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Detection of Antibiotics Produced by Soil and Rhizosphere Microbes In Situ

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Book cover Secondary Metabolites in Soil Ecology

Part of the book series: Soil Biology ((SOILBIOL,volume 14))

It has long been known that certain antibiotic-producing soil microorganisms are inhibitory to plant pathogens, both in the laboratory and in the field (Stallings 1954). The exploitation of these natural antagonistic interactions has been a driving force in research on the biological control of plant pathogens over the past century, but only in recent decades has pathogen control by antibiotics produced at biologically relevant levels in the environment been demonstrated conclusively. This progress, resulting from conceptual and technological advances made initially in the laboratory and then extended to the field, has set new standards for biocontrol research involving antibiotics. More generally, the approaches used in these studies may be useful in exploring the significance of other bioactive metabolites produced by microorganisms in their native habitats.

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References

  • Bakker PA, Glandorf DC, Viebahn M, Ouwens TW, Smit E, Leeflang P, Wernars K, Thomashow LS, Thomas-Oates JE, van Loon LC (2002) Effects of Pseudomonas putida modified to produce phenazine-1-carboxylic acid and 2,4-diacetylphloroglucinol on the microflora of field grown wheat. Antonie Van Leeuwenhoek 81:617–624

    Article  PubMed  CAS  Google Scholar 

  • Blouin-Bankhead S, Landa B, Lutton E, Weller DM, McSpadden Gardener B (2004) Minimal changes in rhizobacterial population structure following root colonization by wild type and transgenic biocontrol strains. FEMS Microbiol Ecol 49:307–318

    Article  CAS  Google Scholar 

  • Blum U, Worsham AD, King LD, Gerig TM (1994) Use of water and EDTA extractions to estimate available (free and reversibly bound) phenolic acids in Cecil soils. J Chem Ecol 20:341–359

    Article  CAS  Google Scholar 

  • Bonsall RF, Weller DM Thomashow LS (1997) Quantification of 2,4-diacetylphloroglucinol produced by fluorescent Pseudomonas spp. in vitro and in the rhizosphere of wheat. Appl Environ Microbiol 63:951–955

    PubMed  CAS  Google Scholar 

  • Bottiglieri M, Keel C (2006) Characterization of PhlG, a hydrolase that specifically degrades the antifungal compound 2,4-diacetylphloroglucinol. Appl Environ Microbiol 72:418–427

    Article  PubMed  CAS  Google Scholar 

  • Chander Y, Kumar K, Goyal SM, Gupta SC (2005) Antibacterial activity of soil-bound antibiotics. J Environ Qual 34:1952–1957

    Article  PubMed  CAS  Google Scholar 

  • Chin-A-Woeng TFC, Bloemberg GV, van der Bij AJ, van der Drift KMGM, Schripsema J, Kroon B, Scheffer RJ, Keel C, Bakker PAHM, Tichy J-V, de Bruijn FJ, Thomas-Oates JE, Lugtenberg BJJ (1998) Biocontrol by phenazine-1-carboxamide-producing Pseudomonas chlororaphis PCL 1391 of tomato root rot caused by Fusarium oxysporum f. sp. radicis-lycopersici. Mol Plant Microbe Interact 11:1069–1077

    Article  CAS  Google Scholar 

  • Chiou CT (1989) Theoretical considerations of the partition uptake of nonionic organic compounds by soil organic matter. In: Sawhney BL, Brown K (eds) Reactions and movement of organic chemicals in soils. SSSA special publication 22. Soil Science Society of America, Madison, pp 1–29

    Google Scholar 

  • Dalton BR, Weed SB, Blum U (1989) Differential sorption of exogenously applied ferulic.p-coumaric, p-hydroxybenzoic, and vanillic acids in soil. Soil Sci Soc Am J 51:1515–1521

    Google Scholar 

  • De La Fuente L, Mavrodi DV, Landa BB, Thomashow LS, Weller DM (2006) phlD-based genetic diversity and detection of genotypes of 2,4-diacetylphloroglucinol-producing Pseudomonas fluorescens. FEMS Microbiol Ecol 56:64–78

    Article  PubMed  CAS  Google Scholar 

  • De Leij FAAM, Sutton EJ, Whipps JM, Fenton JS, Lynch JM (1995) Impact of a field release of genetically modified Pseudomonas fluorescens on indigenous microbial populations of wheat. Appl Environ Microbiol 61:3443–3453

    PubMed  CAS  Google Scholar 

  • Delaney SM, Mavrodi DV, Bonsall RF, Thomashow LS (2001) phzO, a gene for biosynthesis of 2-hydroxylated phenazine compounds in Pseudomonas aureofaciens 30–84. J Bacteriol 183:318–327

    Article  PubMed  CAS  Google Scholar 

  • Díaz-Cruz MS, Barceló, D (2005) LC-MS2 trace analysis of antimicrobials in water, sediment and soil. Trends Anal Chem 24:645–657

    Article  CAS  Google Scholar 

  • Glandorf DC, Verheggen P, Jansen T, Jorritsma JW, Smit E, Leeflang P, Wernars K, Thomashow LS, Laureijs E, Thomas-Oates JE, Bakker PA, van Loon LC (2001) Effect of genetically modified Pseudomonas putida WCS358r on the fungal rhizosphere microflora of field-grown wheat. Appl Environ Microbiol 67:3371–3378

    Article  PubMed  CAS  Google Scholar 

  • Gross H, Stockwell VO, Henkels MD, Nowak-Thompson B, Loper JE, Gerwick, WH (2007) The genomisotopic approach: A systematic method to isolate products of orphan biosynthetic gene clusters. Chem Biol 14:53–63

    Article  PubMed  CAS  Google Scholar 

  • Haas D, Keel C (2003) Regulation of antibiotic production in root-colonizing Pseudomonas spp. and relevance for biological control of plant disease. Annu Rev Phytopathol 41:117–153

    Article  PubMed  CAS  Google Scholar 

  • Haas D, Blumer C, Keel C (2000) Biocontrol ability of fluorescent pseudomonads genetically dissected: importance of positive feedback regulation. Curr Opin Biotechnol 11:290–297

    Article  PubMed  CAS  Google Scholar 

  • Huang Z, Bonsall RF, Mavrodi DV, Weller DM, Thomashow LS (2004) Transformation of Pseudomonas fluorescens with genes for biosynthesis of phenazine-1-carboxylic acid improves biocontrol of Rhizoctonia root rot and in situ antibiotic production. FEMS Microbiol Ecol 49:243–251

    Article  PubMed  CAS  Google Scholar 

  • Iavicoli A, Boutet E, Buchala A, Métraux JP (2003) Induced systemic resistance in Arabidopsis thaliana in response to root inoculation with Pseudomonas fluorescens CHA0. Mol Plant Microbe Interact 16:851–858

    Article  PubMed  CAS  Google Scholar 

  • Jacobsen AM, Halling-Sørensen B, Ingerslev F, Hansen SH (2004) Simultaneous extraction of tetracycline, macrolide and sulfonamide antibiotics from agricultural soils using pressurised liquid extraction, followed by solid-phase extraction and liquid chromatography-tandem mass spectrometry. J Chromatogr A 1038:157–170

    Article  PubMed  CAS  Google Scholar 

  • Kim S-C, Carlson K (2005) LS-MS2 for quantifying trace amounts of pharmaceutical compounds in soil and sediment matrices. Trends Anal Chem 24:635–644

    Article  CAS  Google Scholar 

  • Kim SC, Carlson K (2006) Occurrence of ionophore antibiotics in water and sediments of a mixed-landscape watershed. Water Res 40:2549–2560

    Article  PubMed  CAS  Google Scholar 

  • Leeflang P, Smit E, Glandorf DCM, van Hannen EJ, Wernars K (2002) Effects of Pseudomonas putida WCS358r and its genetically modified phenazine producing derivative on the Fusarium population in a field experiment, as determined by 18S rDNA analysis. Soil Biol Biochem 34:1021–1025

    Article  CAS  Google Scholar 

  • Loper JE, Lindow SE (2002) Reporter gene systems useful in evaluating in situ gene expression by soil- and plant-associated bacteria. In: Hurst CJ, Crawford RL, Knudsen GR, McInerney MJ, Stetzenbach LD (eds) Manual of environmental microbiology, 2nd edn. American Society of Microbiology, Washington, pp 627–637

    Google Scholar 

  • Lehmann RG, Cheng HH, Harsh JB (1987) Oxidation of phenolic acids by soil iron and manganese oxides. Soil Sci Soc Am J 51:352–356

    CAS  Google Scholar 

  • Mavrodi OV, Mavrodi DV, Thomashow LS, Weller DM (2007) Quantification of 2,4-diacetylphloroglucinol-producing Pseudomonas fluorescens in the plant rhizosphere by real-time PCR. Appl Environ Microbiol 73:5531–5538

    Article  PubMed  CAS  Google Scholar 

  • Mavrodi OV, McSpadden-Gardener BB, Mavrodi DV, Bonsall RF, Weller DM, Thomashow LS (2001). Genetic diversity of phlD from 2,4-diacetylphloroglucinol-producing fluorescent Pseudomonas spp. Phytopathology 91:35–43

    Article  PubMed  CAS  Google Scholar 

  • McSpadden-Gardener BB, Mavrodi DV, Thomashow LS, Weller DM (2001) A rapid polymerase chain reaction-based assay characterizing rhizosphere populations of 2,4-diacetylphloroglucinol-producing bacteria. Phytopathology 91:44–54

    Article  PubMed  CAS  Google Scholar 

  • Metsä-Ketalä M, Salo V, Halo L, Hautala A, Hakala J, Mäntsälä P, Ylihonko K (1999) An efficient approach for screening minimal PKS genes from Streptomyces. FEMS Microbiol Lett 180:1–6

    Google Scholar 

  • Moënne-Loccoz Y, Tichy HV, O’Donnell A, Simon R, O’Gara F (2001) Impact of 2,4-diacetylphloroglucinol-producing biocontrol strain Pseudomonas fluorescens F113 on intraspecific diversity of resident culturable fluorescent pseudomonads associated with the roots of field-grown sugar beet seedlings. Appl Environ Microbiol 67:3418–3425

    Article  PubMed  Google Scholar 

  • Nakayama T, Homma Y, Hashidoko Y, Mizutani J, Tahara S (1999) Possible role of xanthobaccins produced by Stenotrophomonas sp. strain SB-K88 in suppression of sugar beet damping-off disease. Appl Environ Microbiol 65:4334–4339

    PubMed  CAS  Google Scholar 

  • Natsch A, Keel C, Hebecker N, Laasik E, Défago G (1998) Impact of Pseudomonas fluorescens strain CHA0 and a derivative with improved biocontrol activity on the culturable resident bacterial community on cucumber roots. FEMS Microbiol Ecol 27:365–380

    Article  CAS  Google Scholar 

  • Nielsen TH, Sørensen J (2003) Production of cyclic lipopeptides by Pseudomonas fluorescens strains in bulk soil and in the sugar beet rhizosphere. Appl Environ Microbiol 69:861–868

    Article  PubMed  CAS  Google Scholar 

  • Ownley BH, Duffy BK, Weller DM (2003) Identification and manipulation of soil properties to improve the biological control performance of phenazine-producing Pseudomonas fluorescens. Appl Environ Microbiol 69:3333–3343

    Article  PubMed  CAS  Google Scholar 

  • Pessi C, Blumer C, Haas D (2002) lacZ fusions report gene expression, don’t they? Microbiology 147:1993–1995

    Google Scholar 

  • Petrović M, Hernando MD, Díaz-Cruz MS, Barceló D (2005) Liquid chromatography-tandem mass spectrometry for the analysis of pharmaceutical residues in environmental samples: a review. J Chromatogr A 1067:1–14

    Article  PubMed  CAS  Google Scholar 

  • Picard C, di Cello F, Ventura M, Fani R, Gluckert A (2000) Frequency and biodiversity of 2,4-diacetylphloroglucinol-producing bacteria isolated from the maize rhizosphere at different stages of plant growth. Appl Environ Microbiol 66:948–955

    Article  PubMed  CAS  Google Scholar 

  • Raaijmakers JM, Weller DM, Thomashow LS (1997) Frequency of antibiotic-producing Pseudomonas spp. in natural environments. Appl Environ Microbiol 63:881–887

    PubMed  CAS  Google Scholar 

  • Raaijmakers JM, Bonsall RF, Weller DM (1999) Effect of population density of Pseudomonas fluorescens on production of 2,4-diacetylphloroglucinol in the rhizosphere of wheat. Phytopathology 89:470–475

    Article  PubMed  CAS  Google Scholar 

  • Ramos L, Kristenson EM, Brinkman UAT (2002) Current use of pressurised liquid extraction and subcritical water extraction in environmental analysis. J Chromatogr A 975:3–29

    Article  PubMed  CAS  Google Scholar 

  • Renew JE, Huang CH (2004) Simultaneous determination of fluoroquinolone, sulfonamide, and trimethoprim antibiotics in wastewater using tandem solid phase extraction and liquid chromatography-electrospray mass spectrometry. J Chromatogr A 1042:113–121

    Article  PubMed  CAS  Google Scholar 

  • Seow KT, Meurer G, Gerlitz M, Wendt-Pienkowski E, Hutchinson CR, Davies J (1997) A study of iterative type II polyketide synthases, using bacterial genes cloned from soil DNA: a means to access and use genes from uncultured microorganisms. J Bacteriol 179:7360–7368

    PubMed  CAS  Google Scholar 

  • Shanahan P, Borro A, O’Gara F, Glennon JD (1992) Isolation, trace enrichment and liquid chromatographic analysis of diacetylphloroglucinol in culture and soil samples using UV and amperometric detection. J Chromatogr 606:171–177

    Article  CAS  Google Scholar 

  • Stallings JH (1954) Soil produced antibiotics-plant disease and insect control. Bacteriol Rev 18:131–146

    PubMed  CAS  Google Scholar 

  • Stoob K, Singer HP, Stettler S, Hartmann N, Mueller S, Stamm CH (2006) Exhaustive extraction of sulfonamide antibiotics from aged agricultural soils using pressurized liquid extraction. J Chromatogr A 1128:1–9

    Article  PubMed  CAS  Google Scholar 

  • ter Laak TL, Gebbink WA, Tolls J (2006a) The effect of pH and ionic strength on the sorption.of sulfachloropyridazine, tylosin, and oxytetracycline to soil. Environ Toxicol Chem 25:904–911

    Article  PubMed  Google Scholar 

  • ter Laak TL, Gebbink WA, Tolls J (2006b) Estimation of soil sorption coefficients of veterinary pharmaceuticals from soil properties. Environ Toxicol Chem 25:933–941

    Article  PubMed  Google Scholar 

  • Thiele-Bruhn S, Seibicke T, Schulten HR, Leinweber P (2004) Sorption of sulfonamide pharmaceutical antibiotics on whole soils and particle-size fractions. J Environ Qual 33:1331–1342

    Article  PubMed  CAS  Google Scholar 

  • Thirup L, Johnsen K, Winding A (2001) Succession of indigenous Pseudomonas spp. and actinomycetes on barley roots affected by the antagonistic strain Pseudomonas fluorescens DR54 and the fungicide imazalil. Appl Environ Microbiol 67:1147–1153

    Article  PubMed  CAS  Google Scholar 

  • Thomashow LS, Weller DM, Bonsall RF, Pierson LS (1990) Production of the antibiotic phenazine-1-carboxylic acid by fluorescent Pseudomonas species in the rhizosphere of wheat. Appl Environ Microbiol 56:908–912

    PubMed  CAS  Google Scholar 

  • Thomashow LS, Bonsall RF, Weller DM (1997) Antibiotic production by soil and rhizosphere microbes in situ. In: Hurst CJ, Knudsen GR, McInerney MJ, Stetzenbach LD, Walter MV (eds) Manual of environmental microbiology, 1st edn. American Society of Microbiology, Washington, pp 493–499

    Google Scholar 

  • Thomashow LS, Bonsall RF, Weller DM (2002) Antibiotic production by soil and rhizosphere microbes in situ. In: Hurst CJ, Crawford RL, Knudsen, GR, McInerney MJ, Stetzenbach LD (eds) Manual of environmental microbiology, 2nd edn. American Society of Microbiology, Washington, DC, pp 636–647

    Google Scholar 

  • Timms-Wilson TM, Kilshaw K, Bailey MJ (2004) Risk assessment for engineered bacteria used in biocontrol of fungal disease in agricultural crops. Plant Soil 266:57–67

    Article  CAS  Google Scholar 

  • Tolls J (2001) Sorption of veterinary pharmaceuticals in soils: a review. Environ Sci Technol 35:3397–3406

    Article  PubMed  CAS  Google Scholar 

  • Validov S, Mavrodi O, De La Fuente, L, Boronin A, Weller D, Thomashow L, Mavrodi D (2005) Antagonistic activity among 2,4-diacetylphloroglucinol-producing fluorescent Pseudomonas spp. FEMS Microbiol Lett 242:249–256

    Article  PubMed  CAS  Google Scholar 

  • Viebahn M, Glandorf DCM, Ouwens TWM, Smit E, Leeflang P, Wernars K, Thomashow L, van Loon LC, Bakker PAHM (2003) Repeated introduction of genetically modified Pseudomonas putida WCS358r without intensified effects on the indigenous microflora of field-grown wheat. Appl Environ Microbiol 69:3110–3118

    Article  PubMed  CAS  Google Scholar 

  • Viebahn M, Veenman C, Wernars K, van Loon LC, Smit E, Bakker PAHM (2005a) Assessment of differences in ascomycete communities in the rhizosphere of field-grown wheat and potato. FEMS Microbiol Ecol 53:245–253

    Article  PubMed  CAS  Google Scholar 

  • Viebahn M, Doornbos R, Wernars K, van Loon LC, Smit E, Bakker PAHM (2005b) Ascomycete communities in the rhizosphere of field-grown wheat are not affected by introductions of genetically modified Pseudomonas putida WCS358r. Environ Microbiol 7:1775–1785

    Article  PubMed  CAS  Google Scholar 

  • Weber JB, Miller CT (1989) Organic chemical movement over and through soil. In: Sawhney BL, Brown K (eds) Reactions and movement of organic chemicals in soils. SSSA special publication 22. Soil Science Society of America, Madison, pp 305–354

    Google Scholar 

  • Winding A, Binnerup SJ, Pritchard H (2004) Non-target effects of bacterial biological control agents suppressing root pathogenic fungi. FEMS Microbiol Ecol 47:129–141

    Article  PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. USDA, ARS Washington State University, Pullman, WA, USA

    Linda S. Thomashow

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  1. Linda S. Thomashow
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  2. Robert F. Bonsall
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  3. David M. Weller
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  1. Molecular Phytopathology and Mycotoxin Research, University of Göttingen, Grisebachstraße 6, 37077, Göttingen, Germany

    Petr Karlovsky

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Thomashow, L.S., Bonsall, R.F., Weller, D.M. (2008). Detection of Antibiotics Produced by Soil and Rhizosphere Microbes In Situ. In: Karlovsky, P. (eds) Secondary Metabolites in Soil Ecology. Soil Biology, vol 14. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-74543-3_2

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