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Isolation and identification of antimicrobial secondary metabolites from Bacillus cereus associated with a rhabditid entomopathogenic nematode

Annals of Microbiology volume 64, pages 209–218 (2014)Cite this article

Abstract

The cell-free culture filtrate of Bacillus cereus associated with an entomopathogenic nematode, Rhabditis (Oscheius) sp., exhibited strong antimicrobial activity. The ethyl acetate extract of the bacterial culture filtrate was purified by silica gel column chromatography to obtain six bioactive compounds. The structure and absolute stereochemistry of these compounds were determined based on extensive spectroscopic analyses (LCMS, FABMS, 1H NMR, 13C NMR, 1H −1H COSY, 1H −13C HMBC) and Marfey’s method. The compounds were identified as cyclo(D-Pro-D-Leu), cyclo(L-Pro-D-Met), cyclo (L-Pro-D-Phe), cyclo (L-Pro-L-Val), 3,5-dihydroxy-4-ethyl-trans-stilbene, and 3,5-dihydroxy-4-isopropylstilbene, respectively. Compounds recorded antibacterial activity against all four tested bacteria strains of Bacillus subtilis, Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. 3,5-dihydroxy-4-isopropylstilbene recorded activity only against Gram-positive bacteria while cyclo(L-Pro-L-Val) recorded no antibacterial activity. Best antibacterial activity was recorded by 3,5-dihydroxy-4-ethyl-trans-stilbene (4 μg/ml) against Escherichia coli. The six compounds recorded significant antifungal activities against five fungal strains tested (Aspergillus flavus, Candida albicans, Fusarium oxysporum, Rhizoctonia solani and Penicillium expansum) and they were more effective than bavistin, the standard fungicide. The activity of cyclo(D-Pro-D-Leu), cyclo(L-Pro-D-Met), 3,5-dihydroxy-4-ethyl-trans-stilbene, and 3,5-dihydroxy-4-isopropylstilbene against Candida albicans was better than amphotericin B. To the best of our knowledge, this is the first report of antifungal activity of the bioactive compounds against the plant pathogenic fungi Fusarium oxysporum, Rhizoctonia solani, and Penicillium expansum. We conclude that the Bacillus cereus strain associated with entomopathogenic nematode is a promising source of natural bioactive secondary metabolites which may receive great benefit as potential sources of new drugs in the agricultural and pharmacological industry.

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References

  • Akhurst RJ (1982) Antibiotic activity of Xenorhabdus spp., bacteria symbiotically associated with insect pathogenic nematodes of the families Hettrorhabditidae and Steinernematidae. J Gen Microbiol 128:3061–3065

    CAS  PubMed  Google Scholar 

  • Anteunis MJO (1978) The cyclic dipeptides: proper model compounds in peptide research. Bull Chem Soc Belg 87:627–650

    Article  CAS  Google Scholar 

  • Bavykin SG, Lysov YP, Zakhariev V, Kelly JJ, Jackman J, Stahl DA, Cherni A (2004) Use of 16S rRNA, 23S rRNA, and gyrB gene sequence analysis to determine phylogenetic relationships of Bacillus cereus group microorganisms. J Clin Microbiol 42:3711–3730

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Boszormeny E, Rsek TE, Fodor A, Fodor AM, Szldes FL, Hevesi M, Hogan JS, Katona Z, Klein MG, Kormány A, Pekár S, Szentirmai A, Sztaricskai F, Taylor RAJ (2009) Isolation and activity of Xenorhabdus antimicrobial compounds against the plant pathogens Erwinia amylovora and Phytophthora nicotianae. J Appl Microbiol 107:746–759

    Article  Google Scholar 

  • Chen G, Dunphy GB, Webster JM (1994) Antifungal activity of two Xenorhabdus species and Photorhabdus luminescens, bacteria associated with the nematodes Steinernema species and Heterorhabditis megidis. Biol Control 4:157–162

    Article  Google Scholar 

  • Chen G, Maxwell P, Dunphy GB, Webster JM (1996) Culture conditions for Xenorhabdus and Photorhabdus symbionts of entomopathogenic nematodes. Nematologica 42:124–127

    Article  Google Scholar 

  • CLSI, Clinical and Laboratory Standards Institute (2006) Methods for dilution antimicrobial susceptibility tests for bacteria that grow aerobically. CLSI documents M27-S3. 940 West Valley Road, Suite 1400, Wayne, Pennsylvania 19087–1898 USA

  • CLSI, Clinical and Laboratory Standards Institute (2008) Reference methods for broth dilution antifungal susceptibility tests of yeasts. CLSI documents M27-S3. 940 West Valley Road, Suite 1400, Wayne, Pennsylvania 19087–1898 USA

  • Dal Bello F, Clarke CI, Ryan LAM, Ulmer H, Schober TJ, Ström K, Sjögren J, van Sinderen D, Schnürer J, Arendt EK (2007) Improvement of the quality and shelf life of wheat bread by fermentation with the antifungal strain Lactobacillus plantarum FST 1.7. J Cereal Sci 45:309–318

    Article  CAS  Google Scholar 

  • De Rosa S, Mitova M, Tommonaro G (2003) Marine bacteria associated with sponge as source of cyclic peptides. Biomol Eng 20:311–316

    Article  PubMed  Google Scholar 

  • Deepa I, Mohandas C, Makesh KT, Siji JV, Prakash KBS, Babu B (2010) Identification of new entomopathogenic nematodes (EPNs) based on sequences of D2-D3 expansion fragments of the 28SrRNA. J Root Crops 36(2):227–232

    Google Scholar 

  • Degrassi G, Aguilar C, Bosco M, Zahariev S, Pongor S, Venturi V (2002) Plant growth-promoting Pseudomonas putida WCS358 produces and secrets four cyclic dipeptides: cross-talk with quorum sensing bacterial sensors. Curr Microbiol 45:250–254

    Article  CAS  PubMed  Google Scholar 

  • Fdhila F, Vazquez V, Sanchez JL, Riguera R (2003) DD-Diketopiperazines: antibiotics active against Vibrio anguillarum isolated from marine bacteria associated with cultures of Pecten maximus. J Nat Prod 66:1299–1301

    Article  CAS  PubMed  Google Scholar 

  • Forst S, Nealson KH (1996) Molecular biology of the symbiotic–pathogenic bacteria Xenorhabdus spp. and Photorhabdus spp. Microbiol Rev 60:21–43

    CAS  PubMed Central  PubMed  Google Scholar 

  • Forst S, Dowds B, Boemare N, Stackebrandt E (1997) Xenorhabdus and Photorhabdus spp. Bugs that kill bugs. Annu Rev Microbiol 51:47–72

    Article  CAS  PubMed  Google Scholar 

  • Gaugler R, Kaya HK (1990) Entomopathogenic nematodes in biological control. CRC, Boca Raton, pp 75–90

    Google Scholar 

  • Graz M, Hunt A, Jamie H, Grant G, Milne P (1999) Antimicrobial activity of selected cyclic dipeptides. Pharmazie 54:772–775

    CAS  PubMed  Google Scholar 

  • Gualtieri M, Aumelasm A, Thaler JO (2009) Identification of a new antimicrobial lysine-rich cyclolipopeptide family from Xenorhabdus nematophila. J Antibiot 62:295–302

    Article  CAS  PubMed  Google Scholar 

  • Guo Q, Guo D, Zhao B, Xu J, Li R (2007) Two cyclic dipeptides from Pseudomonas fluorescens GcM5-1A carried by the pine wood nematode and their toxicities to Japanese black pine suspension cells and seedlings in vitro. J Nematol 39(3):243–247

    CAS  PubMed Central  PubMed  Google Scholar 

  • Holden MTG, Chhabra SR, de Nys R, Stead P, Bainton NJ, Hill PJ, Manefield M, Kumar N, Labatte M, England D, Rice S, Givskov M, Salmond GPC, Stewart GSAB, Bycroft BW, Kjelleberg SA, Williams P (1999) Quorem- sensing cross talk: isolation and chemical characterization of cyclic dipeptides from Pseudomonas aeruginosa and other gram negative bacteria. Mol Microbiol 33:1254

    Article  CAS  PubMed  Google Scholar 

  • Houston DR, Synstad B, Eijsink VG, Stark MJ, Eggleston IM, van Aalten DM (2004) Structure-based exploration of cyclic dipeptide chitinase inhibitors. J Med Chem 47:5713–5720

    Article  CAS  PubMed  Google Scholar 

  • Hsieh PW, Hsu LC, Lai CH, Wu CC, Hwang TL, Lin YK, Wu YC (2009) Evaluation of the bioactivities of extracts of endophytes isolated from Taiwanese herbal plants. World J Microbiol Biotechnol 25:1461–1469

    Article  Google Scholar 

  • Hu K, Li J, Wang W, Wu H, Lin H, Webster JM (1998) Comparison of metabolites produced in vitro and in vivo by Photorhabdus luminescens, a bacterial symbiont of the entomopathogenic nematode Heterorhabditis megidis. Can J Microbiol 44:1072–1077

    Article  CAS  Google Scholar 

  • Jayatilake GS, Thornton MP, Leonard AC, Grimwade JE, Baker BJ (1996) Metabolites from an antarctic sponge-associated bacterium, Pseudomonas aeruginosa. J Nat Prod 59:293–296

    Article  CAS  PubMed  Google Scholar 

  • Ji DJ, Yi YK, Kang GH (2004) Identification of an antibacterial compound, benzylideneacetone, from Xenorhabdus nematophila against major plant-pathogenic bacteria. FEMS Microbiol Lett 239:241–248

    Article  CAS  PubMed  Google Scholar 

  • Joyce SA, Brachmann AO, Itamar G, Lea L, Gertrud S, David C, Bode HB (2008) Bacterial biosynthesis of a multipotent stilbene. Angew Chem Int Ed 47:1942–1945

    Article  CAS  Google Scholar 

  • Lang G, Kalvelage T, Peters A, Wiese J, Imhoff JF (2008) Peptides from the entomopathogenic bacterium Xenorhabdus nematophilus. J Nat Prod 71:1074–1077

    Article  CAS  PubMed  Google Scholar 

  • Li J, Chen GH, Wu HM, Webster JM (1995) Identification of two pigments and a hydroxystilbene antibiotic from Photorhabdus luminescens. Appl Environ Microbiol 61:4329–4333

    CAS  PubMed Central  PubMed  Google Scholar 

  • Li JX, Chen GH, Webster JM (1997) Nematophin, a novel antimicrobial substance produced by Xenorhabdus nematophilus (Enterobactereaceae). Can J Microbiol 43:770–773

    Article  CAS  PubMed  Google Scholar 

  • Li X, Sergey D, Ying X, Xiao X, Oi H, Qian P (2006) Antifouling diketopiperazines produced by a deep-sea bacterium. Streptomyces fungicidicus. Biofouling 22:201

    Article  CAS  PubMed  Google Scholar 

  • Marfey P (1984) Determination of D-amino acids. II. Use of a bifunctional reagents, 1,5-difluoro-2,4-dinitrobenzene. Carlsberg Res Commun 49:591–596

    Article  CAS  Google Scholar 

  • Martins MB, Carvalho I (2007) Diketopiperazines: biological activity and synthesis. Tetrahedron 63:9923–9932

    Article  CAS  Google Scholar 

  • McInerney BV, Gregson RP, Lacey MJ, Akhurst RJ, Lyons GR, Rhodes SH, Smith DRJ, Engelhardt LM (1991a) Biologically active metabolites from Xenorhabdus spp. Part 1. Dithiolopyrrolone derivatives with antibiotic activity. J Nat Prod 54:774–784

    Article  CAS  PubMed  Google Scholar 

  • McInerney BV, Taylor WC, Lacey MJ, Akhurst RJ, Gregson RP (1991b) Biologically active metabolites from Xenorhabdus spp. Part 2 Benzopyran-1-one derivatives with gastroprotective activity. J Nat Prod 54:785–795

    Article  CAS  PubMed  Google Scholar 

  • Mohandas C, Sheeba M, Firoza AJ, Rajamma P (2007) Bacteria associated with Rhabditis (Oscheius) spp. (Rhabditidae: Nematoda) for the biocontrol of insect pests. Proc Nat Seminar on Achievements and Opportunities in Post harvest Management and Value Addition in Root and Tuber Crops (NSRTC–2), p 195–198

  • Murray PR, Baron EJ, Pfaller MA, Tenover FC, Yolke RH (1995) Manual clinic microbiol, vol 6. ASM, Washington, DC

    Google Scholar 

  • Nicholson B, Lloyd GK, Miller BR, Palladino MA, Kiso Y, Hayashi Y, Neuteboom ST (2006) NPI-2358 is a tubulin-depolymerizing agent: in-vitro evidence for activity as a tumor vascular-disrupting agent. Anticancer Drugs 17:25–31

    Article  CAS  PubMed  Google Scholar 

  • Paul VJ, Frautschy S, Fenical W, Nealson KH (1981) Antibiotics in microbial ecology, isolation and structure assignment of several new antibacterial compounds from the insect symbiotic bacteria Xenorhabdus spp. J Chem Ecol 7:589–597

    Article  CAS  PubMed  Google Scholar 

  • Prasad C (1995) Bioactive cyclic dipeptides. Peptides 16:151–164

    Article  CAS  PubMed  Google Scholar 

  • Rhee KH (2002) Isolation and characterization of Streptomyces sp. KH-614 producing anti-VRE (vancomycin-resistant enterococci) antibiotics. J Gen Appl Microbiol 48:327–331

    Article  Google Scholar 

  • Rhee KH (2003) Purification and identification of an antifungal agent from Streptomyces sp. KH-614 antagonistic to rice blast fungus, Pyricularia oryzae. J Microbiol Biotechnol 13(6):984–988

    CAS  Google Scholar 

  • Rhee KH (2004) Cyclic dipeptides exhibit synergistic, broad spectrum antimicrobial effects and have anti-mutagenic properties. Int J Antimicrob Agents 24:423–427

    Article  CAS  PubMed  Google Scholar 

  • Rhee KH (2006) In vitro activity of cyclic dipeptides against gram-positive and gram- negative anaerobic bacteria and radioprotective effect on lung cells. J Microbiol Biotechnol 16(1):158–162

    CAS  Google Scholar 

  • Richardson WH, Schmidt TM, Nealson KH (1988) Identification of an anthraquinone pigment and a hydroxystilbene antibiotic from Xenorhabdus luminescens. Appl Environ Microbiol 54:1602–1605

    CAS  PubMed Central  PubMed  Google Scholar 

  • Rollas S, Kalyoncuoglu N, Sur-Altiner D, Yegenglu Y (1993) 5-(4-Aminophenyl)-4-substituted 2,4-dihydro-3H-1,2,4-triazole-3-thiones: synthesis, antibacterial and antifungal activities. Pharmazie 48:308–309

    CAS  PubMed  Google Scholar 

  • Rudi A, Kashman Y, Benayahu Y, Schleyer M (1994) Amino acid derivatives from the marine sponge Jaspis digonoxea. J Nat Prod 57:829

    Article  CAS  PubMed  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  • Shin HJ, Mojid Mondol MA, Yu TK, Lee HS, Lee YJ, Jin HJ, Kim JH, Kwon HJ (2010) An angiogenesis inhibitor isolated from a marine-derived actinomycete, Nocardiopsis sp. 03N67. Phytochem Lett 3:194–197

    Article  CAS  Google Scholar 

  • Smith-Palmer A, Stewart J, Fyfe L (1998) Antimicrobial properties of plant essential oils and essences against five important food-borne pathogens. Lett Appl Microbiol 26:118–122

    Article  CAS  PubMed  Google Scholar 

  • Song MK, Hwang IK, Rosenthal MJ, Harris DM, Yamaguchi DT, Yip I, Go VLW (2003) Anti-hyperglycemic activity of zinc plus cyclo(His-Pro) in genetically diabetic goto-kakizaki and aged rats. Exp Biol Med 228:1338–1345

    CAS  Google Scholar 

  • Stierle AC, Cardellina JH, Strobel GA (1988) Maculosin, a host-specific phytotoxin for spotted knapweed from Alternaria alternate. Proc Natl Acad Sci USA 85(21):8008–8011

    Article  CAS  PubMed  Google Scholar 

  • Strom K, Sjogren J, Broberg A, Schnurer J (2002) Lactobacillus plantarum MiLAB 393 produces the antifungal cyclic dipeptides cyclo(L-Phe-L-Pro) and cyclo(L-Phe-trans-4-OH-L-pro) and 3-phenyllactic acid. Appl Environ Microbiol 68:4322–4327

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Tailliez P, Laroui C, Ginibre N, Paule A, Page S, Boemare N (2010) Phylogeny of Photorhabdus and Xenorhabdus based on universally conserved protein-coding sequences and implications for the taxonomy of these two genera. Proposal of new taxa: X. vietnamensis sp. nov., P. luminescens subsp. Caribbeanensis subsp. nov., P. luminescens subsp. hainanensis subsp. nov., P. temperata subsp. Khanii subsp. nov., P. temperata subsp. Tasmaniensis subsp. nov., and the reclassification of P. luminescens subsp. thracensis as P. temperate subsp. thracensis comb. nov. Syst Evol Microbiol 60:1921–1937

    Article  Google Scholar 

  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731–2739

    Article  CAS  PubMed  Google Scholar 

  • Thompson JD, Higgins DG, Gibson TJ (1994) Clustal-W—Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • van der Merwe E, Huang D, Peterson D, Kilian G, Milne PJ, Van de Venter M, Frost C (2008) The synthesis and anticancer activity of selected diketopiperazines. Peptides 29:1305–1311

    Article  PubMed  Google Scholar 

  • Wang Y, Mueller UG, Clardy J (1999) Antifungal diketopiperazines from symbiotic fungus of fungus-growing ant Cyphomyrmex minutus Antifungal. J Chem Ecol 25(4):245–257

    Google Scholar 

  • Wang G, Dai S, Chen M, Wu H, Lianwu X, Xiongming L, Li Z (2010) Two diketopiperazine Cyclo(Pro-Phe) isomers from marine bacteria Bacillus subtilis sp. 13-2. Chem Nat Comps 46(4):583–585

    Article  CAS  Google Scholar 

  • Yan PS, Song Y, Sakuno E, Nakajima H, Nakagawa H, Yabe K (2004) Cyclo(Lleucyl-L-prolyl) produced by Achromobacter xylosoxidans inhibits aflatoxin production by Aspergillus parasiticus. Appl Environ Microbiol 70:7466–7473

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Yang L, Tan R, Wang Q, Huang W, Yinc Y (2002) Antifungal cyclopeptides from Halobacillus litoralis YS3106 of marine origin. Tetrahedron Letts 43:6545–6548

    Article  CAS  Google Scholar 

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Acknowledgments

The authors are grateful to the Indian Council Medical Research (ICMR), Government of India for funding. We thank the Director, CTCRI, for providing facilities for the work.

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Authors and Affiliations

  1. Division of Crop Protection, Division of Crop Utilisation, Central Tuber Crops Research Institute, Sreekariyam, Thiruvananthapuram, 695017, India

    Sasidharan Nishanth Kumar, Bala Nambisan & Chellapan Mohandas

  2. Division of Agroprocessing and Natural Products, NIIST, Trivandrum, India

    Andikkannu Sundaresan

  3. Integrated Cancer Research Program, Division of Cancer Research, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India

    Ruby John Anto

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  1. Sasidharan Nishanth Kumar
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Correspondence to Sasidharan Nishanth Kumar.

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Kumar, S.N., Nambisan, B., Sundaresan, A. et al. Isolation and identification of antimicrobial secondary metabolites from Bacillus cereus associated with a rhabditid entomopathogenic nematode. Ann Microbiol 64, 209–218 (2014). https://doi.org/10.1007/s13213-013-0653-6

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Keywords

  • Bacillus cereus
  • Secondary metabolite
  • Purification
  • Antimicrobial