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Cunha IDCMD, Silva AVRD, Boleta EHM, Pellegrinetti TA, Zagatto LFG, Zagatto SDSS, Chaves MGD, Mendes R, Patreze CM, Tsai SM, Mendes LW. The interplay between the inoculation of plant growth-promoting rhizobacteria and the rhizosphere microbiome and their impact on plant phenotype. Microbiol Res 2024; 283:127706. [PMID: 38574431 DOI: 10.1016/j.micres.2024.127706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/06/2024]
Abstract
Microbial inoculation stands as a pivotal strategy, fostering symbiotic relationships between beneficial microorganisms and plants, thereby enhancing nutrient uptake, bolstering resilience against environmental stressors, and ultimately promoting healthier and more productive plant growth. However, while the advantageous roles of inoculants are widely acknowledged, the precise and nuanced impacts of inoculation on the intricate interactions of the rhizosphere microbiome remain significantly underexplored. This study explores the impact of bacterial inoculation on soil properties, plant growth, and the rhizosphere microbiome. By employing various bacterial strains and a synthetic community (SynCom) as inoculants in common bean plants, the bacterial and fungal communities in the rhizosphere were assessed through 16 S rRNA and ITS gene sequencing. Concurrently, soil chemical parameters, plant traits, and gene expression were evaluated. The findings revealed that bacterial inoculation generally decreased pH and V%, while increasing H+Al and m% in the rhizosphere. It also decreased gene expression in plants related to detoxification, photosynthesis, and defense mechanisms, while enhancing bacterial diversity in the rhizosphere, potentially benefiting plant health. Specific bacterial strains showed varied impacts on rhizosphere microbiome assembly, predominantly affecting rhizospheric bacteria more than fungi, indirectly influencing soil conditions and plants. Notably, Paenibacillus polymyxa inoculation improved plant nitrogen (by 5.2%) and iron levels (by 28.1%), whereas Bacillus cereus boosted mycorrhization rates (by 70%). Additionally, inoculation led to increased complexity in network interactions within the rhizosphere (∼15%), potentially impacting plant health. Overall, the findings highlight the significant impact of introducing bacteria to the rhizosphere, enhancing nutrient availability, microbial diversity, and fostering beneficial plant-microbe interactions.
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Affiliation(s)
- Izadora de Cássia Mesquita da Cunha
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil; Luiz de Queiroz College of Agriculture ESALQ, University of São Paulo USP, Piracicaba, SP 13418-900, Brazil
| | - Ana Vitória Reina da Silva
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Eduardo Henrique Marcandalli Boleta
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Thierry Alexandre Pellegrinetti
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Luis Felipe Guandalin Zagatto
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil; Department of Terrestrial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen NL-6700 AB, the Netherlands
| | - Solange Dos Santos Silva Zagatto
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Miriam Gonçalves de Chaves
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariuna 18020-000, Brazil
| | - Camila Maistro Patreze
- Institute of Biosciences, Federal University of the State of Rio de Janeiro, Rio de Janeiro, RJ 22290-240, Brazil
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil.
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2
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Nabi Z, Manzoor S, Nabi SU, Wani TA, Gulzar H, Farooq M, Arya VM, Baloch FS, Vlădulescu C, Popescu SM, Mansoor S. Pattern-Triggered Immunity and Effector-Triggered Immunity: crosstalk and cooperation of PRR and NLR-mediated plant defense pathways during host-pathogen interactions. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:587-604. [PMID: 38737322 PMCID: PMC11087456 DOI: 10.1007/s12298-024-01452-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 05/14/2024]
Abstract
The elucidation of the molecular basis underlying plant-pathogen interactions is imperative for the development of sustainable resistance strategies against pathogens. Plants employ a dual-layered immunological detection and response system wherein cell surface-localized Pattern Recognition Receptors (PRRs) and intracellular Nucleotide-Binding Leucine-Rich Repeat Receptors (NLRs) play pivotal roles in initiating downstream signalling cascades in response to pathogen-derived chemicals. Pattern-Triggered Immunity (PTI) is associated with PRRs and is activated by the recognition of conserved molecular structures, known as Pathogen-Associated Molecular Patterns. When PTI proves ineffective due to pathogenic effectors, Effector-Triggered Immunity (ETI) frequently confers resistance. In ETI, host plants utilize NLRs to detect pathogen effectors directly or indirectly, prompting a rapid and more robust defense response. Additionally epigenetic mechanisms are participating in plant immune memory. Recently developed technologies like CRISPR/Cas9 helps in exposing novel prospects in plant pathogen interactions. In this review we explore the fascinating crosstalk and cooperation between PRRs and NLRs. We discuss epigenomic processes and CRISPR/Cas9 regulating immune response in plants and recent findings that shed light on the coordination of these defense layers. Furthermore, we also have discussed the intricate interactions between the salicylic acid and jasmonic acid signalling pathways in plants, offering insights into potential synergistic interactions that would be harnessed for the development of novel and sustainable resistance strategies against diverse group of pathogens.
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Affiliation(s)
- Zarka Nabi
- Division of Plant Pathology, FOA-SKUAST-K, Wadura, 193201 India
| | - Subaya Manzoor
- Division of Plant Pathology, FOA-SKUAST-K, Wadura, 193201 India
| | - Sajad Un Nabi
- ICAR-Central Institute of Temperate Horticulture, Srinagar, 191132 India
| | | | - Humira Gulzar
- Division of Plant Pathology, FOA-SKUAST-K, Wadura, 193201 India
| | - Mehreena Farooq
- Division of Plant Pathology, FOH-SKUAST-K, Shalimar, Srinagar, 190025 India
| | - Vivak M. Arya
- Division of Soil Science and Agriculture Chemistry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Jammu, India
| | - Faheem Shehzad Baloch
- Department of Biotechnology, Faculty of Science, Mersin University, 33100 Yenişehir, Mersin Turkey
| | - Carmen Vlădulescu
- Department of Biology and Environmental Engineering, University of Craiova, A. I. Cuza 13, 200585 Craiova, Romania
| | - Simona Mariana Popescu
- Department of Biology and Environmental Engineering, University of Craiova, A. I. Cuza 13, 200585 Craiova, Romania
| | - Sheikh Mansoor
- Department of Plant Resources and Environment, Jeju National University, Jeju, 63243 Republic of Korea
- Subtropical/Tropical Organism Gene Bank, Jeju National University, Jeju, 63243 Republic of Korea
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3
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Boo A, Toth T, Yu Q, Pfotenhauer A, Fields BD, Lenaghan SC, Stewart CN, Voigt CA. Synthetic microbe-to-plant communication channels. Nat Commun 2024; 15:1817. [PMID: 38418817 PMCID: PMC10901793 DOI: 10.1038/s41467-024-45897-6] [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: 02/10/2023] [Accepted: 02/07/2024] [Indexed: 03/02/2024] Open
Abstract
Plants and microbes communicate to collaborate to stop pests, scavenge nutrients, and react to environmental change. Microbiota consisting of thousands of species interact with each other and plants using a large chemical language that is interpreted by complex regulatory networks. In this work, we develop modular interkingdom communication channels, enabling bacteria to convey environmental stimuli to plants. We introduce a "sender device" in Pseudomonas putida and Klebsiella pneumoniae, that produces the small molecule p-coumaroyl-homoserine lactone (pC-HSL) when the output of a sensor or circuit turns on. This molecule triggers a "receiver device" in the plant to activate gene expression. We validate this system in Arabidopsis thaliana and Solanum tuberosum (potato) grown hydroponically and in soil, demonstrating its modularity by swapping bacteria that process different stimuli, including IPTG, aTc and arsenic. Programmable communication channels between bacteria and plants will enable microbial sentinels to transmit information to crops and provide the building blocks for designing artificial consortia.
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Affiliation(s)
- Alice Boo
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Tyler Toth
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Qiguo Yu
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Alexander Pfotenhauer
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Brandon D Fields
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Scott C Lenaghan
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - C Neal Stewart
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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4
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Krzyżanowska DM, Jabłońska M, Kaczyński Z, Czerwicka-Pach M, Macur K, Jafra S. Host-adaptive traits in the plant-colonizing Pseudomonas donghuensis P482 revealed by transcriptomic responses to exudates of tomato and maize. Sci Rep 2023; 13:9445. [PMID: 37296159 PMCID: PMC10256816 DOI: 10.1038/s41598-023-36494-6] [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: 01/24/2023] [Accepted: 06/05/2023] [Indexed: 06/12/2023] Open
Abstract
Pseudomonads are metabolically flexible and can thrive on different plant hosts. However, the metabolic adaptations required for host promiscuity are unknown. Here, we addressed this knowledge gap by employing RNAseq and comparing transcriptomic responses of Pseudomonas donghuensis P482 to root exudates of two plant hosts: tomato and maize. Our main goal was to identify the differences and the common points between these two responses. Pathways upregulated only by tomato exudates included nitric oxide detoxification, repair of iron-sulfur clusters, respiration through the cyanide-insensitive cytochrome bd, and catabolism of amino and/or fatty acids. The first two indicate the presence of NO donors in the exudates of the test plants. Maize specifically induced the activity of MexE RND-type efflux pump and copper tolerance. Genes associated with motility were induced by maize but repressed by tomato. The shared response to exudates seemed to be affected both by compounds originating from the plants and those from their growth environment: arsenic resistance and bacterioferritin synthesis were upregulated, while sulfur assimilation, sensing of ferric citrate and/or other iron carriers, heme acquisition, and transport of polar amino acids were downregulated. Our results provide directions to explore mechanisms of host adaptation in plant-associated microorganisms.
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Affiliation(s)
- Dorota M Krzyżanowska
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdańsk, ul. A. Abrahama 58, 80-307, Gdańsk, Poland
| | - Magdalena Jabłońska
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdańsk, ul. A. Abrahama 58, 80-307, Gdańsk, Poland
| | - Zbigniew Kaczyński
- Laboratory of Structural Biochemistry, Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Małgorzata Czerwicka-Pach
- Laboratory of Structural Biochemistry, Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Katarzyna Macur
- Laboratory of Mass Spectrometry, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdańsk, ul. A. Abrahama 58, 80-307, Gdańsk, Poland
| | - Sylwia Jafra
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdańsk, ul. A. Abrahama 58, 80-307, Gdańsk, Poland.
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5
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Gonçalves OS, Souza TS, Gonçalves GDC, Fernandes AS, Veloso TGR, Tupy SM, Garcia EA, Santana MF. Harnessing Novel Soil Bacteria for Beneficial Interactions with Soybean. Microorganisms 2023; 11:300. [PMID: 36838264 PMCID: PMC9964534 DOI: 10.3390/microorganisms11020300] [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: 12/17/2022] [Revised: 01/16/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
It is claimed that one g of soil holds ten billion bacteria representing thousands of distinct species. These bacteria play key roles in the regulation of terrestrial carbon dynamics, nutrient cycles, and plant productivity. Despite the overwhelming diversity of bacteria, most bacterial species remain largely unknown. Here, we used an oligotrophic medium to isolate novel soil bacteria for positive interaction with soybean. Strictly 22 species of bacteria from the soybean rhizosphere were selected. These isolates encompass ten genera (Kosakonia, Microbacterium, Mycobacterium, Methylobacterium, Monashia, Novosphingobium, Pandoraea, Anthrobacter, Stenotrophomonas, and Rhizobium) and have potential as novel species. Furthermore, the novel bacterial species exhibited plant growth-promoting traits in vitro and enhanced soybean growth under drought stress in a greenhouse experiment. We also reported the draft genome sequences of Kosakonia sp. strain SOY2 and Agrobacterium sp. strain SOY23. Along with our analysis of 169 publicly available genomes for the genera reported here, we demonstrated that these bacteria have a repertoire of genes encoding plant growth-promoting proteins and secondary metabolite biosynthetic gene clusters that directly affect plant growth. Taken together, our findings allow the identification novel soil bacteria, paving the way for their application in crop production.
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Affiliation(s)
- Osiel Silva Gonçalves
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast BT9 5DL, UK
- Grupo de Genômica Evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa CEP 36570-900, MG, Brazil
| | - Thamires Santos Souza
- Grupo de Genômica Evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa CEP 36570-900, MG, Brazil
| | - Guilherme de Castro Gonçalves
- Grupo de Genômica Evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa CEP 36570-900, MG, Brazil
| | - Alexia Suellen Fernandes
- Grupo de Genômica Evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa CEP 36570-900, MG, Brazil
| | - Tomás Gomes Reis Veloso
- Grupo de Genômica Evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa CEP 36570-900, MG, Brazil
| | - Sumaya Martins Tupy
- Grupo de Genômica Evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa CEP 36570-900, MG, Brazil
| | - Ediones Amaro Garcia
- Grupo de Genômica Evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa CEP 36570-900, MG, Brazil
| | - Mateus Ferreira Santana
- Grupo de Genômica Evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa CEP 36570-900, MG, Brazil
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6
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Neelam A, Tabassum S. Optical Sensing Technologies to Elucidate the Interplay between Plant and Microbes. MICROMACHINES 2023; 14:195. [PMID: 36677256 PMCID: PMC9866067 DOI: 10.3390/mi14010195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Plant-microbe interactions are critical for ecosystem functioning and driving rhizosphere processes. To fully understand the communication pathways between plants and rhizosphere microbes, it is crucial to measure the numerous processes that occur in the plant and the rhizosphere. The present review first provides an overview of how plants interact with their surrounding microbial communities, and in turn, are affected by them. Next, different optical biosensing technologies that elucidate the plant-microbe interactions and provide pathogenic detection are summarized. Currently, most of the biosensors used for detecting plant parameters or microbial communities in soil are centered around genetically encoded optical and electrochemical biosensors that are often not suitable for field applications. Such sensors require substantial effort and cost to develop and have their limitations. With a particular focus on the detection of root exudates and phytohormones under biotic and abiotic stress conditions, novel low-cost and in-situ biosensors must become available to plant scientists.
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Affiliation(s)
| | - Shawana Tabassum
- Department of Electrical Engineering, The University of Texas at Tyler, Tyler, TX 75799, USA
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7
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Ishida K, Noutoshi Y. The function of the plant cell wall in plant-microbe interactions. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 192:273-284. [PMID: 36279746 DOI: 10.1016/j.plaphy.2022.10.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 09/07/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
The plant cell wall is an interface of plant-microbe interactions. The ability of microbes to decompose cell wall polysaccharides contributes to microbial pathogenicity. Plants have evolved mechanisms to prevent cell wall degradation. However, the role of the cell wall in plant-microbe interactions is not well understood. Here, we discuss four functions of the plant cell wall-physical defence, storage of antimicrobial compounds, production of cell wall-derived elicitors, and provision of carbon sources-in the context of plant-microbe interactions. In addition, we discuss the four families of cell surface receptors associated with plant cell walls (malectin-like receptor kinase family, wall-associated kinase family, leucine-rich repeat receptor-like kinase family, and lysin motif receptor-like kinase family) that have been the subject of several important studies in recent years. This review summarises the findings on both plant cell wall and plant immunity, improving our understanding and may provide impetus to various researchers.
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Affiliation(s)
- Konan Ishida
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Yoshiteru Noutoshi
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan.
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8
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Das PP, Singh KR, Nagpure G, Mansoori A, Singh RP, Ghazi IA, Kumar A, Singh J. Plant-soil-microbes: A tripartite interaction for nutrient acquisition and better plant growth for sustainable agricultural practices. ENVIRONMENTAL RESEARCH 2022; 214:113821. [PMID: 35810815 DOI: 10.1016/j.envres.2022.113821] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/24/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Plants can achieve their proper growth and development with the help of microorganisms associated with them. Plant-associated microbes convert the unavailable nutrients to available form and make them useful for plants. Besides nutrient acquisition, soil microbes also inhibit the pathogens that cause harm to plant growth and induces defense response. Due to the beneficial activities of soil nutrient-microbe-plant interactions, it is necessary to study more on this topic and develop microbial inoculant technology in the agricultural field for better crop improvement. The soil microbes can be engineered, and plant growth-promoting rhizobacteria (PGPR) and plant growth-promoting bacteria (PGPB) technology can be developed as well, as its application can be improved for utilization as biofertilizer, biopesticides, etc., instead of using harmful chemical biofertilizers. Moreover, plant growth-promoting microbe inoculants can enhance crop productivity. Although, scientists have discussed several tools and techniques by omics and gene editing approaches for crop improvement to avoid biotic and abiotic stress and make the plant healthier and more nutritive. However, beneficial soil microbes that help plants with the nutrient acquisition, development, and stress resistance were ignored, and farmers started utilizing chemical fertilizers. Thus, this review attempts to summarize the interaction system of plant microbes, the role of beneficiary soil microbes in the rhizosphere zone, and their role in plant health promotion, particularly in the nutrition acquisition of the plant. The review will also provide a better understanding of soil microbes that can be exploited as biofertilizers and plant growth promoters in the field to create environmentally friendly, sustainable agriculture systems.
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Affiliation(s)
- Prajna Priyadarshini Das
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
| | - Kshitij Rb Singh
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 211005, India
| | - Gunjan Nagpure
- Department of Biotechnology, Faculty of Science, Indira Gandhi National Tribal University, Amarkantak, Madhya Pradesh, 484887, India
| | - Aadil Mansoori
- Department of Botany, Faculty of Science, Indira Gandhi National Tribal University, Amarkantak, Madhya Pradesh, 484887, India
| | - Ravindra Pratap Singh
- Department of Biotechnology, Faculty of Science, Indira Gandhi National Tribal University, Amarkantak, Madhya Pradesh, 484887, India
| | - Irfan Ahmad Ghazi
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
| | - Anirudh Kumar
- Department of Botany, Faculty of Science, Indira Gandhi National Tribal University, Amarkantak, Madhya Pradesh, 484887, India.
| | - Jay Singh
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 211005, India.
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9
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Jiang W, Chen R, Zhao L, Qin L, Fan H, Chen X, Wang Y, Yin C, Mao Z. Chemical fumigants control apple replant disease: Microbial community structure-mediated inhibition of Fusarium and degradation of phenolic acids. JOURNAL OF HAZARDOUS MATERIALS 2022; 440:129786. [PMID: 36007363 DOI: 10.1016/j.jhazmat.2022.129786] [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: 06/17/2022] [Revised: 07/31/2022] [Accepted: 08/13/2022] [Indexed: 06/15/2023]
Abstract
Fusarium and phenolic acids in apple replant soil have deleterious effects on soil, which affects the growth of young replanted apple trees. Here, we studied the effects of different chemical fumigants (metham sodium, dazomet, calcium cyanamide, 1,3-dichloropropene, and methyl bromide) on Fusarium and phenolic acids in soil. The chemical fumigants disturbed the apple replant soil microbial community to different degrees in the order from highest to the lowest as methyl bromide > 1,3-dichloropropene > dazomet > metham sodium > calcium cyanamide. Compared with the control, the total numbers of Operational Taxonomic Unit (OTU) were 104.63 % and 9.38 % lower in the methyl bromide and calcium cyanamide treatments, respectively while the average contents of Fusarium were 88.04 % and 59.18% lower in these treatments, respectively. Higher disturbance degrees resulted in a slower recovery rate of the soil microbial community, which facilitated the transformation of the soil into a disease-suppressing state. During the recovery process, the roots recruited Streptomyces OTU2796 and Bacillus OTU2243, which alleviated Fusarium-induced stress via the synthesis of polyketones and macrolides. The roots also recruited Sphingomonas OTU3488, OTU5572, and OTU8147, which alleviated phenolic acid-induced stress through the degradation of benzoate and polycyclic aromatic hydrocarbons.
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Affiliation(s)
- Weitao Jiang
- State Key Laboratory of Crop Biology College of Horticulture Science and Engineering Shandong Agricultural University Tai'an, Shandong 271018, PR China
| | - Ran Chen
- State Key Laboratory of Crop Biology College of Horticulture Science and Engineering Shandong Agricultural University Tai'an, Shandong 271018, PR China
| | - Lei Zhao
- State Key Laboratory of Crop Biology College of Horticulture Science and Engineering Shandong Agricultural University Tai'an, Shandong 271018, PR China
| | - Lei Qin
- State Key Laboratory of Crop Biology College of Horticulture Science and Engineering Shandong Agricultural University Tai'an, Shandong 271018, PR China
| | - Hai Fan
- College of Chemistry and Material Science Shandong Agricultural University Tai'an, Shandong 271018, PR China
| | - Xuesen Chen
- State Key Laboratory of Crop Biology College of Horticulture Science and Engineering Shandong Agricultural University Tai'an, Shandong 271018, PR China
| | - Yanfang Wang
- College of Chemistry and Material Science Shandong Agricultural University Tai'an, Shandong 271018, PR China
| | - Chengmiao Yin
- State Key Laboratory of Crop Biology College of Horticulture Science and Engineering Shandong Agricultural University Tai'an, Shandong 271018, PR China
| | - Zhiquan Mao
- State Key Laboratory of Crop Biology College of Horticulture Science and Engineering Shandong Agricultural University Tai'an, Shandong 271018, PR China.
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10
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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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Guajardo-Leiva S, Alarcón J, Gutzwiller F, Gallardo-Cerda J, Acuña-Rodríguez IS, Molina-Montenegro M, Crandall KA, Pérez-Losada M, Castro-Nallar E. Source and acquisition of rhizosphere microbes in Antarctic vascular plants. Front Microbiol 2022; 13:916210. [PMID: 36160194 PMCID: PMC9493328 DOI: 10.3389/fmicb.2022.916210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/12/2022] [Indexed: 11/27/2022] Open
Abstract
Rhizosphere microbial communities exert critical roles in plant health, nutrient cycling, and soil fertility. Despite the essential functions conferred by microbes, the source and acquisition of the rhizosphere are not entirely clear. Therefore, we investigated microbial community diversity and potential source using the only two native Antarctic plants, Deschampsia antarctica (Da) and Colobanthus quitensis (Cq), as models. We interrogated rhizosphere and bulk soil microbiomes at six locations in the Byers Peninsula, Livingston Island, Antarctica, both individual plant species and their association (Da.Cq). Our results show that host plant species influenced the richness and diversity of bacterial communities in the rhizosphere. Here, the Da rhizosphere showed the lowest richness and diversity of bacteria compared to Cq and Da.Cq rhizospheres. In contrast, for rhizosphere fungal communities, plant species only influenced diversity, whereas the rhizosphere of Da exhibited higher fungal diversity than the Cq rhizosphere. Also, we found that environmental geographic pressures (i.e., sampling site, latitude, and altitude) and, to a lesser extent, biotic factors (i.e., plant species) determined the species turnover between microbial communities. Moreover, our analysis shows that the sources of the bacterial communities in the rhizosphere were local soils that contributed to homogenizing the community composition of the different plant species growing in the same sampling site. In contrast, the sources of rhizosphere fungi were local (for Da and Da.Cq) and distant soils (for Cq). Here, the host plant species have a specific effect in acquiring fungal communities to the rhizosphere. However, the contribution of unknown sources to the fungal rhizosphere (especially in Da and Da.Cq) indicates the existence of relevant stochastic processes in acquiring these microbes. Our study shows that rhizosphere microbial communities differ in their composition and diversity. These differences are explained mainly by the microbial composition of the soils that harbor them, acting together with plant species-specific effects. Both plant species acquire bacteria from local soils to form part of their rhizosphere. Seemingly, the acquisition process is more complex for fungi. We identified a significant contribution from unknown fungal sources due to stochastic processes and known sources from soils across the Byers Peninsula.
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Affiliation(s)
- Sergio Guajardo-Leiva
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Universidad de Talca, Talca, Chile
- Centro de Ecología Integrativa, Universidad de Talca, Talca, Chile
| | - Jaime Alarcón
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Florence Gutzwiller
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Jorge Gallardo-Cerda
- Laboratorio de Ecología Integrativa, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | | | - Marco Molina-Montenegro
- Centro de Ecología Integrativa, Universidad de Talca, Talca, Chile
- Laboratorio de Ecología Integrativa, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Centro de Estudios Avanzados en Zonas Áridas, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile
- Centro de Investigación en Estudios Avanzados del Maule, Universidad Católica del Maule, Talca, Chile
| | - Keith A. Crandall
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, George Washington University, Washington, DC, United States
| | - Marcos Pérez-Losada
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, George Washington University, Washington, DC, United States
- Division of Emergency Medicine, Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Children’s National Hospital, Washington, DC, United States
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Eduardo Castro-Nallar
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Universidad de Talca, Talca, Chile
- Centro de Ecología Integrativa, Universidad de Talca, Talca, Chile
- *Correspondence: Eduardo Castro-Nallar,
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Dolatabadian A, Fernando WGD. Genomic Variations and Mutational Events Associated with Plant-Pathogen Interactions. BIOLOGY 2022; 11:421. [PMID: 35336795 PMCID: PMC8945218 DOI: 10.3390/biology11030421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 12/23/2022]
Abstract
Phytopathologists are actively researching the molecular basis of plant-pathogen interactions. The mechanisms of responses to pathogens have been studied extensively in model crop plant species and natural populations. Today, with the rapid expansion of genomic technologies such as DNA sequencing, transcriptomics, proteomics, and metabolomics, as well as the development of new methods and protocols, data analysis, and bioinformatics, it is now possible to assess the role of genetic variation in plant-microbe interactions and to understand the underlying molecular mechanisms of plant defense and microbe pathogenicity with ever-greater resolution and accuracy. Genetic variation is an important force in evolution that enables organisms to survive in stressful environments. Moreover, understanding the role of genetic variation and mutational events is essential for crop breeders to produce improved cultivars. This review focuses on genetic variations and mutational events associated with plant-pathogen interactions and discusses how these genome compartments enhance plants' and pathogens' evolutionary processes.
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Affiliation(s)
- Aria Dolatabadian
- Department of Plant Science, Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada;
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Coban O, De Deyn GB, van der Ploeg M. Soil microbiota as game-changers in restoration of degraded lands. Science 2022; 375:abe0725. [PMID: 35239372 DOI: 10.1126/science.abe0725] [Citation(s) in RCA: 121] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Land degradation reduces soil functioning and, consequently, the services that soil provides. Soil hydrological functions are critical to combat soil degradation and promote soil restoration. Soil microorganisms affect soil hydrology, but the role of soil microbiota in forming and sustaining soil is not well explored. Case studies indicate the potential of soil microorganisms as game-changers in restoring soil functions. We review the state of the art of microorganism use in land restoration technology, the groups of microorganisms with the greatest potential for soil restoration, knowledge of the effect of microorganisms on soil physical properties, and proposed strategies for the long-term restoration of degraded lands. We also emphasize the need to advance the emerging research field of biophysical landscape interactions to support soil-plant ecosystem restoration practices.
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Affiliation(s)
- Oksana Coban
- Department of Environmental Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Gerlinde B De Deyn
- Department of Environmental Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Martine van der Ploeg
- Department of Environmental Sciences, Wageningen University & Research, Wageningen, Netherlands
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Song GC, Jeon JS, Sim HJ, Lee S, Jung J, Kim SG, Moon SY, Ryu CM. Dual functionality of natural mixtures of bacterial volatile compounds on plant growth. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:571-583. [PMID: 34679179 DOI: 10.1093/jxb/erab466] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 10/21/2021] [Indexed: 06/13/2023]
Abstract
Bacteria emit volatile compounds that modulate plant growth. Previous studies reported the impacts of bacterial volatile compounds on plant growth; however, the results varied depending on bacterial nutrient availability. We investigated whether the effects of plant growth-inhibiting volatiles (PGIVs) and plant growth-promoting volatiles (PGPVs) depended on the perceived dose by evaluating the growth of Arabidopsis thaliana seedlings placed at 7, 14, and 21 cm away from Bacillus amyloliquefaciens GB03 colonies growing in rich medium. A large bacterial colony (500 μl inoculum) inhibited plant growth at 7 cm and promoted growth at 21 cm, whereas a small bacterial colony (100 μl inoculum) induced the opposite pattern of response. We identified pyrazine and 2,5-dimethylpyrazine as candidate PGIVs that significantly reduced plant growth at a distance of 7 cm. PGIV effects were validated by exposing plants to synthetic 2,5-dimethylpyrazine and bacteria emitting PGPVs, which showed that PGIVs overwhelm PGPVs to rapidly increase salicylic acid content and related gene expression. This is referred to as the defence-growth trade-off. Our results indicate that high PGIV concentrations suppress plant growth and promote immunity, whereas low PGPV concentrations promote growth. This study provides novel insights into the complex effects of bacterial volatile mixtures and fine-tuning of bacteria-plant interactions.
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Affiliation(s)
- Geun Cheol Song
- Molecular Phytobacteriology Laboratory, KRIBB, Daejeon 34141, S. Korea
| | - Je-Seung Jeon
- Molecular Phytobacteriology Laboratory, KRIBB, Daejeon 34141, S. Korea
| | - Hee-Jung Sim
- Center for Genome Engineering, Institute for Basic Science (IBS), Daejeon 34126, S. Korea
- Environmental Safety Assessment Center, Korea Institute of Toxicology (KIT), 17 Jegok-gil, Munsan-eup, Jinju 52834, South Korea
| | - Soohyun Lee
- Molecular Phytobacteriology Laboratory, KRIBB, Daejeon 34141, S. Korea
| | - Jihye Jung
- Molecular Phytobacteriology Laboratory, KRIBB, Daejeon 34141, S. Korea
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Sang-Gyu Kim
- Center for Genome Engineering, Institute for Basic Science (IBS), Daejeon 34126, S. Korea
| | - Sun Young Moon
- Center for Genome Engineering, Institute for Basic Science (IBS), Daejeon 34126, S. Korea
| | - Choong-Min Ryu
- Molecular Phytobacteriology Laboratory, KRIBB, Daejeon 34141, S. Korea
- Biosystems and Bioengineering Program, University of Science and Technology (UST), Daejeon 34113, S. Korea
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Deb S, Choudhury A, Kharbyngar B, Satyawada RR. Applications of CRISPR/Cas9 technology for modification of the plant genome. Genetica 2022; 150:1-12. [PMID: 35018532 DOI: 10.1007/s10709-021-00146-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/02/2021] [Indexed: 12/26/2022]
Abstract
The CRISPR/Cas (Clustered regularly interspaced short palindromic repeats/ CRISPR associated protein 9) system was discovered in bacteria and archea as an acquired immune response to protect the cells from infection. This technology has now evolved to become an efficient genome editing tool, and is replacing older gene editing technologies. This technique uses programmable sgRNAs to guide the Cas9 endonuclease to the target DNA location. sgRNA is a vital component of the CRISPR technology, since without it the Cas nuclease cannot reach to its target location. Over the years, many tools have been developed for designing sgRNAs, the details of which have been extensively reviewed here. It has proven to be a promising tool in the field of genetic engineering and has successfully generated many plant varieties with better and desirable qualities. In the present review, we attempted to collect,collate and summarize information related to the development of CRISPR/Cas9 system as a tool and subsequently into a technique having a wide array of applications in the field of plant genome editing in attaining desirable traits like resistance to various diseases, nutritional enhancement etc. In addition, the probable future prospects and the various bio-safety concerns associated with CRISPR gene editing technology have been discussed in detail.
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Affiliation(s)
- Sohini Deb
- Plant Biotechnology Laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya, 793022, India
| | - Amrita Choudhury
- Plant Biotechnology Laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya, 793022, India
| | - Banridor Kharbyngar
- Plant Biotechnology Laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya, 793022, India
| | - Rama Rao Satyawada
- Plant Biotechnology Laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya, 793022, India.
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Nadarajah K, Abdul Rahman NSN. Plant-Microbe Interaction: Aboveground to Belowground, from the Good to the Bad. Int J Mol Sci 2021; 22:ijms221910388. [PMID: 34638728 PMCID: PMC8508622 DOI: 10.3390/ijms221910388] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/14/2021] [Accepted: 09/17/2021] [Indexed: 02/06/2023] Open
Abstract
Soil health and fertility issues are constantly addressed in the agricultural industry. Through the continuous and prolonged use of chemical heavy agricultural systems, most agricultural lands have been impacted, resulting in plateaued or reduced productivity. As such, to invigorate the agricultural industry, we would have to resort to alternative practices that will restore soil health and fertility. Therefore, in recent decades, studies have been directed towards taking a Magellan voyage of the soil rhizosphere region, to identify the diversity, density, and microbial population structure of the soil, and predict possible ways to restore soil health. Microbes that inhabit this region possess niche functions, such as the stimulation or promotion of plant growth, disease suppression, management of toxicity, and the cycling and utilization of nutrients. Therefore, studies should be conducted to identify microbes or groups of organisms that have assigned niche functions. Based on the above, this article reviews the aboveground and below-ground microbiomes, their roles in plant immunity, physiological functions, and challenges and tools available in studying these organisms. The information collected over the years may contribute toward future applications, and in designing sustainable agriculture.
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Mishra R, Mohanty JN, Mahanty B, Joshi RK. A single transcript CRISPR/Cas9 mediated mutagenesis of CaERF28 confers anthracnose resistance in chilli pepper (Capsicum annuum L.). PLANTA 2021; 254:5. [PMID: 34132917 DOI: 10.1007/s00425-021-03660-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/10/2021] [Indexed: 05/09/2023]
Abstract
T-DNA-free homozygous mutant lines developed through a single transcript CRISPR/Cas9 system harboring the desired modification in the CaERF28 locus exhibited significantly enhanced resistance to the anthracnose pathogen Colletotrichum truncatum coupled with the improved expression of defense responsive genes. Anthracnose, caused by Colletotrichum species, is a major disease of chilli (Capsicum annuum) accounting for significant pre- and post-harvest yield losses across the tropical and subtropical regions of the world. Management of chilli anthracnose using traditional methods have not met with noticeable success. In the present study, we have demonstrated an enhanced anthracnose resistance through a single transcript unit CRISPR/Cas9 mediated alteration of the susceptibility gene CaERF28 in C. annuum. A construct with a single Pol II promoter-driven expression of Cas9, sgRNA and a hammerhead ribozyme (RZ) was designed to modify the CaERF28 gene in the susceptible chilli genotype Arka Lohit. Fourty-five C-ERF28-induced mutant lines (72.5%) were identified from 62 T0 transgenic plants. Further, simultaneously targeted multiple sites within CaERF28 showed increased mutation (85.7%) efficiency. DNA sequence analysis showed that these plants harboured multiple InDels at the target site. The allelic mutants of C-ERF28 were transferred to the following generations by simple Mendelian inheritance. Segregation in the T1 and T2 generations resulted in the identification of T-DNA free and marker-free C-ERF28 mutant lines. Five homozygous mutants demonstrated enhanced resistance to anthracnose compared to wild type as demonstrated by reduced spore count and fungal growth as well as induced expression of defense-related genes. Our results demonstrated that the STU-CRISPR/Cas9 mediated editing of the CaERF28 gene is a rapid, safe and versatile approach for enhancing anthracnose resistance in chilli pepper and pave way for its utilization in the improvement of other solanaceous crops.
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Affiliation(s)
- Rukmini Mishra
- School of Applied Science, Centurion University of Technology and Management, Bhubaneswar, 752050, India
| | - Jatindra Nath Mohanty
- Centre for Biomedical Informatics, Siksha O Anusandhan University, Bhubaneswar, 751003, India
| | - Bijayalaxmi Mahanty
- Department of Biotechnology, Rama Devi Women's University, Vidya Vihar, Bhubaneswar, 751022, India
| | - Raj Kumar Joshi
- Department of Biotechnology, Rama Devi Women's University, Vidya Vihar, Bhubaneswar, 751022, India.
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Chaudhary T, Gera R, Shukla P. Emerging Molecular Tools for Engineering Phytomicrobiome. Indian J Microbiol 2021; 61:116-124. [PMID: 33927453 DOI: 10.1007/s12088-020-00915-1] [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: 02/18/2020] [Accepted: 12/05/2020] [Indexed: 10/22/2022] Open
Abstract
Microbial plant interaction plays a major role in the sustainability of plants. The understanding of phytomicrobiome interactions enables the gene-editing tools for the construction of the microbial consortia. In this interaction, microbes share several common secondary metabolites and terpenoid metabolic pathways with their host plants that ensure a direct connection between the microbiome and associated plant metabolome. In this way, the CRISPR-mediated gene-editing tool provides an attractive approach to accomplish the creation of microbial consortia. On the other hand, the genetic manipulation of the host plant with the help of CRISPR-Cas9 can facilitate the characterization and identification of the genetic determinants. It leads to the enhancement of microbial capacity for more trait improvement. Many plant characteristics like phytovolatilization, phytoextraction, phytodesalination and phytodegradation are targeted by these approaches. Alternatively, chemical communications by PGPB are accomplished by the exchange of different signal molecules. For example, quorum-sensing is the way of the cell to cell communication in bacteria that lead to the detection of metabolites produced by pathogens during adverse conditions and also helpful in devising some tactics towards understanding plant immunity. Along with quorum-sensing, different volatile organic compounds and N-acyl homoserine lactones play a significant role in cell to cell communication by microbe to plant and among the plants respectively. Therefore, it is necessary to get details of all the significant approaches that are useful in exploring cell to cell communications. In this review, we have described gene-editing tools and the cell to cell communication process by quorum-sensing based signaling. These signaling processes via CRISPR- Cas9 mediated gene editing can improve the microbe-plant community in adverse climatic conditions.
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Affiliation(s)
- Twinkle Chaudhary
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, 124001 India
| | - Rajesh Gera
- Department of Microbiology, Chaudhary Charan Singh Haryana Agricultural University, Hisar, 125004 India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, 124001 India.,Present Address: School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005 India
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Tyagi S, Kumar R, Kumar V, Won SY, Shukla P. Engineering disease resistant plants through CRISPR-Cas9 technology. GM CROPS & FOOD 2021; 12:125-144. [PMID: 33079628 PMCID: PMC7583490 DOI: 10.1080/21645698.2020.1831729] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 09/13/2020] [Accepted: 09/27/2020] [Indexed: 01/08/2023]
Abstract
Plants are susceptible to phytopathogens, including bacteria, fungi, and viruses, which cause colossal financial shortfalls (pre- and post-harvest) and threaten global food safety. To combat with these phytopathogens, plant possesses two-layer of defense in the form of PAMP-triggered immunity (PTI), or Effectors-triggered immunity (ETI). The understanding of plant-molecular interactions and revolution of high-throughput molecular techniques have opened the door for innovations in developing pathogen-resistant plants. In this context, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) has transformed genome editing (GE) technology and being harnessed for altering the traits. Here we have summarized the complexities of plant immune system and the use of CRISPR-Cas9 to edit the various components of plant immune system to acquire long-lasting resistance in plants against phytopathogens. This review also sheds the light on the limitations of CRISPR-Cas9 system, regulation of CRISPR-Cas9 edited crops and future prospective of this technology.
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Affiliation(s)
- Swati Tyagi
- Genomic Division, National Institute of Agriculture Science, Rural Development Administration, Jeonju, Republic of Korea
| | - Robin Kumar
- Department of Soil Science and Agricultural Chemistry, Acharya Narendra Dev University of Agriculture and Technology, Kumarganj, Ayodhya, India
- Department of Agriculture Engineering, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, India
| | - Vivak Kumar
- Department of Agriculture Engineering, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, India
| | - So Youn Won
- Genomic Division, National Institute of Agriculture Science, Rural Development Administration, Jeonju, Republic of Korea
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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Hu W, Pan L, Chen H, Tang M. VBA-AMF: A VBA Program Based on the Magnified Intersections Method for Quantitative Recording of Root Colonization by Arbuscular Mycorrhizal Fungi. Indian J Microbiol 2020; 60:374-378. [PMID: 32647395 PMCID: PMC7329954 DOI: 10.1007/s12088-020-00866-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 04/01/2020] [Indexed: 02/07/2023] Open
Abstract
The extent of mycorrhizal fungi colonization is an important factor for determining the function of mycorrhizal fungi in fungi-host interaction, and quantifying the extent of mycorrhizal fungi colonization is a fundamental and essential task for researchers engaged in mycorrhizal studies. Intersect methods, such as the gridline intersect and magnified intersections methods, are accurate and objective, and are widely used to assess the colonization status of arbuscular mycorrhizal (AM) fungus. However, no convenient procedures or add-ins for Excel spreadsheets have been developed to simplify these methods. Here, we propose a procedure using the Visual Basic for Application (VBA) program in Excel that is based on the magnified intersections method, which we refer to as VBA-AMF (arbuscular mycorrhizal fungi). Time-saving and convenience are the two most prominent advantages of the VBA-AMF procedure, as it enables researchers to compute the colonization rate of AM fungi in roots, and consequently the extent of root colonization by AM fungi. VBA-AMF can also be modified to measure the status of other fungal colonizations in plant roots following the same strategy.
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Affiliation(s)
- Wentao Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 People’s Republic of China
| | - Lan Pan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 People’s Republic of China
| | - Hui Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 People’s Republic of China
| | - Ming Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 People’s Republic of China
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Jaswal R, Kiran K, Rajarammohan S, Dubey H, Singh PK, Sharma Y, Deshmukh R, Sonah H, Gupta N, Sharma TR. Effector Biology of Biotrophic Plant Fungal Pathogens: Current Advances and Future Prospects. Microbiol Res 2020; 241:126567. [PMID: 33080488 DOI: 10.1016/j.micres.2020.126567] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 07/21/2020] [Accepted: 07/25/2020] [Indexed: 12/13/2022]
Abstract
The interaction of fungal pathogens with their host requires a novel invading mechanism and the presence of various virulence-associated components responsible for promoting the infection. The small secretory proteins, explicitly known as effector proteins, are one of the prime mechanisms of host manipulation utilized by the pathogen to disarm the host. Several effector proteins are known to translocate from fungus to the plant cell for host manipulation. Many fungal effectors have been identified using genomic, transcriptomic, and bioinformatics approaches. Most of the effector proteins are devoid of any conserved signatures, and their prediction based on sequence homology is very challenging, therefore by combining the sequence consensus based upon machine learning features, multiple tools have also been developed for predicting apoplastic and cytoplasmic effectors. Various post-genomics approaches like transcriptomics of virulent isolates have also been utilized for identifying active consortia of effectors. Significant progress has been made in understanding biotrophic effectors; however, most of it is underway due to their complex interaction with host and complicated recognition and signaling networks. This review discusses advances, and challenges in effector identification and highlighted various features of the potential effector proteins and approaches for understanding their genetics and strategies for regulation.
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Affiliation(s)
- Rajdeep Jaswal
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India; Department of Microbiology, Panjab University, Chandigarh, Punjab, 160014, India
| | - Kanti Kiran
- ICAR-National Institute for Plant Biotechnology, Pusa Campus New Delhi, 110012, India
| | | | - Himanshu Dubey
- ICAR-National Institute for Plant Biotechnology, Pusa Campus New Delhi, 110012, India
| | - Pankaj Kumar Singh
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India
| | - Yogesh Sharma
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India
| | - Naveen Gupta
- Department of Microbiology, Panjab University, Chandigarh, Punjab, 160014, India.
| | - T R Sharma
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India.
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22
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Sahu J, Vaishnav A, Singh HB. Insights in Plant-Microbe Interaction through Genomics Approach (Part 1). Curr Genomics 2020; 21:155. [PMID: 33071608 PMCID: PMC7521037 DOI: 10.2174/138920292103200625161718] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Jagajjit Sahu
- 1National Center for Cell Sciences (NCCS), University of Pune Campus, University Road, Ganeshkhind, Pune-411007, Maharashtra, India; 2Somvanshi Research Foundation, 13/21 Vikas Nagar, Lucknow-226022, Uttar Pradesh, India; 3Department of Biotechnology, Institute of Applied Sciences and Humanities, GLA University, Mathura-281121, Uttar Pradesh, India
| | - Anukool Vaishnav
- 1National Center for Cell Sciences (NCCS), University of Pune Campus, University Road, Ganeshkhind, Pune-411007, Maharashtra, India; 2Somvanshi Research Foundation, 13/21 Vikas Nagar, Lucknow-226022, Uttar Pradesh, India; 3Department of Biotechnology, Institute of Applied Sciences and Humanities, GLA University, Mathura-281121, Uttar Pradesh, India
| | - Harikesh B Singh
- 1National Center for Cell Sciences (NCCS), University of Pune Campus, University Road, Ganeshkhind, Pune-411007, Maharashtra, India; 2Somvanshi Research Foundation, 13/21 Vikas Nagar, Lucknow-226022, Uttar Pradesh, India; 3Department of Biotechnology, Institute of Applied Sciences and Humanities, GLA University, Mathura-281121, Uttar Pradesh, India
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23
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Kumar A, Dubey A. Rhizosphere microbiome: Engineering bacterial competitiveness for enhancing crop production. J Adv Res 2020; 24:337-352. [PMID: 32461810 PMCID: PMC7240055 DOI: 10.1016/j.jare.2020.04.014] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/15/2020] [Accepted: 04/25/2020] [Indexed: 12/29/2022] Open
Abstract
Plants in nature are constantly exposed to a variety of abiotic and biotic stresses which limits their growth and production. Enhancing crop yield and production to feed exponentially growing global population in a sustainable manner by reduced chemical fertilization and agrochemicals will be a big challenge. Recently, the targeted application of beneficial plant microbiome and their cocktails to counteract abiotic and biotic stress is gaining momentum and becomes an exciting frontier of research. Advances in next generation sequencing (NGS) platform, gene editing technologies, metagenomics and bioinformatics approaches allows us to unravel the entangled webs of interactions of holobionts and core microbiomes for efficiently deploying the microbiome to increase crops nutrient acquisition and resistance to abiotic and biotic stress. In this review, we focused on shaping rhizosphere microbiome of susceptible host plant from resistant plant which comprises of specific type of microbial community with multiple potential benefits and targeted CRISPR/Cas9 based strategies for the manipulation of susceptibility genes in crop plants for improving plant health. This review is significant in providing first-hand information to improve fundamental understanding of the process which helps in shaping rhizosphere microbiome.
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Affiliation(s)
- Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar 470003, M.P., India
| | - Anamika Dubey
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar 470003, M.P., India
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24
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Pathak RK, Baunthiyal M, Pandey D, Kumar A. Computational analysis of microarray data of Arabidopsis thaliana challenged with Alternaria brassicicola for identification of key genes in Brassica. J Genet Eng Biotechnol 2020; 18:17. [PMID: 32607787 PMCID: PMC7326868 DOI: 10.1186/s43141-020-00032-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 04/30/2020] [Indexed: 11/10/2022]
Abstract
BACKGROUND Alternaria blight, a recalcitrant disease caused by Alternaria brassicae and Alternaria brassicicola, has been recognized for significant losses of oilseed crops especially rapeseed-mustard throughout the world. Till date, no resistance source is available against the disease; hence, plant breeding methods cannot be used to develop disease-resistant varieties. Therefore, in the present study, efforts have been made to identify resistance and defense-related genes as well as key components of JA-SA-ET-mediated pathway involved in resistance against Alternaria brasscicola through computational analysis of microarray data and network biology approach. Microarray profiling data from wild type and mutant Arabidopsis plants challenged with Alternaria brassicicola along with control plant were obtained from the Gene Expression Omnibus (GEO) database. The data analysis, including DEGs extraction, functional enrichment, annotation, and network analysis, was used to identify genes associated with disease resistance and defense response. RESULTS A total of 2854 genes were differentially expressed in WT9C9; among them, 1327 genes were upregulated and 1527 genes were downregulated. A total of 1159 genes were differentially expressed in JAM9C9; among them, 809 were upregulated and 350 were downregulated. A total of 2516 genes were differentially expressed in SAM9C9; among them, 1355 were upregulated and 1161 were downregulated. A total of 1567 genes were differentially expressed in ETM9C9; among them, 917 were upregulated and 650 were downregulated. Besides, a total of 2965 genes were differentially expressed in contrast WT24C24; among them, 1510 genes were upregulated and 1455 genes were downregulated. A total of 4598 genes were differentially expressed in JAM24C24; among them, 2201 were upregulated and 2397 were downregulated. A total of 3803 genes were differentially expressed in SAM24C24; among them, 1819 were upregulated and 1984 were downregulated. A total of 4164 genes were differentially expressed in ETM24C24; among them, 1895 were upregulated and 2269 were downregulated. The upregulated genes of Arabidopsis thaliana were mapped and annotated with CDS sequences of Brassica rapa obtained from PlantGDB database. Additionally, PPI network of these genes were constructed to investigate the key components of hormone-mediated pathway involved in resistance during pathogenesis. CONCLUSION The obtained information from present study can be used to engineer resistance to Alternaria blight caused by Alternaria brasscicola through molecular breeding or genetic manipulation-based approaches for improving Brassica oilseed productivity.
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Affiliation(s)
- Rajesh Kumar Pathak
- Department of Biotechnology, Govind Ballabh Pant Institute of Engineering & Technology, Pauri Garhwal, Uttarakhand 246194 India
| | - Mamta Baunthiyal
- Department of Biotechnology, Govind Ballabh Pant Institute of Engineering & Technology, Pauri Garhwal, Uttarakhand 246194 India
| | - Dinesh Pandey
- Department of Molecular Biology & Genetic Engineering, College of Basic Sciences & Humanities, G. B. Pant University of Agriculture & Technology, Pantnagar, Uttarakhand 263145 India
| | - Anil Kumar
- Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh 284003 India
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25
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Yadav R, Ror P, Rathore P, Ramakrishna W. Bacteria from native soil in combination with arbuscular mycorrhizal fungi augment wheat yield and biofortification. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 150:222-233. [PMID: 32155450 DOI: 10.1016/j.plaphy.2020.02.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 02/24/2020] [Accepted: 02/25/2020] [Indexed: 05/16/2023]
Abstract
Plant growth promoting bacteria (PGPB) have been used to enhance crop productivity. The effect of native PGPB and arbuscular mycorrhizal (AM) fungi in combination on wheat yield, biofortification and soil enzymatic activity is a relatively unexplored area. Twenty seven bacterial isolates from three different soils were characterized for their plant growth promoting traits. A total of three native and five non-native bacteria were used with and without arbuscular mycorrhizal (AM) fungi in an open greenhouse pot experiment with two wheat varieties to evaluate their effect on wheat yield, nutrient uptake, and soil health parameters. Wheat plants subjected to native PGPB (CP4) (Bacillus subtilis) and AM fungi treatment gave the best results with reference to macronutrient (nitrogen and phosphorus), micronutrient (iron and zinc) content in wheat grains and yield-related parameters, including thousand grain weight, number of grains per spike and total tillers per plant in both wheat cultivars. Treatment with CP4 and CP4 plus AM fungi enhanced total chlorophyll in wheat leaves indicating higher photosynthetic activity. Significant improvement in soil health-related parameters, including soil organic matter and dehydrogenase activity, was observed. Significant correlation among grain yield-related parameters, nutrient enhancement, and soil health parameters was observed in PGPB and AM fungi treated plants, especially HD-3086. These results provide a roadmap for utilizing native PGPB and AM fungi for enhancing wheat production in Punjab state of India and exploring their utility in other parts of the country with different soil and environmental conditions.
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Affiliation(s)
| | - Pankaj Ror
- Department of Biochemistry, Central University of Punjab, India
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26
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Techniques for improving formulations of bioinoculants. 3 Biotech 2020; 10:199. [PMID: 32300515 DOI: 10.1007/s13205-020-02182-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 03/24/2020] [Indexed: 12/13/2022] Open
Abstract
Bioinoculants are eco-friendly microorganisms having a variety of products commonly utilized for improving the potential of soil and providing the nutrient requirements to the host plant. The usage of chemical fertilizers is not beneficial because it affects the soil microbial communities on large scale. The toxicity of chemical fertilizer decreases the fertility of soil and causes microbial disruption. Bioinoculants that are used as PGPR play an important role in the enhancement of crop production and beneficial for both producers and consumers economically by protecting the soil during unfavourable conditions. The utilization of PGPR in the bioinoculant form imparts successfully sustain agricultural yield production and such formulated products contain living microbial cells of bioinoculants that also helps in seed treatment and enhances the mobilization process of nutrients by the low-cost process. This review mainly focuses on different bioinoculant formulations related to its recent approaches such as metabolite formulations, liquid formulations, solid carrier-based formulations and synthetic polymer-based formulations. This review also gives an overview of some aspects of the bioinoculant efficiency and their appropriate formulation, production and storage condition of microbial cells.
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27
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Chaudhary T, Shukla P. Bioinoculant capability enhancement through metabolomics and systems biology approaches. Brief Funct Genomics 2019; 18:159-168. [PMID: 31232454 DOI: 10.1093/bfgp/elz011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/30/2019] [Accepted: 04/26/2019] [Indexed: 02/07/2023] Open
Abstract
Bioinoculants are eco-friendly microorganisms, and their products are utilized for improving the potential of soil and fulfill the nutrients requirement for the host plant. The agricultural yield has increased due to the use of bioinoculants over chemical-based fertilizers, and thus it generates interest in understanding the innovation process by various methods. By gene-editing tool, the desired gene product can be changed for engineered microbial inoculants. We have also described various modern biotechnological tools like constraint-based modeling, OptKnock, flux balance analysis and modeling of the biological network for enhancing the bioinoculant capability. These fluxes give the fascinating perception of the metabolic network in the absence of comprehensive kinetic information. These tools also help in the stimulation of the metabolic networks by incorporation of enzyme-encoding genes. The present review explains the use of systems biology and gene-editing tools for improving the capability of bioinoculants. Moreover, this review also emphasizes on the challenges and future perspective of systems biology and its multidisciplinary facets.
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Affiliation(s)
- Twinkle Chaudhary
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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28
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Saghafi D, Delangiz N, Lajayer BA, Ghorbanpour M. An overview on improvement of crop productivity in saline soils by halotolerant and halophilic PGPRs. 3 Biotech 2019; 9:261. [PMID: 31192086 PMCID: PMC6557925 DOI: 10.1007/s13205-019-1799-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 06/06/2019] [Indexed: 12/18/2022] Open
Abstract
Salinity of water and soil are of the most important factors limiting the production of crops. Moreover, with the increasing population of the planet and saline fields worldwide there is no choice but to use saline soil and water in the near future. Therefore, to increase plant growth under saline stress condition, provision of sustainable and environmentally friendly management for the use of saline water and soil resources is necessary. The development of saline resistant plants is a potent approach to solve this problem. Generally, soil salinity negatively affects the plant growth through ion toxicity, oxidative stress, osmotic stress and ethylene generation. In recent years, scientists through genetic engineering techniques, which are based on molecular and physiological characteristics of plants, have made salt tolerance plants. However, the validation of the present technique is restricted to laboratory condition and it is not easily applied in the agronomy research under field environment. Another option would be to isolate and utilize salinity resistant microorganisms from the rhizosphere of halophyte plants, namely plant growth-promoting rhizobacteria (PGPR). The mechanisms of these bacteria includes; ACC-deaminase and exopolysachared production, osmolite accumulation, antioxidant system activation, ion hemostasis and etc. In this review, we will discuss mechanisms of PGPR in producing tolerate plants under salt stress and how to improve the plant-microbe interactions in future for increasing agricultural productivity to feed all of the world's people.
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Affiliation(s)
- Davood Saghafi
- Department of Soil Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Nasser Delangiz
- Department of Plant Biotechnology and Breeding, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Behnam Asgari Lajayer
- Department of Soil Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Manour Ghorbanpour
- Department of Medicinal Plants, Faculty of Agriculture and Natural Resources, Arak University, Arak, 38156-8-8349 Iran
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29
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Dubey KK, Luke GA, Knox C, Kumar P, Pletschke BI, Singh PK, Shukla P. Vaccine and antibody production in plants: developments and computational tools. Brief Funct Genomics 2019; 17:295-307. [PMID: 29982427 DOI: 10.1093/bfgp/ely020] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Plants as bioreactors have been widely used to express efficient vaccine antigens against viral, bacterial and protozoan infections. To date, many different plant-based expression systems have been analyzed, with a growing preference for transient expression systems. Antibody expression in diverse plant species for therapeutic applications is well known, and this review provides an overview of various aspects of plant-based biopharmaceutical production. Here, we highlight conventional and gene expression technologies in plants along with some illustrative examples. In addition, the portfolio of products that are being produced and how they relate to the success of this field are discussed. Stable and transient gene expression in plants, agrofiltration and virus infection vectors are also reviewed. Further, the present report draws attention to antibody epitope prediction using computational tools, one of the crucial steps of vaccine design. Finally, regulatory issues, biosafety and public perception of this technology are also discussed.
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Affiliation(s)
- Kashyap Kumar Dubey
- Department of Biotechnology, Central University of Haryana, Jant-Pali Mahendergarh, Haryana, India.,Microbial Process Development Laboratory, University Institute of Engineering and Technology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Garry A Luke
- Centre for Biomolecular Sciences, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, Scotland
| | - Caroline Knox
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, Eastern Cape, South Africa
| | - Punit Kumar
- Microbial Process Development Laboratory, University Institute of Engineering and Technology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Brett I Pletschke
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, Eastern Cape, South Africa
| | - Puneet Kumar Singh
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
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30
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Meeting the challenge of developing food crops with improved nutritional quality and food safety: leveraging proteomics and related omics techniques. Biotechnol Lett 2019; 41:471-481. [PMID: 30820711 DOI: 10.1007/s10529-019-02655-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 02/21/2019] [Indexed: 10/27/2022]
Abstract
Eliminating malnutrition remains an imminent priority in our efforts to achieve food security and providing adequate calories, proteins, and micronutrients to the growing world population. Malnutrition may be attributed to socio-economic factors (poverty and limited accessibility to nutritional food), dietary preferences, inherent nutrient profiles of traditional food crops, and to a combination of all such factors. Modern advancements in "omics" technology have made it possible to reliably predict, diagnose, and suggest ways to remedy the low protein content and bioavailability of key micronutrients in food crops. In this review, we briefly describe how proteomics techniques can potentially be used for improving the nutrient profile of major crops, through high throughput multiplexed assays. Food safety is another important issue where proteomics and related platforms can offer solution for absolute quantitation of food allergens and mycotoxins present in the plant-based food. The purpose of the present review is to discuss the proteomic-based strategies in food crops to meet the challenges of overcoming malnutrition throughout the world.
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31
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Bioinoculants for Bioremediation Applications and Disease Resistance: Innovative Perspectives. Indian J Microbiol 2019; 59:129-136. [PMID: 31031426 DOI: 10.1007/s12088-019-00783-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 01/23/2019] [Indexed: 02/02/2023] Open
Abstract
Soil microbial species that act as PGPR or bioinoculants have the capability of improving plant health and promoting its growth. They facilitate plants for uptake nutrients from their surroundings. They provide resistivity to pathogenic pests and also play many roles in the bioremediation process. Bioremediation is the biological approach for the elimination of toxic contaminants by the approach of beneficial microbes. By the consortium of beneficial microbes and plant, a large number of heavy metal and organic contaminants can be controlled. With this advancement of bioremediation, microbial species that act as bioinoculants also help in the enhancement of induced systemic resistance (ISR) and their consortium triggers it by controlling SA, JA, ET and hormonal signaling pathways. Here, this review discusses the progress made on these areas and how the beneficial microbes that act as bioinoculants towards triggering bioremediation and ISR mechanism.
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32
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Yang JY, Fang YL, Wang P, Ye JR, Huang L. Pleiotropic Roles of ChSat4 in Asexual Development, Cell Wall Integrity Maintenance, and Pathogenicity in Colletotrichum higginsianum. Front Microbiol 2018; 9:2311. [PMID: 30405539 PMCID: PMC6208185 DOI: 10.3389/fmicb.2018.02311] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 09/10/2018] [Indexed: 01/31/2023] Open
Abstract
Potassium has an important role to play in multiple cellular processes. In Saccharomyces cerevisiae, the serine/threonine (S/T) kinase Sat4/Hal4 is required for potassium accumulation, and thus, regulates the resistance to sodium salts and helps in the stabilization of other plasma membrane transporters. However, the functions of Sat4 in filamentous phytopathogenic fungi are largely unknown. In this study, ChSat4, the yeast Sat4p homolog in Colletotrichum higginsianum, has been identified. Target deletion of ChSAT4 resulted in defects in mycelial growth and sporulation. Intracellular K+ accumulation was significantly decreased in the ChSAT4 deletion mutant. Additionally, the ΔChsat4 mutant showed defects in cell wall integrity, hyperoxide stress response, and pathogenicity. Localization pattern analysis indicated ChSat4 was localized in the cytoplasm. Furthermore, ChSat4 showed high functional conservation with the homolog FgSat4 in Fusarium graminearum. Taken together, our data indicated that ChSat4 was important for intracellular K+ accumulation and infection morphogenesis in C. higginsianum.
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Affiliation(s)
- Ji-Yun Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yu-Lan Fang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Ping Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Jian-Ren Ye
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Lin Huang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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33
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Villena J, Kitazawa H, Van Wees SCM, Pieterse CMJ, Takahashi H. Receptors and Signaling Pathways for Recognition of Bacteria in Livestock and Crops: Prospects for Beneficial Microbes in Healthy Growth Strategies. Front Immunol 2018; 9:2223. [PMID: 30319660 PMCID: PMC6170637 DOI: 10.3389/fimmu.2018.02223] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 09/07/2018] [Indexed: 01/24/2023] Open
Abstract
Modern animal and crop production practices are associated with the regular use of antimicrobials, potentially increasing selection pressure on bacteria to become resistant. Alternative approaches are needed in order to satisfy the demands of the growing human population without the indiscriminate use of antimicrobials. Researchers have brought a different perspective to solve this problem and have emphasized the exploitation of animal- and plant-associated microorganisms that are beneficial to their hosts through the modulation of the innate immune system. There is increasing evidence that plants and animals employ microbial perception and defense pathways that closely resemble each other. Formation of pattern recognition receptor (PRR) complexes involving leucine-rich repeat (LRR)-containing proteins, mitogen-activated protein kinase (MAPK)-mediated activation of immune response genes, and subsequent production of antimicrobial products and reactive oxygen species (ROS) and nitric oxide (NO) to improve defenses against pathogens, add to the list of similarities between both systems. Recent pioneering work has identified that animal and plant cells use similar receptors for sensing beneficial commensal microbes that are important for the maintenance of the host's health. Here, we reviewed the current knowledge about the molecular mechanisms involved in the recognition of pathogenic and commensal microbes by the innate immune systems of animal and plants highlighting their differences and similarities. In addition, we discuss the idea of using beneficial microbes to modulate animal and plant immune systems in order to improve the resistance to infections and reduce the use of antimicrobial compounds.
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Affiliation(s)
- Julio Villena
- Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli (CERELA-CONICET), Tucuman, Argentina.,Food and Feed Immunology Group, Laboratory of Animal Products Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Haruki Kitazawa
- Food and Feed Immunology Group, Laboratory of Animal Products Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan.,Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Saskia C M Van Wees
- Plant-Microbe Interactions, Department of Biology, Science4life, Utrecht University, Utrecht, Netherlands
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4life, Utrecht University, Utrecht, Netherlands
| | - Hideki Takahashi
- Laboratory of Plant Pathology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan.,Plant Immunology Unit, International Education and Research Center for Food Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
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34
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Czedik‐Eysenberg A, Seitner S, Güldener U, Koemeda S, Jez J, Colombini M, Djamei A. The 'PhenoBox', a flexible, automated, open-source plant phenotyping solution. THE NEW PHYTOLOGIST 2018; 219:808-823. [PMID: 29621393 PMCID: PMC6485332 DOI: 10.1111/nph.15129] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 02/22/2018] [Indexed: 05/11/2023]
Abstract
There is a need for flexible and affordable plant phenotyping solutions for basic research and plant breeding. We demonstrate our open source plant imaging and processing solution ('PhenoBox'/'PhenoPipe') and provide construction plans, source code and documentation to rebuild the system. Use of the PhenoBox is exemplified by studying infection of the model grass Brachypodium distachyon by the head smut fungus Ustilago bromivora, comparing phenotypic responses of maize to infection with a solopathogenic Ustilago maydis (corn smut) strain and effector deletion strains, and studying salt stress response in Nicotiana benthamiana. In U. bromivora-infected grass, phenotypic differences between infected and uninfected plants were detectable weeks before qualitative head smut symptoms. Based on this, we could predict the infection outcome for individual plants with high accuracy. Using a PhenoPipe module for calculation of multi-dimensional distances from phenotyping data, we observe a time after infection-dependent impact of U. maydis effector deletion strains on phenotypic response in maize. The PhenoBox/PhenoPipe system is able to detect established salt stress responses in N. benthamiana. We have developed an affordable, automated, open source imaging and data processing solution that can be adapted to various phenotyping applications in plant biology and beyond.
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Affiliation(s)
- Angelika Czedik‐Eysenberg
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna BioCenter (VBC)Dr. Bohr‐Gasse 31030ViennaAustria
| | - Sebastian Seitner
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna BioCenter (VBC)Dr. Bohr‐Gasse 31030ViennaAustria
| | - Ulrich Güldener
- Department of Genome‐oriented BioinformaticsTechnische Universität MünchenWissenschaftszentrum WeihenstephanFreisingGermany
| | - Stefanie Koemeda
- Vienna Biocenter Core Facilities (VBCF)Dr. Bohr‐Gasse 31030ViennaAustria
| | - Jakub Jez
- Vienna Biocenter Core Facilities (VBCF)Dr. Bohr‐Gasse 31030ViennaAustria
| | - Martin Colombini
- Workshop, Research Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)Campus‐Vienna‐Biocenter 11030ViennaAustria
| | - Armin Djamei
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna BioCenter (VBC)Dr. Bohr‐Gasse 31030ViennaAustria
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35
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Tyagi S, Mulla SI, Lee KJ, Chae JC, Shukla P. VOCs-mediated hormonal signaling and crosstalk with plant growth promoting microbes. Crit Rev Biotechnol 2018; 38:1277-1296. [PMID: 29862848 DOI: 10.1080/07388551.2018.1472551] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In the natural environment, plants communicate with various microorganisms (pathogenic or beneficial) and exhibit differential responses. In recent years, research on microbial volatile compounds (MVCs) has revealed them to be simple, effective and efficient groups of compounds that modulate plant growth and developmental processes. They also interfere with the signaling process. Different MVCs have been shown to promote plant growth via improved photosynthesis rates, increased plant resistance to pathogens, activated phytohormone signaling pathways, or, in some cases, inhibit plant growth, leading to death. Regardless of these exhibited roles, the molecules responsible, the underlying mechanisms, and induced specific metabolic/molecular changes are not fully understood. Here, we review current knowledge on the effects of MVCs on plants, with particular emphasis on their modulation of the salicylic acid, jasmonic acid/ethylene, and auxin signaling pathways. Additionally, opportunities for further research and potential practical applications presented.
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Affiliation(s)
- Swati Tyagi
- a Division of Biotechnology , Chonbuk National University , Iksan , Republic of Korea
| | - Sikandar I Mulla
- a Division of Biotechnology , Chonbuk National University , Iksan , Republic of Korea
| | - Kui-Jae Lee
- a Division of Biotechnology , Chonbuk National University , Iksan , Republic of Korea
| | - Jong-Chan Chae
- a Division of Biotechnology , Chonbuk National University , Iksan , Republic of Korea
| | - Pratyoosh Shukla
- b Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology , Maharshi Dayanand University , Rohtak , India
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Podia V, Milioni D, Martzikou M, Haralampidis K. The role of Arabidopsis thaliana RASD1 gene in ABA-dependent abiotic stress response. PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20:307-317. [PMID: 29125669 DOI: 10.1111/plb.12662] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 11/06/2017] [Indexed: 06/07/2023]
Abstract
Abiotic stress is one of the key parameters affecting plant productivity. Drought and soil salinity, in particular, challenge plants to activate various response mechanisms to withstand these adverse growth conditions. While the molecular events that take place are complex and to a large extent unclear, the plant hormone abscisic acid (ABA) is considered a major player in mediating the adaptation of plants to stress. Here we report the identification of an ABA-insensitive mutant from Arabidopsis thaliana. A combination of molecular, genetic and physiology approaches were implemented, to characterise the AtRASD1 locus (RESPONSIVENESS TO ABA SALT AND DROUGHT 1) and to investigate its role in plant development. RASD1 is expressed predominantly in the vascular system of A. thaliana and encodes a peptide of unknown function with no similarity to any known sequence to date. The protein is localised in the nucleus and the cytoplasm, and RASD1-impaired plants are drought-intolerant and insensitive to exogenous ABA and NaCl during germination and root growth. Our data indicate that RASD1 is involved in ABA-dependent signal transduction pathways and therefore in enabling plants to activate response mechanisms related to seed germination and abiotic stress.
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Affiliation(s)
- V Podia
- Faculty of Biology, Department of Botany, National and Kapodistrian University of Athens, Athens, Greece
| | - D Milioni
- Department of Agricultural Biotechnology, Agricultural University of Athens, Athens, Greece
| | - M Martzikou
- Faculty of Biology, Department of Botany, National and Kapodistrian University of Athens, Athens, Greece
| | - K Haralampidis
- Faculty of Biology, Department of Botany, National and Kapodistrian University of Athens, Athens, Greece
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Mostafa M, Amal-Asran, Almoammar H, Abd-Elsalam KA. Nanoantimicrobials Mechanism of Action. NANOTECHNOLOGY IN THE LIFE SCIENCES 2018:281-322. [DOI: 10.1007/978-3-319-91161-8_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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Shanmugam G, Jeon J. Computer-Aided Drug Discovery in Plant Pathology. THE PLANT PATHOLOGY JOURNAL 2017; 33:529-542. [PMID: 29238276 PMCID: PMC5720600 DOI: 10.5423/ppj.rw.04.2017.0084] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 09/06/2017] [Accepted: 09/06/2017] [Indexed: 05/31/2023]
Abstract
Control of plant diseases is largely dependent on use of agrochemicals. However, there are widening gaps between our knowledge on plant diseases gained from genetic/mechanistic studies and rapid translation of the knowledge into target-oriented development of effective agrochemicals. Here we propose that the time is ripe for computer-aided drug discovery/design (CADD) in molecular plant pathology. CADD has played a pivotal role in development of medically important molecules over the last three decades. Now, explosive increase in information on genome sequences and three dimensional structures of biological molecules, in combination with advances in computational and informational technologies, opens up exciting possibilities for application of CADD in discovery and development of agrochemicals. In this review, we outline two categories of the drug discovery strategies: structure- and ligand-based CADD, and relevant computational approaches that are being employed in modern drug discovery. In order to help readers to dive into CADD, we explain concepts of homology modelling, molecular docking, virtual screening, and de novo ligand design in structure-based CADD, and pharmacophore modelling, ligand-based virtual screening, quantitative structure activity relationship modelling and de novo ligand design for ligand-based CADD. We also provide the important resources available to carry out CADD. Finally, we present a case study showing how CADD approach can be implemented in reality for identification of potent chemical compounds against the important plant pathogens, Pseudomonas syringae and Colletotrichum gloeosporioides.
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Affiliation(s)
| | - Junhyun Jeon
- Corresponding author. Phone) +82-53-810-3030, FAX) +82-53-810-4769, E-mail)
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Howell M, Daniel JJ, Brown PJB. Live Cell Fluorescence Microscopy to Observe Essential Processes During Microbial Cell Growth. J Vis Exp 2017. [PMID: 29286454 DOI: 10.3791/56497] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Core cellular processes such as DNA replication and segregation, protein synthesis, cell wall biosynthesis, and cell division rely on the function of proteins which are essential for bacterial survival. A series of target-specific dyes can be used as probes to better understand these processes. Staining with lipophilic dyes enables the observation of membrane structure, visualization of lipid microdomains, and detection of membrane blebs. Use of fluorescent-d-amino acids (FDAAs) to probe the sites of peptidoglycan biosynthesis can indicate potential defects in cell wall biogenesis or cell growth patterning. Finally, nucleic acid stains can indicate possible defects in DNA replication or chromosome segregation. Cyanine DNA stains label living cells and are suitable for time-lapse microscopy enabling real-time observations of nucleoid morphology during cell growth. Protocols for cell labeling can be applied to protein depletion mutants to identify defects in membrane structure, cell wall biogenesis, or chromosome segregation. Furthermore, time-lapse microscopy can be used to monitor morphological changes as an essential protein is removed and can provide additional insights into protein function. For example, the depletion of essential cell division proteins results in filamentation or branching, whereas the depletion of cell growth proteins may cause cells to become shorter or rounder. Here, protocols for cell growth, target-specific labeling, and time-lapse microscopy are provided for the bacterial plant pathogen Agrobacterium tumefaciens. Together, target-specific dyes and time-lapse microscopy enable characterization of essential processes in A. tumefaciens. Finally, the protocols provided can be readily modified to probe essential processes in other bacteria.
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Current understanding of pattern-triggered immunity and hormone-mediated defense in rice (Oryza sativa) in response to Magnaporthe oryzae infection. Semin Cell Dev Biol 2017; 83:95-105. [PMID: 29061483 DOI: 10.1016/j.semcdb.2017.10.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 09/21/2017] [Accepted: 10/20/2017] [Indexed: 11/22/2022]
Abstract
Plant pathogens represent a huge threat to world food security, affecting both crop production and quality. Although significant progress has been made in improving plant immunity by expressing key, defense-related genes and proteins from different species in transgenic crops, a challenge remains for molecular breeders and biotechnologists to successfully engineer elite, transgenic crop varieties with improved resistance against critical plant pathogens. Upon pathogen attack, including infection of rice (Oryza sativa) by Magnaporthe oryzae, host plants initiate a complex defense response at molecular, biochemical and physiological levels. Plants perceive the presence of pathogens by detecting microbe-associated molecular patterns via pattern recognition receptors, and initiate a first line of innate immunity, the so-called pattern-triggered immunity (PTI). This results in a series of downstream defense responses, including the production of hormones, which collectively function to fend off pathogen attacks. A variety of studies have demonstrated that many genes are involved in the defense response of rice to M. oryzae. In this review, the current understanding of mechanisms that improve rice defense response to M. oryzae will be discussed, with special focus on PTI and the phytohormones ethylene, jasmonic acid, salicylic acid, and abscisic acid; as well as on the mediation of defense signaling mechanisms by PTI and these hormones. Potential target genes that may serve as promising candidates for improving rice immunity against M. oryzae will also be discussed.
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Brader G, Compant S, Vescio K, Mitter B, Trognitz F, Ma LJ, Sessitsch A. Ecology and Genomic Insights into Plant-Pathogenic and Plant-Nonpathogenic Endophytes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:61-83. [PMID: 28489497 DOI: 10.1146/annurev-phyto-080516-035641] [Citation(s) in RCA: 199] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Plants are colonized on their surfaces and in the rhizosphere and phyllosphere by a multitude of different microorganisms and are inhabited internally by endophytes. Most endophytes act as commensals without any known effect on their plant host, but multiple bacteria and fungi establish a mutualistic relationship with plants, and some act as pathogens. The outcome of these plant-microbe interactions depends on biotic and abiotic environmental factors and on the genotype of the host and the interacting microorganism. In addition, endophytic microbiota and the manifold interactions between members, including pathogens, have a profound influence on the function of the system plant and the development of pathobiomes. In this review, we elaborate on the differences and similarities between nonpathogenic and pathogenic endophytes in terms of host plant response, colonization strategy, and genome content. We furthermore discuss environmental effects and biotic interactions within plant microbiota that influence pathogenesis and the pathobiome.
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Affiliation(s)
- Günter Brader
- Center for Health and Bioresources, Bioresources Unit, Austrian Institute of Technology (AIT), 3430 Tulln, Austria
| | - Stéphane Compant
- Center for Health and Bioresources, Bioresources Unit, Austrian Institute of Technology (AIT), 3430 Tulln, Austria
| | - Kathryn Vescio
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003;
| | - Birgit Mitter
- Center for Health and Bioresources, Bioresources Unit, Austrian Institute of Technology (AIT), 3430 Tulln, Austria
| | - Friederike Trognitz
- Center for Health and Bioresources, Bioresources Unit, Austrian Institute of Technology (AIT), 3430 Tulln, Austria
| | - Li-Jun Ma
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003;
| | - Angela Sessitsch
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003;
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Imam J, Mandal NP, Variar M, Shukla P. Allele Mining and Selective Patterns of Pi9 Gene in a Set of Rice Landraces from India. FRONTIERS IN PLANT SCIENCE 2016; 7:1846. [PMID: 28018384 PMCID: PMC5156731 DOI: 10.3389/fpls.2016.01846] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 11/22/2016] [Indexed: 05/31/2023]
Abstract
Allelic variants of the broad-spectrum blast resistance gene, Pi9 (nucleotide binding site-leucine-rich repeat region) have been analyzed in Indian rice landraces. They were selected from the list of 338 rice landraces phenotyped in the rice blast nursery at central Rainfed Upland Rice Research Station, Hazaribag. Six of them were further selected on the basis of their resistance and susceptible pattern for virulence analysis and selective pattern study of Pi9 gene. The sequence analysis and phylogenetic study illustrated that such sequences are vastly homologous and clustered into two groups. All the blast resistance Pi9 alleles were grouped into one cluster, whereas Pi9 alleles of susceptible landraces formed another cluster even though these landraces have a low level of DNA polymorphisms. A total number of 136 polymorphic sites comprising of transitions, transversions, and insertion and deletions (InDels) were identified in the 2.9 kb sequence of Pi9 alleles. Lower variation in the form of mutations (77) (Transition + Transversion), and InDels (59) were observed in the Pi9 alleles isolated from rice landraces studied. The results showed that the Pi9 alleles of the selected rice landraces were less variable, suggesting that the rice landraces would have been exposed to less number of pathotypes across the country. The positive Tajima's D (0.33580), P > 0.10 (not significant) was observed among the seven rice landraces, which suggests the balancing selection of Pi9 alleles. The value of synonymous substitution (-0.43337) was less than the non-synonymous substitution (0.78808). The greater non-synonymous substitution than the synonymous means that the coding region, mainly the leucine-rich repeat domain was under diversified selection. In this study, the Pi9 gene has been subjected to balancing selection with low nucleotide diversity which is different from the earlier reports, this may be because of the closeness of the rice landraces, cultivated in the same region, and under low pathotype pressure.
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Affiliation(s)
- Jahangir Imam
- Biotechnology Laboratory, Central Rainfed Upland Rice Research StationHazaribagh, India
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand UniversityRohtak, India
| | - Nimai P. Mandal
- Biotechnology Laboratory, Central Rainfed Upland Rice Research StationHazaribagh, India
| | - Mukund Variar
- Biotechnology Laboratory, Central Rainfed Upland Rice Research StationHazaribagh, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand UniversityRohtak, India
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