ENDOPHYTIC FUNGUS AND USES THEREFOR

• US 20110182862A1
• Filed: 04/02/2010
• Published: 07/28/2011
• Est. Priority Date: 04/03/2009
• Status: Abandoned Application

• Current Assignee: Synthetic Genomics, Inc.
• Original Assignee: Synthetic Genomics, Inc.
• Inventors: Richardson, Toby H., Herrgard, Markus J., Mathur, Eric J., Schwartz, Ariel S., Green, Wayne A., Kerovuo, Janne S., Strobel, Gary A., Lomelin, David
• Application Number:
  US12/753,760
• Publication Number:
  US 20110182862A1
• Time in Patent Office: Days
• US Class Current: 424/93.5
• CPC Class Codes: A01N 63/30 Microbial fungi; Substances produced thereby or obtained therefrom
• CPC Class Codes: C12N 1/145 Fungal isolates
• CPC Class Codes: C12R 2001/645 Fungi ; Processes using fungi

Abstract

The present invention provides novel microorganisms, compositions and methods of use thereof, for treating, inhibiting or preventing the developing of a plant pathogenic disease and for killing or inhibiting growth of a variety of pests or pathogens. Provided are compositions comprising a novel endophytic fungal organism effective to inhibit the growth of or kill pests and pathogenic microbes, including Ganoderma boninense. Invention compositions are especially useful in preventing and treating basal stem rot in the oil palm, and can be applied on or in the vicinity of the plant or used to sterilize the plant growth medium prior to or concurrent with plant growth therein. The disclosure further provides substantially purified polynucleotides and polypeptides encoded thereby, together with methods of using those products, for example for making transgenic organism.

Claims

1. An isolated culture of a strain of Muscodor strobelii.

3. A culture of Muscodor strobelii according to claim 1, wherein the strain is capable of producing isobutyric acid or a derivative of any thereof.

4. A culture of Muscodor strobelii according to claim 1, wherein the strain is capable of producing one or more of aristolene, bergamotene, caryophyllene, gurjunene, isolongifolene, patchoulene, or a derivative of any thereof.

5. A culture of Muscodor strobelii according to claim 1, further comprising an agriculturally effective amount of a compound or composition selected from the group consisting of a bactericide, a fungicide, an insecticide, a microbicide, a nematicide, a fertilizer, and a food preservative.

6. A composition comprising a culture of Muscodor strobelii according to claim 1 and a carrier.

7. A composition according to claim 6, wherein the carrier is a seed.

8. A composition according to claim 6, wherein the composition is in the form of a powder, a granule, a pellet, a gel, an aqueous suspension, a solution, or an emulsion.

9. A method for treating, inhibiting or preventing the development of a plant pathogenic disease, said method comprising applying a culture of Muscodor strobelii according to claim 1 on or in the vicinity of a host plant.

10. A method according to claim 9, wherein the pathogen is selected from the group consisting of Aspergillus fumigatus, Botrytis cinerea, Cerpospora betae, Curvularia sp., Ganoderma boninense, Geotrichum candidum, Mycosphaerella filiensis, Phytophthora palmivora, Phytophthora ramorum, Pythium ultimum, Rhizoctonia solani, Rhizopus sp., Schizophyllum sp., Sclerotinia sclerotiorum, Verticillium dahliae, and Xanthomonas axonopodis.

11. A method according to claim 9, wherein the host plant is susceptible to Ganoderma boninense.

12. A method according to claim 9, wherein the host plant is an oil palm plant.

13. A method according to claim 9, wherein Muscodor strobelii is established as an endophyte on the plant.

17. A method for killing a plant pathogen, said method comprising growing a culture of Muscodor strobelii according to claim 1 in the vicinity of the plant pathogen.

18. A method for treating, inhibiting or preventing the development of a plant pathogenic disease, said method comprising growing a culture of Muscodor strobelii according to claim 1 in a growth medium or soil of a host plant prior to or concurrent with host plant growth in said growth medium or soil.

19. A method of screening microbial strains, said method comprising (i) co-culturing a Muscodor strobelii strain according to claim 1 with one or more candidate microbial strains, (ii) selecting one or more viable microbial strains after the co-culturing, and (iii) characterizing the one or more selected microbial strains;

wherein said method identifies one or more microbial strains useful for treating, inhibiting or preventing the development of a plant pathogenic disease.

20. An isolated microbial strain obtainable by a method according to claim 19.

21. A method for killing, inhibiting or preventing the development of an organism selected from the group consisting of a fungus, a bacterium, a microorganism, a nematode, and an insect, said method comprising exposing the organism to an effective amount of a culture of Muscodor strobelii according to claim 1.

2. An isolated strain of Muscodor strobelii, wherein the strain is Agricultural Research Service Culture Collection accession number NRRL 50288.

14. A non-naturally occurring oil palm cultivar that is an oil palm infected with an isolated culture of Muscodor strobelii.

15. Seed, reproductive tissue, vegetative tissue, plant parts, or progeny of a non-naturally occurring oil palm cultivar according to claim 14.

16. A product comprising material derived from a non-naturally occurring cultivar according to claim 14.

22. A substantially purified nucleic acid molecule comprising:

(i) a nucleotide sequence hybridizing under high stringency conditions to any one of the nucleotide sequences in the Sequence Listing, a complement thereof or a fragment of either;

(ii) a nucleotide sequence exhibiting a 70% or greater identity to any one of the nucleotide sequences in the Sequence Listing, a complement thereof or a fragment of either;

(iii) a nucleotide sequence encoding an amino acid sequence exhibiting a 50% or greater identity to any one of the polypeptides in the Sequence Listing;

or

(iv) a nucleotide sequence that is an interfering RNA to a nucleotide sequence according to any one of paragraphs (i)-(iii).

24. A transformed cell comprising a first nucleic acid molecule according to claim 22, wherein said first nucleic acid molecule is operably linked to a second nucleic acid molecule that is heterologous with respect to said first nucleic acid.

25. A transgenic organism comprising the transformed cell of claim 24.

26. The transgenic organism of claim 25, wherein said organism is an endophyte or a plant.

23. A substantially purified polypeptide, wherein said polypeptide is encoded by a nucleic acid molecule comprising:

(i) a nucleotide sequence hybridizing under high stringency conditions to any one of the nucleotide sequences in the Sequence Listing, a complement thereof or a fragment of either;

(ii) a nucleotide sequence exhibiting a 70% or greater identity to any one of the nucleotide sequences in the Sequence Listing, a complement thereof or a fragment of either;

or

(iii) a nucleotide sequence encoding an amino acid sequence exhibiting a 50% or greater identity to any one of the polypeptides in the Sequence Listing.