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Gandham P, Vadla N, Saji A, Srinivas V, Ruperao P, Selvanayagam S, Saxena RK, Rathore A, Gopalakrishnan S, Thakur V. Genome assembly, comparative genomics, and identification of genes/pathways underlying plant growth-promoting traits of an actinobacterial strain, Amycolatopsis sp. (BCA-696). Sci Rep 2024; 14:15934. [PMID: 38987320 PMCID: PMC11237095 DOI: 10.1038/s41598-024-66835-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 07/04/2024] [Indexed: 07/12/2024] Open
Abstract
The draft genome sequence of an agriculturally important actinobacterial species Amycolatopsis sp. BCA-696 was developed and characterized in this study. Amycolatopsis BCA-696 is known for its biocontrol properties against charcoal rot and also for plant growth-promotion (PGP) in several crop species. The next-generation sequencing (NGS)-based draft genome of Amycolatopsis sp. BCA-696 comprised of ~ 9.05 Mb linear chromosome with 68.75% GC content. In total, 8716 protein-coding sequences and 61 RNA-coding sequences were predicted in the genome. This newly developed genome sequence has been also characterized for biosynthetic gene clusters (BGCs) and biosynthetic pathways. Furthermore, we have also reported that the Amycolatopsis sp. BCA-696 produces the glycopeptide antibiotic vancomycin that inhibits the growth of pathogenic gram-positive bacteria. A comparative analysis of the BCA-696 genome with publicly available closely related genomes of 14 strains of Amycolatopsis has also been conducted. The comparative analysis has identified a total of 4733 core and 466 unique orthologous genes present in the BCA-696 genome The unique genes present in BCA-696 was enriched with antibiotic biosynthesis and resistance functions. Genome assembly of the BCA-696 has also provided genes involved in key pathways related to PGP and biocontrol traits such as siderophores, chitinase, and cellulase production.
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Affiliation(s)
- Prasad Gandham
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, USA
| | - Nandini Vadla
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Angeo Saji
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Vadlamudi Srinivas
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pradeep Ruperao
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Gujarat Biotechnology University, Gandhinagar, Gujarat, India
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- Excellence in Breeding, International Maize and Wheat Improvement Center (CIMMYT), Hyderabad, India.
| | - Subramaniam Gopalakrishnan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- International Institute of Tropical Agriculture (IITA), Dar es Salaam, Tanzania.
| | - Vivek Thakur
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India.
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Dahar GY, Wang HW, Rajer FU, Jin P, Xu P, Abro MA, Qureshi AS, Karim A, Miao W. Comparative genomic analysis of Bacillus atrophaeus HAB-5 reveals genes associated with antimicrobial and plant growth-promoting activities. Front Microbiol 2024; 15:1384691. [PMID: 38989016 PMCID: PMC11233526 DOI: 10.3389/fmicb.2024.1384691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 06/07/2024] [Indexed: 07/12/2024] Open
Abstract
Bacillus atrophaeus HAB-5 is a plant growth-promoting rhizobacterium (PGPR) that exhibits several biotechnological traits, such as enhancing plant growth, colonizing the rhizosphere, and engaging in biocontrol activities. In this study, we conducted whole-genome sequencing of B. atrophaeus HAB-5 using the single-molecule real-time (SMRT) sequencing platform by Pacific Biosciences (PacBio; United States), which has a circular chromosome with a total length of 4,083,597 bp and a G + C content of 44.21%. The comparative genomic analysis of B. atrophaeus HAB-5 with other strains, Bacillus amyloliquefaciens DSM7, B. atrophaeus SRCM101359, Bacillus velezensis FZB42, B. velezensis HAB-2, and Bacillus subtilis 168, revealed that these strains share 2,465 CDSs, while 599 CDSs are exclusive to the B. atrophaeus HAB-5 strain. Many gene clusters in the B. atrophaeus HAB-5 genome are associated with the production of antimicrobial lipopeptides and polypeptides. These gene clusters comprise distinct enzymes that encode three NRPs, two Transat-Pks, one terpene, one lanthipeptide, one T3PKS, one Ripp, and one thiopeptide. In addition to the likely IAA-producing genes (trpA, trpB, trpC, trpD, trpE, trpS, ywkB, miaA, and nadE), there are probable genes that produce volatile chemicals (acoA, acoB, acoR, acuB, and acuC). Moreover, HAB-5 contained genes linked to iron transportation (fbpA, fetB, feuC, feuB, feuA, and fecD), sulfur metabolism (cysC, sat, cysK, cysS, and sulP), phosphorus solubilization (ispH, pstA, pstC, pstS, pstB, gltP, and phoH), and nitrogen fixation (nif3-like, gltP, gltX, glnR, glnA, nadR, nirB, nirD, nasD, narl, narH, narJ, and nark). In conclusion, this study provides a comprehensive genomic analysis of B. atrophaeus HAB-5, pinpointing the genes and genomic regions linked to the antimicrobial properties of the strain. These findings advance our knowledge of the genetic basis of the antimicrobial properties of B. atrophaeus and imply that HAB-5 may employ a variety of commercial biopesticides and biofertilizers as a substitute strategy to increase agricultural output and manage a variety of plant diseases.
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Affiliation(s)
- Ghulam Yaseen Dahar
- Key Laboratory of Green Prevention and Control of Tropical Plant Disease and Pests, Ministry of Education, College of Plant Protection, Hainan University Haikou, Haikou, China
| | - Huan Wei Wang
- Key Laboratory of Green Prevention and Control of Tropical Plant Disease and Pests, Ministry of Education, College of Plant Protection, Hainan University Haikou, Haikou, China
| | - Faheem Uddin Rajer
- Department of Plant Pathology, Faculty of Crop Protection, Sindh Agriculture University, Tando Jam, Pakistan
| | - Pengfie Jin
- Key Laboratory of Green Prevention and Control of Tropical Plant Disease and Pests, Ministry of Education, College of Plant Protection, Hainan University Haikou, Haikou, China
| | - Peidong Xu
- Key Laboratory of Green Prevention and Control of Tropical Plant Disease and Pests, Ministry of Education, College of Plant Protection, Hainan University Haikou, Haikou, China
| | - Manzoor Ali Abro
- Department of Plant Pathology, Faculty of Crop Protection, Sindh Agriculture University, Tando Jam, Pakistan
| | - Abdul Sattar Qureshi
- Institute of Biotechnology and Genetic Engineering, University of Sindh, Jamshoro, Pakistan
| | - Asad Karim
- Jamil-Ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Weiguo Miao
- Key Laboratory of Green Prevention and Control of Tropical Plant Disease and Pests, Ministry of Education, College of Plant Protection, Hainan University Haikou, Haikou, China
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Buragohain K, Tamuly D, Sonowal S, Nath R. Impact of Drought Stress on Plant Growth and Its Management Using Plant Growth Promoting Rhizobacteria. Indian J Microbiol 2024; 64:287-303. [PMID: 39011023 PMCID: PMC11246373 DOI: 10.1007/s12088-024-01201-0] [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: 04/18/2023] [Accepted: 01/06/2024] [Indexed: 07/17/2024] Open
Abstract
Drought stress is a significant environmental challenge affecting global agriculture, leading to substantial reductions in crop yields and overall plant productivity. It induces a cascade of physiological and biochemical changes in plants, including reduced water uptake, stomatal closure, and alterations in hormonal balance, all of which contribute to impaired growth and development. Drought stress diminishes crop production by impacting crucial plant metabolic pathways. Plants possess the ability to activate or deactivate specific sets of genes, leading to changes in their physiological and morphological characteristics. This adaptive response enables plants to evade, endure, or prevent the effects of drought stress. Drought stress triggers the activation of various genes, transcription factors, and signal transduction pathways in plants. In this context, imposing plant growth-promoting rhizobacteria (PGPR) emerges as a promising strategy. PGPR, employing diverse mechanisms such as osmotic adjustments, antioxidant activity, and phytohormone production, not only ensures the plant's survival during drought conditions but also enhances its overall growth. This comprehensive review delves into the various mechanisms through which PGPR enhances drought stress resistance, offering a thorough exploration of recent molecular and omics-based approaches to unravel the role of drought-responsive genes. The manuscript encompasses a detailed mechanistic analysis, along with the development of PGPR-based drought stress management in plants.
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Affiliation(s)
- Kabyashree Buragohain
- Microbiology Laboratory, Department of Life Sciences, Dibrugarh University, Dibrugarh, Assam 786004 India
| | | | - Sukanya Sonowal
- Microbiology Laboratory, Department of Life Sciences, Dibrugarh University, Dibrugarh, Assam 786004 India
| | - Ratul Nath
- Microbiology Laboratory, Department of Life Sciences, Dibrugarh University, Dibrugarh, Assam 786004 India
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Long M, Wang Q, Li S, Liu C, Chen S, Yang Y, Ma H, Guo L, Fan G, Sun X, Ma G. Additive effect of the Streptomyces albus XJC2-1 and dimethomorph control pepper blight (Capsicum annuum L.). PEST MANAGEMENT SCIENCE 2023; 79:3871-3882. [PMID: 37254281 DOI: 10.1002/ps.7591] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 05/18/2023] [Accepted: 05/31/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND Pepper blight, caused by Phytophthora capsici, is a destructive soilborne disease, which poses a serious threat to pepper, Capsicum annuum L., production. Chemical fungicides, which mainly are used to control pepper blight, have a negative effect on the environment, rendering biological control as a promising alternative to maintain the balance between ecology and pest management. The purpose of this study was to screen the biocontrol bacteria, reduce the dosage of fungicides and increase the stability of biocontrol bacteria, and to find the mixing ratio of biocontrol bacteria and fungicides giving the best control effect. RESULTS We isolated actinomycetes strains from the soil surrounding the roots of healthy pepper plants amongst field-grown plants infected with P. capsici. Of these, Streptomyces albus XJC2-1 showed a strong inhibition effect on the growth of P. capsici, with an inhibition rate of ≤85%. XJC2-1 effectively inhibited the formation of sporangium and release of zoospores of P. capsici as well as directly destroyed its hyphae, to achieve the inhibitory effect. Transcriptomic profiling of pepper leaves, postirrigation of plants with the XJC2-1 fermentation broth, revealed upregulation of genes related to the photosynthesis pathway in pepper. Furthermore, XJC2-1 treatment improved the net photosynthetic rate and intercellular CO2 concentration, thereby improving the pepper plant's resistance to pathogens. The combination of XJC2-1 with the fungicide dimethomorph (8 μg mL-1 ) displayed strong synergism in inhibition of P. capsici infection, with a control efficiency as high as 75.16%, thus providing a basis for its application in the field. CONCLUSION Our study demonstrated that S. albus XJC2-1 inhibited Phytophthora pathogens from infecting pepper plants and enhanced plant host resistance. The combination of XJC2-1 and dimethomorph displayed a more stable and stronger control effect on pepper blight, showing potential for the future application of XJC2-1 in the field of biological control. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Meimei Long
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
| | - Qiuyue Wang
- Institute of Characteristic Crops, Chongqing Academy of Agricultural Sciences, Chongqing, China
| | - Shanshan Li
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
| | - Changyun Liu
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
| | - Shan Chen
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
| | - Yanhui Yang
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
| | - Haoyue Ma
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
| | - Lulu Guo
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
| | - Guangjin Fan
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
| | - Xianchao Sun
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
| | - Guanhua Ma
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
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Genome insights into the plant growth-promoting bacterium Saccharibacillus brassicae ATSA2 T. AMB Express 2023; 13:9. [PMID: 36680648 PMCID: PMC9867790 DOI: 10.1186/s13568-023-01514-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 01/09/2023] [Indexed: 01/22/2023] Open
Abstract
Endophytes can facilitate the improvement of plant growth and health in agriculturally important crops, yet their genomes and secondary metabolites remain largely unexplored. We previously isolated Saccharibacillus brassicae strain ATSA2T from surface-sterilized seeds of kimchi cabbage and represented a novel species of the genus Saccharibacillus. In this study, we evaluated the plant growth-promoting (PGP) effect of strain ATSA2T in kimchi cabbage, bok choy, and pepper plants grown in soils. We found a significant effect on the shoot and root biomass, and chlorophyll contents following strain ATSA2T treatment. Strain ATSA2T displayed PGP traits such as indole acetic acid (IAA, 62.9 μg/mL) and siderophore production, and phosphate solubilization activity. Furthermore, genome analysis of this strain suggested the presence of gene clusters involved in iron acquisition (fhuABD, afuABC, fbpABC, and fepCDG) and phosphate solubilization (pstABCHS, phoABHLU, and phnCDEP) and other phytohormone biosynthesis genes, including indole-3-acetic acid (trpABCDEFG), in the genome. Interestingly, the secondary metabolites cerecidin, carotenoid, siderophore (staphylobactin), and bacillaene underlying plant growth promotion were found in the whole genome via antiSMASH analysis. Overall, physiological testing and genome analysis data provide comprehensive insights into plant growth-promoting mechanisms, suggesting the relevance of strain ATSA2T in agricultural biotechnology.
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Ojuederie OB, Babalola OO. Growth enhancement and extenuation of drought stress in maize inoculated with multifaceted ACC deaminase producing rhizobacteria. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2023. [DOI: 10.3389/fsufs.2022.1076844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
IntroductionMaize is a major staple cereal crop grown and consumed globally. However, due to climate change, extreme heat and drought stresses are greatly affecting its production especially in sub-Saharan Africa. The use of a bio-based approach to mitigate drought stress is therefore suggested using plant growth-promoting rhizobacteria (PGPR).MethodsThis study investigated the abilities of 1-aminocyclopropane-1-carboxylate (ACC) deaminase producing PGPR Pseudomonas sp. MRBP4, Pseudomonas sp. MRBP13 and Bacillus sp. MRBP10 isolated from maize rhizosphere soil, to ameliorate the effect of drought stress in maize genotypes MR44 and S0/8/W/I137TNW//CML550 under two water regimes; mild drought stress (50% FC) and well-watered conditions (100% FC). The rhizobacterial strains were identified by 16S rRNA sequencing and biochemical tests, and evaluated for plant growth-promoting and abiotic stress tolerance traits.Results and discussionThe synergistic effect of the bacterial strains had a highly significant (p < 0.001) effect on the total soluble sugar, soil moisture content and relative water content, which were enhanced under water-stress in the inoculated plants. Relative water content was significantly highest (p < 0.001) in maize plants co-inoculated with Pseudomonas sp. MRBP4 + Bacillus sp. MRBP10 (60.55%). Total chlorophyll content was significantly enhanced in maize seedlings sole inoculated with Pseudomonas sp. MRBP4, Pseudomonas sp. MRBP13, and co-inoculated with Pseudomonas sp. MRBP13 + Bacillus sp. MRBP10 by 15.91%, 14.99% and 15.75% respectively, over the un-inoculated control. Soil moisture content increased by 28.67% and 30.71% compared to the un-inoculated control when plants were inoculated with Pseudomonas sp. MRBP4 + Bacillus sp. MRBP10 and Pseudomonas sp. MRBP4 + Bacillus sp. MRBP10 respectively. The interactive effect of genotype × bacteria significantly enhanced biomass production. Leaf area was highest in maize plants co-inoculated with Pseudomonas sp. MRBP4 + Pseudomonas sp. MRBP13 (212.45 ± 0.87 cm2) under drought stress. Treatment of maize seeds with Pseudomonas sp. MRBP 4 + Pseudomonas sp. MRBP13 + Bacillus sp. MRBP10 significantly increased the root length (10.32 ± 0.48 cm) which enhanced survival of the maize seedlings. Bioinoculation of maize seeds with these strains could boost maize production cultivated in arid regions.
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Gopalakrishnan S, Srinivas V, Chand U, Pratyusha S, Samineni S. Streptomyces consortia-mediated plant growth-promotion and yield performance in chickpea. 3 Biotech 2022; 12:318. [PMID: 36276473 PMCID: PMC9548453 DOI: 10.1007/s13205-022-03389-8] [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: 06/13/2022] [Accepted: 09/30/2022] [Indexed: 11/01/2022] Open
Abstract
Fourteen Streptomyces strains reported earlier as plant growth promoters (PGP) in chickpea were characterized for production of ammonia and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase and solubilization of silica and zinc. The results showed that nine (CAI-17, CAI-78, KAI-26, CAI-21, CAI-26, MMA-32, CAI-140, CAI-155 and KAI-180) and six (CAI-17, CAI-21, CAI-26, CAI-13, CAI-93 and KAI-180) strains were found to produce ammonia and ACC deaminase, respectively, while one (KAI-180) and eight (CAI-17, CAI-21, CAI-26, MMA-32, CAI-13, CAI-85, CAI-93 and KAI-180) strains solubilized silica and zinc, respectively. The selected 14 Streptomyces strains were categorized into three consortia groups, consortium-1 (CAI-17, CAI-68, CAI-78, KAI-26 and KAI-27), consortium-2 (CAI-21, CAI-26 and MMA-32) and consortium-3 (CAI-13, CAI-85, CAI-93, CAI-140, CAI-155 and KAI-180), based on their compatibility, and evaluated for their PGP traits in chickpea. The experiment was conducted under field conditions with two chickpea varieties over two years. The consortia-treated plots enhanced nodule number up to 23%, nodule weight up to 36%, root weight up to 27% and shoot weight up to 26% at 30 days after sowing and pod weight up to 35%, pod number up to 34% and grain yield up to 24% at harvest over the un-inoculated control plots. The harvested grains of consortia treatments were found to enhance crude protein up to 14%, crude fibre up to 17% and crude fat up to 16% over the grains from un-inoculated control. The rhizosphere soils of the consortia-treated plots enhanced total nitrogen up to 21%, organic carbon up to 8% and available phosphorous up to 16% over the un-inoculated control plots. This investigation demonstrated the potential use of the selected consortium of Streptomyces strains in the farmers' fields to improve the chickpea yields and soil fertility.
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Affiliation(s)
- Subramaniam Gopalakrishnan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502 324 India
| | - Vadlamudi Srinivas
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502 324 India
| | - Uttam Chand
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502 324 India
| | - Sambangi Pratyusha
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502 324 India
| | - Srinivas Samineni
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502 324 India
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Nonthakaew N, Panbangred W, Songnuan W, Intra B. Plant growth-promoting properties of Streptomyces spp. isolates and their impact on mung bean plantlets’ rhizosphere microbiome. Front Microbiol 2022; 13:967415. [PMID: 36090067 PMCID: PMC9453592 DOI: 10.3389/fmicb.2022.967415] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 07/26/2022] [Indexed: 12/02/2022] Open
Abstract
Phytophthora is an important, highly destructive pathogen of many plants, which causes considerable crop loss, especially durians in Thailand. In this study, we selectively isolated Streptomyces from the rhizosphere soil with a potent anti-oomycete activity against Phytophthora palmivora CbP03. Two strains (SNN087 and SNN289) demonstrated exceptional plant growth-promoting properties in pot experiment. Both strains promoted mung bean (Vigna radiate) growth effectively in both sterile and non-sterile soils. Metagenomic analysis revealed that Streptomyces sp. SNN289 may modify the rhizosphere microbial communities, especially promoting microbes beneficial for plant growth. The relative abundance of bacterial genera Bacillus, Sphingomonas, Arthrobacter, and Pseudarthrobacter, and fungal genera Coprinellus and Chaetomium were noticeably increased, whereas a genus Fusarium was slightly reduced. Interestingly, Streptomyces sp. SNN289 exhibited an exploratory growth, which allows it to survive in a highly competitive environment. Based on whole genome sequence analysis combined with an ANI and dDDH values, this strain should be classifiable as a new species. Functional annotation was also used to characterize plant-beneficial genes in SNN087 and SNN289 genomes for production of siderophores, 3-indole acetic acid (IAA), ammonia, and solubilized phosphate. AntiSMASH genome analysis and preliminary annotation revealed biosynthetic gene clusters with possible secondary metabolites. These findings emphasize the potential for application of strain SNN289 as a bioinoculant for sustainable agricultural practice.
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Affiliation(s)
- Napawit Nonthakaew
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Osaka Collaborative Research Center for Bioscience and Biotechnology, Mahidol University-Osaka, Bangkok, Thailand
| | - Watanalai Panbangred
- Research, Innovation, and Partnerships Office (Office of the President), King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Wisuwat Songnuan
- Department of Plant Science, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Bungonsiri Intra
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Osaka Collaborative Research Center for Bioscience and Biotechnology, Mahidol University-Osaka, Bangkok, Thailand
- *Correspondence: Bungonsiri Intra,
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Nano-biofertilizers on soil health, chemistry, and microbial community: benefits and risks. PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY 2022. [DOI: 10.1007/s43538-022-00094-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Ahmad HM, Fiaz S, Hafeez S, Zahra S, Shah AN, Gul B, Aziz O, Mahmood-Ur-Rahman, Fakhar A, Rafique M, Chen Y, Yang SH, Wang X. Plant Growth-Promoting Rhizobacteria Eliminate the Effect of Drought Stress in Plants: A Review. FRONTIERS IN PLANT SCIENCE 2022; 13:875774. [PMID: 36035658 PMCID: PMC9406510 DOI: 10.3389/fpls.2022.875774] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/23/2022] [Indexed: 07/21/2023]
Abstract
Plants evolve diverse mechanisms to eliminate the drastic effect of biotic and abiotic stresses. Drought is the most hazardous abiotic stress causing huge losses to crop yield worldwide. Osmotic stress decreases relative water and chlorophyll content and increases the accumulation of osmolytes, epicuticular wax content, antioxidant enzymatic activities, reactive oxygen species, secondary metabolites, membrane lipid peroxidation, and abscisic acid. Plant growth-promoting rhizobacteria (PGPR) eliminate the effect of drought stress by altering root morphology, regulating the stress-responsive genes, producing phytohormones, osmolytes, siderophores, volatile organic compounds, and exopolysaccharides, and improving the 1-aminocyclopropane-1-carboxylate deaminase activities. The use of PGPR is an alternative approach to traditional breeding and biotechnology for enhancing crop productivity. Hence, that can promote drought tolerance in important agricultural crops and could be used to minimize crop losses under limited water conditions. This review deals with recent progress on the use of PGPR to eliminate the harmful effects of drought stress in traditional agriculture crops.
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Affiliation(s)
- Hafiz Muhammad Ahmad
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Sumaira Hafeez
- Department of Plant Breeding and Molecular Genetics, University of Poonch, Rawalakot, Pakistan
| | - Sadaf Zahra
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Bushra Gul
- Department of Biosciences, University of Wah, Wah, Pakistan
| | - Omar Aziz
- Department of Soil and Environmental Science, University of Agriculture, Faisalabad, Pakistan
| | - Mahmood-Ur-Rahman
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Ali Fakhar
- Department of Soil and Climate Change, The University of Haripur, Haripur, Pakistan
| | - Mazhar Rafique
- Department of Soil and Climate Change, The University of Haripur, Haripur, Pakistan
| | - Yinglong Chen
- School of Agriculture and Environment, UWA Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, South Korea
| | - Xiukang Wang
- College of Life Sciences, Yan’an University, Yan’an, China
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Ashraf N, Zafar S, Makitrynskyy R, Bechthold A, Spiteller D, Song L, Anwar MA, Luzhetskyy A, Khan AN, Akhtar K, Khaliq S. Revealing Genome-Based Biosynthetic Potential of Streptomyces sp. BR123 Isolated from Sunflower Rhizosphere with Broad Spectrum Antimicrobial Activity. Antibiotics (Basel) 2022; 11:antibiotics11081057. [PMID: 36009926 PMCID: PMC9405382 DOI: 10.3390/antibiotics11081057] [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: 07/02/2022] [Revised: 07/30/2022] [Accepted: 08/01/2022] [Indexed: 11/16/2022] Open
Abstract
Actinomycetes, most notably the genus Streptomyces, have great importance due to their role in the discovery of new natural products, especially for finding antimicrobial secondary metabolites that are useful in the medicinal science and biotechnology industries. In the current study, a genome-based evaluation of Streptomyces sp. isolate BR123 was analyzed to determine its biosynthetic potential, based on its in vitro antimicrobial activity against a broad range of microbial pathogens, including gram-positive and gram-negative bacteria and fungi. A draft genome sequence of 8.15 Mb of Streptomyces sp. isolate BR123 was attained, containing a GC content of 72.63% and 8103 protein coding genes. Many antimicrobial, antiparasitic, and anticancerous compounds were detected by the presence of multiple biosynthetic gene clusters, which was predicted by in silico analysis. A novel metabolite with a molecular mass of 1271.7773 in positive ion mode was detected through a high-performance liquid chromatography linked with mass spectrometry (HPLC-MS) analysis. In addition, another compound, meridamycin, was also identified through a HPLC-MS analysis. The current study reveals the biosynthetic potential of Streptomyces sp. isolate BR123, with respect to the synthesis of bioactive secondary metabolites through genomic and spectrometric analysis. Moreover, the comparative genome study compared the isolate BR123 with other Streptomyces strains, which may expand the knowledge concerning the mechanism involved in novel antimicrobial metabolite synthesis.
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Affiliation(s)
- Neelma Ashraf
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, PO Box 577, Faisalabad 38000, Pakistan
- Department of Chemical Ecology/Biological Chemistry, University of Konstanz, 78457 Konstanz, Germany
- Correspondence: (N.A.); (S.K.); Tel.: +92-41-9201316 (S.K.); Fax: +92-41-92014722 (S.K.)
| | - Sana Zafar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, PO Box 577, Faisalabad 38000, Pakistan
| | - Roman Makitrynskyy
- Department of Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, University of Freiburg, 79104 Freiburg im Breisgau, Germany
| | - Andreas Bechthold
- Department of Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, University of Freiburg, 79104 Freiburg im Breisgau, Germany
| | - Dieter Spiteller
- Department of Chemical Ecology/Biological Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Lijiang Song
- Department of Chemistry, University of Warwick Coventry, Coventry CV4 7AL, UK
| | - Munir Ahmad Anwar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, PO Box 577, Faisalabad 38000, Pakistan
| | - Andriy Luzhetskyy
- Pharmaceutical Biotechnology Campus, Saarland University, Building C2.3, 66123 Saarbrucken, Germany
| | - Ali Nisar Khan
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, PO Box 577, Faisalabad 38000, Pakistan
| | - Kalsoom Akhtar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, PO Box 577, Faisalabad 38000, Pakistan
| | - Shazia Khaliq
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, PO Box 577, Faisalabad 38000, Pakistan
- Correspondence: (N.A.); (S.K.); Tel.: +92-41-9201316 (S.K.); Fax: +92-41-92014722 (S.K.)
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Choi B, Jeong S, Kim E. Variation of the seed endophytic bacteria among plant populations and their plant growth‐promoting activities in a wild mustard plant species,
Capsella bursa‐pastoris. Ecol Evol 2022; 12:e8683. [PMID: 35309752 PMCID: PMC8901890 DOI: 10.1002/ece3.8683] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 01/29/2022] [Accepted: 02/10/2022] [Indexed: 12/26/2022] Open
Affiliation(s)
- Byungwook Choi
- School of Earth Sciences and Environmental Engineering Gwangju Institute of Science and Technology Gwangju South Korea
| | - Seorin Jeong
- School of Earth Sciences and Environmental Engineering Gwangju Institute of Science and Technology Gwangju South Korea
| | - Eunsuk Kim
- School of Earth Sciences and Environmental Engineering Gwangju Institute of Science and Technology Gwangju South Korea
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Rangseekaew P, Barros-Rodríguez A, Pathom-aree W, Manzanera M. Plant Beneficial Deep-Sea Actinobacterium, Dermacoccus abyssi MT1.1T Promote Growth of Tomato (Solanum lycopersicum) under Salinity Stress. BIOLOGY 2022; 11:biology11020191. [PMID: 35205058 PMCID: PMC8869415 DOI: 10.3390/biology11020191] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 01/24/2022] [Accepted: 01/24/2022] [Indexed: 12/23/2022]
Abstract
Simple Summary Salt stress is an important environmental problem that negatively affects agricultural and food production in the world. Currently, the use of plant beneficial bacteria for plant growth promotion is attractive due to the demand for eco-friendly and sustainable agriculture. In this study, salt tolerant deep-sea actinobacterium, Dermacoccus abyssi MT1.1T was investigated plant growth promotion and salt stress mitigation in tomato seedlings. In addition, D. abyssi MT1.1T whole genome was analyzed for plant growth promoting traits and genes related to salt stress alleviation in plants. We also evaluated the biosafety of this strain on human health and organisms in the environment. Our results highlight that the inoculation of D. abyssi MT1.1T could reduce the negative effects of salt stress in tomato seedlings by growth improvement, total soluble sugars accumulation and hydrogen peroxide reduction. Moreover, this strain could survive and colonize tomato roots. Biosafety testing and genome analysis of D. abyssi MT1.1T showed no pathogenicity risk. In conclusion, we provide supporting evidence on the potential of D. abyssi MT1.1T as a safe strain for use in plant growth promotion under salt stress. Abstract Salt stress is a serious agricultural problem threatens plant growth and development resulted in productivity loss and global food security concerns. Salt tolerant plant growth promoting actinobacteria, especially deep-sea actinobacteria are an alternative strategy to mitigate deleterious effects of salt stress. In this study, we aimed to investigate the potential of deep-sea Dermacoccus abyssi MT1.1T to mitigate salt stress in tomato seedlings and identified genes related to plant growth promotion and salt stress mitigation. D. abyssi MT1.1T exhibited plant growth promoting traits namely indole-3-acetic acid (IAA) and siderophore production and phosphate solubilization under 0, 150, 300, and 450 mM NaCl in vitro. Inoculation of D. abyssi MT1.1T improved tomato seedlings growth in terms of shoot length and dry weight compared with non-inoculated seedlings under 150 mM NaCl. In addition, increased total soluble sugar and total chlorophyll content and decreased hydrogen peroxide content were observed in tomato inoculated with D. abyssi MT1.1T. These results suggested that this strain mitigated salt stress in tomatoes via osmoregulation by accumulation of soluble sugars and H2O2 scavenging activity. Genome analysis data supported plant growth promoting and salt stress mitigation potential of D. abyssi MT1.1T. Survival and colonization of D. abyssi MT1.1T were observed in roots of inoculated tomato seedlings. Biosafety testing on D. abyssi MT1.1T and in silico analysis of its whole genome sequence revealed no evidence of its pathogenicity. Our results demonstrate the potential of deep-sea D. abyssi MT1.1T to mitigate salt stress in tomato seedlings and as a candidate of eco-friendly bio-inoculants for sustainable agriculture.
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Affiliation(s)
- Pharada Rangseekaew
- Doctor of Philosophy Program in Applied Microbiology (International Program) in Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
- Graduate School, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Adoración Barros-Rodríguez
- Department of Microbiology, Institute for Water Research, University of Granada, 18071 Granada, Spain; (A.B.-R.); (M.M.)
| | - Wasu Pathom-aree
- Research Center in Bioresources for Agriculture, Industry and Medicine, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence: ; Tel.: +66-53943346-48
| | - Maximino Manzanera
- Department of Microbiology, Institute for Water Research, University of Granada, 18071 Granada, Spain; (A.B.-R.); (M.M.)
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Handayani I, Saad H, Ratnakomala S, Lisdiyanti P, Kusharyoto W, Krause J, Kulik A, Wohlleben W, Aziz S, Gross H, Gavriilidou A, Ziemert N, Mast Y. Mining Indonesian Microbial Biodiversity for Novel Natural Compounds by a Combined Genome Mining and Molecular Networking Approach. Mar Drugs 2021; 19:316. [PMID: 34071728 PMCID: PMC8227522 DOI: 10.3390/md19060316] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/22/2021] [Accepted: 05/25/2021] [Indexed: 11/17/2022] Open
Abstract
Indonesia is one of the most biodiverse countries in the world and a promising resource for novel natural compound producers. Actinomycetes produce about two thirds of all clinically used antibiotics. Thus, exploiting Indonesia's microbial diversity for actinomycetes may lead to the discovery of novel antibiotics. A total of 422 actinomycete strains were isolated from three different unique areas in Indonesia and tested for their antimicrobial activity. Nine potent bioactive strains were prioritized for further drug screening approaches. The nine strains were cultivated in different solid and liquid media, and a combination of genome mining analysis and mass spectrometry (MS)-based molecular networking was employed to identify potential novel compounds. By correlating secondary metabolite gene cluster data with MS-based molecular networking results, we identified several gene cluster-encoded biosynthetic products from the nine strains, including naphthyridinomycin, amicetin, echinomycin, tirandamycin, antimycin, and desferrioxamine B. Moreover, 16 putative ion clusters and numerous gene clusters were detected that could not be associated with any known compound, indicating that the strains can produce novel secondary metabolites. Our results demonstrate that sampling of actinomycetes from unique and biodiversity-rich habitats, such as Indonesia, along with a combination of gene cluster networking and molecular networking approaches, accelerates natural product identification.
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Affiliation(s)
- Ira Handayani
- Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen (IMIT), Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (I.H.); (J.K.); (A.K.); (W.W.)
- Research Center for Biotechnology, Indonesian Institute of Sciences (LIPI), Jl. Raya Jakarta-Bogor KM.46, Cibinong, West Java 16911, Indonesia; (P.L.); (W.K.)
| | - Hamada Saad
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany; (H.S.); (S.A.); (H.G.)
- Department of Phytochemistry and Plant Systematics, Division of Pharmaceutical Industries, National Research Centre, Dokki, Cairo 12622, Egypt
| | - Shanti Ratnakomala
- Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Raya Jakarta-Bogor KM.46, Cibinong, West Java 16911, Indonesia;
| | - Puspita Lisdiyanti
- Research Center for Biotechnology, Indonesian Institute of Sciences (LIPI), Jl. Raya Jakarta-Bogor KM.46, Cibinong, West Java 16911, Indonesia; (P.L.); (W.K.)
| | - Wien Kusharyoto
- Research Center for Biotechnology, Indonesian Institute of Sciences (LIPI), Jl. Raya Jakarta-Bogor KM.46, Cibinong, West Java 16911, Indonesia; (P.L.); (W.K.)
| | - Janina Krause
- Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen (IMIT), Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (I.H.); (J.K.); (A.K.); (W.W.)
| | - Andreas Kulik
- Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen (IMIT), Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (I.H.); (J.K.); (A.K.); (W.W.)
| | - Wolfgang Wohlleben
- Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen (IMIT), Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (I.H.); (J.K.); (A.K.); (W.W.)
| | - Saefuddin Aziz
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany; (H.S.); (S.A.); (H.G.)
| | - Harald Gross
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany; (H.S.); (S.A.); (H.G.)
| | - Athina Gavriilidou
- Applied Natural Products Genome Mining, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (A.G.); (N.Z.)
| | - Nadine Ziemert
- Applied Natural Products Genome Mining, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (A.G.); (N.Z.)
- German Center for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Yvonne Mast
- Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen (IMIT), Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (I.H.); (J.K.); (A.K.); (W.W.)
- German Center for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
- Department of Bioresources for Bioeconomy and Health Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
- Department of Microbiology, Technical University of Braunschweig, 38124 Braunschweig, Germany
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Ankati S, Srinivas V, Pratyusha S, Gopalakrishnan S. Streptomyces consortia-mediated plant defense against Fusarium wilt and plant growth-promotion in chickpea. Microb Pathog 2021; 157:104961. [PMID: 34033892 DOI: 10.1016/j.micpath.2021.104961] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/30/2021] [Accepted: 05/07/2021] [Indexed: 11/15/2022]
Abstract
Three strains of Streptomyces griseus (CAI-24, CAI-121 and CAI-127) and one strain each of Streptomyces africanus (KAI-32) and Streptomyces coelicolor (KAI-90) were reported by us as biocontrol agents against Fusarium wilt, caused by Fusarium oxysporum f. sp. ciceri (FOC), and as plant growth-promoters (PGP) in chickpea. In the present study, the combined effect of these Streptomyces strains as a consortium were assessed for their biocontrol potential against Fusarium wilt and PGP in chickpea. Based on their compatibility, biocontrol ability and PGP performance, two consortia were assembled, consortium-1 having all the five strains of Streptomyces sp. and consortium-2 having the two promising strains (CAI-127 and KAI-32). Under greenhouse conditions, consortium-1 and consortium-2 were found to reduce the Fusarium wilt disease incidence by 55% and 74%, while under field conditions, these were by 86% and 96% in year-1 and by 54% and 69% in year-2, respectively, when compared to the positive control (only FOC treated). Shoot samples treated with consortia + FOC contained significantly enhanced antioxidant enzymes such as superoxide dismutase, catalase, ascorbate peroxidase, guaiacol peroxidase, glutathione reductase and phenylalanine ammonia-lyase, when compared to the positive control (only FOC treated) or the negative control samples (neither FOC nor consortia treated). When the consortia were evaluated for their PGP traits under field conditions in two chickpea cultivars, JG11 and ICCV2, and in two consecutive years, nodule number was found to enhance up to 25%, nodule weight up to 49%, leaf area up to 37%, leaf weight up to 43%, root weight up to 23%, shoot weight up to 35%, seed weight up to 30%, seed number up to 29%, total dry matter up to 22% and grain yield up to 22% over the un-inoculated control plants. This study had demonstrated that the selected consortium of Streptomyces spp. has a greater potential for biological control of Fusarium wilt disease and PGP in chickpea.
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Affiliation(s)
- Sravani Ankati
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Telangana, India
| | - Vadlamudi Srinivas
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Telangana, India
| | - Sambangi Pratyusha
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Telangana, India
| | - Subramaniam Gopalakrishnan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Telangana, India.
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The Impact of Growth-Promoting Streptomycetes Isolated from Rhizosphere and Bulk Soil on Oilseed Rape (Brassica napus L.) Growth Parameters. SUSTAINABILITY 2021. [DOI: 10.3390/su13105704] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Inoculation of Streptomyces to improve oilseed rape (Brassica napus L.) yields and minimise the use of chemical fertilisers is a promising sustainable strategy. In this study, we isolated 72 actinobacterial strains from rhizosphere of oilseed rape and maize and from bulk soil for screening and characterising their antimicrobial activity. Nine promising strains, identified as Streptomyces sp. by morphology, physiological characteristics, and 16S rRNA gene sequencing, were selected for their plant growth-promoting traits and in planta experiments. The actinobacterial strains were positive for IAA production, siderophore production, and HCN production. In planta experiments were conducted by soaking the oilseed rape seeds in the actinobacterial suspension, followed by plant growth under controlled conditions in a cultivate chamber (22–28 °C, 8 h dark/16 h light, constant humidity 80%). We recorded root and shoot length (cm) and seedling fresh weight (g). For most of the abovementioned parameters, a significant enhancement was observed with strain KmiRC20A118 treatment. The length of the root increased by 53.14%, the shoot length increased by 65.6%, and the weight of the fresh plant by 60% compared to the control. The integrated application of PGPS (Plant Growth Promoting Streptomyces) from the rhizosphere of oilseed rape is a promising strategy to improve the growth of oilseed rape.
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Soumare A, Diédhiou AG, Arora NK, Tawfeeq Al-Ani LK, Ngom M, Fall S, Hafidi M, Ouhdouch Y, Kouisni L, Sy MO. Potential Role and Utilization of Plant Growth Promoting Microbes in Plant Tissue Culture. Front Microbiol 2021; 12:649878. [PMID: 33854489 PMCID: PMC8039301 DOI: 10.3389/fmicb.2021.649878] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/01/2021] [Indexed: 11/04/2022] Open
Abstract
Plant growth promoting microbes (PGPMs) play major roles in diverse ecosystems, including atmospheric nitrogen fixation, water uptake, solubilization, and transport of minerals from the soil to the plant. Different PGPMs are proposed as biofertilizers, biostimulants, and/or biocontrol agents to improve plant growth and productivity and thereby to contribute to agricultural sustainability and food security. However, little information exists regarding the use of PGPMs in micropropagation such as the in vitro plant tissue culture. This review presents an overview of the importance of PGPMs and their potential application in plant micropropagation. Our analysis, based on published articles, reveals that the process of in vitro classical tissue culture techniques, under strictly aseptic conditions, deserves to be reviewed to allow vitroplants to benefit from the positive effect of PGPMs. Furthermore, exploiting the potential benefits of PGPMs will lead to lessen the cost production of vitroplants during micropropagation process and will make the technique of plant tissue culture more efficient. The last part of the review will indicate where research is needed in the future.
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Affiliation(s)
- Abdoulaye Soumare
- AgroBioSciences Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco.,Laboratoire Commun de Microbiologie (LCM) IRD/ISRA/UCAD, Centre de Recherche de Bel Air, Dakar, Senegal.,Centre d'Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA-AGRISAN), UCAD, Dakar, Senegal
| | - Abdala G Diédhiou
- Laboratoire Commun de Microbiologie (LCM) IRD/ISRA/UCAD, Centre de Recherche de Bel Air, Dakar, Senegal.,Centre d'Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA-AGRISAN), UCAD, Dakar, Senegal.,Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Senegal
| | - Naveen Kumar Arora
- Department of Environmental Science, School of Earth and Environmental Sciences, BBA University, Lucknow, India
| | - Laith Khalil Tawfeeq Al-Ani
- Department of Plant Protection, College of Agriculture Engineering Sciences, University of Baghdad, Baghdad, Iraq.,School of Biology Science, Universiti Sains Malaysia, Penang, Malaysia
| | - Mariama Ngom
- Laboratoire Commun de Microbiologie (LCM) IRD/ISRA/UCAD, Centre de Recherche de Bel Air, Dakar, Senegal.,Laboratoire Campus de Biotechnologies Végétales (LCBV), Département de Biologie Végétale, Faculté des Sciences et Techniques, UCAD, Dakar, Senegal
| | - Saliou Fall
- Laboratoire Commun de Microbiologie (LCM) IRD/ISRA/UCAD, Centre de Recherche de Bel Air, Dakar, Senegal
| | - Mohamed Hafidi
- AgroBioSciences Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco.,Laboratory of Microbial Biotechnologies, Agrosciences and Environment, Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakesh, Morocco
| | - Yedir Ouhdouch
- AgroBioSciences Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco.,Laboratory of Microbial Biotechnologies, Agrosciences and Environment, Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakesh, Morocco
| | - Lamfeddal Kouisni
- AgroBioSciences Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Mame Ourèye Sy
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Senegal.,Laboratoire Campus de Biotechnologies Végétales (LCBV), Département de Biologie Végétale, Faculté des Sciences et Techniques, UCAD, Dakar, Senegal
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Plant Growth-Promoting Bacteria as an Emerging Tool to Manage Bacterial Rice Pathogens. Microorganisms 2021; 9:microorganisms9040682. [PMID: 33810209 PMCID: PMC8065915 DOI: 10.3390/microorganisms9040682] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 01/16/2023] Open
Abstract
As a major food crop, rice (Oryza sativa) is produced and consumed by nearly 90% of the population in Asia with less than 9% produced outside Asia. Hence, reports on large scale grain losses were alarming and resulted in a heightened awareness on the importance of rice plants' health and increased interest against phytopathogens in rice. To serve this interest, this review will provide a summary on bacterial rice pathogens, which can potentially be controlled by plant growth-promoting bacteria (PGPB). Additionally, this review highlights PGPB-mediated functional traits, including biocontrol of bacterial rice pathogens and enhancement of rice plant's growth. Currently, a plethora of recent studies address the use of PGPB to combat bacterial rice pathogens in an attempt to replace existing methods of chemical fertilizers and pesticides that often lead to environmental pollutions. As a tool to combat bacterial rice pathogens, PGPB presented itself as a promising alternative in improving rice plants' health and simultaneously controlling bacterial rice pathogens in vitro and in the field/greenhouse studies. PGPB, such as Bacillus, Pseudomonas, Enterobacter, Streptomyces, are now very well-known. Applications of PGPB as bioformulations are found to be effective in improving rice productivity and provide an eco-friendly alternative to agroecosystems.
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Chandra A, Chandra P, Tripathi P. Whole genome sequence insight of two plant growth-promoting bacteria (B. subtilis BS87 and B. megaterium BM89) isolated and characterized from sugarcane rhizosphere depicting better crop yield potentiality. Microbiol Res 2021; 247:126733. [PMID: 33676313 DOI: 10.1016/j.micres.2021.126733] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 12/13/2022]
Abstract
Since sugarcane is a ratoon crop, genome analysis of plant growth-promoting bacteria that exist in its soil rhizosphere, can provide opportunity to better understand their characteristics and use of such bacteria in turn, may especially improve perennial crop productivity. In the present study, genome of two bacterial strains, one each of B. megaterium (BM89) and B. subtilis (BS87), isolated and reported earlier (Chandra et al., 2018), were sequenced and characterized. Though both strains have demonstrated plant growth promoting properties and enhanced in-vitro plant growth responses, functional annotation and analysis of genes indicated superiority of BS87 as it possessed more plant growth promotion attributable genes over BM89. Apart from some common genes, trehalose metabolism, glycine betaine production, peroxidases, super oxide dismutase, cold shock proteins and phenazine production associated genes were selectively identified in BS87 genome indicating better plant growth performances and survival potential under harsh environmental conditions. Genes for chitinase, d-cysteine desulfhydrase and γ-aminobutyric acid (GABA), as found in BM89, propose its selective utilization in defense and bio-control measures. Concomitant with better settlings' growth, scanning electron micrographs indicated these isolated and characterized bacteria exhibiting healthy colonization within root of sugarcane crop. Kegg pathways' assignment also revealed added pathways namely carbohydrate and amino acid metabolism attached to B. subtilis strain BS87, a preferable candidate for bio-fertilizer and its utilization to promote growth of both plant and ratoon crops of sugarcane usually experiencing harsh environmental conditions.
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Affiliation(s)
- Amaresh Chandra
- ICAR-Indian Institute of Sugarcane Research, Rae Bareli Road, Lucknow, 26002, India.
| | - Priyanka Chandra
- ICAR-Central Soil Salinity Research Institute, Karnal, 132001, India
| | - Pramila Tripathi
- ICAR-Indian Institute of Sugarcane Research, Rae Bareli Road, Lucknow, 26002, India
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Gopalakrishnan S, Srinivas V, Naresh N, Pratyusha S, Ankati S, Madhuprakash J, Govindaraj M, Sharma R. Deciphering the antagonistic effect of Streptomyces spp. and host-plant resistance induction against charcoal rot of sorghum. PLANTA 2021; 253:57. [PMID: 33532924 DOI: 10.1007/s00425-021-03577-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/21/2021] [Indexed: 06/12/2023]
Abstract
The findings of this study suggest that the selected five strains of Streptomyces spp. could be used for biological control of charcoal rot disease in sorghum. Two strains each of Streptomyces albus (CAI-17 and KAI-27) and Streptomyces griseus (KAI-26 and MMA-32) and one strain of Streptomyces cavourensis (SAI-13) previously reported to have plant growth-promotion activity in chickpea, rice and sorghum were evaluated for their antagonistic potential against Macrophomina phaseolina, which causes charcoal rot in sorghum. The antagonistic potential of these strains against M. phaseolina was assessed through dual culture assay, metabolite production assay, blotter paper assay in greenhouse and field disease screens. In both dual culture and metabolite production assays, the selected strains significantly inhibited the growth of M. phaseolina (63-74%). In the blotter paper assay, all the five strains of Streptomyces spp. inhibited the pathogen (80-90%). When these five strains were tested for their antagonistic potential under the greenhouse (two times) and field (two seasons) conditions by toothpick method of inoculation, significant differences were observed for charcoal rot severity. Principal component analysis capturing 91.3% phenotypic variations, revealed that the shoot samples treated with both Streptomyces and the pathogen exhibited significantly enhanced antioxidant parameters including superoxide dismutase, catalase, ascorbate peroxidase, guaiacol peroxidase, glutathione reductase, phenylalanine ammonia-lyase, polyphenol oxidase, and total phenolic contents when compared to shoot samples treated with only M. phaseolina. Scanning electron microscope analysis revealed that the phloem and xylem tissues of the Streptomyces treated stem samples were intact compared to that of pathogen inoculated plants. This study indicated that the selected strains of Streptomyces spp. have the potential for biological control of charcoal rot disease in sorghum.
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Affiliation(s)
- Subramaniam Gopalakrishnan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, Telangana, India.
| | - Vadlamudi Srinivas
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, Telangana, India
| | - Nimmala Naresh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, Telangana, India
| | - Sambangi Pratyusha
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, Telangana, India
| | - Sravani Ankati
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, Telangana, India
| | - Jogi Madhuprakash
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, 500 046, Hyderabad, Telangana, India
| | - Mahalingam Govindaraj
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, Telangana, India.
| | - Rajan Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, Telangana, India.
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Chandra A, Gaur V, Tripathi P. Microbiome analysis of rhizospheres of plant and winter-initiated ratoon crops of sugarcane grown in sub-tropical India: utility to improve ratoon crop productivity. 3 Biotech 2021; 11:34. [PMID: 33457168 DOI: 10.1007/s13205-020-02603-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/19/2020] [Indexed: 11/29/2022] Open
Abstract
One plant and one to two ratoon crops are the predominant patterns of sugarcane cultivation in sub-tropical part of India. Despite high agricultural inputs, yield of ratoon crop gets dwindled in the subsequent years. The microbial community, particularly bacteria and fungi, in the rhizosphere and their interaction with the root system, in general influences plant productivity. For the present study, an early maturing sugarcane variety (CoLk 94184), was used to establish plant and winter-initiated ratoon crops in 2016-2018. Soils pertaining to both plant and ratoon rhizospheres were subjected to biochemical analysis, microbial DNA isolation and high-throughput sequencing of 16S rRNA genes to assess the microbial diversity and associated characteristics impacting cane yield. Although alpha diversity of bacterial community was observed high in the soils of both plant and ratoon crops, the species richness/diversity was more in plant crop. Bacterial community structure in the rhizosphere of plant crop was predominantly consisted of phyla Actinobacteria (35.68%), Gemmatimonadetes (29.26%), Chloroflexi (26.73%) and Proteobacteria (16.68%), while ratoon rhizosphere revealed dominance of Acidobacteria (20.77%) and Bacteroidetes (10.7%). Though studies revealed the presence of rich bacterial community in the rhizospheres of both plant and ratoon crops of sugarcane, dominance of Acidobacteria and meager proportion of Actinobacteria and Proteobacteria in ratoon crop possibly limited its productivity. Along with high total phenols (7.27 mg/g dry wt), ratoon crop depicted less active root system as revealed by scanning electron microscopy. Dominance of thermophilic bacterial phyla Chloroflexi and Gemmatimonadetes which was observed in sugarcane rhizosphere supports better crop growth in drought. However, management of soil microbial community is required to improve the ratoon crop productivity.
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Affiliation(s)
- Amaresh Chandra
- ICAR-Indian Institute of Sugarcane Research, Rae Bareli Road, Lucknow, 26002 India
| | - Vivek Gaur
- Lucknow Campus, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, 226010 India
| | - Pramila Tripathi
- ICAR-Indian Institute of Sugarcane Research, Rae Bareli Road, Lucknow, 26002 India
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Identification and Characterization of a Streptomyces albus Strain and Its Secondary Metabolite Organophosphate against Charcoal Rot of Sorghum. PLANTS 2020; 9:plants9121727. [PMID: 33297539 PMCID: PMC7762395 DOI: 10.3390/plants9121727] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/01/2020] [Accepted: 12/01/2020] [Indexed: 12/05/2022]
Abstract
Streptomycesalbus strain CAI-21 has been previously reported to have plant growth-promotion abilities in chickpea, pigeonpea, rice, and sorghum. The strain CAI-21 and its secondary metabolite were evaluated for their biocontrol potential against charcoal rot disease in sorghum caused by Macrophomina phaseolina. Results exhibited that CAI-21 significantly inhibited the growth of the pathogen, M. phaseolina, in dual-culture (15 mm; zone of inhibition), metabolite production (74% inhibition), and blotter paper (90% inhibition) assays. When CAI-21 was tested for its biocontrol potential under greenhouse and field conditions following inoculation of M. phaseolina by toothpick method, it significantly reduced the number of internodes infected (75% and 45% less, respectively) and length of infection (75% and 51% less, respectively) over the positive control (only M. phaseolina inoculated) plants. Under greenhouse conditions, scanning electron microscopic analysis showed that the phloem and xylem tissues of the CAI-21-treated shoot samples were intact compared to those of the diseased stem samples. The culture filtrate of the CAI-21 was purified by various chromatographic techniques, and the active compound was identified as “organophosphate” by NMR and MS. The efficacy of organophosphate was found to inhibit the growth of M. phaseolina in the poisoned food technique. This study indicates that S.albus CAI-21 and its active metabolite organophosphate have the potential to control charcoal rot in sorghum.
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