foodmetaFOOD METAENGINEERINGFOOD METAENGINEERING2949-6497All-Russian Dairy Research Institute10.37442/fme.2024.1.44foodmeta-44Research ArticleОбзорная статьяScoping ReviewПрименение методов omics в изучении эндофитных микроорганизмов: обзор предметного поляApplication of omics methods to the study of endophytic microorganisms: Scoping Reviewhttps://orcid.org/0000-0002-5630-3196ПросековАлександр ЮрьевичProsekovAlexander Yurievich

главный научный сотрудник

SPIN-код: 5203-5725, AuthorID: 130915

Chief Scientific OfficerSPIN code: 5203-5725, AuthorID: 130915

bionano_kem@mail.ruКемеровский государственный университетРоссияKemerovo State UniversityRussian Federation202407042024213450Copyright © Просеков А.Ю., 20242024Просеков А.Ю.Prosekov A.Y.Данная работа распространяется под лицензией Creative Commons Attribution 4.0.This work is licensed under a Creative Commons Attribution 4.0 License.https://www.fme-journal.org/jour/article/view/44Введение

Введение: Зерновые культуры являются основой продовольственной безопасности во многих регионах, в том числе в Кузбассе, но сталкиваются с угрозой снижения урожайности из-за биотических стрессов. Эффективным решением может стать использование эндофитных микроорганизмов, однако их взаимодействие с растениями еще недостаточно изучено. Omics-технологии предоставляют возможность детально изучить эти взаимоотношения, открывая путь к повышению продуктивности зерновых.

Цель и исследовательские вопросы: обобщение и систематизация знаний об эндофитных микроорганизмах, полученных с применением omics-ных технологий.

Материалы и методы

Материалы и методы: Поиск производился в период с 4 по 18 декабря 2023 г в базах данных Scopus, ScienceDirect, GoogleSchoolar по ключевым словам endophytes, endosphere, RNA, transcriptome, genes, wheat, barley, oats. Поиск не ограничивали по временному периоду. Из 239 релевантных с точки зрения ключевых слов публикаций, 62 соответствовали критериям включения. Обзор предметного поля опирается на протокол PRISMA-ScR.

Результаты

Результаты: В результате поиска обнаружено 62 источника, посвященных изучению эндофитного поведения с применением современных молекулярно-генетических методов исследования. Проведенный анализ позволил выявить следующие тренды применения эндофитных микроорганизмов: разработка микробных биостимуляторов сельскохозяйственных культур; применение в качестве агентов биологического контроля инфекционных заболеваний растений. Выявленные тренды согласуются с предыдущими обзорами данной предметной области. В отличие от ранних исследований, акцент смещен на реализацию генетического потенциала микробиоты, рассматриваются возможности модернизации генетической информации микроорганизмов.

Выводы

Выводы: Необходимо развитие сферы применения молекулярно-генетических методов для изучения эндофитных микроорганизмов, так как их применение в качестве биоконтроля может стать многообещающей стратегией устойчивого развития агропромышленного комплекса. Особенный акцент необходимо сделать на изучение взаимосвязи данных микроорганизмов и зерновых культур, так как на данный момент сведений в современной научной литературе недостаточно.

Introduction: Grain crops form the basis of food security in many regions, including Kuzbass. However, they face the threat of decreasing yields due to biotic stressors. An effective solution might be the use of endophytic microorganisms. Their interaction with plants, however, has not been sufficiently studied yet. Omics technology provides an opportunity to investigate these relationships in depth, leading to increased grain productivity. Purpose and Research Questions: Generalization and systematization of knowledge regarding endophytic microbes obtained through omics techniques.Materials and methods: A search was conducted from December 4 to 18, 2023, in the databases of Scopus, ScienceDirect, and GoogleScholar using keywords such as endophytes, endosphere, RNA, transcriptome, genes, wheat, barley, and oats. No time limit was set for the search. Out of 239 relevant publications, 62 were selected based on inclusion criteria. The subject field review was conducted using the PRISMA-ScR protocol.Results: As a result of the search, 62 sources were found dedicated to the study of endophytic behavior using modern molecular genetic research methods. The analysis revealed the following trends in the utilization of endophyte microorganisms: the development of microbial bio-stimulators for agricultural crops and the use as agents for biological control of plant diseases. These trends are consistent with earlier reviews on this subject area, but in contrast to previous studies, there is a focus on realizing the genetic potential of microbiota and exploring the possibilities of modernizing microbial genetic information.Conclusions: It is necessary to expand the scope of molecular genetic methods in the study of endophytic microorganisms, as their use as biocontrol agents could become a promising strategy for sustainable development in the agro-industry. Special attention should be paid to the investigation of the relationship between these microbes and cereals, as there is currently insufficient information available in the scientific literature on this subject.

omics-ные технологииэндофитные микроорганизмыбиоконтрольomics technologiesendophytic microorganismsbiocontrolReferencesAhmed, A., He, P., He, Y., Singh, B. K., Wu, Y., Munir, S., & He, P. (2023). Biocontrol of plant pathogens in omics era - With special focus on endophytic bacilli. Critical Reviews in Biotechnology, 43, 1–19. https://doi.org/10.1080/07388551.2023.2183379Ali, S., Duan, J., Charles, T. C., & Glick, B. R. (2014). A bioinformatics approach to the determination of genes involved in endophytic behavior in Burkholderia spp. Journal of Theoretical Biology, 343, 193–198. https://doi.org/10.1016/j.jtbi.2013.10.007Ali, S., Duan, J., Charles, T. C., & Glick, B. R. (2014). A bioinformatics approach to the determination of genes involved in endophytic behavior in Burkholderia spp. Journal of Theoretical Biology, 343, 193–198. https://doi.org/10.1016/j.jtbi.2013.10.007Alkan, M., Özer, G., İmren, M., Özdemir, F., Morgounov, A., & Dababat, A. A. (2021). First Report of Fusarium culmorum and Microdochium bolleyi Causing Root Rot on Triticale in Kazakhstan. Plant Disease, 105(7), 2015. https://doi.org/10.1094/PDIS-12-20-2659-PDNAlkan, M., Özer, G., İmren, M., Özdemir, F., Morgounov, A., & Dababat, A. A. (2021). First report of Fusarium culmorum and Microdochium bolleyi causing root rot on triticale in Kazakhstan. Plant Disease, 105(7), 2015. https://doi.org/10.1094/PDIS-12-20-2659-PDNAl-Sadi, A. M. (2021). Bipolaris sorokiniana-Induced Black Point, Common Root Rot, and Spot Blotch Diseases of Wheat: A Review. Frontiers in Cellular and Infection Microbiology, 11, 584899. https://doi.org/10.3389/fcimb.2021.584899Al-Sadi, A. M. (2021). Bipolaris sorokiniana-induced black point, common root rot, and spot blotch diseases of wheat: A review. Frontiers in Cellular and Infection Microbiology, 11, 584899. https://doi.org/10.3389/fcimb.2021.584899Ambrose, K. V., Tian, Z., Wang, Y., Smith, J., Zylstra, G., Huang, B., &Ambrose, K. V., Tian, Z., Wang, Y., Smith, J., Zylstra, G., Huang, B., & Belanger, F. C. (2015). Functional characterization of salicylate hydroxylase from the fungal endophyte Epichloë festucae. Scientific Reports, 5(1), 10939. https://doi.org/10.1038/srep10939Belanger, F. C. (2015). Functional characterization of salicylate hydroxylase from the fungal endophyte Epichloë festucae. Scientific Reports, 5(1), 10939. https://doi.org/10.1038/srep10939Baymiev, A. K., Gumenko, R. S., Vladimirova, A. A., Akimova, E. S., Vershinina, Z. R., & Baymiev, A. K. (2019). Artificial activation of NIF gene expression in nodule bacteria Ex Planta. Ecological Genetics, 17(2), 35–42. https://doi.org/10.17816/ecogen17235-42Baymiev, A. K., Gumenko, R. S., Vladimirova, A. A., Akimova, E. S.,Becker, Y., Eaton, C. J., Brasell, E., May, K. J., Becker, M., Hassing, B., Cartwright, G. M., Reinhold, L., & Scott, B. (2015). The fungal cell-wall integrity MAPK cascade is crucial for рyphal network formation and maintenance of restrictive growth of Epichloë festucae in symbiosis with Lolium perenne. Molecular Plant-Microbe Interactions®, 28(1), 69–85. https://doi.org/10.1094/MPMI-06-14-0183-RVershinina, Z. R., & Baymiev, A. K. (2019). Artificial activation of nif gene expression in nodule bacteria Ex Planta. Ecological Genetics, 17(2), 35–42. https://doi.org/10.17816/ecogen17235-42Bertalan, M., Albano, R., De Pádua, V., Rouws, L., Rojas, C., Hemerly, A., Teixeira, K., Schwab, S., Araujo, J., Oliveira, A., França, L., Magalhães, V., Alquéres, S., Cardoso, A., Almeida, W., Loureiro, M. M., Nogueira, E., Cidade, D., Oliveira, D., Simão, T., Macedo, Jacyara, Valadão, A., Dreschsel, M., Freitas, F., Vidal, M., Guedes, H., Rodrigues, E., Meneses, C., Brioso, P., Pozzer, L., Figueiredo, D., Montano, H., Junior, J., De Souza Filho, G., Martin Quintana Flores, V., Ferreira, B., Branco, A., Gonzalez, P., Guillobel, H., Lemos, M., Seibel, L., Macedo, José, Alves-Ferreira, M., Sachetto-Martins, G., Coelho, A., Santos, E., Amaral, G., Neves, A., Pacheco, A. B., Carvalho, D., Lery, L., Bisch, P., Rössle, S. C., Ürményi, T., Rael Pereira, A., Silva, R., Rondinelli, E., Von Krüger, W., Martins, O., Baldani, J. I., Ferreira, P. C. (2009). Complete genome sequence of the sugarcane nitrogen-fixing endophyte Gluconacetobacter diazotrophicus Pal5. BMC Genomics, 10(1), 450. https://doi.org/10.1186/1471-2164-10-450Becker, Y., Eaton, C. J., Brasell, E., May, K. J., Becker, M., Hassing, B., Cartwright, G. M., Reinhold, L., & Scott, B. (2015). The Fungal Cell-Wall Integrity MAPK Cascade Is Crucial for Hyphal Network Formation and Maintenance of Restrictive Growth of Epichloë festucae in Symbiosis With Lolium perenne. Molecular Plant-Microbe Interactions®, 28(1), 69–85. https://doi.org/10.1094/MPMI-06-14-0183-RBoyer, F., Fichant, G., Berthod, J., Vandenbrouck, Y., & Attree, I. (2009). Dissecting the bacterial type VI secretion system by a genome wide in silico analysis: What can be learned from available microbial genomic resources? BMC Genomics, 10(1), 104. https://doi.org/10.1186/1471-2164-10-104Bertalan, M., Albano, R., De Pádua, V., Rouws, L., Rojas, C., Hemerly, A., Teixeira, K., Schwab, S., Araujo, J., Oliveira, A., França, L., Magalhães, V., Alquéres, S., Cardoso, A., Almeida, W., Loureiro, M. M., Nogueira, E., Cidade, D., Oliveira, D., … Ferreira, P. C. (2009). Complete genome sequence of the sugarcane nitrogen-fixing endophyte Gluconacetobacter diazotrophicus Pal5. BMC Genomics, 10(1), 450. https://doi.org/10.1186/1471-2164-10-450Card, S. D., Faville, M. J., Simpson, W. R., Johnson, R. D., Voisey, C. R.,Boyer, F., Fichant, G., Berthod, J., Vandenbrouck, Y., & Attree, I. (2009). Dissecting the bacterial type VI secretion system by a genome wide in silico analysis: What can be learned from available microbial genomic resources? BMC Genomics, 10(1), 104. https://doi.org/10.1186/1471-2164-10-104De Bonth, A. C. M., & Hume, D. E. (2014). Mutualistic fungal endophytes in the Triticeae –Survey and description. FEMS Microbiology Ecology, 88(1), 94–106. https://doi.org/10.1111/1574-6941.12273Card, S. D., Faville, M. J., Simpson, W. R., Johnson, R. D., Voisey, C. R.,Chetia, H., Kabiraj, D., Bharali, B., Ojha, S., Barkataki, M. P., Saikia, D., Singh, T., Mosahari, P. V., Sharma, P., & Bora, U. (2019). Exploring the benefits of endophytic fungi via omics. In B. P. Singh (Ed.), Advances in Endophytic Fungal Research (pp. 51–81). Springer International Publishing. https://doi.org/10.1007/978-3-030-03589-1_4De Bonth, A. C. M., & Hume, D. E. (2014). Mutualistic fungal endophytes in the Triticeae –Survey and description. FEMS Microbiology Ecology, 88(1), 94–106. https://doi.org/10.1111/1574-6941.12273Comby, M., Gacoin, M., Robineau, M., Rabenoelina, F., Ptas, S., Dupont, J.,Comby, M., Gacoin, M., Robineau, M., Rabenoelina, F., Ptas, S., Dupont, J.,Profizi, C., & Baillieul, F. (2017). Screening of wheat endophytes as biological control agents against Fusarium head blight using two different in vitro tests. Microbiological Research, 202, 11–20. https://doi.org/10.1016/j.micres.2017.04.014Profizi, C., & Baillieul, F. (2017). Screening of wheat endophytes as biological control agents against Fusarium head blight using two different in vitro tests. Microbiological Research, 202, 11–20. https://doi.org/10.1016/j.micres.2017.04.014Constantin, M. E., De Lamo, F. J., Vlieger, B. V., Rep, M., & Takken, F. L. W. (2019). Endophyte-mediated resistance in tomato to Fusarium oxysporum is independent of ET, JA, and SA. Frontiers in Plant Science, 10, 979. https://doi.org/10.3389/fpls.2019.00979Constantin, M. E., De Lamo, F. J., Vlieger, B. V., Rep, M., & Takken, F. L. W. (2019). Endophyte-Mediated Resistance in Tomato to Fusarium oxysporum Is Independent of ET, JA, and SA. Frontiers in Plant Science, 10, 979. https://doi.org/10.3389/fpls.2019.00979De Palma, M., Salzano, M., Villano, C., Aversano, R., Lorito, M., Ruocco, M., Docimo, T., Piccinelli, A. L., D’Agostino, N., & Tucci, M. (2019). Transcriptome reprogramming, epigenetic modifications and alternative splicing orchestrate the tomato root response to the beneficial fungus Trichoderma harzianum. Horticulture Research, 6(1), 5. https://doi.org/10.1038/s41438-018-0079-1De Palma, M., Salzano, M., Villano, C., Aversano, R., Lorito, M., Ruocco, M., Docimo, T., Piccinelli, A. L., D’Agostino, N., & Tucci, M. (2019). Transcriptome reprogramming, epigenetic modifications and alternative splicing orchestrate the tomato root response to the beneficial fungus Trichoderma harzianum. Horticulture Research, 6(1), 5. https://doi.org/10.1038/s41438-018-0079-1Demtröder, L., Pfänder, Y., Schäkermann, S., Bandow, J. E., & Masepohl, B. (2019). NifA is the master regulator of both nitrogenase systems in Rhodobacter capsulatus. MicrobiologyOpen, 8(12), e921. https://doi.org/10.1002/mbo3.921Demtröder, L., Pfänder, Y., Schäkermann, S., Bandow, J. E., & Masepohl, B. (2019). NifA is the master regulator of both nitrogenase systems in Rhodobacter capsulatus. MicrobiologyOpen, 8(12), e921. https://doi.org/10.1002/mbo3.921Downie, J. A. (2010). The roles of extracellular proteins, polysaccharides and signals in the interactions of rhizobia with legume roots. FEMS Microbiology Reviews, 34(2), 150–170. https://doi.org/10.1111/j.1574-6976.2009.00205.xDownie, J. A. (2010). The roles of extracellular proteins, polysaccharides and signals in the interactions of rhizobia with legume roots. FEMS Microbiology Reviews, 34(2), 150–170. https://doi.org/10.1111/j.1574-6976.2009.00205.xEida, A. A., Alzubaidy, H. S., De Zélicourt, A., Synek, L., Alsharif, W., Lafi, F. F., Hirt, H., & Saad, M. M. (2019). Phylogenetically diverse endophytic bacteria from desert plants induce transcriptional changes of tissue-specific ion transporters and salinity stress in Arabidopsis thaliana. Plant Science, 280, 228–240. https://doi.org/10.1016/j.plantsci.2018.12.002Eida, A. A., Alzubaidy, H. S., De Zélicourt, A., Synek, L., Alsharif, W., Lafi, F. F., Hirt, H., & Saad, M. M. (2019). Phylogenetically diverse endophytic bacteria from desert plants induce transcriptional changes of tissue-specific ion transporters and salinity stress in Arabidopsis thaliana. Plant Science, 280, 228–240. https://doi.org/10.1016/j.plantsci.2018.12.002Fadiji, A. E., Ayangbenro, A. S., & Babalola, O. O. (2021). Unveiling the putative functional genes present in root-associated endophytic microbiome from maize plant using the shotgun approach. Journal of Applied Genetics, 62(2), 339–351. https://doi.org/10.1007/s13353-021-00611-wFigueroa, M., Hammond-Kosack, K. E., & Solomon, P. S. (2018). A review of wheat diseases – a field perspective. Molecular Plant Pathology, 19(6), 1523–1536. https://doi.org/10.1111/mpp.12618Fadiji, A. E., & Babalola, O. O. (2020). Exploring the potentialities of beneficial endophytes for improved plant growth. Saudi Journal of Biological Sciences, 27(12), 3622–3633. https://doi.org/10.1016/j.sjbs.2020.08.002Fouts, D. E., Tyler, H. L., DeBoy, R. T., Daugherty, S., Ren, Q., Badger, J. H., Durkin, A. S., Huot, H., Shrivastava, S., Kothari, S., Dodson, R. J., Mohamoud, Y., Khouri, H., Roesch, L. F. W., Krogfelt, K. A., Struve, C., Triplett, E. W., & Methé, B. A. (2008). Complete Genome Sequence of the N2-Fixing Broad Host Range Endophyte Klebsiella pneumoniae 342 and Virulence Predictions Verified in Mice. PLoS Genetics, 4(7), e1000141. https://doi.org/10.1371/journal.pgen.1000141Figueroa, M., Hammond-Kosack, K. E., & Solomon, P. S. (2018). A review of wheat diseases – a field perspective. Molecular Plant Pathology, 19(6), 1523–1536. https://doi.org/10.1111/mpp.12618Ghaffari, M. R., Ghabooli, M., Khatabi, B., Hajirezaei, M. R., Schweizer, P., & Salekdeh, G. H. (2016). Metabolic and transcriptional response of central metabolism affected by root endophytic fungus Piriformospora indica under salinity in barley. Plant Molecular Biology, 90(6), 699–717. https://doi.org/10.1007/s11103-016-0461-zFouts, D. E., Tyler, H. L., DeBoy, R. T., Daugherty, S., Ren, Q., Badger, J. H., Durkin, A. S., Huot, H., Shrivastava, S., Kothari, S., Dodson, R. J., Mohamoud, Y., Khouri, H., Roesch, L. F. W., Krogfelt, K. A., Struve, C., Triplett, E. W., & Methé, B. A. (2008). Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice. PLoS Genetics, 4(7), e1000141. https://doi.org/10.1371/journal.pgen.1000141Gil-Gil, T., Cuesta, T., Hernando-Amado, S., Reales-Calderón, J. A., Corona, F., Linares, J. F., & Martínez, J. L. (2023). Virulence and metabolism crosstalk: Impaired activity of the Type three Secretion System (T3SS) in a Pseudomonas aeruginosa crc-defective mutant. International Journal of Molecular Sciences, 24(15), 12304. https://doi.org/10.3390/ijms241512304Ghaffari, M. R., Ghabooli, M., Khatabi, B., Hajirezaei, M. R., Schweizer, P., & Salekdeh, G. H. (2016). Metabolic and transcriptional response of central metabolism affected by root endophytic fungus Piriformospora indica under salinity in barley. Plant Molecular Biology, 90(6), 699–717. https://doi.org/10.1007/s11103-016-0461-zGranzow, S., Kaiser, K., Wemheuer, B., Pfeiffer, B., Daniel, R., Vidal, S., & Wemheuer, F. (2017). The Effects of Cropping Regimes on Fungal and Bacterial Communities of Wheat and Faba Bean in a Greenhouse Pot Experiment Differ between Plant Species and Compartment. Frontiers in Microbiology, 8, 902. https://doi.org/10.3389/fmicb.2017.00902Gil-Gil, T., Cuesta, T., Hernando-Amado, S., Reales-Calderón, J. A., Corona, F., Linares, J. F., & Martínez, J. L. (2023). Virulence and metabolism crosstalk: Impaired activity of the Type three Secretion System (T3SS) in a Pseudomonas aeruginosa crc-defective mutant. International Journal of Molecular Sciences, 24(15), 12304. https://doi.org/10.3390/ijms241512304Hao, K., Wang, F., Nong, X., McNeill, M. R., Liu, S., Wang, G., Cao, G., & Zhang, Z. (2017). Response of peanut Arachis hypogaea roots to the presence of beneficial and pathogenic fungi by transcriptome analysis. Scientific Reports, 7(1), 964. https://doi.org/10.1038/s41598-017-01029-3Granzow, S., Kaiser, K., Wemheuer, B., Pfeiffer, B., Daniel, R., Vidal, S., & Wemheuer, F. (2017). The effects of cropping regimes on fungal and bacterial communities of wheat and faba bean in a greenhouse pot experiment differ between plant species and compartment. Frontiers in Microbiology, 8, 902. https://doi.org/10.3389/fmicb.2017.00902Hashem, A., Abd_Allah, E. F., Alqarawi, A. A., Radhakrishnan, R., & Kumar, A. (2017). Plant defense approach of Bacillus subtilis (BERA 71) against Macrophomina phaseolina (Tassi) Goid in mung bean. Journal of Plant Interactions, 12(1), 390–401. https://doi.org/10.1080/17429145.2017.1373871Hao, K., Wang, F., Nong, X., McNeill, M. R., Liu, S., Wang, G., Cao, G., & Zhang, Z. (2017). Response of peanut Arachis hypogaea roots to the presence of beneficial and pathogenic fungi by transcriptome analysis. Scientific Reports, 7(1), 964. https://doi.org/10.1038/s41598-017-01029-3Ikram, M., Ali, N., Jan, G., Jan, F. G., & Khan, N. (2020). Endophytic fungal diversity and their interaction with plants for agriculture sustainability under stressful condition. Recent Patents on Food, Nutrition & Agriculture, 11(2), 115–123. https://doi.org/10.2174/2212798410666190612130139Hashem, A., Abd_Allah, E. F., Alqarawi, A. A., Radhakrishnan, R., & Kumar, A. (2017). Plant defense approach of Bacillus subtilis (BERA 71) against Macrophomina phaseolina (Tassi) Goid in mung bean. Journal of Plant Interactions, 12(1), 390–401. https://doi.org/10.1080/17429145.2017.1373871Jiang, C.-H., Xie, Y.-S., Zhu, K., Wang, N., Li, Z.-J., Yu, G.-J., & Guo, J.-H. (2019). Volatile organic compounds emitted by Bacillus sp. JC03 promote plant growth through the action of auxin and strigolactone. Plant Growth Regulation, 87(2), 317–328. https://doi.org/10.1007/s10725-018-00473-zSang, H., Lee, H. B., Molecular Mechanisms of Succinate Dehydrogenase Inhibitor Resistance in Phytopathogenic Fungi. (2020). Res. Plant Dis, 26(1), 1–7. https://doi.org/10.5423/RPD.2020.26.1.1Jiang, Y., Wang, L., Lu, S., Xue, Y., Wei, X., Lu, J., & Zhang, Y. (2019). Transcriptome sequencing of Salvia miltiorrhiza after infection by its endophytic fungi and identification of genes related to tanshinone biosynthesis. Pharmaceutical Biology, 57(1), 760–769. https://doi.org/10.1080/13880209.2019.1680706Ikram, M., Ali, N., Jan, G., Jan, F. G., & Khan, N. (2020). Endophytic fungal diversity and their interaction with plants for agriculture sustainability under stressful condition. Recent Patents on Food, Nutrition & Agriculture, 11(2), 115–123. https://doi.org/10.2174/2212798410666190612130139Kage, U., Karre, S., Kushalappa, A. C., & McCartney, C. (2017). Identification and characterization of a fusarium head blight resistance gene Ta ACT in wheat QTL ‐2 DL. Plant Biotechnology Journal, 15(4), 447–457. https://doi.org/10.1111/pbi.12641Jiang, C.-H., Xie, Y.-S., Zhu, K., Wang, N., Li, Z.-J., Yu, G.-J., & Guo, J.-H. (2019). Volatile organic compounds emitted by Bacillus sp. JC03 promote plant growth through the action of auxin and strigolactone. Plant Growth Regulation, 87(2), 317–328. https://doi.org/10.1007/s10725-018-00473-zKarlsson, I., Friberg, H., Kolseth, A., Steinberg, C., & Persson, P. (2017). Organic farming increases richness of fungal taxa in the wheat phyllosphere. Molecular Ecology, 26(13), 3424–3436. https://doi.org/10.1111/mec.14132Jiang, Y., Wang, L., Lu, S., Xue, Y., Wei, X., Lu, J., & Zhang, Y. (2019). Transcriptome sequencing of Salvia miltiorrhiza after infection by its endophytic fungi and identification of genes related to tanshinone biosynthesis. Pharmaceutical Biology, 57(1), 760–769. https://doi.org/10.1080/13880209.2019.1680706Kothe, E., & Turnau, K. (2018). Editorial: Mycorrhizosphere Communication: Mycorrhizal Fungi and Endophytic Fungus-Plant Interactions. Frontiers in Microbiology, 9, 3015. https://doi.org/10.3389/fmicb.2018.03015Kage, U., Karre, S., Kushalappa, A. C., & McCartney, C. (2017). Identification and characterization of a fusarium head blight resistance gene Ta ACT in wheat QTL‐2 DL. Plant Biotechnology Journal, 15(4), 447–457. https://doi.org/10.1111/pbi.12641Kumar, J., Ramlal, A., Mallick, D., & Mishra, V. (2021). An Overview of Some Biopesticides and Their Importance in Plant Protection for Commercial Acceptance. Plants, 10(6), 1185. https://doi.org/10.3390/plants10061185Karlsson, I., Friberg, H., Kolseth, A., Steinberg, C., & Persson, P. (2017). Organic farming increases richness of fungal taxa in the wheat phyllosphere. Molecular Ecology, 26(13), 3424–3436. https://doi.org/10.1111/mec.14132Kwak, M.-J., Song, J. Y., Kim, S.-Y., Jeong, H., Kang, S. G., Kim, B. K., Kwon, S.-K., Lee, C. H., Yu, D. S., Park, S.-H., & Kim, J. F. (2012). Complete Genome Sequence of the Endophytic Bacterium Burkholderia sp. Strain KJ006. Journal of Bacteriology, 194(16), 4432–4433. https://doi.org/10.1128/JB.00821-12Khare, E., Mishra, J., & Arora, N. K. (2018). Multifaceted Interactions Between Endophytes and Plant: Developments and Prospects. Frontiers in Microbiology, 9, 2732. https://doi.org/10.3389/fmicb.2018.02732Lahrmann, U., & Zuccaro, A. (2012). Opprimo ergo sum – Evasion and Suppression in the Root Endophytic Fungus Piriformospora indica. Molecular Plant-Microbe Interactions®, 25(6), 727–737. https://doi.org/10.1094/MPMI-11-11-0291Kothe, E., & Turnau, K. (2018). Editorial: mycorrhizosphere communication: mycorrhizal fungi and endophytic fungus-plant interactions. Frontiers in Microbiology, 9, 3015. https://doi.org/10.3389/fmicb.2018.03015Larran, S., Simón, M. R., Moreno, M. V., Siurana, M. P. S., & Perelló, A. (2016). Endophytes from wheat as biocontrol agents against tan spot disease. Biological Control, 92, 17–23. https://doi.org/10.1016/j.biocontrol.2015.09.002Kumar, J., Ramlal, A., Mallick, D., & Mishra, V. (2021). An overview of some biopesticides and their importance in plant protection for commercial acceptance. Plants, 10(6), 1185. https://doi.org/10.3390/plants10061185Latz, M. A. C., Jensen, B., Collinge, D. B., & Jørgensen, H. J. L. (2018). Endophytic fungi as biocontrol agents: Elucidating mechanisms inKwak, M.-J., Song, J. Y., Kim, S.-Y., Jeong, H., Kang, S. G., Kim, B. K., Kwon, S.-K., Lee, C. H., Yu, D. S., Park, S.-H., & Kim, J. F. (2012). Complete genome sequence of the endophytic bacterium Burkholderia sp. Strain KJ006. Journal of Bacteriology, 194(16), 4432–4433. https://doi.org/10.1128/JB.00821-12disease suppression. Plant Ecology & Diversity, 11(5–6), 555–567. https://doi.org/10.1080/17550874.2018.1534146Lahrmann, U., & Zuccaro, A. (2012). Opprimo ergo sum – evasion and suppression in the root endophytic fungus Piriformospora indica. Molecular Plant-Microbe Interactions®, 25(6), 727–737. https://doi.org/10.1094/MPMI-11-11-0291Lengai, G. M. W., & Muthomi, J. W. (2018). Biopesticides and Their Role in Sustainable Agricultural Production. Journal of Biosciences and Medicines, 06(06), 7–41. https://doi.org/10.4236/jbm.2018.66002Larran, S., Simón, M. R., Moreno, M. V., Siurana, M. P. S., & Perelló, A. (2016). Endophytes from wheat as biocontrol agents against tan spot disease. Biological Control, 92, 17–23. https://doi.org/10.1016/j.biocontrol.2015.09.002Lu, C., Liu, H., Jiang, D., Wang, L., Jiang, Y., Tang, S., Hou, X., Han, X., Liu, Z., Zhang, M., Chu, Z., & Ding, X. (2019). Paecilomyces variotii extracts (ZNC) enhance plant immunity and promote plant growth. Plant and Soil, 441(1–2), 383–397. https://doi.org/10.1007/s11104-019-04130-wLatz, M. A. C., Jensen, B., Collinge, D. B., & Jørgensen, H. J. L. (2018). Endophytic fungi as biocontrol agents: Elucidating mechanisms inLu, H., Wei, T., Lou, H., Shu, X., & Chen, Q. (2021). A Critical Review on Communication Mechanism within Plant-Endophytic Fungi Interactions to Cope with Biotic and Abiotic Stresses. Journal of Fungi, 7(9), 719. https://doi.org/10.3390/jof7090719disease suppression. Plant Ecology & Diversity, 11(5–6), 555–567. https://doi.org/10.1080/17550874.2018.1534146Mahoney, A. K., Yin, C., & Hulbert, S. H. (2017). Community Structure, Species Variation, and Potential Functions of Rhizosphere-Associated Bacteria of Different Winter Wheat (Triticum aestivum) Cultivars. Frontiers in Plant Science, 8. https://doi.org/10.3389/fpls.2017.00132Lengai, G. M. W., & Muthomi, J. W. (2018). Biopesticides and their role in sustainable agricultural production. Journal of Biosciences and Medicines, 06(06), 7–41. https://doi.org/10.4236/jbm.2018.66002Malinich, E. A., Wang, K., Mukherjee, P. K., Kolomiets, M., & Kenerley, C. M. (2019). Differential expression analysis of Trichoderma virens RNA reveals a dynamic transcriptome during colonization of Zea mays roots. BMC Genomics, 20(1), 280. https://doi.org/10.1186/s12864-019-5651-zLi, J., Wu, H., Pu, Q., Zhang, C., Chen, Y., Lin, Z., Hu, X., Li, O. (2023). Complete genome of Sphingomonas paucimobilis ZJSH1, an endophytic bacterium from Dendrobium officinale with stress resistance and growth promotion potential. Archives of Microbiology, 205(4), 132. https://doi.org/10.1007/s00203-023-03459-2Molecular Mechanisms of Succinate Dehydrogenase Inhibitor Resistance in Phytopathogenic Fungi. (2020). Research in Plant Disease, 26(1), 1–7. https://doi.org/10.5423/RPD.2020.26.1.1Lu, C., Liu, H., Jiang, D., Wang, L., Jiang, Y., Tang, S., Hou, X., Han, X., Liu, Z., Zhang, M., Chu, Z., & Ding, X. (2019). Paecilomyces variotii extracts (ZNC) enhance plant immunity and promote plant growth. Plant and Soil, 441(1–2),Morales-Cedeño, L. R., Orozco-Mosqueda, Ma. D. C., Loeza-Lara, P. D.,–397. https://doi.org/10.1007/s11104-019-04130-wParra-Cota, F. I., De Los Santos-Villalobos, S., & Santoyo, G. (2021). Plant growth-promoting bacterial endophytes as biocontrol agents of pre- and post-harvest diseases: Fundamentals, methods of application andLu, H., Wei, T., Lou, H., Shu, X., & Chen, Q. (2021). A Critical review on communication mechanism within plant-endophytic fungi interactions to cope with biotic and abiotic stresses. Journal of Fungi, 7(9), 719. https://doi.org/10.3390/jof7090719future perspectives. Microbiological Research, 242, 126612. https://doi.org/10.1016/j.micres.2020.126612Mahoney, A. K., Yin, C., & Hulbert, S. H. (2017). Community sructure, species variation, and potential functions of rhizosphere-associated bacteria of different winter wheat (Triticum aestivum) cultivars. Frontiers in Plant Science, 8. https://doi.org/10.3389/fpls.2017.00132Pandey, V., Ansari, M. W., Tula, S., Yadav, S., Sahoo, R. K., Shukla, N., Bains, G., Badal, S., Chandra, S., Gaur, A. K., Kumar, A., Shukla, A., Kumar, J., &Malinich, E. A., Wang, K., Mukherjee, P. K., Kolomiets, M., & Kenerley, C. M. (2019). Differential expression analysis of Trichoderma virens RNA reveals a dynamic transcriptome during colonization of Zea mays roots. BMC Genomics, 20(1), 280. https://doi.org/10.1186/s12864-019-5651-zTuteja, N. (2016). Dose-dependent response of Trichoderma harzianum in improving drought tolerance in rice genotypes. Planta, 243(5), 1251–1264. https://doi.org/10.1007/s00425-016-2482-xMorales-Cedeño, L. R., Orozco-Mosqueda, Ma. D. C., Loeza-Lara, P. D.,Pankievicz, V. C. S., Camilios-Neto, D., Bonato, P., Balsanelli, E., Tadra-Sfeir, M. Z., Faoro, H., Chubatsu, L. S., Donatti, L., Wajnberg, G., Passetti, F., Monteiro, R. A., Pedrosa, F. O., & Souza, E. M. (2016). RNA-seq transcriptional profiling of Herbaspirillum seropedicae colonizing wheat (Triticum aestivum) roots. Plant Molecular Biology, 90(6), 589–603. https://doi.org/10.1007/s11103-016-0430-6Parra-Cota, F. I., De Los Santos-Villalobos, S., & Santoyo, G. (2021). Plant growth-promoting bacterial endophytes as biocontrol agents of pre- and post-harvest diseases: Fundamentals, methods of application andPlett, J. M., & Martin, F. M. (2018). Know your enemy, embrace your friend: Using omics to understand how plants respond differently to pathogenicfuture perspectives. Microbiological Research, 242, 126612. https://doi.org/10.1016/j.micres.2020.126612and mutualistic microorganisms. The Plant Journal, 93(4), 729–746. https://doi.org/10.1111/tpj.13802Pandey, V., Ansari, M. W., Tula, S., Yadav, S., Sahoo, R. K., Shukla, N., Bains, G., Badal, S., Chandra, S., Gaur, A. K., Kumar, A., Shukla, A., Kumar, J., &Qin, S., Feng, W.-W., Zhang, Y.-J., Wang, T.-T., Xiong, Y.-W., & Xing, K. (2018). Diversity of Bacterial Microbiota of Coastal Halophyte Limonium sinense and Amelioration of Salinity Stress Damage by Symbiotic PlantTuteja, N. (2016). Dose-dependent response of Trichoderma harzianum in improving drought tolerance in rice genotypes. Planta, 243(5), 1251–1264. https://doi.org/10.1007/s00425-016-2482-xGrowth-Promoting Actinobacterium Glutamicibacter halophytocola KLBMP 5180. Applied and Environmental Microbiology, 84(19), e01533-18. https://doi.org/10.1128/AEM.01533-18Pankievicz, V. C. S., Camilios-Neto, D., Bonato, P., Balsanelli, E., Tadra-Sfeir, M. Z., Faoro, H., Chubatsu, L. S., Donatti, L., Wajnberg, G., Passetti, F., Monteiro, R. A., Pedrosa, F. O., & Souza, E. M. (2016). RNA-seq transcriptional profiling of Herbaspirillum seropedicae colonizing wheat (Triticum aestivum) roots. Plant Molecular Biology, 90(6), 589–603. https://doi.org/10.1007/s11103-016-0430-6Reinhold-Hurek, B., & Hurek, T. (2011). Living inside plants: Bacterial endophytes. Current Opinion in Plant Biology, 14(4), 435–443. https://doi.org/10.1016/j.pbi.2011.04.004Plett, J. M., & Martin, F. M. (2018). Know your enemy, embrace your friend: Using omics to understand how plants respond differently to pathogenicRojas, E. C., Jensen, B., Jørgensen, H. J. L., Latz, M. A. C., Esteban, P., Ding, Y., & Collinge, D. B. (2020). Selection of fungal endophytes with biocontrol potential against Fusarium head blight in wheat. Biological Control, 144, 104222. https://doi.org/10.1016/j.biocontrol.2020.104222and mutualistic microorganisms. The Plant Journal, 93(4), 729–746. https://doi.org/10.1111/tpj.13802Sánchez-Vallet, A., Mesters, J. R., & Thomma, B. P. H. J. (2015). The battle for chitin recognition in plant-microbe interactions. FEMS Microbiology Reviews, 39(2), 171–183. https://doi.org/10.1093/femsre/fuu003Qin, S., Feng, W.-W., Zhang, Y.-J., Wang, T.-T., Xiong, Y.-W., & Xing, K. (2018). Diversity of Bacterial Microbiota of Coastal Halophyte Limonium sinense and Amelioration of Salinity Stress Damage by Symbiotic PlantSánchez-Vallet, A., Saleem-Batcha, R., Kombrink, A., Hansen, G., Valkenburg, D.-J., Thomma, B. P., & Mesters, J. R. (2013). Fungal effector Ecp6 outcompetes host immune receptor for chitin binding through intrachain LysM dimerization. eLife, 2, e00790. https://doi.org/10.7554/eLife.00790Growth-Promoting Actinobacterium Glutamicibacter halophytocola KLBMP 5180. Applied and Environmental Microbiology, 84(19), e01533-18. https://doi.org/10.1128/AEM.01533-18Santoyo, G., Moreno-Hagelsieb, G., Del Carmen Orozco-Mosqueda, Ma., &Reinhold-Hurek, B., & Hurek, T. (2011). Living inside plants: Bacterial endophytes. Current Opinion in Plant Biology, 14(4), 435–443. https://doi.org/10.1016/j.pbi.2011.04.004Glick, B. R. (2016). Plant growth-promoting bacterial endophytes. Microbiological Research, 183, 92–99. https://doi.org/10.1016/j.micres.2015.11.008Rojas, E. C., Jensen, B., Jørgensen, H. J. L., Latz, M. A. C., Esteban, P., Ding, Y., & Collinge, D. B. (2020). Selection of fungal endophytes with biocontrol potential against Fusarium head blight in wheat. Biological Control, 144, 104222. https://doi.org/10.1016/j.biocontrol.2020.104222Segmüller, N., Kokkelink, L., Giesbert, S., Odinius, D., Van Kan, J., & Tudzynski, P. (2008). NADPH Oxidases Are Involved in Differentiation and Pathogenicity in Botrytis cinerea. Molecular Plant-Microbe Interactions®, 21(6), 808–819. https://doi.org/10.1094/MPMI-21-6-0808Saini, P., Verma, A., Tiwari, H., Mishra, V., & Gautam, V. (2024). Omics-Based Approaches in Studying Fungal Endophytes and Their Associated Secondary Metabolites. In B. P. Singh, A. M. Abdel-Azeem, V. Gautam, G. Singh, & S. K. Singh (Eds.), Endophytic Fungi (pp. 209–227). Springer International Publishing. https://doi.org/10.1007/978-3-031-49112-2_10Sowa, S. W., Gelderman, G., Leistra, A. N., Buvanendiran, A., Lipp, S., Pitaktong, A., Vakulskas, C. A., Romeo, T., Baldea, M., & Contreras, L. M. (2017). Integrative FourD omics approach profiles the target network of the carbon storage regulatory system. Nucleic Acids Research, gkx048. https://doi.org/10.1093/nar/gkx048Sánchez-Vallet, A., Mesters, J. R., & Thomma, B. P. H. J. (2015). The battle for chitin recognition in plant-microbe interactions. FEMS Microbiology Reviews, 39(2), 171–183. https://doi.org/10.1093/femsre/fuu003Straub, D., Yang, H., Liu, Y., Tsap, T., & Ludewig, U. (2013). Root ethylene signalling is involved in Miscanthus sinensis growth promotion by the bacterial endophyte Herbaspirillum frisingense GSF30T. Journal of Experimental Botany, 64(14), 4603–4615. https://doi.org/10.1093/jxb/ert276Sánchez-Vallet, A., Saleem-Batcha, R., Kombrink, A., Hansen, G., Valkenburg, D.-J., Thomma, B. P., & Mesters, J. R. (2013). Fungal effector Ecp6 outcompetes host immune receptor for chitin binding through intrachain LysM dimerization. eLife, 2, e00790. https://doi.org/10.7554/eLife.00790Sugawara, S., Mashiguchi, K., Tanaka, K., Hishiyama, S., Sakai, T., Hanada, K., Kinoshita-Tsujimura, K., Yu, H., Dai, X., Takebayashi, Y., Takeda-Kamiya, N., Kakimoto, T., Kawaide, H., Natsume, M., Estelle, M., Zhao, Y., Hayashi, K., Kamiya, Y., & Kasahara, H. (2015). Distinct Characteristics of Indole-3-Acetic Acid and Phenylacetic Acid, Two Common Auxins in Plants. Plant and Cell Physiology, 56(8), 1641–1654. https://doi.org/10.1093/pcp/pcv088Santoyo, G., Moreno-Hagelsieb, G., Del Carmen Orozco-Mosqueda, Ma., &Sun, S., Sidhu, V., Rong, Y., & Zheng, Y. (2018). Pesticide Pollution in Agricultural Soils and Sustainable Remediation Methods: A Review. Current Pollution Reports, 4(3), 240–250. https://doi.org/10.1007/s40726-018-0092-xGlick, B. R. (2016). Plant growth-promoting bacterial endophytes. Microbiological Research, 183, 92–99. https://doi.org/10.1016/j.micres.2015.11.008Syed Ab Rahman, S. F., Singh, E., Pieterse, C. M. J., & Schenk, P. M. (2018). Emerging microbial biocontrol strategies for plant pathogens. Plant Science, 267, 102–111. https://doi.org/10.1016/j.plantsci.2017.11.012Segmüller, N., Kokkelink, L., Giesbert, S., Odinius, D., Van Kan, J., & Tudzynski, P. (2008). NADPH oxidases are involved in differentiation and pathogenicity in Botrytis cinerea. Molecular Plant-Microbe Interactions®, 21(6), 808–819. https://doi.org/10.1094/MPMI-21-6-0808Taghavi, S., Garafola, C., Monchy, S., Newman, L., Hoffman, A., Weyens, N.,Sowa, S. W., Gelderman, G., Leistra, A. N., Buvanendiran, A., Lipp, S., Pitaktong, A., Vakulskas, C. A., Romeo, T., Baldea, M., & Contreras, L. M. (2017). Integrative FourD omics approach profiles the target network of the carbon storage regulatory system. Nucleic Acids Research, gkx048. https://doi.org/10.1093/nar/gkx048Barac, T., Vangronsveld, J., & Van Der Lelie, D. (2009). Genome Survey and Characterization of Endophytic Bacteria Exhibiting a Beneficial Effect on Growth and Development of Poplar Trees. Applied and Environmental Microbiology, 75(3), 748–757. https://doi.org/10.1128/AEM.02239-08Straub, D., Yang, H., Liu, Y., Tsap, T., & Ludewig, U. (2013). Root ethylene signalling is involved in Miscanthus sinensis growth promotion by the bacterial endophyte Herbaspirillum frisingense GSF30T. Journal of Experimental Botany, 64(14), 4603–4615. https://doi.org/10.1093/jxb/ert276Tao, Y., Jia, C., Jing, J., Zhang, J., Yu, P., He, M., Wu, J., Chen, L., & Zhao, E. (2021). Occurrence and dietary risk assessment of 37 pesticides in wheat fields in the suburbs of Beijing, China. Food Chemistry, 350, 129245. https://doi.org/10.1016/j.foodchem.2021.129245Sugawara, S., Mashiguchi, K., Tanaka, K., Hishiyama, S., Sakai, T., Hanada, K., Kinoshita-Tsujimura, K., Yu, H., Dai, X., Takebayashi, Y., Takeda-Kamiya, N., Kakimoto, T., Kawaide, H., Natsume, M., Estelle, M., Zhao, Y., Hayashi, K., Kamiya, Y., & Kasahara, H. (2015). Distinct characteristics of Indole-3-Acetic acid and phenylacetic acid, two common auxins in plants. Plant and Cell Physiology, 56(8), 1641–1654. https://doi.org/10.1093/pcp/pcv088Terblanche, J. S., Hoffmann, A. A., Mitchell, K. A., Rako, L., Le Roux, P. C., & Chown, S. L. (2011). Ecologically relevant measures of tolerance to potentially lethal temperatures. Journal of Experimental Biology, 214(22), 3713–3725. https://doi.org/10.1242/jeb.061283Sun, S., Sidhu, V., Rong, Y., & Zheng, Y. (2018). Pesticide pollution in agricultural soils and sustainable remediation methods: a review. Current Pollution Reports, 4(3), 240–250. https://doi.org/10.1007/s40726-018-0092-xUtturkar, S. M., Cude, W. N., Robeson, M. S., Yang, Z. K., Klingeman, D. M., Land, M. L., Allman, S. L., Lu, T.-Y. S., Brown, S. D., Schadt, C. W., Podar, M., Doktycz, M. J., & Pelletier, D. A. (2016). Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis. Applied and Environmental Microbiology, 82(18), 5698–5708. https://doi.org/10.1128/AEM.01285-16Syed Ab Rahman, S. F., Singh, E., Pieterse, C. M. J., & Schenk, P. M. (2018). Emerging microbial biocontrol strategies for plant pathogens. Plant Science, 267, 102–111. https://doi.org/10.1016/j.plantsci.2017.11.012Vahabi, K., Sherameti, I., Bakshi, M., Mrozinska, A., Ludwig, A., & Oelmüller, R. (2015). Microarray analyses during early and later stages of the Arabidopsis/ Piriformospora indica interaction. Genomics Data, 6, 16–18. https://doi.org/10.1016/j.gdata.2015.07.019Taghavi, S., Garafola, C., Monchy, S., Newman, L., Hoffman, A., Weyens, N.,Vandenkoornhuyse, P., Quaiser, A., Duhamel, M., Le Van, A., & Dufresne, A. (2015). The importance of the microbiome of the plant holobiont. New Phytologist, 206(4), 1196–1206. https://doi.org/10.1111/nph.13312Barac, T., Vangronsveld, J., & Van Der Lelie, D. (2009). Genome survey and characterization of endophytic bacteria exhibiting a beneficial effect on growth and development of poplar trees. Applied and Environmental Microbiology, 75(3), 748–757. https://doi.org/10.1128/AEM.02239-08Vibhuti, M., Kumar, A., Sheoran, N., Nadakkakath, A. V., & Eapen, S. J. (2017). Molecular Basis of Endophytic Bacillus megaterium-induced Growth Promotion in Arabidopsis thaliana: Revelation by Microarray-based Gene Expression Analysis. Journal of Plant Growth Regulation, 36(1), 118–130. https://doi.org/10.1007/s00344-016-9624-zTao, Y., Jia, C., Jing, J., Zhang, J., Yu, P., He, M., Wu, J., Chen, L., & Zhao, E. (2021). Occurrence and dietary risk assessment of 37 pesticides in wheat fields in the suburbs of Beijing, China. Food Chemistry, 350, 129245. https://doi.org/10.1016/j.foodchem.2021.129245Ważny, R., Rozpądek, P., Domka, A., Jędrzejczyk, R. J., Nosek, M.,Terblanche, J. S., Hoffmann, A. A., Mitchell, K. A., Rako, L., Le Roux, P. C., & Chown, S. L. (2011). Ecologically relevant measures of tolerance to potentially lethal temperatures. Journal of Experimental Biology, 214(22), 3713–3725. https://doi.org/10.1242/jeb.061283Hubalewska-Mazgaj, M., Lichtscheidl, I., Kidd, P., & Turnau, K. (2021). The effect of endophytic fungi on growth and nickel accumulation in Noccaea hyperaccumulators. Science of The Total Environment, 768, 144666. https://doi.org/10.1016/j.scitotenv.2020.144666Utturkar, S. M., Cude, W. N., Robeson, M. S., Yang, Z. K., Klingeman, D. M., Land, M. L., Allman, S. L., Lu, T.-Y. S., Brown, S. D., Schadt, C. W., Podar, M., Doktycz, M. J., & Pelletier, D. A. (2016). Enrichment of root endophytic bacteria from populus deltoides and single-cell-genomics analysis. Applied and Environmental Microbiology, 82(18), 5698–5708. https://doi.org/10.1128/AEM.01285-16Wei, W., Zhu, W., Cheng, J., Xie, J., Jiang, D., Li, G., Chen, W., & Fu, Y. (2016). Nox Complex signal and MAPK cascade pathway are cross-linked and essential for pathogenicity and conidiation of mycoparasite Coniothyrium minitans. Scientific Reports, 6(1). https://doi.org/10.1038/srep24325Vahabi, K., Sherameti, I., Bakshi, M., Mrozinska, A., Ludwig, A., & Oelmüller, R. (2015). Microarray analyses during early and later stages of the Arabidopsis/ Piriformospora indica interaction. Genomics Data, 6, 16–18. https://doi.org/10.1016/j.gdata.2015.07.019Weilharter, A., Mitter, B., Shin, M. V., Chain, P. S. G., Nowak, J., & Sessitsch, A. (2011). Complete Genome Sequence of the Plant Growth-Promoting Endophyte Burkholderia phytofirmans Strain PsJN. Journal of Bacteriology, 193(13), 3383–3384. https://doi.org/10.1128/JB.05055-11Vandenkoornhuyse, P., Quaiser, A., Duhamel, M., Le Van, A., & Dufresne, A. (2015). The importance of the microbiome of the plant holobiont. New Phytologist, 206(4), 1196–1206. https://doi.org/10.1111/nph.13312Yan, Y., Yang, J., Dou, Y., Chen, M., Ping, S., Peng, J., Lu, W., Zhang, W., Yao, Z., Li, H., Liu, W., He, S., Geng, L., Zhang, X., Yang, F., Yu, H., Zhan, Y., Li, D., Lin, Z., … Jin, Q. (2008). Nitrogen fixation island and rhizosphere competence traits in the genome of root-associated Pseudomonas stutzeri A1501. Proceedings of the National Academy of Sciences, 105(21), 7564–7569. https://doi.org/10.1073/pnas.0801093105Vibhuti, M., Kumar, A., Sheoran, N., Nadakkakath, A. V., & Eapen, S. J. (2017). Molecular basis of endophytic Bacillus megaterium-induced growth promotion in arabidopsis thaliana: revelation by microarray-based gene expression analysis. Journal of Plant Growth Regulation, 36(1), 118–130. https://doi.org/10.1007/s00344-016-9624-zYin, C., Mueth, N., Hulbert, S., Schlatter, D., Paulitz, T. C., Schroeder, K.,Ważny, R., Rozpądek, P., Domka, A., Jędrzejczyk, R. J., Nosek, M.,Prescott, A., & Dhingra, A. (2017). Bacterial Communities on Wheat Grown Under Long-Term Conventional Tillage and No-Till in the Pacific Northwest of the United States. Phytobiomes Journal, 1(2), 83–90. https://doi.org/10.1094/PBIOMES-09-16-0008-RHubalewska-Mazgaj, M., Lichtscheidl, I., Kidd, P., & Turnau, K. (2021). The effect of endophytic fungi on growth and nickel accumulation in Noccaea hyperaccumulators. Science of The Total Environment, 768, 144666. https://doi.org/10.1016/j.scitotenv.2020.144666Zhang, W., Wang, J., Xu, L., Wang, A., Huang, L., Du, H., Qiu, L., & Oelmüller, R. (2018). Drought stress responses in maize are diminished by Piriformospora indica. Plant Signaling & Behavior, 13(1), e1414121. https://doi.org/10.1080/15592324.2017.1414121Wei, W., Zhu, W., Cheng, J., Xie, J., Jiang, D., Li, G., Chen, W., & Fu, Y. (2016). Nox Complex signal and MAPK cascade pathway are cross-linked and essential for pathogenicity and conidiation of mycoparasite Coniothyrium minitans. Scientific Reports, 6(1). https://doi.org/10.1038/srep24325Zhao, C., Liu, B., Piao, S., Wang, X., Lobell, D. B., Huang, Y., Huang, M., Yao, Y., Bassu, S., Ciais, P., Durand, J.-L., Elliott, J., Ewert, F., Janssens, I. A., Li, T.,Weilharter, A., Mitter, B., Shin, M. V., Chain, P. S. G., Nowak, J., & Sessitsch, A. (2011). Complete genome sequence of the plant growth-promoting endophyte Burkholderia phytofirmans Strain PsJN. Journal of Bacteriology, 193(13), 3383–3384. https://doi.org/10.1128/JB.05055-11Lin, E., Liu, Q., Martre, P., Müller, C., … Asseng, S. (2017). Temperature increase reduces global yields of major crops in four independent estimates. Proceedings of the National Academy of Sciences of the United States of America, 114(35), 9326–9331. https://doi.org/10.1073/pnas.1701762114Yan, Y., Yang, J., Dou, Y., Chen, M., Ping, S., Peng, J., Lu, W., Zhang, W., Yao, Z., Li, H., Liu, W., He, S., Geng, L., Zhang, X., Yang, F., Yu, H., Zhan, Y., Li, D., Lin, Z., … Jin, Q. (2008). Nitrogen fixation island and rhizosphere competence traits in the genome of root-associated Pseudomonas stutzeri A1501. Proceedings of the National Academy of Sciences, 105(21), 7564–7569. https://doi.org/10.1073/pnas.0801093105Zhou, J., Li, X., Huang, P.-W., & Dai, C.-C. (2018). Endophytism or saprophytism: Decoding the lifestyle transition of the generalist fungusYin, C., Mueth, N., Hulbert, S., Schlatter, D., Paulitz, T. C., Schroeder, K.,Phomopsis liquidambari. Microbiological Research, 206, 99–112. https://doi.org/10.1016/j.micres.2017.10.005Prescott, A., & Dhingra, A. (2017). Bacterial communities on wheat grown under long-term conventional tillage and no-till in the pacific northwest of the united states. Phytobiomes Journal, 1(2), 83–90. https://doi.org/10.1094/PBIOMES-09-16-0008-RPrescott, A., & Dhingra, A. (2017). Bacterial communities on wheat grown under long-term conventional tillage and no-till in the pacific northwest of the united states. Phytobiomes Journal, 1(2), 83–90. https://doi.org/10.1094/PBIOMES-09-16-0008-RZhang, W., Wang, J., Xu, L., Wang, A., Huang, L., Du, H., Qiu, L., & Oelmüller, R. (2018). Drought stress responses in maize are diminished by Piriformospora indica. Plant Signaling & Behavior, 13(1), e1414121. https://doi.org/10.1080/15592324.2017.1414121Zhang, W., Wang, J., Xu, L., Wang, A., Huang, L., Du, H., Qiu, L., & Oelmüller, R. (2018). Drought stress responses in maize are diminished by Piriformospora indica. Plant Signaling & Behavior, 13(1), e1414121. https://doi.org/10.1080/15592324.2017.1414121Zhao, C., Liu, B., Piao, S., Wang, X., Lobell, D. B., Huang, Y., Huang, M., Yao, Y., Bassu, S., Ciais, P., Durand, J.-L., Elliott, J., Ewert, F., Janssens, I. A., Li, T.,Zhao, C., Liu, B., Piao, S., Wang, X., Lobell, D. B., Huang, Y., Huang, M., Yao, Y., Bassu, S., Ciais, P., Durand, J.-L., Elliott, J., Ewert, F., Janssens, I. A., Li, T.,Lin, E., Liu, Q., Martre, P., Müller, C., Peng, S., Peñuelas, J., Ruane, A. C., Wallach, D., Wang, T., Wu, D., Liu, Z., Zhu, Y., Zhu, Z., Asseng, S. (2017). Temperature increase reduces global yields of major crops in four independent estimates. Proceedings of the National Academy of Sciences of the United States of America, 114(35), 9326–9331. https://doi.org/10.1073/pnas.1701762114Lin, E., Liu, Q., Martre, P., Müller, C., Peng, S., Peñuelas, J., Ruane, A. C., Wallach, D., Wang, T., Wu, D., Liu, Z., Zhu, Y., Zhu, Z., Asseng, S. (2017). Temperature increase reduces global yields of major crops in four independent estimates. Proceedings of the National Academy of Sciences of the United States of America, 114(35), 9326–9331. https://doi.org/10.1073/pnas.1701762114Zhou, J., Li, X., Huang, P.-W., & Dai, C.-C. (2018). Endophytism or saprophytism: Decoding the lifestyle transition of the generalist fungusZhou, J., Li, X., Huang, P.-W., & Dai, C.-C. (2018). Endophytism or saprophytism: Decoding the lifestyle transition of the generalist fungusPhomopsis liquidambari. Microbiological Research, 206, 99–112. https://doi.org/10.1016/j.micres.2017.10.005Phomopsis liquidambari. Microbiological Research, 206, 99–112. https://doi.org/10.1016/j.micres.2017.10.005

The authors declare that there are no conflicts of interest present.