{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T05:04:23Z","timestamp":1783919063170,"version":"3.55.0"},"reference-count":102,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T00:00:00Z","timestamp":1783468800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Origanum L. (Lamiaceae) is a commercially important medicinal and aromatic plant genus worldwide. Endophytic bacterial communities are recognized for promoting plant growth and physiology, although their interactions with host metabolism remain insufficiently understood. In this work, an in vitro model of axenic Origanum heracleoticum plants was established to investigate the relationship between endophytic bacteria and their tissue of origin. Specifically, we evaluated the adaptation of two strains, Bacillus sp. OHL2 and Pseudomonas sp. OHS18, and the potential role of Bacillus sp. OHL2 in modulating plant physiology and secondary metabolism. Bacterial inoculation and re-isolation highlighted niche-specific adaptation and possible co-evolution within the host, suggesting an active role of the plant in regulating bacterial colonization within the endosphere. Inoculation with Bacillus sp. OHL2 significantly enhanced photosynthetic rate, leaf area, dry weight, and chlorophyll content. No substantial overall changes in secondary metabolism were detected. Rosmarinic acid was the predominant phenolic, while monoterpenes dominated, with carvacrol dominant. A significant tissue-by-inoculation interaction was observed for \u03b1-humulene, which decreased in leaves of inoculated plants. Overall, the in vitro system provides a valuable platform to study plant\u2013endophyte interactions and bacterial mechanisms underlying the stimulation of plant growth and metabolic responses.<\/jats:p>","DOI":"10.3390\/microorganisms14071497","type":"journal-article","created":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T15:40:09Z","timestamp":1783525209000},"page":"1497","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Plant\u2013Endophyte Cross-Talk in Origanum heracleoticum L. In Vitro Axenic Culture: Endosphere-Driven Bacterial Interactions and Plant Metabolic Responses"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6210-8197","authenticated-orcid":false,"given":"Giulia","family":"Semenzato","sequence":"first","affiliation":[{"name":"Institute for Sustainable Plant Protection, National Research Council of Italy, 50019 Sesto Fiorentino, Florence, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6615-6014","authenticated-orcid":false,"given":"Sara","family":"Barberini","sequence":"additional","affiliation":[{"name":"Institute for Sustainable Plant Protection, National Research Council of Italy, 50019 Sesto Fiorentino, Florence, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Felicia","family":"Menicucci","sequence":"additional","affiliation":[{"name":"Institute for Sustainable Plant Protection, National Research Council of Italy, 50019 Sesto Fiorentino, Florence, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2140-718X","authenticated-orcid":false,"given":"Giulia","family":"Atzori","sequence":"additional","affiliation":[{"name":"Institute for Sustainable Plant Protection, National Research Council of Italy, 50019 Sesto Fiorentino, Florence, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8531-6076","authenticated-orcid":false,"given":"Cecilia","family":"Brunetti","sequence":"additional","affiliation":[{"name":"Institute for Sustainable Plant Protection, National Research Council of Italy, 50019 Sesto Fiorentino, Florence, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giovanni","family":"Marino","sequence":"additional","affiliation":[{"name":"Institute for Sustainable Plant Protection, National Research Council of Italy, 50019 Sesto Fiorentino, Florence, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valeria","family":"Palchetti","sequence":"additional","affiliation":[{"name":"Institute for Sustainable Plant Protection, National Research Council of Italy, 50019 Sesto Fiorentino, Florence, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9114-2335","authenticated-orcid":false,"given":"Renato","family":"Fani","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Florence, 50019 Sesto Fiorentino, Florence, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3739-1397","authenticated-orcid":false,"given":"Mauro","family":"Centritto","sequence":"additional","affiliation":[{"name":"Institute for Sustainable Plant Protection, National Research Council of Italy, 50019 Sesto Fiorentino, Florence, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1264-8002","authenticated-orcid":false,"given":"Giovanni","family":"Emiliani","sequence":"additional","affiliation":[{"name":"Institute for Sustainable Plant Protection, National Research Council of Italy, 50019 Sesto Fiorentino, Florence, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,8]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Nurzy\u0144ska-Wierdak, R., and Walasek-Janusz, M. (2025). Chemical Composition, Biological Activity, and Potential Uses of Oregano (Origanum vulgare L.) and Oregano Essential Oil. Pharmaceuticals, 18.","DOI":"10.3390\/ph18020267"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Pontes-Quero, G.M., Esteban-Rubio, S., P\u00e9rez Cano, J., Aguilar, M.R., and V\u00e1zquez-Lasa, B. (2021). Oregano Essential Oil Micro- and Nanoencapsulation With Bioactive Properties for Biotechnological and Biomedical Applications. Front. Bioeng. Biotechnol., 9.","DOI":"10.3389\/fbioe.2021.703684"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1016\/j.indcrop.2011.06.029","article-title":"Emerging Cultivation of Oregano in Sicily: Sensory Evaluation of Plants and Chemical Composition of Essential Oils","volume":"35","author":"Bonfanti","year":"2012","journal-title":"Ind. Crops Prod."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Napoli, E., Giovino, A., Carrubba, A., Siong, V.H.Y., Rinoldo, C., Nina, O., and Ruberto, G. (2020). Variations of Essential Oil Constituents in Oregano (Origanum vulgare subsp. viridulum (= O. heracleoticum) over Cultivation Cycles. Plants, 9.","DOI":"10.3390\/plants9091174"},{"key":"ref_5","first-page":"50","article-title":"Comparative Investigation about the Trichome Morphology of Common Oregano (Origanum vulgare L. subsp. vulgare) and Greek Oregano (Origanum vulgare L. subsp. hirtum)","volume":"1","author":"Hardt","year":"2014","journal-title":"J. Appl. Res. Med. Aromat. Plants"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1128\/MMBR.00050-14","article-title":"The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes","volume":"79","author":"Hardoim","year":"2015","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"4532","DOI":"10.1111\/1462-2920.15197","article-title":"More than Words: The Chemistry behind the Interactions in the Plant Holobiont","volume":"22","author":"Romero","year":"2020","journal-title":"Environ. Microbiol."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Rutkowska, N., Dro\u017cd\u017cy\u0144ski, P., Ryngaj\u0142\u0142o, M., and Marchut-Miko\u0142ajczyk, O. (2023). Plants as the Extended Phenotype of Endophytes\u2014The Actual Source of Bioactive Compounds. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms241210096"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1038\/s41588-017-0012-9","article-title":"Genomic Features of Bacterial Adaptation to Plants","volume":"50","author":"Levy","year":"2018","journal-title":"Nat. Genet."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"100161","DOI":"10.1016\/j.cpb.2020.100161","article-title":"Plant Microbiome\u2013an Account of the Factors That Shape Community Composition and Diversity","volume":"23","author":"Dastogeer","year":"2020","journal-title":"Curr. Plant Biol."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Rossmann, M., Sarango-Flores, S.W., Chiaramonte, J.B., Kmit, M.C.P., and Mendes, R. (2017). Plant Microbiome: Composition and Functions in Plant Compartments. The Brazilian Microbiome, Springer International Publishing.","DOI":"10.1007\/978-3-319-59997-7_2"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"650905","DOI":"10.1155\/2014\/650905","article-title":"Linking Bacterial Endophytic Communities to Essential Oils: Clues from Lavandula Angustifolia Mill","volume":"2014","author":"Emiliani","year":"2014","journal-title":"Evid.-Based Complement. Altern. Med."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"963401","DOI":"10.6064\/2012\/963401","article-title":"Plant Growth-Promoting Bacteria: Mechanisms and Applications","volume":"2012","author":"Glick","year":"2012","journal-title":"Scientifica"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1094\/PHYTO-07-18-0262-R","article-title":"A Bacterial Endophyte from Apoplast Fluids Protects Canola Plants from Different Phytopathogens via Antibiosis and Induction of Host Resistance","volume":"109","author":"Romero","year":"2019","journal-title":"Phytopathology"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"155665","DOI":"10.1016\/j.scitotenv.2022.155665","article-title":"Environmental Factors, Bacterial Interactions and Plant Traits Jointly Regulate Epiphytic Bacterial Community Composition of Two Alpine Grassland Species","volume":"836","author":"Li","year":"2022","journal-title":"Sci. Total Environ."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1016\/j.jenvman.2016.02.047","article-title":"Beneficial Role of Bacterial Endophytes in Heavy Metal Phytoremediation","volume":"174","author":"Ma","year":"2016","journal-title":"J. Environ. Manag."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1186\/s40168-017-0241-2","article-title":"Structural Variability and Niche Differentiation in the Rhizosphere and Endosphere Bacterial Microbiome of Field-Grown Poplar Trees","volume":"5","author":"Beckers","year":"2017","journal-title":"Microbiome"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"968","DOI":"10.1016\/j.tplants.2022.07.009","article-title":"Leaf Photosynthesis: Do Endophytes Have a Say?","volume":"27","author":"Suryanarayanan","year":"2022","journal-title":"Trends Plant Sci."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1104\/pp.86.1.200","article-title":"Do Stomata Respond to CO 2 Concentrations Other than Intercellular?","volume":"86","author":"Mott","year":"1988","journal-title":"Plant Physiol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1186\/s40168-018-0445-0","article-title":"Microbial Interactions within the Plant Holobiont","volume":"6","author":"Hassani","year":"2018","journal-title":"Microbiome"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"856","DOI":"10.1038\/s41564-022-01132-w","article-title":"Mapping Phyllosphere Microbiota Interactions in Planta to Establish Genotype\u2013Phenotype Relationships","volume":"7","author":"Vogel","year":"2022","journal-title":"Nat. Microbiol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"eadf5121","DOI":"10.1126\/science.adf5121","article-title":"Metabolic Interaction Models Recapitulate Leaf Microbiota Ecology","volume":"381","author":"Pacheco","year":"2023","journal-title":"Science"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"115997","DOI":"10.1016\/j.indcrop.2022.115997","article-title":"Exploring the Nexus between the Composition of Essential Oil and the Bacterial Phytobiome Associated with Different Compartments of the Medicinal Plants Origanum vulgare ssp. vulgare, O. vulgare ssp. hirtum, and O. heracleoticum","volume":"191","author":"Semenzato","year":"2023","journal-title":"Ind. Crops Prod."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"fiy118","DOI":"10.1093\/femsec\/fiy118","article-title":"Antagonism and Antibiotic Resistance Drive a Species-Specific Plant Microbiota Differentiation in Echinacea spp.","volume":"94","author":"Maggini","year":"2018","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Pontonio, E., Di Cagno, R., Tarraf, W., Filannino, P., De Mastro, G., and Gobbetti, M. (2018). Dynamic and Assembly of Epiphyte and Endophyte Lactic Acid Bacteria During the Life Cycle of Origanum vulgare L.. Front. Microbiol., 9.","DOI":"10.3389\/fmicb.2018.01372"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"2824","DOI":"10.1111\/j.1462-2920.2008.01703.x","article-title":"The Microbial Community of Vetiver Root and Its Involvement into Essential Oil Biogenesis","volume":"10","author":"Massardo","year":"2008","journal-title":"Environ. Microbiol."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Pang, Z., Chen, J., Wang, T., Gao, C., Li, Z., Guo, L., Xu, J., and Cheng, Y. (2021). Linking Plant Secondary Metabolites and Plant Microbiomes: A Review. Front. Plant Sci., 12.","DOI":"10.3389\/fpls.2021.621276"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"5450","DOI":"10.1038\/s41598-018-23716-5","article-title":"Endophytes of Withania somnifera Modulate in Planta Content and the Site of Withanolide Biosynthesis","volume":"8","author":"Pandey","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Li, R., Duan, W., Ran, Z., Chen, X., Yu, H., Fang, L., Guo, L., and Zhou, J. (2023). Diversity and Correlation Analysis of Endophytes and Metabolites of Panax quinquefolius L. in Various Tissues. BMC Plant Biol., 23, Erratum in BMC Plant Biol. 2023, 23, 341. https:\/\/doi.org\/10.1186\/s12870-023-04340-6.","DOI":"10.1186\/s12870-023-04282-z"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"120528","DOI":"10.1016\/j.indcrop.2025.120528","article-title":"Endophytes Drive the Biosynthesis and Accumulation of Sesquiterpenoids in Atractylodes lancea (Thunb.) DC","volume":"225","author":"Han","year":"2025","journal-title":"Ind. Crops Prod."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"16924","DOI":"10.1038\/s41598-017-17110-w","article-title":"Plant-Endophytes Interaction Influences the Secondary Metabolism in Echinacea purpurea (L.) Moench: An in Vitro Model","volume":"7","author":"Maggini","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Maggini, V., Mengoni, A., Gallo, E.R., Biffi, S., Fani, R., Firenzuoli, F., and Bogani, P. (2019). Tissue Specificity and Differential Effects on in Vitro Plant Growth of Single Bacterial Endophytes Isolated from the Roots, Leaves and Rhizospheric Soil of Echinacea purpurea. BMC Plant Biol., 19.","DOI":"10.1186\/s12870-019-1890-z"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"2232","DOI":"10.1080\/14786419.2019.1579810","article-title":"Volatile Profile of Echinacea purpurea Plants after in Vitro Endophyte Infection","volume":"34","author":"Maggini","year":"2019","journal-title":"Nat. Prod. Res."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1038\/s42003-025-07527-9","article-title":"Role of Metabolism, Resistance, and\/or Antagonism as Drivers of Endomicrobiomes Assemblage in Origanum heracleoticum L.","volume":"8","author":"Semenzato","year":"2025","journal-title":"Commun. Biol."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Semenzato, G., Alonso-V\u00e1squez, T., Del Duca, S., Vassallo, A., Riccardi, C., Zaccaroni, M., Mucci, N., Padula, A., Emiliani, G., and Piccionello, A.P. (2022). Genomic analysis of endophytic Bacillus-related strains isolated from the medicinal plant Origanum vulgare L. revealed the presence of metabolic pathways involved in the biosynthesis of bioactive compounds. Microorganisms, 10.","DOI":"10.3390\/microorganisms10050919"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1101\/gr.215087.116","article-title":"Canu: Scalable and Accurate Long-Read Assembly via Adaptive k-Mer Weighting and Repeat Separation","volume":"27","author":"Koren","year":"2017","journal-title":"Genome Res."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: Quality Assessment Tool for Genome Assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","article-title":"High Throughput ANI Analysis of 90K Prokaryotic Genomes Reveals Clear Species Boundaries","volume":"9","author":"Jain","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: Rapid Prokaryotic Genome Annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Patz, S., Gautam, A., Becker, M., Ruppel, S., Rodr\u00edguez-Palenzuela, P., and Huson, D.H. (2021). PLaBAse: A Comprehensive Web Resource for Analyzing the Plant Growth-Promoting Potential of Plant-Associated Bacteria. bioRxiv.","DOI":"10.1101\/2021.12.13.472471"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Sprouffske, K., and Wagner, A. (2016). Growthcurver: An R Package for Obtaining Interpretable Metrics from Microbial Growth Curves. BMC Bioinform., 17.","DOI":"10.1186\/s12859-016-1016-7"},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Wickham, H. (2016). Ggplot2: Elegant Graphics for Data Analysis, Springer.","DOI":"10.1007\/978-3-319-24277-4_9"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1111\/j.1399-3054.1962.tb08052.x","article-title":"A Revised Medium for Rapid Growth and Bio Assays with Tobacco Tissue Cultures","volume":"15","author":"Murashige","year":"1962","journal-title":"Physiol. Plant."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1038\/nmeth.2089","article-title":"NIH Image to ImageJ: 25 Years of Image Analysis","volume":"9","author":"Schneider","year":"2012","journal-title":"Nat. Methods"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1016\/S0176-1617(11)81192-2","article-title":"The Spectral Determination of Chlorophylls a and b, as Well as Total Carotenoids, Using Various Solvents with Spectrophotometers of Different Resolution","volume":"144","author":"Wellburn","year":"1994","journal-title":"J. Plant Physiol."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Bolivar-Anillo, H.J., Gonz\u00e1lez-Rodr\u00edguez, V.E., Cantoral, J.M., Garc\u00eda-S\u00e1nchez, D., Collado, I.G., and Garrido, C. (2021). Endophytic Bacteria Bacillus subtilis, Isolated from Zea mays, as Potential Biocontrol Agent against Botrytis Cinerea. Biology, 10.","DOI":"10.3390\/biology10060492"},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Shukla, N., Singh, D., Tripathi, A., Kumari, P., Gupta, R.K., Singh, S., Shanker, K., and Singh, A. (2022). Synergism of Endophytic Bacillus subtilis and Klebsiella aerogenes Modulates Plant Growth and Bacoside Biosynthesis in Bacopa Monnieri. Front. Plant Sci., 13.","DOI":"10.3389\/fpls.2022.896856"},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Oteino, N., Lally, R.D., Kiwanuka, S., Lloyd, A., Ryan, D., Germaine, K.J., and Dowling, D.N. (2015). Plant Growth Promotion Induced by Phosphate Solubilizing Endophytic Pseudomonas Isolates. Front. Microbiol., 6.","DOI":"10.3389\/fmicb.2015.00745"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1016\/j.plaphy.2016.01.026","article-title":"Volatiles Released by Endophytic Pseudomonas fluorescens Promoting the Growth and Volatile Oil Accumulation in Atractylodes lancea","volume":"101","author":"Zhou","year":"2016","journal-title":"Plant Physiol. Biochem."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1164","DOI":"10.1002\/jsfa.10125","article-title":"Effect of Endophytic Bacillus megaterium Colonization on Structure Strengthening, Microbial Community, Chemical Composition and Stabilization Properties of Hybrid Pennisetum","volume":"100","author":"Shah","year":"2020","journal-title":"J. Sci. Food Agric."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"20190602","DOI":"10.1098\/rstb.2019.0602","article-title":"Compartmentalization Drives the Evolution of Symbiotic Cooperation","volume":"375","author":"Chomicki","year":"2020","journal-title":"Philos. Trans. R. Soc. B Biol. Sci."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"798","DOI":"10.1111\/nph.13697","article-title":"Plant Compartment and Biogeography Affect Microbiome Composition in Cultivated and Native Agave Species","volume":"209","author":"Desgarennes","year":"2016","journal-title":"New Phytol."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Wei, G., Ning, K., Zhang, G., Yu, H., Yang, S., Dai, F., Dong, L., and Chen, S. (2021). Compartment Niche Shapes the Assembly and Network of Cannabis Sativa-Associated Microbiome. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.714993"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1007\/s00248-011-9883-y","article-title":"Endophytes of Grapevine Flowers, Berries, and Seeds: Identification of Cultivable Bacteria, Comparison with Other Plant Parts, and Visualization of Niches of Colonization","volume":"62","author":"Compant","year":"2011","journal-title":"Microb. Ecol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"fiaa053","DOI":"10.1093\/femsec\/fiaa053","article-title":"Endophytic Microbial Assemblage in Grapevine","volume":"96","author":"Deyett","year":"2020","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref_56","doi-asserted-by":"crossref","unstructured":"Wang, Y., Wang, C., Gu, Y., Wang, P., Song, W., Ma, J., and Yang, X. (2020). The Variability of Bacterial Communities in Both the Endosphere and Ectosphere of Different Niches in Chinese Chives (Allium tuberosum). PLoS ONE, 15.","DOI":"10.1371\/journal.pone.0227671"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"1812","DOI":"10.1111\/1462-2920.15240","article-title":"The Plant Endosphere World\u2014Bacterial Life within Plants","volume":"23","author":"Compant","year":"2021","journal-title":"Environ. Microbiol."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"1445","DOI":"10.1038\/s41396-023-01459-0","article-title":"Metabolic Resource Overlap Impacts Competition among Phyllosphere Bacteria","volume":"17","author":"Schlechter","year":"2023","journal-title":"ISME J."},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Ossowicki, A., Jafra, S., and Garbeva, P. (2017). The Antimicrobial Volatile Power of the Rhizospheric Isolate Pseudomonas Donghuensis P482. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0174362"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"101754","DOI":"10.1016\/j.pmpp.2021.101754","article-title":"Plant-Associated Bacillus and Pseudomonas Antimicrobial Activities in Plant Disease Suppression via Biological Control Mechanisms\u2014A Review","volume":"117","author":"Janakiev","year":"2022","journal-title":"Physiol. Mol. Plant Pathol."},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Khatoon, Z., del Carmen Orozco-Mosqueda, M., Huang, S., Nascimento, F.X., and Santoyo, G. (2022). Peptide Antibiotics Produced by Bacillus Species: First Line of Attack in the Biocontrol of Plant Diseases. Bacilli in Agrobiotechnology: Bacilli in Climate Resilient Agriculture and Bioprospecting, Springer.","DOI":"10.1007\/978-3-030-85465-2_2"},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"MacNair, C.R., Tsai, C.N., Rutherford, S.T., and Tan, M.-W. (2023). Returning to Nature for the Next Generation of Antimicrobial Therapeutics. Antibiotics, 12.","DOI":"10.3390\/antibiotics12081267"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1016\/j.tim.2023.02.003","article-title":"Frenemies of the Soil: Bacillus and Pseudomonas Interspecies Interactions","volume":"31","author":"Lyng","year":"2023","journal-title":"Trends Microbiol."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1016\/j.chom.2014.06.002","article-title":"Agrobacterium Tumefaciens Deploys a Superfamily of Type VI Secretion DNase Effectors as Weapons for Interbacterial Competition In Planta","volume":"16","author":"Ma","year":"2014","journal-title":"Cell Host Microbe"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1146\/annurev-phyto-121423-084620","article-title":"Function, Evolution, and Ecology of Type VI Secretion Systems of Plant-Associated Bacteria","volume":"63","author":"Hsieh","year":"2025","journal-title":"Annu. Rev. Phytopathol."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"ycaf158","DOI":"10.1093\/ismeco\/ycaf158","article-title":"The Pseudomonas putida Type VI Secretion Systems Shape the Tomato Rhizosphere Microbiota","volume":"5","author":"Civantos","year":"2025","journal-title":"ISME Commun."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"5772","DOI":"10.1038\/s41598-021-85218-1","article-title":"Pseudomonas fluorescens F113 Type VI Secretion Systems Mediate Bacterial Killing and Adaption to the Rhizosphere Microbiome","volume":"11","author":"Bernal","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"972","DOI":"10.1038\/ismej.2016.169","article-title":"The Pseudomonas putida T6SS Is a Plant Warden against Phytopathogens","volume":"11","author":"Bernal","year":"2017","journal-title":"ISME J."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"1675","DOI":"10.1007\/s11104-025-07291-z","article-title":"Priority Effects of Inoculation Timing of Plant Growth-Promoting Microbial Inoculants: Role, Mechanisms and Perspectives","volume":"513","author":"Kong","year":"2025","journal-title":"Plant Soil"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"2313","DOI":"10.1007\/s00299-011-1158-z","article-title":"Intense Association of Non-Culturable Endophytic Bacteria with Antibiotic-Cleansed in Vitro Watermelon and Their Activation in Degenerating Cultures","volume":"30","author":"Thomas","year":"2011","journal-title":"Plant Cell Rep."},{"key":"ref_71","doi-asserted-by":"crossref","unstructured":"Cornell, C., Kokkoris, V., Richards, A., Horst, C., Rosa, D., Bennett, J.A., and Hart, M.M. (2021). Do Bioinoculants Affect Resident Microbial Communities? A Meta-Analysis. Front. Agron., 3.","DOI":"10.3389\/fagro.2021.753474"},{"key":"ref_72","doi-asserted-by":"crossref","unstructured":"Semenzato, G., and Fani, R. (2024). Endophytic Bacteria: A Sustainable Strategy for Enhancing Medicinal Plant Cultivation and Preserving Microbial Diversity. Front. Microbiol., 15.","DOI":"10.3389\/fmicb.2024.1477465"},{"key":"ref_73","doi-asserted-by":"crossref","unstructured":"Tabacchioni, S., Passato, S., Ambrosino, P., Huang, L., Caldara, M., Cantale, C., Hett, J., Del Fiore, A., Fiore, A., and Schl\u00fcter, A. (2021). Identification of Beneficial Microbial Consortia and Bioactive Compounds with Potential as Plant Biostimulants for a Sustainable Agriculture. Microorganisms, 9.","DOI":"10.3390\/microorganisms9020426"},{"key":"ref_74","doi-asserted-by":"crossref","unstructured":"Tripathi, A., Pandey, P., Tripathi, S.N., and Kalra, A. (2022). Perspectives and Potential Applications of Endophytic Microorganisms in Cultivation of Medicinal and Aromatic Plants. Front. Plant Sci., 13.","DOI":"10.3389\/fpls.2022.985429"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1080\/15427528.2020.1824168","article-title":"Leveraging Photosynthetic Efficiency toward Improving Crop Yields","volume":"35","author":"Miglani","year":"2021","journal-title":"J. Crop Improv."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"1317","DOI":"10.1007\/s00344-023-11185-8","article-title":"Siderophore-Producing Spinacia Oleracea Bacterial Endophytes Enhance Nutrient Status and Vegetative Growth Under Iron-Deficit Conditions","volume":"43","author":"Misra","year":"2024","journal-title":"J. Plant Growth Regul."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1007\/s12275-014-4002-7","article-title":"Bacterial Endophyte Sphingomonas Sp. LK11 Produces Gibberellins and IAA and Promotes Tomato Plant Growth","volume":"52","author":"Khan","year":"2014","journal-title":"J. Microbiol."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"127602","DOI":"10.1016\/j.micres.2024.127602","article-title":"Bacterial Indole-3-Acetic Acid: A Key Regulator for Plant Growth, Plant-Microbe Interactions, and Agricultural Adaptive Resilience","volume":"281","author":"Etesami","year":"2024","journal-title":"Microbiol. Res."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"654","DOI":"10.1007\/s00344-014-9415-3","article-title":"Bacterial Biosynthesis of 1-Aminocyclopropane-1-Carboxylate (ACC) Deaminase and Indole-3-Acetic Acid (IAA) as Endophytic Preferential Selection Traits by Rice Plant Seedlings","volume":"33","author":"Etesami","year":"2014","journal-title":"J. Plant Growth Regul."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1007\/s00344-021-10571-4","article-title":"Biochemical Characterization and Potential of Bacillus Safensis Strain SCAL1 to Mitigate Heat Stress in Solanum lycopersicum L.","volume":"42","author":"Mukhtar","year":"2023","journal-title":"J. Plant Growth Regul."},{"key":"ref_81","doi-asserted-by":"crossref","unstructured":"Katsenios, N., Andreou, V., Sparangis, P., Djordjevic, N., Giannoglou, M., Chanioti, S., Stergiou, P., Xanthou, M.Z., Kakabouki, I., and Vlachakis, D. (2021). Evaluation of Plant Growth Promoting Bacteria Strains on Growth, Yield and Quality of Industrial Tomato. Microorganisms, 9.","DOI":"10.3390\/microorganisms9102099"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"e0051923","DOI":"10.1128\/spectrum.00519-23","article-title":"Identification of Bioactive Compounds of Bacillus Velezensis HNA3 That Contribute to Its Dual Effects as Plant Growth Promoter and Biocontrol against Post-Harvested Fungi","volume":"11","author":"Zaid","year":"2023","journal-title":"Microbiol. Spectr."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/j.jbiotec.2021.03.008","article-title":"Effects of Plant Growth-Promoting Rhizobacteria Strains Producing ACC Deaminase on Photosynthesis, Isoprene Emission, Ethylene Formation and Growth of Mucuna pruriens (L.) DC. in Response to Water Deficit","volume":"331","author":"Brunetti","year":"2021","journal-title":"J. Biotechnol."},{"key":"ref_84","doi-asserted-by":"crossref","unstructured":"Berg, G., Kusstatscher, P., Abdelfattah, A., Cernava, T., and Smalla, K. (2021). Microbiome Modulation\u2014Toward a Better Understanding of Plant Microbiome Response to Microbial Inoculants. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.650610"},{"key":"ref_85","doi-asserted-by":"crossref","unstructured":"Wang, Y., Chen, N., Deng, K., Zhong, X., Li, Z., Li, L., and Xu, D. (2025). Effects and Molecular Mechanism of Endophytic Elicitors on the Accumulation of Secondary Metabolites in Medicinal Plants. Front. Microbiol., 16.","DOI":"10.3389\/fmicb.2025.1558567"},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"e14382","DOI":"10.1111\/1751-7915.14382","article-title":"Unlocking the Potential of Bacterial Endophytes from Medicinal Plants for Drug Discovery","volume":"17","author":"Zotchev","year":"2024","journal-title":"Microb. Biotechnol."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"5294","DOI":"10.1021\/jf020408a","article-title":"Antioxidant Activities and Phenolic Composition of Extracts from Greek Oregano, Greek Sage, and Summer Savory","volume":"50","author":"Exarchou","year":"2002","journal-title":"J. Agric. Food Chem."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1016\/S0031-9422(02)00513-7","article-title":"Rosmarinic Acid","volume":"62","author":"Petersen","year":"2003","journal-title":"Phytochemistry"},{"key":"ref_89","doi-asserted-by":"crossref","unstructured":"Guan, H., Luo, W., Bao, B., Cao, Y., Cheng, F., Yu, S., Fan, Q., Zhang, L., Wu, Q., and Shan, M. (2022). A comprehensive review of rosmarinic acid: From phytochemistry to pharmacology and its new insight. Molecules, 27.","DOI":"10.3390\/molecules27103292"},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"946","DOI":"10.2478\/s11535-011-0057-1","article-title":"Rosmarinic Acid Content in Basil Plants Grown in Vitro and in Hydroponics","volume":"6","author":"Kiferle","year":"2011","journal-title":"Open Life Sci."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1007\/s11101-013-9282-8","article-title":"Rosmarinic Acid: New Aspects","volume":"12","author":"Petersen","year":"2013","journal-title":"Phytochem. Rev."},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1007\/BF00232160","article-title":"Growth and Rosmarinic Acid Production in Cell Suspension Cultures of Salvia Officinalis L.","volume":"11","author":"Hippolyte","year":"1992","journal-title":"Plant Cell Rep."},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1007\/s11240-013-0300-8","article-title":"Molecular Cloning of SoHPPR Encoding a Hydroxyphenylpyruvate Reductase, and Its Expression in Cell Suspension Cultures of Salvia Officinalis","volume":"114","author":"Barberini","year":"2013","journal-title":"Plant Cell Tissue Organ Cult. (PCTOC)"},{"key":"ref_94","doi-asserted-by":"crossref","unstructured":"Savona, M., Barberini, S., Bassolino, L., Mozzanini, E., Pistelli, L., Pistelli, L., and Ruffoni, B. (2017). Strategies for Optimization of the Production of Rosmarinic Acid in Salvia officinalis L. and Salvia dolomitica Codd Biomass with Several Biotechnological Approaches. Salvia Biotechnology, Springer International Publishing.","DOI":"10.1007\/978-3-319-73900-7_6"},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"1847","DOI":"10.1021\/acs.jafc.8b05647","article-title":"Differential Production of Phenylpropanoid Metabolites in Callus Cultures of Ocimum basilicum L. with Distinct In Vitro Antioxidant Activities and In Vivo Protective Effects against UV Stress","volume":"67","author":"Nazir","year":"2019","journal-title":"J. Agric. Food Chem."},{"key":"ref_96","doi-asserted-by":"crossref","unstructured":"Ekiert, H.M., Kubica, P., Kwiecie\u0144, I., Jafernik, K., Klimek-Szczykutowicz, M., and Szopa, A. (2022). Cultures of medicinal plants in vitro as a potential rich source of antioxidants. Plant Antioxidants and Health, Springer International Publishing.","DOI":"10.1007\/978-3-030-78160-6_37"},{"key":"ref_97","doi-asserted-by":"crossref","unstructured":"Kakalis, A., Tsekouras, V., Mavrikou, S., Moschopoulou, G., Kintzios, S., Evergetis, E., Iliopoulos, V., Koulocheri, S.D., and Haroutounian, S.A. (2023). Farm or Lab? A Comparative Study of Oregano\u2019s Leaf and Callus Volatile Isolates Chemistry and Cytotoxicity. Plants, 12.","DOI":"10.3390\/plants12071472"},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1080\/10412905.2010.9700284","article-title":"Essential Oils From Wild and Micropropagated Plants of Origanum minutiflorum O. Schwarz et Davis","volume":"22","author":"Tipirdamaz","year":"2010","journal-title":"J. Essent. Oil Res."},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"692","DOI":"10.1111\/nph.14178","article-title":"Why Do Plants Produce so Many Terpenoid Compounds?","volume":"220","author":"Pichersky","year":"2018","journal-title":"New Phytol."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"3227","DOI":"10.1111\/pce.14945","article-title":"Nitrogen-mediated Volatilisation of Defensive Metabolites in Tomato Confers Resistance to Herbivores","volume":"47","author":"Li","year":"2024","journal-title":"Plant Cell Environ."},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"2534","DOI":"10.1111\/gcb.14973","article-title":"Variation and Evolution of C:N Ratio among Different Organs Enable Plants to Adapt to N-limited Environments","volume":"26","author":"Zhang","year":"2020","journal-title":"Glob. Chang. Biol."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.micres.2018.04.006","article-title":"Bacterial Endophytes Modulates the Withanolide Biosynthetic Pathway and Physiological Performance in Withania somnifera under Biotic Stress","volume":"212\u2013213","author":"Mishra","year":"2018","journal-title":"Microbiol. Res."}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/14\/7\/1497\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T04:11:49Z","timestamp":1783915909000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/14\/7\/1497"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,8]]},"references-count":102,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2026,7]]}},"alternative-id":["microorganisms14071497"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms14071497","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,8]]}}}