Methods of use of seed-origin endophyte populations

• US 9,532,572 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, Flavell, Richard Bailey, Toledo, Gerardo V., Djonovic, Slavica, Marquez, Luis Miguel, Johnston, David Morris, Millet, Yves Alain, Lyford, Jeffrey, Naydich, Alexander, Sadowski, Craig
• Primary Examiner(s): IBRAHIM, MEDINA AHMED
• Application Number:
  US15/017,525
• Publication Number:
  US 20160150796A1
• 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 synthetic combination comprising a purified bacterial population in association with a seed of a cereal agricultural plant, wherein the purified bacterial population comprises a seed bacterial endophyte that is heterologous to the seed, 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, 588, 658, 710, 856 and 1447, and is capable of producing an auxin or acetoin, and wherein the seed bacterial endophyte is present in the synthetic combination at a concentration of at least 10³ CFU/seed on the surface of a seed and in an amount effective to increase tolerance to drought of a cereal agricultural plant produced from the seed as compared to a reference plant grown under the same conditions.

2. A population comprising at least 1000 synthetic combinations of claim 1, wherein the synthetic combinations are disposed within a package and are shelf stable.

3. A population comprising at least 1000 cereal agricultural plants produced by planting a population of synthetic combinations of claim 1, wherein the plants are grown in a field.

4. The synthetic combination of claim 1, wherein the seed bacterial endophyte is obtainable from an interior seed compartment.

5. The synthetic combination of claim 1, wherein the seed bacterial endophyte is obtainable from an exterior surface of a seed.

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

7. The synthetic combination of claim 1, wherein the seed bacterial endophyte colonizes the roots of the cereal agricultural plant.

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

9. The synthetic combination of claim 1, wherein the synthetic combination further comprises a purified fungal population.

10. The synthetic combination of claim 1, wherein the bacterial population includes two or more bacterial endophytes.

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

521.

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

521.

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

533.

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

533.

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

560.

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

560.

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

588.

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

588.

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

658.

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

658.

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

710.

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

710.

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

856.

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

856.

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

1447.

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

1447.

11. A synthetic combination comprising a purified bacterial population in association with a seed of a cereal agricultural plant, wherein the purified bacterial population comprises a first bacterial endophyte and a second bacterial endophyte, wherein the first bacterial endophyte and second bacterial endophyte 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, 588, 658, 710, 856 and 1447, and is capable of producing an auxin or acetoin, wherein the first bacterial endophyte and the second bacterial endophyte have different 16S nucleic acid sequence, and wherein the first bacterial endophyte and second bacterial endophyte are present in the synthetic combination at a concentration of at least 10³ CFU/seed on the surface of a seed and in an amount effective to increase tolerance to drought of a cereal agricultural plant produced from the seed as compared to a reference plant grown under the same conditions.

12. A population comprising at least 1000 synthetic combinations of claim 11, wherein the synthetic combinations are disposed within a package and are shelf stable.

13. A population comprising at least 1000 cereal agricultural plants produced by planting a population of synthetic combinations of claim 11, wherein the plants are grown in a field.

14. The synthetic combination of claim 11, wherein the seed bacterial endophyte is obtainable from an interior seed compartment.

15. The synthetic combination of claim 11, wherein the seed bacterial endophyte is obtainable from an exterior surface of a seed.

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

17. The synthetic combination of claim 11, wherein the seed bacterial endophyte colonizes the roots of the cereal agricultural plant.

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

19. The synthetic combination of claim 11, wherein the synthetic combination further comprises a purified fungal population.

20. The synthetic combination of claim 11, wherein the bacterial population comprises more than two bacterial endophytes.

37. The synthetic combination 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, 710, 856 and 1447.

38. The synthetic combination 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, 710, 856 and 1447.