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Mohan I, Joshi B, Pathania D, Dhar S, Bhau BS. Phytobial remediation advances and application of omics and artificial intelligence: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:37988-38021. [PMID: 38780844 DOI: 10.1007/s11356-024-33690-3] [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: 05/19/2023] [Accepted: 05/11/2024] [Indexed: 05/25/2024]
Abstract
Industrialization and urbanization increased the use of chemicals in agriculture, vehicular emissions, etc., and spoiled all environmental sectors. It causes various problems among living beings at multiple levels and concentrations. Phytoremediation and microbial association are emerging as a potential method for removing heavy metals and other contaminants from soil. The treatment uses plant physiology and metabolism to remove or clean up various soil contaminants efficiently. In recent years, omics and artificial intelligence have been seen as powerful techniques for phytobial remediation. Recently, AI and modeling are used to analyze large data generated by omics technologies. Machine learning algorithms can be used to develop predictive models that can help guide the selection of the most appropriate plant and plant growth-promoting rhizobacteria combination that is most effective at remediation. In this review, emphasis is given to the phytoremediation techniques being explored worldwide in soil contamination.
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Affiliation(s)
- Indica Mohan
- Department of Environmental Sciences, Central University of Jammu, Rahya-Suchani, Bagla, District Samba, Jammu and Kashmir, 181143, India
- Department of Botany, Central University of Jammu, Rahya-Suchani, Bagla, District Samba, Jammu and Kashmir, 181143, India
| | - Babita Joshi
- Plant Molecular Genetics Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, U.P., 226001, India
| | - Deepak Pathania
- Department of Environmental Sciences, Central University of Jammu, Rahya-Suchani, Bagla, District Samba, Jammu and Kashmir, 181143, India
- Department of Botany, Central University of Jammu, Rahya-Suchani, Bagla, District Samba, Jammu and Kashmir, 181143, India
| | - Sunil Dhar
- Department of Environmental Sciences, Central University of Jammu, Rahya-Suchani, Bagla, District Samba, Jammu and Kashmir, 181143, India
- Department of Botany, Central University of Jammu, Rahya-Suchani, Bagla, District Samba, Jammu and Kashmir, 181143, India
| | - Brijmohan Singh Bhau
- Department of Botany, Central University of Jammu, Rahya-Suchani, Bagla, District Samba, Jammu and Kashmir, 181143, India.
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Yuan G, Zhang N, Zou Y, Hao Y, Pan J, Liu Y, Zhang W, Li B. Genome-wide identification and expression analysis of WRKY gene family members in red clover ( Trifolium pratense L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1289507. [PMID: 38130488 PMCID: PMC10733489 DOI: 10.3389/fpls.2023.1289507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023]
Abstract
Trifolium pratense is an important legume forage grass and a key component of sustainable livestock development. Serving as an essential component, the WRKY gene family, a crucial group of regulatory transcription factors in plants, holds significant importance in their response to abiotic stresses. However, there has been no systematic analysis conducted on the WRKY gene family in Trifolium pratense. This study conducted a comprehensive genomic characterization of the WRKY gene family in Trifolium pratense, utilizing the latest genomic data, resulting in the identification of 59 TpWRKY genes. Based on their structural features, phylogenetic characteristics, and conserved motif composition, the WRKY proteins were classified into three groups, with group II further subdivided into five subgroups (II-a, II-b, II-c, II-d, and II-e). The majority of the TpWRKYs in a group share a similar structure and motif composition. Intra-group syntenic analysis revealed eight pairs of duplicate segments. The expression patterns of 59 TpWRKY genes in roots, stems, leaves, and flowers were examined by analyzing RNA-seq data. The expression of 12 TpWRKY genes under drought, low-temperature (4°C), methyl jasmonate (MeJA) and abscisic acid (ABA) stresses was analyzed by RT-qPCR. The findings indicated that TpWRKY46 was highly induced by drought stress, and TpWRKY26 and TpWRKY41 were significantly induced by low temperature stress. In addition, TpWRKY29 and TpWRKY36 were greatly induced by MeJA stress treatment, and TpWRKY17 was significantly upregulated by ABA stress treatment. In this research, we identified and comprehensively analyzed the structural features of the WRKY gene family in T.pratense, along with determined the possible roles of WRKY candidate genes in abiotic stress. These discoveries deepen our understandings of how WRKY transcription factors contribute to species evolution and functional divergence, laying a solid molecular foundation for future exploration and study of stress resistance mechanisms in T.pratense.
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Affiliation(s)
| | | | | | | | | | | | - Weiguo Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
| | - Beibei Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
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Management of Rhizosphere Microbiota and Plant Production under Drought Stress: A Comprehensive Review. PLANTS 2022; 11:plants11182437. [PMID: 36145836 PMCID: PMC9502053 DOI: 10.3390/plants11182437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/13/2022] [Accepted: 09/16/2022] [Indexed: 01/10/2023]
Abstract
Drought generates a complex scenario worldwide in which agriculture should urgently be reframed from an integrative point of view. It includes the search for new water resources and the use of tolerant crops and genotypes, improved irrigation systems, and other less explored alternatives that are very important, such as biotechnological tools that may increase the water use efficiency. Currently, a large body of evidence highlights the role of specific strains in the main microbial rhizosphere groups (arbuscular mycorrhizal fungi, yeasts, and bacteria) on increasing the drought tolerance of their host plants through diverse plant growth-promoting (PGP) characteristics. With this background, it is possible to suggest that the joint use of distinct PGP microbes could produce positive interactions or additive beneficial effects on their host plants if their co-inoculation does not generate antagonistic responses. To date, such effects have only been partially analyzed by using single omics tools, such as genomics, metabolomics, or proteomics. However, there is a gap of information in the use of multi-omics approaches to detect interactions between PGP and host plants. This approach must be the next scale-jump in the study of the interaction of soil–plant–microorganism. In this review, we analyzed the constraints posed by drought in the framework of an increasing global demand for plant production, integrating the important role played by the rhizosphere biota as a PGP agent. Using multi-omics approaches to understand in depth the processes that occur in plants in the presence of microorganisms can allow us to modulate their combined use and drive it to increase crop yields, improving production processes to attend the growing global demand for food.
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Yan Z, Sang L, Ma Y, He Y, Sun J, Ma L, Li S, Miao F, Zhang Z, Huang J, Wang Z, Yang G. A de novo assembled high-quality chromosome-scale Trifolium pratense genome and fine-scale phylogenetic analysis. BMC PLANT BIOLOGY 2022; 22:332. [PMID: 35820796 PMCID: PMC9277957 DOI: 10.1186/s12870-022-03707-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/20/2022] [Indexed: 05/12/2023]
Abstract
BACKGROUND Red clover (Trifolium pratense L.) is a diploid perennial temperate legume with 14 chromosomes (2n = 14) native to Europe and West Asia, with high nutritional and economic value. It is a very important forage grass and is widely grown in marine climates, such as the United States and Sweden. Genetic research and molecular breeding are limited by the lack of high-quality reference genomes. In this study, we used Illumina, PacBio HiFi, and Hi-C to obtain a high-quality chromosome-scale red clover genome and used genome annotation results to analyze evolutionary relationships among related species. RESULTS The red clover genome obtained by PacBio HiFi assembly sequencing was 423 M. The assembly quality was the highest among legume genome assemblies published to date. The contig N50 was 13 Mb, scaffold N50 was 55 Mb, and BUSCO completeness was 97.9%, accounting for 92.8% of the predicted genome. Genome annotation revealed 44,588 gene models with high confidence and 52.81% repetitive elements in red clover genome. Based on a comparison of genome annotation results, red clover was closely related to Trifolium medium and distantly related to Glycine max, Vigna radiata, Medicago truncatula, and Cicer arietinum among legumes. Analyses of gene family expansions and contractions and forward gene selection revealed gene families and genes related to environmental stress resistance and energy metabolism. CONCLUSIONS We report a high-quality de novo genome assembly for the red clover at the chromosome level, with a substantial improvement in assembly quality over those of previously published red clover genomes. These annotated gene models can provide an important resource for molecular genetic breeding and legume evolution studies. Furthermore, we analyzed the evolutionary relationships among red clover and closely related species, providing a basis for evolutionary studies of clover leaf and legumes, genomics analyses of forage grass, the improvement of agronomic traits.
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Affiliation(s)
- Zhenfei Yan
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Lijun Sang
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Yue Ma
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Yong He
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Juan Sun
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Lichao Ma
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Shuo Li
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Fuhong Miao
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Zixin Zhang
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
| | | | - Zengyu Wang
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China.
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China.
| | - Guofeng Yang
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China.
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China.
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Sangiorgio D, Cellini A, Donati I, Ferrari E, Tanunchai B, Fareed Mohamed Wahdan S, Sadubsarn D, Farneti B, Checcucci A, Buscot F, Spinelli F, Purahong W. Taxonomical and functional composition of strawberry microbiome is genotype-dependent. J Adv Res 2022; 42:189-204. [PMID: 36513413 PMCID: PMC9788945 DOI: 10.1016/j.jare.2022.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 02/01/2022] [Accepted: 02/17/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Specific microbial communities are associated to host plants, influencing their phenotype and fitness.Despite the rising interest in plant microbiome, the role of microbial communities associated with perennial fruit plants remains overlooked. OBJECTIVES This work provides the first comprehensive descriptionof the taxonomical and functional bacterial and fungal microbiota of below- and above-ground organsof three commercially important strawberry genotypes under cultural conditions. METHODS Strawberry-associatedfungal and bacterial microbiomes were characterised by Next-Generation Sequencing and the potential functions expressed by the bacterial microbiome were analysed by both in silico and in vitro characterisation of plant growth-promoting abilities of native bacteria. Additionally, the association between the strawberry microbiome, plant disease tolerance, plant mineral nutrient content, and fruit quality was investigated. RESULTS Results showed that thestrawberry core microbiome included 24 bacteria and 15 fungal operational taxonomicunits (OTUs).However, plant organ and genotype had a significant role in determining the taxonomical and functional composition of microbial communities. Interestingly, the cultivar with the highesttolerance against powdery mildew and leaf spot and the highest fruit productivity was the only one able to ubiquitously recruit the beneficial bacterium, Pseudomonasfluorescens, and to establish a mutualistic symbiosis with the arbuscular mycorrhizaRhizophagus irregularis. CONCLUSION This work sheds light on the interaction of cultivated strawberry genotypes with a variety of microbes and highlights the importance of their applications to increase the sustainability of fruit crop production.
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Affiliation(s)
- Daniela Sangiorgio
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - University of Bologna, viale Fanin 46, 40127 Bologna, Italy
| | - Antonio Cellini
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - University of Bologna, viale Fanin 46, 40127 Bologna, Italy
| | | | - Erika Ferrari
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy
| | - Benjawan Tanunchai
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, D-06120 Halle (Saale), Germany
| | - Sara Fareed Mohamed Wahdan
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, D-06120 Halle (Saale), Germany,Department of Botany, Faculty of Science, Suez Canal University, 41522 Ismailia, Egypt
| | - Dolaya Sadubsarn
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, D-06120 Halle (Saale), Germany
| | - Brian Farneti
- Fondazione Edmund Mach, Research and Innovation Centre, Via E. Mach 1, 38010, S. Michele all’Adige, TN, Italy
| | - Alice Checcucci
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - University of Bologna, viale Fanin 46, 40127 Bologna, Italy
| | - François Buscot
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, D-06120 Halle (Saale), Germany,German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103 Leipzig, Germany
| | - Francesco Spinelli
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - University of Bologna, viale Fanin 46, 40127 Bologna, Italy,Corresponding authors.
| | - Witoon Purahong
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, D-06120 Halle (Saale), Germany,Corresponding authors.
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