{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T12:04:27Z","timestamp":1791547467699,"version":"4.3.4"},"reference-count":61,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,1,1]],"date-time":"2025-01-01T00:00:00Z","timestamp":1735689600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001503","name":"Indian Council of Agricultural Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001503","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Aim<\/jats:title>\n                  <jats:p>Bacillus subtilis is usually found in soil, and their biocontrol and plant growth-promoting capabilities are being explored more recently than ever. However, knowledge about metabolite production and genome composition of endophytic B. subtilis from seeds is limited. In the present study, B. subtilis EVCu15 strain isolated from the seeds of Vasconcellea cundinamarcensis (mountain papaya) was subjected to whole genome sequencing and detailed molecular and functional characterization.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods and results<\/jats:title>\n                  <jats:p>Whole genome sequencing and sequence analysis of the endophytic bacterium from mountain papaya seed revealed that the bacterium was B. subtilis, strain EVCu15. The genomic sequence had more than 98% nucleotide similarity with two published whole genome sequences of B. subtilis strains. Some of the important secondary metabolite gene clusters involved in production of bioactive compounds such as surfactin, fengycin, plipastatin, bacillibactin, bacillaene, subtilomycin, subtilosin A, and bacilysin were identified from the whole genome sequence analysis. Genes encoding several plant growth-promoting metabolites, mostly involved in the nutrient metabolism, were identified in the bacterial genome. These included factors coding for nitrogen, phosphorus, iron, sulfur, potassium, and trehalose metabolism. Genes involved in auxin, riboflavin, acetoin biosynthesis, ACC deaminase activity, and xylan degradation were also identified. Proteomic analysis confirmed the biosynthesis and release of several bioactive secondary metabolites in the endophytic B. subtilis strain EVCu15. Liquid chromatography-mass spectrometry-based profiling for hormones and vitamins identified extracellular secretion of several important plant growth-promoting compounds such as IAA, salicylic acid, zeatin, vitamin D1, D2, E, K1, and pyridoxine. The in vitro and in vivo studies with the endophytic B. subtilis against various plant pathogenic fungi showed moderate to high levels of resistance. The B. subtilis EVCu15 compared to B. amyloliquefaciens showed better control over the root-knot nematode Meloidogyne incognita, in terms of egg hatching inhibition and the mortality of J2 juveniles.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusion<\/jats:title>\n                  <jats:p>Overall, this study underscores the biocontrol and plant growth-promoting potential of B. subtilis EVCu15, an endophyte isolated from mountain papaya seeds. Genomic analysis revealed a significant proportion of genes linked to biocontrol and plant growth promotion, corroborating its efficacy against M. incognita and various plant pathogens in vitro and in greenhouse studies. Furthermore, the bacterium\u2019s ability to produce diverse bioactive compounds, including proteins, hormones, and vitamins, was confirmed, highlighting its complex interactions within the plant system.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/jambio\/lxaf010","type":"journal-article","created":{"date-parts":[[2025,1,8]],"date-time":"2025-01-08T02:20:57Z","timestamp":1736302857000},"source":"Crossref","is-referenced-by-count":9,"title":["Molecular characterization of an endophytic strain of <i>Bacillus subtilis<\/i> with plant growth-promoting properties from a wild relative of papaya"],"prefix":"10.1093","volume":"136","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6023-5894","authenticated-orcid":false,"given":"Basavaprabhu L","family":"Patil","sequence":"first","affiliation":[{"name":"ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake Post , Bengaluru 560089 , Karnataka,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amulya M","family":"Gopalkrishna","sequence":"additional","affiliation":[{"name":"ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake Post , Bengaluru 560089 , Karnataka,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandeep Kumar","family":"G M","sequence":"additional","affiliation":[{"name":"ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake Post , Bengaluru 560089 , Karnataka,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Umamaheswari","family":"R","sequence":"additional","affiliation":[{"name":"ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake Post , Bengaluru 560089 , Karnataka,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,1,7]]},"reference":[{"key":"2025013014344641700_bib1","doi-asserted-by":"crossref","first-page":"9","DOI":"10.3923\/ppj.2009.9.16","article-title":"Effect of combined use of Bacillus subtilis CA32 and Trichoderma harzianum RU01 on biological control of Rhizoctonia solani on Solanum melongena and Capsicum annuum","volume":"8","author":"Abeysinghe","year":"2009","journal-title":"Plant Pathology J"},{"key":"2025013014344641700_bib2","first-page":"36","article-title":"Antagonistic activity of endophytic bacteria isolated from Mentha rotundifolia L","volume":"4","author":"Abla","year":"2015","journal-title":"Int J Sci Res"},{"key":"2025013014344641700_bib3","doi-asserted-by":"publisher","first-page":"1776","DOI":"10.3390\/plants10091776","article-title":"Genomic analysis of endophytic Bacillus cereus T4S and its plant growth-promoting traits","volume":"10","author":"Adeleke","year":"2021","journal-title":"Plants"},{"key":"2025013014344641700_bib4","doi-asserted-by":"publisher","first-page":"1159","DOI":"10.1007\/s42161-019-00304-8","article-title":"Evaluation of tomato genotypes for early blight disease resistance caused by Alternaria solani in Pakistan","volume":"101","author":"Akhtar","year":"2019","journal-title":"J Plant Pathol"},{"key":"2025013014344641700_bib5","doi-asserted-by":"publisher","first-page":"566","DOI":"10.1038\/nbt.4163","article-title":"KBase: the United States department of energy systems biology knowledgebase","volume":"36","author":"Arkin","year":"2018","journal-title":"Nat Biotechnol"},{"key":"2025013014344641700_bib6","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s13205-018-1403-z","article-title":"Complete genome sequencing and analysis of endophytic Sphingomonas sp. 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