MOLECULAR PROFILING OF COWPEA RHIZOSPHERIC MICROBES USING METAGENOMICS SEQUENCING
Main Article Content
Abstract
There have been several studies investigating the compositions and structure of microbes residing in the legume root rhizosphere/nodules. Although most of these microbes do not form associations with the rhizosphere/nodules of legumes themselves, but they are usually in great number in the rhizosphere with various activities. The aim of this study was to use metagenomics high-throughput technology (NovaSeq 600 sequencing system) to describe the diversity of microbial communities and functional activities associated with cowpea (Vigna unguiculata L. Walp) root rhizosphere/nodules with respect to the differences in the season of collection, i.e., winter and summer rhizosphere soil samples. On the hierarchy of family, Sphingobacteriaceae, Cytophagaceae, Flavobacteriaceae and Cyclobacteriaceae were more prominent in WS while Planctomycetaceae, Conexibacteriaceae, Streptomycetaceae, Bradyrhizobiaceae, Micrococcaceae and Nocardioidaceae were more abundant in SS at least at 3% =/> in relative abundance. This shows that, there was more diversity of plants growth promoting microbes in SS than WS. This is in conjunction with the results at the functional profiles where the sequence counts for most of the metabolic activities most especially nitrogen, phosphorus and sulphur metabolisms in SS were higher than WS. Although, potassium and iron acquisition metabolisms were more prominent in WS than SS. The presence of these families of microbes were significantly influenced by the soil physiochemical elements and also difference in the season of collection. Therefore, the structural diversity and functional profiles of microbes were more prominent in the summer than winter soil samples.
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Odelade, K. A., Yahya, M., Sulaimon, S. O., Onaolapo, A. A., & Jacobs, P. C. (2025). MOLECULAR PROFILING OF COWPEA RHIZOSPHERIC MICROBES USING METAGENOMICS SEQUENCING. The Bioscientist Journal, 13(2), 132-149. https://doi.org/10.54117/the_bioscientist.v13i1.187
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This work is licensed under a Creative Commons Attribution 4.0 International License.
References
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Guo, G.-X., Deng, H., Qiao, M., Yao, H.-Y. and Zhu, Y.-G. (2013). Effect of long-term wastewater irrigation on potential denitrification and denitrifying communities in soils at the watershed scale. Environmental science and technology, 47, 3105-3113.
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Khan, M. S., Zaidi, A. and Ahmad, E. (2014). Mechanism of phosphate solubilization and physiological functions of phosphate-solubilizing microorganisms. Phosphate solubilizing microorganisms. Springer.
Kieft, T. L. and Simmons, K. A. (2015). Allometry of animal–microbe interactions and global census of animal-associated microbes. Proceedings of the Royal Society B: Biological Sciences, 282, 20150702.
Lakshmanan, V., Selvaraj, G. and Bais, H. P. (2014). Functional soil microbiome: belowground solutions to an aboveground problem. Plant physiology, 166, 689-700.
Lebeis, S. L. 2014. The potential for give and take in plant–microbiome relationships. Frontiers in plant science, 5, 287.
Materechera, S. A. (2018). Soil properties and subsoil constraints of urban and peri-urban agriculture within Mahikeng city in the North West Province (South Africa). Journal of soils and sediments, 18, 494-505.
Meneghine, A. K., Nielsen, S., Varani, A. M., Thomas, T. and Alves, L. M. C. (2017). Metagenomic analysis of soil and freshwater from zoo agricultural area with organic fertilization. PloS one, 12.
Olanrewaju, O. S., Glick, B. R. and Babalola, O. O. (2017). Mechanisms of action of plant growth promoting bacteria. World Journal of Microbiology and Biotechnology, 33, 197.
Poretsky, R., Rodriguez-R, L. M., Luo, C., Tsementzi, D. and Konstantinidis, K. T. (2014). Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics. PloS one, 9.
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Rashid, M. I., Mujawar, L. H., Shahzad, T., Almeelbi, T., Ismail, I. M. and Oves, M. (2016). Bacteria and fungi can contribute to nutrients bioavailability and aggregate formation in degraded soils. Microbiological Research, 183, 26-41.
Saha, M., Sarkar, S., Sarkar, B., Sharma, B. K., Bhattacharjee, S. and Tribedi, P. (2016). Microbial siderophores and their potential applications: a review. Environmental Science and Pollution Research, 23, 3984-3999.
Salam, L. B. and Obayori, O. S. (2019). Structural and functional metagenomic analyses of a tropical agricultural soil. Spanish Journal of Soil Science, 9.
Shaikh, S. S., Sayyed, R. Z. and Reddy, M. (2016). Plant growth-promoting rhizobacteria: an eco-friendly approach for sustainable agroecosystem. Plant, Soil and Microbes. Springer.
Sharma, S. B., Sayyed, R. Z., Trivedi, M. H. and Gobi, T. A. (2013). Phosphate solubilizing microbes: sustainable approach for managing phosphorus deficiency in agricultural soils. SpringerPlus, 2, 587.
Stefan, A., Stredel, C., Gheorgita, G., Cojocaru, D. and Efrose, R. C. (2014). Nitrogen Fixing Efficiency of some Indigenous Rhizobium leguminosarum Strains Isolated from Red Clover (Trifolium pratense, L.) and White Clover (Trifolium repens, L.) Nodules. Analele Stiintifice ale Universitatii" Al. I. Cuza" Din Iasi.(Serie Noua). Sectiunea 2. a. Genetica si Biologie Moleculara, 15, 5.
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Ventosa, A., De La Haba, R. R., Sánchez-Porro, C. and Papke, R. T. (2015). Microbial diversity of hypersaline environments: a metagenomic approach. Current opinion in microbiology, 25, 80-87.
Verma, P., Yadav, A., Shukla, L., Saxena, A. and Suman, A. (2015). Alleviation of cold stress in wheat seedlings by Bacillus amyloliquefaciens. IARI-HHS2-30, an endophytic psychrotolerant K-solubilizing bacterium from NW Indian Himalayas. Natonal Journal of Life Sciences 12: 105–110.
Xia, F., Zhou, X., Liu, Y., Li, Y., Bai, X. and Zhou, X. (2019). Composition and predictive functional analysis of bacterial communities inhabiting Chinese Cordyceps insight into conserved core microbiome. BMC microbiology, 19, 105.
Yousuf, B., Kumar, R., Mishra, A. and Jha, B. (2014). Unravelling the carbon and sulphur metabolism in coastal soil ecosystems using comparative cultivation-independent genome-level characterisation of microbial communities. PLoS One, 9.
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Zou, J., Liu, X., He, C., Zhang, X., Zhong, C., Wang, C. and Wei, J. (2013). Effect of Scripus triqueter of its rhizosphere and root exudates on microbial community structure of simulated diesel-spiked wetland. International Biodeterioration and Biodegradation, 82, 110-116.
Ali, A., Khalid, R., Safdar, A., Akram, Z. and Hayat, R. (2015). Characterization of plant growth promoting rhizobacteria isolated from chickpea (Cicer arietinum). British Microbiology Research Journal, 6, 32.
Bejarano, A., Ramírez-Bahena, M.-H., Velázquez, E. and Peix, A. (2014). Vigna unguiculata is nodulated in Spain by endosymbionts of Genisteae legumes and by a new symbiovar (vignae) of the genus Bradyrhizobium. Systematic and applied microbiology, 37, 533-540.
Bouali, M., Pelletier, E., Chaussonnerie, S., Le Paslier, D., Bakhrouf, A. and Sghir, A. (2013). Characterization of rhizosphere prokaryotic diversity in a horizontal subsurface flow constructed wetland using a PCR cloning-sequencing based approach. Applied microbiology and biotechnology, 97, 4221-4231.
Bulgarelli, D., Garrido-Oter, R., Münch, P. C., Weiman, A., Dröge, J., Pan, Y., Mchardy, A. C. and Schulze-Lefert, P. (2015). Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell host and microbe, 17, 392-403.
Calhoun, S., Korczynska, M., Wichelecki, D. J., San Francisco, B., Zhao, S., Rodionov, D. A., Vetting, M. W., Al-Obaidi, N. F., Lin, H. and O'meara, M. J. (2018). Prediction of enzymatic pathways by integrative pathway mapping. Elife, 7, e31097.
Costa, P. S., Reis, M. P., Avila, M. P., Leite, L. R., De Araújo, F. M., Salim, A. C., Oliveira, G., Barbosa, F., Chartone-Souza, E. and Nascimento, A. M. (2015). Metagenome of a microbial community inhabiting a metal-rich tropical stream sediment. PLoS One, 10.
Dakora, F. D. and Phillips, D. A. (2013). Root exudates as mediators of mineral acquisition in low-nutrient. Food Security in Nutrient-Stressed Environments: Exploiting Plants’ Genetic Capabilities, 95, 201.
De Meyer, S. E., De Beuf, K., Vekeman, B. and Willems, A. (2015). A large diversity of non-rhizobial endophytes found in legume root nodules in Flanders (Belgium). Soil Biology and Biochemistry, 83, 1-11.
Díaz, E., Jiménez, J. I. and Nogales, J. (2013). Aerobic degradation of aromatic compounds. Current opinion in biotechnology, 24, 431-442.
Dudhagara, P., Bhavsar, S., Bhagat, C., Ghelani, A., Bhatt, S. and Patel, R. (2015). Web resources for metagenomics studies. Genomics, proteomics and bioinformatics, 13, 296-303.
Enagbonma, B. J. and Babalola, O. O. (2023). Metagenomics Reveals the Microbiome Multifunctionalities of Environmental Importance from Termite Mound Soils. Bioinformatics and Biology Insights, 17. https://doi.org/10.1177/11779322231184025
Fahad, S. (2012). Growth promotion by P-solubilizing, siderophore and bacteriocin producing rhizobacteria in Zea mays L. Journal of Medicinal Plants Research, 6, 553-559.
Fox, A., Kwapinski, W., Griffiths, B. S. and Schmalenberger, A. (2014). The role of sulfur-and phosphorus-mobilizing bacteria in biochar-induced growth promotion of Lolium perenne. FEMS microbiology ecology, 90, 78-91.
Gahan, J. and Schmalenberger, A. (2014). The role of bacteria and mycorrhiza in plant sulfur supply. Frontiers in plant science, 5, 723.
Gerrano, A. S., Adebola, P. O., Jansen Van Rensburg, W. S. and Laurie, S. M. (2015). Genetic variability in cowpea (Vigna unguiculata (L.) Walp.) genotypes. South African Journal of Plant and Soil, 32, 165-174.
Glick, B. R. (2012). Plant growth-promoting bacteria: mechanisms and applications. Scientifica, 96340. doi:10.6064/2012/963401
Grzywacz, D., Stevenson, P., Mushobozi, W. L., Belmain, S. and Wilson, K. (2014). The use of indigenous ecological resources for pest control in Africa. Food Security, 6, 71-86.
Guo, G.-X., Deng, H., Qiao, M., Yao, H.-Y. and Zhu, Y.-G. (2013). Effect of long-term wastewater irrigation on potential denitrification and denitrifying communities in soils at the watershed scale. Environmental science and technology, 47, 3105-3113.
Gupta, G., Parihar, S. S., Ahirwar, N. K., Snehi, S. K. and Singh, V. (2015). Plant growth promoting rhizobacteria (PGPR): current and future prospects for development of sustainable agriculture. J Microb Biochem Technol, 7, 096-102.
Jing, Y. X., Yan, J. L., He, H. D., Yang, D. J., Xiao, L., Zhong, T., Yuan, M., Cai, X. D. and Li, S. B. (2014). Characterization of bacteria in the rhizosphere soils of Polygonum pubescens and their potential in promoting growth and Cd, Pb, Zn uptake by Brassica napus. International journal of phytoremediation, 16, 321-333.
Khan, M. S., Zaidi, A. and Ahmad, E. (2014). Mechanism of phosphate solubilization and physiological functions of phosphate-solubilizing microorganisms. Phosphate solubilizing microorganisms. Springer.
Kieft, T. L. and Simmons, K. A. (2015). Allometry of animal–microbe interactions and global census of animal-associated microbes. Proceedings of the Royal Society B: Biological Sciences, 282, 20150702.
Lakshmanan, V., Selvaraj, G. and Bais, H. P. (2014). Functional soil microbiome: belowground solutions to an aboveground problem. Plant physiology, 166, 689-700.
Lebeis, S. L. 2014. The potential for give and take in plant–microbiome relationships. Frontiers in plant science, 5, 287.
Materechera, S. A. (2018). Soil properties and subsoil constraints of urban and peri-urban agriculture within Mahikeng city in the North West Province (South Africa). Journal of soils and sediments, 18, 494-505.
Meneghine, A. K., Nielsen, S., Varani, A. M., Thomas, T. and Alves, L. M. C. (2017). Metagenomic analysis of soil and freshwater from zoo agricultural area with organic fertilization. PloS one, 12.
Olanrewaju, O. S., Glick, B. R. and Babalola, O. O. (2017). Mechanisms of action of plant growth promoting bacteria. World Journal of Microbiology and Biotechnology, 33, 197.
Poretsky, R., Rodriguez-R, L. M., Luo, C., Tsementzi, D. and Konstantinidis, K. T. (2014). Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics. PloS one, 9.
Pule-Meulenberg, F., Belane, A. K., Krasova-Wade, T. and Dakora, F. D. (2010). Symbiotic functioning and bradyrhizobial biodiversity of cowpea (Vigna unguiculata L. Walp.) in Africa. BMC microbiology, 10, 89.
Rashid, M. I., Mujawar, L. H., Shahzad, T., Almeelbi, T., Ismail, I. M. and Oves, M. (2016). Bacteria and fungi can contribute to nutrients bioavailability and aggregate formation in degraded soils. Microbiological Research, 183, 26-41.
Saha, M., Sarkar, S., Sarkar, B., Sharma, B. K., Bhattacharjee, S. and Tribedi, P. (2016). Microbial siderophores and their potential applications: a review. Environmental Science and Pollution Research, 23, 3984-3999.
Salam, L. B. and Obayori, O. S. (2019). Structural and functional metagenomic analyses of a tropical agricultural soil. Spanish Journal of Soil Science, 9.
Shaikh, S. S., Sayyed, R. Z. and Reddy, M. (2016). Plant growth-promoting rhizobacteria: an eco-friendly approach for sustainable agroecosystem. Plant, Soil and Microbes. Springer.
Sharma, S. B., Sayyed, R. Z., Trivedi, M. H. and Gobi, T. A. (2013). Phosphate solubilizing microbes: sustainable approach for managing phosphorus deficiency in agricultural soils. SpringerPlus, 2, 587.
Stefan, A., Stredel, C., Gheorgita, G., Cojocaru, D. and Efrose, R. C. (2014). Nitrogen Fixing Efficiency of some Indigenous Rhizobium leguminosarum Strains Isolated from Red Clover (Trifolium pratense, L.) and White Clover (Trifolium repens, L.) Nodules. Analele Stiintifice ale Universitatii" Al. I. Cuza" Din Iasi.(Serie Noua). Sectiunea 2. a. Genetica si Biologie Moleculara, 15, 5.
Thomas, T., Gilbert, J. and Meyer, F. (2012). Metagenomics-a guide from sampling to data analysis. Microbial informatics and experimentation, 2, 3.
Ventosa, A., De La Haba, R. R., Sánchez-Porro, C. and Papke, R. T. (2015). Microbial diversity of hypersaline environments: a metagenomic approach. Current opinion in microbiology, 25, 80-87.
Verma, P., Yadav, A., Shukla, L., Saxena, A. and Suman, A. (2015). Alleviation of cold stress in wheat seedlings by Bacillus amyloliquefaciens. IARI-HHS2-30, an endophytic psychrotolerant K-solubilizing bacterium from NW Indian Himalayas. Natonal Journal of Life Sciences 12: 105–110.
Xia, F., Zhou, X., Liu, Y., Li, Y., Bai, X. and Zhou, X. (2019). Composition and predictive functional analysis of bacterial communities inhabiting Chinese Cordyceps insight into conserved core microbiome. BMC microbiology, 19, 105.
Yousuf, B., Kumar, R., Mishra, A. and Jha, B. (2014). Unravelling the carbon and sulphur metabolism in coastal soil ecosystems using comparative cultivation-independent genome-level characterisation of microbial communities. PLoS One, 9.
Zhang, W., Wu, X., Liu, G., Chen, T., Zhang, G., Dong, Z., Yang, X. and Hu, P. (2013). Pyrosequencing reveals bacterial diversity in the rhizosphere of three Phragmites australis ecotypes. Geomicrobiology Journal, 30, 593-599.
Zou, J., Liu, X., He, C., Zhang, X., Zhong, C., Wang, C. and Wei, J. (2013). Effect of Scripus triqueter of its rhizosphere and root exudates on microbial community structure of simulated diesel-spiked wetland. International Biodeterioration and Biodegradation, 82, 110-116.