IP Library › Granted Patent US 12,686,650
Granted Patent B2
US 12,686,650 · App. 17/027,030 · Granted Jul 21, 2026

Methods and compositions for improving plant traits

Inventors: Karsten Temme (Oakland, CA); Alvin Tamsir (San Francisco, CA); Sarah Bloch (Emeryville, CA); Rosemary Clark (El Cerrito, CA); Emily Tung (Millbrae, CA); Kevin Hammill (Danville, CA); Douglas Higgins (Berkeley, CA); Austin Davis-Richardson (San Francisco, CA)
Assignee: Pivot Bio, Inc.
C05F11/08A01H3/00A01H6/4684A01N63/20C12N1/04C12N1/20C12N1/205C12N15/111C12N15/52C12N15/70C12N15/743C12R2001/01C12R2001/025C12R2001/065C12R2001/07C12R2001/22
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Quick Facts
Patent No.
US 12,686,650
App. No.
17/027,030
Filed
Sep 21, 2020
Granted
Jul 21, 2026
Kind
B2
Art Unit
1662
USPC
800/320.1
Abstract

Methods and systems are provided for generating and utilizing a bacterial composition that comprises at least one genetically engineered bacterial strain that fixes atmospheric nitrogen in an agricultural system that has been fertilized with more than 20 lbs of Nitrogen per acre.

Claims (46)

1 . A method for increasing the available nitrogen for a non-leguminous plant in a field, said method comprising applying to said non-leguminous plant in said field a plurality of engineered diazotrophic bacteria, wherein:

said engineered diazotrophic bacteria have a product of (i) colonization ability under field conditions and (ii) fixed N produced per bacterial cell per hour of at least about 2.5×10 −8 mmol N per gram of fresh weight of plant root tissue per hour; and

said engineered diazotrophic bacteria comprises one or more genetic variations, wherein the one or more genetic variations comprise a complete or partial nifL deletion and insertion of a constitutive promoter operably linked to a nifA gene.

2 . The method of claim 1 , wherein said plurality of engineered diazotrophic bacteria, in planta, produce 5% or more of the available nitrogen in said non-leguminous plant.

3 . The method of claim 1 , wherein said engineered diazotrophic bacteria comprise a bacterium from a species selected from the group consisting of Kosakonia sacchari, Rahnella aquatilis, Klebsiella variicola , and Kosakonia pseudosacchari.

4 . The method of claim 3 , wherein said Kosakonia sacchari bacterium is a bacterium deposited under Patent Depository Designation No. 201701002, 201708004, 201708003, or 201708002.

5 . The method of claim 3 , wherein said Rahnella aquatilis bacterium is a bacterium deposited under Accession No. PTA-122293.

6 . The method of claim 3 , wherein said Klebsiella variicola bacterium is a bacterium deposited under Patent Depository Designation No. 201712002.

7 . A non-leguminous plant colonized with a plurality of engineered diazotrophic bacteria, wherein:

said engineered diazotrophic bacteria have a product of (i) colonization ability under field conditions and (ii) N produced per bacterial cell per hour of at least about 2.5×10 −8 mmol N per gram of fresh weight of plant root tissue per hour; and

said engineered diazotrophic bacteria comprise one or more genetic variations, wherein the one or more genetic variations comprise a complete or partial nifL deletion and insertion of a constitutive promoter operably linked to a nifA gene.

8 . The non-leguminous plant of claim 7 , wherein said non-leguminous plant is selected from the group consisting of corn, rice, wheat, barley, sorghum, millet, oat, rye, and triticale.

9 . A composition comprising:

a) a plurality of engineered diazotrophic bacteria, wherein:

said engineered diazotrophic bacteria have a product of (i) colonization ability under field conditions and (ii) N produced per bacterial cell per hour of at least about 2.5×10 −8 mmol N per gram of fresh weight of non-leguminous plant root tissue per hour; and

said engineered diazotrophic bacteria comprise one or more genetic variations, wherein the one or more genetic variations comprise a complete or partial nifL deletion and insertion of a constitutive promoter operably linked to a nifA gene; and

b) a non-leguminous plant seed, wherein said plurality of engineered diazotrophic bacteria can provide at least one pound of nitrogen per acre per season to a non-leguminous plant produced from said plant seed in a field.

10 . The composition of claim 9 , wherein said plurality of engineered diazotrophic bacteria comprises two or more bacterial strains.

11 . The composition of claim 9 , wherein said plurality of engineered diazotrophic bacteria comprises a bacterium from a species selected from the group consisting of Kosakonia sacchari, Rahnella aquatilis, Klebsiella variicola , and Kosakonia pseudosacchari.

12 . The composition of claim 11 , wherein said Kosakonia sacchari bacterium is a bacterium deposited under Patent Depository Designation No. 201701002, 201708004, 201708003, or 201708002.

13 . The composition of claim 11 , wherein said Rahnella aquatilis bacterium is a bacterium deposited under Accession No. PTA-122293.

14 . The composition of claim 11 , wherein said Klebsiella variicola bacterium is a bacterium deposited under Patent Depository Designation No. 201712002.

15 . The method of claim 1 , wherein said plurality of engineered diazotrophic bacteria comprises a bacterium from a genus selected from the group consisting of Kosakonia, Rahnella , and Klebsiella.

16 . The method of claim 1 , wherein said plurality of engineered diazotrophic bacteria comprises two or more bacterial strains.

17 . The method of claim 16 , wherein said two or more bacterial strains are from a genus independently selected from the group consisting of Kosakonia, Rahnella , and Klebsiella.

18 . The method of claim 16 , wherein at least two bacterial strains of said two or more bacterial strains are from a genus independently selected from the group consisting of Kosakonia and Rahnella.

19 . The method of claim 1 , wherein said one or more genetic variations comprise a partial deletion of nifL and further comprise a partial deletion of glnE.

20 . The method of claim 19 , wherein said partial deletion of glnE results in deletion of the nucleotides encoding the adenylyl-removing domain of the GlnE protein.

21 . The non-leguminous plant of claim 7 , wherein said engineered diazotrophic bacteria comprise a bacterium from a species selected from the group consisting of Kosakonia sacchari, Rahnella aquatilis, Klebsiella variicola , and Kosakonia pseudosacchari.

22 . The non-leguminous plant of claim 21 , wherein said Kosakonia sacchari bacterium is a bacterium deposited under Patent Depository Designation No. 201701002, 201708004, 201708003, or 201708002.

23 . The non-leguminous plant of claim 21 , wherein said Rahnella aquatilis bacterium is a bacterium deposited under Accession No. PTA-122293.

24 . The non-leguminous plant of claim 21 , wherein said Klebsiella variicola bacterium is a bacterium deposited under Patent Depository Designation No. 201712002.

25 . The non-leguminous plant of claim 7 , wherein said plurality of engineered diazotrophic bacteria comprises two or more bacterial strains.

26 . The non-leguminous plant of claim 7 , wherein said plurality of engineered diazotrophic bacteria comprises a bacterium from a genus selected from the group consisting of Kosakonia, Rahnella , and Klebsiella.

27 . The non-leguminous plant of claim 26 , wherein said two or more bacterial strains are from a genus independently selected from the group consisting of Kosakonia, Rahnella , and Klebsiella.

28 . The non-leguminous plant of claim 26 , wherein at least two bacterial strains of said two or more bacterial strains are from a genus independently selected from the group consisting of Kosakonia and Rahnella.

29 . The non-leguminous plant of claim 7 , wherein said one or more genetic variations comprise a partial deletion of nifL and further comprise a partial deletion of glnE.

30 . The non-leguminous plant of claim 29 , wherein said partial deletion of glnE results in deletion of the nucleotides encoding the adenylyl-removing domain of the GlnE protein.

31 . The composition of claim 9 , wherein said plurality of engineered diazotrophic bacteria comprises a bacterium from a genus selected from the group consisting of Kosakonia, Rahnella , and Klebsiella.

32 . The composition of claim 10 , wherein said two or more bacterial strains are from a genus independently selected from the group consisting of Kosakonia, Rahnella , and Klebsiella.

33 . The composition of claim 10 , wherein at least two bacterial strains of said two or more bacterial strains are from a genus independently selected from the group consisting of Kosakonia and Rahnella.

34 . The composition of claim 9 , wherein said one or more genetic variations comprise a partial deletion of nifL and further comprise a partial deletion of glnE.

35 . The composition of claim 34 , wherein said partial deletion of glnE results in deletion of the nucleotides encoding the adenylyl-removing domain of the GlnE protein.

36 . The method of claim 1 , wherein said one or more genetic variations further comprise a complete or partial amtB deletion.

37 . The non-leguminous plant of claim 7 , wherein said one or more genetic variations further comprise a complete or partial amtB deletion.

38 . The composition of claim 9 , wherein said one or more genetic variations further comprise a complete or partial amtB deletion.

Assignments (4)
SECURITY INTEREST Recorded Dec 22, 2025
From: PIVOT BIO, INC.
To: HSBC BANK USA, N.A.
Reel/Frame 073285/0020 →
REASSIGNMENT AND RELEASE OF SECURITY INTEREST AT REEL/FRAME NO. 55743/0625 Recorded Nov 7, 2025
From: HERCULES CAPITAL INC., AS AGENT
To: PIVOT BIO, INC.
Reel/Frame 073567/0605 →
INTELLECTUAL PROPERTY SECURITY AGREEMENT Recorded Mar 26, 2021
From: PIVOT BIO, INC.
To: HERCULES CAPITAL, INC., AS AGENT
Reel/Frame 055743/0625 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Sep 29, 2020
From: TEMME, KARSTEN; TAMSIR, ALVIN; BLOCH, SARAH; CLARK, ROSEMARY; TUNG, EMILY; HAMMILL, KEVIN; HIGGINS, DOUGLAS; DAVIS-RICHARDSON, AUSTIN
To: PIVOT BIO, INC.
Reel/Frame 053915/0915 →
Continuity (9)
Continuation 16159542 · Oct 12, 2018
Continuation PCTUS2018013671 · Jan 12, 2018
Provisional Application 62577147 · Oct 25, 2017
Provisional Application 62566199 · Sep 29, 2017
Provisional Application 62467032 · Mar 3, 2017
Provisional Application 62447889 · Jan 18, 2017
Provisional Application 62445557 · Jan 12, 2017
Provisional Application 62445570 · Jan 12, 2017
Related Publication 20210009483A1 · Jan 14, 2021
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