Seed-origin endophyte populations, compositions, and methods of use

• US 9,113,636 B2
• Filed: 06/26/2014
• Issued: 08/25/2015
• Est. Priority Date: 06/26/2013
• Status: Active Grant

• Current Assignee: Indigo Ag, Inc.
• Original Assignee: Symbiota, Inc.
• Inventors: von Maltzahn, Geoffrey, Flavell, Richard Bailey, Toledo, Gerardo V., Djonovic, Slavica, Mrquez, Luis Miguel, Johnston, David Morris, Millet, Yves Alain, Lyford, Jeffrey, Naydich, Alexander, Sadowski, Craig
• Primary Examiner(s): IBRAHIM, MEDINA AHMED
• Application Number:
  US14/316,469
• Publication Number:
  US 20150020239A1
• Time in Patent Office: 425 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:

522, 658, 588, 560, 536, 1447, 530, is capable of producing an auxin or acetoin, 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 grain yield 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 present at a concentration of at least 10⁴ CFU/seed on the surface of a seed.

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

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

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

8. The synthetic combination of claim 1, wherein the seed bacterial endophyte is present in the synthetic combination in an amount effective to increase the level of at least one protein involved in resistance to oxidative stress within the seed, a seedling produced from the seed, or a cereal plant produced from the seed as compared to a reference seed, seedling or plant grown under the same conditions.

9. The synthetic combination of claim 8, wherein the protein involved in resistance to oxidative stress is involved in scavenging reactive oxygen species.

10. The synthetic combination of claim 9, wherein the protein involved in scavenging reactive oxygen species is a glutathione S-transferase or a peroxidase.

11. The synthetic combination of claim 1, wherein the synthetic combination comprises two or more seed bacterial endophytes.

13. The synthetic combination of claim 1, wherein the bacterial seed endophyte is present in the synthetic combination in an amount effective to increase the level of at least one protein involved in growth promotion within the seed, a seedling produced from the seed, or a cereal plant produced from the seed as compared to a reference seed, seedling or plant grown under the same conditions.

14. The synthetic combination of claim 13, wherein the protein involved growth promotion is a protein involved in cell proliferation.

15. The synthetic combination of claim 14, wherein the protein involved in cell proliferation is a histone.

16. The population of claim 3, wherein at least 60% of the plants in the population are colonized by the seed bacterial endophyte.

12. A synthetic combination of a purified bacterial population in association with a seed of a cereal agricultural plant, wherein the synthetic combination is produced by the step of contacting the seed with a formulation comprising a heterologous purified bacterial population, wherein the purified bacterial population comprises a seed bacterial endophyte that 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:

522, 658, 588, 560, 536, 1447, 530, and is capable of producing an auxin or acetoin, under conditions such that the formulation becomes disposed upon an exterior surface of the seed at a concentration of at least 10³ CFU/seed and in a manner effective for the seed bacterial endophyte to increase grain yield of a cereal agricultural plant produced from the seed, relative to a reference plant grown under the same conditions.

17. 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:

522, 658, 588, 560, 536, 1447, 530, is present at a concentration of at least 10³ CFU/seed on the surface of a seed, and is capable of producing an auxin or acetoin, wherein the seed bacterial endophyte is present in the synthetic combination in an amount effective to increase the level of at least one protein involved in resistance to oxidative stress within the seed, a seedling grown from the seed or a cereal agricultural plant produced by the seed, as compared to a reference seed, seedling or plant grown under the same conditions.

18. The synthetic combination of claim 17, wherein the protein involved in resistance to oxidative stress is involved in scavenging reactive oxygen species.

19. The synthetic combination of claim 18, wherein the protein involved in scavenging reactive oxygen species is a glutathione S-transferase or a peroxidase.

20. A population comprising at least 1000 synthetic combinations of claim 17, wherein the synthetic combinations are disposed within a package and are shelf stable.