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Mian S, Machado ACZ, Hoshino RT, Mosela M, Higashi AY, Shimizu GD, Teixeira GM, Nogueira AF, Giacomin RM, Ribeiro LAB, Koltun A, de Assis R, Gonçalves LSA. Complete genome sequence of Bacillus velezensis strain Ag109, a biocontrol agent against plant-parasitic nematodes and Sclerotinia sclerotiorum. BMC Microbiol 2024; 24:194. [PMID: 38849775 PMCID: PMC11157790 DOI: 10.1186/s12866-024-03282-9] [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: 05/17/2023] [Accepted: 03/28/2024] [Indexed: 06/09/2024] Open
Abstract
Soybean is the main oilseed cultivated worldwide. Even though Brazil is the world's largest producer and exporter of soybean, its production is severely limited by biotic factors. Soil borne diseases are the most damaging biotic stressors since they significantly reduce yield and are challenging to manage. In this context, the present study aimed to evaluate the potential of a bacterial strain (Ag109) as a biocontrol agent for different soil pathogens (nematodes and fungi) of soybean. In addition, the genome of Ag109 was wholly sequenced and genes related to secondary metabolite production and plant growth promotion were mined. Ag109 showed nematode control in soybean and controlled 69 and 45% of the populations of Meloidogyne javanica and Pratylenchus brachyurus, respectively. Regarding antifungal activity, these strains showed activity against Macrophomia phaseolina, Rhizoctonia solani, and Sclerotinia sclerotiorum. For S. sclerotiorum, this strain increased the number of healthy plants and root dry mass compared to the control (with inoculation). Based on the average nucleotide identity and digital DNA-DNA hybridization, this strain was identified as Bacillus velezensis. Diverse clusters of specific genes related to secondary metabolite biosynthesis and root growth promotion were identified, highlighting the potential of this strain to be used as a multifunctional microbial inoculant that acts as a biological control agent while promoting plant growth in soybean.
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Affiliation(s)
- Silas Mian
- Agronomy Department, Universidade Estadual de Londrina, Londrina, Paraná, 86097-570, Brazil
| | | | - Rodrigo Thibes Hoshino
- Agronomy Department, Universidade Estadual de Londrina, Londrina, Paraná, 86097-570, Brazil
| | - Mirela Mosela
- Microbiology Department, Universidade Estadual de Londrina, Londrina, Paraná, 86097-570, Brazil
| | - Allan Yukio Higashi
- Agronomy Department, Universidade Estadual de Londrina, Londrina, Paraná, 86097-570, Brazil
| | - Gabriel Danilo Shimizu
- Agronomy Department, Universidade Estadual de Londrina, Londrina, Paraná, 86097-570, Brazil
| | - Gustavo Manoel Teixeira
- Microbiology Department, Universidade Estadual de Londrina, Londrina, Paraná, 86097-570, Brazil
| | | | - Renata Mussoi Giacomin
- Biology Department, Universidade Estadual Do Centro Oeste, Guarapuava, Paraná, 85015-430, Brazil
| | | | - Alessandra Koltun
- Center for Molecular Biology and Genetic Engineering, UNICAMP, Campinas, São Paulo, 13083-875, Brazil
| | - Rafael de Assis
- Agronomy Department, Universidade Estadual de Londrina, Londrina, Paraná, 86097-570, Brazil
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Han KI, Nam YH, Hwang BS, Kim JT, Jung JO, Kim E, Lee MH. Characterization of Bacillus velezensis TJS119 and its biocontrol potential against insect pathogens. Front Microbiol 2024; 15:1361961. [PMID: 38784813 PMCID: PMC11111924 DOI: 10.3389/fmicb.2024.1361961] [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: 12/27/2023] [Accepted: 04/18/2024] [Indexed: 05/25/2024] Open
Abstract
Introduction The white-spotted flower chafer (Protaetia brevitarsis seulensis), which is widely distributed in Asian countries, is traditionally used in oriental medicine. However, its larvae are prone to severe damage by green muscardine disease (caused by Metarhizium anisopliae) during breeding. The aim of this study was to characterize Bacillus velezensis TJS119, which has been isolated from freshwater, and investigate its potential as a biocontrol agent against M. anisopliae in insects. Methods TJS119 was obtained from freshwater samples in the Republic of Korea and was classified as B. velezensis. We evaluated its in vitro antifungal effect, sequenced the bacterial whole genome, mined genes responsible for the synthesis of secondary metabolites, performed secondary metabolite analysis Ultra performance liquid chromatography-mass spectrometry (UPLC-MS/MS), and conducted bioassays for determining green muscardine disease control ability. Results Bacillus velezensis TJS119 inhibited the mycelial growth of M. anisopliae in vitro. The size of the B. velezensis TJS119 genome was estimated to be 3,890,913 bp with a GC content of 46.67% and 3,750 coding sequences. Biosynthetic gene clusters for secondary metabolites with antifungal activity were identified in the genome. Lipopeptides, including fengycin secreted by TJS119 exhibit antifungal activity. Application of TJS119 for the biocontrol against green muscardine disease increased the viability of white-spotted flower chafer by 94.7% compared to the control. Discussion These results indicate that B. velezensis TJS119 is a potential biocontrol agent for insect pathogens.
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Affiliation(s)
- Kook-Il Han
- Using Technology Development Department, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju, Republic of Korea
| | - Young Ho Nam
- Using Technology Development Department, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju, Republic of Korea
| | - Byung Su Hwang
- Using Technology Development Department, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju, Republic of Korea
| | - Jeong Tae Kim
- Using Technology Development Department, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju, Republic of Korea
| | - Jum Oc Jung
- Using Technology Development Department, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju, Republic of Korea
| | - Eunsun Kim
- Industrial Insect and Sericulture Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, Republic of Korea
| | - Mi-Hwa Lee
- Using Technology Development Department, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju, Republic of Korea
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Bustamante MI, Elfar K, Eskalen A. Evaluation of the Antifungal Activity of Endophytic and Rhizospheric Bacteria against Grapevine Trunk Pathogens. Microorganisms 2022; 10:microorganisms10102035. [PMID: 36296311 PMCID: PMC9611468 DOI: 10.3390/microorganisms10102035] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/13/2022] [Accepted: 10/13/2022] [Indexed: 11/08/2022] Open
Abstract
Grapevine trunk diseases (GTDs) are caused by multiple unrelated fungal pathogens, and their management remains difficult worldwide. Biocontrol is an attractive and sustainable strategy given the current need for a cleaner viticulture. In this study, twenty commercial vineyards were sampled across California to isolate endophytic and rhizospheric bacteria from different grapevine cultivars with the presence and absence of GTD symptoms. A collection of 1344 bacterial isolates were challenged in vitro against Neofusicoccum parvum and Diplodia seriata, from which a subset of 172 isolates exerted inhibition levels of mycelial growth over 40%. Bacterial isolates were identified as Bacillus velezensis (n = 154), Pseudomonas spp. (n = 12), Serratia plymuthica (n = 2) and others that were later excluded (n = 4). Representative isolates of B. velezensis, P. chlororaphis, and S. plymuthica were challenged against six other fungal pathogens responsible for GTDs. Mycelial inhibition levels were consistent across bacterial species, being slightly higher against slow-growing fungi than against Botryosphaeriaceae. Moreover, agar-diffusible metabolites of B. velezensis strongly inhibited the growth of N. parvum and Eutypa lata, at 1, 15, and 30% v/v. The agar-diffusible metabolites of P. chlororaphis and S. plymuthica, however, caused lower inhibition levels against both pathogens, but their volatile organic compounds showed antifungal activity against both pathogens. These results suggest that B. velezensis, P. chlororaphis and S. plymuthica constitute potential biocontrol agents (BCAs) against GTDs and their application in field conditions should be further evaluated.
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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: 0] [Impact Index Per Article: 0] [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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Xu W, Yang Q, Yang F, Xie X, Goodwin PH, Deng X, Tian B, Yang L. Evaluation and Genome Analysis of Bacillus subtilis YB-04 as a Potential Biocontrol Agent Against Fusarium Wilt and Growth Promotion Agent of Cucumber. Front Microbiol 2022; 13:885430. [PMID: 35756052 PMCID: PMC9218633 DOI: 10.3389/fmicb.2022.885430] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/06/2022] [Indexed: 12/13/2022] Open
Abstract
Cucumber wilt caused by Fusarium oxysporum f.sp. cucumerinum (Foc) is a highly destructive disease that leads to reduced yield in cucumbers. In this study, strain YB-04 was isolated from wheat straw and identified as Bacillus subtilis. It displayed strong antagonistic activity against F. oxysporum f.sp. cucumerinum in dual culture and exhibited significant biocontrol of cucumber Fusarium wilt with a higher control effect than those of previously reported Bacillus strains and displayed pronounced growth promotion of cucumber seedlings. B. subtilis YB-04 could secrete extracellular protease, amylase, cellulose, and β-1,3-glucanase and be able to produce siderophores and indole acetic acid. Inoculation with B. subtilis YB-04 or Foc increased cucumber defense-related enzyme activities for PPO, SOD, CAT, PAL, and LOX. However, the greatest increase was with the combination of B. subtilis YB-04 and Foc. Sequencing the genome of B. subtilis YB-04 showed that it had genes for the biosynthesis of various secondary metabolites, carbohydrate-active enzymes, and assimilation of nitrogen, phosphorous, and potassium. B. subtilis YB-04 appears to be a promising biological control agent against the Fusarium wilt of cucumber and promotes cucumber growth by genomic, physiological, and phenotypic analysis.
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Affiliation(s)
- Wen Xu
- Henan International Joint Laboratory of Crop Protection, Henan Biopesticide Engineering Research Center, Institute of Plant Protection Research, Graduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Qian Yang
- Henan International Joint Laboratory of Crop Protection, Henan Biopesticide Engineering Research Center, Institute of Plant Protection Research, Graduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Zhengzhou, China.,School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Fan Yang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xia Xie
- Henan International Joint Laboratory of Crop Protection, Henan Biopesticide Engineering Research Center, Institute of Plant Protection Research, Graduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Paul H Goodwin
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Xiaoxu Deng
- Henan International Joint Laboratory of Crop Protection, Henan Biopesticide Engineering Research Center, Institute of Plant Protection Research, Graduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Baoming Tian
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Lirong Yang
- Henan International Joint Laboratory of Crop Protection, Henan Biopesticide Engineering Research Center, Institute of Plant Protection Research, Graduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Zhengzhou, China
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Genome analysis uncovers the prolific antagonistic and plant growth-promoting potential of endophyte Bacillus velezensis K1. Gene 2022; 836:146671. [PMID: 35714801 DOI: 10.1016/j.gene.2022.146671] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 05/23/2022] [Accepted: 06/10/2022] [Indexed: 11/24/2022]
Abstract
Insights into the application of endophytic bacilli in sustainable agricultural practices have opened up new avenues for the inhibition of soil-borne pathogens and the improvement of plant health. Bacillus subtilis K1, an endophytic bacterium originally isolated from aerial roots of Ficus benghalensis is a potential biocontrol agent secreting a mixture of surfactins, iturins and fengycins. The current study extends the characterization of this bacterium through genomic and comparative genomics approaches. The sequencing of the bacterial genome at Illumina MiSeq platform revealed that it possessed a 4,103,502-bp circular chromosome with 45.98% GC content and 4325 predicted protein-coding sequences. Based on phylogenomics and whole-genome average nucleotide identity, the B. subtilis K1 was taxonomically classified as Bacillus velezensis. The formerly evaluated phenotypic traits viz. C-source utilization and lipopeptide-mediated fungal antagonism were correlated to their molecular determinants. The genome also harbored several genes associated with induced systemic resistance and plant growth promotion i.e, phytohormone production, nitrogen assimilation and reduction, siderophore production, phosphate solubilization, biofilm formation, swarming motility, acetoin and butanediol synthesis. The production of antifungal volatile organic compounds and plant growth promotion was experimentally demonstrated by volatile compound assay and seed germination assay on cumin and groundnut. The isolate also holds great prospects for application as a soil inoculant as indicated by enhancement in the growth of groundnut via in planta pot studies. Bacterial pan-genome analysis based on a comparison of whole genomes with eighteen other Bacillus strains was also conducted. Comparative examination of biosynthetic gene clusters across all genomes indicated that the largest number of gene clusters were harbored by the K1 genome. Based on the findings, we propose K1 as a model for scrutinizing non-ribosomally synthesized peptide synthetase and polyketide synthetase derived molecules.
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Ge Z, Kuang Z, Chen J, Chen J, Liu T, She Z, Lu Y. Comparative genomics analysis of Bacillus velezensis LOH112 isolated from a nonagenarian provides insights into its biocontrol and probiotic traits. Gene 2022; 835:146644. [PMID: 35680027 DOI: 10.1016/j.gene.2022.146644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/28/2022] [Accepted: 06/02/2022] [Indexed: 11/17/2022]
Abstract
Bacillus velezensis has recently received increasing attention as a biological fungicide and a potential probiotic agent because of its broad spectrum of antibacterial and antifungal activities. Here, we evaluated the beneficial traits of a newly isolated B. velezensis strain LOH112 using comprehensive bioinformatics and comparative genomic analyses and in vitro experimental approaches. Whole genome sequencing and assembly results showed that the genome of LOH112 consists of a circular chromosome and a circular plasmid, which encodes proteins involved in important biological processes such as sporulation, quorum sensing, and antibiotic synthesis. LOH112 contains 13 secondary metabolism gene clusters responsible for the production of antimicrobial compounds. In vitro experiments showed that LOH112 effectively inhibits several fungi and Gram-positive pathogenic bacteria, hydrolyzes protein and cellulose, and is capable of forming strong adhesive biofilms. Furthermore, comparative genomics revealed that LOH112 contains 34 strain-specific orthologous gene clusters, including two caseinolytic protease P (clpP) genes responsible for proteomic homeostasis. Selective pressure analysis indicated that the transmembrane transporter and ATP-dependent alanine/valine adenylase genes were strongly positively selected, which may endow LOH112 with better biocontrol ability and potential probiotic properties. Collectively, these results not only provide insights into a deeper understanding of the genomic characterization of LOH112 but also imply the potential application of LOH112 as biocontrol and probiotic agents.
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Affiliation(s)
- Zhenhuang Ge
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; School of Chemistry, Sun Yat-sen University, Guangzhou 510275, China; Run Ze Laboratory for Gastrointestinal Microbiome Study, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhiqi Kuang
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Run Ze Laboratory for Gastrointestinal Microbiome Study, Sun Yat-sen University, Guangzhou 510275, China
| | - Jiahao Chen
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Run Ze Laboratory for Gastrointestinal Microbiome Study, Sun Yat-sen University, Guangzhou 510275, China
| | - Junyi Chen
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Run Ze Laboratory for Gastrointestinal Microbiome Study, Sun Yat-sen University, Guangzhou 510275, China
| | - Tianhao Liu
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Run Ze Laboratory for Gastrointestinal Microbiome Study, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhigang She
- School of Chemistry, Sun Yat-sen University, Guangzhou 510275, China
| | - Yongjun Lu
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Run Ze Laboratory for Gastrointestinal Microbiome Study, Sun Yat-sen University, Guangzhou 510275, China.
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Amarouchi Z, Esmaeel Q, Sanchez L, Jacquard C, Hafidi M, Vaillant-Gaveau N, Ait Barka E. Beneficial Microorganisms to Control the Gray Mold of Grapevine: From Screening to Mechanisms. Microorganisms 2021; 9:microorganisms9071386. [PMID: 34202293 PMCID: PMC8304954 DOI: 10.3390/microorganisms9071386] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 11/16/2022] Open
Abstract
In many vineyards around the world, Botrytis cinerea (B. cinerea) causes one of the most serious diseases of aerial grapevine (Vitis vinifera L.) organs. The control of the disease relies mainly on the use of chemical products whose use is increasingly challenged. To develop new sustainable methods to better resist B. cinerea, beneficial bacteria were isolated from vineyard soil. Once screened based on their antimicrobial effect through an in vivo test, two bacterial strains, S3 and S6, were able to restrict the development of the pathogen and significantly reduced the Botrytis-related necrosis. The photosynthesis analysis showed that the antagonistic strains also prevent grapevines from considerable irreversible PSII photo-inhibition four days after infection with B. cinerea. The 16S rRNA gene sequences of S3 exhibited 100% similarity to Bacillus velezensis, whereas S6 had 98.5% similarity to Enterobacter cloacae. On the other hand, the in silico analysis of the whole genome of isolated strains has revealed the presence of “biocontrol-related” genes supporting their plant growth and biocontrol activities. The study concludes that those bacteria could be potentially useful as a suitable biocontrol agent in harvested grapevine.
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Affiliation(s)
- Zakaria Amarouchi
- Université de Reims Champagne-Ardenne, RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France; (Z.A.); (Q.E.); (L.S.); (C.J.); (N.V.-G.)
- Laboratoire de Biotechnologie Végétale et Valorisation des Bio-Ressources, Faculté des Sciences, Université Moulay Ismail, Meknès B.P. 11201, Morocco;
| | - Qassim Esmaeel
- Université de Reims Champagne-Ardenne, RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France; (Z.A.); (Q.E.); (L.S.); (C.J.); (N.V.-G.)
| | - Lisa Sanchez
- Université de Reims Champagne-Ardenne, RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France; (Z.A.); (Q.E.); (L.S.); (C.J.); (N.V.-G.)
| | - Cédric Jacquard
- Université de Reims Champagne-Ardenne, RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France; (Z.A.); (Q.E.); (L.S.); (C.J.); (N.V.-G.)
| | - Majida Hafidi
- Laboratoire de Biotechnologie Végétale et Valorisation des Bio-Ressources, Faculté des Sciences, Université Moulay Ismail, Meknès B.P. 11201, Morocco;
| | - Nathalie Vaillant-Gaveau
- Université de Reims Champagne-Ardenne, RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France; (Z.A.); (Q.E.); (L.S.); (C.J.); (N.V.-G.)
| | - Essaid Ait Barka
- Université de Reims Champagne-Ardenne, RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France; (Z.A.); (Q.E.); (L.S.); (C.J.); (N.V.-G.)
- Correspondence: ; Tel.: +33-326913221
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de Carvalho Silveira T, Gomes WE, Tonon GC, Beatto TG, Spogis N, Cunha LHD, Lattaro BP, Nogueira AB, Mendes RK, Alvarenga DO, Etchegaray A. Residual biomass from surfactin production is a source of arginase and adsorbed surfactin that is useful for environmental remediation. World J Microbiol Biotechnol 2021; 37:123. [PMID: 34160683 DOI: 10.1007/s11274-021-03094-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 06/01/2021] [Indexed: 10/21/2022]
Abstract
Lipopeptides are important secondary metabolites produced by microbes. They find applications in environmental decontamination and in the chemical, pharmaceutical and food industries. However, their production is expensive. In the present work we propose three strategies to lower the production costs of surfactin. First, the coproduction of surfactin and arginase in a single growth. Second, extract the fraction of surfactin that adsorbs to the biomass and is removed from the growth medium through centrifugation. Third, use microbial biomass for the remediation of organic and inorganic contaminants. The coproduction of surfactin and arginase was evaluated by factorial design experiments using the LB medium supplemented with arginine. The best conditions for surfactin production were 22 h of growth at 37 °C using LB supplemented with arginine 7.3 g/L. Almost similar conditions were found to produce highest levels of arginase, 24 h and 6.45 g/L arginine. Decontamination of phenol and copper from artificial samples was attained by treatment with residues from lipopeptide production. Thus, cell suspensions and wash-waters used to extract surfactin from the biomass. Cell suspensions were used to successfully remove hydroquinone. Cell suspensions and wash-waters containing surfactin were successfully used to recover copper from solution. Specific monitoring methods were used for phenol and metal solutions, respectively a biosensor based on tyrosinase and either atomic absorption flame ionization spectrometry or absorbance coupled to the Arduino™ platform. Therefore, we report three alternative strategies to lower the production costs in lipopeptide production, which include the effective recovery of copper and phenol from contaminated waters using residues from surfactin production. Sustainable and profitable production of surfactin can be achieved by a coproduction strategy of lipopeptides and enzymes. Lipopeptides are collected in the supernatant and enzymes in the biomass. In addition, lipopeptides that coprecipitate with biomass can be recovered by washing. Lipopeptide wash-waters find applications in remediation and cells can also be used for environmental decontamination.
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Affiliation(s)
- Thais de Carvalho Silveira
- Programa de Pós-Graduação em Ciências da Saúde, Centro de Ciências da Vida, Pontifícia Universidade Católica de Campinas, Campinas, SP, Brasil
| | - Wyllerson Evaristo Gomes
- Programa de Pós-Graduação em Sistemas de Infraestrutura Urbana, Centro de Ciências Ambientais e de Tecnologias, Pontifícia Universidade Católica de Campinas, Campinas, SP, Brasil
| | - Giovana Chinaglia Tonon
- Faculdade de Química, Centro de Ciências Ambientais e de Tecnologias, Pontifícia Universidade Católica de Campinas (PUC-Campinas), Rua Professor Doutor Euryclides de Jesus Zerbini n° 1.516, Parque Rural Fazenda Santa Cândida, CEP 13087571, Campinas, SP, Brasil
| | - Thainá Godoy Beatto
- Programa de Pós-Graduação em Sistemas de Infraestrutura Urbana, Centro de Ciências Ambientais e de Tecnologias, Pontifícia Universidade Católica de Campinas, Campinas, SP, Brasil.,Faculdade de Química, Centro de Ciências Ambientais e de Tecnologias, Pontifícia Universidade Católica de Campinas (PUC-Campinas), Rua Professor Doutor Euryclides de Jesus Zerbini n° 1.516, Parque Rural Fazenda Santa Cândida, CEP 13087571, Campinas, SP, Brasil
| | - Nicolas Spogis
- Faculdade de Química, Centro de Ciências Ambientais e de Tecnologias, Pontifícia Universidade Católica de Campinas (PUC-Campinas), Rua Professor Doutor Euryclides de Jesus Zerbini n° 1.516, Parque Rural Fazenda Santa Cândida, CEP 13087571, Campinas, SP, Brasil
| | - Luiz Henrique Dallan Cunha
- Faculdade de Química, Centro de Ciências Ambientais e de Tecnologias, Pontifícia Universidade Católica de Campinas (PUC-Campinas), Rua Professor Doutor Euryclides de Jesus Zerbini n° 1.516, Parque Rural Fazenda Santa Cândida, CEP 13087571, Campinas, SP, Brasil
| | - Bruno Pera Lattaro
- Faculdade de Química, Centro de Ciências Ambientais e de Tecnologias, Pontifícia Universidade Católica de Campinas (PUC-Campinas), Rua Professor Doutor Euryclides de Jesus Zerbini n° 1.516, Parque Rural Fazenda Santa Cândida, CEP 13087571, Campinas, SP, Brasil
| | - Alessandra Borin Nogueira
- Faculdade de Química, Centro de Ciências Ambientais e de Tecnologias, Pontifícia Universidade Católica de Campinas (PUC-Campinas), Rua Professor Doutor Euryclides de Jesus Zerbini n° 1.516, Parque Rural Fazenda Santa Cândida, CEP 13087571, Campinas, SP, Brasil
| | - Renata Kelly Mendes
- Programa de Pós-Graduação em Sistemas de Infraestrutura Urbana, Centro de Ciências Ambientais e de Tecnologias, Pontifícia Universidade Católica de Campinas, Campinas, SP, Brasil.,Faculdade de Química, Centro de Ciências Ambientais e de Tecnologias, Pontifícia Universidade Católica de Campinas (PUC-Campinas), Rua Professor Doutor Euryclides de Jesus Zerbini n° 1.516, Parque Rural Fazenda Santa Cândida, CEP 13087571, Campinas, SP, Brasil
| | | | - Augusto Etchegaray
- Programa de Pós-Graduação em Ciências da Saúde, Centro de Ciências da Vida, Pontifícia Universidade Católica de Campinas, Campinas, SP, Brasil. .,Faculdade de Química, Centro de Ciências Ambientais e de Tecnologias, Pontifícia Universidade Católica de Campinas (PUC-Campinas), Rua Professor Doutor Euryclides de Jesus Zerbini n° 1.516, Parque Rural Fazenda Santa Cândida, CEP 13087571, Campinas, SP, Brasil.
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10
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Comparative genomic and secretomic characterisation of endophytic Bacillus velezensis LC1 producing bioethanol from bamboo lignocellulose. Arch Microbiol 2021; 203:3089-3099. [PMID: 33792738 DOI: 10.1007/s00203-021-02306-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/30/2022]
Abstract
Bacillus is an excellent organic matter degrader, and it has exhibited various abilities required for lignocellulose degradation. Several B. velezensis strains encode lignocellulosases, however their ability to efficiently transform biomass has not been appreciated. In the present study, through the comparative genomic analysis of the whole genome sequences of 21 B. velezensis strains, CAZyome related to lignocellulose degradation was identified and their similarities and differences were compared. Subsequently, the secretome of B. velezensis LC1 by liquid chromatography-tandem mass spectrometry (LC-MS/MS) were identified and confirmed that a considerable number of proteins were involved in lignocellulose degradation. Moreover, after 6-day treatment, the degradation efficiency of the B. velezensis LC1 toward cellulose, hemicellulose and lignin were 59.90%, 75.44% and 23.41%, respectively, the hydrolysate was subjected to ethanol fermentation with Saccharomyces cerevisiae and Escherichia coli KO11, yielded 10.44 g/L ethanol after 96 h. These results indicate that B. velezensis LC1 has the ability to effectively degrade bamboo lignocellulose and has the potential to be used in bioethanol production.
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11
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Ngalimat MS, Yahaya RSR, Baharudin MMAA, Yaminudin SM, Karim M, Ahmad SA, Sabri S. A Review on the Biotechnological Applications of the Operational Group Bacillus amyloliquefaciens. Microorganisms 2021; 9:microorganisms9030614. [PMID: 33802666 PMCID: PMC8002464 DOI: 10.3390/microorganisms9030614] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/27/2022] Open
Abstract
Bacteria under the operational group Bacillus amyloliquefaciens (OGBa) are all Gram-positive, endospore-forming, and rod-shaped. Taxonomically, the OGBa belongs to the Bacillus subtilis species complex, family Bacillaceae, class Bacilli, and phylum Firmicutes. To date, the OGBa comprises four bacterial species: Bacillus amyloliquefaciens, Bacillus siamensis, Bacillus velezensis and Bacillus nakamurai. They are widely distributed in various niches including soil, plants, food, and water. A resurgence in genome mining has caused an increased focus on the biotechnological applications of bacterial species belonging to the OGBa. The members of OGBa are known as plant growth-promoting bacteria (PGPB) due to their abilities to fix nitrogen, solubilize phosphate, and produce siderophore and phytohormones, as well as antimicrobial compounds. Moreover, they are also reported to produce various enzymes including α-amylase, protease, lipase, cellulase, xylanase, pectinase, aminotransferase, barnase, peroxidase, and laccase. Antimicrobial compounds that able to inhibit the growth of pathogens including non-ribosomal peptides and polyketides are also produced by these bacteria. Within the OGBa, various B. velezensis strains are promising for use as probiotics for animals and fishes. Genome mining has revealed the potential applications of members of OGBa for removing organophosphorus (OPs) pesticides. Thus, this review focused on the applicability of members of OGBa as plant growth promoters, biocontrol agents, probiotics, bioremediation agents, as well as producers of commercial enzymes and antibiotics. Here, the bioformulations and commercial products available based on these bacteria are also highlighted. This review will better facilitate understandings of members of OGBa and their biotechnological applications.
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Affiliation(s)
- Mohamad Syazwan Ngalimat
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (M.S.N.); (R.S.R.Y.); (M.M.A.-a.B.)
| | - Radin Shafierul Radin Yahaya
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (M.S.N.); (R.S.R.Y.); (M.M.A.-a.B.)
| | - Mohamad Malik Al-adil Baharudin
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (M.S.N.); (R.S.R.Y.); (M.M.A.-a.B.)
| | - Syafiqah Mohd. Yaminudin
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (S.M.Y.); (M.K.)
| | - Murni Karim
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (S.M.Y.); (M.K.)
- Laboratory of Sustainable Aquaculture, International Institute of Aquaculture and Aquatic Sciences, Universiti Putra Malaysia, Port Dickson 71050, Negeri Sembilan, Malaysia
| | - Siti Aqlima Ahmad
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia;
| | - Suriana Sabri
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (M.S.N.); (R.S.R.Y.); (M.M.A.-a.B.)
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Correspondence: ; Tel.: +603-97698298
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12
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Chen L, Zhao Z, Yu W, Zheng L, Li L, Gu W, Xu H, Wei B, Yan X. Nutritional quality improvement of soybean meal by Bacillus velezensis and Lactobacillus plantarum during two-stage solid- state fermentation. AMB Express 2021; 11:23. [PMID: 33547539 PMCID: PMC7865068 DOI: 10.1186/s13568-021-01184-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 01/23/2021] [Indexed: 02/07/2023] Open
Abstract
Bacillus velezensis is widely used for agricultural biocontrol, due to its ability to enhance plant growth while suppressing the growth of microbial pathogens. However, there are few reports on its application in fermented feed. Here, a two-stage solid-state fermentation process using Bacillus velezensis followed by Lactobacillus plantarum was developed to degrade antinutritional factors (ANFs) and improve soybean meal (SBM) nutrition for animal feed. The process was evaluated for performance in degrading SBM antinutritional factors, dynamic changes in physicochemical characteristics, microorganisms and metabolites. After two-stage fermentation, degradation rates of glycinin and β-conglycinin contents reached 78.60% and 72.89%, respectively. The pH of fermented SBM (FSBM) decreased to 4.78 ± 0.04 and lactic acid content reached 183.38 ± 4.86 mmol/kg. NSP-degrading enzymes (Non-starch polysaccharide, NSPases) and protease were detected from the fermented product, which caused the changed microstructure of SBM. Compared to uninoculated SBM, FSBM exhibited increased proportions of crude protein (51.97 ± 0.44% vs. 47.28 ± 0.34%), Ca, total phosphorus (P), and trichloroacetic acid-soluble protein (11.79 ± 0.13% vs. 5.07 ± 0.06%). Additionally, cellulose and hemicellulose proportions declined by 22.10% and 39.15%, respectively. Total amino acid content increased by 5.05%, while the difference of AA content between the 24 h, 48 h and 72 h of fermentation was not significant (P > 0.05). Furthermore, FSBM also showed antibacterial activity against Staphylococcus aureus and Escherichia coli. These results demonstrated that two-stage SBM fermentation process based on Bacillus velezensis 157 and Lactobacillus plantarum BLCC2-0015 is an effective approach to reduce ANFs content and improve the quality of SBM feed.
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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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14
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Complete genome sequence and antimicrobial activity of Bacillus velezensis JT3-1, a microbial germicide isolated from yak feces. 3 Biotech 2020; 10:231. [PMID: 32399381 DOI: 10.1007/s13205-020-02235-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/27/2020] [Indexed: 12/12/2022] Open
Abstract
Bacillus velezensis JT3-1 was isolated from feces of the domestic yak (Bos grunniens) in Gansu province of China. Aim to know whether B. velezensis JT3-1 has the potency to be developed as a probiotic bacterium, works on the complete genome sequence, antimicrobial activity, growth performance in calves, and treatment effect on calf diarrhea of B. velezensis JT3-1 were carried out. The results showed that the complete genome of B. velezensis JT3-1 contains one gapless circular chromosome which is 3,929,799 bp, and has 3761 protein-encoding genes with an average GC content of 46.50%. From the antimicrobial activity results, B. velezensis JT3-1 has shown strong antagonistic activities against Listeria monocytogenes, Staphylococcus aureus, Escherichia coli, Salmonella Typhimurium, Mannheimia haemolytica, Staphylococcus hominis, Clostridium perfringens, and Mycoplasma bovis. Compared with the control group, the average weight of the experiment animals from Bv1 group and Bv2 group which were supplemented with B. velezensis JT3-1 was significantly increased (P < 0.05). Meanwhile, the Bv1 and Bv2 supplement significantly improved the level of IgA, IgG, IgM, and IFN-γ in calves as compared with the controls (P < 0.05), but the IL-2 level was not obviously changed between the three groups. In addition, B. velezensis JT3-1 showed a good effect against diarrhea, as the cure rate reached 95.0% (171/180) in newborn calves (Angus cattle) in Xinjiang, and 100.0% (149/149) in yak calves in Qinghai, respectively. Our study will lay a good foundation for the elucidation of the molecular mechanisms of its antimicrobial activity, and supports the hypothesis that JT3-1 has the potential to be developed as a probiotic bacterium in cattle.
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Zeng Q, Xie J, Li Y, Gu X, Wang Q. Draft genome sequence data of Bacillus subtilis strain 9407, isolated from healthy apples in China. Data Brief 2020; 29:105143. [PMID: 32140503 PMCID: PMC7052065 DOI: 10.1016/j.dib.2020.105143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/24/2019] [Accepted: 01/10/2020] [Indexed: 11/30/2022] Open
Abstract
Bacillus subtilis strain 9407 is an endophyte which was isolated from healthy apples from an infested orchard that exhibits strong inhibitory activity against Botryosphaeria dothidea. Whole-genome sequencing of B. subtilis 9407 was performed using the Illumina Hiseq platforms. Here, we report the draft genome sequence of B. subtilis strain 9407 containing 16 scaffolds (4,062,615 bp), 4033 coding sequences, and an average 43.66% G + C content. The genome contains genes responsible for the production of several bioactive secondary metabolites, including the lipopeptides fengycin and surfactin. The genome information will provide fundamental knowledge of the organism. This whole-genome shotgun data has been deposited at DDBJ/EMBL/GenBank under the accession numbers PISO00000000.
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Affiliation(s)
- Qingchao Zeng
- College of Plant Protection, Key Laboratory of Plant Pathology, Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Jianbo Xie
- College of Biological Sciences and Technology, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
| | - Yan Li
- College of Plant Protection, Key Laboratory of Plant Pathology, Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Xiaofei Gu
- College of Plant Protection, Key Laboratory of Plant Pathology, Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Qi Wang
- College of Plant Protection, Key Laboratory of Plant Pathology, Ministry of Agriculture, China Agricultural University, Beijing, China
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Pan H, Tian X, Shao M, Xie Y, Huang H, Hu J, Ju J. Genome mining and metabolic profiling illuminate the chemistry driving diverse biological activities of Bacillus siamensis SCSIO 05746. Appl Microbiol Biotechnol 2019; 103:4153-4165. [DOI: 10.1007/s00253-019-09759-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 03/07/2019] [Accepted: 03/10/2019] [Indexed: 10/27/2022]
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17
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Xu WF, Ren HS, Ou T, Lei T, Wei JH, Huang CS, Li T, Strobel G, Zhou ZY, Xie J. Genomic and Functional Characterization of the Endophytic Bacillus subtilis 7PJ-16 Strain, a Potential Biocontrol Agent of Mulberry Fruit Sclerotiniose. MICROBIAL ECOLOGY 2019; 77:651-663. [PMID: 30178387 DOI: 10.1007/s00248-018-1247-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/13/2018] [Indexed: 06/08/2023]
Abstract
Bacillus sp. 7PJ-16, an endophytic bacterium isolated from a healthy mulberry stem and previously identified as Bacillus tequilensis 7PJ-16, exhibits strong antifungal activity and has the capacity to promote plant growth. This strain was studied for its effectiveness as a biocontrol agent to reduce mulberry fruit sclerotiniose in the field and as a growth-promoting agent for mulberry in the greenhouse. In field studies, the cell suspension and supernatant of strain 7PJ-16 exhibited biocontrol efficacy and the lowest disease incidence was reduced down to only 0.80%. In greenhouse experiments, the cell suspension (1.0 × 106 and 1.0 × 105 CFU/mL) and the cell-free supernatant (100-fold and 1000-fold dilution) stimulated mulberry seed germination and promoted mulberry seedling growth. In addition, to accurately identify the 7PJ-16 strain and further explore the mechanisms of its antifungal and growth-promoting properties, the complete genome of this strain was sequenced and annotated. The 7PJ-16 genome is comprised of two circular plasmids and a 4,209,045-bp circular chromosome, containing 4492 protein-coding genes and 116 RNA genes. This strain was ultimately designed as Bacillus subtilis based on core genome sequence analyses using a phylogenomic approach. In this genome, we identified a series of gene clusters that function in the synthesis of non-ribosomal peptides (surfactin, fengycin, bacillibactin, and bacilysin) as well as the ribosome-dependent synthesis of tasA and bacteriocins (subtilin, subtilosin A), which are responsible for the biosynthesis of numerous antimicrobial metabolites. Additionally, several genes with function that promote plant growth, such as indole-3-acetic acid biosynthesis, the production of volatile substances, and siderophores synthesis, were also identified. The information described in this study has established a good foundation for understanding the beneficial interactions between endophytes and host plants, and facilitates the further application of B. subtilis 7PJ-16 as an agricultural biofertilizer and biocontrol agent.
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Affiliation(s)
- Wei-Fang Xu
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, 400715, People's Republic of China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing, 400715, People's Republic of China
| | - Hui-Shuang Ren
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, 400715, People's Republic of China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing, 400715, People's Republic of China
| | - Ting Ou
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, 400715, People's Republic of China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing, 400715, People's Republic of China
| | - Ting Lei
- Institute of Sericulture Science and Technology Research, Chongqing, 400700, People's Republic of China
| | - Jun-Hong Wei
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, 400715, People's Republic of China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing, 400715, People's Republic of China
| | - Chuan-Shu Huang
- Institute of Sericulture Science and Technology Research, Chongqing, 400700, People's Republic of China
| | - Tian Li
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, 400715, People's Republic of China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing, 400715, People's Republic of China
| | - Gary Strobel
- Department of Plant Sciences, Montana State University, Bozeman, MT, 59717, USA
| | - Ze-Yang Zhou
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, 400715, People's Republic of China.
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing, 400715, People's Republic of China.
- College of Life Science, Chongqing Normal University, Chongqing, 400047, People's Republic of China.
| | - Jie Xie
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, 400715, People's Republic of China.
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing, 400715, People's Republic of China.
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18
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Adeniji AA, Loots DT, Babalola OO. Bacillus velezensis: phylogeny, useful applications, and avenues for exploitation. Appl Microbiol Biotechnol 2019; 103:3669-3682. [PMID: 30911788 DOI: 10.1007/s00253-019-09710-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/21/2019] [Accepted: 02/22/2019] [Indexed: 02/06/2023]
Abstract
Some members of the Bacillus velezensis (Bv) group (e.g., Bv FZB42T and AS3.43) were previously assigned grouping with B. subtilis and B. amyloliquefaciens, based on the fact that they shared a 99% DNA-DNA percentage phylogenetic similarity. However, hinging on current assessments of the pan-genomic reassignments, the differing phylogenomic characteristics of Bv from B. subtilis and B. amyloliquefaciens are now better understood. Within this re-grouping/reassignment, the various strains within the Bv share a close phylogenomic resemblance, and a number of these strains have received a lot of attention in recent years, due to their genomic robustness, and the growing evidence for their possible utilization in the agricultural industry for managing plant diseases. Only a few applications for their use medicinally/pharmaceutically, environmentally, and in the food industry have been reported, and this may be due to the fact that the majority of those strains investigated are those typically occurring in soil. Although the intracellular unique biomolecules of Bv strains have been revealed via in silico genome modeling and investigated using transcriptomics and proteomics, a further inquisition into the Bv metabolome using newer technologies such as metabolomics could elucidate additional applications of this economically relevant Bacillus species, beyond that of primarily the agricultural sector.
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Affiliation(s)
- Adetomiwa Ayodele Adeniji
- Faculty of Natural and Agricultural Science, North-West University, Food Security and Safety, Private Bag X2046, Mmabatho, 2735, South Africa.,Faculty of Natural and Agricultural Science, North-West University, Human Metabolomics Private Bag X6001, Box 269, Potchefstroom, 2531, South Africa
| | - Du Toit Loots
- Faculty of Natural and Agricultural Science, North-West University, Human Metabolomics Private Bag X6001, Box 269, Potchefstroom, 2531, South Africa
| | - Olubukola Oluranti Babalola
- Faculty of Natural and Agricultural Science, North-West University, Food Security and Safety, Private Bag X2046, Mmabatho, 2735, South Africa.
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Adeniji AA, Aremu OS, Babalola OO. Selecting lipopeptide-producing, Fusarium-suppressing Bacillus spp.: Metabolomic and genomic probing of Bacillus velezensis NWUMFkBS10.5. Microbiologyopen 2018; 8:e00742. [PMID: 30358165 PMCID: PMC6562122 DOI: 10.1002/mbo3.742] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 09/03/2018] [Accepted: 09/10/2018] [Indexed: 12/29/2022] Open
Abstract
The results of this study indicate that the maize rhizosphere remains a reservoir for microbial strains with unique beneficial properties. The study sought to provide an indigenous Bacillus strain with a bioprotective potential to alleviate maize fusariosis in South Africa. We selected seven Bacillus isolates (MORWBS1.1, MARBS2.7, VERBS5.5, MOREBS6.3, MOLBS8.5, MOLBS8.6, and NWUMFkBS10.5) with biosuppressive effects against two maize fungal pathogens (Fusarium graminearum and Fusarium culmorum) based on 16S rDNA gene characterization and lipopeptide gene analysis. The PCR analysis revealed that lipopeptide genes encoding the synthesis of iturin, surfactin, and fengycin might be responsible for their antifungal activities. Few of the isolates also showed possible biosurfactant capability, and their susceptibility to known antibiotics is indicative of their eco‐friendly attributes. In addition, in silico genomic analysis of our best isolate (Bacillus velezensis NWUMFkBS10.5) and characterization of its active metabolite with FTIR, NMR, and ESI‐Micro‐Tof MS confirmed the presence of valuable genes clusters and metabolic pathways. The versatile genomic potential of our Bacillus isolate emphasizes the continued relevance of Bacillus spp. in biological management of plant diseases.
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Affiliation(s)
- Adetomiwa Ayodele Adeniji
- Department of Biological Sciences, Faculty of Natural and Agriculture Science, North-West University, Mmabatho, South Africa.,Food Security and Safety Niche Area, Faculty of Natural and Agriculture Science, North-West University, Mmabatho, South Africa
| | - Oluwole Samuel Aremu
- Department of Chemistry, Faculty of Natural and Agriculture Science, North-West University, Mmabatho, South Africa
| | - Olubukola Oluranti Babalola
- Department of Biological Sciences, Faculty of Natural and Agriculture Science, North-West University, Mmabatho, South Africa.,Food Security and Safety Niche Area, Faculty of Natural and Agriculture Science, North-West University, Mmabatho, South Africa
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Chen L, Gu W, Xu HY, Yang GL, Shan XF, Chen G, Kang YH, Wang CF, Qian AD. Comparative genome analysis of Bacillus velezensis reveals a potential for degrading lignocellulosic biomass. 3 Biotech 2018; 8:253. [PMID: 29765811 DOI: 10.1007/s13205-018-1270-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 04/30/2018] [Indexed: 02/07/2023] Open
Abstract
Genomes of 24 sequenced Bacillus velezensis strains were characterized to identity shared and unique genes of lignocellulolytic enzymes and predict potential to degrade lignocellulose. All 24 strains had genes that encoded lignocellulolytic enzymes, with potential to degrade cellulose and hemicelluloses. Several lignocellulosic genes related to cellulose degradation were universally present, including one GH5 (endo-1,4-β-glucanase), one GH30 (glucan endo-1,6-β-glucosidase), two GH4 (6-phospho-β-glucosidase, 6-phospho-α-glucosidase), one GH1 (6-phospho-β-galactosidase), one GH16 (β-glucanase) and three GH32 (two sucrose-6-phosphate hydrolase and levanase). However, in the absence of gene(s) for cellobiohydrolase, it was predicted that none of the 24 strains would be able to directly hydrolyse cellulose. Regarding genes for hemicellulose degradation, four GH43 (1,4-β-xylosidase; except strain 9912D), one GH11 (endo-1,4-β-xylanase), three GH43 (two arabinan endo-1,5-α-L-arabinosidase and one arabinoxylan arabinofuranohydrolase), two GH51 (α-N-arabinofuranosidase), one GH30 (glucuronoxylanase), one GH26 (β-mannosidase) and one GH53 (arabinogalactan endo-1,4-β-galactosidase) were present. In addition, two PL1 (pectate lyase) and one PL9 (pectate lyase) with potential for pectin degradation were conserved among all 24 strains. In addition, all 24 Bacillus velezensis had limited representation of the auxiliary activities super-family, consistent with a limited ability to degrade lignin. Therefore, it was predicted that for these bacteria to degrade lignin, pretreatment of lignocellulosic substrates may be required. Finally, based on in silico studies, we inferred that Bacillus velezensis strains may degrade a range of polysaccharides in lignocellulosic biomasses.
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Affiliation(s)
- Long Chen
- 1College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118 People's Republic of China
| | - Wei Gu
- Shandong BaoLai-LeeLai Bioengineering Co. Ltd, Tai'an, 271000 Shandong People's Republic of China
| | - Hai-Yan Xu
- Shandong BaoLai-LeeLai Bioengineering Co. Ltd, Tai'an, 271000 Shandong People's Republic of China
| | - Gui-Lian Yang
- 1College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118 People's Republic of China
- 4Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, 130118 People's Republic of China
- 5Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, 130118 People's Republic of China
| | - Xiao-Feng Shan
- 1College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118 People's Republic of China
| | - Guang Chen
- 3College of Life Sciences, Jilin Agricultural University, Changchun, 130118 People's Republic of China
| | - Yuan-Huan Kang
- 1College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118 People's Republic of China
| | - Chun-Feng Wang
- 1College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118 People's Republic of China
- 4Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, 130118 People's Republic of China
- 5Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, 130118 People's Republic of China
| | - Ai-Dong Qian
- 1College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118 People's Republic of China
- 4Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, 130118 People's Republic of China
- 5Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, 130118 People's Republic of China
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Ye M, Tang X, Yang R, Zhang H, Li F, Tao F, Li F, Wang Z. Characteristics and Application of a Novel Species of Bacillus: Bacillus velezensis. ACS Chem Biol 2018; 13:500-505. [PMID: 29309732 DOI: 10.1021/acschembio.7b00874] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacillus velezensis has been investigated and applied more and more widely recently because it can inhibit fungi and bacteria and become a potential biocontrol agent. In order to provide more clear and comprehensive understanding of B. velezensis for researchers, we collected the recent relevant articles systematically and reviewed the discovery and taxonomy, secondary metabolites, characteristics and application, gene function, and molecular research of B. velezensis. This review will give some direction to the research and application of this strain for the future.
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Affiliation(s)
- Miao Ye
- College of Life Science, Anhui Agricultural University, Anhui Hefei 230036, Peoples’ Republic of China
| | - Xiangfang Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ru Yang
- College of Life Science, Anhui Agricultural University, Anhui Hefei 230036, Peoples’ Republic of China
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fangshu Li
- College of Life Science, Anhui Agricultural University, Anhui Hefei 230036, Peoples’ Republic of China
| | - Fangzheng Tao
- College of Life Science, Anhui Agricultural University, Anhui Hefei 230036, Peoples’ Republic of China
| | - Fei Li
- College of Life Science, Anhui Agricultural University, Anhui Hefei 230036, Peoples’ Republic of China
| | - Zaigui Wang
- College of Life Science, Anhui Agricultural University, Anhui Hefei 230036, Peoples’ Republic of China
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Chen L, Gu W, Xu HY, Yang GL, Shan XF, Chen G, Wang CF, Qian AD. Complete genome sequence of Bacillus velezensis 157 isolated from Eucommia ulmoides with pathogenic bacteria inhibiting and lignocellulolytic enzymes production by SSF. 3 Biotech 2018; 8:114. [PMID: 29430375 PMCID: PMC5801104 DOI: 10.1007/s13205-018-1125-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 01/16/2018] [Indexed: 10/18/2022] Open
Abstract
Bacillus velezensis 157 was isolated from the bark of Eucommia ulmoides, and exhibited antagonistic activity against a broad spectrum of pathogenic bacteria and fungi. Moreover, B. velezensis 157 also showed various lignocellulolytic activities including cellulase, xylanase, α-amylase, and pectinase, which had the ability of using the agro-industrial waste (soybean meal, wheat bran, sugarcane bagasse, wheat straw, rice husk, maize flour and maize straw) under solid-state fermentation and obtained several industrially valuable enzymes. Soybean meal appeared to be the most efficient substrate for the single fermentation of B. velezensis 157. Highest yield of pectinase (19.15 ± 2.66 U g-1), cellulase (46.69 ± 1.19 U g-1) and amylase (2097.18 ± 15.28 U g-1) was achieved on untreated soybean meal. Highest yield of xylanase (22.35 ± 2.24 U g-1) was obtained on untreated wheat bran. Here, we report the complete genome sequence of the B. velezensis 157, composed of a circular 4,013,317 bp chromosome with 3789 coding genes and a G + C content of 46.41%, one circular 8439 bp plasmid and a G + C content of 40.32%. The genome contained a total of 8 candidate gene clusters (bacillaene, difficidin, macrolactin, butirosin, bacillibactin, bacilysin, fengycin and surfactin), and dedicates over 15.8% of the whole genome to synthesize secondary metabolite biosynthesis. In addition, the genes encoding enzymes involved in degradation of cellulose, xylan, lignin, starch, mannan, galactoside and arabinan were found in the B. velezensis 157 genome. Thus, the study of B. velezensis 157 broadened that B. velezensis can not only be used as biocontrol agents, but also has potentially a wide range of applications in lignocellulosic biomass conversion.
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Affiliation(s)
- Long Chen
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118 People’s Republic of China
| | - Wei Gu
- Shandong BaoLai-LeeLai Bioengineering Co. Ltd., Tai’an, 271000 Shandong People’s Republic of China
| | - Hai-yan Xu
- Shandong BaoLai-LeeLai Bioengineering Co. Ltd., Tai’an, 271000 Shandong People’s Republic of China
| | - Gui-Lian Yang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118 People’s Republic of China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, 130118 People’s Republic of China
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, 130118 People’s Republic of China
| | - Xiao-Feng Shan
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118 People’s Republic of China
| | - Guang Chen
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118 People’s Republic of China
| | - Chun-Feng Wang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118 People’s Republic of China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, 130118 People’s Republic of China
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, 130118 People’s Republic of China
| | - Ai-Dong Qian
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118 People’s Republic of China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, 130118 People’s Republic of China
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, 130118 People’s Republic of China
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Complete Genome Sequence of Bacillus velezensis GQJK49, a Plant Growth-Promoting Rhizobacterium with Antifungal Activity. GENOME ANNOUNCEMENTS 2017; 5:5/35/e00922-17. [PMID: 28860261 PMCID: PMC5578859 DOI: 10.1128/genomea.00922-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Bacillus velezensis GQJK49 is a plant growth-promoting rhizobacterium with antifungal activity, which was isolated from Lycium barbarum L. rhizosphere. Here, we report the complete genome sequence of B. velezensis GQJK49. Twelve gene clusters related to its biosynthesis of secondary metabolites, including antifungal and antibacterial antibiotics, were predicted.
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Complete genome sequence of Bacillus velezensis LM2303, a biocontrol strain isolated from the dung of wild yak inhabited Qinghai-Tibet plateau. J Biotechnol 2017; 251:124-127. [PMID: 28461206 DOI: 10.1016/j.jbiotec.2017.04.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 04/28/2017] [Accepted: 04/28/2017] [Indexed: 11/20/2022]
Abstract
Bacillus velezensis LM2303 is a biocontrol strain with a broad inhibitory spectrum against plant pathogens, isolated from the dung of wild yak inhabited Qinghai-Tibet plateau, China. Here we present its complete genome sequence, which consists of a single, circular chromosome of 3,989,393bp with a 46.68% G+C content. Genome analysis revealed genes encoding specialized functions for the biosynthesis of antifungal metabolites and antibacterial metabolites, the promotion of plant growth, the alleviation of oxidative stress and nutrient utilization. And the biosynthesis of antimicrobial metabolites in strain LM2303 was confirmed by biochemical analysis, while its plant growth promoting traits were confirmed by inoculation tests. Our results will establish a better foundation for further studies and biocontrol application of B. velezensis LM2303.
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