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Nematicidal lipopeptides from Bacillus paralicheniformis and Bacillus subtilis: A comparative study. Appl Microbiol Biotechnol 2023; 107:1537-1549. [PMID: 36719435 DOI: 10.1007/s00253-023-12391-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 12/26/2022] [Accepted: 01/15/2023] [Indexed: 02/01/2023]
Abstract
The aim of this work was to develop a comparative study between Bacillus paralicheniformis TB197 and B. subtilis ATCC 21332 strains in terms of growth, cyclic lipopeptide production, nematicidal activity, and active lipopeptide characteristics. Crude lipopeptide extracts (CLEs) from their fermentation broths were obtained, and their nematicidal activity (NA) was estimated as the mean lethal dose (LD50), employing Caenorhabditis elegans. Using a bioguided approach, CLE components were fractionated by semipreparative thin layer chromatography, and active lipopeptides were characterized by mass spectrometry. Both strains produced similar concentrations of CLEs (p ≥ 0.05) (0.99 ± 0.11 and 1.14 ± 0.15 mg/mL by TB197 and ATCC 21332, respectively). The estimated LD50 values of CLEs from the TB197 and ATCC 21332 strains were 3.88 and 8.15 mg/mL, respectively, showing that the NA of the TB197 strain CLE was 2.1-fold higher (p ≤ 0.05). Mass spectrometry revealed that strain TB197 synthesizes several families of lipopeptides, namely, fengycin A (C14-C17), fengycin B (C16-C17), surfactin (C15-C17), and lichenysin (C12, C13, C14, and C16), from which fengycins and lichenysins possess the highest NA (100 and 60% mortality in C. elegans larvae, respectively), while the ATCC 21332 strain produces mainly surfactin (C13-C17) (NA 63% mortality). The main differences found in this study were that the TB197 strain has a higher tolerance to inhibition by the product, and the lipopeptides they synthesize have a higher nematicidal activity due to the diversity of families compared to ATCC 21332. Likewise, it was shown that more polar lipopeptides (fengycins) are more effective at causing mortality in C. elegans larvae. KEY POINTS: • The nematicidal activity of lipopeptides from TB197 is higher than from ATCC 21332 • TB197 produces surfactin, lichenysin, and fengycin, while ATCC 21332 mainly produces surfactin • The most polar lipopeptides (fengycins) cause more mortality in C. elegans L2.
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Świątczak J, Kalwasińska A, Wojciechowska A, Brzezinska MS. Physiological properties and genomic insights into the plant growth-promoting rhizobacterium Brevibacillus laterosporus K75 isolated from maize rhizosphere. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:1432-1441. [PMID: 36181696 DOI: 10.1002/jsfa.12238] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 08/20/2022] [Accepted: 10/01/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND When looking for a safer alternative to pesticides that are potentially harmful to living organisms, one of the directions worth looking at are plant growth-promoting rhizobacteria. The purpose of the research was a comprehensive characterization of Brevibacillus laterosporus K75, a strain isolated from maize rhizosphere. Many studies have proved B. laterosporus to be a biocontrol agent; however, little is known about B. laterosporus as a plant growth-promoting rhizobacterium. RESULTS Ninety strains were screened for plant growth-promoting activities. Four strains with the best plant growth-promoting traits (Rhodococcus qingshengii K8, Bacillus subtilis subsp. stercoris K73, Brevibacillus laterosporus K75, and Brevibacillus laterosporus K89) were used to research their effect on maize growth. Under sterile conditions, B. laterosporus K75 showed the best stimulatory effect, significantly improving the weight of roots, shoots and leaves, and considerably increasing content of chlorophyll. In unsterilized soil, B. laterosporus K75 significantly improved length of roots and weight of leaves compared to the K73, K89, and untreated control. Moreover, B. laterosporus K75 significantly increased specific leaf area compared to the untreated control and to other inoculant treatments. The genome of B. laterosporus K75 was compared to the recently published B. laterosporus MG64. Genome-mining displayed differences in identified plant growth-promoting genes and biosynthetic gene clusters of secondary metabolites. The B. laterosporus K75 genome possessed additional genes involved in indole-3-acetic acid production and phosphate solubilization that could be attributed to its ability to enhance maize growth. CONCLUSION Our study demonstrated that B. laterosporus K75 is a promising candidate for use in inoculant formulation, effectively facilitating maize growth. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Joanna Świątczak
- Department of Environmental Microbiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Torun, Torun, Poland
| | - Agnieszka Kalwasińska
- Department of Environmental Microbiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Torun, Torun, Poland
| | - Anna Wojciechowska
- Department of Geobotany and Landscape Planning, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Torun, Torun, Poland
| | - Maria Swiontek Brzezinska
- Department of Environmental Microbiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Torun, Torun, Poland
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Babar TK, Glare TR, Hampton JG, Hurst MRH, Narciso JO. Isolation, Purification, and Characterisation of a Phage Tail-Like Bacteriocin from the Insect Pathogenic Bacterium Brevibacillus laterosporus. Biomolecules 2022; 12:biom12081154. [PMID: 36009048 PMCID: PMC9406221 DOI: 10.3390/biom12081154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/13/2022] [Accepted: 08/16/2022] [Indexed: 11/23/2022] Open
Abstract
The Gram-positive and spore-forming bacterium Brevibacillus laterosporus (Bl) belongs to the Brevibacillus brevis phylogenetic cluster. Isolates of the species have demonstrated pesticidal potency against a wide range of invertebrate pests and plant diseases. Two New Zealand isolates, Bl 1821L and Bl 1951, are under development as biopesticides for control of diamondback moth and other pests. However, due to the often-restricted growth of these endemic isolates, production can be an issue. Based on the previous work, it was hypothesised that the putative phages might be involved. During investigations of the cause of the disrupted growth, electron micrographs of crude lysate of Bl 1821L showed the presence of phages’ tail-like structures. A soft agar overlay method with PEG 8000 precipitation was used to differentiate between the antagonistic activity of the putative phage and phage tail-like structures (bacteriocins). Assay tests authenticated the absence of putative phage activity. Using the same method, broad-spectrum antibacterial activity of Bl 1821L lysate against several Gram-positive bacteria was found. SDS-PAGE of sucrose density gradient purified and 10 kD MWCO concentrated lysate showed a prominent protein band of ~48 kD, and transmission electron microscopy revealed the presence of polysheath-like structures. N-terminal sequencing of the ~48 kD protein mapped to a gene with weak predicted amino acid homology to a Bacillus PBSX phage-like element xkdK, the translated product of which shared >90% amino acid similarity to the phage tail-sheath protein of another Bl published genome, LMG15441. Bioinformatic analysis also identified an xkdK homolog in the Bl 1951 genome. However, genome comparison of the region around the xkdK gene between Bl 1821L and Bl 1951 found differences including two glycine rich protein encoding genes which contain imperfect repeats (1700 bp) in Bl 1951, while a putative phage region resides in the analogous Bl 1821L region. Although comparative analysis of the genomic organisation of Bl 1821L and Bl 1951 PBSX-like region with the defective phages PBSX, PBSZ, and PBP 180 of Bacillus subtilis isolates 168 and W23, and Bacillus phage PBP180 revealed low amino acids similarity, the genes encode similar functional proteins in similar arrangements, including phage tail-sheath (XkdK), tail (XkdO), holin (XhlB), and N-acetylmuramoyl-l-alanine (XlyA). AMPA analysis identified a bactericidal stretch of 13 amino acids in the ~48 kD sequenced protein of Bl 1821L. Antagonistic activity of the purified ~48 kD phage tail-like protein in the assays differed remarkably from the crude lysate by causing a decrease of 34.2% in the number of viable cells of Bl 1951, 18 h after treatment as compared to the control. Overall, the identified inducible phage tail-like particle is likely to have implications for the in vitro growth of the insect pathogenic isolate Bl 1821L.
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Affiliation(s)
- Tauseef K. Babar
- Bio-Protection Research Centre, Lincoln University, Lincoln 7674, New Zealand
- Department of Entomology, Faculty of Agriculture Sciences & Technology, Bahauddin Zakariya University, Multan 60000, Pakistan
- Correspondence:
| | - Travis R. Glare
- Bio-Protection Research Centre, Lincoln University, Lincoln 7674, New Zealand
| | - John G. Hampton
- Bio-Protection Research Centre, Lincoln University, Lincoln 7674, New Zealand
| | - Mark R. H. Hurst
- Resilient Agriculture, AgResearch, Lincoln Research Centre, Christchurch 8140, New Zealand
| | - Josefina O. Narciso
- Bio-Protection Research Centre, Lincoln University, Lincoln 7674, New Zealand
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Gonçalves KB, Appel RJC, Bôas LAV, Cardoso PF, Bôas GTV. Genomic insights into the diversity of non-coding RNAs in Bacillus cereus sensu lato. Curr Genet 2022; 68:449-466. [PMID: 35552506 DOI: 10.1007/s00294-022-01240-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 03/20/2022] [Accepted: 03/30/2022] [Indexed: 11/28/2022]
Abstract
Bacillus cereus sensu lato is a group of bacteria of medical and agricultural importance in different ecological niches and with controversial taxonomic relationships. Studying the composition of non-coding RNAs (ncRNAs) in several bacterial groups has been an important tool for identifying genetic information and better understanding genetic regulation towards environment adaptation. However, to date, no comparative genomics study of ncRNA has been performed in this group. Thus, this study aimed to identify and characterize the set of ncRNAs from 132 strains of Bacillus cereus, Bacillus thuringiensis and Bacillus anthracis to obtain an overview of the diversity and distribution of these genetic elements in these species. We observed that the number of ncRNAs differs in the chromosomes of the three species, but not in the plasmids, when species or phylogenetic clusters were compared. The prevailing functional/structural category was Cis-reg and the most frequent class was Riboswitch. However, in plasmids, the class Group II intron was the most frequent. Also, nine ncRNAs were selected for validation in the strain B. thuringiensis 407 by RT-PCR, which allowed to identify the expression of the ncRNAs. The wide distribution and diversity of ncRNAs in the B. cereus group, and more intensely in B. thuringiensis, may help improve the abilities of these species to adapt to various environmental changes. Further studies should address the expression of these genetic elements in different conditions.
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Affiliation(s)
- Kátia B Gonçalves
- Depto Biologia Geral, Universidade Estadual de Londrina, Londrina, Brazil
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Xiong D, Wen J, Lu G, Li T, Long M. Isolation, Purification, and Characterization of a Laccase-Degrading Aflatoxin B1 from Bacillus amyloliquefaciens B10. Toxins (Basel) 2022; 14:toxins14040250. [PMID: 35448859 PMCID: PMC9028405 DOI: 10.3390/toxins14040250] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/29/2022] [Accepted: 03/29/2022] [Indexed: 01/27/2023] Open
Abstract
Aflatoxins, widely found in feed and foodstuffs, are potentially harmful to human and animal health because of their high toxicity. In this study, a strain of Bacillus amyloliquefaciens B10 with a strong ability to degrade aflatoxin B1 (AFB1) was screened; it could degrade 2.5 μg/mL of AFB1 within 96 h. The active substances of Bacillus amyloliquefaciens B10 for the degradation of AFB1 mainly existed in the culture supernatant. A new laccase with AFB1-degrading activity was separated by ammonium sulfate precipitation, diethylaminoethyl (DEAE) and gel filtration chromatography. The results of molecular docking showed that B10 laccase and aflatoxin had a high docking score. The coding sequence of the laccase was successfully amplified from cDNA by PCR and cloned into E. coli. The purified laccase could degrade 79.3% of AFB1 within 36 h. The optimum temperature for AFB1 degradation was 40 °C, and the optimum pH was 6.0–8.0. Notably, Mg2+ and dimethyl sulfoxide (DMSO) could enhance the AFB1-degrading activity of B10 laccase. Mutation of the three key metal combined sites of B10 laccase resulted in the loss of AFB1-degrading activity, indicating that these three metal combined sites of B10 laccase play an essential role in the catalytic degradation of AFB1.
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Asaturova AM, Bugaeva LN, Homyak AI, Slobodyanyuk GA, Kashutina EV, Yasyuk LV, Sidorov NM, Nadykta VD, Garkovenko AV. Bacillusvelezensis Strains for Protecting Cucumber Plants from Root-Knot Nematode Meloidogyne incognita in a Greenhouse. PLANTS (BASEL, SWITZERLAND) 2022; 11:275. [PMID: 35161255 PMCID: PMC8838184 DOI: 10.3390/plants11030275] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Meloidogyne incognita Kofoid et White is one of the most dangerous root-knot nematodes in greenhouses. In this study, we evaluated two Bacillus strains (Bacillus velezensis BZR 86 and Bacillus velezensis BZR 277) as promising microbiological agents for protecting cucumber plants from the root-knot nematode M. incognita Kof. The morphological and cultural characteristics and enzymatic activity of the strains have been studied and the optimal conditions for its cultivation have been developed. We have shown the nematicidal activity of these strains against M. incognita. Experiments with the cucumber variety Courage were conducted under greenhouse conditions in 2016-2018. We determined the effect of plant damage with M. incognita to plants on the biometric parameters of underground and aboveground parts of cucumber plants, as well as on the gall formation index and yield. It was found that the treatment of plants with Bacillus strains contributed to an increase in the height of cucumber plants by 7.4-43.1%, an increase in leaf area by 2.7-17.8%, and an increase in root mass by 3.2-16.1% compared with the control plants without treatment. The application of these strains was proved to contribute to an increase in yield by 4.6-45.8% compared to control. Our experiments suggest that the treatment of cucumber plants with two Bacillus strains improved plant health and crop productivity in the greenhouse. B. velezensis BZR 86 and B. velezensis BZR 277 may form the basis for bionematicides to protect cucumber plants from the root-knot nematode M. incognita.
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Affiliation(s)
- Anzhela M. Asaturova
- Federal Research Center of Biological Plant Protection, p/o 39, 350039 Krasnodar, Russia; (A.M.A.); (N.M.S.); (V.D.N.)
| | - Ludmila N. Bugaeva
- Lazarevskaya Experimental Plant Protection Station, the Affiliated Branch of the Federal Research Centre of Biological Plant Protection, l. 200, Sochi Highway-77, 354200 Sochi, Russia; (L.N.B.); (G.A.S.); (E.V.K.); (L.V.Y.)
| | - Anna I. Homyak
- Federal Research Center of Biological Plant Protection, p/o 39, 350039 Krasnodar, Russia; (A.M.A.); (N.M.S.); (V.D.N.)
| | - Galina A. Slobodyanyuk
- Lazarevskaya Experimental Plant Protection Station, the Affiliated Branch of the Federal Research Centre of Biological Plant Protection, l. 200, Sochi Highway-77, 354200 Sochi, Russia; (L.N.B.); (G.A.S.); (E.V.K.); (L.V.Y.)
| | - Evgeninya V. Kashutina
- Lazarevskaya Experimental Plant Protection Station, the Affiliated Branch of the Federal Research Centre of Biological Plant Protection, l. 200, Sochi Highway-77, 354200 Sochi, Russia; (L.N.B.); (G.A.S.); (E.V.K.); (L.V.Y.)
| | - Larisa V. Yasyuk
- Lazarevskaya Experimental Plant Protection Station, the Affiliated Branch of the Federal Research Centre of Biological Plant Protection, l. 200, Sochi Highway-77, 354200 Sochi, Russia; (L.N.B.); (G.A.S.); (E.V.K.); (L.V.Y.)
| | - Nikita M. Sidorov
- Federal Research Center of Biological Plant Protection, p/o 39, 350039 Krasnodar, Russia; (A.M.A.); (N.M.S.); (V.D.N.)
| | - Vladimir D. Nadykta
- Federal Research Center of Biological Plant Protection, p/o 39, 350039 Krasnodar, Russia; (A.M.A.); (N.M.S.); (V.D.N.)
| | - Alexey V. Garkovenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia;
- Laboratory of Molecular Genetic Research in the Agroindustrial Complex, Department of Biotechnology, Biochemistry and Biophysics, Trubilin Kuban State Agrarian University, Kalinina Str. 13, 350044 Krasnodar, Russia
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Khanna K, Kohli SK, Ohri P, Bhardwaj R. Plants-nematodes-microbes crosstalk within soil: A trade-off among friends or foes. Microbiol Res 2021; 248:126755. [PMID: 33845302 DOI: 10.1016/j.micres.2021.126755] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/18/2021] [Accepted: 03/27/2021] [Indexed: 11/28/2022]
Abstract
Plants interact with enormous biotic and abiotic components within ecosystem. For instance, microbes, insects, herbivores, animals, nematodes etc. In general, these interactions are studied independently with plants, that condenses only specific information about the interaction. However, the limitation to study the cross-interactions masks the collaborative role of organisms within ecosystem. Beneficial microbes are most prominent organisms that are needed to be studied due to their bidirectional nature towards plants. Fascinatingly, Plant-Parasitic Nematodes (PPNs) have been profoundly observed to cause mass destruction of agricultural crops worldwide. The huge demand for agriculture for present-day population requires optimization of production potential by curbing the damage caused by PPNs. Chemical nematicides combats their proliferation, but their extended usage has abruptly affected flora, fauna and human populations. Because of consistent pressing issues in regard to environment, the use of biocontrol agents are most favourable alternatives for managing agriculture. However, this association is somehow, tug of war, and understanding of plant-nematode-microbial relation would enable the agriculturists to monitor the overall development of plants along with limiting the use of agrochemicals. Soil microbes are contemporary bio-nematicides emerging in the market, that stimulates the plant growth and impedes PPNs populations. They form natural enemies and trap nematodes, henceforth, it is crucial to understand these interactions for ecological and biotechnological perspectives for commercial use. Moreover, acquiring the diversity of their relationship and molecular-based mechanisms, outlines their cascade of signaling events to serve as biotechnological ecosystem engineers. The omics based mechanisms encompassing hormone gene regulatory pathways and elicitors released by microbes are able to modulate pathogenesis-related (PR) genes within plants. This is achieved via Induced Systemic Resistance (ISR) or acquired systemic channels. Taking into account all these validations, the present review mainly advocates the relationship among microbes and nematodes in plants. It is believed that this review will boost zest and zeal within researchers to effectively understand the plant-nematodes-microbes relations and their ecological perspectives.
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Affiliation(s)
- Kanika Khanna
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, 143005, Punjab, India.
| | - Sukhmeen Kaur Kohli
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, 143005, Punjab, India
| | - Puja Ohri
- Department of Zoology, Guru Nanak Dev University, Amritsar, 143005, Punjab, India.
| | - Renu Bhardwaj
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, 143005, Punjab, India.
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Zhang L, Wei Y, Tao Y, Zhao S, Wei X, Yin X, Liu S, Niu Q. Molecular mechanism of the smart attack of pathogenic bacteria on nematodes. Microb Biotechnol 2020; 13:683-705. [PMID: 31730281 PMCID: PMC7111092 DOI: 10.1111/1751-7915.13508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 10/16/2019] [Accepted: 10/20/2019] [Indexed: 11/28/2022] Open
Abstract
Nematode-bacterial associations are far-reaching subjects in view of their impact on ecosystems, economies, agriculture and human health. There is still no conclusion regarding which pathogenic bacteria sense nematodes. Here, we found that the pathogenic bacterium Bacillus nematocida B16 was sensitive to C. elegans and could launch smart attacks to kill the nematodes. Further analysis revealed that the spores of B. nematocida B16 are essential virulence factors. Once gaseous molecules (morpholine) produced from C. elegans were sensed, the sporulation of B16 was greatly accelerated. Then, B16 showed maximum attraction to C. elegans during the spore-forming process but had no attraction until all the spores were formed. The disruption of either the spore formation gene spo0A or the germination gene gerD impaired colonization and attenuated infection in B16. In contrast, complementation with the intact genes restored most of the above-mentioned deficient phenotypes, which indicated that the spo0A gene was a key factor in the smart attack of B16 on C. elegans. Further, transcriptome, molecular simulations and quantitative PCR analysis showed that morpholine from C. elegans could promote sporulation and initiate infection by increasing the transcription of the spo0A gene by decreasing the transcription of the rapA and spo0E genes. The overexpression of rapA or spo0E decreased the induced sporulation effect, and morpholine directly reduced the level of phosphorylation of purified recombinant RapA and Spo0E compared to that of Spo0A. Collectively, these findings further support a 'Trojan horse-like' infection model. The significance of our paper is that we showed that the soil-dwelling bacterium B. nematocida B16 has the ability to actively detect, attract and attack their host C. elegans. These studies are the first report on the behaviours, signalling molecules and mechanism of the smart attack of B16 on nematodes and also reveal new insights into microbe-host interactions.
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Affiliation(s)
- Lin Zhang
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
- State Key Laboratory of Cotton BiologyHenan Key Laboratory of Plant Stress BiologySchool of Life SciencesHenan UniversityKaifengHenan475001China
| | - Yuping Wei
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
| | - Ye Tao
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
| | - Suya Zhao
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
| | - Xuyang Wei
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
| | - Xiaoyan Yin
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
| | - Suyao Liu
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
| | - Qiuhong Niu
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
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Whole Genome Sequencing and Comparative Genomics of Two Nematicidal Bacillus Strains Reveals a Wide Range of Possible Virulence Factors. G3-GENES GENOMES GENETICS 2020; 10:881-890. [PMID: 31919110 PMCID: PMC7056983 DOI: 10.1534/g3.119.400716] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Bacillus firmus nematicidal bacterial strains are used to control plant parasitic nematode infestation of crops in agricultural production. Proteases are presumed to be the primary nematode virulence factors in nematicidal B. firmus degrading the nematode cuticle and other organs. We determined and compared the whole genome sequences of two nematicidal strains. Comparative genomics with a particular focus on possible virulence determinants revealed a wider range of possible virulence factors in a B. firmus isolate from a commercial bionematicide and a wild type Bacillus sp. isolate with nematicidal activity. The resulting 4.6 Mb B. firmus I-1582 and 5.3 Mb Bacillus sp. ZZV12-4809 genome assemblies contain respectively 18 and 19 homologs to nematode-virulent proteases, two nematode-virulent chitinase homologs in ZZV12-4809 and 28 and 36 secondary metabolite biosynthetic clusters, projected to encode antibiotics, small peptides, toxins and siderophores. The results of this study point to the genetic capability of B. firmus and related species for nematode virulence through a range of direct and indirect mechanisms.
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Ghahremani Z, Escudero N, Beltrán-Anadón D, Saus E, Cunquero M, Andilla J, Loza-Alvarez P, Gabaldón T, Sorribas FJ. Bacillus firmus Strain I-1582, a Nematode Antagonist by Itself and Through the Plant. FRONTIERS IN PLANT SCIENCE 2020; 11:796. [PMID: 32765537 PMCID: PMC7381289 DOI: 10.3389/fpls.2020.00796] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 05/19/2020] [Indexed: 05/21/2023]
Abstract
Bacillus firmus I-1582 is approved in Europe for the management of Meloidogyne on vegetable crops. However, little information about its modes of action and temperature requirements is available, despite the effect of these parameters in its efficacy. The cardinal temperatures for bacterial growth and biofilm formation were determined. The bacteria was transformed with GFP to study its effect on nematode eggs and root colonization of tomato (Solanum lycopersicum) and cucumber (Cucumis sativus) by laser-scanning confocal microscopy. Induction of plant resistance was determined in split-root experiments and the dynamic regulation of genes related to jasmonic acid (JA) and salicylic acid (SA) by RT-qPCR at three different times after nematode inoculation. The bacteria was able to grow and form biofilms between 15 and 45°C; it degraded egg-shells and colonized eggs; it colonized tomato roots more extensively than cucumber roots; it induced systemic resistance in tomato, but not in cucumber; SA and JA related genes were primed at different times after nematode inoculation in tomato, but only the SA-related gene was up-regulated at 7 days after nematode inoculation in cucumber. In conclusion, B. firmus I-1582 is active at a wide range of temperatures; its optimal growth temperature is 35°C; it is able to degrade Meloidogyne eggs, and to colonize plant roots, inducing systemic resistance in a plant dependent species manner.
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Affiliation(s)
- Zahra Ghahremani
- Departament d’Enginyeria Agroalimentària i Biotecnologia, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Nuria Escudero
- Departament d’Enginyeria Agroalimentària i Biotecnologia, Universitat Politècnica de Catalunya, Barcelona, Spain
- *Correspondence: Nuria Escudero,
| | - Daniel Beltrán-Anadón
- Departament d’Enginyeria Agroalimentària i Biotecnologia, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Ester Saus
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Marina Cunquero
- Institut de Ciències Fotòniques (ICFO), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jordi Andilla
- Institut de Ciències Fotòniques (ICFO), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Pablo Loza-Alvarez
- Institut de Ciències Fotòniques (ICFO), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Toni Gabaldón
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - F. Javier Sorribas
- Departament d’Enginyeria Agroalimentària i Biotecnologia, Universitat Politècnica de Catalunya, Barcelona, Spain
- F. Javier Sorribas,
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Glare TR, Durrant A, Berry C, Palma L, Ormskirk MM, Cox MP. Phylogenetic determinants of toxin gene distribution in genomes of Brevibacillus laterosporus. Genomics 2019; 112:1042-1053. [PMID: 31226484 PMCID: PMC6978878 DOI: 10.1016/j.ygeno.2019.06.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 05/16/2019] [Accepted: 06/17/2019] [Indexed: 11/24/2022]
Abstract
Brevibacillus laterosporus is a globally ubiquitous, spore forming bacterium, strains of which have shown toxic activity against invertebrates and microbes and several have been patented due to their commercial potential. Relatively little is known about this bacterium. Here, we examined the genomes of six published and five newly determined genomes of B. laterosporus, with an emphasis on the relationships between known and putative toxin encoding genes, as well as the phylogenetic relationships between strains. Phylogenetically, strain relationships are similar using average nucleotide identity (ANI) values and multi-gene approaches, although PacBio sequencing revealed multiple copies of the 16S rDNA gene which lessened utility at the strain level. Based on ANI values, the New Zealand isolates were distant from other isolates and may represent a new species. While all of the genomes examined shared some putative toxicity or virulence related proteins, many specific genes were only present in a subset of strains. We examined genomes of 11 Brevibacillus laterosporus, a bacterium which is antagonistic to invertebrates and/or microbes Multiple phylogenetic methods showed New Zealand isolates more distant than all other isolates Each genome could contain 11–13 copies of the 16S rDNA gene, some of which were not identical Many putative toxin encoding genes were present in the genomes, but the toxin complement varied from isolate to isolate Variation in occurrence of toxin-encoding genes indicates the potential to find strains with new combinations of activities
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Affiliation(s)
- Travis R Glare
- Bio-Protection Research Centre, PO Box 85084, Lincoln University, Lincoln, New Zealand.
| | - Abigail Durrant
- Bio-Protection Research Centre, PO Box 85084, Lincoln University, Lincoln, New Zealand
| | - Colin Berry
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, UK
| | - Leopoldo Palma
- Universidad Nacional de Villa María, Instituto A.P. de Ciencias Básicas y Aplicadas, Av. Arturo Jauretche 1555, Villa María 5900, Córdoba, Argentina
| | - M Marsha Ormskirk
- Bio-Protection Research Centre, PO Box 85084, Lincoln University, Lincoln, New Zealand
| | - Murray P Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand
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12
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Wan L, Lin J, Du H, Zhang Y, Bravo A, Soberón M, Sun M, Peng D. Bacillus thuringiensistargets the host intestinal epithelial junctions for successful infection ofCaenorhabditis elegans. Environ Microbiol 2019; 21:1086-1098. [DOI: 10.1111/1462-2920.14528] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 12/02/2018] [Accepted: 12/12/2018] [Indexed: 01/28/2023]
Affiliation(s)
- Liting Wan
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University Wuhan 430070 Hubei People's Republic of China
| | - Jian Lin
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University Wuhan 430070 Hubei People's Republic of China
| | - Hongwen Du
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University Wuhan 430070 Hubei People's Republic of China
| | - Yulan Zhang
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University Wuhan 430070 Hubei People's Republic of China
| | - Alejandra Bravo
- Instituto de BiotecnologíaUniversidad Nacional Autónoma de México Apdo. postal 510‐3, Cuernavaca, 62250 Morelos Mexico
| | - Mario Soberón
- Instituto de BiotecnologíaUniversidad Nacional Autónoma de México Apdo. postal 510‐3, Cuernavaca, 62250 Morelos Mexico
| | - Ming Sun
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University Wuhan 430070 Hubei People's Republic of China
| | - Donghai Peng
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University Wuhan 430070 Hubei People's Republic of China
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13
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Shanmugam G, Dubey A, Ponpandian LN, Rim SO, Seo ST, Bae H, Jeon J. Genomic Insights into Nematicidal Activity of a Bacterial Endophyte, Raoultella ornithinolytica MG against Pine Wilt Nematode. THE PLANT PATHOLOGY JOURNAL 2018; 34:250-255. [PMID: 29887781 PMCID: PMC5985651 DOI: 10.5423/ppj.oa.10.2017.0217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 03/09/2018] [Accepted: 03/11/2018] [Indexed: 06/08/2023]
Abstract
Pine wilt disease, caused by the nematode Bursaphelenchus xylophilus, is one of the most devastating conifer diseases decimating several species of pine trees on a global scale. Here, we report the draft genome of Raoultella ornithinolytica MG, which is isolated from mountain-cultivated ginseng plant as an bacterial endophyte and shows nematicidal activity against B. xylophilus. Our analysis of R. ornithinolytica MG genome showed that it possesses many genes encoding potential nematicidal factors in addition to some secondary metabolite biosynthetic gene clusters that may contribute to the observed nematicidal activity of the strain. Furthermore, the genome was lacking key components of avermectin gene cluster, suggesting that nematicidal activity of the bacterium is not likely due to the famous anthelmintic agent of wide-spread use, avermectin. This genomic information of R. ornithinolytica will provide basis for identification and engineering of genes and their products toward control of pine wilt disease.
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Affiliation(s)
- Gnanendra Shanmugam
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541,
Korea
| | - Akanksha Dubey
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541,
Korea
| | | | - Soon Ok Rim
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541,
Korea
| | - Sang-Tae Seo
- Division of Forest Insect Pests and Diseases, National Institute of Forest Science Seoul 02455,
Korea
| | - Hanhong Bae
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541,
Korea
| | - Junhyun Jeon
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541,
Korea
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14
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Marche MG, Mura ME, Falchi G, Ruiu L. Spore surface proteins of Brevibacillus laterosporus are involved in insect pathogenesis. Sci Rep 2017; 7:43805. [PMID: 28256631 PMCID: PMC5335551 DOI: 10.1038/srep43805] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 01/30/2017] [Indexed: 12/21/2022] Open
Abstract
Outer spore envelope proteins of pathogenic bacteria often present specific virulence factors and tools to evade the defence system of their hosts. Brevibacillus laterosporus, a pathogen of invertebrates and an antimicrobial-producing species, is characterised by a unique spore coat and canoe-shaped parasporal body (SC-CSPB) complex surrounding the core spore. In the present study, we identified and characterised major proteins of the SC-CSPB complex of B. laterosporus, and we investigated their entomopathogenic role. Employing a proteomic approach and a B. laterosporus-house fly study model, we found four highly conserved proteins (ExsC, CHRD, CpbA and CpbB) that function as insect virulence factors. CpbA was associated with a significantly higher mortality of flies and greater relative gene expression levels during sporulation, compared to the other SC-CSPB proteins. Taken together, we suggest that spore surface proteins are a part of a complex set of toxins and virulence factors that B. laterosporus employs in its pathogenicity against flies.
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Affiliation(s)
| | - Maria Elena Mura
- Dipartimento di Agraria, University of Sassari, Sassari, 07100, Italy
| | - Giovanni Falchi
- Dipartimento di Agraria, University of Sassari, Sassari, 07100, Italy
| | - Luca Ruiu
- Dipartimento di Agraria, University of Sassari, Sassari, 07100, Italy
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15
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Du C, Cao S, Shi X, Nie X, Zheng J, Deng Y, Ruan L, Peng D, Sun M. Genetic and Biochemical Characterization of a Gene Operon for trans-Aconitic Acid, a Novel Nematicide from Bacillus thuringiensis. J Biol Chem 2017; 292:3517-3530. [PMID: 28087696 DOI: 10.1074/jbc.m116.762666] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 12/31/2016] [Indexed: 12/31/2022] Open
Abstract
trans-Aconitic acid (TAA) is an isomer of cis-aconitic acid (CAA), an intermediate of the tricarboxylic acid cycle that is synthesized by aconitase. Although TAA production has been detected in bacteria and plants for many years and is known to be a potent inhibitor of aconitase, its biosynthetic origins and the physiological relevance of its activity have remained unclear. We have serendipitously uncovered key information relevant to both of these questions. Specifically, in a search for novel nematicidal factors from Bacillus thuringiensis, a significant nematode pathogen harboring many protein virulence factors, we discovered a high yielding component that showed activity against the plant-parasitic nematode Meloidogyne incognita and surprisingly identified it as TAA. Comparison with CAA, which displayed a much weaker nematicidal effect, suggested that TAA is specifically synthesized by B. thuringiensis as a virulence factor. Analysis of mutants deficient in plasmids that were anticipated to encode virulence factors allowed us to isolate a TAA biosynthesis-related (tbr) operon consisting of two genes, tbrA and tbrB We expressed the corresponding proteins, TbrA and TbrB, and characterized them as an aconitate isomerase and TAA transporter, respectively. Bioinformatics analysis of the TAA biosynthetic gene cluster revealed the association of the TAA genes with transposable elements relevant for horizontal gene transfer as well as a distribution across B. cereus bacteria and other B. thuringiensis strains, suggesting a general role for TAA in the interactions of B. cereus group bacteria with nematode hosts in the soil environment. This study reveals new bioactivity for TAA and the TAA biosynthetic pathway, improving our understanding of virulence factors employed by B. thuringiensis pathogenesis and providing potential implications for nematode management applications.
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Affiliation(s)
- Cuiying Du
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shiyun Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiangyu Shi
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiangtao Nie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yun Deng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lifang Ruan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Donghai Peng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
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16
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Complete genome sequence of Fictibacillus arsenicus G25-54, a strain with toxicity to nematodes. J Biotechnol 2017; 241:98-100. [PMID: 27902921 DOI: 10.1016/j.jbiotec.2016.11.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/23/2016] [Accepted: 11/25/2016] [Indexed: 02/01/2023]
Abstract
Root-knot nematodes (RKNs) can infect almost all crops and cause huge economic losses in agriculture worldwide. An in-depth understanding of bacteria with nematicidal activity is essential for an effective and environmentally friendly control of RKNs. Fictibacillus arsenicus G25-54, a gram-positive and spore-forming bacterium isolated from a submerged sand bank, shows nematicidal activity against free-living Caenorhabditis elegans and RKNs. Here, we report the complete genome of F. arsenicus G25-54, which contains a circular chromosome and encodes ten potential nematicidal factors with twelve secondary metabolite gene clusters. Additionally, it encodes five arsenic resistance and transformation related proteins, which may provide the potential arsenic-resistance activity.
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17
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Zheng Z, Zheng J, Liu H, Peng D, Sun M. Complete genome sequence of Fictibacillus phosphorivorans G25-29, a strain toxic to nematodes. J Biotechnol 2016; 239:20-22. [PMID: 27677407 DOI: 10.1016/j.jbiotec.2016.09.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 09/18/2016] [Accepted: 09/23/2016] [Indexed: 11/17/2022]
Abstract
Root-knot nematodes (RKNs) which can infect almost all crops lead to huge economic losses in agriculture around the world. Unavailability of effective and environmentally friendly control of RKNs provides an opportunity to nematicidal bacteria. Fictibacillus phosphorivorans G25-29 is a gram-positive and spore-forming bacterium with nematicidal capability against root-knot nematodes and free-living nematode Caenorhabditis elegans. Here, we report the complete genome of F. phosphorivorans G25-29, containing a circular chromosome and encoding nine potential nematicidal factors which may contribute to its nematicidal activity.
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Affiliation(s)
- Ziqiang Zheng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hualin Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Donghai Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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