They are not only an important source of natural products, but also play important roles in the interactions and life cycle between bacteria and the environment. Up to now, research on Bacillus has mostly adopted integrated omics models and bioinformatics calculation methods, focusing on the mechanisms of Bacillus resistance formation, biofilm formation, colonization, growth promotion, and induction of plant stress resistance. With the continuous deepening of research, the gene regulatory mechanisms, protein expression, and metabolic pathways in the biocontrol process of Bacillus will be further elucidated, which will help discover new biocontrol active substances and optimize biocontrol strategies. This article reviews the research progress of multi-omics techniques such as genomics, transcriptomics, proteomics, and metabonomics on Bacillus. It aims to provide reference for the analysis of the biocontrol mechanism of Bacillus and the in-depth study of biocontrol strain improvement.

Key words: Bacillus, genomics, transcriptomics, proteomics, metabonomics

许沛冬, 易剑锋, 陈迪, 陈浩, 谢丙炎, 赵文军. 组学技术在生防芽胞杆菌的应用进展[J]. 生物技术通报, 2024, 40(10): 208-220.

XU Pei-dong, YI Jian-feng, CHEN Di, CHEN Hao, XIE Bing-yan, ZHAO Wen-jun. Progress in the Application of Omics Technology in Biocontrol Bacillus[J]. Biotechnology Bulletin, 2024, 40(10): 208-220.

图/表 1

参考文献 143

[1]	Karačić V, Miljaković D, Marinković J, et al. Bacillus species: excellent biocontrol agents against tomato diseases[J]. Microorganisms, 2024, 12(3): 457.
[2]	Tudi M, Ruan HD, Wang L, et al. Agriculture development, pesticide application and its impact on the environment[J]. Int J Environ Res Public Health, 2021, 18(3): 1112.
[3]	Tripathi S, Srivastava P, Devi RS, et al. Influence of synthetic fertilizers and pesticides on soil health and soil microbiology[M]// Agrochemicals Detection, Treatment and Remediation. Amsterdam: Elsevier, 2020: 25-54.
[4]	中华人民共和国农业农村部. 关于印发《食用农产品“治违禁控药残促提升”三年行动方案》的通知[EB/OL]. 2021-5-31. http://www.moa.gov.cn/nybgb/2021/202107/202111/t20211104_6381340.htm.
	Ministry of Agriculture and Rural Affairs of the People's Republic of China. Notice on issuing <the Three Year Action Plan for the Treatment of Prohibitions, Control of Drug Residues, and Promotion of Improvement in Edible Agricultural Products>[EB/OL]. 2021-5-31. http://www.moa.gov.cn/nybgb/2021/202107/202111/t20211104_6381340.htm.
[5]	He DC, He MH, Amalin DM, et al. Biological control of plant diseases: an evolutionary and eco-economic consideration[J]. Pathogens, 2021, 10(10): 1311.
[6]	Hirozawa MT, Ono MA, Suguiura IMS, et al. Lactic acid bacteria and Bacillus spp. as fungal biological control agents[J]. J Appl Microbiol, 2023 134(2): lxac083.
[7]	Jacobsen BJ, Zidack NK, Larson BJ. The role of bacillus-based biological control agents in integrated pest management systems: plant diseases[J]. Phytopathology, 2004, 94(11): 1272-1275. doi: 10.1094/PHYTO.2004.94.11.1272 pmid: 18944466
[8]	Miljaković D, Marinković J, Balešević-Tubić S. The significance of Bacillus spp. in disease suppression and growth promotion of field and vegetable crops[J]. Microorganisms, 2020, 8(7): 1037.
[9]	Soni R, Keharia H. Phytostimulation and biocontrol potential of Gram-positive endospore-forming Bacilli[J]. Planta, 2021, 254(3): 49. doi: 10.1007/s00425-021-03695-0 pmid: 34383174
[10]	Cohn F. Untersuchungen über Bakterien[M]//In: Cohn F(eds), Beiträge zur Biologie der Pflanzen 1(Heft 2), 1872, Max Müller, Breslau, 1875: 127-224.
[11]	Skerman VBD, Sneath PHA, McGowan V. Approved lists of bacterial names[J]. Int J Syst Evol Microbiol, 1980, 30(1): 225-420.
[12]	Göker M, Oren A. Valid publication of names of two domains and seven Kingdoms of prokaryotes[J]. Int J Syst Evol Microbiol, 2024, 74(1): 10.1099/ijsem.0.006242.
[13]	Zhang N, Wang ZQ, Shao JH, et al. Biocontrol mechanisms of Bacillus: improving the efficiency of green agriculture[J]. Microb Biotechnol, 2023, 16(12): 2250-2263. doi: 10.1111/1751-7915.14348 pmid: 37837627
[14]	Chowdhury SP, Hartmann A, Gao XW, et al. Biocontrol mechanism by root-associated Bacillus amyloliquefaciens FZB42 - a review[J]. Front Microbiol, 2015, 6: 780. doi: 10.3389/fmicb.2015.00780 pmid: 26284057
[15]	许沛冬, 易剑锋, 陈迪, 等. 贝莱斯芽孢杆菌生防次级代谢产物研究进展[J]. 生物技术通报, 2024, 40(3): 75-88. doi: 10.13560/j.cnki.biotech.bull.1985.2023-0867
	Xu PD, Yi JF, Chen D, et al. Research progress on secondary metabolites of biological control of Bacillus velezensis[J]. Biotechnol Bull, 2024, 40(3): 75-88.
[16]	Molina-Santiago C, Pearson JR, Navarro Y, et al. The extracellular matrix protects Bacillus subtilis colonies from Pseudomonas invasion and modulates plant co-colonization[J]. Nat Commun, 2019, 10(1): 1919. doi: 10.1038/s41467-019-09944-x pmid: 31015472
[17]	Berlanga-Clavero MV, Molina-Santiago C, Caraballo-Rodríguez AM, et al. Bacillus subtilis biofilm matrix components target seed oil bodies to promote growth and anti-fungal resistance in melon[J]. Nat Microbiol, 2022, 7(7): 1001-1015. doi: 10.1038/s41564-022-01134-8 pmid: 35668112
[18]	Dimopoulou A, Theologidis I, Benaki D, et al. Direct antibiotic activity of bacillibactin broadens the biocontrol range of Bacillus amyloliquefaciens MBI600[J]. mSphere, 2021, 6(4): e0037621.
[19]	Xia LM, Miao YZ, Cao AL, et al. Biosynthetic gene cluster profiling predicts the positive association between antagonism and phylogeny in Bacillus[J]. Nat Commun, 2022, 13(1): 1023.
[20]	Lahlali R, Ezrari S, Radouane N, et al. Biological control of plant pathogens: a global perspective[J]. Microorganisms, 2022, 10(3): 596.
[21]	Ongena M, Jourdan E, Adam A, et al. Surfactin and fengycin lipopeptides of Bacillus subtilis as elicitors of induced systemic resistance in plants[J]. Environ Microbiol, 2007, 9(4): 1084-1090. doi: 10.1111/j.1462-2920.2006.01202.x pmid: 17359279
[22]	Gowtham HG, Murali M, Singh SB, et al. Plant growth promoting rhizobacteria- Bacillus amyloliquefaciens improves plant growth and induces resistance in chilli against anthracnose disease[J]. Biol Contr, 2018, 126: 209-217.
[23]	Wu LM, Huang ZY, Li X, et al. Stomatal closure and SA-, JA/ET-signaling pathways are essential for Bacillus amyloliquefaciens FZB42 to restrict leaf disease caused by Phytophthora nicotianae in Nicotiana benthamiana[J]. Front Microbiol, 2018, 9: 847.
[24]	Faure D, Dessaux Y. Quorum sensing as a target for developing control strategies for the plant pathogen Pectobacterium[J]. Eur J Plant Pathol, 2007, 119(3): 353-365.
[25]	Blake C, Christensen MN, Kovács ÁT. Molecular aspects of plant growth promotion and protection by Bacillus subtilis[J]. Mol Plant Microbe Interact, 2021, 34(1): 15-25.
[26]	Lyng M, Jørgensen JPB, Schostag MD, et al. Competition for iron shapes metabolic antagonism between Bacillus subtilis and Pseudomonas marginalis[J]. ISME J, 2024, 18(1): wrad001.
[27]	Morales Moreira ZP, Chen MY, Yanez Ortuno DL, et al. Engineering plant microbiomes by integrating eco-evolutionary principles into current strategies[J]. Curr Opin Plant Biol, 2023, 71: 102316.
[28]	Sorokan A, Gabdrakhmanova V, Kuramshina Z, et al. Plant-associated Bacillus thuringiensis and Bacillus cereus: inside agents for biocontrol and genetic recombination in phytomicrobiome[J]. Plants, 2023, 12(23): 4037.
[29]	王世伟, 王卿惠, 翟丽萍, 等. 多组学分析在解淀粉芽孢杆菌相关功能机制研究中的应用进展[J]. 湖南农业大学学报: 自然科学版, 2020, 46(4): 410-418.
	Wang SW, Wang QH, Zhai LP, et al. Advances in application of multi-component analysis on the functional mechanism study of Bacillus amyloliquefaciens[J]. J Hunan Agric Univ Nat Sci, 2020, 46(4): 410-418.
[30]	Cimermancic P, Medema MH, Claesen J, et al. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters[J]. Cell, 2014, 158(2): 412-421. doi: S0092-8674(14)00826-5 pmid: 25036635
[31]	Dejong CA, Chen GM, Li HX, et al. Polyketide and nonribosomal peptide retro-biosynthesis and global gene cluster matching[J]. Nat Chem Biol, 2016, 12: 1007-1014. doi: 10.1038/nchembio.2188 pmid: 27694801
[32]	Blin K, Shaw S, Steinke K, et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline[J]. Nucleic Acids Res, 2019, 47(W1): W81-W87. doi: 10.1093/nar/gkz310
[33]	Xu PD, Xie SQ, Liu WB, et al. Comparative genomics analysis provides new strategies for bacteriostatic ability of Bacillus velezensis HAB-2[J]. Front Microbiol, 2020, 11: 594079.
[34]	Lee H, Jung DH, Seo DH, et al. Genome analysis of 1-deoxynojirimycin(1-DNJ)-producing Bacillus velezensis K26 and distribution of Bacillus sp. harboring a 1-DNJ biosynthetic gene cluster[J]. Genomics, 2021, 113(1 Pt 2):647-653.
[35]	Zaid DS, Cai SY, Hu C, et al. Comparative genome analysis reveals phylogenetic identity of Bacillus velezensis HNA3 and genomic insights into its plant growth promotion and biocontrol effects[J]. Microbiol Spectr, 2022, 10(1): e0216921.
[36]	Andryukov B, Mikhailov V, Besednova N. The biotechnological potential of secondary metabolites from marine bacteria[J]. J Mar Sci Eng, 2019, 7(6): 176.
[37]	Kizhakkekalam VK, Chakraborty K, Joy M. Oxygenated elansolid-type of polyketide spanned macrolides from a marine heterotrophic Bacillus as prospective antimicrobial agents against multidrug-resistant pathogens[J]. Int J Antimicrob Agents, 2020, 55(3): 105892.
[38]	Sun Y, Shuai WJ, Nie L, et al. Investigating the role of OrbF in biofilm biosynthesis and regulation of biofilm-associated genes in Bacillus cereus BC1[J]. Foods, 2024, 13(5): 638.
[39]	Ashajyothi M, Mahadevakumar S, Venkatesh YN, et al. Comprehensive genomic analysis of Bacillus subtilis and Bacillus paralicheniformis associated with the pearl millet panicle reveals their antimicrobial potential against important plant pathogens[J]. BMC Plant Biol, 2024, 24(1): 197. doi: 10.1186/s12870-024-04881-4 pmid: 38500040
[40]	Comba-González NB, Chaves-Moreno D, Santamaría-Vanegas J, et al. A pan-genomic assessment: Delving into the genome of the marine epiphyte Bacillus altitudinis strain 19_A and other very close Bacillus strains from multiple environments[J]. Heliyon, 2024, 10(7): e27820.
[41]	闫晓妮, 马天有, 杜仁佳, 等. 解淀粉芽胞杆菌胞外抑菌活性物质研究现状[J]. 中国微生态学杂志, 2018, 30(2): 229-234, 249.
	Yan XN, Ma TY, Du RJ, et al. Extracellular antibacterial compounds produced by Bacillus amyloliquefaciens: research progress[J]. Chin J Microecol, 2018, 30(2): 229-234, 249.
[42]	Förster M, Rathmann I, Yüksel M, et al. Genome-wide transformation reveals extensive exchange across closely related Bacillus species[J]. Nucleic Acids Res, 2023, 51(22): 12352-12366. doi: 10.1093/nar/gkad1074 pmid: 37971327
[43]	Thanh Tam LT, Jähne J, Luong PT, et al. Two plant-associated Bacillus velezensis strains selected after genome analysis, metabolite profiling, and with proved biocontrol potential, were enhancing harvest yield of coffee and black pepper in large field trials[J]. Front Plant Sci, 2023, 14: 1194887.
[44]	Hossain MJ, Ran C, Liu K, et al. Deciphering the conserved genetic loci implicated in plant disease control through comparative genomics of Bacillus amyloliquefaciens subsp. plantarum[J]. Front Plant Sci, 2015, 6: 631.
[45]	Belbahri L, Chenari Bouket A, Rekik I, et al. Comparative genomics of Bacillus amyloliquefaciens strains reveals a core genome with traits for habitat adaptation and a secondary metabolites rich accessory genome[J]. Front Microbiol, 2017, 8: 1438. doi: 10.3389/fmicb.2017.01438 pmid: 28824571
[46]	Ryan RP, Dow JM. Diffusible signals and interspecies communication in bacteria[J]. Microbiology, 2008, 154(Pt 7): 1845-1858. doi: 10.1099/mic.0.2008/017871-0 pmid: 18599814
[47]	Straight PD, Kolter R. Interspecies chemical communication in bacterial development[J]. Annu Rev Microbiol, 2009, 63: 99-118. doi: 10.1146/annurev.micro.091208.073248 pmid: 19566421
[48]	Romero D, Traxler MF, López D, et al. Antibiotics as signal molecules[J]. Chem Rev, 2011, 111(9): 5492-5505. doi: 10.1021/cr2000509 pmid: 21786783
[49]	López D, Fischbach MA, Chu F, et al. Structurally diverse natural products that cause potassium leakage trigger multicellularity in Bacillus subtilis[J]. Proc Natl Acad Sci USA, 2009, 106(1): 280-285.
[50]	López D, Vlamakis H, Losick R, et al. Paracrine signaling in a bacterium[J]. Genes Dev, 2009, 23(14): 1631-1638.
[51]	Traxler MF, Kolter R. Natural products in soil microbe interactions and evolution[J]. Nat Prod Rep, 2015, 32(7): 956-970. doi: 10.1039/c5np00013k pmid: 26000872
[52]	Yang H, Li X, Li X, et al. Identification of lipopeptide isoforms by MALDI-TOF-MS/MS based on the simultaneous purification of iturin, fengycin, and surfactin by RP-HPLC[J]. Anal Bioanal Chem, 2015, 407(9): 2529-2542. doi: 10.1007/s00216-015-8486-8 pmid: 25662934
[53]	Müller S, Strack SN, Hoefler BC, et al. Bacillaene and sporulation protect Bacillus subtilis from predation by Myxococcus xanthus[J]. Appl Environ Microbiol, 2014, 80(18): 5603-5610.
[54]	Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics[J]. Nat Rev Genet, 2009, 10(1): 57-63. doi: 10.1038/nrg2484 pmid: 19015660
[55]	Haas BJ, Zody MC. Advancing RNA-Seq analysis[J]. Nat Biotechnol, 2010, 28(5): 421-423. doi: 10.1038/nbt0510-421 pmid: 20458303
[56]	Garber M, Grabherr MG, Guttman M, et al. Computational methods for transcriptome annotation and quantification using RNA-seq[J]. Nat Methods, 2011, 8(6): 469-477. doi: 10.1038/nmeth.1613 pmid: 21623353
[57]	Hu HJ, Wang C, Li X, et al. RNA-Seq identification of candidate defense genes targeted by endophytic Bacillus cereus-mediated induced systemic resistance against Meloidogyne incognita in tomato[J]. Pest Manag Sci, 2018, 74(12): 2793-2805.
[58]	Liao YL, Huang LG, Wang B, et al. The global transcriptional landscape of Bacillus amyloliquefaciens XH7 and high-throughput screening of strong promoters based on RNA-seq data[J]. Gene, 2015, 571(2): 252-262.
[59]	Li X, Li MT, Liu XK, et al. RNA-seq provides insights into the mechanisms underlying Ilyonectria robusta responding to secondary metabolites of Bacillus methylotrophicus NJ13[J]. J Fungi, 2022, 8(8): 779.
[60]	Liu D, Li KY, Hu JL, et al. Biocontrol and action mechanism of Bacillus amyloliquefaciens and Bacillus subtilis in soybean Phytophthora blight[J]. Int J Mol Sci, 2019, 20(12): 2908.
[61]	Yeo IC, Lee NK, Yang BW, et al. RNA-seq analysis of antibiotic-producing Bacillus subtilis SC-8 in response to signal peptide PapR of Bacillus cereus[J]. Appl Biochem Biotechnol, 2014, 172(2): 580-594.
[62]	Tahir HAS, Ali Q, Rajer FU, et al. Transcriptomic analysis of Ralstonia solanacearum in response to antibacterial volatiles of Bacillus velezensis FZB42[J]. Arch Microbiol, 2023, 205(11): 358.
[63]	Zhang J, Zhu WQ, Goodwin PH, et al. Response of Fusarium pseudograminearum to biocontrol agent Bacillus velezensis YB-185 by phenotypic and transcriptome analysis[J]. J Fungi, 2022, 8(8): 763.
[64]	Fan B, Li L, Chao YJ, et al. dRNA-seq reveals genomewide TSSs and noncoding RNAs of plant beneficial rhizobacterium Bacillus amyloliquefaciens FZB42[J]. PLoS One, 2015, 10(11): e0142002.
[65]	Kröber M, Verwaaijen B, Wibberg D, et al. Comparative transcriptome analysis of the biocontrol strain Bacillus amyloliquefaciens FZB42 as response to biofilm formation analyzed by RNA sequencing[J]. J Biotechnol, 2016, 231: 212-223.
[66]	Liu SF, Hao HT, Lu X, et al. Transcriptome profiling of genes involved in induced systemic salt tolerance conferred by Bacillus amyloliquefaciens FZB42 in Arabidopsis thaliana[J]. Sci Rep, 2017, 7(1): 10795.
[67]	Dergham Y, Le Coq D, Nicolas P, et al. Direct comparison of spatial transcriptional heterogeneity across diverse Bacillus subtilis biofilm communities[J]. Nat Commun, 2023, 14(1): 7546.
[68]	Sadiq FA, Flint S, Sakandar HA, et al. Molecular regulation of adhesion and biofilm formation in high and low biofilm producers of Bacillus licheniformis using RNA-Seq[J]. Biofouling, 2019, 35(2): 143-158.
[69]	Yang W, Yan HX, Dong GH, et al. Comparative transcriptomics reveal different genetic adaptations of biofilm formation in Bacillus subtilis isolate 1JN2 in response to Cd²⁺ treatment[J]. Front Microbiol, 2022, 13: 1002482.
[70]	Ku YS, Liao YJ, Chiou SP, et al. From trade-off to synergy: microbial insights into enhancing plant growth and immunity[J]. Plant Biotechnol J, 2024,(5).
[71]	Liu H, Wang J, Sun HM, et al. Transcriptome profiles reveal the growth-promoting mechanisms of Paenibacillus polymyxa YC0136 on tobacco(Nicotiana tabacum L.)[J]. Front Microbiol, 2020, 11: 584174.
[72]	Samaras A, Roumeliotis E, Ntasiou P, et al. Bacillus subtilis MBI600 promotes growth of tomato plants and induces systemic resistance contributing to the control of soilborne pathogens[J]. Plants, 2021, 10(6): 1113.
[73]	He TT, Xu YF, Li X, et al. A linear and circular dual-conformation noncoding RNA involved in oxidative stress tolerance in Bacillus altitudinis[J]. Nat Commun, 2023, 14(1): 5722.
[74]	Ogura M, Matsutani M, Asai K, et al. Glucose controls manganese homeostasis through transcription factors regulating known and newly identified manganese transporter genes in Bacillus subtilis[J]. J Biol Chem, 2023, 299(8): 105069.
[75]	Li M, Zhang ZL, Li SW, et al. Study on the mechanism of production of γ-PGA and nattokinase in Bacillus subtilis natto based on RNA-seq analysis[J]. Microb Cell Fact, 2021, 20(1): 83.
[76]	Yang PZ, Wu WJ, Zhang DF, et al. AFB₁ microbial degradation by Bacillus subtilis WJ6 and its degradation mechanism exploration based on the comparative transcriptomics approach[J]. Metabolites, 2023, 13(7): 785.
[77]	Stults JT, Arnott D. Proteomics[M]// Methods in Enzymology. Amsterdam: Elsevier, 2005: 245-289.
[78]	姚婷, 石海林, 杨琦, 等. 蛋白质组学技术在微生物农药苏云金杆菌中的应用进展[J]. 农药, 2020, 59(12): 867-870, 887.
	Yao T, Shi HL, Yang Q, et al. Application of proteomic technologies in microbial pesticide Bacillus thuringiensis[J]. Agrochemicals, 2020, 59(12): 867-870, 887.
[79]	Antelmann H, Bernhardt J, Schmid R, et al. First steps from a two-dimensional protein index towards a response-regulation map for Bacillus subtilis[J]. Electrophoresis, 1997, 18(8): 1451-1463. pmid: 9298659
[80]	Tobisch S, Zühlke D, Bernhardt J, et al. Role of CcpA in regulation of the central pathways of carbon catabolism in Bacillus subtilis[J]. J Bacteriol, 1999, 181(22): 6996-7004. pmid: 10559165
[81]	Bernhardt J, Weibezahn J, Scharf C, et al. Bacillus subtilis during feast and famine: visualization of the overall regulation of protein synthesis during glucose starvation by proteome analysis[J]. Genome Res, 2003, 13(2): 224-237. pmid: 12566400
[82]	Reuβ DR, Altenbuchner J, Mäder U, et al. Large-scale reduction of the Bacillus subtilis genome: consequences for the transcriptional network, resource allocation, and metabolism[J]. Genome Res, 2017, 27(2): 289-299.
[83]	Maass S, Sievers S, Zühlke D, et al. Efficient, global-scale quantification of absolute protein amounts by integration of targeted mass spectrometry and two-dimensional gel-based proteomics[J]. Anal Chem, 2011, 83(7): 2677-2684. doi: 10.1021/ac1031836 pmid: 21395229
[84]	Muntel J, Fromion V, Goelzer A, et al. Comprehensive absolute quantification of the cytosolic proteome of Bacillus subtilis by data independent, parallel fragmentation in liquid chromatography/mass spectrometry(LC/MS(E))[J]. Mol Cell Proteomics, 2014, 13(4): 1008-1019. doi: 10.1074/mcp.M113.032631 pmid: 24696501
[85]	Chavez JD, Lee CF, Caudal A, et al. Chemical crosslinking mass spectrometry analysis of protein conformations and super complexes in heart tissue[J]. Cell Syst, 2018, 6(1): 136-141.e5. doi: S2405-4712(17)30487-8 pmid: 29199018
[86]	O'Reilly FJ, Xue L, Graziadei A, et al. In-cell architecture of an actively transcribing-translating expressome[J]. Science, 2020, 369(6503): 554-557. doi: 10.1126/science.abb3758 pmid: 32732422
[87]	O'Reilly FJ, Graziadei A, Forbrig C, et al. Protein complexes in cells by AI-assisted structural proteomics[J]. Mol Syst Biol, 2023, 19(4): e11544.
[88]	Qiu MH, Xu ZH, Li XX, et al. Comparative proteomics analysis of Bacillus amyloliquefaciens SQR9 revealed the key proteins involved in in situ root colonization[J]. J Proteome Res, 2014, 13(12): 5581-5591.
[89]	Goodson JR, Klupt S, Zhang CX, et al. LoaP is a broadly conserved antiterminator protein that regulates antibiotic gene clusters in Bacillus amyloliquefaciens[J]. Nat Microbiol, 2017, 2: 17003.
[90]	Liu XY, Zhao FK, Wang XH, et al. Prediction and validation of enzymatic degradation of aflatoxin M₁: Genomics and proteomics analysis of Bacillus pumilus E-1-1-1 enzymes[J]. Sci Total Environ, 2023, 900: 165720.
[91]	Li BX, Jin ZC, Yang F, et al. Proteomic investigation reveals the role of bacterial laccase from Bacillus pumilus in oxidative stress defense[J]. J Proteomics, 2024, 292: 105047.
[92]	Shimokawa-Chiba N, Müller C, Fujiwara K, et al. Release factor-dependent ribosome rescue by BrfA in the Gram-positive bacterium Bacillus subtilis[J]. Nat Commun, 2019, 10(1): 5397. doi: 10.1038/s41467-019-13408-7 pmid: 31776341
[93]	Senges CHR, Stepanek JJ, Wenzel M, et al. Comparison of proteomic responses as global approach to antibiotic mechanism of action elucidation[J]. Antimicrob Agents Chemother, 2020, 65(1): e01373-e01320.
[94]	Vázquez-Hernández M, Leedom SL, Keiler KC, et al. Physiology of trans-translation deficiency in Bacillus subtilis-a comparative proteomics study[J]. Proteomics, 2023, 23(18): e2200474.
[95]	Caballero J, Jiménez-Moreno N, Orera I, et al. Unraveling the composition of insecticidal crystal proteins in Bacillus thuringiensis: a proteomics approach[J]. Appl Environ Microbiol, 2020, 86(12): e00476-e00420.
[96]	Yang Q, Tang SJ, Rang J, et al. Detection of toxin proteins from Bacillus thuringiensis strain 4.0718 by strategy of 2D-LC-MS/MS[J]. Curr Microbiol, 2015, 70(4): 457-463. doi: 10.1007/s00284-014-0747-9 pmid: 25477065
[97]	Khorramnejad A, Gomis-Cebolla J, Talaei-Hassanlouei R, et al. Genomics and proteomics analyses revealed novel candidate pesticidal proteins in a lepidopteran-toxic Bacillus thuringiensis strain[J]. Toxins, 2020, 12(11): 673.
[98]	Gray EJ, Di Falco M, Souleimanov A, et al. Proteomic analysis of the bacteriocin thuricin 17 produced by Bacillus thuringiensis NEB17[J]. FEMS Microbiol Lett, 2006, 255(1): 27-32.
[99]	Chen DJ, Xu D, Li MS, et al. Proteomic analysis of Bacillus thuringiensis ΔphaC mutant BMB171/PHB(-1)reveals that the PHB synthetic pathway warrants normal carbon metabolism[J]. J Proteomics, 2012, 75(17): 5176-5188.
[100]	张虹, 蒋红亮, 赵辅昆, 等. 高表达PGA的枯草芽孢杆菌蛋白质组学研究[J]. 浙江理工大学学报, 2011, 28(1): 116-121.
	Zhang H, Jiang HL, Zhao FK, et al. Proteomics analysis of B. S₁₆₈ overproducing PGA[J]. J Zhejiang Sci Tech Univ Nat Sci Ed, 2011, 28(1): 116-121.
[101]	Zhao JF, Cao L, Zhang C, et al. Differential proteomics analysis of Bacillus amyloliquefaciens and its genome-shuffled mutant for improving surfactin production[J]. Int J Mol Sci, 2014, 15(11): 19847-19869.
[102]	Mashego MR, Rumbold K, De Mey M, et al. Microbial metabolomics: past, present and future methodologies[J]. Biotechnol Lett, 2007, 29(1): 1-16. doi: 10.1007/s10529-006-9218-0 pmid: 17091378
[103]	Saito K, Matsuda F. Metabolomics for functional genomics, systems biology, and biotechnology[J]. Annu Rev Plant Biol, 2010, 61: 463-489. doi: 10.1146/annurev.arplant.043008.092035 pmid: 19152489
[104]	Beale DJ, Kouremenos KA, Palombo. Microbial Metabolomics[M]. 1rd ed.ed. Australia: Springer Cham, 2016.
[105]	Garcia DE, Baidoo EE, Benke PI, et al. Separation and mass spectrometry in microbial metabolomics[J]. Curr Opin Microbiol, 2008, 11(3): 233-239. doi: 10.1016/j.mib.2008.04.002 pmid: 18538626
[106]	Baidoo EEK, Benke PI, Keasling JD. Mass spectrometry-based microbial metabolomics[J]. Methods Mol Biol, 2012, 881: 215-278. doi: 10.1007/978-1-61779-827-6_9 pmid: 22639216
[107]	Gao P, Xu GW. Mass-spectrometry-based microbial metabolomics: recent developments and applications[J]. Anal Bioanal Chem, 2015, 407(3): 669-680. doi: 10.1007/s00216-014-8127-7 pmid: 25216964
[108]	Wishart DS. Quantitative metabolomics using NMR[J]. Trac Trends Anal Chem, 2008, 27(3): 228-237.
[109]	Kind T, Wohlgemuth G, Lee DY, et al. FiehnLib: mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometry[J]. Anal Chem, 2009, 81(24): 10038-10048. doi: 10.1021/ac9019522 pmid: 19928838
[110]	Dehaven CD, Evans AM, Dai HP, et al. Organization of GC/MS and LC/MS metabolomics data into chemical libraries[J]. J Cheminform, 2010, 2(1): 9.
[111]	Ntasi G, Tsarbopoulos A, Mikros E, et al. Targeted metabolomics: the LC-MS/MS based quantification of the metabolites involved in the methylation biochemical pathways[J]. Metabolites, 2021, 11(7): 416.
[112]	Zhang LY, Jin MS, Shi X, et al. Macrolactin metabolite production by Bacillus sp. ZJ318 isolated from marine sediment[J]. Appl Biochem Biotechnol, 2022, 194(6): 2581-2593.
[113]	Wu CH, Tang JW, Limlingan Malit JJ, et al. Bathiapeptides: polythiazole-containing peptides from a marine biofilm-derived Bacillus sp[J]. J Nat Prod, 2022, 85(7): 1751-1762.
[114]	Koilybayeva M, Shynykul Z, Ustenova G, et al. Gas chromatography-mass spectrometry profiling of volatile metabolites produced by some Bacillus spp. and evaluation of their antibacterial and antibiotic activities[J]. Molecules, 2023, 28(22): 7556.
[115]	Ntemafack A, Chouhan R, Kapoor N, et al. Protective effect of Bacillus species associated with Rumex dentatus against postharvest soil borne disease in potato tubers and GC-MS metabolite profile[J]. Arch Microbiol, 2022, 204(9): 583. doi: 10.1007/s00203-022-03213-0 pmid: 36042050
[116]	Hou YP, Braun DR, Michel CR, et al. Microbial strain prioritization using metabolomics tools for the discovery of natural products[J]. Anal Chem, 2012, 84(10): 4277-4283. doi: 10.1021/ac202623g pmid: 22519562
[117]	Farzand A, Moosa A, Zubair M, et al. Suppression of Sclerotinia sclerotiorum by the induction of systemic resistance and regulation of antioxidant pathways in tomato using fengycin produced by Bacillus amyloliquefaciens FZB42[J]. Biomolecules, 2019, 9(10): 613.
[118]	Zhang YJ, Meng ZN, Li SL, et al. Two antimicrobial peptides derived from Bacillus and their properties[J]. Molecules, 2023, 28(23): 7899.
[119]	Zhao M, Liu DM, Liang ZH, et al. Antagonistic activity of Bacillus subtilis CW14 and its β-glucanase against Aspergillus ochraceus[J]. Food Contr, 2022, 131: 108475.
[120]	Chandwani S, Dewala S, Chavan SM, et al. Genomic, LC-MS, and FTIR analysis of plant probiotic potential of Bacillus albus for managing Xanthomonas oryzae via different modes of application in rice(Oryza sativa L.)[J]. Probiotics Antimicrob Proteins, 2024, 16(5): 1541-1552.
[121]	Ye QL, Zhong Z, Chao SF, et al. Antifungal effect of Bacillus velezensis ZN-S10 against plant pathogen Colletotrichum changpingense and its inhibition mechanism[J]. Int J Mol Sci, 2023, 24(23): 16694.
[122]	Silveira RD, Veras FF, Bach E, et al. Aspergillus carbonarius-derived ochratoxins are inhibited by Amazonian Bacillus spp. used as a biocontrol agent in grapes[J]. Food Addit Contam Part A Chem Anal Control Expo Risk Assess, 2022, 39(1): 158-169.
[123]	Jinal HN, Sakthivel K, Amaresan N. Characterisation of antagonistic Bacillus paralicheniformis(strain EAL)by LC-MS, antimicrobial peptide genes, and ISR determinants[J]. Antonie Van Leeuwenhoek, 2020, 113(8): 1167-1177.
[124]	Ravi A, Rajan S, Khalid NK, et al. Impact of supplements on enhanced activity of Bacillus amyloliquefaciens BmB1 against Pythium aphanidermatum through lipopeptide modulation[J]. Probiotics Antimicrob Proteins, 2021, 13(2): 367-374.
[125]	Zhou DY, Hu FX, Lin JZ, et al. Genome and transcriptome analysis of Bacillus velezensis BS-37, an efficient surfactin producer from glycerol, in response to d-/ l-leucine[J]. MicrobiologyOpen, 2019, 8(8): e00794.
[126]	Tian DD, Song XP, Li CS, et al. Antifungal mechanism of Bacillus amyloliquefaciens strain GKT04 against Fusarium wilt revealed using genomic and transcriptomic analyses[J]. MicrobiologyOpen, 2021, 10(3): e1192.
[127]	Liu ZS, Fan CX, Xiao JW, et al. Metabolomic and transcriptome analysis of the inhibitory effects of Bacillus subtilis strain Z-14 against Fusarium oxysporum causing vascular wilt diseases in cucumber[J]. J Agric Food Chem, 2023, 71(5): 2644-2657.
[128]	Zhang H, Yang QL, Zhao JJ, et al. Metabolites from Bacillus subtilis J-15 affect seedling growth of Arabidopsis thaliana and cotton plants[J]. Plants, 2022, 11(23): 3205.
[129]	Park MK, Hong CP, Kim BS, et al. Integrated-omics study on the transcriptomic and metabolic changes of Bacillus licheniformis, a main microorganism of fermented soybeans, according to alkaline pH and osmotic stress[J]. J Agric Food Chem, 2023, 71(39): 14379-14389.
[130]	Li QY, Lin W, Zhang XF, et al. Transcriptomics integrated with metabolomics reveal the competitive relationship between co-cultured Trichoderma asperellum HG1 and Bacillus subtilis Tpb55[J]. Microbiol Res, 2024, 280: 127598.
[131]	Tang JZ, Ding YX, Nan J, et al. Transcriptome sequencing and ITRAQ reveal the detoxification mechanism of Bacillus GJ1, a potential biocontrol agent for Huanglongbing[J]. PLoS One, 2018, 13(8): e0200427.
[132]	Fu L, Penton CR, Ruan YZ, et al. Inducing the rhizosphere microbiome by biofertilizer application to suppress banana Fusarium wilt disease[J]. Soil Biol Biochem, 2017, 104: 39-48.
[133]	Altena K, Guder A, Cramer C, et al. Biosynthesis of the lantibiotic mersacidin: organization of a type B lantibiotic gene cluster[J]. Appl Environ Microbiol, 2000, 66(6): 2565-2571.
[134]	Torres-Sánchez A, Pardo-Cacho J, López-Moreno A, et al. Antimicrobial effects of potential probiotics of Bacillus spp. isolated from human microbiota: in vitro and in silico methods[J]. Microorganisms, 2021, 9(8): 1615.
[135]	Casjens SR. Comparative genomics and evolution of the tailed-bacteriophages[J]. Curr Opin Microbiol, 2005, 8(4): 451-458. pmid: 16019256
[136]	Varani AM, Monteiro-Vitorello CB, Nakaya HI, et al. The role of prophage in plant-pathogenic bacteria[J]. Annu Rev Phytopathol, 2013, 51: 429-451. doi: 10.1146/annurev-phyto-081211-173010 pmid: 23725471
[137]	Wang XX, Kim Y, Ma Q, et al. Cryptic prophages help bacteria cope with adverse environments[J]. Nat Commun, 2010, 1: 147. doi: 10.1038/ncomms1146 pmid: 21266997
[138]	Fortier LC, Sekulovic O. Importance of prophages to evolution and virulence of bacterial pathogens[J]. Virulence, 2013, 4(5): 354-365.
[139]	Loh B, Chen JY, Manohar P, et al. A biological inventory of prophages in A. baumannii genomes reveal distinct distributions in classes, length, and genomic positions[J]. Front Microbiol, 2020, 11: 579802.
[140]	Nakayama K, Takashima K, Ishihara H, et al. The R-type pyocin of Pseudomonas aeruginosa is related to P2 phage, and the F-type is related to lambda phage[J]. Mol Microbiol, 2000, 38(2): 213-231. doi: 10.1046/j.1365-2958.2000.02135.x pmid: 11069649
[141]	Prigigallo MI, Gómez-Lama Cabanás C, Mercado-Blanco J, et al. Designing a synthetic microbial community devoted to biological control: the case study of Fusarium wilt of banana[J]. Front Microbiol, 2022, 13: 967885.
[142]	Minchev Z, Kostenko O, Soler R, et al. Microbial consortia for effective biocontrol of root and foliar diseases in tomato[J]. Front Plant Sci, 2021, 12: 756368.
[143]	Santhanam R, Luu VT, Weinhold A, et al. Native root-associated bacteria rescue a plant from a sudden-wilt disease that emerged during continuous cropping[J]. Proc Natl Acad Sci USA, 2015, 112(36): E5013-E5020.