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Marik D, Sharma P, Chauhan NS, Jangir N, Shekhawat RS, Verma D, Mukherjee M, Abiala M, Roy C, Yadav P, Sadhukhan A. Peribacillus frigoritolerans T7-IITJ, a potential biofertilizer, induces plant growth-promoting genes of Arabidopsis thaliana. J Appl Microbiol 2024; 135:lxae066. [PMID: 38486365 DOI: 10.1093/jambio/lxae066] [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: 12/04/2023] [Revised: 01/28/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024]
Abstract
AIMS This study aimed to isolate plant growth and drought tolerance-promoting bacteria from the nutrient-poor rhizosphere soil of Thar desert plants and unravel their molecular mechanisms of plant growth promotion. METHODS AND RESULTS Among our rhizobacterial isolates, Enterobacter cloacae C1P-IITJ, Kalamiella piersonii J4-IITJ, and Peribacillus frigoritolerans T7-IITJ, significantly enhanced root and shoot growth (4-5-fold) in Arabidopsis thaliana under PEG-induced drought stress. Whole genome sequencing and biochemical analyses of the non-pathogenic bacterium T7-IITJ revealed its plant growth-promoting traits, viz., solubilization of phosphate (40-73 µg/ml), iron (24 ± 0.58 mm halo on chrome azurol S media), and nitrate (1.58 ± 0.01 µg/ml nitrite), along with production of exopolysaccharides (125 ± 20 µg/ml) and auxin-like compounds (42.6 ± 0.05 µg/ml). Transcriptome analysis of A. thaliana inoculated with T7-IITJ and exposure to drought revealed the induction of 445 plant genes (log2fold-change > 1, FDR < 0.05) for photosynthesis, auxin and jasmonate signalling, nutrient uptake, redox homeostasis, and secondary metabolite biosynthesis pathways related to beneficial bacteria-plant interaction, but repression of 503 genes (log2fold-change < -1) including many stress-responsive genes. T7-IITJ enhanced proline 2.5-fold, chlorophyll 2.5-2.8-fold, iron 2-fold, phosphate 1.6-fold, and nitrogen 4-fold, and reduced reactive oxygen species 2-4.7-fold in plant tissues under drought. T7-IITJ also improved the germination and seedling growth of Tephrosia purpurea, Triticum aestivum, and Setaria italica under drought and inhibited the growth of two plant pathogenic fungi, Fusarium oxysporum, and Rhizoctonia solani. CONCLUSIONS P. frigoritolerans T7-IITJ is a potent biofertilizer that regulates plant genes to promote growth and drought tolerance.
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Affiliation(s)
- Debankona Marik
- Department of Bioscience and Bioengineering, IIT Jodhpur, Jodhpur 342030, India
| | - Pinki Sharma
- Department of Biochemistry, Maharshi Dayanand University, Rohtak 124001, India
| | - Nar Singh Chauhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak 124001, India
| | - Neelam Jangir
- Department of Bioscience and Bioengineering, IIT Jodhpur, Jodhpur 342030, India
| | | | - Devanshu Verma
- Department of Bioscience and Bioengineering, IIT Jodhpur, Jodhpur 342030, India
| | - Manasi Mukherjee
- Jodhpur City Knowledge and Innovation Foundation, IIT Jodhpur, Jodhpur 342030, India
| | - Moses Abiala
- Department of Biological Sciences, College of Basic and Applied Sciences, Mountain Top University, Prayer City 110106, Nigeria
| | - Chandan Roy
- Department of Genetics and Plant Breeding, Agriculture University Jodhpur, Jodhpur 342304, India
| | - Pankaj Yadav
- Department of Bioscience and Bioengineering, IIT Jodhpur, Jodhpur 342030, India
| | - Ayan Sadhukhan
- Department of Bioscience and Bioengineering, IIT Jodhpur, Jodhpur 342030, India
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Świątczak J, Kalwasińska A, Brzezinska MS. Plant growth-promoting rhizobacteria: Peribacillus frigoritolerans 2RO30 and Pseudomonas sivasensis 2RO45 for their effect on canola growth under controlled as well as natural conditions. FRONTIERS IN PLANT SCIENCE 2024; 14:1233237. [PMID: 38259930 PMCID: PMC10800854 DOI: 10.3389/fpls.2023.1233237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024]
Abstract
Even though canola is one of the most important industrial crops worldwide, it has high nutrient requirements and is susceptible to pests and diseases. Therefore, natural methods are sought to support the development of these plants. One of those methods could be a plant growth-promoting rhizobacteria (PGPR) that have a beneficial effect on plant development. The aim of this study was a genomic comparison of two PGPR strains chosen based on their effect on canola growth: Peribacillus frigoritolerans 2RO30, which stimulated canola growth only in sterile conditions, and Pseudomonas sivasensis 2RO45, which promoted canola growth in both sterile and non-sterile conditions. First of all, six bacterial strains: RO33 (Pseudomonas sp.), RO37 (Pseudomonas poae), RO45 (Pseudomonas kairouanensis), 2RO30 (Peribacillus frigoritolerans), 2RO45 (Pseudomonas sivasensis), and 3RO30 (Pseudomonas migulae), demonstrating best PGP traits in vitro, were studied for their stimulating effect on canola growth under sterile conditions. P. frigoritolerans 2RO30 and P. sivasensis 2RO45 showed the best promoting effect, significantly improving chlorophyll content index (CCI) and roots length compared to the non-inoculated control and to other inoculated seedlings. Under non-sterile conditions, only P. sivasensis 2RO45 promoted the canola growth, significantly increasing CCI compared to the untreated control and to other inoculants. Genome comparison revealed that the genome of P. sivasensis 2RO45 was enriched with additional genes responsible for ACC deaminase (acdA), IAA (trpF, trpG), and siderophores production (fbpA, mbtH, and acrB) compared to 2RO30. Moreover, P. sivasensis 2RO45 showed antifungal effect against all the tested phytopathogens and harbored six more biosynthetic gene clusters (BGC), namely, syringomycin, pyoverdin, viscosin, arylpolyene, lankacidin C, and enterobactin, than P. frigoritolerans 2RO30. These BGCs are well known as antifungal agents; therefore, it can be assumed that these BGCs were responsible for the antifungal activity of P. sivasensis 2RO45 against all plant pathogens. This study is the first report describing P. sivasensis 2RO45 as a canola growth promoter, both under controlled and natural conditions, thus suggesting its application in improving canola yield, by improving nutrient availability, enhancing stress tolerance, and reducing environmental impact of farming practices.
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Affiliation(s)
- Joanna Świątczak
- Department of Environmental Microbiology and Biotechnology, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | | | - Maria Swiontek Brzezinska
- Department of Environmental Microbiology and Biotechnology, Nicolaus Copernicus University in Toruń, Toruń, Poland
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Rudra B, Gupta RS. Phylogenomics studies and molecular markers reliably demarcate genus Pseudomonas sensu stricto and twelve other Pseudomonadaceae species clades representing novel and emended genera. Front Microbiol 2024; 14:1273665. [PMID: 38249459 PMCID: PMC10797017 DOI: 10.3389/fmicb.2023.1273665] [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: 08/07/2023] [Accepted: 11/17/2023] [Indexed: 01/23/2024] Open
Abstract
Genus Pseudomonas is a large assemblage of diverse microorganisms, not sharing a common evolutionary history. To clarify their evolutionary relationships and classification, we have conducted comprehensive phylogenomic and comparative analyses on 388 Pseudomonadaceae genomes. In phylogenomic trees, Pseudomonas species formed 12 main clusters, apart from the "Aeruginosa clade" containing its type species, P. aeruginosa. In parallel, our detailed analyses on protein sequences from Pseudomonadaceae genomes have identified 98 novel conserved signature indels (CSIs), which are uniquely shared by the species from different observed clades/groups. Six CSIs, which are exclusively shared by species from the "Aeruginosa clade," provide reliable demarcation of this clade corresponding to the genus Pseudomonas sensu stricto in molecular terms. The remaining 92 identified CSIs are specific for nine other Pseudomonas species clades and the genera Azomonas and Azotobacter which branch in between them. The identified CSIs provide strong independent evidence of the genetic cohesiveness of these species clades and offer reliable means for their demarcation/circumscription. Based on the robust phylogenetic and molecular evidence presented here supporting the distinctness of the observed Pseudomonas species clades, we are proposing the transfer of species from the following clades into the indicated novel genera: Alcaligenes clade - Aquipseudomonas gen. nov.; Fluvialis clade - Caenipseudomonas gen. nov.; Linyingensis clade - Geopseudomonas gen. nov.; Oleovorans clade - Ectopseudomonas gen. nov.; Resinovorans clade - Metapseudomonas gen. nov.; Straminea clade - Phytopseudomonas gen. nov.; and Thermotolerans clade - Zestomonas gen. nov. In addition, descriptions of the genera Azomonas, Azotobacter, Chryseomonas, Serpens, and Stutzerimonas are emended to include information for the CSIs specific for them. The results presented here should aid in the development of a more reliable classification scheme for Pseudomonas species.
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Affiliation(s)
| | - Radhey S. Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
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Manetsberger J, Caballero Gómez N, Soria-Rodríguez C, Benomar N, Abriouel H. Simply Versatile: The Use of Peribacillus simplex in Sustainable Agriculture. Microorganisms 2023; 11:2540. [PMID: 37894197 PMCID: PMC10608964 DOI: 10.3390/microorganisms11102540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 09/30/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Peribacillus simplex is a Gram-positive, spore-forming bacterium derived from a vast range of different origins. Notably, it is part of the plant-growth-promoting rhizobacterial community of many crops. Although members of the Bacillaceae family have been widely used in agriculture, P. simplex has, so far, remained in the shadow of its more famous relatives, e.g., Bacillus subtilis or Bacillus thuringiensis. Recent studies have, however, started to uncover the bacterium's highly promising and versatile properties, in particular in agricultural and environmental applications. Hence, here, we review the plant-growth-promoting features of P. simplex, as well as its biocontrol activity against a variety of detrimental plant pests in different crops. We further highlight the bacterium's potential as a bioremediation agent for environmental contaminants, such as metals, pesticide residues, or (crude) oil. Finally, we examine the recent developments in the European regulatory landscape to facilitate the use of microorganisms in plant protection products. Undoubtedly, further studies on P. simplex will reveal additional benefits for agricultural and environmentally friendly applications.
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Affiliation(s)
- Julia Manetsberger
- Area of Microbiology, Department of Health Sciences, Faculty of Experimental Sciences, University of Jaén, 23071 Jaén, Spain
| | - Natacha Caballero Gómez
- Area of Microbiology, Department of Health Sciences, Faculty of Experimental Sciences, University of Jaén, 23071 Jaén, Spain
| | - Carlos Soria-Rodríguez
- Area of Public International Law and International Relations, Department of Public and European Common Law, University of Jaén, 23071 Jaén, Spain
| | - Nabil Benomar
- Area of Microbiology, Department of Health Sciences, Faculty of Experimental Sciences, University of Jaén, 23071 Jaén, Spain
| | - Hikmate Abriouel
- Area of Microbiology, Department of Health Sciences, Faculty of Experimental Sciences, University of Jaén, 23071 Jaén, Spain
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Gupta RS, Kanter-Eivin DA. AppIndels.com server: a web-based tool for the identification of known taxon-specific conserved signature indels in genome sequences. Validation of its usefulness by predicting the taxonomic affiliation of >700 unclassified strains of Bacillus species. Int J Syst Evol Microbiol 2023; 73. [PMID: 37159410 DOI: 10.1099/ijsem.0.005844] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
Taxon-specific conserved signature indels (CSIs) in genes/proteins provide reliable molecular markers (synapomorphies) for unambiguous demarcation of taxa of different ranks in molecular terms and for genetic, biochemical and diagnostic studies. Because of their predictive abilities, the shared presence of known taxon-specific CSIs in genome sequences has proven useful for taxonomic purposes. However, the lack of a convenient method for identifying the presence of known CSIs in genome sequences has limited their utility for taxonomic and other studies. We describe here a web-based tool/server (AppIndels.com) that identifies the presence of known and validated CSIs in genome sequences and uses this information for predicting taxonomic affiliation. The utility of this server was tested by using a database of 585 validated CSIs, which included 350 CSIs specific for ≈45 Bacillales genera, with the remaining CSIs being specific for members of the orders Neisseriales, Legionellales and Chlorobiales, family Borreliaceae, and some Pseudomonadaceae species/genera. Using this server, genome sequences were analysed for 721 Bacillus strains of unknown taxonomic affiliation. Results obtained showed that 651 of these genomes contained significant numbers of CSIs specific for the following Bacillales genera/families: Alkalicoccus, 'Alkalihalobacillaceae', Alteribacter, Bacillus Cereus clade, Bacillus Subtilis clade, Caldalkalibacillus, Caldibacillus, Cytobacillus, Ferdinandcohnia, Gottfriedia, Heyndrickxia, Lederbergia, Litchfieldia, Margalitia, Mesobacillus, Metabacillus, Neobacillus, Niallia, Peribacillus, Priestia, Pseudalkalibacillus, Robertmurraya, Rossellomorea, Schinkia, Siminovitchia, Sporosarcina, Sutcliffiella, Weizmannia and Caryophanaceae. Validity of the taxon assignment made by the server was examined by reconstructing phylogenomic trees. In these trees, all Bacillus strains for which taxonomic predictions were made correctly branched with the indicated taxa. The unassigned strains likely correspond to taxa for which CSIs are lacking in our database. Results presented here show that the AppIndels server provides a useful new tool for predicting taxonomic affiliation based on shared presence of the taxon-specific CSIs. Some caveats in using this server are discussed.
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario CA L8N 3Z5, Canada
| | - David A Kanter-Eivin
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario CA L8N 3Z5, Canada
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Wufuer R, Li W, Wang S, Duo J. Isolation and Degradation Characteristics of PBAT Film Degrading Bacteria. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:17087. [PMID: 36554967 PMCID: PMC9779299 DOI: 10.3390/ijerph192417087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
In recent years, PBAT (polybutylene adipate-co-terephthalate) mulch has become one of the most commonly used biodegradable mulching films. In this paper, five potential strains of PBAT film degrading bacteria were screened from the soil sample using PBAT film as the sole carbon source. A highly efficient PBAT degrading strain JZ1 was isolated by comparing the degradation performance of PBAT mulching film identified as Peribacillus frigoritolerans S2313 by 16S rDNA sequence analysis. The capacity of the strain to degrade PBAT film was optimized by adjusting the cultivation conditions such as nitrogen source, pH, and inoculum volume. After 8 weeks of cultivation, the actual degradation rate of the strain to PBAT mulch film reached 12.45%. SEM (scanning electron microscopy) coupled with EDX (energy dispersive spectroscopy) analysis showed that microbial degradation is an oxidation process and is mainly due to the amorphous regions of the PBAT film. The biodegradation of PBAT film by Peribacillus frigoritolerans may provide a promising method for regulating the degradation progress of PBAT film in the farmlands.
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Affiliation(s)
- Rehemanjiang Wufuer
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Wenfeng Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Shuzhi Wang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Jia Duo
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
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Montecillo JAV, Bae H. In silico analysis of koranimine, a cyclic imine compound from Peribacillus frigoritolerans reveals potential nematicidal activity. Sci Rep 2022; 12:18883. [PMID: 36344604 PMCID: PMC9640594 DOI: 10.1038/s41598-022-20461-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2022] Open
Abstract
Pine wilt disease (PWD) is a destructive vector-borne forest disease caused by the nematode Bursaphelenchus xylophilus. To date, several options are available for the management of pine wilt disease; however constant development and search for natural products with potential nematicidal activity are imperative to diversify management options and to cope with the possible future emergence of resistance in parasitic nematodes. Here, a combined metabolomics and genomics approach was employed to investigate the chemical repertoire and biosynthetic potential of the bacterial endophyte Peribacillus frigoritolerans BE93, previously characterized to exhibit nematicidal activity against B. xylophilus. Feature-based molecular networking revealed the presence of diverse secondary metabolites. A cyclic imine heptapeptide, koranimine, was found to be among the most abundant secondary metabolites produced. Genome mining displayed the presence of several putative biosynthetic gene clusters (BGCs), including a dedicated non-ribosomal peptide synthase (NRPS) BGC for koranimine. Given the non-ribosomal peptide nature of koranimine, in silico molecular docking analysis was conducted to investigate its potential nematicidal activity against the target receptor ivermectin-sensitive invertebrate α glutamate-gated chloride channel (GluCl). Results revealed the binding of koranimine at the allosteric site of the channel-the ivermectin binding site. Moreover, the ligand-receptor interactions observed were mostly shared between koranimine and ivermectin when bound to the α GluCl receptor thus, suggesting a possibly shared mechanism of potential nematicidal activity. This study highlights the efficiency of combined metabolomics and genomics approach in the identification of candidate compounds.
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Affiliation(s)
- Jake Adolf V. Montecillo
- grid.413028.c0000 0001 0674 4447Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541 Republic of Korea
| | - Hanhong Bae
- grid.413028.c0000 0001 0674 4447Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541 Republic of Korea
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