DETAILED ACTION
Applicant’s amendment filed on 10/8/2025 is acknowledged. Claims 1, 160, and 169 are currently amended. Claims 2-159 and 161-162 are canceled. Claims 1, 160, and 163-177 are pending and the subject of this office action.
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 10/8/2025 has been entered.
Priority
The instant application is a National Phase of PCT/US2019/068152 filed on 12/20/2019 and claims domestic benefit to U.S. Provisional Application No. 62/784,277 filed on 12/21/2018. Claims 1, 160, and 163-177 find support in the international application and are afforded an effective filing date of 12/20/2019.
Response to Amendment
Applicant’s amendment to claim 169 renders moot the 35 U.S.C. § 112(a) new matter rejection previously set forth in the Final Rejection mailed on 7/8/2025. Accordingly, the rejection is withdrawn.
Claim Rejections - 35 USC § 112(a) – New Matter
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claim 169 is rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventors, at the time the application was filed, had possession of the claimed invention.
Newly added claim 169 recites new matter. Claim 169 recites “further comprising applying the modified bacterial strain to a plant, wherein the plant is the same type of plant as the plant root exudate.” The limitation “wherein the plant is the same type of plant as the plant root exudate” fails to receive support in the specification or priority documents. None of the specification paragraphs cited by Applicant in the remarks (see p.6, 7th paragraph) provide implicit or explicit support for the newly added limitation. Paragraphs [0106], [0108], and [0248] disclose inoculating plants with bacteria but do not disclose the plant is the same species of plant from which the plant exudate is obtained. The examples of the instant specification disclose generating corn root exudate, analyzing growth and nitrogen fixation activity of bacteria in the corn root exudate, and applying the bacteria to the soil above corn seeds and to corn seeds (see Examples 3-7). However, this disclosed species does not provide support for the claimed genus of “applying the modified bacterial strain to a plant, wherein the plant is the same type of plant as the plant root exudate” since the only species of plant described is corn and the claim is generically drawn to all plants. Moreover, “plant type” is not defined in the specification, and as discussed in the 35 U.S.C. § 112(b) rejection below, is used ambiguously in the relevant art. Therefore, new claim 169 recites new matter.
Claim Rejections - 35 USC § 112(b) – Indefinite
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 169 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 169 recites the limitation “type of plant” in line 2. The phrase “type of plant” receives an ambiguous meaning in the art. The specification mentions “plant types” once in paragraph [0163] but provides no clear definition of the term. NC State Extension describes there are over 350,000 types of plants with new species being discovered regularly and others going extinct (see Appendix A – p.3, 1st passage). Later, it is described that the Kingdom Plantae is divided into two types of land plants: nonvascular and vascular (see p.4, 2nd-3rd passages). Thus, in botanical communities, the term type with respect to plants is not clearly defined and accords multiple uses. One of ordinary skill in the art would not be able to determine the metes and bounds of the claim. Therefore, claim 169 is indefinite.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
New Rejection Necessitated by Amendment: Claims 1 and 164-170 are rejected under 35 U.S.C. 103 as being unpatentable over to Thomas et al. (US2019/0209636 A1 published 7/11/2019; Of Record) in view of Islam et al. (Front. Microbiol., 2016, Vol. 6, Article 1360; Of Record) and Temme et al. (US2018/0002243; of record in IDS filed 9/9/2021).
Regarding claim 1, Thomas teaches methods for screening, identifying, and producing microorganisms capable of imparting beneficial properties to plants (see Abstract and paragraph [0005]). Thomas teaches that improved plant-associated soil microorganisms (PASMs) are generated by experimental evolution using a plant root exudate or root exudate compound (see Abstract and paragraphs [0029] and [0044]-[0046]). Thomas teaches that the PASMs are plant rhizosphere microbiota including Bacillus species as reduced in the Examples of their disclosure (see paragraphs [0031]-[0034], [0037], and [0063]-[0092] and Figs. 1-11). Thomas teaches 1) growing a genetically-uniform population of PASM cells in or on a first medium comprising an aliquot of root exudate produced by a plant of interest; 2) harvesting at least some of the resulting PASM cells and growing the harvested PASM cells in or on a second medium comprising an aliquot of root exudate produced by the plant of interest; 3) repeating step 2) at least one time; and 4) selecting, identifying, and/or producing at least one PASM cell that is different compared to the genetically-uniform population (see paragraph [0006]). Thomas further teaches the selected PASM cell has an improved ability to confer at least one beneficial phenotypic trait to a plant compared to the genetically-uniform population (see paragraphs [0006] and [0050]). Thomas teaches the passages of PASMs in medium containing root exudate drives microbial evolution and co-adaptation to enhance the performance of microbial strains for improving plants, and is targeted at improving rhizosphere competency of a microbe by using the crop root exudate (see paragraphs [0006], [0029], [0035]-[0037], [0044]-[0045], and [0063]-[0070]). Thomas specifically teaches culturing Bacillus spores to log phase in a soybean root exudate as media and repeating the process 13 times to obtain variant Bacillus cells (see paragraphs [0063] and [0065]). Thomas teaches the soybean root exudate is generated by growing sterilized soybeans in deep well blocks of 1 mL of water, and after 1 week, harvesting the root exudate (see paragraph [0064]). Thomas teaches plant roots secrete a vast array of compounds including amino acids, organic acids, carbohydrates, sugars, mucilage, vitamins, and proteins, and thus reads on the limitation for generating the PEM of the claimed invention (see paragraphs [0031]-[0033]). Thomas teaches collecting variants and assaying for rate of growth/bacterial cell growth kinetics of the variants when grown in soybean root exudate, which reads on assaying colonization ability of a genetically modified microbial strain in a plant exudate medium comprising root exudate, thereby producing an in vitro colonization ability, wherein said in vitro colonization ability of said genetically modified microbial strain is assayed by determining, in said PEM, growth rate (see paragraphs [0065]-[0066] and [0069] and Fig. 1).
Thomas does not teach wherein said generating comprises using transposon mutagenesis or site-directed mutagenesis to introduce one or more mutations into a gene of the bacterial strain, assaying nitrogen fixation activity of a genetically modified bacterial strain in vitro in a plant exudate medium (PEM) comprising root exudate, thereby producing an in vitro nitrogen fixation activity, wherein assaying said in vitro nitrogen fixation activity of said genetically modified microbial strain consists of using an acetylene reduction assay of the strain in said PEM; and (c) based on said in vitro nitrogen fixation activity of the genetically modified bacterial strain, predicting the nitrogen fixation activity of the genetically modified bacterial strain in a plant.
Islam teaches that rhizobacteria that benefit plants by stimulating growth and suppressing disease are referred to as plant growth promoting rhizobacteria and are widely recognized for their mechanisms of plant growth promotion by production of phytohormones, diazotrophic fixation of nitrogen, and solubilization of phosphate (see p.2, left column, 1st paragraph). Islam teaches methods of characterizing plant growth promoting rhizobacteria in vitro that includes testing the nitrogenase activity of isolates via the acetylene reduction assay (see Abstract, p.3, right column, 2nd passage). This is considered to read on assaying the nitrogen fixation activity of said microbial strain by using an acetylene reduction assay of the strain.
Therefore, it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have included an acetylene reduction assay, as taught by Islam, in the method for screening, identifying, and producing microorganisms capable of imparting beneficial properties to plants, as taught by Thomas, to arrive at the claimed invention. One of ordinary skill in the art would have been motivated to because Islam teaches plant growth promoting rhizobacteria, of which Thomas teaches the use of in their methods, promote plant growth by providing nitrogen fixation, and teaches an assay for determining the nitrogen fixation activity of plant growth promoting rhizobacteria by acetylene reduction assay, which would yield predictable results. One of ordinary skill in the art would have been motivated to select the best rhizobacteria for nitrogen fixation to provide plants with increased nitrogen and would have had a reasonable expectation of success because Islam teaches this assay is performed in rhizobacteria cultured in vitro and the method of Thomas is also performed in vitro using rhizobacteria.
Islam does not teach wherein said generating comprises using transposon mutagenesis or site-directed mutagenesis to introduce one or more mutations into a gene of the bacterial strain.
Temme teaches a method of producing one or more bacteria including isolating bacteria from tissue or soil of a first plant, introducing one or more genetic variations into one or more of the bacteria to produce one or more variant bacteria, exposing plants to the variant bacteria, isolating bacteria from tissue or soil wherein the plant from which the bacteria is isolated has an improved trait relative to other plants (see paragraph [0028]). Temme further teaches the improved trait may be enhanced nitrogen fixation in the plant from which the bacteria are isolated and/or in plants exposed to the bacteria (see paragraph [0028]). Temme teaches the genetic variation can be in a gene of the bacteria’s nitrogen fixation or assimilation genetic regulatory network selected from: nifA, nifL, ntrB, ntrC, glnA, glnB, glnK, draT, amtB, glnD, glnE, nifJ, nifH, nifD, nifK, nifY, nifE, nifN, nifU, nifS, nifV, nifW, nifZ, nifM, nifF, nifB, and nifQ (see paragraphs [0026] and [0028]). Temme further teaches the genetic variation is a mutation that results in one or more of increased expression or activity of NifA or glutaminase, decreased expression or activity of NifL, NtrB, glutamine synthetase, GlnB, GlnK, DraT, and AmtB, decreased adenylyl-removing activity of GlnE, or decreased uridylyl-removing activity of GlnD (see paragraphs [0026] and [0028]). Temme teaches site specific mutagenesis can be used to alter the activity of an enzyme, reading on site-directed mutagenesis to introduce one or more mutations into a gene of the bacterial strain (see paragraphs [0101], [0106], and [0108]).
Therefore, it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have substituted producing one or more bacteria that improve a trait of a plant by introducing one or more genetic variations by site specific mutagenesis, as taught by Temme, for the PASM bacteria used in the passages in medium containing root exudate to drive microbial evolution and co-adaptation to enhance the performance of microbial strains for improving plants, as taught by Thomas, to arrive at the claimed invention. One of ordinary skill in the art would have been substituting bacteria intended for improving traits of a plant, yielding predictable results.
Regarding claim 164, Temme teaches introducing one or more genetic variations by site specific (site-directed) mutagenesis in which the mutation may be a single base change, multiple base change, deletion, insertion, or a combination (see paragraphs [0106] and [0108]).
Regarding claim 165, Temme teaches a native or endogenous control sequence of genes of the present disclosure are replaced with one or more intrageneric control sequences, reading on wherein the one or more mutations comprise an intrageneric modification of the gene (see paragraph [0068]). It would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have further modified a bacteria for improving a trait of a plant with one or more genetic variations, as taught by the method of Thomas in view of Islam and Temme, by replacing a native control sequence with an intrageneric control sequence, as taught by Temme, to arrive at the claimed invention.
Regarding claims 166-168, Temme teaches the one or more genetic variations can be in a gene of the bacteria’s nitrogen fixation or assimilation genetic regulatory network selected from: nifA, nifL, ntrB, ntrC, glnA, glnB, glnK, draT, amtB, glnD, glnE, nifJ, nifH, nifD, nifK, nifY, nifE, nifN, nifU, nifS, nifV, nifW, nifZ, nifM, nifF, nifB, and nifQ (see paragraphs [0026] and [0028]). Temme further teaches the genetic variation is a mutation that results in one or more of increased expression or activity of NifA or glutaminase, decreased expression or activity of NifL, NtrB, glutamine synthetase, GlnB, GlnK, DraT, and AmtB, decreased adenylyl-removing activity of GlnE, or decreased uridylyl-removing activity of GlnD (see paragraphs [0026] and [0028]). It would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have produced bacteria that improve the trait of a plant by any one or more of a genetic variation to a bacteria’s nitrogen fixation or assimilation genetic regulatory network as disclosed by Temme.
Regarding claim 169, the limitation “type of plant” is interpreted as being an identical plant to that which the root exudate was obtained light of this limitation being indefinite. Thomas further teaches applying the improved bacterial cells produced in their methods to a plant in an amount sufficient to result in stable or transient colonization of the plant (see paragraphs [0011] and [0027]). The examples of Thomas demonstrate the generation of soybean root exudate to assay bacteria and then applying the improved bacteria to soybean seeds (see Examples 1-3). Thus, it would have been obvious to apply the bacteria produced to the identical plant that the plant root exudate was obtained since the bacteria were optimized to root exudate produced by that plant, and one of ordinary skill would expect transferrable results in the plant based on the results obtained in the assay using the plant root exudate.
Regarding claim 170, Thomas teaches the improved bacteria is applied to a plant of interest such as soybean or corn plants (see paragraph [0054] and Examples 1-3).
Thus, claims 1 and 164-170 are prima facie obvious over Thomas in view of Islam and Temme.
Claims 160, 163, and 171-177 are rejected under 35 U.S.C. 103 as being unpatentable over to Thomas et al. (US2019/0209636 A1 published 7/11/2019; Of Record) in view of Islam et al. (Front. Microbiol., 2016, Vol. 6, Article 1360; Of Record) and Temme et al. (US2018/0002243; of record in IDS filed 9/9/2021), as applied to claims 1 and 164-170 above, and further in view of Baudoin et al. (Soil Biol. & Biochem., 2003, Vol. 35, p.1183-1192; Of record).
Regarding claim 160, Thomas in view of Islam and Temme teach every limitation of the claimed invention, as outlined in the rejection of claim 1 above, except for a synthetic plant exudate medium, as claimed.
Baudoin teaches testing the impact of artificial root exudates on the bacterial community and structure in bulk soil and maize rhizosphere and discovered that their artificial root exudate which comprised glucose, fructose, saccharose, citric acid, lactic acid, succinic acid, alanine, serine, and glutamic acid, reading on the limitations of claim 163, significantly increased bacterial densities both in vitro and in situ (see Abstract, p.1184, left column, last two paragraphs, full right column, Fig. 1, and Fig. 4).
Therefore, it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have substituted the artificial root exudate of Baudoin for the root exudate of Thomas, as modified by Islam and Temme above, to arrive at the claimed invention. One of ordinary skill in the art would have been motivated to because Baudoin teaches their artificial root exudate significantly increased bacterial densities in soil and maize rhizosphere and they would have been substituting equivalents known for the same purpose, yielding predictable results. See MPEP § 2144.06(II). Thus, claims 160 and 163 are prima facie obvious.
Regarding claim 171, Temme teaches introducing one or more genetic variations by site specific (site-directed) mutagenesis in which the mutation may be a single base change, multiple base change, deletion, insertion, or a combination (see paragraphs [0106] and [0108]).
Regarding claim 172, Temme teaches a native or endogenous control sequence of genes of the present disclosure are replaced with one or more intrageneric control sequences, reading on wherein the one or more mutations comprise an intrageneric modification of the gene (see paragraph [0068]). It would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have further modified a bacteria for improving a trait of a plant with one or more genetic variations, as taught by the method of Thomas in view of Islam and Temme, by replacing a native control sequence with an intrageneric control sequence, as taught by Temme, to arrive at the claimed invention.
Regarding claims 173-175, Temme teaches the one or more genetic variations can be in a gene of the bacteria’s nitrogen fixation or assimilation genetic regulatory network selected from: nifA, nifL, ntrB, ntrC, glnA, glnB, glnK, draT, amtB, glnD, glnE, nifJ, nifH, nifD, nifK, nifY, nifE, nifN, nifU, nifS, nifV, nifW, nifZ, nifM, nifF, nifB, and nifQ (see paragraphs [0026] and [0028]). Temme further teaches the genetic variation is a mutation that results in one or more of increased expression or activity of NifA or glutaminase, decreased expression or activity of NifL, NtrB, glutamine synthetase, GlnB, GlnK, DraT, and AmtB, decreased adenylyl-removing activity of GlnE, or decreased uridylyl-removing activity of GlnD (see paragraphs [0026] and [0028]). It would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have produced bacteria that improve the trait of a plant by any one or more of a genetic variation to a bacteria’s nitrogen fixation or assimilation genetic regulatory network as disclosed by Temme.
Regarding claim 176, Thomas further teaches applying the improved bacterial cells produced in their methods to a plant in an amount sufficient to result in stable or transient colonization of the plant (see paragraphs [0011] and [0027]).
Regarding claim 177, Thomas teaches the improved bacteria is applied to a plant of interest such as soybean or corn plants (see paragraph [0054] and Examples 1-3).
Thus, claims 160, 163, and 171-177 are prima facie obvious over Thomas in view of Islam and Temme and further in view of Baudoin.
Response to Arguments
Applicant's arguments filed 10/8/2025 have been fully considered but they are not persuasive.
In Applicant’s Remarks, see p.6, 7th paragraph, Applicant argues that the amendment to recite “same type of plant” receives support in the Examples of the specification and is not new matter. This is not found persuasive. Firstly, the term ”type” with regards to plants receives different uses in the relevant art. NC State Extension describes there are over 350,000 types of plants with new species being discovered regularly and others going extinct (see Appendix A – p.3, 1st passage). Later, it is described that the Kingdom Plantae is divided into two types of land plants: nonvascular and vascular (see p.4, 2nd-3rd passages). Thus, in botanical communities, the term type with respect to plants is not clearly defined and accords multiple uses. The specification only mentions plant type once in paragraph [0163] and does not provide a clear definition for a type of plant. Absent a clear definition and in view of the ambiguous use of the phrase “type of plant” in the relevant art, claim 169 still embraces new matter.
In Applicant’s Remarks, see p.8, 1st passage, Applicant argues that since Islam states that all isolates, including the two that demonstrated no acetylene reduction activity, enhanced the nitrogen content of cucumber, a person of ordinary skill in the art would not have been prompted to carry out a method as claimed to rely solely on the acetylene reduction assay (ARA) for predicting nitrogen fixation activity. Applicant further argues that Islam’s teachings would lead a person of ordinary skill in the art to possibly try another or additional in vitro method to assess the nitrogen fixation activity of bacterial strain in a plant. This is not found persuasive. Islam still found that 8 of the 10 isolates studied that were found to have ARA enhanced the nitrogen content of the cucumber plants tested (see p.9, paragraph bridging left and right columns). Furthermore, Islam states that acetylene reduction activity is a widely accepted surrogate for nitrogenase activity and N2-fixing potential. Thus, one of ordinary skill in the art would have a reasonable expectation of success predicting in planta nitrogen fixation activity from the in vitro ARA assay since it showed 80% predictive capability in Islam.
In Applicant’s Remarks, see paragraph bridging p.9-10, Applicant reiterates the arguments set forth above. These arguments are not found persuasive for the same reasons discussed above.
Conclusion
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/J.P.S./Examiner, Art Unit 1657
/MELENIE L GORDON/Supervisory Patent Examiner, Art Unit 1657