Examining the Range of Genes in Soil Microbes and Their Ability to Make Biopolymers Using RNA identification and DNA Extraction
Meneliti Kisaran Gen pada Mikroba Tanah dan Kemampuannya Membuat Biopolimer Menggunakan Identifikasi RNA dan Ekstraksi DNA
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(1) * Nadia Altaee
Babylon university. College of science for women. Department of biology
Iraq
(2) Mustafa Jasim Aljozary Department of Applied Biotechnology, College of Biotechnology, Al-Qasim Green University
Iraq
(3) Murtadha Kadhim Hasan Department of Biology College of science for women University of Babylon
Iraq
(*) Corresponding Author
Abstract
This research was conducted to investigate the genetic diversity and functional capabilities of microbes in agricultural soils in Iraq. The study involved soil sampling from various agricultural farms located in the regions of Oil production station in Baghdad encompassing a range of soil types including sandy loam, clay loam, and silty clay. The research explores the genetic diversity and functional capabilities of microbes in agricultural soils, focusing on macrophages' potential to produce biopolymers through practical experiments. Diversity of the soil microbial communities was high, with an average Shannon index of 6.1. Analysis of the RNA sequencing revealed Proteobacteria (28.7%), Actinobacteria (24.5%) and Bacteroidetes (13.2%) as the main phyla and Streptomyces (9.8%), Bradyrhizobium (6.7%) and Pseudomonas (4.6%) as the most abundant genera. The most abundant functional categories in the soil microbiome as determined through metagenomic analysis were carbohydrate metabolism, amino acid metabolism and protein metabolism. Potentials of the soil, mainly of the clay loam from Basra, for PHA production were tested in biopolymer production assays, where 1.2 mg/g was produced in the clay loam from Basra. We performed differential abundance analysis and identified 500 significantly different OTUs, with Streptomyces and Bradyrhizobium as most significantly enriched, and Nitrospira and Nitrosomonas as most significantly depleted. Finally, the soil microbiome in Iraq shows a rich diversity, a high functional potential and biotechnological relevance. The study findings reveal considerable diversity and functional potential within soil microbial communities, highlighting their roles in sustainable agriculture. Understanding the genetic resources provided by soil microbes could help harness their abilities to improve crop yields while minimizing environmental impacts.
Highlights:
- High microbial diversity in Iraqi agricultural soils, Shannon index 6.1.
- Abundant Proteobacteria, Actinobacteria, functional potential in metabolism, biopolymer production.
- Soil microbes crucial for sustainable agriculture and improved crop yields.
Keywords: Soil microbiome, Metagenomics, RNA sequencing, Biopolymers, Sustainable agriculture, Poly-hydroxy-alkenoates
References
A. Abdelnaby, D. H. Assar, A. Salah, A. Atiba, A. M. El-Nokrashy, A. E. Elshafey, A. El-Far, and Z. I. Elbialy, "Extracted Marine Collagen From Nile Tilapia (Oreochromis Niloticus L.) Skin Accelerates Burn Healing: Histopathological, Immunohistochemical and Gene Expression Analysis," Egyptian Journal of Veterinary Sciences, vol. 56, no. 8, pp. 1849-1865, 2025.
A. Ahmedou, I. I. Al-Hawary, M. Alsayadi, T. Yassine, A. Elshafey, and Z. I. Elbialy, "Assessment of Quality and Safety of Some Imported and Locally Sourced Fish in the Egyptian Markets," Egyptian Journal of Veterinary Sciences, vol. 56, no. 2, pp. 273-287, 2025.
M. A. Anthony, S. F. Bender, and M. G. van der Heijden, "Enumerating Soil Biodiversity," Proceedings of the National Academy of Sciences, vol. 120, no. 33, p. e2304663120, 2023.
M. Azeem, P. G. Soundari, A. Ali, M. I. Tahir, M. Imran, S. Bashir, M. Irfan, G. Li, Y.-G. Zhu, and Z. Zhang, "Soil Metaphenomics: A Step Forward in Metagenomics," Archives of Agronomy and Soil Science, vol. 68, no. 12, pp. 1645-1663, 2022.
G. Bravo-Porras, L. A. Fernández-Güelfo, C. J. Álvarez-Gallego, M. Carbú, D. Sales, and L. I. Romero-García, "Influence of the Total Concentration and the Profile of Volatile Fatty Acids on Polyhydroxyalkanoates (PHA) Production by Mixed Microbial Cultures," Biomass Conversion and Biorefinery, vol. 14, no. 1, pp. 239-253, 2024.
J. Chow, P. Perez‐Garcia, R. Dierkes, and W. R. Streit, "Microbial Enzymes Will Offer Limited Solutions to the Global Plastic Pollution Crisis," Microbial Biotechnology, vol. 16, no. 2, pp. 195-217, 2023.
N. Ezzat, I. Al-Hawary, A. Elshafey, N. Althobaiti, and Z. I. Elbialy, "Effect of Seasonal Changes in Heavy Metals on the Histomorphology of the Liver and Gills of Nile Tilapia (Oreochromis Niloticus L.) in Burullus Lake, Egypt," Egyptian Journal of Veterinary Sciences, vol. 55, no. 6, pp. 1705-1716, 2024.
C. Fang, T. Xu, C. Ye, L. Huang, Q. Wang, and W. Lin, "Method for RNA Extraction and cDNA Library Construction from Microbes in Crop Rhizosphere Soil," World Journal of Microbiology and Biotechnology, vol. 30, pp. 783-789, 2014.
A. M. Ghobish, A. M. El-Nokrashy, A. E. Elshafey, and A. A. Tayel, "Investigating the Potential of Chitosan-Nanocomposites as a Bio-Based Adsorbent for Sustainable Aflatoxin Eradication from Fish Feed," Egyptian Journal of Veterinary Sciences, 2025.
B. Hamid, M. Zaman, S. Farooq, S. Fatima, R. Z. Sayyed, Z. A. Baba, T. A. Sheikh, M. S. Reddy, H. El Enshasy, and A. Gafur, "Bacterial Plant Biostimulants: A Sustainable Way Towards Improving Growth, Productivity, and Health of Crops," Sustainability, vol. 13, no. 5, p. 2856, 2021.
M. Hartmann and J. Six, "Soil Structure and Microbiome Functions in Agroecosystems," Nature Reviews Earth & Environment, vol. 4, no. 1, pp. 4-18, 2023.
J. Herbert, A. H. Beckett, and S. C. Robson, "A Review of Cross-Disciplinary Approaches for the Identification of Novel Industrially Relevant Plastic-Degrading Enzymes," Sustainability, vol. 14, no. 23, p. 15898, 2022.
A. Hussein, "Molecular Techniques to Assess Microbial Community Structure, Function, and Dynamics in the Environment," International Journal of Emerging Trends in Science and Technology, pp. 4-14, 2021.
C. Lazcano, E. Boyd, G. Holmes, S. Hewavitharana, A. Pasulka, and K. Ivors, "The Rhizosphere Microbiome Plays a Role in the Resistance to Soil-Borne Pathogens and Nutrient Uptake of Strawberry Cultivars Under Field Conditions," Scientific Reports, vol. 11, no. 1, p. 3188, 2021.
A. Mikić, A. Alomari, and D. M. Gowers, "Classical Recombinant DNA Cloning," in DNA Manipulation and Analysis, Springer, 2023, pp. 1-24.
J. M. Nduko and S. Taguchi, "Microbial Production of Biodegradable Lactate-Based Polymers and Oligomeric Building Blocks from Renewable and Waste Resources," Frontiers in Bioengineering and Biotechnology, vol. 8, p. 618077, 2021.
M. Ofek-Lalzar, N. Sela, M. Goldman-Voronov, S. J. Green, Y. Hadar, and D. Minz, "Niche and Host-Associated Functional Signatures of the Root Surface Microbiome," Nature Communications, vol. 5, p. 4950, 2014.
Z. Pang, F. Dong, Q. Liu, W. Lin, C. Hu, and Z. Yuan, "Soil Metagenomics Reveals Effects of Continuous Sugarcane Cropping on the Structure and Functional Pathway of Rhizospheric Microbial Community," Frontiers in Microbiology, vol. 12, p. 627569, 2021.
M. A. Sandoval-Powers, "Discovery, Expression, and Characterization of Biosynthetic Gene Clusters Encoding Antimicrobial Secondary Metabolites from a Soil Metagenome and Cultured Actinobacteria," Auburn University, 2022.
M. Semenov, "Metabarcoding and Metagenomics in Soil Ecology Research: Achievements, Challenges, and Prospects," Biology Bulletin Reviews, vol. 11, no. 1, pp. 40-53, 2021.
L. Shafea, J. Yap, N. Beriot, V. J. Felde, E. D. Okoffo, C. E. Enyoh, and S. Peth, "Microplastics in Agroecosystems: A Review of Effects on Soil Biota and Key Soil Functions," Journal of Plant Nutrition and Soil Science, vol. 186, no. 1, pp. 5-22, 2023.
C. M. Singleton, F. Petriglieri, J. M. Kristensen, R. H. Kirkegaard, T. Y. Michaelsen, M. H. Andersen, Z. Kondrotaite, S. M. Karst, M. S. Dueholm, and P. H. Nielsen, "Connecting Structure to Function with the Recovery of Over 1000 High-Quality Metagenome-Assembled Genomes from Activated Sludge Using Long-Read Sequencing," Nature Communications, vol. 12, no. 1, p. 2009, 2021.
M. Tartaglia, F. Bastida, R. Sciarrillo, and C. Guarino, "Soil Metaproteomics for the Study of the Relationships Between Microorganisms and Plants: A Review of Extraction Protocols and Ecological Insights," International Journal of Molecular Sciences, vol. 21, no. 22, p. 8455, 2020.
D. J. Uhlenhopp, E. O. Then, T. Sunkara, and V. Gaduputi, "Epidemiology of Esophageal Cancer: Update in Global Trends, Etiology and Risk Factors," Clinical Journal of Gastroenterology, vol. 13, no. 6, pp. 1010-1021, 2020.
X. Wei, B. Xie, C. Wan, R. Song, W. Zhong, S. Xin, and K. Song, "Enhancing Soil Health and Plant Growth Through Microbial Fertilizers: Mechanisms, Benefits, and Sustainable Agricultural Practices," Agronomy, vol. 14, no. 3, p. 609, 2024.
M. D. Weinroth, A. D. Belk, C. Dean, N. Noyes, D. K. Dittoe, M. J. Rothrock Jr, S. C. Ricke, P. R. Myer, M. T. Henniger, and G. A. Ramírez, "Considerations and Best Practices in Animal Science 16S Ribosomal RNA Gene Sequencing Microbiome Studies," Journal of Animal Science, vol. 100, no. 2, p. skab346, 2022.
E. Wołejko, A. Jabłońska-Trypuć, U. Wydro, A. Butarewicz, and B. Łozowicka, "Soil Biological Activity as an Indicator of Soil Pollution with Pesticides–A Review," Applied Soil Ecology, vol. 147, p. 103356, 2020.
B. Xiong, Q. Fang, T. Wei, Z. Wang, R. Shen, M. Cheng, and W. Zhou, "Chemical Digestion Method to Promote Activated Sludge Cell Wall Breaking and Optimize the Polyhydroxyalkanoate (PHA) Extraction Process," International Journal of Biological Macromolecules, vol. 240, p. 124369, 2023.
