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Tkachuk N, Zelena L. Inhibition of heterotrophic bacterial biofilm in the soil ferrosphere by Streptomyces spp. and Bacillus velezensis. BIOFOULING 2022; 38:916-925. [PMID: 36440643 DOI: 10.1080/08927014.2022.2151362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 11/14/2022] [Accepted: 11/18/2022] [Indexed: 06/16/2023]
Abstract
The soil microbiome is involved in the processes of microbial corrosion, in particular, by the formation of biofilm. It has been proposed that an environmentally friendly solution to this corrosion might be through biological control. Bacillus velezensis NUChC C2b, Streptomyces gardneri ChNPU F3 and S. canus NUChC F2 were investigated as potentially 'green' biocides to prevent attachment to glass as a model surface and the formation of heterotrophic bacterial biofilm which participates in the corrosion process. Results showed high antagonistic and antibiofilm properties of S. gardneri ChNPU F3; which may be related to the formation of secondary antimicrobial metabolites by this strain. B. velezensis NUChC C2b and S. gardneri ChNPU F3 could be incorporated into green biocides - as components of antibiofilm agents that will protect material from bacterial corrosion or as agents that will prevent historical heritage damage.
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Affiliation(s)
- Nataliia Tkachuk
- Department of Biology, T.H. Shevchenko National University "Chernihiv Colehium", Chernihiv, Ukraine
| | - Liubov Zelena
- Department of Physiology of Industrial Microorganisms of the Danylo Zabolotny Institute of Microbiology and Virology, NAS of Ukraine, Kyiv, Ukraine
- Department of Biotechnology, Leather and Fur, Kyiv National University of Technologies and Design, Kyiv, Ukraine
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Luo Y, Chen L, Lu Z, Zhang W, Liu W, Chen Y, Wang X, Du W, Luo J, Wu H. Genome sequencing of biocontrol strain Bacillus amyloliquefaciens Bam1 and further analysis of its heavy metal resistance mechanism. BIORESOUR BIOPROCESS 2022; 9:74. [PMID: 38647608 PMCID: PMC10991351 DOI: 10.1186/s40643-022-00563-x] [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: 01/01/2022] [Accepted: 07/01/2022] [Indexed: 11/10/2022] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) or Biocontrol strains inevitably encounter heavy metal excess stress during the product's processing and application. Bacillus amyloliquefaciens Bam1 was a potential biocontrol strain with strong heavy metal resistant ability. To understand its heavy metal resistance mechanism, the complete genome of Bam1 had been sequenced, and the comparative genomic analysis of Bam1 and FZB42, an industrialized PGPR and biocontrol strain with relatively lower heavy metal tolerance, was conducted. The comparative genomic analysis of Bam1 and the other nine B. amyloliquefaciens strains as well as one Bacillus velezensis (genetically and physiologically very close to B. amyloliquefaciens) was also performed. Our results showed that the complete genome size of Bam1 was 3.95 Mb, 4219 coding sequences were predicted, and it possessed the highest number of unique genes among the eleven analyzed strains. Nine genes related to heavy metal resistance were detected within the twelve DNA islands of Bam1, while only two of them were detected within the seventeen DNA islands of FZB42. When compared with B. amyloliquefaciens type strain DSM7, Bam1 lacked contig L, whereas FZB42 lacked contig D and I, as well as just possessed contig B with a very small size. Our results could also deduce that Bam1 promoted its essential heavy metal resistance mainly by decreasing the import and increasing the export of heavy metals with the corresponding homeostasis systems, which are regulated by different metalloregulators. While Bam1 promoted its non-essential heavy metal resistance mainly by the activation of some specific or non-specific exporters responding to different heavy metals. The variation of the genes related to heavy metal resistance and the other differences of the genomes, including the different number and arrangement of contigs, as well as the number of the heavy metal resistant genes in Prophages and Genomic islands, led to the significant different resistance of Bam1 and FZB42 to heavy metals.
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Affiliation(s)
- Yuanchan Luo
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Lei Chen
- Department of Plant Quarantine, Shanghai Extension and Service Center of Agriculture Technology, Shanghai, 201103, China
| | - Zhibo Lu
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Weijian Zhang
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Wentong Liu
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Yuwei Chen
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Xinran Wang
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Wei Du
- Agricultural Technology Extension Station of Ningxia, 2, West Shanghai Road, Yinchuan, 750001, China
| | - Jinyan Luo
- Department of Plant Quarantine, Shanghai Extension and Service Center of Agriculture Technology, Shanghai, 201103, China.
| | - Hui Wu
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai, 200237, China.
- Key Laboratory of Bio-Based Material Engineering of China National Light Industry Council, 130 Meilong Road, Shanghai, 200237, China.
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Cruz-Magalhães V, Guimarães RA, da Silva JC, de Faria AF, Pedroso MP, Campos VP, Marbach PA, de Medeiros FH, De Souza JT. The combination of two Bacillus strains suppresses Meloidogyne incognita and fungal pathogens, but does not enhance plant growth. PEST MANAGEMENT SCIENCE 2022; 78:722-732. [PMID: 34689397 DOI: 10.1002/ps.6685] [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: 07/06/2021] [Revised: 09/18/2021] [Accepted: 10/24/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The combination of biocontrol agents is a desirable strategy to improve control efficacy against the root-knot nematode (RKN) Meloidogyne incognita under field conditions. However, strains compatibility is generally tested in vitro and incompatible combinations are normally not further examined in experiments in planta. Therefore, there is virtually no information on the performance of incompatible strains. In this study, we evaluated two Bacillus strains previously described as incompatible in vitro for effects on plant growth and suppression of M. incognita, pathogenic fungi and nematophagous fungi. RESULTS Strains BMH and INV were shown to be closely related to Bacillus velezensis. These strains, when applied individually, reduced the number of galls and eggs of M. incognita by more than 90% in tomato roots. When BMH and INV were combined (BMH + INV), RKN suppression and tomato shoot weight were lower compared to single-strain applications. Additionally, metabolites in cell-free supernatants and volatile organic compounds (VOCs) from strains BMH and INV had strong effects against the plant pathogens M. incognita, Fusarium oxysporum, Rhizoctonia solani and Sclerotium rolfsiii, but not against three species of nematophagous fungi. Although strain INV and the combination BMH + INV emitted fewer VOCs than strain BMH, they were still capable of killing second-stage juveniles of M. incognita. CONCLUSIONS Bacillus strains BMH and INV inhibited M. incognita and fungal pathogens, and promoted tomato growth. However, strain INV emitted fewer VOCs and the combination BMH + INV did not enhance the activity of the biocontrol strains against the RKN or their capacity to promote plant growth. © 2021 Society of Chemical Industry.
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Affiliation(s)
| | - Rafaela A Guimarães
- Department of Phytopathology, Universidade Federal de Lavras, Lavras, Brazil
| | - Julio Cp da Silva
- Department of Phytosanitary Defense, CCR, Universidade Federal de Santa Maria, Santa Maria, Brazil
| | - Amanda F de Faria
- Department of Phytopathology, Universidade Federal de Lavras, Lavras, Brazil
| | - Márcio P Pedroso
- Department of Chemistry, Universidade Federal de Lavras, Lavras, Brazil
| | - Vicente P Campos
- Department of Phytopathology, Universidade Federal de Lavras, Lavras, Brazil
| | - Phellippe As Marbach
- Center for Agricultural, Biological and Environmental Sciences, Universidade Federal do Recôncavo da Bahia, Cruz das Almas, Brazil
| | | | - Jorge T De Souza
- Department of Phytopathology, Universidade Federal de Lavras, Lavras, Brazil
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R S, Nakkeeran S, Saranya N, Senthilraja C, Renukadevi P, Krishnamoorthy A, El Enshasy HA, El-Adawi H, Malathi V, Salmen SH, Ansari MJ, Khan N, Sayyed RZ. Mining the Genome of Bacillus velezensis VB7 (CP047587) for MAMP Genes and Non-Ribosomal Peptide Synthetase Gene Clusters Conferring Antiviral and Antifungal Activity. Microorganisms 2021; 9:microorganisms9122511. [PMID: 34946111 PMCID: PMC8708206 DOI: 10.3390/microorganisms9122511] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 11/25/2021] [Accepted: 11/30/2021] [Indexed: 11/16/2022] Open
Abstract
Chemical pesticides have an immense role in curbing the infection of plant viruses and soil-borne pathogens of high valued crops. However, the usage of chemical pesticides also contributes to the development of resistance among pathogens. Hence, attempts were made in this study to identify a suitable bacterial antagonist for managing viral and fungal pathogens infecting crop plants. Based on our earlier investigations, we identified Bacillus amyloliquefaciens VB7 as a potential antagonist for managing Sclerotinia sclerotiorum infecting carnation, tobacco streak virus infecting cotton and groundnut bud necrosis infecting tomato. Considering the multifaceted action of B. amyloliquefaciens VB7, attempts were made for whole-genome sequencing to assess the antiviral activity against tomato spotted wilt virus infecting chrysanthemum and antifungal action against Fusarium oxysporum f. sp. cubense (Foc). Genome annotation of the isolate B. amyloliquefaciens VB7 was confirmed as B. velezensis VB7 with accession number CP047587. Genome analysis revealed the presence of 9,231,928 reads with an average read length of 149 bp. Assembled genome had 1 contig, with a total length of 3,021,183 bp and an average G+C content of 46.79%. The protein-coding sequences (CDS) in the genome was 3090, transfer RNA (tRNA) genes were 85 with 29 ribosomal RNA (rRNA) genes and 21 repeat regions. The genome of B. velezensis VB7 had 506 hypothetical proteins and 2584 proteins with functional assignments. VB7 genome had the presence of flagellin protein FlaA with 987 nucleotides and translation elongation factor TU (Ef-Tu) with 1191 nucleotides. The identified ORFs were 3911 with 47.22% GC content. Non ribosomal pepide synthetase cluster (NRPS) gene clusters in the genome of VB7, coded for the anti-microbial peptides surfactin, butirosin A/butirosin B, fengycin, difficidin, bacillibactin, bacilysin, and mersacidin the Ripp lanthipeptide. Antiviral action of VB7 was confirmed by suppression of local lesion formation of TSWV in the local lesion host cowpea (Co-7). Moreover, combined application of B. velezensis VB7 with phyto-antiviral principles M. Jalapa and H. cupanioides increased shoot length, shoot diameter, number of flower buds per plant, flower diameter, and fresh weight of chrysanthemum. Further, screening for antifungal action of VB7 expressed antifungal action against Foc in vitro by producing VOC/NVOC compounds, including hexadecanoic acid, linoelaidic acid, octadecanoic acid, clindamycin, formic acid, succinamide, furanone, 4H-pyran, nonanol and oleic acid, contributing to the total suppression of Foc apart from the presence of NRPS gene clusters. Thus, our study confirmed the scope for exploring B. velezensis VB7 on a commercial scale to manage tomato spotted wilt virus, groundnut bud necrosis virus, tobacco streak virus, S. sclerotiorum, and Foc causing panama wilt of banana.
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Affiliation(s)
- Saravanan R
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.R.); (C.S.); (P.R.); (A.S.K.); (V.G.M.)
| | - S Nakkeeran
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.R.); (C.S.); (P.R.); (A.S.K.); (V.G.M.)
- Correspondence: (S.N.); (R.Z.S.)
| | - N Saranya
- Department of Plant Biotechnology and Bioinformatics, Tamil Nadu Agricultural University, Coimbatore 641003, India;
| | - C Senthilraja
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.R.); (C.S.); (P.R.); (A.S.K.); (V.G.M.)
| | - P Renukadevi
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.R.); (C.S.); (P.R.); (A.S.K.); (V.G.M.)
| | - A.S. Krishnamoorthy
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.R.); (C.S.); (P.R.); (A.S.K.); (V.G.M.)
| | - Hesham Ali El Enshasy
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.R.); (C.S.); (P.R.); (A.S.K.); (V.G.M.)
- Institute of Bioproduct Development (IBD), Universiti Teknologi Malaysia (UTM), Skudai, Johor Bahru 81310, Malaysia;
- Faculty of Engineering School of Chemical and Energy Engineering, Universiti Teknologi Malaysia (UTM), Skudai, Johor Bahru 81310, Malaysia
- City of Scientific Research and Technology Applications (SRTA), New Burg Al Arab, Alexandria 21934, Egypt;
| | - Hala El-Adawi
- City of Scientific Research and Technology Applications (SRTA), New Burg Al Arab, Alexandria 21934, Egypt;
| | - V.G. Malathi
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.R.); (C.S.); (P.R.); (A.S.K.); (V.G.M.)
| | - Saleh H. Salmen
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia;
| | - M. J. Ansari
- Department of Botany, Hindu College Moradabad (Mahatma Jyotiba Phule Rohilkhand University, Bareilly 244001, India;
| | - Naeem Khan
- Department of Agronomy, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA;
| | - R. Z. Sayyed
- Department of Microbiology, PSGVP Mandal’s Arts, Science, and Commerce College, Shahada 425409, India
- Asian PGPR Society for Sustainable Agriculture, Auburn University, Auburn, AL 36830, USA
- Correspondence: (S.N.); (R.Z.S.)
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Sultana OF, Lee S, Seo H, Mahmud HA, Kim S, Seo A, Kim M, Song HY. Biodegradation and Removal of PAHs by Bacillus velezensis Isolated from Fermented Food. J Microbiol Biotechnol 2021; 31:999-1010. [PMID: 34024889 PMCID: PMC9705940 DOI: 10.4014/jmb.2104.04023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 12/15/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous in the environment. They are highly toxigenic and carcinogenic. Probiotic bacteria isolated from fermented foods were tested to check their ability to degrade and/or detoxify PAHs. Five probiotic bacteria with distinct morphologies were isolated from a mixture of 26 fermented foods co-cultured with benzo(a)pyrene (BaP) containing Bushnell Haas minimal broth. Among them, B. velezensis (PMC10) significantly reduced the abundance of BaP in the broth. PMC10 completely degraded BaP presented at a lower concentration in broth culture. B. velezensis also showed a clear zone of degradation on a BaP-coated Bushnell Haas agar plate. Gene expression profiling showed significant increases of PAH ringhydroxylating dioxygenases and 4-hydroxybenzoate 3-monooxygenase genes in B. velezensis in response to BaP treatment. In addtion, both live and heat-killed B. velezensis removed BaP and naphthalene (Nap) from phosphate buffer solution. Live B. velezensis did not show any cytotoxicity to macrophage or human dermal fibroblast cells. Live-cell and cell-free supernatant of B. velezensis showed potential anti-inflammatory effects. Cell-free supernatant and extract of B. velezensis also showed free radical scavenging effects. These results highlight the prospective ability of B. velezensis to biodegrade and remove toxic PAHs from the human body and suggest that the biodegradation of BaP might be regulated by ring-hydroxylating dioxygenase-initiated metabolic pathway.
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Affiliation(s)
- Omme Fatema Sultana
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea
| | - Saebim Lee
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan 31538, Republic of Korea
| | - Hoonhee Seo
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan 31538, Republic of Korea
| | - Hafij Al Mahmud
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan 31538, Republic of Korea
| | - Sukyung Kim
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan 31538, Republic of Korea
| | - Ahyoung Seo
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan 31538, Republic of Korea
| | - Mijung Kim
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan 31538, Republic of Korea
| | - Ho-Yeon Song
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea,Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan 31538, Republic of Korea,Corresponding author Phone: +82-41-570-2412 Fax: +82-41-577-2415 E-mail:
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Hou Q, Kolodkin-Gal I. Harvesting the complex pathways of antibiotic production and resistance of soil bacilli for optimizing plant microbiome. FEMS Microbiol Ecol 2021; 96:5872479. [PMID: 32672816 DOI: 10.1093/femsec/fiaa142] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/13/2020] [Indexed: 01/04/2023] Open
Abstract
A sustainable future increasing depends on our capacity to utilize beneficial plant microbiomes to meet our growing needs. Plant microbiome symbiosis is a hallmark of the beneficial interactions between bacteria and their host. Specifically, colonization of plant roots by biocontrol agents and plant growth-promoting bacteria can play an important role in maintaining the optimal rhizosphere environment, supporting plant growth and promoting its fitness. Rhizosphere communities confer immunity against a wide range of foliar diseases by secreting antibiotics and activating plant defences. At the same time, the rhizosphere is a highly competitive niche, with multiple microbial species competing for space and resources, engaged in an arms race involving the production of a vast array of antibiotics and utilization of a variety of antibiotic resistance mechanisms. Therefore, elucidating the mechanisms that govern antibiotic production and resistance in the rhizosphere is of great significance for designing beneficial communities with enhanced biocontrol properties. In this review, we used Bacillus subtilis and B. amyloliquefaciens as models to investigate the genetics of antibiosis and the potential for its translation of into improved plant microbiome performance.
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Affiliation(s)
- Qihui Hou
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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Choi J, Nam J, Seo MH. Complete genome sequence of Bacillus velezensis NST6 and comparison with the species belonging to operational group B. amyloliquefaciens. Genomics 2020; 113:380-386. [PMID: 33316360 DOI: 10.1016/j.ygeno.2020.12.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/06/2020] [Accepted: 12/06/2020] [Indexed: 01/12/2023]
Abstract
Bacillus spp. play important roles in production of bioactive natural products with potential agricultural and medical applications. The three families of lipopeptides produced by Bacillus spp. have been most recognized for their antagonistic activity against other microbes, i.e. fengycin, iturin, and surfactin. A novel strain NST6 was isolated from soil and identified as B. velezensis based on phylogenomic analysis. Genome analysis revealed 21 putative biosynthetic gene clusters including the ones responsible for producing bacillomycin and surfactin. However, fengycin cluster was compromised with absence or partial disruption of three non-ribosomal peptide synthetases. Distribution of biosynthetic gene clusters showed that clusters for iturin families were well conserved in 327 genomes of the species belonging to the operational group B. amyloliquefaciens. However, clusters for fengycin and surfactin showed dynamic distribution at gene level. Comparative analysis of closely related species would provide new insights to the diversity in genetic elements for secondary metabolites.
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Affiliation(s)
- Jaeyoung Choi
- Smart Farm Research Center, Korea Institute of Science and Technology, Gangneung 25451, Republic of Korea.
| | - Jiyoung Nam
- Natural Product Research Center, Korea Institute of Science and Technology, Gangneung 25451, Republic of Korea
| | - Moon-Hyeong Seo
- Natural Product Research Center, Korea Institute of Science and Technology, Gangneung 25451, Republic of Korea.
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