Biocontrol of plant pathogens in omics era—with special focus on endophytic bacilli

References

• Ab Rahman SFS, Singh E, Pieterse CM, et al. Emerging microbial biocontrol strategies for plant pathogens. Plant Sci. 2018;267:102–111.
   PubMed Web of Science ®Google Scholar
• Waghunde RR, Khunt MD, Shelake RM, et al. Culturable plant-associated endophytic microbial communities from leguminous and nonleguminous crops. In: Advances in plant microbiome and sustainable agriculture. Singapore: Springer; 2020. p. 83–103.
   Google Scholar
• Dean R, Van Kan JA, Pretorius ZA, et al. The Top 10 fungal pathogens in molecular plant pathology. Mol Plant Pathol. 2012;13(4):414–430.
   PubMed Web of Science ®Google Scholar
• Mansfield J, Genin S, Magori S, et al. Top 10 plant pathogenic bacteria in molecular plant pathology. Mol Plant Pathol. 2012;13(6):614–629.
   PubMed Web of Science ®Google Scholar
• Schwelm A, Badstöber J, Bulman S, et al. Not in your usual Top 10: protists that infect plants and algae. Mol Plant Pathol. 2018;19(4):1029–1044.
   PubMed Web of Science ®Google Scholar
• Pais M, Yoshida K, Giannakopoulou A, et al. Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen. BMC Evol Biol. 2018;18(1):93.
   PubMedGoogle Scholar
• Donnelly JS. Great Irish potato famine. UK: Oxford University Press; 2002.
   Google Scholar
• Singh BK, Trivedi P. Microbiome and the future for food and nutrient security. Microb Biotechnol. 2017;10(1):50–53.
   PubMed Web of Science ®Google Scholar
• Dhananjayan V, Jayanthi P, Jayakumar S, et al. Agrochemicals impact on ecosystem and bio-monitoring. In: Resources use efficiency in agriculture. Singapore: Springer; 2020. p. 349–388.
   Google Scholar
• Mandal A, Sarkar B, Mandal S, et al. Impact of agrochemicals on soil health. In: Agrochemicals detection, treatment and remediation. UK: Butterworth-Heinemann; 2020. p. 161–187.
   Google Scholar
• Meena RS, Kumar S, Datta R, et al. Impact of agrochemicals on soil microbiota and management: a review. Land. 2020;9(2):34.
   Web of Science ®Google Scholar
• Haney CH, Samuel BS, Bush J, et al. Associations with rhizosphere bacteria can confer an adaptive advantage to plants. Nature plants. 2015;1(6):1–9.
   Web of Science ®Google Scholar
• Trivedi P, Leach JE, Tringe SG, et al. Plant–microbiome interactions: from community assembly to plant health. Nature Rev Microbiol. 2020;18(11):607–621.
   PubMed Web of Science ®Google Scholar
• Singh BK, Trivedi P, Egidi E, et al. Crop microbiome and sustainable agriculture. Nature Rev Microbiol. 2020;18(11):601–602.
   PubMed Web of Science ®Google Scholar
• Toju H, Peay KG, Yamamichi M, et al. Core microbiomes for sustainable agroecosystems. Nature Plants. 2018;4(5):247–257.
   PubMed Web of Science ®Google Scholar
• Nataraja KN, Suryanarayanan T, Shaanker RU, et al. Plant–microbe interaction: prospects for crop improvement and management. Plant Physiol Rep. 2019;24(4):461–462.
   Google Scholar
• Zicca S, De Bellis P, Masiello M, et al. Antagonistic activity of olive endophytic bacteria and of Bacillus spp. strains against Xylella fastidiosa. Microbiol Res. 2020;236:126467.
   PubMedGoogle Scholar
• Munir S, Ahmed A, Li Y, et al. The hidden treasures of citrus: finding Huanglongbing cure where it was lost. Crit Rev Biotechnol. 2021;42(4):1–16.
   PubMed Web of Science ®Google Scholar
• Fan B, Wang C, Song X, et al. Bacillus velezensis FZB42 in 2018: the Gram-positive model strain for plant growth promotion and biocontrol. Front Microbiol. 2018;9:2491.
   PubMed Web of Science ®Google Scholar
• Barkodia M, Joshi U, Rami N, et al. Endophytes: a hidden treasure inside plant. IJCS. 2018;6(5):1660–1665.
   Google Scholar
• Brader G, Compant S, Vescio K, et al. Ecology and genomic insights into plant-pathogenic and plant-nonpathogenic endophytes. Annu Rev Phytopathol. 2017;55:61–83.
   PubMed Web of Science ®Google Scholar
• Babalola OO, Fadiji AE, Enagbonma BJ, et al. The nexus between plant and plant microbiome: revelation of the networking strategies. Front Microbiol. 2020;11:2128.
   Web of Science ®Google Scholar
• Fadiji AE, Babalola OO. Metagenomics methods for the study of plant-associated microbial communities: a review. J Microbiol Methods. 2020;170:105860.
   PubMed Web of Science ®Google Scholar
• Khalaf EM, Raizada MN. Bacterial seed endophytes of domesticated cucurbits antagonize fungal and oomycete pathogens including powdery mildew. Front Microbiol. 2018;9:42.
   PubMed Web of Science ®Google Scholar
• Pandit MA, Kumar J, Gulati S, et al. Major biological control strategies for plant pathogens. Pathogens. 2022;11(2):273.
   PubMed Web of Science ®Google Scholar
• Shen F-T, Yen J-H, Liao C-S, et al. Screening of rice endophytic biofertilizers with fungicide tolerance and plant growth-promoting characteristics. Sustainability. 2019;11(4):1133.
   Web of Science ®Google Scholar
• Rangjaroen C, Lumyong S, Sloan WT, et al. Herbicide-tolerant endophytic bacteria of rice plants as the biopriming agents for fertility recovery and disease suppression of unhealthy rice seeds. BMC Plant Biol. 2019;19(1):1–16.
   PubMed Web of Science ®Google Scholar
• Gamalero E, Glick BR. Bacterial modulation of plant ethylene levels. Plant Physiol. 2015;169(1):13–22.
   PubMed Web of Science ®Google Scholar
• Singh R, Dubey AK. Diversity and applications of endophytic actinobacteria of plants in special and other ecological niches. Front Microbiol. 2018;9:1767.
   PubMed Web of Science ®Google Scholar
• Bodhankar S, Grover M, Hemanth S, et al. Maize seed endophytic bacteria: dominance of antagonistic, lytic enzyme-producing Bacillus spp. 3 Biotech. 2017;7(4):232.
   PubMedGoogle Scholar
• Ranjith S, Kalaiselvi T, Muthusami M, et al. Maize apoplastic fluid bacteria alter feeding characteristics of herbivore (Spodoptera frugiperda) in maize. Microorganisms. 2022;10(9):1850.
   PubMed Web of Science ®Google Scholar
• Thomas P, Reddy KM. Microscopic elucidation of abundant endophytic bacteria colonizing the cell wall–plasma membrane peri-space in the shoot-tip tissue of banana. AoB Plants. 2013;5:1–12.
   Web of Science ®Google Scholar
• de Almeida CV, Andreote FD, Yara R, et al. Bacteriosomes in axenic plants: endophytes as stable endosymbionts. World J Microbiol Biotechnol. 2009;25(10):1757–1764.
   Web of Science ®Google Scholar
• White JF, Torres MS, Johnson H, et al. A functional view of plant microbiomes: endosymbiotic systems that enhance plant growth and survival. In: Advances in endophytic research. New Delhi: Springer; 2014. p. 425–439.
   Google Scholar
• Yadav AN, Verma P, Kour D, et al. Plant microbiomes and its beneficial multifunctional plant growth promoting attributes. Int J Environ Sci Nat Resour. 2017;3(1):1–8.
   Google Scholar
• Compant S, Mitter B, Colli-Mull JG, et al. Endophytes of grapevine flowers, berries, and seeds: identification of cultivable bacteria, comparison with other plant parts, and visualization of niches of colonization. Microbial Ecol. 2011;62(1):188–197.
   PubMed Web of Science ®Google Scholar
• Sessitsch A, Hardoim P, Döring J, et al. Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis. Mol Plant Microbe Interact. 2012;25(1):28–36.
   PubMed Web of Science ®Google Scholar
• Edwards J, Johnson C, Santos-Medellín C, et al. Structure, variation, and assembly of the root-associated microbiomes of rice. Proc Natl Acad Sci U S A. 2015;112(8):E911–E920.
   PubMed Web of Science ®Google Scholar
• Santoyo G, Moreno-Hagelsieb G, del Carmen Orozco-Mosqueda M, et al. Plant growth-promoting bacterial endophytes. Microbiol Res. 2016;183:92–99.
   PubMed Web of Science ®Google Scholar
• Afzal I, Shinwari ZK, Sikandar S, et al. Plant beneficial endophytic bacteria: mechanisms, diversity, host range and genetic determinants. Microbiol Res. 2019;221:36–49.
   PubMed Web of Science ®Google Scholar
• Ghiasian M. Endophytic microbiomes: biodiversity, current status, and potential agricultural applications. In: Advances in plant microbiome and sustainable agriculture. Singapore: Springer; 2020. p. 61–82.
   Google Scholar
• Jackson CR, Randolph KC, Osborn SL, et al. Culture dependent and independent analysis of bacterial communities associated with commercial salad leaf vegetables. BMC Microbiol. 2013;13(1):274.
   PubMedGoogle Scholar
• Hardoim PR, Hardoim CC, Van Overbeek LS, et al. Dynamics of seed-borne rice endophytes on early plant growth stages. PLoS One. 2012;7(2):e30438.
   PubMed Web of Science ®Google Scholar
• Shehzadi M, Afzal M, Khan MU, et al. Enhanced degradation of textile effluent in constructed wetland system using Typha domingensis and textile effluent-degrading endophytic bacteria. Water Res. 2014;58:152–159.
   PubMed Web of Science ®Google Scholar
• Mora-Ruiz MDR, Font-Verdera F, Orfila A, et al. Endophytic microbial diversity of the halophyte Arthrocnemum macrostachyum across plant compartments. FEMS Microbiol Ecol. 2016;92(9):fiw145.
   PubMed Web of Science ®Google Scholar
• Kampapongsa D, Kaewkla O. Biodiversity of endophytic actinobacteria from jasmine rice (Oryza sativa L. KDML 105) grown in Roi-Et Province, Thailand and their antimicrobial activity against rice pathogens. Ann Microbiol. 2016;66(2):587–595.
   Web of Science ®Google Scholar
• Jog R, Pandya M, Nareshkumar G, et al. Mechanism of phosphate solubilization and antifungal activity of Streptomyces spp. isolated from wheat roots and rhizosphere and their application in improving plant growth. Microbiology. 2014;160(4):778–788.
   PubMedGoogle Scholar
• Bulgarelli D, Rott M, Schlaeppi K, et al. Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature. 2012;488(7409):91–95.
   PubMed Web of Science ®Google Scholar
• Liu H, Carvalhais LC, Schenk PM, et al. Effects of jasmonic acid signalling on the wheat microbiome differ between body sites. Sci Rep. 2017;7(1):1–8.
   PubMedGoogle Scholar
• Haruna E, Zin NM, Kerfahi D, et al. Extensive overlap of tropical rainforest bacterial endophytes between soil, plant parts, and plant species. Microbial Ecol. 2018;75(1):88–103.
   PubMed Web of Science ®Google Scholar
• Hameed A, Yeh M-W, Hsieh Y-T, et al. Diversity and functional characterization of bacterial endophytes dwelling in various rice (Oryza sativa L.) tissues, and their seed-borne dissemination into rhizosphere under gnotobiotic P-stress. Plant Soil. 2015;394(1-2):177–197.
   Web of Science ®Google Scholar
• Hamonts K, Trivedi P, Garg A, et al. Field study reveals core plant microbiota and relative importance of their drivers. Environ Microbiol. 2018;20(1):124–140.
   PubMed Web of Science ®Google Scholar
• Philippot L, Raaijmakers JM, Lemanceau P, et al. Going back to the roots: the microbial ecology of the rhizosphere. Nature Rev Microbiol. 2013;11(11):789–799.
   PubMed Web of Science ®Google Scholar
• Tosi M, Gaiero J, Linton N, et al. Bacterial endophytes: diversity, functional importance, and potential for manipulation. In: Rhizosphere biology: interactions between microbes and plants. Singapore: Springer; 2020. p. 1–49.
   Google Scholar
• Turner TR, James EK, Poole PS. The plant microbiome. Genome Biol. 2013;14(6):1–10.
   Web of Science ®Google Scholar
• Knief C, Ramette A, Frances L, et al. Site and plant species are important determinants of the Methylobacterium community composition in the plant phyllosphere. ISME J. 2010;4(6):719–728.
   PubMed Web of Science ®Google Scholar
• Li L, Sinkko H, Montonen L, et al. Biogeography of symbiotic and other endophytic bacteria isolated from medicinal G lycyrrhiza species in China. FEMS Microbiol Ecol. 2012;79(1):46–68.
   PubMed Web of Science ®Google Scholar
• Kandel SL, Joubert PM, Doty SL. Bacterial endophyte colonization and distribution within plants. Microorganisms. 2017;5(4):77.
   PubMed Web of Science ®Google Scholar
• van Dam NM, Bouwmeester HJ. Metabolomics in the rhizosphere: tapping into belowground chemical communication. Trends Plant Sci. 2016;21(3):256–265.
   PubMed Web of Science ®Google Scholar
• Bulgarelli D, Schlaeppi K, Spaepen S, et al. Structure and functions of the bacterial microbiota of plants. Ann Rev Plant Biol. 2013;64:807–838.
   PubMed Web of Science ®Google Scholar
• Chagas FO, de Cassia Pessotti R, Caraballo-Rodriguez AM, et al. Chemical signaling involved in plant–microbe interactions. Chem Soc Rev. 2018;47(5):1652–1704.
   PubMed Web of Science ®Google Scholar
• Liu H, Carvalhais LC, Crawford M, et al. Inner plant values: diversity, colonization and benefits from endophytic bacteria. Front Microbiol. 2017;8:2552.
   PubMed Web of Science ®Google Scholar
• Pathak P, Rai VK, Can H, et al. Plant-endophyte interaction during biotic stress management. Plants. 2022;11(17):2203.
   Google Scholar
• Yu K, Liu Y, Tichelaar R, et al. Rhizosphere-associated Pseudomonas suppress local root immune responses by gluconic acid-mediated lowering of environmental pH. Curr Biol. 2019;29(22):3913.e4–3920.e4.
   Web of Science ®Google Scholar
• Liu Z, Beskrovnaya P, Melnyk RA, et al. A genome-wide screen identifies genes in rhizosphere-associated Pseudomonas required to evade plant defenses. MBio. 2018;9(6):e00433–e00518.
   Web of Science ®Google Scholar
• Zhou F, Emonet A, Tendon VD, et al. Co-incidence of damage and microbial patterns controls localized immune responses in roots. Cell. 2020;180(3):440.e18–453.e18.
   Web of Science ®Google Scholar
• Lundberg DS, Lebeis SL, Paredes SH, et al. Defining the core Arabidopsis thaliana root microbiome. Nature. 2012;488(7409):86–90.
   PubMed Web of Science ®Google Scholar
• Jones P, Garcia B, Furches A, et al. Plant host-associated mechanisms for microbial selection. Front Plant Sci. 2019;10:862.
   PubMed Web of Science ®Google Scholar
• Russo A, Pollastri S, Ruocco M, et al. Volatile organic compounds in the interaction between plants and beneficial microorganisms. J Plant Interact. 2022;17(1):840–852.
   Web of Science ®Google Scholar
• Zhang YZ, Wang ET, Li M, et al. Effects of rhizobial inoculation, cropping systems and growth stages on endophytic bacterial community of soybean roots. Plant Soil. 2011;347(1):147–161.
   Web of Science ®Google Scholar
• White JF, Kingsley KL, Zhang Q, et al. Endophytic microbes and their potential applications in crop management. Pest Manag Sci. 2019;75(10):2558–2565.
   PubMed Web of Science ®Google Scholar
• Beltran-Garcia MJ, White JF Jr, Prado FM, et al. Nitrogen acquisition in Agave tequilana from degradation of endophytic bacteria. Sci Rep. 2014;4:6938.
   PubMed Web of Science ®Google Scholar
• Verma SK, Kingsley K, Irizarry I, et al. Seed‐vectored endophytic bacteria modulate development of rice seedlings. J Appl Microbiol. 2017;122(6):1680–1691.
   PubMed Web of Science ®Google Scholar
• Verma SK, Kingsley KL, Bergen M, et al. Fungal disease protection in rice (Oryza sativa) seedlings by growth promoting seed-associated endophytic bacteria from invasive Phragmites australis. Microorganisms. 2018;6:21.
   PubMed Web of Science ®Google Scholar
• Irizarry I, White J. Application of bacteria from non‐cultivated plants to promote growth, alter root architecture and alleviate salt stress of cotton. J Appl Microbiol. 2017;122(4):1110–1120.
   PubMed Web of Science ®Google Scholar
• Soares MA, Li H-Y, Bergen M, et al. Functional role of an endophytic Bacillus amyloliquefaciens in enhancing growth and disease protection of invasive English ivy (Hedera helix L.). Plant Soil. 2016;405(1-2):107–123.
   Web of Science ®Google Scholar
• Pitzschke A. Developmental peculiarities and seed-borne endophytes in quinoa: omnipresent, robust bacilli contribute to plant fitness. Front Microbiol. 2016;7(2):1–15.
   PubMedGoogle Scholar
• Cope‐Selby N, Cookson A, Squance M, et al. Endophytic bacteria in miscanthus seed: implications for germination, vertical inheritance of endophytes, plant evolution and breeding. GCB Bioenergy. 2017;9(1):57–77.
   Google Scholar
• Verma SK, Kharwar RN, White JF. The role of seed-vectored endophytes in seedling development and establishment. Symbiosis. 2019;78(2):107–113.
   Web of Science ®Google Scholar
• Verma SK, Kingsley K, Bergen M, et al. Bacterial endophytes from rice cut grass (Leersia oryzoides L.) increase growth, promote root gravitropic response, stimulate root hair formation, and protect rice seedlings from disease. Plant Soil. 2018;422(1-2):223–238.
   Web of Science ®Google Scholar
• Glick BR. Plant growth-promoting bacteria: mechanisms and applications. Scientifica. 2012;2012:1–15.
   Google Scholar
• Mitter B, Petric A, SG Chain P, et al. Genome analysis, ecology, and plant growth promotion of the endophyte Burkholderia phytofirmans strain PsJN. Mol Microbial Ecol Rhizosphere. 2013;1:865–874.
   Google Scholar
• Coutinho BG, Licastro D, Mendonça-Previato L, et al. Plant-influenced gene expression in the rice endophyte Burkholderia kururiensis M130. Mol Plant Microbe Interact. 2015;28(1):10–21.
   PubMed Web of Science ®Google Scholar
• Puri A, Padda KP, Chanway CP. Nitrogen-fixation by endophytic bacteria in agricultural crops: recent advances. In: Amanullah, Fahad S, editors. Nitrogen in agriculture – updates. London: IntechOpen; 2018. p. 73–94.
   Google Scholar
• Hassan SE-D. Plant growth-promoting activities for bacterial and fungal endophytes isolated from medicinal plant of Teucrium polium L. J Adv Res. 2017;8(6):687–695.
   PubMed Web of Science ®Google Scholar
• Lebeis SL, Paredes SH, Lundberg DS, et al. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science. 2015;349(6250):860–864.
   PubMed Web of Science ®Google Scholar
• Faria PSA, de Oliveira Marques V, Selari PJRG, et al. Multifunctional potential of endophytic bacteria from Anacardium othonianum Rizzini in promoting in vitro and ex vitro plant growth. Microbiol Res. 2020;242:126600.
   PubMedGoogle Scholar
• ALKahtani MD, Fouda A, Attia KA, et al. Isolation and characterization of plant growth promoting endophytic bacteria from desert plants and their application as bioinoculants for sustainable agriculture. Agronomy. 2020;10(9):1325.
   Google Scholar
• Naveed M, Mitter B, Reichenauer TG, et al. Increased drought stress resilience of maize through endophytic colonization by Burkholderia phytofirmans PsJN and Enterobacter sp. FD17. Environ Exp Bot. 2014;97:30–39.
   Web of Science ®Google Scholar
• Vaishnav A, Shukla AK, Sharma A, et al. Endophytic bacteria in plant salt stress tolerance: current and future prospects. J Plant Growth Regulat. 2019;38(2):650–668.
   Web of Science ®Google Scholar
• Etesami H, Noori F, Ebadi A, et al. Alleviation of stress-induced ethylene-mediated negative impact on crop plants by bacterial ACC deaminase: perspectives and applications in stressed agriculture management. Plant Microbiomes Sustain Agric. 2020;25:287–315.
   Google Scholar
• Lata R, Chowdhury S, Gond SK, et al. Induction of abiotic stress tolerance in plants by endophytic microbes. Lett Appl Microbiol. 2018;66(4):268–276.
   PubMed Web of Science ®Google Scholar
• Afridi MS, Mahmood T, Salam A, et al. Induction of tolerance to salinity in wheat genotypes by plant growth promoting endophytes: involvement of ACC deaminase and antioxidant enzymes. Plant Physiol Biochem. 2019;139:569–577.
   PubMed Web of Science ®Google Scholar
• Nascimento FX, Rossi MJ, Glick BR. Ethylene and 1-aminocyclopropane-1-carboxylate (ACC) in plant–bacterial interactions. Front Plant Sci. 2018;9:114.
   PubMed Web of Science ®Google Scholar
• Su F, Jacquard C, Villaume S, et al. Burkholderia phytofirmans PsJN reduces impact of freezing temperatures on photosynthesis in Arabidopsis thaliana. Front Plant Sci. 2015;6:810.
   PubMed Web of Science ®Google Scholar
• Vargas L, Santa Brigida AB, Mota Filho JP, et al. Drought tolerance conferred to sugarcane by association with Gluconacetobacter diazotrophicus: a transcriptomic view of hormone pathways. PLoS One. 2014;9(12):e114744.
   PubMed Web of Science ®Google Scholar
• Jha Y, Subramanian R, Patel S. Combination of endophytic and rhizospheric plant growth promoting rhizobacteria in Oryza sativa shows higher accumulation of osmoprotectant against saline stress. Acta Physiol Plant. 2011;33(3):797–802.
   Web of Science ®Google Scholar
• Fernandez O, Theocharis A, Bordiec S, et al. Burkholderia phytofirmans PsJN acclimates grapevine to cold by modulating carbohydrate metabolism. Mol Plant Microbe Interact. 2012;25(4):496–504.
   PubMed Web of Science ®Google Scholar
• Babu AG, Shea PJ, Sudhakar D, et al. Potential use of Pseudomonas koreensis AGB-1 in association with Miscanthus sinensis to remediate heavy metal (loid)-contaminated mining site soil. J Environ Manag. 2015;151:160–166.
   PubMed Web of Science ®Google Scholar
• Mukherjee G, Saha C, Naskar N, et al. An endophytic bacterial consortium modulates multiple strategies to improve arsenic phytoremediation efficacy in Solanum nigrum. Sci Rep. 2018;8(1):1–16.
   PubMed Web of Science ®Google Scholar
• Asaf S, Numan M, Khan AL, et al. Sphingomonas: from diversity and genomics to functional role in environmental remediation and plant growth. Crit Rev Biotechnol. 2020;40(2):138–152.
   PubMed Web of Science ®Google Scholar
• Raymaekers K, Ponet L, Holtappels D, et al. Screening for novel biocontrol agents applicable in plant disease management–a review. Biol Control. 2020;114:104240.
   Google Scholar
• Omomowo OI, Babalola OO. Bacterial and fungal endophytes: tiny giants with immense beneficial potential for plant growth and sustainable agricultural productivity. Microorganisms. 2019;7(11):481.
   PubMed Web of Science ®Google Scholar
• Ahmed A, Munir S, He P, et al. Biocontrol arsenals of bacterial endophyte: an imminent triumph against clubroot disease. Microbiol Res. 2020;241:126565.
   PubMedGoogle Scholar
• Constantin ME, de Lamo FJ, Vlieger BV, et al. Endophyte-mediated resistance in tomato to Fusarium oxysporum is independent of ET, JA, and SA. Front Plant Sci. 2019;10:979.
   PubMed Web of Science ®Google Scholar
• Griffin MR. Biocontrol and bioremediation: two areas of endophytic research which hold great promise. In: Advances in endophytic research. New Delhi: Springer; 2014. p. 257–282.
   Google Scholar
• Latz MA, Jensen B, Collinge DB, et al. Endophytic fungi as biocontrol agents: elucidating mechanisms in disease suppression. Plant Ecol Divers. 2018;11(5-6):555–567.
   Web of Science ®Google Scholar
• Pohjanen J, Koskimäki JJ, Pirttilä AM. Interactions of meristem-associated endophytic bacteria. In: Advances in endophytic research. New Delhi: Springer; 2014. p. 103–113.
   Google Scholar
• Kramer J, Özkaya Ö, Kümmerli R. Bacterial siderophores in community and host interactions. Nature Rev Microbiol. 2019;18:1–12.
   Web of Science ®Google Scholar
• Martinuz A, Schouten A, Sikora R. Systemically induced resistance and microbial competitive exclusion: implications on biological control. Phytopathology. 2012;102(3):260–266.
   PubMed Web of Science ®Google Scholar
• Fadiji AE, Babalola OO. Elucidating mechanisms of endophytes used in plant protection and other bioactivities with multifunctional prospects. Front Bioeng Biotechnol. 2020;8:467.
   PubMed Web of Science ®Google Scholar
• Palmieri D, Vitale S, Lima G, et al. A bacterial endophyte exploits chemotropism of a fungal pathogen for plant colonization. Nature Commun. 2020;11(1):1–11.
   PubMed Web of Science ®Google Scholar
• Law JW-F, Ser H-L, Khan TM, et al. The potential of Streptomyces as biocontrol agents against the rice blast fungus, Magnaporthe oryzae (Pyricularia oryzae). Front Microbiol. 2017;8:3.
   PubMed Web of Science ®Google Scholar
• Swarnalakshmi K, Senthilkumar M, Ramakrishnan B. Endophytic actinobacteria: nitrogen fixation, phytohormone production, and antibiosis. In: Plant growth promoting actinobacteria. Singapore: Springer; 2016. p. 123–145.
   Google Scholar
• González V, Armijos E, Garcés-Claver A. Fungal endophytes as biocontrol agents against the main soil-borne diseases of melon and watermelon in Spain. Agronomy. 2020;10(6):820.
   Google Scholar
• Rajani P, Rajasekaran C, Vasanthakumari M, et al. Inhibition of plant pathogenic fungi by endophytic Trichoderma spp. through mycoparasitism and volatile organic compounds. Microbiol Res. 2020;242:126595.
   PubMedGoogle Scholar
• Inayati A, Sulistyowati L, Aini LQ, et al. Mycoparasitic activity of indigenous Trichoderma virens strains against mungbean soil borne pathogen Rhizoctonia solani: hyperparasite and hydrolytic enzyme production. AGRIVITA J Agric Sci. 2020;42(2):229–242.
   Google Scholar
• Rai S, Solanki MK. Beneficial endophytic Trichoderma functions in plant health management. In: Microbial endophytes and plant growth. USA: Academic Press; 2023. p. 233–244.
   Google Scholar
• Sheoran N, Nadakkakath AV, Munjal V, et al. Genetic analysis of plant endophytic Pseudomonas putida BP25 and chemo-profiling of its antimicrobial volatile organic compounds. Microbiol Res. 2015;173:66–78.
   PubMed Web of Science ®Google Scholar
• Raaijmakers JM, De Bruijn I, Nybroe O, et al. Natural functions of lipopeptides from Bacillus and Pseudomonas: more than surfactants and antibiotics. FEMS Microbiol Rev. 2010;34(6):1037–1062.
   PubMed Web of Science ®Google Scholar
• Brader G, Compant S, Mitter B, et al. Metabolic potential of endophytic bacteria. Curr Opin Biotechnol. 2014;27:30–37.
   PubMed Web of Science ®Google Scholar
• Li X-Y, Mao Z-C, Wang Y-H, et al. Diversity and active mechanism of fengycin-type cyclopeptides from Bacillus subtilis XF-1 against Plasmodiophora brassicae. J Microbiol Biotechnol. 2013;23(3):313–321.
   PubMed Web of Science ®Google Scholar
• He P, Cui W, Munir S, et al. Plasmodiophora brassicae root hair interaction and control by Bacillus subtilis XF-1 in Chinese cabbage. Biol Control. 2019;128:56–63.
   Web of Science ®Google Scholar
• Santoyo G, Sánchez-Yáñez JM, de los Santos-Villalobos S. Methods for detecting biocontrol and plant growth-promoting traits in rhizobacteria. In: Methods in rhizosphere biology research. Singapore: Springer; 2019. p. 133–149.
   Google Scholar
• Villarreal-Delgado MF, Villa-Rodríguez ED, Cira-Chávez LA, et al. The genus Bacillus as a biological control agent and its implications in the agricultural biosecurity. Mex J Phytopathol. 2018;36:95–130.
   Google Scholar
• Mehnaz S. Rhizotrophs: plant growth promotion to bioremediation. Vol. 2. Singapore: Springer; 2017.
   Google Scholar
• Khan AR, Mustafa A, Hyder S, et al. Bacillus spp. as bioagents: uses and application for sustainable agriculture. Biology. 2022;11(12):1763.
   PubMedGoogle Scholar
• Ngo VA, Wang S-L, Nguyen VB, et al. Phytophthora antagonism of endophytic bacteria isolated from roots of black pepper (Piper nigrum L.). Agronomy. 2020;10(2):286.
   Google Scholar
• Netzker T, Shepherdson EM, Zambri MP, et al. Bacterial volatile compounds: functions in communication, cooperation, and competition. Annu Rev Microbiol. 2020;74:409–430.
   PubMed Web of Science ®Google Scholar
• Agisha VN, Kumar A, Eapen SJ, et al. Broad-spectrum antimicrobial activity of volatile organic compounds from endophytic Pseudomonas putida BP25 against diverse plant pathogens. Biocontrol Sci Technol. 2019;29(11):1069–1089.
   Web of Science ®Google Scholar
• Etminani F, Harighi B, Mozafari AA. Effect of volatile compounds produced by endophytic bacteria on virulence traits of grapevine crown gall pathogen, Agrobacterium tumefaciens. Sci Rep. 2022;12(1):1–13.
   PubMed Web of Science ®Google Scholar
• Pieterse CM, Zamioudis C, Berendsen RL, et al. Induced systemic resistance by beneficial microbes. Annu Rev Phytopathol. 2014;52:347–375.
   PubMed Web of Science ®Google Scholar
• Abdul Malik NA, Kumar IS, Nadarajah K. Elicitor and receptor molecules: orchestrators of plant defense and immunity. Int J Mol Sci. 2020;21(3):963.
   PubMed Web of Science ®Google Scholar
• Fouda A, Hassan SED, Eid AM, et al. The interaction between plants and bacterial endophytes under salinity stress. In: Endophytes and Secondary Metabolites. Cham: Springer; 2019. p. 591–607.
   Google Scholar
• Tyagi S, Mulla SI, Lee K-J, et al. VOCs-mediated hormonal signaling and crosstalk with plant growth promoting microbes. Crit Rev Biotechnol. 2018;38(8):1277–1296.
   PubMed Web of Science ®Google Scholar
• Asghari S, Harighi B, Ashengroph M, et al. Induction of systemic resistance to Agrobacterium tumefaciens by endophytic bacteria in grapevine. Plant Pathol. 2020;69(5):827–837.
   Web of Science ®Google Scholar
• Dhanya S, Varghese S, Divya K, et al. Pseudomonas taiwanensis (MTCC11631) mediated induction of systemic resistance in Anthurium andreanum L against blight disease and visualisation of defence related secondary metabolites using confocal laser scanning microscopy. Biocatal Agric Biotechnol. 2020;24:101561.
   Web of Science ®Google Scholar
• Jiao R, Munir S, He P, et al. Biocontrol potential of the endophytic Bacillus amyloliquefaciens YN201732 against tobacco powdery mildew and its growth promotion. Biological Control. 2019;143:104160.
   Web of Science ®Google Scholar
• Liu H, Li J, Carvalhais LC, et al. Evidence for the plant recruitment of beneficial microbes to suppress soil‐borne pathogens. New Phytologist. 2021;229(5):2873–2885.
   PubMed Web of Science ®Google Scholar
• Safara S, Harighi B, Bahramnejad B, et al. Antibacterial activity of endophytic bacteria against sugar beet root rot agent by volatile organic compound production and induction of systemic resistance. Front Microbiol. 2022;13:1–14.
   Web of Science ®Google Scholar
• Nambirajan G, Ashok G, Baskaran K, et al. Bacillus and endomicrobiome: biodiversity and potential applications in agriculture. In: Advances in plant microbiome and sustainable agriculture. Singapore: Springer; 2020. p. 189–205.
   Google Scholar
• Kumar RV, Singh RP, Mishra P. Endophytes as emphatic communication barriers of quorum sensing in Gram-positive and Gram-negative bacteria—a review. Environ Sustain. 2019;2:455–468.
   Google Scholar
• Helman Y, Chernin L. Silencing the mob: disrupting quorum sensing as a means to fight plant disease. Mol Plant Pathol. 2015;16(3):316–329.
   PubMed Web of Science ®Google Scholar
• Akbari Kiarood SL, Rahnama K, Golmohammadi M, et al. Quorum‐quenching endophytic bacteria inhibit disease caused by Pseudomonas syringae pv. syringae in citrus cultivars. J Basic Microbiol. 2020;60(9):746–757.
   PubMed Web of Science ®Google Scholar
• Berde CV, Salvi SP, Rawool PP, et al. Role of medicinal plants and endophytic bacteria of medicinal plants in inhibition of biofilm formation: interference in quorum sensing. In: Implication of quorum sensing and biofilm formation in medicine, agriculture and food industry. Singapore: Springer; 2019. p. 177–188.
   Google Scholar
• Miljaković D, Marinković J, Balešević-Tubić S. The significance of Bacillus spp. in disease suppression and growth promotion of field and vegeTable crops. Microorganisms. 2020;8(7):1037.
   PubMed Web of Science ®Google Scholar
• De Silva NI, Brooks S, Lumyong S, et al. Use of endophytes as biocontrol agents. Fungal Biol Rev. 2019;33(2):133–148.
   Web of Science ®Google Scholar
• Bhattacharyya P, Goswami M, Bhattacharyya L. Perspective of beneficial microbes in agriculture under changing climatic scenario: a review. J Phytol. 2016;8:26–41.
   Google Scholar
• Prashar P, Kapoor N, Sachdeva S. Rhizosphere: its structure, bacterial diversity and significance. Rev Environ Sci Bio/Technol. 2014;13(1):63–77.
   Web of Science ®Google Scholar
• Wu L, Wu H-J, Qiao J, et al. Novel routes for improving biocontrol activity of Bacillus based bioinoculants. Front Microbiol. 2015;6:1395.
   PubMed Web of Science ®Google Scholar
• Lastochkina O, Seifikalhor M, Aliniaeifard S, et al. Bacillus spp.: efficient biotic strategy to control postharvest diseases of fruits and vegetables. Plants. 2019;8(4):97.
   Google Scholar
• Pandey PK, Singh MC, Singh S, et al. Inside the plants: endophytic bacteria and their functional attributes for plant growth promotion. Int J Curr Microbiol Appl Sci. 2017;6:11–21.
   Google Scholar
• Souza Rd, Ambrosini A, Passaglia LM. Plant growth-promoting bacteria as inoculants in agricultural soils. Genet Mol Biol. 2015;38(4):401–419.
   PubMed Web of Science ®Google Scholar
• Frank AC, Saldierna Guzmán JP, Shay JE. Transmission of bacterial endophytes. Microorganisms. 2017;5(4):70.
   PubMed Web of Science ®Google Scholar
• Vinodkumar S, Nakkeeran S, Renukadevi P, et al. Diversity and antiviral potential of rhizospheric and endophytic Bacillus species and phyto-antiviral principles against tobacco streak virus in cotton. Agric Ecosyst Environ. 2018;267:42–51.
   Web of Science ®Google Scholar
• Yang F, Zhang R, Wu X, et al. An endophytic strain of the genus Bacillus isolated from the seeds of maize (Zea mays L.) has antagonistic activity against maize pathogenic strains. Microbial Pathog. 2020;142:104074.
   PubMed Web of Science ®Google Scholar
• Jing R, Li N, Wang W, et al. An endophytic strain JK of genus bacillus isolated from the seeds of super hybrid rice (Oryza sativa L., Shenliangyou 5814) has antagonistic activity against rice blast pathogen. Microbial Pathog. 2020;147:104422.
   PubMed Web of Science ®Google Scholar
• Cui L, Yang C, Wei L, et al. Isolation and identification of an endophytic bacteria Bacillus velezensis 8-4 exhibiting biocontrol activity against potato scab. Biol Control. 2020;141:104156.
   Web of Science ®Google Scholar
• Zhang P, Zhu Y, Ma D, et al. Screening, identification, and optimization of fermentation conditions of an antagonistic endophyte to wheat head blight. Agronomy. 2019;9(9):476.
   Google Scholar
• Abdallah RAB, Jabnoun-Khiareddine H, Nefzi A, et al. Evaluation of the growth-promoting potential of endophytic bacteria recovered from healthy tomato plants. J Hortic For. 2018;5(2):1–10.
   Google Scholar
• Denner W. The legislative aspects of the industrial enzymes in the manufacture of food and food ingredients. Ind Enzymol. 1996:397–411.
   Google Scholar
• Aloo BN, Makumba B, Mbega ER. The potential of Bacilli rhizobacteria for sustainable crop production and environmental sustainability. Microbiol Res. 2019;219:26–39.
   PubMed Web of Science ®Google Scholar
• Caulier S, Nannan C, Gillis A, et al. Overview of the antimicrobial compounds produced by members of the Bacillus subtilis group. Front Microbiol. 2019;10:302.
   PubMed Web of Science ®Google Scholar
• Shivaji S, Chaturvedi P, Suresh K, et al. Bacillus aerius sp. nov., Bacillus aerophilus sp. nov., Bacillus stratosphericus sp. nov. and Bacillus altitudinis sp. nov., isolated from cryogenic tubes used for collecting air samples from high altitudes. Int J Syst Evol Microbiol. 2006;56(7):1465–1473.
   PubMedGoogle Scholar
• Sumpavapol P, Tongyonk L, Tanasupawat S, et al. Bacillus siamensis sp. nov., isolated from salted crab (poo-khem) in Thailand. Int J Syst Evol Microbiol. 2010;60(10):2364–2370.
   PubMedGoogle Scholar
• Lai Q, Liu Y, Shao Z. Bacillus xiamenensis sp. nov., isolated from intestinal tract contents of a flathead mullet (Mugil cephalus). Antonie van Leeuwenhoek. 2014;105(1):99–107.
   PubMed Web of Science ®Google Scholar
• Dunlap CA, Saunders LP, Schisler DA, et al. Bacillus nakamurai sp. nov., a black-pigment-producing strain. Int J Syst Evol Microbiol. 2016;66(8):2987–2991.
   PubMedGoogle Scholar
• Dunlap CA. Taxonomy of registered Bacillus spp. strains used as plant pathogen antagonists. Biol Control. 2019;134:82–86.
   Web of Science ®Google Scholar
• Fan B, Blom J, Klenk H-P, et al. Bacillus amyloliquefaciens, Bacillus velezensis, and Bacillus siamensis form an “operational group B. amyloliquefaciens” within the B. subtilis species complex. Front Microbiol. 2017;8:22.
   PubMed Web of Science ®Google Scholar
• Fira D, Dimkić I, Berić T, et al. Biological control of plant pathogens by Bacillus species. J Biotechnol. 2018;285:44–55.
   PubMed Web of Science ®Google Scholar
• Kushwaha P, Kashyap PL, Srivastava AK, et al. Plant growth promoting and antifungal activity in endophytic Bacillus strains from pearl millet (Pennisetum glaucum). Br J Microbiol. 2020;51(1):229–241.
   PubMed Web of Science ®Google Scholar
• Kaspar F, Neubauer P, Gimpel M. Bioactive secondary metabolites from Bacillus subtilis: a comprehensive review. J Nat Prod. 2019;82(7):2038–2053.
   PubMed Web of Science ®Google Scholar
• Ding T, Su B, Chen X, et al. An endophytic bacterial strain isolated from Eucommia ulmoides inhibits southern corn leaf blight. Front Microbiol. 2017;8:903.
   PubMed Web of Science ®Google Scholar
• Xie S, Liu J, Gu S, et al. Antifungal activity of volatile compounds produced by endophytic Bacillus subtilis DZSY21 against Curvularia lunata. Ann Microbiol. 2020;70(1):1–10.
   Web of Science ®Google Scholar
• Rabbee MF, Ali M, Choi J, et al. Bacillus velezensis: a valuable member of bioactive molecules within plant microbiomes. Molecules. 2019;24(6):1046.
   PubMed Web of Science ®Google Scholar
• Dhouib H, Zouari I, Abdallah DB, et al. Potential of a novel endophytic Bacillus velezensis in tomato growth promotion and protection against Verticillium wilt disease. Biol Control. 2019;139:104092.
   Web of Science ®Google Scholar
• Lopes R, Tsui S, Gonçalves PJ, et al. A look into a multifunctional toolbox: endophytic Bacillus species provide broad and underexploited benefits for plants. World J Microbiol Biotechnol. 2018;34(7):94.
   PubMed Web of Science ®Google Scholar
• Pršić J, Ongena M. Elicitors of plant immunity triggered by beneficial bacteria. Front Plant Sci. 2020;11:594530.
   PubMed Web of Science ®Google Scholar
• Andrić S, Meyer T, Ongena M. Bacillus responses to plant-associated fungal and bacterial communities. Front Microbiol. 2020;11:1350.
   PubMedGoogle Scholar
• Yamamoto S, Shiraishi S, Suzuki S. Are cyclic lipopeptides produced by Bacillus amyloliquefaciens S13‐3 responsible for the plant defence response in strawberry against Colletotrichum gloeosporioides? Lett Appl Microbiol. 2015;60(4):379–386.
   PubMed Web of Science ®Google Scholar
• Gond SK, Bergen MS, Torres MS, et al. Endophytic Bacillus spp. produce antifungal lipopeptides and induce host defence gene expression in maize. Microbiol Res. 2015;172:79–87.
   PubMed Web of Science ®Google Scholar
• Hasan N, Farzand A, Heng Z, et al. Antagonistic potential of novel endophytic bacillus strains and mediation of plant defense against verticillium wilt in upland cotton. Plants. 2020;9(11):1438.
   Google Scholar
• Köhl J, Kolnaar R, Ravensberg WJ. Mode of action of microbial biological control agents against plant diseases: relevance beyond efficacy. Front Plant Sci. 2019;10:845.
   PubMed Web of Science ®Google Scholar
• Ray P, Lakshmanan V, Labbé JL, et al. Microbe to microbiome: a paradigm shift in the application of microorganisms for sustainable agriculture. Front Microbiol. 2020;11:3323.
   Web of Science ®Google Scholar
• Rajamanickam S, Karthikeyan G, Kavino M, et al. Biohardening of micropropagated banana using endophytic bacteria to induce plant growth promotion and restrain rhizome rot disease caused by Pectobacterium carotovorum subsp. Carotovorum. Sci Hortic. 2018;231:179–187.
   Web of Science ®Google Scholar
• Egamberdieva D, Wirth SJ, Shurigin VV, et al. Endophytic bacteria improve plant growth, symbiotic performance of chickpea (Cicer arietinum L.) and induce suppression of root rot caused by Fusarium solani under salt stress. Front Microbiol. 2017;8:1887.
   PubMed Web of Science ®Google Scholar
• Saha C, Mukherjee G, Agarwal‐Banka P, et al. A consortium of non‐rhizobial endophytic microbes from Typha angustifolia functions as probiotic in rice and improves nitrogen metabolism. Plant Biol. 2016;18(6):938–946.
   PubMed Web of Science ®Google Scholar
• Bradáčová K, Florea AS, Bar-Tal A, et al. Microbial consortia versus single-strain inoculants: an advantage in PGPM-assisted tomato production? Agronomy. 2019;9(2):105.
   Web of Science ®Google Scholar
• Wang Q, Zhou Q, Huang L, et al. Cadmium phytoextraction through Brassica juncea L. under different consortia of plant growth-promoting bacteria from different ecological niches. Ecotoxicol Environ Saf. 2022;237:113541.
   PubMed Web of Science ®Google Scholar
• Rosier A, Beauregard PB, Bais HP. Quorum quenching activity of the PGPR Bacillus subtilis UD1022 alters nodulation efficiency of Sinorhizobium meliloti on Medicago truncatula. Front Microbiol. 2021;11(3476):1–13.
   Google Scholar
• Niu B, Wang W, Yuan Z, et al. Microbial interactions within multiple-strain biological control agents impact soil-borne plant disease. Front Microbiol. 2020;11(2452):1–16.
   PubMedGoogle Scholar
• Qiu Z, Egidi E, Liu H, et al. New frontiers in agriculture productivity: optimised microbial inoculants and in situ microbiome engineering. Biotechnology advances. 2019;37(6):107371.
   PubMed Web of Science ®Google Scholar
• Vannier N, Agler M, Hacquard S. Microbiota-mediated disease resistance in plants. PLoS Pathog. 2019;15(6):e1007740.
   PubMed Web of Science ®Google Scholar
• Sessitsch A, Pfaffenbichler N, Mitter B. Microbiome applications from lab to field: facing complexity. Trends Plant Sci. 2019;24(3):194–198.
   PubMed Web of Science ®Google Scholar
• Xiong C, Zhu YG, Wang JT, et al. Host selection shapes crop microbiome assembly and network complexity. New Phytol. 2021;229(2):1091–1104.
   PubMed Web of Science ®Google Scholar
• Fitzpatrick CR, Salas-González I, Conway JM, et al. The plant microbiome: from ecology to reductionism and beyond. Annu Rev Microbiol. 2020;74:81–100.
   PubMed Web of Science ®Google Scholar
• Cordovez V, Dini-Andreote F, Carrión VJ, et al. Ecology and evolution of plant microbiomes. Annu Rev Microbiol. 2019;73:69–88.
   PubMed Web of Science ®Google Scholar
• Feng H, Zhang N, Du W, et al. Identification of chemotaxis compounds in root exudates and their sensing chemoreceptors in plant-growth-promoting rhizobacteria Bacillus amyloliquefaciens SQR9. Mol Plant Microbe Interact. 2018;31(10):995–1005.
   PubMed Web of Science ®Google Scholar
• Cregger M, Veach A, Yang Z, et al. The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome. Microbiome. 2018;6(1):31.
   PubMedGoogle Scholar
• Yu P, Wang C, Baldauf JA, et al. Root type and soil phosphate determine the taxonomic landscape of colonizing fungi and the transcriptome of field‐grown maize roots. New Phytol. 2018;217(3):1240–1253.
   PubMed Web of Science ®Google Scholar
• Hartman K, van der Heijden MG, Wittwer RA, et al. Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming. Microbiome. 2020;8(1):66.
   PubMed Web of Science ®Google Scholar
• Hiruma K, Gerlach N, Sacristán S, et al. Root endophyte Colletotrichum tofieldiae confers plant fitness benefits that are phosphate status dependent. Cell. 2016;165(2):464–474.
   PubMed Web of Science ®Google Scholar
• Stringlis IA, Yu K, Feussner K, et al. MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health. Proc Natl Acad Sci U S A. 2018;115(22):5213–5222.
   PubMed Web of Science ®Google Scholar
• Ganin H, Kemper N, Meir S, et al. Indole derivatives maintain the status quo between beneficial biofilms and their plant hosts. Mol Plant Microbe Interact. 2019;32(8):1013–1025.
   PubMed Web of Science ®Google Scholar
• Tewari S, Shrivas VL, Hariprasad P, et al. Harnessing endophytes as biocontrol agents. In: Plant health under biotic stress. Singapore: Springer; 2019. p. 189–218.
   Google Scholar
• Munir S, Li Y, He P, et al. Unraveling the metabolite signature of citrus showing defense response towards Candidatus Liberibacter asiaticus after application of endophyte Bacillus subtilis L1-21. Microbiol Res. 2020;234:126425.
   PubMedGoogle Scholar
• Yadav A, Yadav K. Exploring the potential of endophytes in agriculture: a minireview. Adv Plants Agric Res. 2017;6(4):102–106.
   Google Scholar
• Christakis CA, Daskalogiannis G, Chatzakis A, et al. Halophytic bacterial endophytome: a potential source of beneficial microbes for a sustainable agriculture. bioRxiv. 2020;7:1–54.
   Google Scholar
• Sarhan MS, Patz S, Hamza MA, et al. G3 PhyloChip analysis confirms the promise of plant-based culture media for unlocking the composition and diversity of the maize root microbiome and for recovering unculturable candidate divisions/phyla. Microb Environ. 2018;33(3):317–325.
   PubMed Web of Science ®Google Scholar
• Elsawey H, Patz S, Nemr RA, et al. Plant broth-(not bovine-) based culture media provide the most compatible vegan nutrition for in vitro culturing and in situ probing of plant microbiota. Diversity. 2020;12(11):418.
   Google Scholar
• Yousaf S, Bulgari D, Bergna A, et al. Pyrosequencing detects human and animal pathogenic taxa in the grapevine endosphere. Front Microbiol. 2014;5:327.
   PubMed Web of Science ®Google Scholar
• Singh M, Kumar A, Singh R, et al. Endophytic bacteria: a new source of bioactive compounds. 3 Biotech. 2017;7(5):315.
   PubMedGoogle Scholar
• Gadhave KR, Devlin PF, Ebertz A, et al. Soil inoculation with Bacillus spp. modifies root endophytic bacterial diversity, evenness, and community composition in a context-specific manner. Microbial Ecol. 2018;76(3):741–750.
   PubMed Web of Science ®Google Scholar
• Prasannakumar M, Mahesh H, Desai RU, et al. Metagenome sequencing of fingermillet-associated microbial consortia provides insights into structural and functional diversity of endophytes. 3 Biotech. 2020;10(1):15.
   PubMedGoogle Scholar
• Paolinelli M, Escoriaza G, Cesari C, et al. Metatranscriptomic approach for microbiome characterization and host gene expression evaluation for “Hoja de malvón” disease in Vitis vinifera cv. Malbec. 2020.
   Google Scholar
• Liu D, Li K, Hu J, et al. Biocontrol and action mechanism of Bacillus amyloliquefaciens and Bacillus subtilis in soybean phytophthora blight. Int J Mol Sci. 2019;20(12):2908.
   PubMed Web of Science ®Google Scholar
• Asaf S, Khan AL, Khan MA, et al. Complete genome sequencing and analysis of endophytic Sphingomonas sp. LK11 and its potential in plant growth. 3 Biotech. 2018;8(9):389.
   PubMedGoogle Scholar
• Frank AC. The genomes of endophytic bacteria. In: Endophytes of forest trees. Cham: Springer; 2018. p. 141–176.
   Google Scholar
• Dahmani MA, Desrut A, Moumen B, et al. Unearthing the plant growth-promoting traits of Bacillus megaterium RmBm31, an endophytic bacterium isolated from root nodules of Retama monosperma. Front Plant Sci. 2020;11:124.
   PubMed Web of Science ®Google Scholar
• Chen C, Yue Z, Chu C, et al. Complete genome sequence of bacillus sp. strain wr11, an endophyte isolated from wheat root providing genomic insights into its plant growth-promoting effects. Mol Plant Microbe Interact. 2020:876–879.
   PubMed Web of Science ®Google Scholar
• Naik S, Tsang A, Ramanan US, et al. Genome sequence resource of Bacillus velezensis EB14, a native endophytic bacterial strain with biocontrol potential against the poplar stem canker causative pathogen, Sphaerulina musiva. Phytopathology. 2020;111(5):890–892.
   Web of Science ®Google Scholar
• Pérez-Equihua A, Santoyo G. Draft genome sequence of Bacillus sp. strain E25, a biocontrol and plant growth-promoting bacterial endophyte isolated from Mexican Husk Tomato Roots (Physalis ixocarpa Brot. Ex Horm.). Microbiol Resour Announc. 2021;10(1):e01112-20.
   PubMed Web of Science ®Google Scholar
• Chen L, Shi H, Heng J, et al. Antimicrobial, plant growth-promoting and genomic properties of the peanut endophyte Bacillus velezensis LDO2. Microbiol Res. 2019;218:41–48.
   PubMedGoogle Scholar
• Utturkar SM, Cude WN, Robeson MS, et al. Enrichment of root endophytic bacteria from Populus deltoides and single-cell-genomics analysis. Appl Environ Microbiol. 2016;82(18):5698–5708.
   PubMed Web of Science ®Google Scholar
• Murphy BR, Doohan FM, Hodkinson TR. From concept to commerce: developing a successful fungal endophyte inoculant for agricultural crops. J Fungi. 2018;4(1):24.
   Web of Science ®Google Scholar
• Morelli M, Bahar O, Papadopoulou KK, et al. Role of endophytes in plant health and defense against pathogens. Front Plant Sci. 2020;11(2020):1312.
   PubMedGoogle Scholar
• Rao HY, Mohana NC, Satish S. Biocommercial aspects of microbial endophytes for sustainable agriculture. In: Microbial endophytes. UK: Woodhead Publishing; 2020. p. 323–347.
   Google Scholar
• Santos URd, Costa MC, de Freitas GJ, et al. Exposition to biological control agent Trichoderma stromaticum increases the development of cancer in mice injected with murine melanoma. Front Cell Infect Microbiol. 2020;10:252.
   PubMed Web of Science ®Google Scholar
• Whitaker BK, Bakker MG. Bacterial endophyte antagonism toward a fungal pathogen in vitro does not predict protection in live plant tissue. FEMS Microbiol Ecol. 2019;95(2):fiy237.
   Web of Science ®Google Scholar