WO2014149241A1 - Souche bactérienne isolée du genre burkholderia et métabolites pesticides correspondants - Google Patents

Souche bactérienne isolée du genre burkholderia et métabolites pesticides correspondants Download PDF

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Publication number
WO2014149241A1
WO2014149241A1 PCT/US2014/015799 US2014015799W WO2014149241A1 WO 2014149241 A1 WO2014149241 A1 WO 2014149241A1 US 2014015799 W US2014015799 W US 2014015799W WO 2014149241 A1 WO2014149241 A1 WO 2014149241A1
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Prior art keywords
weed
composition
burkholderia
isolated
sedge
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PCT/US2014/015799
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English (en)
Inventor
Ratnakar Asolkar
Marja Koivunen
Pamela Marrone
Huazhang Huang
Ana Lucia Cordova-Kreylos
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Marrone Bio Innovations, Inc.
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Priority claimed from US13/843,971 external-priority patent/US8822193B2/en
Application filed by Marrone Bio Innovations, Inc. filed Critical Marrone Bio Innovations, Inc.
Publication of WO2014149241A1 publication Critical patent/WO2014149241A1/fr

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N1/00—Microorganisms, e.g. protozoa; Compositions thereof; Processes of propagating, maintaining or preserving microorganisms or compositions thereof; Processes of preparing or isolating a composition containing a microorganism; Culture media therefor
    • C12N1/20—Bacteria; Culture media therefor
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01N—PRESERVATION OF BODIES OF HUMANS OR ANIMALS OR PLANTS OR PARTS THEREOF; BIOCIDES, e.g. AS DISINFECTANTS, AS PESTICIDES OR AS HERBICIDES; PEST REPELLANTS OR ATTRACTANTS; PLANT GROWTH REGULATORS
    • A01N43/00—Biocides, pest repellants or attractants, or plant growth regulators containing heterocyclic compounds
    • A01N43/72—Biocides, pest repellants or attractants, or plant growth regulators containing heterocyclic compounds having rings with nitrogen atoms and oxygen or sulfur atoms as ring hetero atoms
    • A01N43/74—Biocides, pest repellants or attractants, or plant growth regulators containing heterocyclic compounds having rings with nitrogen atoms and oxygen or sulfur atoms as ring hetero atoms five-membered rings with one nitrogen atom and either one oxygen atom or one sulfur atom in positions 1,3
    • A01N43/76—1,3-Oxazoles; Hydrogenated 1,3-oxazoles
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01N—PRESERVATION OF BODIES OF HUMANS OR ANIMALS OR PLANTS OR PARTS THEREOF; BIOCIDES, e.g. AS DISINFECTANTS, AS PESTICIDES OR AS HERBICIDES; PEST REPELLANTS OR ATTRACTANTS; PLANT GROWTH REGULATORS
    • A01N63/00—Biocides, pest repellants or attractants, or plant growth regulators containing microorganisms, viruses, microbial fungi, animals or substances produced by, or obtained from, microorganisms, viruses, microbial fungi or animals, e.g. enzymes or fermentates
    • A01N63/20—Bacteria; Substances produced thereby or obtained therefrom
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N1/00—Microorganisms, e.g. protozoa; Compositions thereof; Processes of propagating, maintaining or preserving microorganisms or compositions thereof; Processes of preparing or isolating a composition containing a microorganism; Culture media therefor
    • C12N1/20—Bacteria; Culture media therefor
    • C12N1/205—Bacterial isolates
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12R—INDEXING SCHEME ASSOCIATED WITH SUBCLASSES C12C - C12Q, RELATING TO MICROORGANISMS
    • C12R2001/00—Microorganisms ; Processes using microorganisms
    • C12R2001/01—Bacteria or Actinomycetales ; using bacteria or Actinomycetales

Definitions

  • Burkholderia sp with no known pathogenicity to vertebrates, such as mammals, fish and birds but exhibits herbicidal activity. Also provided are products derived from a culture of said species and methods of controlling germination and growth of dicotyiedenous, monocoryledonous, and sedge weeds.
  • the Burkholderia genus ⁇ -subdivisioii of the proteobacteria, comprises more than 40 species that inhabit diverse ecological iches (Compant et al., FEMS Microbiol. Rev. 32:607- 626, 2008).
  • the bacterial species in the genus Burkholderia are ubiquiious organisms in soil and rhizosphere (Coenye et al., Environ. Microbiol. 5:719-729, 2003; Parke et al., Ann. Rev. Phytopathology 39:225-258, 2001), Traditionally, they have been known as plant pathogens, B.
  • cepacia being the first one discovered and identified as the pathogen causing disease in onions (Burkholder, Phytopathology 40: 1 15- 1 17, 1950).
  • Burkholderia species have developed beneficial interactions with their plant hosts (see, for example, Cabballero- Mellado et al., Int. J. Sysi. Evol. Microbiol. 54: 1 165-1 172, 2004, Chen et al, Int. J. Sysl. Evol. Microbiol. 57: 1055-1059, 2007).
  • Some Biirkhoideria species have also been found to be opportunistic human pathogens (see, for example, Cheng et al. Clin. Microbiol. 18:383- 416, 2005 and Nierman et al, PNAS 101 : 14246-14251, 2004). Additionally, some
  • Burkholderia species have been found to have potential as biocontrol products (see for example, Burkhead et al, Appl. Environ. Microbiol. 60:2031-2039, 1994; Knudsen et al, Plant Disease 71 :442-445, 1987; Jansiewicz et al., Phytopathology 78: 1697-1700, 1988; US Pub. No. 2003/0082147; US Patent No. 6,077,505; US Patent No. 6,689,357;
  • the A396 strain is a non-Burkholderia cepacia, non-Burkholderia plantari, xioa-Burkholderia gladioli, Burkholderia sp. that has the following characteristics:
  • Has a 16S rRNA gene sequence comprising a forward sequences having at least 99.0% identity to the sequences set forth in SEQ ID NQs:8, 1 1, and 12 and a reverse sequence having at least 99.0% identity to SEQ ID NOs:9, 10, and 13-15;
  • d. is non-pathogenic (non-infectious) to vertebrate animals, such as mammals, birds and fish;
  • e. is susceptible to kanamycin, chloramphenicol, ciprofloxacin, piperacillin,
  • imipenem and a combination of sulphamethoxazole and trimethoprim;
  • £ contains the fatty acids 16:0, cyclo 17:0, 16:0 3- OH, 14:0, cyclo 19:0 U)8c, 18:0.
  • a method for modulating emergence and/or growth of a monocotyledonous, sedge, or dicotyledonous weed comprising applying to said weed or soil prior to emergence of said weed or after emergence of said weed a composition comprising an isolated strain of Burkholderia sp. A396 or a composition derived therefrom, in an amount effective to modulate emergence and/or growth of the monocotyledonous, sedge, or dicotyledonous weed.
  • the composition may be a whole cell broth comprising the isolated strain of Burkholderia sp. A396. In another embodiment, the composition may be a supernatant or an extract obtained from the composition comprising the isolated strain of Burkholderia sp. A396.
  • a method for modulating emergence and/or growth of a monocotyledonous, sedge, or dicotyledonous weed comprising applying to the weed or soil a composition comprising an isolated templazole A or templazole B in an amount effective to modulate emergence and/or growth of the monocotyledonous, sedge, or dicotyledonous weed.
  • the weeds may be grass weeds (e.g., Digiiaria sanguinalis, Echinochloa crus-gali, Phalaris minor and Lolium perenne), sedge weeds (e.g., Cyperus difformis) or broadleaf weeds (e.g., Brassica juncea, TrifoUum repens, Conyza canadensis, Conyza bonariensis, Amaranthus palmeri, Amaranthus rudis, Ambrosia artemisifolia, Ambrosia trifida, Kochia scoparia, Solanum nigrum, Oxalis stricta, Chenopodium album, Medicago poiymorpha, Taraxacum oficinale, Convolvulus arvensos, Pueraria lobata, Malva parviflora, and Gallium aparine). Further provided are seeds coated with the cultures, extracts, strains, compounds, supernatant, whole cell broth
  • Figure 1 shows the comparison of the growth rate of Burkholderia A396 to
  • Burkholderia multivorans ATCC 17616 Burkholderia multivorans ATCC 17616.
  • Figure 2 shows the effect of Burkholderia A396 extract on bindweed.
  • Figure 3 shows the effect of Burkholderia A396 extract on pigweed.
  • Figure 4 is a schematic representation of purification scheme for obtaining the templazole and templamide compounds.
  • derived from means directly isolated or obtained from a particular source or alternatively having identify ing characteristics of a substance or organism isolated or obtained from a particular source.
  • an "isolated compound” is essentially free of other compounds or substances, e.g., at least about 20% pure, preferably at least about 40% pure, more preferably about 60% pure, even more preferably about 80% pure, most preferably about 90% pure, and even most preferably about 95% pure, as determined by analytical methods, including but not limited to chromatographic methods, electrophoretic methods.
  • whole cell broth refers to a liquid culture containing both cells and media. If bacteria are grown on a plate the ceils can be harvested in water or other liquid, whole culture.
  • filtrate refers to liquid from a whole broth culture that has passed through a. membrane.
  • extract refers to a liquid substance removed from cells by a solvent (water, detergent, buffer, chemical such as acetone) and separated from the cells by centrifugation, filtration or other method.
  • the Burkhoideria strain set forth herein is a non-Burkholderia cepacia complex, non- Burkhoideria plantar i, non-Burkholderia gladioli, Burkhoideria sp and non-pathogenic to vertebrates, such as birds, mammals and fish.
  • This strain may be isolated from a soil sample using procedures known in the art and described by Lorch et al., In Methods in Applied Soil Microbiology and Biochemistry, K. Alef and P. Nannipieri, Eds, San Diego, CA, Academic Press, p. 146-161, 1995.
  • the Burkhoideria strain may be isolated from many different types of soil or growth medium.
  • the sample is then plated on potato dextrose agar (PDA).
  • PDA potato dextrose agar
  • the bacteria are gram negative, and it forms round, opaque cream-colored colonies that change to pink and pinkish-brown, in color and mucoid or slimy over time.
  • Colonies are isolated from the potato dextrose agar plates and screened for those that have biological, genetic, biochemical and/or enzymatic characteristics of the Burkhoideria strain of the present invention sei forth in the Examples below .
  • the Burkhoideria strain of the present invention sei forth in the Examples below .
  • Burkhoideria strain has a 16S rRNA gene comprising a forward sequence that is at least about 99.0%, preferably about 99.5%, more preferably about 99.9% and most preferably about 100% identical to the sequence set forth in SEQ ID NOs: 8, 1 1 and 12 and a forward sequence that is at least about 99.0%, preferably about 99.5%, more preferably about 99.9% and most preferably about 100% identical to the sequence set forth in SEQ ID NOs: 9, 10, 13, 14 and 15 as determined by clustal analysis. Furthermore, as set forth below, this
  • Burritiideria strain has, as sei forth below, pesticidal activity, particularly, herbieidal activity. It is not pathogenic to vertebrate animals, such as mammals, birds, and fish.
  • the Burkhoideria strain produces at least templazole A and templazole
  • the Burkhoideria strain is susceptible to kanamyein, chloramphenicol, ciprofloxacin, piperacillin , imipenem, and a combination of sulphamethoxazole and trimethoprim and contains the fatty acids 16:0, cyclo 17:0, 16:0 3- OH, 14:0, cyclo 19:0, 18:0.
  • This Burkhoideria strain may be obtained by culturing a microorganism having the identifying characteristics of Burkhoideria A396 (NRRL Accession No. B-50319) on Potato Dextrose Agar (PDA) or in a fermentation medium containing defined carbon sources such as glucose, maltose, fructose, galactose, and undefined nitrogen sources such as peptone, tryptone, soytone, and NZ amine.
  • PDA Potato Dextrose Agar
  • the herbieidal compounds disclosed herein may be produced by culturing the Burkarideria strain described herein and producing the compounds.
  • the compounds may be isolated from the culture or supernatant of the Burkhoideria strain. Alternatively, the compounds may be synthesized by methods known in the art.
  • the herbieidal compounds obtainable from the
  • Burritiideria strain is templazole A and templazole B having the following structures:
  • Templazole A and templazoie B are shown to have herbicidal activity in the Example section below.
  • a substantially pure culture, whole ceil broth, ceil fraction, supernatant, extract, and compounds of the Burkholderia strain of the present invention may be formulated into herbicidal compositions.
  • Non-limiting formulation examples include but are not limited to emulsiflable concentrates (EC), wettable powders (WP), soluble liquids (SL), aerosols, ultra- low volume concentrate solutions (ULV), soluble powders (SP), microencapsulation, water dispersed granules, flowables (FL), microemulsions (ME), nano-emulsions (NE), etc.
  • EC emulsiflable concentrates
  • WP wettable powders
  • SL soluble liquids
  • UUV ultra- low volume concentrate solutions
  • SP soluble powders
  • microencapsulation water dispersed granules, flowables (FL), microemulsions (ME), nano-emulsions (NE), etc.
  • the concentrate, powders, granules and emulsions may be ireeze-dried.
  • percent of the active ingredient is within a range of 0.01% to 99.99%.
  • compositions may be in the form of a liquid, gel or solid.
  • Liquid compositions comprise pesticidal compounds derived from said Burkholderia strain, e.g. Burkholderia A396 (NRRL Accession No. B-50319).
  • a solid composition can be prepared by suspending a solid carrier in a solution of pesticidal compounds and drying the suspension under mild conditions, such as evaporation at room temperature or vacuum evaporation at 65°C or lower.
  • a composition of the invention may comprise gel-encapsulated compounds derived from the Biirkhoideria strain of the present invention.
  • Such gel-encapsulated materials can be prepared by mixing a gel-forming agent (e.g., gelatin, cellulose, or lignin) with a solution of pesticidal compounds used in the method of the invention; and inducing gel formation of the agent.
  • a gel-forming agent e.g., gelatin, cellulose, or lignin
  • the composition may additionally comprise a surfactant to be used for the purpose of emulsification, dispersion, wetting, spreading, integration, disintegration control, stabilization of active ingredients, and improvement of fluidity or rust inhibition.
  • a surfactant to be used for the purpose of emulsification, dispersion, wetting, spreading, integration, disintegration control, stabilization of active ingredients, and improvement of fluidity or rust inhibition.
  • the surfactant is a non-phytotoxic non-ionic surfactant which preferably belongs to EPA List 4B.
  • the nonionic surfactant is
  • polyoxyethyiene (20) monolaurate The concentration of surfactants may range between 0.1 - 35% of the total formulation, preferred range is 5-25%.
  • concentration of surfactants may range between 0.1 - 35% of the total formulation, preferred range is 5-25%.
  • dispersing and emulsifying agents such as non-ionic, anionic, amphoteric and canonic dispersing and emulsifying agents, and the amount employed is determined by the nature of the composition and the ability of the agent to facilitate the dispersion of these compositions.
  • the composition may further comprise another microorganism and/or pesticide (e.g, nematocide, fungicide, insecticide).
  • the microorganism may include but is not limited to an agent derived from Bacillus sp., Pseudomonas sp processed Brevabacillus sp., Lecanicillium sp., non- Ampelomyces sp., Pseudozyma sp., Slreptomyces sp, Burkholderia sp, Trichoderma sp, and Gliocladium sp.
  • the agent may be a natural oil or oil-product having fungicidal and/or insecticidal activity (e.g., paraffinic oil, tea tree oil, lemongrass oil, clove oil, cinnamon oil, citrus oil, rosemary oil).
  • the composition may further comprise an insecticide.
  • the insecticide may include but is not limited to avermectin, Bacillus thuringiensis, neem oil and azadiractin, spinosads, Chromobacterium subtsugae, eucalyptus extract, entomopathogenic bacterium or fungi such a Beauveria hassiana, and Metarrhizium anisopliae and chemical insecticides including but not limited to organochlorine compounds, organophosphorous compounds, carbamates, pyrethroids, and neonicotinoids.
  • the composition my further comprise a nematicide.
  • the nematicide may include, but is not limited to chemical nematicides such as tenamiphos, aldicarb, oxamyl, carbofuran, natural product neamtieide, avermectin, the fungi Paecilomyces lilacinas and Muscodor spp. , the bacteria Bacillus firmus and other Bacillus spp. and Pasteuria penetrans.
  • composition may further comprise a biofungicide such as extract of R.
  • fungicides include, but are not limited to, a single site anti-fungal agent which may include but is not limited to benzimidazole, a demethylation inhibitor (DMT) (e.g., imidazole, piperazine, pyrimidine, triazole), morpholme, hydroxypyiimidine, anilinopyrimidine, phosphorothioiate, quinone outside inhibitor, quinoline, dicarboximide, carboximide, phenyiamide, anilinopyrimidine, phenylpyrrole, aromatic hydrocarbon, cinnamic acid, hydroxyanilide, antibiotic, polyoxin, acylamine, phthalimide, benzenoid (xylylalanine).
  • DMT demethylation inhibitor
  • morpholme e.g., imidazole, piperazine, pyrimidine, triazole
  • morpholme e.g., imidazole, piperazine, pyrim
  • the antifungal agent is a demethylation inhibitor selected from the group consisting of imidazole (e.g., triflumizole), piperazine, pyrimidine and triazole (e.g., bitertanol, myclobutaniL penconazole, propiconazole, triadimefon, bromuconazole, cyproconazole, diniconazole, fenbuconazole, hexaconazole, tebuconazole, tetraconazole, propiconazole).
  • imidazole e.g., triflumizole
  • piperazine pyrimidine
  • triazole e.g., bitertanol, myclobutaniL penconazole, propiconazole, triadimefon, bromuconazole, cyproconazole, diniconazole, fenbuconazole, hexaconazole, tebuconazole,
  • the antimicrobial agent may also be a multi-site non-inorganic, chemical fungicide selected from a nitrile (e.g., chloronitrile or fludioxonii), quinoxaline, suiphamide, phosphonate, phosphite, dithiocarbamate, chioraikythios, phenylpyridm-amine, cyano- acetamide, and oxinie.
  • a nitrile e.g., chloronitrile or fludioxonii
  • compositions may be applied using methods .known in the art. Specifically, these compositions may be applied to plants or plant parts. Plants are to be understood as meaning in the present context all plants and plant populations such as desired and undesired wild plants or crop plants (including naturally occurring crop plants and weeds). Crop plants can be plants which can be obtained by conventional plant breeding and optimization methods or by biotechnological and genetic engineering methods or by combinations of these methods, including the transgenic plants and including the plant cuitivars protectable or not protectable by plant breeders' rights.
  • Plant parts are to be understood as meaning all parts and organs of plants above and below the ground, such as shoot, leaf, flower and root, examples which may be mentioned being leaves, needles, stalks, stems, flowers, fruit bodies, fruits, seeds, roots, tubers and rhizomes.
  • the plant parts also include harvested material, and vegetative and generative propagation material, for example cuttings, tubers, rhizomes, offshoots and seeds.
  • compositions set forth above Treatment of the plants and plant parts with the compositions set forth above may be carried out directly or by allowing the compositions to act on their surroundings, habitat or storage space by, for example, immersion, spraying, evaporation, fogging, scattering, painting on, injecting.
  • the composition may be applied to the seed as one or more coats prior to planting the seed using one or more coats using methods known in the art.
  • compositions may be herbicidal compositions.
  • the composition may further comprise one or more herbicides. These may include, but are not limited to, a bioherbicide and/or a chemical herbicide.
  • the bioherbicide may be selected from the group consisting of clove, cinnamon, lemongrass, citrus oils, orange peel oil, tentoxin, comexistisi, AAL-toxin, leptospermone, thaxtomin, sarmentine, momilactone B, sorgoleone, ascaulatoxin and ascaulatoxin aglycone.
  • the chemical herbicide may include, but is not limited to, difiufenzopyr and salts thereof, dicamba and salts thereof, topramezone, tenibotrione, S- metofach!or, atrazine, mesotrione, primisulfuron-methyl, 2,4- dichlorophenoxyacetic acid, nicosulfuron, thifensulfuron-methyl, asulam, metrihuzin, diclofop-methyl, fluazifop, fenoxaprop-p-ethyl, asulam, oxyfiuorfen, rimsuifuron, mecoprop, and quinciorac, thiobencarb, clomazone, cyhalofop, propanil, bensulfuron-methyl, penoxsulam, triclopyr, iniazethapyr, halosulfuron-methyl, pendimethalin, bispyribac- sodium, carfentrazone e
  • Herbicidal compositions may be applied in liquid or solid form as pre-emergence or post-emergence formulations.
  • the granule size of the carrier is typically 1 -2 mm (diameter) but the granules can be either smaller or larger depending on the required ground coverage.
  • Granules may comprise porous or non-porous particles.
  • the formulation components used may contain smectite clays, attapulgite clays and similar swelling clays, thickeners such as xanthan gums, gum Arabic and other polysaccharide thickeners as well as dispersion stabilizers such as nonionic surfactants (for example polyoxyethylene (20) monolaurate).
  • thickeners such as xanthan gums, gum Arabic and other polysaccharide thickeners as well as dispersion stabilizers such as nonionic surfactants (for example polyoxyethylene (20) monolaurate).
  • compositions and compounds derived from the Burkholderia strain set forth herein may be used as pesticides, particularly as herbicides.
  • the substances and compositions may be used to modulate emergence in either a pre- emergent or post-emergent formulation of monocotyledonous, sedge or dicotyledonous weeds.
  • the weeds may be Chenopodium sp. (e.g., Chenopodium album, Chenopodium. murale), Abutilon sp. (e.g., Abutilo theophrasU), Helianthus sp. (e.g., Helianthus artnuus), Ambrosia sp. (e.g... Ambrosia artemesifolia. Ambrosia trifida),
  • Amaranthus sp. e.g., Amaranthus retroflexus, Amaranthus palmer i, Amaranthus rudis, Amaranthus spinosus, Amaranthus tuberculatus
  • Convolvulus sp. e.g., Convolvulus arvensis
  • Brassica sp. e.g., Brassica kaber
  • Taraxacum sp. e.g., Taraxacum officinale
  • Solanum sp. e.g., Solanum nigrum, Solanum elaeagnifolium, Solanum physalifolium,
  • Solanum ptycanthum Malva sp. (e.g., Malva neglecta, Malva parvijlora), Setaria sp. (e.g., Setaria lutescens), Bromus sp. (e.g., Bromus tectorum, Bromus diandrus, Bromus hordeaceus), Poa sp. (e.g., Poa annua, Poa pratensis), Lolium sp. (e.g., Lolium perenne, Lolium rigidum, Lolium multiflorum L. var. Pace), Fesiuca sp.
  • Malva sp. e.g., Malva neglecta, Malva parvijlora
  • Setaria sp. e.g., Setaria lutescens
  • Bromus sp. e.g., Bromus tectorum, Bromus diandrus, Bromus hordeaceus
  • Echinochloa sp. e.g., Echinochloa crus-galli, Echinochloa colona
  • Oxalis sp. e.g., Oxalis stricta, Oxalis pes-caprae, Oxalis corniculata
  • Cyperus sp. e.g., Cyperus difformis, Cyperus esculentum, Cyperus rotundas, Cyperus brevifolius
  • Conyza sp. e.g., Conyza canadensis, Conyza sumairensis. Conyza honarien is); Sagina sp.
  • Veronica sp. e.g., Veronica nederafoiia
  • Steilaria sp. e.g., Slellaria media
  • Rorippa sp. e.g., Rorippa islandica
  • Senecio sp. e.g., Senecio vulgaris
  • Lamium sp. e.g., Lamium amplexicaule
  • Digitaria sp. e.g., Digitaria sanguinalis, Digitaria ischaemum
  • Trifolium repens Trifolium hirtum, Trifolium incarnatum, Trifolium pratense
  • Alhagi maurorum Astragalus spp.
  • Medicago sp. e.g. Medicago lupulina, Medicago pol morpha
  • Melilolus sp. Seshania sp. (e.g. Sesbania punicea, Sesbania exaltata), Vicia sp. (e.g. Vicia sativa, Vicia villosa), Gallium sp. (e.g., Gallium aparine), Galinsoga sp.
  • Cardamine sp. e.g., Cardamine jlexuosa, Cardamine hirsu(a), Kochia sp. (e.g., Kochia scoparia), Eleusine sp. (e.g., Eleusine indica), Portulaca sp. (e.g., Portulaca oleraceae), Plantago sp. (e.g., Plantago lanceolata), Euphorbia sp. (e.g., Euphomia supina, Euphorbia maculate, Euphorbia esula. Euphorbia prostrata), Erodium sp.
  • Cardamine sp. e.g., Cardamine jlexuosa, Cardamine hirsu(a), Kochia sp. (e.g., Kochia scoparia), Eleusine sp. (e.g., Eleusine indica), Portulaca sp. (e.g., Portulaca
  • sp e.g., Paspalum dilatatum
  • Gnaphalium sp. Cynodon sp, (e.g., Cynodon dactylon, Cynodon hirsutus), Polygonum sp. (e.g.. Polygonum arenastrum, Polygonum lapalhifolium,), Avena falua, Horaeum sp. (e.g., Horaeum leporinum), Urtica sp. (e.g., Urtica wens), Tribulus terrestris, Sisymbrium sp. (e.g., Sisymbrium irio), Cenckrus sp., Salsola sp.
  • Amsinckia sp. e.g., Amsinckia lycopsoides
  • Ipomoea sp. Claytonia perfoliala
  • Polypogon sp. e.g., Polypogon monspeliensis
  • Xanthium sp. Hypochaeris radicata
  • Urochloa platyphylla Urochloa panicoides
  • Leersia sp. Seshania sp. ⁇ Sesbania herbacea
  • Rotala sp. Ammonia sp., Alternaihera philoxeroides
  • Commelina sp. Sorghum halepense
  • Parlhenium hysterophorus Parlhenium hysterophorus
  • Chloris truncata species in the Fabaceae family.
  • compositions and methods set forth above will be further illustrated in the following, non- limiting Examples.
  • the examples are illustrative of various embodiments only and do not limit the claimed invention regarding the materials, conditions, weight ratios, process parameters and the like recited herein.
  • the microbe is isolated using established techniques know to the art from a soil sample collected under an e vergreen tree at (he Rinnoji Temple, Nikko, Japan.
  • the isolation is done using potato dextrose agar (PDA) using a procedure described in detail by Lorch et al., In Methods in Applied Soil Microbiology and Biochemistry, K. Aief and P. Nannipieri, Eds, San Diego, CA, Academic Press, p. 146- 161 , 1995.
  • the soil sample is first diluted in sterile water, after which it is plated in a solid agar maxim such as potato dextrose agar (PDA).
  • the plates are grown at 25°C for five days, after which individual microbial colonies are isolated into separate PDA plates.
  • the isolated bacterium is gram negative, and it forms round, opaque cream-colored colonies that change to pink and pinkish- brown in color and mucoid or slimy over time.
  • the microbe is identified based on gene sequencing using universal bacterial primers to amplify the 1 6S rRNA region.
  • the following protocol is used: Burkholderia sp A396 is cultured on potato-dextrose agar plates. Growth from a 24 hour-old plate is scraped with a sterile loop and re-suspended in DNA extraction buffer, DNA is extracied using the MoBio Liitra Clean Microbial DNA extraction kit, D A extract is checked for quality/quantity by miming 5 ⁇ 1 on a 1% agarose gel.
  • PC reactions are set up as follows: 2 ⁇ DNA extract, 5 ⁇ PGR buffer, 1 ⁇ dNTPs (10 mM each), 1.25 ⁇ forward primer (27F; 5 ' - AGAGTTTG A.TCCTG G CTCAG- 3 ' (SEQ ID NO: 1 ), 1.25 ⁇ reverse primer (907R; 5 '-CCGTCAATTCCTTTG AGTTT-3 ' (SEQ ID NO:2)) and 0.25 ⁇ Taq enzyme.
  • the reaction volume is made up to 50 ⁇ using sterile nuclease- free water.
  • the PCR reaction includes an initial denaturation step at 95°C for 10 minutes, followed by 30 cycles of 94°C/30 sec, 57°C/20 sec, 72°C/30 sec, and a final extension step at 72°C for 10 minutes.
  • the product's approximate concentration and size is calculated by running a 5 ⁇ volume on a 1% agarose gel and comparing the product band to a mass ladder.
  • strain A396 The 16S rRNA gene sequence of strain A396 is compared with the available 16s rRNA gene sequences of representatives of the ⁇ -proteobacteria using BLAST.
  • Strain A395 A396 is closely related to members of the Burkholderia cepacia complex, with 99% or higher similarity to several isolates of Burkholderia multivorans, Burkholderia Vietnam ens is, and Burkholderia cepacia.
  • a BLAST search excluding the B. cepacia complex showed 98% similarity to B. plantarii, B. gladioli and Burkholderia sp. isolates.
  • a distance tree of results using the neighbor joining method showed that A396 is related to Burkholderia multivorans and other Burkholderi cepacia complex isolates, Burkholderia plantarii and Burkholderia glumae grouped in a separate branch of the tree.
  • the isolated Burkholderia strain was found to contain the following sequences:
  • reverse sequence 824 bp using primer 907R (SEQ NO: 10); forward sequence 1 152 bp using primer 530F (SEQ ID NO: l 1); forward sequence 1067 bp using 11 14F primer (SEQ ID NO: 12); reverse sequence 1223 bp using 1525R primer (SEQ NO: 13); reverse sequence 1216 bp using 1 100R primer (SEQ ID NO: 14); reverse sequence i 194 bp using 519R primer (SEQ ID NO: 15).
  • Burkholderia multivorans is a known member of the Burkholderia cepacia complex. Efforts are focused on PGR of recA genes, as described by Mahenthiralingam et aL, 2000. The following primers are used: (a) BCR1 and BCR2 set forth in Mahenthiralingam et a!,, 2000 to confirm B. cepacia complex match and (b) BCRBM1 and BCRBM2 set forth Mahenthiralingam et af, 2000 to confirm B. multivorans match. A product-yielding PGR reaction for the first primer set would confirm ihai ihe microbe belongs to the B. cepacia complex. A product-yielding PGR reaction for the second primer set would confirm that the microbe is indeed B.
  • A396 is a new species of Burkholderia
  • a DNA-DNA hybridization experiment with Burkholderia multivorans (the closest 16S rRNA sequence match) is conducted.
  • Biomass for both A396 and B. multivorans is produced in 1SP2 broth, grown over 48 hours at 200 rpm/25 c C in Fernbach flasks. The biomass is aseptically harvested by centrifugation. The broth is decanted and the cell pellet is resuspended in a 1 : 1 solution of water: isopropanoJ.
  • DNA-DNA hybridization experiments are performed by the DSMZ, the German Collection of Microorganisms and Cell Cultures in Germany.
  • DNA is isolated using a French pressure cell (Thermo Spectronic) and is purified by chromatography on hydroxyapatite as described by Cashion et al,, Anal Biochem. 81 :461-466 (1977), DNA- DNA. hybridization is carried out as described by De Ley et al, Eur, J. Biochem. 12: 133-142 (1970) under consideration of the modifications described by Huss et al, System. Appl.
  • A396 is grown overnight on Potato Dextrose Agar (PDA).
  • PDA Potato Dextrose Agar
  • the culture is transferred to BUG agar to produce an adequate culture for Biolog experiments as recommended by the manufacturer (Biolog, Hayward, CA).
  • the biochemical profile of the microorganism is determined by inoculating onto a Biolog GN2 plate and reading the plate after a 24-hour incubation using the MicroLog 4- automated microstation system. Identification of the unknown bacteria is attempted by comparing its carbon utilization pattern with the Microlog 4 Gram negative database.
  • Cis-aconitic acid - D-Lactose - Citric acid Lactulose
  • a ioopful of well-grown ceils are harv ested and fatty acid methyl esters are prepared, separated and identified using the Sherlock Microbial identification System (MIDI) as described (see Vandamme et al., Int. J. Syst. BActeriol. 42:344-356, 1992).
  • MIDI Sherlock Microbial identification System
  • the predominant fatty acids present in the Burkholderia A396 are as follows: 16:0 (24.4%), cycle 1 7:0 (7.1 %), 16:0 3- OH (4.4%), 14:0 (3.6%), 19:0 ⁇ o8c (2.6%) cycle, 18:0 (1.0%).
  • Summed feature 8 (comprising 18: 1 (o7c) and summed feature 3 (comprising of 16: 1 0)7e and 16: 1 co6c) corresponded to 26.2% and 20.2 % of the total peak area, respectively.
  • Summed feature 2 comprising 12:0 ALDE, 16: 1 iso I, and 14:0 3-OH) corresponded to 5.8% of the total peak area while summed feature 5 comprising 1 8:0 ANTE and 18:2 a)6,9c corresponded to 0.4%.
  • Table 2 Susceptibility of ⁇ -2 ⁇ 6 to various antibiotics. +++ very susceptible, ++ susceptible, - resistant
  • Burkholderia A396 is quite different from pathogenic B. cepacia complex strains. Burkholderia A396 is susceptible to kanamycin, chloramphenicol, ciprofloxacin, piperacillin, imipenem, and a combination of sulphamethoxazole and trimethoprim.
  • Zhou et al,, Antimicrobial Agents and Chemotherapy 51 : 1085-1088, 2007 tested the susceptibility of 2,621 different strains in B, cepacia complex isolated from cystic fibrosis patients, and found that only 7% and 5% of all strains were susceptible to imipenem or ciprofloxacin, respectively. They also found 85% of all strains to be resistant to chloramphenicol (15% susceptible), and 95% to be resistant (5% susceptible) to the combination of sulphamethoxazole and trimethoprim. Results of
  • a novel strain of Burkholderia sp. A396 is gro wn in an undefined mineral medium for 5 days (25°C, 200 rpm).
  • the whole cell broth is extracted using XAD7 resin.
  • the dried crude extract is resuspended in 4% ethanol and 0.2 % non-ionic surfactant at a concentration of 10 mg/mL, and further diluted to concentrations of 5.0, 2.5, and 1.25 mg/mL. All four test solutions are then tested on the following broadieaf and grass weed species listed in Table 3:
  • a solution of 0.2 % glycosperse and Roundup at 6 fl oz per gallon rate is used as negative and positive controls, respectively.
  • Ail plant species are tested in 4"x4" plastic pots in three replicates.
  • the untreated control plants are sprayed with the carrier solution (4% Ethanol, 0.2% glycosperse) and the positive control plants with Roundup at a rate corresponding to 6 fl. oz/acre.
  • Treated plants are kept in a greenhouse under 12h light/12h dark conditions.
  • Phytotoxicity data taken 22 days after treatment for species #1 -8 and 12 days for species #9- 12 are presented in Tables 5 and 6, respectively. The rating scale for both tables is shown in Table 4:
  • Seedlings are evaluated 7 days after treatment. Observed symptoms include: burning, warping, bleaching Herbicidal activity is observed in the next leaf above the treated leaf in Ragweed, Mustard and Nightshade. No systemic activity is observed in the tested grasses. In a second experiment, five fractions of the same crude extract (10 mg/ml) are evaluated using the same experimenta l design as described abo v e. Seedlings of Mustard, Wheat and Crabgrass are treated.
  • the culture broth derived from the 10-L fermentation Burkholderia (A396) in Hy soy growth medium is extracted with Amberlite XAD-7 resin (Asolkar et a]., J. Nat. Prod, 69: 1756-1759, 2006) by shaking the cell suspension with resin at 225 rpm for two hours at room temperature.
  • the resin and cell mass are collected by filtration through cheesecloth and washed with DI water to remove salts.
  • the resin, cell mass, and cheesecloth are then soaked for 2 h in acetone after which the acetone is filtered and dried under vacuum using rotary evaporator to give the crude extract.
  • the crude extract is then fractionated by using reversed- phase CI 8 vacuum liquid chromatography (H 2 O/CH 3 OH; gradient 90:20 to 0: 100%) to give 10 fractions. These fractions are then concentrated to dryness using rotary evaporator and the resulting dry residues are screened for biological activity using 96 well plate lettuce seeding assay.
  • the active fractions are then subjected to reversed phase FIPLC (Spectra System P4000 (Thermo Scientific) to give pure compounds, which are then screened in above mentioned bioassays to locate/identify the active compounds. To confirm the identity of the compound, additional spectroscopic data such as LC/MS and NMR is recorded.
  • the active fraction 4 is purified further by using HPLC C- 18 column (Phenomenex, Luna l Ou CI 8(2) 100 A, 250 x 30), watenacetonitrile gradient solvent system (0- 10 min; 80% aqueous CHjCN, 10-25 min; 80 - 65% aqueous CH 3 CN, 25-50 min; 65 - 50 % aqueous CH 3 CN, 50-60 min; 50-70% CH 3 CN, 60-80 min; 70-0% aqueous CH 3 C , 80-85 min; 0 - 20% aqueous CH 3 CN) at 8 mL/min flow rate and UV detection of 210 nm, to give templazole B, retention time 46.65 min.
  • HPLC C- 18 column Phenomenex, Luna l Ou CI 8(2) 100 A, 250 x 30
  • watenacetonitrile gradient solvent system (0- 10 min; 80% aqueous CHjCN, 10-25 min; 80 - 65% aqueous CH 3
  • the other active fraction 6 is also purified using HPLC C- 18 column (Phenomenex, Luna lOu CI 8(2) 100 A, 250 x 30), water:acetonitrile gradient solvent sysiem (0- 10 min; 80 % aqueous C3 ⁇ 4CN, 10-25 min; 80 - 60 % aqueous C3 ⁇ 4CN, 25-50 min; 60 - 40% aqueous CH 3 CN, 50-60 min; 40% CH 3 CN, 60-80 min; 40-0% aqueous CFI 3 C , 80-85 min; 0-20 % aqueous CH 3 CN) at 8 mL/min flow rate and UV detection of 210 mn. to give templazole A, retention time 70.82 min.
  • LCQ Deca XP Plus electrospray (EST) instrument using both positive and negative ionization modes in a full scan mode (m/z 100-1500 Da) on a LCQ DECA XP plu£i Mass Spectrometer (Thermo Electron Corp., San Jose, CA).
  • Thermo high performance liquid chromatography (FTPLC) instrument equipped with Finnigan Surveyor PDA plus detector, autosampler plus, MS pump and a 4.6 mm x 100 mm Luna CT 8 5 um column (Phenomenex).
  • the solvent system consists of water (solvent A) and acetonitrile (solvent B).
  • the mobile phase begins at 10% solvent B and is linearly increased to 100% solvent B over 20 min and then kept for 4 min, and finally returned to 10% solvent B over 3 min and kept for 3 min.
  • the flow rate is 0.5 mL/min.
  • the injection volume was 10 and the samples are kept at room temperature in an auto sampler.
  • the compounds are analyzed by LC-MS utilizing the LC and reversed phase chromatography. Mass spectroscopy analysis of the present compounds is performed under the following conditions: The flow rate of the nitrogen gas was fixed at 30 and 15 arb for the sheath and aux/sweep gas flow rate, respectively, Electrospray ionization was performed with a spray voltage set at 5000 V and a capillary voltage at 35.0 V. The capillary temperature was set at 400°C.
  • the data was analyzed on Xcalibur software.
  • the active compound templazole A has a molecular mass of 298 and showed m/z ion at 297.34 in negative ionization mode.
  • the LC-MS chromatogram for templazole B suggests a molecular mass of 258 and exhibited m/z ion at 257.74 in negative ionization mode.
  • the purified compound with a molecular weight 298 is further analyzed using a 500 MHz NMR instrument, and has ⁇ NMR ⁇ values at 8.44, 8.74, 8.19, 7.47, 7.31, 3.98, 2.82, 2.33, 1.08 and has 13 C NMR ⁇ values of 163.7, 161.2, 154.8, 136.1 , 129.4, 125.4, 123.5, 123.3, 121.8, 121.5, 1 1 1.8, 104.7, 52.2, 37.3, 28.1, 22.7, 22.7.
  • Templazole A has UV absorption bands at 226, 275, 327 nm, which suggested the presence of indole and oxazole rings.
  • ⁇ - ⁇ COSY and HMBC also indicated the presence of a carboxylic acid methyl ester group and a -CH 2 -CH-(C3 ⁇ 4)2 side chain.
  • C carboxylic acid methyl ester
  • HMBC hematoma-butyl side chain
  • the second herbicidally active compound, templazole B, with a molecular weight 258 is further analyzed using a 500 MHz NMR instrument, and has ! H NMR ⁇ values at 7.08, 7.06, 6.75, 3.75, 2.56, 2.15, 0.93, 0.93 and i3 C NMR values of ⁇ 158.2, 156.3, 155.5, 132.6, 129.5, 129.5, 127.3, 121.8, 1 15.2, 1 15.2, 41.2, 35.3, 26.7, 21.5, 21.5.
  • the molecular formula is assigned as C15H1 SN2Q2, which is determined by interpretation of ⁇ , J i C NMR and mass data. The l 3 C NMR.
  • the H-l ' signal in the isobutyl moiety correlated with the olefmic carbon (C-2, ⁇ 156.3), and the oiefmic proton H-4 correlated with (C-5, ⁇ 155,5; C-2, 156.3 & C- l ", 41.2).
  • the methylene signal at ⁇ 3.75 correlated with C-5, C-4 as well as the C-2" of the para-substituted aromatic moiety. All these observed correlations suggested the connectivity among the isobutyl, and the para-substituted benzyl moieties for the skeleton of the structure as shown.
  • the carboxamide group is assigned at the para position of the benzyl moiety based 011 the HMBC correlation from the aromatic proton at H-4"& H-6" position.
  • the structure was designated as templazole B, shown below.
  • Example 4 Herbicidal Effect of Burkholderi sp. A396 Formulations (Pre-Emergent) To determine the spectrum of pre-emergence activity, tests were conducted in a petri dish or small pot conditions. Tn laboratory testing, 35 seeds were placed on a ring of blotter paper inside a 3 cm petri dish and supplied with 4 ml of MBI-010 ( ⁇ ().1 mg MBI-()()5/ml). Water was used as a negative control and oryzalin applied as a positive control. Petri dishes were randomly placed in a growth room at 25 °C and 50% RH. Treatments were replicated three times and germinated seeds were counted 7 and 14 days after application; water was added as necessary to maintain moisture levels inside each petri dish.
  • potting soil was placed into 4 inch square pot, into which were then inserted five weed tubers, rhizomes or other underground perennation structure, according to species. Pots were drenched with 20 mL MBI-010 (Burkholderia sp. A396) at a range of dilutions with water. Treatments, including water as the negative control and glyphosate as the positive control, were replicated five times. Treatments were evaluated visually as number of germinating plants per pot and above-ground fresh weights per container were taken.
  • Results in Table 7 indicate broad spectrum activity on both annual grasses and hroadieaves, as well as on some perennials.
  • Example S Herbkidal Effect of B rkholderia sp, A396 Formulations (Post-Emergent)
  • MBI-010 Basing on the species
  • Negative controls were sprayed with water and positive controls with glufosinate. Pots were randomly placed in a growth room at 25 °C and 50% RH, and watered as necessary.
  • Treatments were replicated five times and evaluated at 7 and 14 days for visual % damage, with 0% indicating no damage and 100% indicating plant death.
  • potting soil was placed into 4 inch square pots containing plants at the 2 -3 leaf stage. Pots were drenched with 20 mL MBI-010 (Burkholderia sp. A396) at a range of dilutions with water. Treatments, including water as the negative control and oryzalin as the positive control, were replicated five times and kept in a growth room as described above. Treatments were evaluated visually on a percent control basis and above- ground fresh weights per container were taken.
  • Table 8 Post-Emergent Effect of B rkholderia sp, A396 Formulations. An S indicates an assay that successfully showed systemic activity, a 0 indicates no activity.
  • CE is concentrated extract; WCB is whole ceil broth and Prototype Formulation is whole cell broth with added surfactants (e.g. hostaphat or genapol).
  • surfactants e.g. hostaphat or genapol.
  • the herbicidal activity of the active compounds templazole A and B were tested in a laboratory assay using one-week old lettuce seedlings in a 96 -well plate platform.
  • One lettuce seedling was placed in each of the wells containing 99 microliters of deionized water, into each well, a one microliter aliquot of the pure compound in ethanol (10 mg/mL) was added, and the plate was sealed with a lid.
  • One microliter of ethanol in 99 microliters of water was used as a negative control.
  • the treatments were done in eight replicates, and the sealed plate was incubated in a greenhouse under artificial lights (12 hr light/dark cycle). After five days, the results were read by visual inspection.
  • Table 9 Herbicidal bioassay data for templazole A and templazole B. Samples were tested at 100 ug/ ' mL concentration per well.
  • the strain has been deposited under conditions that assure that access to the culture will be available during the pendency of this patent application to one determined by the Commissioner of Patents and Trademarks to be entitled thereto under 37 C.F.R. ⁇ 1.14 and 35 U.S.C. ⁇ 122,
  • the deposit represents a substantially pure culture of the deposited strain.
  • the deposit is available as required by foreign patent laws in countries wherein counterparts of the subjeci application, or its progeny are filed. However, it should be understood that the availability of a deposit does not constitute a license to practice the subject invention in derogation of patent rights granted by government action.

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Abstract

L'invention concerne une espèce de Burkholderia sp. sans pathogénicité connue pour les vertébrés mais présentant une activité herbicide. L'invention concerne également des produits issus d'une culture de ladite espèce, ainsi que des procédés de lutte contre les mauvaises herbes au moyen desdits produits.
PCT/US2014/015799 2013-03-15 2014-02-11 Souche bactérienne isolée du genre burkholderia et métabolites pesticides correspondants WO2014149241A1 (fr)

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US6077505A (en) * 1997-06-11 2000-06-20 Wisconsin Alumni Research Foundation Biological seed treatment to improve emergence, vigor, uniformity and yield of sweet corn
US20090175837A1 (en) * 2004-02-27 2009-07-09 Daiju Yuki Method and agent for controlling plant disease using bacteria of genus bacillus
US20110207604A1 (en) * 2010-02-25 2011-08-25 Marrone Bio Innovations Isolated bacterial strain of the genus burkholderia and pesticidal metabolites therefrom

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* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6077505A (en) * 1997-06-11 2000-06-20 Wisconsin Alumni Research Foundation Biological seed treatment to improve emergence, vigor, uniformity and yield of sweet corn
US20090175837A1 (en) * 2004-02-27 2009-07-09 Daiju Yuki Method and agent for controlling plant disease using bacteria of genus bacillus
US20110207604A1 (en) * 2010-02-25 2011-08-25 Marrone Bio Innovations Isolated bacterial strain of the genus burkholderia and pesticidal metabolites therefrom

Non-Patent Citations (2)

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Title
SCHWEIZER , HERBERT P.: "Mechanisms of antibiotic resistance in Burkholderia pseudomallei: implications for treatment of melioidosis", FUTURE MICROBIOL., vol. 7, no. 12, December 2012 (2012-12-01), pages 1389 - 1399 *
STOKELL, JOSHUA R. ET AL.: "Rapid emergence of a ceftazidime-resistant Burkholderia multivorans strain in a cystic fibrosis patient", J. CYST. FIBROS., vol. 12, no. 6, 9 March 2013 (2013-03-09), pages 812 - 816 *

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