A review of plant microbiome: Its functions and components
Keywords:
Microbiome, phyllosphere, endosphere, rhizosphere, endophyte
Abstract
Microbes are living organisms that are lived everywhere in our environment. They occupy a place in, on, and around humans, plants, and animals. They have mutualistic, parasitic, and commensalism relationships with other organisms. The study of these microorganisms which live in a special habitat is called the microbiome. Plant microbiome function and their types have been discussed. Phyllosphere, endosphere, and rhizosphere microbiomes take important roles in plant growth by multiple mechanisms. It has been declared that Microbiome is important for us, animals, and as well as plants. Mutualistic microorganisms support animals' and plants' health and protect them from diseases and pests. The phyllosphere, endosphere, and rhizosphere are the components of the plant that live plenty of microbes there. They fix nitrogen, dissolve nutrients, decompose organic materials, and promote plant growth. To sum up, microbes clean up our environment, decompose wastes, help diet, support survival, and do many tasks in, on, and around organisms.
References
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Kumari, B., Mani, M., Solanki, A. C., Solanki, M. K., Hora, A., & Mallick, M. A. (2020). Phytobiome engineering and its impact on next-generation agriculture. Phytobiomes: current insights and future vistas, 381-403.
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Lebeis, S. L. (2015). Greater than the sum of their parts: characterizing plant microbiomes at the community-level. Current opinion in plant biology, 24, 82-86.
Leveau, J. H. (2015). Life of microbes on aerial plant parts. Principles of Plant-Microbe Interactions: Microbes for Sustainable Agriculture, 17-24.
Lindow, S. E., &Brandl, M. T. (2003). Microbiology of the phyllosphere. Applied and environmental microbiology, 69(4), 1875-1883.
Lugtenberg, B. (2015). Life of microbes in the rhizosphere. Principles of plant-microbe interactions: microbes for sustainable agriculture, 7-15.
Mendes, R., Garbeva, P., &Raaijmakers, J. M. (2013). The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS microbiology reviews, 37(5), 634-663.
Miransari, M. (2013). Soil microbes and the availability of soil nutrients. Acta physiologiae plantarum, 35(11), 3075-3084.
Mokrani, S., & El-Hafid, N. (2020). Rhizospheric microbiome: biodiversity, current advancement and potential biotechnological applications. Advances in Plant Microbiome and Sustainable Agriculture: Diversity and Biotechnological Applications, 39-60.
Nadarajah, K. K. (2019). Microbes: an important resource for sustainable agriculture. Microbiome in Plant Health and Disease: Challenges and Opportunities, 53-77.
Panke-Buisse, K., Poole, A. C., Goodrich, J. K., Ley, R. E., & Kao-Kniffin, J. (2015). Selection on soil microbiomes reveals reproducible impacts on plant function. The ISME journal, 9(4), 980.
Philippot, L., Raaijmakers, J. M., Lemanceau, P., & Van Der Putten, W. H. (2013). Going back to the roots: the microbial ecology of the rhizosphere. Nature Reviews Microbiology, 11(11), 789.
Postgate, J. (2000). Microbes and man. Cambridge University Press.
Prieto, P., Schilirò, E., Maldonado-González, M. M., Valderrama, R., Barroso-Albarracín, J. B., & Mercado-Blanco, J. (2011). Root hairs play a key role in the endophytic colonization of olive roots by Pseudomonas spp. with biocontrol activity. Microbial ecology, 62(2), 435-445.
Rossmann, M., Sarango-Flores, S. W., Chiaramonte, J. B., Kmit, M. C. P., & Mendes, R. (2017). Plant Microbiome: Composition and Functions in Plant Compartments. In The Brazilian Microbiome (pp. 7-20). Springer, Cham.
Saha, M., Sarkar, A., Roy, T., Biswas, S. S., & Mandal, A. (2020). Phytobiomes: role in nutrient stewardship and soil health. Phytobiomes: Current Insights and Future Vistas, 1-28.
Saleem, M. (2015). Microbiome ecosystem ecology: unseen majority in an anthropogenic ecosystem. In Microbiome Community Ecology (pp. 1-11). Springer International Publishing.
Saleem, M., & Saleem, M. (2015). Loss of microbiome ecological niches and diversity by global change and trophic downgrading. Microbiome Community Ecology: Fundamentals and Applications, 89-113.
Schulz, B., & Boyle, C. (2005). The endophytic continuum. Mycological research, 109(6), 661-686
Singh, S. P., Bhattacharya, A., Gupta, R., Mishra, A., Zaidi, F. A., & Srivastava, S. (2020). Endophytic Phytobiomes as Defense Elicitors: Current Insights and Future Prospects. Phytobiomes: Current Insights and Future Vistas, 299-334.
Subrahmanyam, G., Kumar, A., Sandilya, S. P., Chutia, M., & Yadav, A. N. (2020). Diversity, plant growth promoting attributes, and agricultural applications of rhizospheric microbes. Plant microbiomes for sustainable agriculture, 1-52.
Sugiyama, A., Ueda, Y., Zushi, T., Takase, H., & Yazaki, K. (2014). Changes in the bacterial community of soybean rhizospheres during growth in the field. PLoS One, 9(6), e100709.
Taylor, L. L., Leake, J. R., Quirk, J., Hardy, K., Banwart, S. A., &Beerling, D. J. (2009). Biological weathering and the long‐term carbon cycle: integrating mycorrhizal evolution and function into the current paradigm. Geobiology, 7(2), 171-191.
Toal, M. E., Yeomans, C., Killham, K., &Meharg, A. A. (2000). A review of rhizosphere carbon flow modelling. Plant and soil, 222(1-2), 263-281.
Trivedi, P., Batista, B. D., Bazany, K. E., & Singh, B. K. (2022). Plant–microbiome interactions under a changing world: Responses, consequences and perspectives. New Phytologist, 234(6), 1951-1959.
Turner, T. R., James, E. K., & Poole, P. S. (2013). The plant microbiome. Genome biology, 14(6), 209.
Ursell, L. K., Metcalf, J. L., Parfrey, L. W., & Knight, R. (2012). Defining the human microbiome. Nutrition reviews, 70 (suppl 1), 38-44.
Van Loon, L. C. (2007). Plant responses to plant growth-promoting rhizobacteria. European Journal of Plant Pathology, 119(3), 243-254.
Velázquez, E., Menéndez, E., Juanes, F. S., Daza, N. V., Yépez, J. P., Barrios, M. L., ... & Buitrago, J. M. G. (2016). Identification of Human Pathogenic Bacteria in Plant Roots by Using MALDI-TOF MS Methodology. In Biological Nitrogen Fixation and Beneficial Plant-Microbe Interaction. Springer International Publishing. (pp. 3-12).
Verma, N., & Kumar, V. (2019). Perceptions of Microbe–Microbe and Plant–Microbiome Interfaces: The Metagenomic Maneuver. Microbiome in Plant Health and Disease: Challenges and Opportunities, 483-505.
Villa, T. G., &Viñas, M. (2016). Introductory Chapter. In New Weapons to Control Bacterial Growth. Springer International Publishing (pp. 1-13).
Whipps, J., Hand, P., Pink, D., & Bending, G. D. (2008). Phyllosphere microbiology with special reference to diversity and plant genotype. Journal of applied microbiology, 105(6), 1744-1755.
Anal, A. K. D., Rai, S., Singh, M., & Solanki, M. K. (2020). Plant mycobiome: Current research and applications. Phytobiomes: Current insights and future vistas, 81-104.
Andreote, F. D., Gumiere, T., &Durrer, A. (2014). Exploring interactions of plant microbiomes. Scientia agrícola, 71(6), 528-539.
Bais, H. P., Weir, T. L., Perry, L. G., Gilroy, S., &Vivanco, J. M. (2006). The role of root exudates in rhizosphere interactions with plants and other organisms. Annu. Rev. Plant Biol., 57, 233-266.
Berendsen, R. L., Pieterse, C. M., & Bakker, P. A. (2012). The rhizosphere microbiome and plant health. Trends in plant science, 17(8), 478-486.
Berg, G., Erlacher, A., & Grube, M. (2015). The edible plant microbiome: importance and health issues. In Principles of plant-microbe interactions (pp. 419-426). Springer, Cham.
Berg, G., Grube, M., Schloter, M., &Smalla, K. (2014). The plant microbiome and its importance for plant and human health. Frontiers in microbiology, 5, 1.
Borriss, R. (2020). Phytostimulation and biocontrol by the plant-associated Bacillus amyloliquefaciens FZB42: an update. Phyto-microbiome in stress regulation, 1-20.
Carvalhais, L. C., Dennis, P. G., Fan, B., Fedoseyenko, D., Kierul, K., Becker, A., ... &Borriss, R. (2013). Linking plant nutritional status to plant-microbe interactions. PLoS One, 8(7), e68555.
Delmotte, N., Knief, C., Chaffron, S., Innerebner, G., Roschitzki, B., Schlapbach, R., ... &Vorholt, J. A. (2009). Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proceedings of the National Academy of Sciences, 106(38), 16428-16433.
DeSalle, R., & Perkins, S. L. (2015). Welcome to the Microbiome: Getting to Know the Trillions of Bacteria and Other Microbes In, On, and Around You. Yale University Press.
Djikeng, A., Nelson, B. J., & Nelson, K. E. (2011). Implications of human microbiome research for the developing world. In Metagenomics of the Human Body (pp. 317-336). Springer, New York, NY.
Doty, S. L. (2017). Functional Importance of the Plant Endophytic Microbiome: Implications for Agriculture, Forestry, and Bioenergy. In Functional Importance of the Plant Microbiome (pp. 1-5). Springer, Cham.
Hashimi, M. H. (2016). The Effects of Urea and Organic Manure on Egyptian clover. Research for academic ranking, Shaikh Zayed University-Khost, Afghanistan. Pp. 6-47. (Pashto language)
Hassan, S., &Mathesius, U. (2012). The role of flavonoids in root–rhizosphere signalling: opportunities and challenges for improving plant–microbe interactions. Journal of experimental botany, 63(9), 3429-3444.
Jeong, H., Choi, S. K., Kloepper, J. W., & Ryu, C. M. (2014). Genome sequence of the plant endophyte Bacillus pumilus INR7, triggering induced systemic resistance in field crops. Genome announcements, 2(5), e01093-14.
Krishnaraj, P. U., & Pasha, M. A. (2017). Metagenome of Rhizosphere and Endophytic Ecosystem. In Understanding Host-Microbiome Interactions-An Omics Approach (pp. 125-156). Springer, Singapore.
Kumar, V. V. (2019). Influence of the rhizospheric microbiome in plant health management. Microbiome in Plant Health and Disease: Challenges and Opportunities, 215-230.
Kumari, B., Mani, M., Solanki, A. C., Solanki, M. K., Hora, A., & Mallick, M. A. (2020). Phytobiome engineering and its impact on next-generation agriculture. Phytobiomes: current insights and future vistas, 381-403.
Laksmanan, V., Selvaraj, G., &Bais, H. (2014). Functional soil microbiome: belowground solutions to an aboveground problem. Plant physiology, pp-114.
Lareen, A., Burton, F., & Schäfer, P. (2016). Plant root-microbe communication in shaping root microbiomes. Plant molecular biology, 90(6), 575-587.
Lebeis, S. L. (2015). Greater than the sum of their parts: characterizing plant microbiomes at the community-level. Current opinion in plant biology, 24, 82-86.
Leveau, J. H. (2015). Life of microbes on aerial plant parts. Principles of Plant-Microbe Interactions: Microbes for Sustainable Agriculture, 17-24.
Lindow, S. E., &Brandl, M. T. (2003). Microbiology of the phyllosphere. Applied and environmental microbiology, 69(4), 1875-1883.
Lugtenberg, B. (2015). Life of microbes in the rhizosphere. Principles of plant-microbe interactions: microbes for sustainable agriculture, 7-15.
Mendes, R., Garbeva, P., &Raaijmakers, J. M. (2013). The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS microbiology reviews, 37(5), 634-663.
Miransari, M. (2013). Soil microbes and the availability of soil nutrients. Acta physiologiae plantarum, 35(11), 3075-3084.
Mokrani, S., & El-Hafid, N. (2020). Rhizospheric microbiome: biodiversity, current advancement and potential biotechnological applications. Advances in Plant Microbiome and Sustainable Agriculture: Diversity and Biotechnological Applications, 39-60.
Nadarajah, K. K. (2019). Microbes: an important resource for sustainable agriculture. Microbiome in Plant Health and Disease: Challenges and Opportunities, 53-77.
Panke-Buisse, K., Poole, A. C., Goodrich, J. K., Ley, R. E., & Kao-Kniffin, J. (2015). Selection on soil microbiomes reveals reproducible impacts on plant function. The ISME journal, 9(4), 980.
Philippot, L., Raaijmakers, J. M., Lemanceau, P., & Van Der Putten, W. H. (2013). Going back to the roots: the microbial ecology of the rhizosphere. Nature Reviews Microbiology, 11(11), 789.
Postgate, J. (2000). Microbes and man. Cambridge University Press.
Prieto, P., Schilirò, E., Maldonado-González, M. M., Valderrama, R., Barroso-Albarracín, J. B., & Mercado-Blanco, J. (2011). Root hairs play a key role in the endophytic colonization of olive roots by Pseudomonas spp. with biocontrol activity. Microbial ecology, 62(2), 435-445.
Rossmann, M., Sarango-Flores, S. W., Chiaramonte, J. B., Kmit, M. C. P., & Mendes, R. (2017). Plant Microbiome: Composition and Functions in Plant Compartments. In The Brazilian Microbiome (pp. 7-20). Springer, Cham.
Saha, M., Sarkar, A., Roy, T., Biswas, S. S., & Mandal, A. (2020). Phytobiomes: role in nutrient stewardship and soil health. Phytobiomes: Current Insights and Future Vistas, 1-28.
Saleem, M. (2015). Microbiome ecosystem ecology: unseen majority in an anthropogenic ecosystem. In Microbiome Community Ecology (pp. 1-11). Springer International Publishing.
Saleem, M., & Saleem, M. (2015). Loss of microbiome ecological niches and diversity by global change and trophic downgrading. Microbiome Community Ecology: Fundamentals and Applications, 89-113.
Schulz, B., & Boyle, C. (2005). The endophytic continuum. Mycological research, 109(6), 661-686
Singh, S. P., Bhattacharya, A., Gupta, R., Mishra, A., Zaidi, F. A., & Srivastava, S. (2020). Endophytic Phytobiomes as Defense Elicitors: Current Insights and Future Prospects. Phytobiomes: Current Insights and Future Vistas, 299-334.
Subrahmanyam, G., Kumar, A., Sandilya, S. P., Chutia, M., & Yadav, A. N. (2020). Diversity, plant growth promoting attributes, and agricultural applications of rhizospheric microbes. Plant microbiomes for sustainable agriculture, 1-52.
Sugiyama, A., Ueda, Y., Zushi, T., Takase, H., & Yazaki, K. (2014). Changes in the bacterial community of soybean rhizospheres during growth in the field. PLoS One, 9(6), e100709.
Taylor, L. L., Leake, J. R., Quirk, J., Hardy, K., Banwart, S. A., &Beerling, D. J. (2009). Biological weathering and the long‐term carbon cycle: integrating mycorrhizal evolution and function into the current paradigm. Geobiology, 7(2), 171-191.
Toal, M. E., Yeomans, C., Killham, K., &Meharg, A. A. (2000). A review of rhizosphere carbon flow modelling. Plant and soil, 222(1-2), 263-281.
Trivedi, P., Batista, B. D., Bazany, K. E., & Singh, B. K. (2022). Plant–microbiome interactions under a changing world: Responses, consequences and perspectives. New Phytologist, 234(6), 1951-1959.
Turner, T. R., James, E. K., & Poole, P. S. (2013). The plant microbiome. Genome biology, 14(6), 209.
Ursell, L. K., Metcalf, J. L., Parfrey, L. W., & Knight, R. (2012). Defining the human microbiome. Nutrition reviews, 70 (suppl 1), 38-44.
Van Loon, L. C. (2007). Plant responses to plant growth-promoting rhizobacteria. European Journal of Plant Pathology, 119(3), 243-254.
Velázquez, E., Menéndez, E., Juanes, F. S., Daza, N. V., Yépez, J. P., Barrios, M. L., ... & Buitrago, J. M. G. (2016). Identification of Human Pathogenic Bacteria in Plant Roots by Using MALDI-TOF MS Methodology. In Biological Nitrogen Fixation and Beneficial Plant-Microbe Interaction. Springer International Publishing. (pp. 3-12).
Verma, N., & Kumar, V. (2019). Perceptions of Microbe–Microbe and Plant–Microbiome Interfaces: The Metagenomic Maneuver. Microbiome in Plant Health and Disease: Challenges and Opportunities, 483-505.
Villa, T. G., &Viñas, M. (2016). Introductory Chapter. In New Weapons to Control Bacterial Growth. Springer International Publishing (pp. 1-13).
Whipps, J., Hand, P., Pink, D., & Bending, G. D. (2008). Phyllosphere microbiology with special reference to diversity and plant genotype. Journal of applied microbiology, 105(6), 1744-1755.
Published
2023-02-28
How to Cite
Hashimi, M. H., Abad, Q., & Noori, G. H. (2023). A review of plant microbiome: Its functions and components. IJO - International Journal of Agriculture and Research ( ISSN 2814-189X ), 6(02), 10-17. Retrieved from https://www.ijojournals.com/index.php/ar/article/view/639
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