Methods of use of seed-origin endophyte populations

• US 9,532,573 B2
• Filed: 02/05/2016
• Issued: 01/03/2017
• Est. Priority Date: 06/26/2013
• Status: Active Grant

• Current Assignee: Indigo Ag, Inc.
• Original Assignee: Indigo Ag, Inc.
• Inventors: von Maltzahn, Geoffrey, Sadowski, Craig, Flavell, Richard Bailey, Toledo, Gerardo V., Djonovic, Slavica, Marquez, Luis Miguel, Johnston, David Morris, Millet, Yves Alain, Lyford, Jeffrey, Naydich, Alexander
• Primary Examiner(s): IBRAHIM, MEDINA AHMED
• Application Number:
  US15/017,531
• Publication Number:
  US 20160150794A1
• Time in Patent Office: 333 Days
• Field of Search: None
• US Class Current: 1/1
• CPC Class Codes: A01C 1/00 Apparatus, or methods of use thereof, for testing or treating seed, roots, or the like, prior to sowing or planting
• CPC Class Codes: A01C 1/06 Coating or dressing seed
• CPC Class Codes: A01N 25/00 Biocides, pest repellants or attractants, or plant growth regulators, characterised by their forms, or by their non-active ingredients or by their methods of application , e.g. seed treatment or sequential application; Substances for reducing the noxious effect of the active ingredients to organisms other than pests
• CPC Class Codes: A01N 63/20 Bacteria; Substances produced thereby or obtained therefrom
• CPC Class Codes: A01N 63/30 Microbial fungi; Substances produced thereby or obtained therefrom
• CPC Class Codes: G01N 33/5097 involving plant cells immunoassays of plant cells G01N33/56961

Abstract

This application relates to methods and materials for providing a benefit to a seed or seedling of an agricultural plant (e.g., an agricultural grass plant), or the agricultural plant derived from the seed or seedling. For example, this application provides purified bacterial populations that include novel seed-origin bacterial endophytes, and synthetic combinations of seeds and/or seedlings (e.g., cereal seeds and/or seedlings) with heterologous seed-derived bacterial endophytes.

Claims

1. A method of treating seeds of a cereal agricultural plant, comprising mechanically or manually contacting a plurality of seeds with a composition comprising a purified bacterial population that comprises a seed bacterial endophyte that is capable of producing an auxin or acetoin, and has a 16S nucleic acid sequence that is at least 97% identical to a 16S nucleic acid sequence selected from the group consisting of SEQ ID NO:

521, 533, 560, 710, 856, 1447, 530, 536, 588, and 658, and the endophyte is heterologously disposed to the seed in an amount effective to colonize the plant and to increase germination efficiency of the treated seed as compared to a reference seed sowed under the same conditions.

2. The method of claim 1, wherein the bacterial endophyte is obtainable from an interior seed compartment.

3. The method of claim 1, wherein the bacterial endophyte is obtainable from an exterior surface of a seed.

4. The method of claim 1, wherein the bacterial endophyte is obtainable from a different cultivar, variety or crop as compared to the seed.

5. The method of claim 1, wherein the bacterial endophyte colonizes the roots of a seedling germinated from the treated seed.

6. The method of claim 1, wherein the composition further comprises a purified fungal population.

7. The method of claim 1, wherein the bacterial population includes two or more bacterial endophytes.

8. The method of claim 1, wherein the bacterial endophyte is obtained from rice seed, maize seed, wheat seed, or barley seed.

9. The method of claim 1, wherein the increased germination efficiency occurs under conditions of abiotic stress.

10. The method of claim 9, wherein the abiotic stress is selected from the group consisting of water stress, salt stress, heat stress, cold stress, high metal content stress and low nutrient stress.

21. The method of claim 1, wherein the effective amount is at least 10^3 CFU of endophyte per seed surface.

23. The method of claim 1, wherein the seed bacterial endophyte has a 16S nucleic acid sequence that is 97% identical to SEQ ID NO:

521.

24. The method of claim 1, wherein the seed bacterial endophyte has a 16S nucleic acid sequence that is 100% identical to SEQ ID NO:

521.

25. The method of claim 1, wherein the seed bacterial endophyte has a 16S nucleic acid sequence that is 97% identical to SEQ ID NO:

533.

26. The method of claim 1, wherein the seed bacterial endophyte has a 16S nucleic acid sequence that is 100% identical to SEQ ID NO:

533.

27. The method of claim 1, wherein the seed bacterial endophyte has a 16S nucleic acid sequence that is 97% identical to SEQ ID NO:

560.

28. The method of claim 1, wherein the seed bacterial endophyte has a 16S nucleic acid sequence that is 100% identical to SEQ ID NO:

560.

29. The method of claim 1, wherein the seed bacterial endophyte has a 16S nucleic acid sequence that is 97% identical to SEQ ID NO:

710.

30. The method of claim 1, wherein the seed bacterial endophyte has a 16S nucleic acid sequence that is 100% identical to SEQ ID NO:

710.

31. The method of claim 1, wherein the seed bacterial endophyte has a 16S nucleic acid sequence that is 97% identical to SEQ ID NO:

856.

32. The method of claim 1, wherein the seed bacterial endophyte has a 16S nucleic acid sequence that is 100% identical to SEQ ID NO:

856.

33. The method of claim 1, wherein the seed bacterial endophyte has a 16S nucleic acid sequence that is 97% identical to SEQ ID NO:

1447.

34. The method of claim 1, wherein the seed bacterial endophyte has a 16S nucleic acid sequence that is 100% identical to SEQ ID NO:

1447.

35. The method of claim 1, wherein the seed bacterial endophyte has a 16S nucleic acid sequence that is 97% identical to SEQ ID NO:

530.

36. The method of claim 1, wherein the seed bacterial endophyte has a 16S nucleic acid sequence that is 100% identical to SEQ ID NO:

530.

37. The method of claim 1, wherein the seed bacterial endophyte has a 16S nucleic acid sequence that is 97% identical to SEQ ID NO:

536.

38. The method of claim 1, wherein the seed bacterial endophyte has a 16S nucleic acid sequence that is 100% identical to SEQ ID NO:

536.

39. The method of claim 1, wherein the seed bacterial endophyte has a 16S nucleic acid sequence that is 97% identical to SEQ ID NO:

588.

40. The method of claim 1, wherein the seed bacterial endophyte has a 16S nucleic acid sequence that is 100% identical to SEQ ID NO:

588.

41. The method of claim 1, wherein the seed bacterial endophyte has a 16S nucleic acid sequence that is 97% identical to SEQ ID NO:

658.

42. The method of claim 1, wherein the seed bacterial endophyte has a 16S nucleic acid sequence that is 100% identical to SEQ ID NO:

658.

43. The method of claim 10, wherein the abiotic stress is water stress.

11. A method of treating seeds of a cereal agricultural plant, comprising mechanically or manually contacting a plurality of seeds with a composition comprising a purified bacterial population that comprises a first bacterial endophyte and a second bacterial endophyte, wherein the first bacterial endophyte and second bacterial endophyte have a 16S nucleic acid sequence that is at least 97% identical to a 16S nucleic acid sequence selected from the group consisting of SEQ ID NO:

521, 533, 560, 588, 658 and 856, and is capable of producing an auxin or acetoin, wherein the first bacterial endophyte and second bacterial endophyte have different 16S nucleic acid sequence, wherein the first and second endophytes are heterologously disposed to the seed in an amount effective to colonize the plant and to increase germination efficiency of the treated seed as compared to a reference seed sowed under the same conditions.

12. The method of claim 11, wherein the bacterial endophyte is obtainable from an interior seed compartment.

13. The method of claim 11, wherein the bacterial endophyte is obtainable from an exterior surface of a seed.

14. The method of claim 11, wherein the bacterial endophyte is obtainable from a different cultivar, variety or crop as compared to the seed.

15. The method of claim 11, wherein the bacterial endophyte colonizes the roots of a seedling germinated from the treated seed.

16. The method of claim 11, wherein the composition further comprises a purified fungal population.

17. The method of claim 11, wherein the bacterial population comprises more than two bacterial endophytes.

18. The method of claim 11, wherein the bacterial endophyte is obtained from rice seed, maize seed, wheat seed, or barley seed.

19. The method of claim 11, wherein the increased germination efficiency occurs under conditions of abiotic stress.

20. The method of claim 19, wherein the abiotic stress is selected from the group consisting of water stress, salt stress, heat stress, cold stress, high metal content stress and low nutrient stress.

22. The method of claim 11, wherein the effective amount is at least 10^3 CFU of each endophyte per seed surface.

44. The method of claim 11, wherein the first bacterial endophyte 16S nucleic acid sequence is 100% identical to a 16S nucleic acid sequence selected from the group consisting of SEQ ID NO:

521, 533, 560, 588, 658 and 856.

45. The method of claim 11, wherein the second bacterial endophyte 16S nucleic acid sequence is 100% identical to a 16S nucleic acid sequence selected from the group consisting of SEQ ID NO:

521, 533, 560, 588, 658 and 856.

46. The method of claim 20, wherein the abiotic stress is water stress.