Plant Viruses and Plant Growth Promoting Rhizobacteria (PGPR) Relationships: A Shiny Application

Faruk Öncü, Kubilay Kurtuluş Baştaş


In the face of climate change, the point of view of existing agricultural production systems is changing, and biological issues are gaining importance in terms of sustainable agriculture. Environmentally friendly biological solutions come to the forefront in the management of diseases and pests that put pressure on sustainable agriculture. It has been proven by many studies that plant growth promoting rhizobacteria (PGPR) have positive effects on plant growth, as well as reduce or prevent viral diseases. However, determining the targeted virus species, the PGPR strains used, or the plant strains tested requires a serious literature review and reading. In this study, which can be considered as a preliminary study, a database of PGPR and plant virus relations literature was created in a dynamic infrastructure that can be constantly updated, and a web interface was developed as an R/shiny application. Thanks to this preliminary study, which has examples in different fields, it is thought that it is possible for researchers to quickly access the literature on the subject, plan cost-effective projects, and identify the missing or potential points of the subject. According to the information in the database, it was determined that CMV was the most targeted virus, different strains of Bacillus and Pseudomonas genera were used the most as PGPR agent, tomato (Solanum lycopersicum) and cucumber (Cucumis sativus) were the most tested plant species, and single applications were tested more. It is thought that this and similar studies will enable researchers to gain a quick perspective on the subject, facilitate the management of the information they have acquired, and contribute to effective planning in their new studies.


biological control; database; PGPR; plant viruses; Shiny; Web interface

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Antezana E, Kuiper M, Mironov V (2009). Biological knowledge management: the emerging role of the Semantic Web technologies. Brief Bioinformatics 10:392–407.

Chang W, Cheng J, Allaire J, Xie Y, McPherson J (2017). Shiny: web application framework for R. R package version 1:2017

Chávez‐Dulanto PN, Thiry AAA, Glorio‐Paulet P, Vögler O, Carvalho FP (2021). Increasing the impact of science and technology to provide more people with healthier and safer food. Food Energy Secur 10.

Corrêa FB, Saraiva JP, Stadler PF, da Rocha UN (2020). TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes. Nucleic Acids Res 48:D626-D632.

Dowle M, Srinivasan A (2022). data.table: Extension of ‘data.frame‘,,

Dubey A, Malla MA, Khan F, Chowdhary K, Yadav S, Kumar A, Sharma S, Khare PK, Khan ML (2019). Soil microbiome: a key player for conservation of soil health under changing climate. Biodivers Conserv 28:2405–2429.

Fanidis D, Moulos P, Aidinis V (2021). Fibromine is a multi-omics database and mining tool for target discovery in pulmonary fibrosis. Sci Rep 11:21712.

Giorgi FM, Ceraolo C, Mercatelli D (2022). The R Language: An Engine for Bioinformatics and Data Science. Life (Basel) 12.

Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods 15:475–476.

Jia L, Yao W, Jiang Y, Li Y, Wang Z, Li H, Huang F, Li J, Chen T, Zhang H (2022). Development of interactive biological web applications with R/Shiny. Brief Bioinformatics 23.

Khoshru B, Mitra D, Khoshmanzar E, Myo EM, Uniyal N, Mahakur B, Mohapatra PKD, Panneerselvam P, Boutaj H, Alizadeh M, Cely MVT, Senapati A, Rani A (2020). Current scenario and future prospects of plant growth-promoting rhizobacteria: an economic valuable resource for the agriculture revival under stressful conditions. Journal of Plant Nutrition 43:3062–3092.

Maksimov IV, Sorokan AV, Burkhanova GF, Veselova SV, Alekseev VY, Shein M, Avalbaev AM, Dhaware PD, Mehetre GT, Singh BP, Khairullin RM (2019). Mechanisms of Plant Tolerance to RNA Viruses Induced by Plant-Growth-Promoting Microorganisms. Plants (Basel) 8.

Nhemachena C, Nhamo L, Matchaya G, Nhemachena CR, Muchara B, Karuaihe ST, Mpandeli S (2020). Climate Change Impacts on Water and Agriculture Sectors in Southern Africa: Threats and Opportunities for Sustainable Development. Water 12:2673.

Priya P, Aneesh B, Harikrishnan K (2021). Genomics as a potential tool to unravel the rhizosphere microbiome interactions on plant health. J Microbiol Methods 185:106215.

R Core Team (2021). R: A Language and Environment for Statistical Computing: R Foundation for Statistical Computing

RStudio Team (2013). shiny: Easy web applications in R

RStudio Team (2020). RStudio: Integrated Development Environment for R

Satyahadewi N, Perdana H (2021). Web Application Development for Inferential Statistics using R Shiny. In: Proceedings of the 1st International Conference on Mathematics and Mathematics Education (ICMMEd 2020). Atlantis PressParis, France

Schoch CL, Ciufo S, Domrachev M, Hotton CL, Kannan S, Khovanskaya R, Leipe D, Mcveigh R, O’Neill K, Robbertse B, Sharma S, Soussov V, Sullivan JP, Sun L, Turner S, Karsch-Mizrachi I (2020). NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database (Oxford) 2020.

Sievert C (2020). Interactive web-based data visualization with r, plotly, and shiny, 1st edn. Chapman & Hall/CRC the R series. Chapman & Hall/CRC, Boca Raton

Targen S, Kaya T, Avci ME, Gunes D, Keskus AG, Konu O (2020). ZenoFishDb v1.1: A Database for Xenotransplantation Studies in Zebrafish. Zebrafish 17:305–318.

Walker PJ, Siddell SG, Lefkowitz EJ, Mushegian AR, Adriaenssens EM, Alfenas-Zerbini P, Dempsey DM, Dutilh BE, García ML, Curtis Hendrickson R, Junglen S, Krupovic M, Kuhn JH, Lambert AJ, Łobocka M, Oksanen HM, Orton RJ, Robertson DL, Rubino L, Sabanadzovic S, Simmonds P, Smith DB, Suzuki N, van Doorslaer K, Vandamme A-M, Varsani A, Zerbini FM (2022). Recent changes to virus taxonomy ratified by the International Committee on Taxonomy of Viruses (2022). Arch Virol 167:2429–2440.

Wang C, Chen L, Zhang M, Yang Y, Wong G (2020). PDmethDB: A curated Parkinson’s disease associated methylation information database. Comput Struct Biotechnol J 18:3745–3749.

Wickham H, Averick M, Bryan J, Chang W, McGowan L, François R, Grolemund G, Hayes A, Henry L, Hester J, Kuhn M, Pedersen T, Miller E, Bache S, Müller K, Ooms J, Robinson D, Seidel D, Spinu V, Takahashi K, Vaughan D, Wilke C, Woo K, Yutani H (2019). Welcome to the Tidyverse. JOSS 4:1686.

Xu C, Ma D, Ding Q, Zhou Y, Zheng H-L (2022). PlantPhoneDB: A manually curated pan-plant database of ligand-receptor pairs infers cell-cell communication. Plant Biotechnol J.

Yadav AN (2020). Plant Microbiomes for Sustainable Agriculture: Current Research and Future Challenges. In: Plant Microbiomes for Sustainable Agriculture. Springer, Cham, pp 475–482.


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