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Halema AA, El-Beltagi HS, Al-Dossary O, Alsubaie B, Henawy AR, Rezk AA, Almutairi HH, Mohamed AA, Elarabi NI, Abdelhadi AA. Omics technology draws a comprehensive heavy metal resistance strategy in bacteria. World J Microbiol Biotechnol 2024; 40:193. [PMID: 38709343 DOI: 10.1007/s11274-024-04005-y] [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: 03/21/2024] [Accepted: 04/24/2024] [Indexed: 05/07/2024]
Abstract
The rapid industrial revolution significantly increased heavy metal pollution, becoming a major global environmental concern. This pollution is considered as one of the most harmful and toxic threats to all environmental components (air, soil, water, animals, and plants until reaching to human). Therefore, scientists try to find a promising and eco-friendly technique to solve this problem i.e., bacterial bioremediation. Various heavy metal resistance mechanisms were reported. Omics technologies can significantly improve our understanding of heavy metal resistant bacteria and their communities. They are a potent tool for investigating the adaptation processes of microbes in severe conditions. These omics methods provide unique benefits for investigating metabolic alterations, microbial diversity, and mechanisms of resistance of individual strains or communities to harsh conditions. Starting with genome sequencing which provides us with complete and comprehensive insight into the resistance mechanism of heavy metal resistant bacteria. Moreover, genome sequencing facilitates the opportunities to identify specific metal resistance genes, operons, and regulatory elements in the genomes of individual bacteria, understand the genetic mechanisms and variations responsible for heavy metal resistance within and between bacterial species in addition to the transcriptome, proteome that obtain the real expressed genes. Moreover, at the community level, metagenome, meta transcriptome and meta proteome participate in understanding the microbial interactive network potentially novel metabolic pathways, enzymes and gene species can all be found using these methods. This review presents the state of the art and anticipated developments in the use of omics technologies in the investigation of microbes used for heavy metal bioremediation.
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Affiliation(s)
- Asmaa A Halema
- Genetics Department, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Hossam S El-Beltagi
- Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, 31982, Saudi Arabia.
- Biochemistry Department, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt.
| | - Othman Al-Dossary
- Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Bader Alsubaie
- Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Ahmed R Henawy
- Microbiology Department, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Adel A Rezk
- Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
- Plant Virology Department, Plant Pathology Research Institute, Agriculture Research Center, Giza, 12619, Egypt
| | - Hayfa Habes Almutairi
- Chemistry Department, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Amal A Mohamed
- Chemistry Dept, Al-Leith University College, Umm Al-Qura University, P.O. Box 6725- 21955, Makkah, Saudi Arabia
| | - Nagwa I Elarabi
- Genetics Department, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
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Dhanapal A, Thiruvengadam M, Vairavanathan J, Venkidasamy B, Easwaran M, Ghorbanpour M. Nanotechnology Approaches for the Remediation of Agricultural Polluted Soils. ACS OMEGA 2024; 9:13522-13533. [PMID: 38559935 PMCID: PMC10975622 DOI: 10.1021/acsomega.3c09776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 04/04/2024]
Abstract
Soil pollution from various anthropogenic and natural activities poses a significant threat to the environment and human health. This study explored the sources and types of soil pollution and emphasized the need for innovative remediation approaches. Nanotechnology, including the use of nanoparticles, is a promising approach for remediation. Diverse types of nanomaterials, including nanobiosorbents and nanobiosurfactants, have shown great potential in soil remediation processes. Nanotechnology approaches to soil pollution remediation are multifaceted. Reduction reactions and immobilization techniques demonstrate the versatility of nanomaterials in mitigating soil pollution. Nanomicrobial-based bioremediation further enhances the efficiency of pollutant degradation in agricultural soils. A literature-based screening was conducted using different search engines, including PubMed, Web of Science, and Google Scholar, from 2010 to 2023. Keywords such as "soil pollution, nanotechnology, nanoremediation, heavy metal remediation, soil remediation" and combinations of these were used. The remediation of heavy metals using nanotechnology has demonstrated promising results and offers an eco-friendly and sustainable solution to address this critical issue. Nanobioremediation is a robust strategy for combatting organic contamination in soils, including pesticides and herbicides. The use of nanophytoremediation, in which nanomaterials assist plants in extracting and detoxifying pollutants, represents a cutting-edge and environmentally friendly approach for tackling soil pollution.
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Affiliation(s)
- Anand
Raj Dhanapal
- Chemistry
and Bioprospecting Division, Institute of Forest Genetics and Tree
Breeding (IFGTB), Forest Campus, Indian
Council of Forestry Research and Education (ICFRE), Coimbatore 641 002, Tamil Nadu, India
| | - Muthu Thiruvengadam
- Department
of Crop Science, College of Sanghuh Life Science, Konkuk University, Seoul 05029, Republic
of Korea
- Center
for Global Health Research, Saveetha Medical College, Saveetha Institute
of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, 600077, India
| | - Jayavarshini Vairavanathan
- Department
of Biotechnology, Karpagam Academy of Higher
Education, Coimbatore 641 021, Tamil Nadu, India
| | - Baskar Venkidasamy
- Department
of Oral & Maxillofacial Surgery, Saveetha Dental College and Hospitals,
Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai 600 077, Tamil
Nadu, India
| | - Maheswaran Easwaran
- Department
of Research Analytics, Saveetha Dental College and Hospitals, Saveetha
Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai 600 077, Tamil Nadu, India
| | - Mansour Ghorbanpour
- Department
of Medicinal Plants, Faculty of Agriculture and Natural Resources, Arak University, Arak 38156-8-8349, Iran
- Institute
of Nanoscience and Nanotechnology, Arak
University, Arak 38156-8-8349, Iran
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Wang L, Chen M, Zheng X, Li X. Comparative genomics of fungal mutants provides a systemic view of extreme cadmium tolerance in eukaryotic microbes. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133354. [PMID: 38154183 DOI: 10.1016/j.jhazmat.2023.133354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/09/2023] [Accepted: 12/21/2023] [Indexed: 12/30/2023]
Abstract
Whether eukaryotic organisms can evolve for higher heavy metal resistance in laboratory conditions remains unknown. In this study, we challenged a macrofungi, Pleurotus ostreatus, in a designed microbial evolution and growth arena (MEGA)-plate with an extreme Cd gradient. Within months, the wild-type strain developed 10 mutants, exhibiting a maximum three-fold increase in Cd tolerance and slower growth rates. Genomic sequencing and re-sequencing of the wild-type and ten mutant strains generated about 51 GB data, allowing a comprehensive comparative genomics analysis. As a result, a total of 2512 common single nucleotide polymorphisms, 70 inserts and deletes, 39 copy number variations and 21 structural variations were found in the 10 mutants. The mutant genes were primarily involved in substrate transport. In combination with transcriptome analysis, we discovered that the ten mutants had a distinct Cd-resistant mechanism compared to the wild-type strain. Genes involved in oxidation-reduction, ion transmembrane transport, and metal compartment/efflux are primarily responsible for the extreme Cd tolerance in the P. ostreatus mutants. Our findings contribute to the understanding of eukaryotic Cd resistance at the genome level and establish a foundation for developing bioremediation tools utilizing highly tolerant macrofungi.
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Affiliation(s)
- Likun Wang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | | | - Xin Zheng
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Xiaofang Li
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China.
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Liu H, Li C, Lin Y, Chen YJ, Zhang ZJ, Wei KH, Lei M. Biochar and organic fertilizer drive the bacterial community to improve the productivity and quality of Sophora tonkinensis in cadmium-contaminated soil. Front Microbiol 2024; 14:1334338. [PMID: 38260912 PMCID: PMC10800516 DOI: 10.3389/fmicb.2023.1334338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024] Open
Abstract
Excessive Cd accumulation in soil reduces the production of numerous plants, such as Sophora tonkinensis Gagnep., which is an important and widely cultivated medicinal plant whose roots and rhizomes are used in traditional Chinese medicine. Applying a mixture of biochar and organic fertilizers improved the overall health of the Cd-contaminated soil and increased the yield and quality of Sophora. However, the underlying mechanism between this mixed fertilization and the improvement of the yield and quality of Sophora remains uncovered. This study investigated the effect of biochar and organic fertilizer application (BO, biochar to organic fertilizer ratio of 1:2) on the growth of Sophora cultivated in Cd-contaminated soil. BO significantly reduced the total Cd content (TCd) in the Sophora rhizosphere soil and increased the soil water content, overall soil nutrient levels, and enzyme activities in the soil. Additionally, the α diversity of the soil bacterial community had been significantly improved after BO treatment. Soil pH, total Cd content, total carbon content, and dissolved organic carbon were the main reasons for the fluctuation of the bacterial dominant species. Further investigation demonstrated that the abundance of variable microorganisms, including Acidobacteria, Proteobacteria, Bacteroidetes, Firmicutes, Chloroflexi, Gemmatimonadetes, Patescibacteria, Armatimonadetes, Subgroups_ 6, Bacillus and Bacillus_ Acidiceler, was also significantly changed in Cd-contaminated soil. All these alterations could contribute to the reduction of the Cd content and, thus, the increase of the biomass and the content of the main secondary metabolites (matrine and oxymatrine) in Sophora. Our research demonstrated that the co-application of biochar and organic fertilizer has the potential to enhance soil health and increase the productivity and quality of plants by regulating the microorganisms in Cd-contaminated soil.
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Affiliation(s)
- Han Liu
- National Center for TCM Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Cui Li
- National Center for TCM Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Yang Lin
- National Center for TCM Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Yi-jian Chen
- The Third Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin, China
| | - Zhan-jiang Zhang
- National Center for TCM Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Kun-hua Wei
- National Center for TCM Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Ming Lei
- National Center for TCM Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
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