DETAILED 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 .
Election/Restrictions
Applicant’s election without traverse of Group III comprising claims 25-29, 32 and 34 in the reply filed on 12/26/2025 is acknowledged. There are no species election for Group III.
The Election is made FINAL.
Claims Status
Claims 1, 3-6, 8, 10-11, 14, 16, 18-19, 22, 24-27, 29, 32 and 34 are pending.
Claims 1, 3-6, 8, 10-11, 14, 16, 18-19, 22 and 24 are withdrawn from examination as being part of non-elected groups.
Claims 25-27, 29, 32 and 34 are being examined.
Claim Objections
Claims 29 and 32 are objected to because of the following informalities: Claims 29 recites, “…one or more viable microorganisms …”. Claim 32 recites, “the one or more viable
microorganisms comprise..”.
It is suggested to amend claim 29 in the line of “…one or more viable microorganism(s)..” and amend claim 32 in the line of “…the one or more viable microorganism(s) comprise(s)...”
Appropriate correction is required.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 25-27, 29, 32 and 34 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more. The claims are drawn to an agricultural composition comprising an enriched root associated microbiome (RAM) or a portion thereof, wherein the enriched RAM is obtained from a genetically engineered plant. These are product by process claims. Patentability of the product (i.e., “root associated microbiome (RAM) or a portion thereof”) does not depend on the process including use of genetically engineered plants grown over it, as claimed (i.e., “obtained from a genetically engineered plant”) but on the product itself. Any microbiome (not necessarily by plants, genetically engineered or not ) with enriched RAM would satisfy the claim limitations.
The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because all the viable microorganisms are also naturally occurring. Moreover, the Applicant does not define the term “enriched” in the context of root associated microbiome (RAM) and also does not specify how far (distance wise) the term “root associated” imply from the root(s) of the plant. It is well-known in the art that soil microbiome is naturally enriched when specific type of plants (e.g., nitrogen-fixing naturally occurring legume plants) are grown over it. Claims 25-29, 32, and 34 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception without significantly more.
The composition of independent claim 25 comprises an “enriched root associated microbiome or a portion thereof”. Root associated microbiomes (RAM) occur in nature. The instant claims recite “enriched” RAM. However, as discussed in the rejection under 35 U.S.C. 112(b) below, the term “enriched” is not defined in the specification. Claim 25 also recites that the enriched RAM “is obtained from a genetically engineered plant”. However, a RAM is not actually in a plant, but rather is in the soil surrounding the roots of plants. Further, the specification in [0034] teaches, “A “genetically engineered plant” can refer to a plant that has been genetically manipulated”, which includes “other forms of altering the amount, nature, or activity of nucleic acids in a plant, such as mutagenizing plant by exposing it to a mutagen such as UV light”. Therefore, a “genetically engineered plant” includes naturally-occurring mutated plants, as plants in nature are exposed to UV radiation in sunlight. An “enriched RAM” may also be the RAM surrounding the roots of such plants.
When a claim recites a nature-based product limitation, the markedly different characteristics analysis is used to evaluate the nature-based product limitation (MPEP 2106.04(b)(II)). Given it is unclear what is encompassed by the term “enriched” in the context of the invention (as discussed below), an “enriched root associated microbiome” encompasses RAM that occur in nature. As mentioned above, claim 25 does not require the RAM surrounding the roots of a genetically engineered plant to be any different (in any specific way) from that surrounding a corresponding non-engineered plant. Further, the definition for “genetically engineered plant” in the specification encompasses naturally occurring plants mutagenized by UV in sunlight. Furthermore, the claim encompasses “a portion” of the enriched RAM. Neither the claims nor the specification place restrictions on this “portion”. Therefore, the “portion” encompasses any contents of the enriched RAM, including, for example, nutrients and microorganisms. Such “portions” are not markedly different from the naturally-occurring nutrients and microorganisms in naturally occurring RAM.
Claim 26 recites that the genetically-engineered plant overexpresses a type 1 H+-pyrophospatase. However, again, the specification does not define “enriched”. And the claim encompasses any “portion” of an enriched RAM, which includes naturally occurring soil nutrients and microorganims.
Claim 27 only limits the genetically engineered plant to being Arabidopsis. A RAM is not actually in a plant.
Claim 29 recites a Markush list of viable microorganisms comprised in the enriched RAM. Note, all of the Markush group members occur in nature, and constitute a “portion” of the enriched RAM.
Claim 32 depends from claim 29 and requires the viable microorganisms to comprise enriched fermentation capacity. However, as discussed further in the rejection under 35 U.S.C. 112(b), the specification does not provide an unambiguous definition of “enriched fermentation capacity” that distinguishes from non-enriched fermentation capacity. For example, paragraph [0060] states, “For example, the enriched fermentation capacity can comprise 0-5% over those normally present,….”.
Claim 34 recites a Markush group of metabolites that the enriched RAM further comprises. However, this list also encompasses naturally-occurring substances (“at least one other plant nutrient”, at least).
The claims also do not recite any limitations that integrate the JEs into a practical application.
The claims recite, “The agricultural composition”. The specification in paragraph [0075] indicates that an agricultural composition “can refer to a composition that can improve the rate of growth or health of plants…and/or improving or change the environments where the plants grow”. The term “can” indicates that the composition does not necessarily improve the growth or health of plants or change the environment where they grow. Further, this is an intended use. The claims do not recite elements that add significantly more to the claims.
Thus, the claims are not directed to significantly more than the products of nature.
Claim Rejections - 35 USC § 112(b)
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.
Claims 25-27, 29, 32 and 34 are 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.
The term “enriched” in claims 25-27, 29, 32 and 34 is a relative term which renders the claim indefinite. The term “enriched” is not defined by the claim, the specification also does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention.
It is not clear to the Examiner what the term “enriched” refer to. There is no definition of the term in the specification.
Moreover, the Applicant describes, “enriched fermentation capacity” (as recited in claim 32) arising due to enriched RAM “can comprise 0-5% over those normally present” (page 21, para 0060, line 1) indicating that even zero percentage increase/enrichment can be included in enriched RAM. It is also unclear what is meant by “enriched fermentation capacity”, given that the fermentation capacity can have no difference from the capacity ‘normally present’.
Claim Rejections - 35 USC § 102(a)(1)
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 25-27, 29, 32 and 34 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Kumar et al. (Rhizosphere microbiome: Engineering bacterial competitiveness for enhancing crop production, 2020, Journal of Advanced Research, 24:337–352), in evidence of Kimura et al. (Trends in the application of Bacillus in fermented foods, 2019, Current Opinion in Biotechnology, 56:36-42) and Ferraiuolo1 et al. (Streptomycetes as platform for biotechnological production processes of drugs, 2021, Applied Microbiology and Biotechnology,105:551–56; First published on 4 January 2021).
Kumar et al. teaches targeted application of beneficial (reads on to “enriched”) plant microbiome including rhizosphere microbiome (which reads on to “root associated microbiome”) and their cocktails (which, cumulatively, reads on to “agricultural composition”) to counteract abiotic and biotic stresses in plants (abstract, line 4-5). Kumar et al. describes shaping rhizosphere microbiome of a susceptible host plant from a resistant plant which comprises specific type of microbial community with multiple potential benefits, and manipulation of susceptibility genes in crop plants for improving plant health (abstract, line 9-12). Kumar et al. also describes manipulating the pH of the rhizosphere by using genetically engineered or transgenic Arabidopsis plants (as recited in claims 25 and 27) overexpressing AVP1 H+ pyrophosphatase, which is a known type I pyrophosphatase1(as recited in claim 26), producing different phenotypes including elevation of H+ -efflux from the roots of the plant, creates a more acidic environment in the rhizosphere which result in enhanced growth at lower pH, phosphate mineralization or plant mineral nutrition and exhibit enhanced resistance towards drought stress in AVP1 overexpressing Arabidopsis plants (page 344, left column, para 3, line 23-32). Kumar et al. also describes enriched RAM comprising different groups of bacteria (as recited in claim 29) including phosphate solubilizing bacteria (PSB), siderophore producing bacteria, and AMF increase accessibility of diverse plant nutrients such as iron, phosphorous, zinc, cooper, and cadmium (page 341, right column, para 4, line 18-21), as recited in claim 34. These rhizobacteria are also recognized as potential and commercially valuable biocontrol agents, like Bacillus, Streptomyces and Pseudomonads and produces antibiotic as well as antifungal compounds (page 341, right column, para 4, line 21-24).
Bacillus spp (Kimura et al.; abstract) and Streptomyces spp. (Ferraiuolo1 et al.; page 553, left column, line 3-5) are well known for their ability to produce various commercially important products including antibiotics via fermentation. Thus, microbiome enriched in Bacillus spp and/or Streptomyces spp., as described by Kumar et al., would be having enriched fermentation capacity, as recited in claim 32.
Alternatively, if it is determined that Kumar et al. does not explicitly describe or characterize or isolate enriched RAM, then it would have been obvious to an ordinarily skilled artisan to measure/characterize and isolate specific microbiome enrichment in the rhizosphere of the AVP1 H+ pyrophosphatase overexpressing plants of Kumar, as described below.
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.
Claims 25-27, 29, 32 and 34 are rejected under 35 U.S.C. 103 as being unpatentable over Kumar et al. in view of Kawasaki et al. (Microbiome and Exudates of the Root and Rhizosphere of Brachypodium distachyon, a Model for Wheat, 2016, PLoS ONE 11:e0164533).
Claim 25 is drawn to agricultural composition comprising an enriched root associated microbiome (RAM), wherein the enriched RAM is obtained from a genetically engineered plant.
Kumar et al. describes an agricultural composition comprising an enriched root associated microbiome (RAM) wherein the enriched RAM is obtained from a genetically engineered plant, as discussed above.
Kumar et al. also describes different groups of phosphate solubilizing bacteria (PSB), siderophore producing bacteria, and AMF increase accessibility of diverse nutrients such as iron, phosphorous, zinc, cooper, and cadmium (page 341, right column, para 4, line 18-21). Kumar et al. teaches manipulating the pH of the rhizosphere by using genetically engineered Arabidopsis plants overexpressing AVP1 H+ pyrophosphatase (as recited in claims 25-27) producing different phenotypes like the elevation of H+ -efflux from the roots of the plant, creates a more acidic environment in the rhizosphere, which result in enhanced growth at lower pH, phosphate mineralization or plant mineral nutrition and exhibit enhanced resistance towards drought stress in AVP1 overexpressing Arabidopsis plants (page 344, left column, para 3, line 23-32).
Kumar et al. also describes enriched RAM comprising different groups of bacteria (as recited in claim 29) including phosphate solubilizing bacteria (PSB), siderophore producing bacteria, and AMF increase accessibility of diverse plant nutrients such as iron, phosphorous, zinc, cooper, and cadmium (page 341, right column, para 4, line 18-21), as recited in claim 34. These rhizobacteria are also recognized as potential biocontrol agents, like Bacillus, Streptomyces and Pseudomonads and produces antibiotic as well as antifungal compounds (page 341, right column, para 4, line 21-24). Bacillus spp and Streptomyces sp are well known for their ability to produce various commercially important products including antibiotics via fermentation. Thus, microbiome enriched in Bacillus spp and/or Streptomyces spp would be having enriched fermentation capacity, as recited in claim 32.
However, Kumar et al. does not explicitly describe or characterize a root associated microbiome of genetically engineered Arabidopsis plants overexpressing H+ pyrophosphatase.
Kawasaki et al. describes rhizosphere microbiome is regulated by plant genotype, root exudates and environment (abstract, line 1). Naturally, there is substantial interest in breeding and managing crops that host root microbial communities that increase crop productivity (abstract, line 2-3). Kawasaki et al. teaches that there is a requirement to understand the plant-soil interface sufficiently well to allow the rhizosphere to be engineered to benefit plant fitness. Kawasaki et al. teaches that characterizing the core microbial communities in the rhizosphere and identifying the major root exudates are critical inputs to such models (page 2, para 4, line 1-5).
It would have been obvious to an ordinarily skilled artisan to characterize and isolate the agricultural composition comprising the core microbial communities in the rhizosphere and identifying the major root exudates that help enriching the RAM, as described by Kawasaki et al., of genetically engineered Arabidopsis plants overexpressing H+ pyrophosphatase, as described by Kumar et al.
The ordinarily skilled artisan would have bene motivated to produce and characterize and isolate the agricultural composition comprising the core root associated microbial communities because the rhizosphere around the genetically engineered Arabidopsis plants overexpressing H+ pyrophosphatase creates a more acidic environment in the rhizosphere resulting in commercially important traits like enhanced plant growth at lower pH, enhanced phosphate mineralization or plant mineral nutrition and exhibit enhanced resistance towards drought stress that can then be added to the soil of other plants, to enhance growth.
Conclusion
No claim is allowed.
Communication
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JAY CHATTERJEE whose telephone number is (703)756-1329. The examiner can normally be reached (Mon - Fri) 8.30 am to 5.30 pm..
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Jay Chatterjee
Patent Examiner
Art Unit 1662
/Jay Chatterjee/Examiner, Art Unit 1662
/BRATISLAV STANKOVIC/Supervisory Patent Examiner, Art Units 1661 & 1662
1 Pizzio et al. (Arabidopsis Type I Proton-Pumping Pyrophosphatase Expresses Strongly in Phloem, Where It Is Required for Pyrophosphate Metabolism and Photosynthate Partitioning, 2015, Plant Physiology, 167:541–1553) provides the evidence that AVP1 is a Type I pyrophosphatase (abstract, line 3-4).