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DOCUMENT ID:

BRS-GD-2023-0001

DATE:

TBD

GUIDE FOR SUBMITTING PERMIT APPLICATIONS FOR 

MICROORGANISMS DEVELOPED USING GENETIC 

ENGINEERING UNDER 7 CFR PART 340 

The information contained in this document is intended solely as guidance. Except where noted,

persons may choose to follow APHIS guidance or follow different procedures, practices, or protocols

that meet applicable statutes and regulations.

Language implying that guidance is mandatory (e.g., “shall,” “must,” “required,” or “requirement”)

should not be construed as binding unless the terms are used to refer to a statutory or regulatory

requirement.

Following the guidance contained in this document should not be construed as a guarantee of

compliance with applicable statutes and regulations.

Biotechnology Regulatory Services

Animal and Plant Health Inspection Service

United States Department of Agriculture

4700 River Road

Riverdale, MD 20737
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GUIDE INFORMATION

ISSUING

AGENCY/OFFICE:

Animal and Plant Health Inspection Service (APHIS)/ Biotechnology

Regulatory Services (BRS)

TITLE OF

DOCUMENT:

Guide for Submitting Permit Applications for Microorganisms Developed 

using Genetic Engineering Under 7 CFR part 340

DOCUMENT ID: BRS-GD-2023-0001

DATE OF

ISSUANCE: TBD

REPLACES: N/A

SUMMARY:

This document assists developers with preparing a permit application for 

movement activities with modified microorganisms under 7 CFR part 340 

(Movement of Organisms Modified or Produced Through Genetic 

Engineering). APHIS protects and enhances U.S. agricultural and natural 

resources using a science-based and risk-based regulatory framework to 

ensure the safe movement – including importation, interstate movement, 

and confined environmental release – of organisms developed using genetic 

engineering. APHIS receives its regulatory authority from the Plant 

Protection Act of 2000, and oversees organisms developed using genetic 

engineering in accordance with its regulations under 7 CFR part 340 

(Movement of Organisms Modified or Produced Through Genetic 

Engineering) (85 FR 29790). For more information: 

https://www.aphis.usda.gov/aphis/ourfocus/biotechnology

DISCLAIMER:

The contents of this document do not have the force and effect of law 

and are not meant to bind the public in any way. This document is

intended only to provide clarity to the public regarding existing

requirements under the law or agency regulations.
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TABLE OF CONTENTS

MICROORGANISMS REGULATED UNDER 7 CFR PART 340 ............................................................. 1

Regulated Organisms................................................................................................................................1

Exemptions from Permitting Requirements.............................................................................................2

Select Agents.............................................................................................................................................3

SUBMITTING PERMIT APPLICATIONS FOR MODIFIED MICROORGANISMS.................................... 4

Movement Between Contained Facilities.................................................................................................5

Environmental Release .............................................................................................................................6

APPENDIX I - EXCERPTS PERTINENT TO MODIFIED MICROBES .................................................... 11

RESOURCES ................................................................................................................................... 12
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MICROORGANISMS REGULATED UNDER 7 CFR PART 340

APHIS regulates the importation, interstate movement, and environmental release of certain 

microorganisms developed using genetic engineering under 7 CFR part 340. Genetic engineering is 

defined in § 340.3 as “techniques that use recombinant, synthesized, or amplified nucleic acids to 

modify or create a genome.” Regulated microorganisms include plant pests and other modified 

microorganisms that could pose a plant pest risk. See § 340.2. Developers require a permit for regulated 

activities involving any modified microorganism that: 

• Meets the definition of a plant pest in § 340.3; or

• Is not a plant but has received deoxyribonucleic acid (DNA) from a plant pest, as 

defined in § 340.3, and the DNA from the donor organism either is capable of 

producing an infectious agent that causes plant disease or encodes a compound 

that is capable of causing plant disease; or

• Is a microorganism used to control plant pests and could pose a plant pest risk.

We describe these categories of regulated microorganisms below, followed by exemptions for 

permitting requirements, and information about select agents. For simplicity in this document, 

microorganisms developed using genetic engineering are referred to as “modified microbes.” Modified 

microbes addressed in this guide include bacteria, fungi, oomycetes, viruses, and viroids, and the 

information herein could also be applicable to other taxonomic groups not specifically mentioned such 

as protozoa, algae, or nematodes.

Definitions that come from 7 CFR part 340, are referenced as § 340.3. Other important excerpts are 

referenced with the appropriate regulatory section. See Appendix 1 for a full list of excerpts relevant to

microorganisms. 

Developers may also refer to BRS’ Questions and Answers document for additional information 

regarding work with modified microbes under 7 CFR part 340.

REGULATED ORGANISMS

Microorganisms that are Plant Pests

Modified microbes that meet the definition of a plant pest are regulated under 7 CFR part 340. 

(7 CFR § 340.2(b)).

The regulations define a plant pest as follows:

Plant pest. Any living stage of a protozoan, nonhuman animal, parasitic plant, bacterium, 

fungus, virus or viroid, infectious agent or other pathogen, or any article similar to or allied with 

any of the foregoing, that can directly or indirectly injure, cause damage to, or cause disease in 

any plant or plant product. § 340.3

A modified microbe can meet the definition of a “plant pest” if the modified microbe itself can directly 

or indirectly injure, cause damage to, or cause disease in any plant or plant product. A modified microbe 

could meet the definition of “plant pest” because the unmodified microbe is itself a plant pest or the 

modification imparts changes to a microbe such that it can directly or indirectly injure, cause damage to, 
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or cause disease in a plant or plant product. Plant pathogens that have been modified to reduce 

virulence yet remain capable of causing direct or indirect injury or damage to, or disease in, a plant or 

plant product also meet the definition of “plant pest.” 

Microorganisms Modified with DNA Capable of Causing Plant Disease

Modified microbes that have received DNA from plant pests meeting the criteria below are regulated 

under 7 CFR part 340:

Is not a plant but has received deoxyribonucleic acid (DNA) from a plant pest, as defined in 

§ 340.3, and the DNA from the donor organism either is capable of producing an infectious 

agent that causes plant disease or encodes a compound that is capable of causing plant disease. 

§ 340.2(c)

In these cases, the microbial species in its unmodified state may not necessarily be a plant pest. 

However, because the modified microbe contains DNA that is capable of producing an infectious agent 

that causes plant disease or contains DNA that encodes a compound that is capable of causing plant 

disease, the modified microbe can directly or indirectly injure, cause damage to, or cause disease in a 

plant or plant product and therefore meets the definition of “plant pest.” An example of a modified 

microbe in this category would be a bacterium engineered to express infectious clones of plant viruses, 

for purposes of basic research, or for developing diagnostics or therapeutics.

Microorganisms Used for Biocontrol of Plant Pests

Modified microbes used to control plant pests and that could pose a plant pest risk are regulated under 

7 CFR part 340:

Is a microorganism used to control plant pests...and could pose a plant pest risk 

§ 340.2(d)

Plant pest risk. The potential for direct or indirect injury to, damage to, or disease in any plant 

or plant product resulting from introducing or disseminating a plant pest, or the potential for 

exacerbating the impact of a plant pest. § 340.3

In these cases, if APHIS Plant Protection and Quarantine (PPQ) requires a permit for a wild-type strain 

because it could pose a direct or indirect plant pest risk, APHIS BRS requires a permit for modified 

versions of the wild-type strain. If APHIS PPQ does not require a permit for a wild-type strain, APHIS BRS 

will require a permit for a modified version if the unmodified version has been used as a biocontrol 

organism, or if the modified version is being investigated or proposed for use as a biocontrol organism.

EXEMPTIONS FROM PERMITTING REQUIREMENTS

The following modified microorganisms are exempt from permitting requirements in 7 CFR part 340.

Exemption for GE disarmed Agrobacterium species. A permit for importation or interstate 

movement is not required for any GE disarmed Agrobacterium species, provided that it is moved 

as a secure shipment, the modified genetic material is stably integrated into the genome, and 

the modified material does not include the complete infectious genome of a plant pest. 

§ 340.5(d)
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Exemption for certain microbial pesticides. A permit is not required for the movement of any 

GE microorganism product that is currently registered with the Environmental Protection 

Agency (EPA) as a microbial pesticide, so long as the microorganism is not a plant pest as 

defined in § 340.3. § 340.5(f)

Information regarding EPA biopesticide registrations can be found here: 

https://www.epa.gov/ingredients-used-pesticide-products/biopesticide-active-ingredients.

To facilitate shipments of modified microbes that are exempt from BRS’ permitting requirements (e.g., 

importation of GE disarmed Agrobacterium species meeting the criteria above), developers may request 

a Letter of No Permit Required (LONPR) by emailing BRSNoPermitRequired@usda.gov. An LONPR does 

not expire, and it can be used indefinitely. For this reason, developers may wish to have a permanent 

employee with oversight of the laboratory to which the material will be shipped request the LONPR. 

To request a LONPR, you must provide:

• Name

• Institution

• Full address

• Phone number

• Email

SELECT AGENTS

The Agricultural Bioterrorism Protection Act of 2002 and the Public Health Security and Bioterrorism 

Preparedness and Response Act of 2002 require entities that possess, use, or transfer biological agents 

or toxins deemed a severe threat to animal or plant health or products to notify and register with the 

Federal Select Agent Program. If the modified organism is a select agent or is capable of producing a 

toxin listed in the Federal Select Agent Program website, APHIS BRS cannot issue a permit to authorize 

its use. Select agents that are plant pathogens are regulated specifically by the APHIS PPQ branch of the 

Federal Select Agent Program.

A current list of all select agents and toxins is available at: http://www.selectagents.gov/. 

Bacilli strains are frequently used in biotechnology applications, and taxonomic designations have been 

challenging. For example, note that Bacillus cereus biovar anthracis appears on the list of the U.S. 

Department of Health and Human Services’ (HHS) Select Agents and Toxins, and B. anthracis and B. 

anthracis Pasteur strain appear on the HHS and USDA Overlap List. If the identity of a B.cereus s.l. strain 

in a BRS permit application is not yet determined, then, at a minimum, applicants must be able to 

exclude strains that are designated as select agents.

For questions related to microorganisms that produce select agents and toxins that can cause disease in 

humans, contact Centers for Disease Control and Prevention Division of Select Agents and Toxins at 404-

718-2000; email: LRSAT@cdc.gov; and for those that can cause disease in animals and plants contact 

Animal and Plant Health Inspection Service Division of Agricultural Select Agents and Toxins at 301-851-

2070; email: DASAT@usda.gov.
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SUBMITTING PERMIT APPLICATIONS FOR MODIFIED MICROORGANISMS

APHIS regulates and issues permits for the importation, interstate movement, and environmental 

release of certain modified microbes under 7 CFR part 340. A BRS permit is not required if a developer is 

creating a modified microbe and conducting research activities involving that modified microbe in a 

contained facility designed to prevent the modified microbe’s unauthorized releases into the 

environment and is not moving the microbe across state lines or releasing it into the environment. To 

ensure a facility prevents the unauthorized release of a modified microbe, developers should follow 

containment guidelines specific to microbes. For examples of containment guidelines, see NIH 

Guidelines; CDC Biosafety in Microbiological and Biomedical Laboratories; APHIS PPQ Containment 

Facility Guidance; and Practical Guide to Containment: Plant Biosafety in Research Greenhouses, Adair & 

Irwin (2008). Unauthorized, accidental, or inadvertent release of a modified microbe that would 

otherwise be subject to 7 CFR part 340 is a violation of the regulations. If you are unsure whether your 

contained facility is adequate to prevent an unauthorized release of a modified microbe, please apply 

for a permit following the information below. 

To apply for a BRS permit, the applicant creates a permit application and an associated “Standard 

Operating Procedures” (SOP) using the APHIS eFile electronic permitting system. The APHIS eFile system 

will not accept a BRS permit application unless at least one document with the attachment type of 

“SOP” is uploaded to the SOP/Attachments section of APHIS eFile. The purpose of the SOP is to provide 

a description of how the modified microbe will be: 

• contained during movement and at the points of origin and destination, including 

intermediate destinations, and 

• confined during release into the environment “in a manner so as to prevent its unauthorized 

release, spread, dispersal and/or persistence in the environment” (7 CFR § 340.5(i)(1)).

Details on submitting permit applications can be found on the BRS webpage and on the APHIS eFile 

training page. To minimize redundancy, information that is required for all BRS permits in the APHIS 

eFile electronic permitting system may not necessarily be repeated in this document. For example, 

confidential business information (CBI) must be appropriately designated if applicable (see CBI 

Submission Guidance). Additionally, when submitting a permit application for a modified microbe, use 

the “Traditional” permit application regardless of the intended use. The other permit designation, 

Pharmaceutical, Phytoremediation, and Industrial permits (“PMPI”), is specific to plants, only. 

When completing a permit application, you will need to have the following information on hand 

describing the modified microbe:

• Scientific name: The species name, as well as the strain, isolate, race, and/or pathovar, as 

applicable. For importation or interstate movement of foreign isolates, provide the location 

where the organism was originally collected or isolated.

• Construct elements: All genetic elements used in imparting the modification, including the 

name, donor (source) organism, and a brief description of the function. If applicable, 

describe targeted deletions.

• Phenotype: Brief description of the intended phenotype that the modification(s) are 

expected to confer.
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You will also need to have information related to all activities involving the modified microbe at all 

intermediate and final destinations. As a practical matter, you will describe these activities and 

associated containment and confinement measures in your “Standard Operating Procedures” (SOPs), 

which is a required attachment in the APHIS eFile system that is discussed more fully below.

Multiple species belonging to the same genus may be submitted on a single permit application for 

importation and/or interstate movement if containment protocols are appropriate and all species are 

securely contained during shipment. For release permits, only a single species may be submitted on a 

given permit application.

 

The expected timeline for issuance of a permit that contains all required information is 45 days for 

importation and interstate movement, and 120 days for environmental release.

Special note on greenhouses: BRS has received inquiries regarding permit procedures for greenhouses 

and other semi-contained structures in terms of whether the developer should apply for an interstate 

movement permit, environmental release permit, or both. We recognize that structures referred to as a 

“greenhouse” could represent a range of containment levels. Depending on the measures in place to 

prevent escape into the environment, proposed research in a greenhouse could either be considered as 

a contained destination on a movement permit, or activities in a greenhouse may be more appropriately 

designated as a confined field release. For questions pertaining to greenhouse research with modified 

microbes, please contact BiotechQuery@usda.gov. After the initial inquiry, a consultation may be 

scheduled with BRS subject matter experts. When preparing for such a consultation, it is helpful to 

gather information about the proposed research activities and greenhouse, including transport to/from 

a contained facility, and any history related to previous permits, inspection BRS or PPQ inspections, 

SOPs, and/or photos.

MOVEMENT BETWEEN CONTAINED FACILITIES

Summary of Requirements for SOPs

Your SOPs must describe the procedures you will use to contain the modified microbe during shipment 

and at the destination. In other words, describe how you will prevent the release and dissemination of 

the modified microbe into the environment.

• During shipping: You must secure all shipments of modified microbes. Please refer to the document 

“Suggestions for SOPs Submitted for APHIS BRS permits” (in Section 2.1 Packaging and Shipping) for 

information on what to include in your SOP, such as descriptions of packaging materials, any 

additional biological material that may be present, and devitalization/sterilization procedures upon 

receipt.

• At the destination: To receive regulated modified microbes at a contained facility (e.g., laboratory, 

contained greenhouse, or other contained structure), BRS requires information about the 

destination in the permit application. Containment considerations are case-by-case, but some useful 

resources are provided in the following section.

Note: If the laboratory/facility proposed for work with the modified microbe has been previously 

inspected, either by BRS or PPQ, that information may assist BRS staff in evaluating containment and 

whether any additional measures might be needed. It is recommended for applicants to provide 
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facility numbers, dates of inspection, any BRS or PPQ permits associated with the inspection, and/or 

other pertinent information in the application, if it is known.

Considerations for Containment

Considerations include the following:

• Where will you use the modified microbe (e.g., laboratory, walk-in growth chamber, greenhouse)?

• How will you use the modified microbe (e.g., DNA extraction for genetic analysis, pathogenicity 

testing, vector transmission studies, etc.)?

• How will you securely store and maintain the modified microbe in all areas of the facility for all 

activities?

• How will you devitalize or sterilize the modified microbe and all items in contact with it? This 

includes all plants, growth media, soil, storage containers, laboratory surfaces, etc. Consider the 

biology of the microorganism, such as cell wall structure, and types of plants and media. The choice 

of disinfectant, concentration, and exposure time will be based on each microorganism.

• Will you inoculate plants with the modified microbe? If so, what plants will you use and how will 

they be inoculated?

• How will you prevent dispersal and transmission of the microbe? 

o If air-dispersed, what measures will you take to prevent dissemination in the facility?

o If spore-producing, how will you contain the spores?

o If vectored by insects, how will you control insects and to prevent unintended transmission?

o If water or splash dispersed, how will you prevent splash dispersal, and/or what measures will 

you take to treat the water?

ENVIRONMENTAL RELEASE

Summary of Requirements and Considerations

Summary of Requirements

In addition to the general requirements discussed above, you will need the following information to 

complete a permit application for an environmental release:

• Release site: Provide information such as land area (size), GPS coordinates, and land use 

history at the site and adjacent areas.

• Experimental procedures for confinement (SOPs): Describe how you will maintain the 

modified microbe at the release site and prevent its spread and persistence after the 

termination of a field trial.

• Diagnostics: Describe how you will detect the modified microbe and distinguish it from the 

wild type for monitoring purposes.

• Monitoring: Describe how long and how often you will monitor to ensure modified 

microbes have not spread and will persist in the environment.

• Final disposition for release: Describe how you will devitalize the modified microbes at the

end of the field trial.

Considerations

Permit conditions and procedures carried out by the applicant should prevent the unauthorized release, 

spread, dispersal and/or persistence of the modified microbe in the environment. Additionally, the 
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information supplied in the application, including experimental procedures for confinement (SOPs), will 

help BRS determine the appropriate level of National Environmental Policy Act and Endangered Species 

Act analyses. We encourage developers to consult with BRS early in the planning process to discuss 

confinement procedures, diagnostic testing, and other possible background studies. If you are 

interested in a consult, please write to BiotechQuery@usda.gov.

Additional considerations as applicable may include the following biological properties of the modified 

microbe:

Organism

• Geographic origin: Is the same species/strain of the organism found in the locale of the 

proposed release? Documentation could include external references, the molecular basis for 

the determination, and biological properties of the modified microbe.

• Environment: What is the habitat and environmental conditions that are favorable and/or 

where the microbe is typically found? Are there dormant stages that need to be considered? 

What environmental conditions, habitat, and soil types, for example, are favorable or 

unfavorable for persistence of the microbe?

• Host range (both primary and alternative hosts): Consider all possible host plants of the 

microbe, including, for example, groups of plants typically affected, as well as wild or weed 

species that may act as reservoirs. Consider whether any other primary or alternative host 

plants may be present in the area of the proposed release. If the organism is used for 

biocontrol of invertebrate plant pests, what is the host range of the microbe? 

• Dissemination and spread: How does the modified microbe spread naturally in the 

environment? Is it vectored by another organism, or can it spread via water, wind, or 

adherence to animals or objects such as tools used for cultivation? Can the microbe be 

secondarily spread via seeds or pollen from inoculated plants? Consider all possible routes 

of transmission and dispersal.

• Does/would application of the modified microbe result in changes to the microbial 

community (rhizosphere, phyllosphere, and/or endosphere) that enhance plant pest risk? 

• Are there interactions with other microbes that may need to be considered?

Modification

• Does the modification to the microbe alter any of the aspects described above? For 

example:

o Does the modification involve a change in host range, or allow the microbe to survive 

under different environmental conditions?

o Does the modification affect how the microbe is spread?

• Effects on other organisms

o What is the effect on host plants that may or may not be part of the proposed trial?

o If the modified microbe is a plant pathogen, is there any change in virulence from the 

wild-type?

o Does the modified microbe produce antagonistic compounds such as toxins or 

antibiotics? For example, chitinases, siderophores, proteases, or mycotoxins.

o Is the modified microbe antagonistic to other microbes that benefit plant health?

o Does the modified microbe synergistically interact with a plant pathogen to enhance 

disease severity?
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o Does the modified microbe benefit plant growth? How?

o Does the modified microbe affect invertebrate plant pests? How?

o Does the modified microbe affect invertebrates that benefit plant health?

• Has horizontal gene transfer been considered? For example, on the frequency of 

occurrence and species of organisms that could be potential recipients? For example, 

among strains of Bacillus subtilis, or, for genetic elements that may confer a fitness 

advantage?

• Does the modification involve a conditional switch or other mechanism for reducing 

spread or persistence?

Supporting information can be provided in studies conducted by the applicant in controlled environments 

and/or in peer-reviewed publications.

Experimental Procedures for Confinement (SOPs) 

SOPs are required for all permit applications; the SOP for an environmental release should describe 

procedures to ensure a confined field trial. Procedures should be appropriate to prevent spread beyond 

the trial site (confinement in physical space) and prevent persistence beyond the duration of the trial 

(confinement in time). Readers are referred to Section 3.0 of “Suggestions for SOPs Submitted for APHIS 

BRS permits” for general information about protocols for confined field trials.

You should include the elements described below in an SOP for confinement of modified microbes in a 

field trial. Your SOP should account for your particular trial with the particular modified microbe.

Trial design and execution

• Procedures for application or inoculation of plants or soil, including for example, whether 

plants and/or soil will be inoculated in a greenhouse and then moved to the field. 

• Inoculum: Amount and concentration of the modified microbe and how it will be applied, 

e.g. foliar spray, soil drench, or seed treatment.

• Frequency of applications, i.e., number of environmental releases.

• Duration of the trial.

• Scale (e.g. approximate number of plants, size of the field plot).

• A detailed map and/or diagram of the proposed trial, including GPS coordinates.

• If applicable, describe procedures for packaging and transportation of organism and 

inoculated material to/from the field site, and include these facility locations in the permit 

application. 

• Procedures to prevent dissemination of the modified microbe via air, water, plant parts, or 

vector organisms, as appropriate. For example: 

o Physical isolation from primary and alternative host plants that are not part of the trial 

o Prevention of unintended transmission via vector organisms. 

o Water and irrigation management (e.g. drip or sprinkler irrigation, berms or ditches 

around the release site to manage water runoff).

o Other example methods could include cages, plastic sheeting, bare ground, or

inoculation of potted plants.

• In-trial monitoring procedures to ensure that the modified microbe is not disseminated 

beyond the designated trial site.

o Should describe frequency of sampling, plus number and type of samples.
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o Samples could be from soil (e.g. within trial site, adjacent to trial site, or outside of trial 

site) or from plants (e.g. treatments, controls, or buffer plants).

o Further information on diagnostics is provided below.

Trial termination

To prevent persistence in the environment, procedures should describe how plants, soil, and 

other materials as relevant will be treated to devitalize the modified microbe at the field site. 

Describe methods to devitalize the modified microbe after use (e.g., autoclaving, chemical 

treatment, or burning), or how the regulated material will be returned to and maintained in a 

contained facility.

• Termination and devitalization of inoculated plants. 

• Treatment of soil in the trial zone and buffer zones. 

• If the microbe requires the host plant to survive, how will the plot be kept clear of 

applicable vegetation to prevent persistence of the microbe? For example, will bare ground 

be maintained at the plot for some defined period of time?

• If inoculated plants are not destroyed at the end of the trial, such as trees, how will 

devitalization of the modified microbe be ensured?

• Consider all stages of the life cycle of the modified microbe, including vegetative, 

reproductive, and dormant/overwintering structures as applicable.

• Trial termination must occur on or before the expiration date of the permit unless the 

permit has been renewed.

Post-trial monitoring

Your post-trial monitoring procedures should describe how you will determine that the modified 

microbe does not persist and spread in the environment after conclusion of the field trial. Refer 

above to “Additional Considerations” for some aspects that are relevant to evaluating the 

potential for persistence.

• Should describe duration and frequency of sampling, plus number and type of samples.

• Samples could be from soil, plants (e.g. sentinel plants, or post-treatment trees), water, 

insects, or any other matrix depending on the trial. 

• Further information on diagnostics is provided below.

• Documentation of post-trial monitoring for all BRS release permits is submitted as a 

“Volunteer Monitoring” Report in APHIS eFile.

• Monitoring must be conducted until the modified microbe is no longer detectable for 

consecutive time points. Again, the sampling regime and associated diagnostic test(s) must 

be appropriate for the trial. 

Diagnostics for In-Trial and Post-Trial Monitoring 

Diagnostic assays must be developed for detection of the modified microbe in the intended sample 

matrix. This means distinguishing the modified microbe from the unmodified strain, in field-relevant 

samples (e.g., soil where the microbe is to be released) appropriate for the method of application (e.g., 

seed treatment, soil drench, or foliar spray).

The limit of detection (LOD) of the assay(s) can be determined in controlled settings, but the diagnostic 

method must be able to detect the modified microbe in field-derived samples. At a minimum, validation 
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data should support the specificity (true positives) and selectivity (true negatives) of the assay for the 

taxon of host and microorganism for which it is developed. Selectivity includes healthy host tissue (e.g. 

from control plants) and unrelated microorganisms that may be found with the host (within intended 

purpose). Specificity should demonstrate the assays’ ability to detect all applicable modified strains in 

both simple and complex matrices (e.g., with and without the plant) to exclude false negatives. 

List of Information to be Submitted

• Material and sample preparation:

o Sample collection:

 From relevant soil and/or plant tissues.

 From areas including, for example, from initial inoculation site to other areas of the 

plant.

 At time points from Time 0 (baseline), for a duration to include the trial and post-trial 

monitoring.

o Nucleic acid extraction protocol(s), adapted for sample types: From pure cultures, potting 

media, soil, plant material, and/or vector insects, as applicable.

• Description of the strategy/methodology used, e.g., PCR, Sanger sequencing, or Highthroughput sequencing. 

• Description of the procedures required to perform the diagnostic test from sampling to results 

reporting.

• Specificity: Describe how the diagnostic method specifically detects only the modified microbe. 

Validation of the diagnostic test involves distinguishing: 

o the modified microbe from the unmodified (wild-type) strain, and 

o the modified microbe from closely related species, as well as other species expected to be 

commonly found at the release site.

Information regarding test specificity includes:

o In silico: For example, the description of primer design.

o In vivo: Provide the list of species that were tested in a laboratory and/or greenhouse 

setting to confirm specificity. 

• Sensitivity: Describe how the limit of detection is determined and verified. Diagnostic tests 

should be able to detect the modified microbe in field-derived samples and be appropriate for 

monitoring after the field trial is ended.

• Robustness: sample size and types of samples assessed (e.g. simple or complex matrix, and with 

or without plants used to validate).
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APPENDIX I - EXCERPTS PERTINENT TO MODIFIED MICROBES

From Title IV: Plant Protection Act. 7 USC 7702. SEC. 403. Definitions.

(2) Biological Control Organism.—The term ‘‘biological control organism’’ means any enemy, antagonist, 

or competitor used to control a plant pest or noxious weed.

From 7 CFR 330.200(d): 

Biological control organisms not regulated by this subpart. Paragraph (c) of this section notwithstanding, 

biological control organisms that have undergone genetic engineering, as defined in § 340.3 of this 

chapter, as well as products that are currently under an EPA experimental use permit, a Federal 

Insecticide Fungicide and Rodenticide Act (FIFRA) section 18 emergency exemption, or products that are 

currently registered with EPA as a microbial pesticide product, are not regulated under this subpart. 

Additionally, biological control organisms that are pesticides that are not registered with EPA, but are 

being transferred, sold, or distributed in accordance with EPA’s regulations in 40 CFR 152.30, are not 

regulated under this subpart for their interstate movement or importation. 

From 7 CFR 340.2 Scope:

Except under a permit issued by the Administrator in accordance with § 340.5, no person shall move any 

GE organism that: ...

(b) Meets the definition of a plant pest in § 340.3; or

(c) Is not a plant but has received deoxyribonucleic acid (DNA) from a plant pest, as defined in § 340.3, 

and the DNA from the donor organism either is capable of producing an infectious agent that causes 

plant disease or encodes a compound that is capable of causing plant disease; or

(d) Is a microorganism used to control plant pests, or an invertebrate predator or parasite (parasitoid) 

used to control invertebrate plant pests and could pose a plant pest risk.

From 7 CFR 340.3 Definitions:

• Genetic engineering. Techniques that use recombinant, synthesized, or amplified nucleic acids to 

modify or create a genome.

• Move (moving, movement). To carry, enter, import, mail, ship, or transport; aid, abet, cause, or 

induce the carrying, entering, importing, mailing, shipping, or transporting; to offer to carry, enter, 

import, mail, ship, or transport; to receive to carry, enter, import, mail, ship, or transport; to release 

into the environment; or to allow any of the above activities to occur.

• Plant pest. Any living stage of a protozoan, nonhuman animal, parasitic plant, bacterium, fungus, 

virus or viroid, infectious agent or other pathogen, or any article similar to or allied with any of the 

foregoing, that can directly or indirectly injure, cause damage to, or cause disease in any plant or 

plant product.

• Plant pest risk. The potential for direct or indirect injury to, damage to, or disease in any plant or 

plant product resulting from introducing or disseminating a plant pest, or the potential for 

exacerbating the impact of a plant pest.

• Release into the environment (environmental release). The use of an organism outside the physical 

constraints of a contained facility.

• Secure shipment. Shipment in a container or a means of conveyance of sufficient strength and 

integrity to withstand leakage of contents, shocks, pressure changes, and other conditions incident 

to ordinary handling in transportation.
DRAFT

Microorganisms Guide USDA APHIS BRS

12

RESOURCES

• Q&As on Working with Modified Microorganisms:

https://www.aphis.usda.gov/biotechnology/downloads/faq-modified-microbes.pdf

• Guidance for Submitting Confidential Business Information:

https://www.aphis.usda.gov/brs/pdf/CBI_Submission_Guidance.pdf

• Suggestions for SOPs: https://www.aphis.usda.gov/help/eFile/sop-suggestion-submissions.pdf

• APHIS eFile Training Resources: https://www.aphis.usda.gov/aphis/banner/help/efile/efile-training