COMPARATIVE GENOMIC PROFILING OF PLANT-ASSOCIATED BACTERIA WITH AGRICULTURAL IMPORTANCE
DOI:
https://doi.org/10.53555/gafs.v12i1.2573Keywords:
plant-associated bacteria, comparative genomics, PGPR, genome size, GC content, sustainable agricultureAbstract
Plant-associated bacteria have significant contributions to plant-growth promotion, nutrient cycling, stress tolerance, rhizosphere adaptation and biological control thus are a valuable part of sustainable agriculture. This study was performed to comparatively estimate the genomic characteristics of the plant-associated bacterial genera, which were based on the genome size, GC content, coding sequence abundance, scaffold number, and multivariate genomic patterns. A total of 944 bacterial genome records of 11 genera were studied. The results of descriptive analysis revealed significant differences in the size of the genomes between the genera, with Paraburkholderia, Streptomyces and Bradyrhizobium having relatively large genomes and Streptomyces having the highest mean GC content. The genus-level differences in genome size, GC content, coding sequences, and scaffold number were significant (p < 0.001). We found that abundance of coding sequences (abundance of proteins) was positively correlated with genome size (ρ = 0.964; p < 0.001), suggesting that larger genomes have more protein-coding potential. PCA revealed that the 1st and 2nd principal components accounted for 90.71% of the total genomic variation, indicating a clear distinction among the different groups of bacteria. In general, the results show high genomic diversity within the prokaryotic populations associated with plants that are germplasm resources for agricultural applications, including the identification of taxa that may be useful in biofertilization, biostimulation, nutrient acquisition and biocontrol.
Downloads
References
Alghamdi, A. K., Parween, S., Hirt, H., & Saad, M. M. (2023). Complete genome sequence analysis of plant growth-promoting bacterium, Isoptericola sp. AK164 isolated from the rhizosphere of Avicennia marina growing at the Red Sea coast. Archives of Microbiology, 205(9), 307.
Aloo, B. N., Mbega, E. R., Makumba, B. A., Friedrich, I., Hertel, R., & Daniel, R. (2020). Whole-genome sequences of three plant growth-promoting rhizobacteria isolated from Solanum tuberosum L. rhizosphere in Tanzania. Microbiology Resource Announcements, 9(20), 10-1128.
Aloo, B. N., Tripathi, V., Makumba, B. A., & Mbega, E. R. (2022). Plant growth-promoting rhizobacterial biofertilizers for crop production: The past, present, and future. Frontiers in Plant Science, 13, 1002448.
Ayilara, M. S., Adeleke, B. S., & Babalola, O. O. (2023). Bioprospecting and challenges of plant microbiome research for sustainable agriculture, a review on soybean endophytic bacteria. Microbial ecology, 85(3), 1113-1135.
Babalola, O. O., Agbodjato, N. A., Ayangbenro, A. S., Adjanohoun, A., & Baba-Moussa, L. (2022). Draft Genome Sequences of Four Strains of Plant Growth-Promoting Bacteria Associated with Maize Rhizosphere. Microbiology Resource Announcements, 11(11), e00730-22.
Bandeppa, S., Phule, A. S., Barbadikar, K. M., Govindannagari, R., B, P. B. M., Kavuru, V. P. B., ... & Chandran, L. P. (2022). Draft genome sequence of Paenibacillus sonchi Iirrbnf1, a nitrogen-fixing and plant growth-promoting bacterium isolated from rice Rhizosphere. Microbiology Resource Announcements, 11(5), e00126-22.
Berrios, L. (2021). Complete genome sequence of the plant-growth-promoting bacterium Caulobacter segnis CBR1. Current microbiology, 78(8), 2935-2942.
Bhadrecha, P., Singh, S., & Dwibedi, V. (2023). ‘A plant’s major strength in rhizosphere’: the plant growth promoting rhizobacteria. Archives of Microbiology, 205(5), 165.
Bhanse, P., Kumar, M., Singh, L., Awasthi, M. K., & Qureshi, A. (2022). Role of plant growth-promoting rhizobacteria in boosting the phytoremediation of stressed soils: Opportunities, challenges, and prospects. Chemosphere, 303, 134954.
Carvalho, I. D., Apaza-Castillo, G. A., Paz, I. C. P., Guimarães, A. M., Quecine, M. C., & Bonatelli, M. L. (2023). Draft genome sequence of the plant growth promoter and biocontrol agent Bacillus velezensis strain BIB0110. Microbiology Resource Announcements, 12(6), e00231-23.
Chandra, A., Chandra, P., & Tripathi, P. (2021). Whole genome sequence insight of two plant growth-promoting bacteria (B. subtilis BS87 and B. megaterium BM89) isolated and characterized from sugarcane rhizosphere depicting better crop yield potentiality. Microbiological research, 247, 126733.
Chialva, M., Lanfranco, L., & Bonfante, P. (2022). The plant microbiota: composition, functions, and engineering. Current Opinion in Biotechnology, 73, 135-142.
Chouhan, G. K., Verma, J. P., Jaiswal, D. K., Mukherjee, A., Singh, S., de Araujo Pereira, A. P., ... & Singh, B. K. (2021). Phytomicrobiome for promoting sustainable agriculture and food security: opportunities, challenges, and solutions. Microbiological Research, 248, 126763.
Das, P. P., Singh, K. R., Nagpure, G., Mansoori, A., Singh, R. P., Ghazi, I. A., ... & Singh, J. (2022). Plant-soil-microbes: A tripartite interaction for nutrient acquisition and better plant growth for sustainable agricultural practices. Environmental Research, 214, 113821.
Diwan, D., Rashid, M. M., & Vaishnav, A. (2022). Current understanding of plant-microbe interaction through the lenses of multi-omics approaches and their benefits in sustainable agriculture. Microbiological research, 265, 127180.
Gupta, R., Anand, G., Gaur, R., & Yadav, D. (2021). Plant–microbiome interactions for sustainable agriculture: a review. Physiology and Molecular Biology of Plants, 27(1), 165-179.
Han, S. W., & Yoshikuni, Y. (2022). Microbiome engineering for sustainable agriculture: using synthetic biology to enhance nitrogen metabolism in plant-associated microbes. Current opinion in microbiology, 68, 102172.
Jiao, H., Xu, W., Chen, W., Hu, Y., Tian, R., & Wang, Z. (2022). Complete genome sequence data of Bacillus altitudinis LZP02, a bacterium from the rice rhizosphere, for studying the promotion of plant growth. Molecular Plant-Microbe Interactions, 35(5), 428-431.
Ke, J., Wang, B., & Yoshikuni, Y. (2021). Microbiome engineering: synthetic biology of plant-associated microbiomes in sustainable agriculture. Trends in Biotechnology, 39(3), 244-261.
Khalifa, A., & Alsowayeh, N. (2023). Whole-genome sequence insight into the plant-growth-promoting bacterium Priestia filamentosa strain AZC66 obtained from Zygophyllum coccineum rhizosphere. Plants, 12(10), 1944.
Kumawat, K. C., Nagpal, S., & Sharma, P. (2022). Potential of plant growth-promoting rhizobacteria-plant interactions in mitigating salt stress for sustainable agriculture: A review. Pedosphere, 32(2), 223-245.
Leontidou, K., Genitsaris, S., Papadopoulou, A., Kamou, N., Bosmali, I., Matsi, T., ... & Mellidou, I. (2020). Plant growth promoting rhizobacteria isolated from halophytes and drought-tolerant plants: genomic characterisation and exploration of phyto-beneficial traits. Scientific reports, 10(1), 14857.
Luo, Y., Zhou, M., Zhao, Q., Wang, F., Gao, J., Sheng, H., & An, L. (2020). Complete genome sequence of Sphingomonas sp. Cra20, a drought resistant and plant growth promoting rhizobacteria. Genomics, 112(5), 3648-3657.
Mishra, P., Mishra, J., & Arora, N. K. (2021). Plant growth promoting bacteria for combating salinity stress in plants–Recent developments and prospects: A review. Microbiological Research, 252, 126861.
Mukhia, S., Kumar, A., Kumari, P., & Kumar, R. (2022). Psychrotrophic plant beneficial bacteria from the glacial ecosystem of Sikkim Himalaya: genomic evidence for the cold adaptation and plant growth promotion. Microbiological research, 260, 127049.
Nanjani, S., Soni, R., Paul, D., & Keharia, H. (2022). Genome analysis uncovers the prolific antagonistic and plant growth-promoting potential of endophyte Bacillus velezensis K1. Gene, 836, 146671.
Nugent, C. (2018). Genome information for sequenced organisms [Data set]. Kaggle.
Genome Information for Sequenced Organisms – Kaggle
Downloads
Published
How to Cite
Issue
Section
License
Copyright (c) 2026 International Journal For Research In Agricultural And Food Science
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
In consideration of the journal, Green Publication taking action in reviewing and editing our manuscript, the authors undersigned hereby transfer, assign, or otherwise convey all copyright ownership to the Editorial Office of the Green Publication in the event that such work is published in the journal. Such conveyance covers any product that may derive from the published journal, whether print or electronic. Green Publication shall have the right to register copyright to the Article in its name as claimant, whether separately
or as part of the journal issue or other medium in which the Article is included.
By signing this Agreement, the author(s), and in the case of a Work Made For Hire, the employer, jointly and severally represent and warrant that the Article is original with the author(s) and does not infringe any copyright or violate any other right of any third parties, and that the Article has not been published elsewhere, and is not being considered for publication elsewhere in any form, except as provided herein. Each author’s signature should appear below. The signing author(s) (and, in
