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Wani AK, Qadir F, Elboughdiri N, Rahayu F, Saefudin, Pranowo D, Martasari C, Kosmiatin M, Suhara C, Sudaryono T, Prayogo Y, Yadav KK, Muzammil K, Eltayeb LB, Alreshidi MA, Singh R. Metagenomics and plant-microbe symbioses: Microbial community dynamics, functional roles in carbon sequestration, nitrogen transformation, sulfur and phosphorus mobilization for sustainable soil health. Biotechnol Adv 2025; 82:108580. [PMID: 40246210 DOI: 10.1016/j.biotechadv.2025.108580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2025] [Revised: 03/19/2025] [Accepted: 04/13/2025] [Indexed: 04/19/2025]
Abstract
Biogeochemical cycles are fundamental processes that regulate the flow of essential elements such as carbon, nitrogen, and phosphorus, sustaining ecosystem productivity and global biogeochemical equilibrium. These cycles are intricately influenced by plant-microbe symbioses, which facilitate nutrient acquisition, organic matter decomposition, and the transformation of soil nutrients. Through mutualistic interactions, plants and microbes co-regulate nutrient availability and promote ecosystem resilience, especially under environmental stress. Metagenomics has emerged as a transformative tool for deciphering the complex microbial communities and functional genes driving these cycles. By enabling the high-throughput sequencing and annotation of microbial genomes, metagenomics provides unparalleled insights into the taxonomic diversity, metabolic potential, and functional pathways underlying microbial contributions to biogeochemical processes. Unlike previous reviews, this work integrates recent advancements in metagenomics with complementary omics approaches to provide a comprehensive perspective on how plant-microbe interactions modulate biogeochemical cycles at molecular, genetic, and ecosystem levels. By highlighting novel microbial processes and potential biotechnological applications, this review aims to guide future research in leveraging plant-microbe symbioses for sustainable agriculture, ecosystem restoration, and climate change mitigation.
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Affiliation(s)
- Atif Khurshid Wani
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar 144411, Punjab, India.
| | - Fayzan Qadir
- Department of Civil Engineering, Engineering & Technology, Jamia Millia Islamia-Jamia Nagar, New Delhi 110025, India
| | - Noureddine Elboughdiri
- Chemical Engineering Department, College of Engineering, University of Ha'il, P.O. Box 2440, Ha'il 81441, Saudi Arabia
| | - Farida Rahayu
- Research Center for Genetic Engineering, National Research and Innovation Agency, Bogor 16911, Indonesia
| | - Saefudin
- Research Center for Estate Crop, National Research and Innovation Agency, Bogor 16111, Indonesia
| | - Dibyo Pranowo
- Research Center for Estate Crop, National Research and Innovation Agency, Bogor 16111, Indonesia
| | - Chaireni Martasari
- Research Center for Horticulture, National Research and Innovation Agency, Bogor 16111, Indonesia
| | - Mia Kosmiatin
- Research Center for Horticulture, National Research and Innovation Agency, Bogor 16111, Indonesia
| | - Cece Suhara
- Research Center for Estate Crop, National Research and Innovation Agency, Bogor 16111, Indonesia
| | - Tri Sudaryono
- Research Center for Horticulture, National Research and Innovation Agency, Bogor 16111, Indonesia
| | - Yusmani Prayogo
- Food Crops Research Center, National Research and Innovation Agency, Bogor 16111, Indonesia
| | - Krishna Kumar Yadav
- Department of VLSI Microelectronics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai -602105, Tamil Nadu, India; Environmental and Atmospheric Sciences Research Group, Scientific Research Center, Al-Ayen University, Nasiriyah, Thi-Qar, Iraq
| | - Khursheed Muzammil
- Department of Public Health, College of Applied Medical Sciences, Khamis Mushait, King Khalid University, Abha 62561, Saudi Arabia
| | - Lienda Bashier Eltayeb
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin AbdulAziz University- Al-Kharj, 11942 Riyadh, Saudi Arabia
| | - Maha Awjan Alreshidi
- Department of Chemistry, College of Science, University of Ha'il, Ha'il 81441, Saudi Arabia
| | - Reena Singh
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar 144411, Punjab, India
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Liu M, Xu L, Yin Z, He D, Zhang Y, Liu C. Harnessing the potential of exogenous microbial agents: a comprehensive review on enhancing lignocellulose degradation in agricultural waste composting. Arch Microbiol 2025; 207:51. [PMID: 39893606 DOI: 10.1007/s00203-025-04247-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2024] [Revised: 01/05/2025] [Accepted: 01/15/2025] [Indexed: 02/04/2025]
Abstract
Composting converts organic agricultural wastes into value-added products, yet the presence of significant non-biodegradable lignocelluloses hinders its efficiency. The introduction of various exogenous microbial agents has been shown to effectively addresses this challenge. In this context, basing on the microbial enzymatic mechanism for lignocellulose degradation, this paper synthesizes the latest research advancements and practical applications of exogenous microbial agents in agricultural waste composting. Given that the effectiveness of lignocellulose degradation is highly dependent on the waste's inherent characteristics, it is crucial to carefully consider the composition of fungi and bacteria, the dosage of microbial agents, and the composting process operation, tailored to the specific type of agricultural waste. Moreover, the combination of additives with exogenous microbial agents can further enhance the degradation of lignocelluloses and the humification of organic matters. Furthermore, insights into the future research and application trends of exogenous microbial agents in agricultural waste composting was prospected.
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Affiliation(s)
- Meng Liu
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao, 266520, People's Republic of China
| | - Luxin Xu
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao, 266520, People's Republic of China
| | - Zhixuan Yin
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao, 266520, People's Republic of China.
| | - Deming He
- Shanghai Chengtou Shangjing Ecological Restoration Technology Co., Shanghai, 200120, People's Republic of China
| | - Yujia Zhang
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao, 266520, People's Republic of China
| | - Changqing Liu
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao, 266520, People's Republic of China
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Ji S, Liu B, Han J, Kong N, Yang Y, Zhang J, Wang Y, Liu Z. Bacillus-derived consortium enhances Ginkgo biloba's health and resistance to Alternaria tenuissima. PEST MANAGEMENT SCIENCE 2024; 80:4110-4124. [PMID: 38578650 DOI: 10.1002/ps.8118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/28/2024] [Accepted: 04/05/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND Bacillus, as a plant-growth-promoting rhizobacteria, can enhance the resistance of plants to phytopathogens. In our study, Bacillus strains showing excellent biocontrol were screened and used to control ginkgo leaf blight (Alternaria tenuissima). RESULTS Four biocontrol Bacillus strains-Bsa537, Bam337, Bso544, and Bsu503-were selected from 286 isolates based on their capacity to inhibit pathogens and promote plant growth. The four Bacillus strains significantly improved the resistance of ginkgo to leaf blight. This was especially the case when the four strains were used as a mixture, which contributed to a decrease in lesion area of >40%. Hence, a mixture of Bacillus strains was used to control ginkgo leaf blight in the field. Treatment efficiency varied from 30% to 100% (average 81.5%) and was higher than that of the control (-2% to -18%, average - 8.5%); the antioxidant capacity of the treated ginkgo was also stronger. In addition, ginkgo biomass increased as a result of treatment with the Bacillus mixture, including leaf weight, area, thickness, number of lateral roots and root weight. Furthermore, the Bacillus mixture improved the ginkgo rhizosphere soil by boosting the number of beneficial microorganisms, lowering the number of pathogens and hastening soil catabolism. CONCLUSION The Bacillus mixture improved the health status of ginkgo by protecting it from pathogen attack, promoting its growth and improving the microorganism community in the rhizosphere. This work closes a technological gap in the biological control of ginkgo leaf blight, investigates application methods for compound Bacillus biofertilizers and establishes a framework for the popularity and commercialization of these products. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Shida Ji
- College of Forestry, ShenYang Agricultural University, Shenyang, China
- College of Horticulture, ShenYang Agricultural University, Shenyang, China
| | - Bin Liu
- College of Forestry, ShenYang Agricultural University, Shenyang, China
| | - Jing Han
- College of Forestry, ShenYang Agricultural University, Shenyang, China
| | - Ning Kong
- College of Forestry, ShenYang Agricultural University, Shenyang, China
| | - Yongfeng Yang
- College of Forestry, ShenYang Agricultural University, Shenyang, China
| | - Jianxia Zhang
- College of Forestry, ShenYang Agricultural University, Shenyang, China
| | - Yucheng Wang
- College of Forestry, ShenYang Agricultural University, Shenyang, China
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Zhihua Liu
- College of Forestry, ShenYang Agricultural University, Shenyang, China
- College of Forestry, Northeast Forestry University, Harbin, China
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Wu X, Zhao Z, Zhao Z, Zhang Y, Li M, Yu Q. Analysis of the Potassium-Solubilizing Priestia megaterium Strain NK851 and Its Potassium Feldspar-Binding Proteins. Int J Mol Sci 2023; 24:14226. [PMID: 37762528 PMCID: PMC10531590 DOI: 10.3390/ijms241814226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
Potassium-solubilizing bacteria are an important microbial group that play a critical role in releasing mineral potassium from potassium-containing minerals, e.g., potassium feldspar. Their application may reduce eutrophication caused by overused potassium fertilizers and facilitate plants to utilize environmental potassium. In this study, a high-efficiency potassium-solubilizing bacterium, named NK851, was isolated from the Astragalus sinicus rhizosphere soil. This bacterium can grow in the medium with potassium feldspar as the sole potassium source, releasing 157 mg/L and 222 mg/L potassium after 3 days and 5 days of incubation, respectively. 16S rDNA sequencing and cluster analysis showed that this strain belongs to Priestia megaterium. Genome sequencing further revealed that this strain has a genome length of 5,305,142 bp, encoding 5473 genes. Among them, abundant genes are related to potassium decomposition and utilization, e.g., the genes involved in adherence to mineral potassium, potassium release, and intracellular trafficking. Moreover, the strong potassium-releasing capacity of NK851 is not attributed to the acidic pH but is attributed to the extracellular potassium feldspar-binding proteins, such as the elongation factor TU and the enolase that contains potassium feldspar-binding cavities. This study provides new information for exploration of the bacterium-mediated potassium solubilization mechanisms.
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Affiliation(s)
- Xinyue Wu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; (X.W.); (Z.Z.); (Z.Z.); (M.L.)
| | - Zijian Zhao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; (X.W.); (Z.Z.); (Z.Z.); (M.L.)
| | - Zirun Zhao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; (X.W.); (Z.Z.); (Z.Z.); (M.L.)
| | - Youjun Zhang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China;
| | - Mingchun Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; (X.W.); (Z.Z.); (Z.Z.); (M.L.)
| | - Qilin Yu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; (X.W.); (Z.Z.); (Z.Z.); (M.L.)
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