Comments on APHIS’ Draft Guide for Submitting Permit Applications for Microorganisms Developed Using Genetic Engineering

Submitted by the Institute for Responsible Technology, with support by the undersigned citizens.

The US food supply is vulnerable to potentially devastating impacts of genetically modified (GM) microbes. The USDA, however, fails to address most of the risks by overlooking well-established findings about microbes, microbiomes, and soil biology, and by ignoring research on genetic engineering, including gene editing technology.

This is abundantly clear in the APHIS Draft Guide for Submitting Permit Applications for Microorganisms Developed Using Genetic Engineering. It illustrates how the USDA’s narrow regulatory focus puts food safety and food security at risk.

The Soil Microbiome is Fundamental to Agriculture and Food Security

Soil is fundamental to all terrestrial life. Our food and biodiversity start with the soil. The United Nations Food and Agriculture Organization (FAO) states: “Healthy soils lay at the foundations of agricultural development, healthy and nutritious food production, and essential ecosystem services, which are crucial to our basic survival as well as our planet’s sustainable future[1].”

The soil microbiome is the most complex and richest biodiversity on our planet, especially in the region around the roots of plants, the rhizosphere. There, plants feed the soil microbiome with organic molecules that they create through photosynthesis. These molecules are the basis of organic matter – carbon-based molecules – that life on Earth depends on. Soil organic matter (SOM) is therefore fundamental to all life.

It is also fundamental to life in the soil. Increases in SOM promote the productivity of agricultural systems, including soil fertility, water holding capacity, drought tolerance,[2] and pest and disease resilience. Because SOM comes from carbon dioxide fixed through photosynthesis, increasing SOM can have a significant impact on reversing the climate crisis by drawing down this greenhouse gas.

Research shows that soil microbes produce chemically diverse, stable SOM. According to an article in Nature Communications, “We show that SOM accumulation is driven by distinct microbial communities more so than clay mineralogy, where microbial-derived SOM accumulation is greatest in soils with higher fungal abundances and more efficient microbial biomass production[3].”

FAO states: “Soil organisms act as the primary driving agents of nutrient cycling, regulating the dynamics of soil organic matter, soil carbon sequestration and greenhouse gas emission, modifying soil physical structure and water regimes, enhancing the amount and efficiency of nutrient acquisition by the vegetation and enhancing plant health[4].”

USDA Ignores “Non-Pathogenic” GM Microbes

Just as a healthy soil microbiome can support plants, an unhealthy one can damage them[5]. Imbalances in microbial communities can lead to weed growth, plant disease, intolerance to droughts, etc. Even relatively minor shifts in microbial populations and changes in microbial properties can harm plants[6].

The process of genetic engineering can introduce novel gene sequences and traits into microorganisms that are not the product of billions of years of evolution and did not coevolve or co-exist with plants, animals, humans, or each other. Their impacts are unknown.

Some can certainly cause harm.

Of the countless ways that GM microbes might adversely impact agriculture, only a small proportion is from introducing disease-causing infectious agents. Tragically, this is the narrow focus of how APHIS regulates them. USDA only concerns itself with GM microbes that are known pathogens, or that have received genes from potential pathogens.

Similar to using the obsolete reference to microorganisms as “germs,” it ignores decades of scientific discoveries that have unearthed the critical role of a healthy soil microbiome in supporting ecosystems and plant health.

The distinction is easier to convey in terms of human disease. We may think of catching a cold or flu from germs. A specific infectious agent causes an illness, and the impact is noticeable soon after.

Asthma is not traditionally thought of as coming from microbes. We don’t “catch it.” We now understand, however, that the chances of a child developing asthma at age five is often dependent on whether he or she had a particular microbiome configuration at infancy. The impact was not infectious and not immediate[7].

In the same way, the composition of human gut microbiomes can lead to obesity. Microbes may have a role in dementia or Alzheimer’s. There’s evidence suggesting that our internal microbiome play a role in most diseases[8] [9].

Microbial interactions in soil and agricultural ecosystems may be as complex and impactful as those within our bodies. Until we know otherwise, this should be the default assumption that guides our actions and regulations.

USDA must update its understanding of microbes, microbiomes, and pathogens.

GM Microbes Can Also Become Invasive Species and Pathogens

APHIS protects the United States’ agricultural interests related to non-native plants, animals, insects, and diseases, as well as monitoring and managing existing agricultural pests and diseases. The current list has 18 exotic plant diseases and 26 animal diseases[10].

There is no way of guaranteeing that a genetically modified organism will not, over time, become an exotic invasive species or promote invasive disease species in agricultural, disrupting the soil microbiome, plants, and animals.

The USDA states Terrestrial (land-dwelling) Invasive Pathogens and Diseases include diseases and disease-causing microorganisms (such as bacteria, viruses, fungi, and parasitic protozoa) of terrestrial plants and animals. It lists 30 exotic pathogens and diseases that are causing serious issues in the U.S[11]. But recent evidence shows that new plant diseases, “both endemic and recently emerging, are spreading and exacerbated by climate change, transmission with global food trade networks, pathogen spillover, and evolution of new pathogen lineages.” The introduction of new genetic traits from GM microbes could exacerbate this trend in unpredictable ways[12] [13] [14] [15].

USDA Ignores Most Gene Edited GM Microbes, and More

USDA turns a blind eye to non-pathogenic GM microbes that do not have foreign DNA (from pathogens) inserted into their genomes. GM microbes, however, can cause harm to agriculture whether or not a foreign gene is inserted and whether or not an inserted gene is from a potential pathogen.

By ignoring scientific evidence, USDA exempts the vast majority of GM microbes that can inflict damage. For example, it gives a pass to most microbes that are created with gene editing technologies such as CRISPR, which will likely be the source of the greatest variety of GM microbes produced going forward.

CRISPR can be used to knock out genes, without inserting new genetic material. Such changes, however, can have far reaching impacts.

A change to a single bacterial gene involved in the formation of biofilm confers a communication disruption and change in the entire bacterial community structure[16].

The presence and proper functioning of iron sequestering genes can, in theory, determine if a pathogen thrives or dies[17].

Small changes to the rhizosphere microbiome can impact a plant’s susceptibility to pathogens[18].

Some genes have multiple impacts that are not yet identified. Knocking out a single gene might have unpredictable, but serious effects in gene edited microbes.

Some microbes have single antivirulence genes, which, if accidentally silenced during the gene editing process, could transform a non-pathogen into an infectious agent[19].

USDA Overlooks Side Effects and Collateral Damage from Genetic Engineering

Decades of research on genetically engineered plants, animals, and microbes have revealed the presence of consistent side effects—mutations, deletions, and additions—resulting from the process. This occurs frequently as a result of the original forms of engineering (biolistics and agrobacterium) as well as the recently developed gene-editing techniques.

Unfortunately, those creating GMOs using any of the methods typically do not sufficiently evaluate the presence and extent of damage to the genome. They further neglect to look for altered transcriptomes, proteomes, and metabolomes, the presence of truncated proteins, or altered activity and interactions of the modified cells or organisms. Consequently, developers are unaware of a wide range of potential dangers associated with their novel organisms.

USDA reinforces these risks by not requiring more thorough, state-of-the-art evaluations by those seeking permits.

Collateral Damage from Gene Editing is Extensive

The biotech industry falsely portrays gene editing as safe and predictable. It appears that USDA has accepted these baseless claims, and therefore refuses to require safety assessments for most GMOs created by gene editing. Although the draft guidance under discussion is focused on microbes, we are compelled to include research on the side effects of gene editing cells from plants, animals, and humans as well, in order to convey the weight of evidence that contradicts USDA’s assumptions and policies across the board.

Gene-editing tools, especially CRISPR, are prone to causing mutations to the organism’s DNA at locations other than the intended edit site[20] [21].

Side effects of CRISPR were discovered years after it was used to create organisms for food, feed, and soil[22].

Large deletions and rearrangements of the genome have been observed following CRISPR gene editing[23] [24] [25] [26] [27].

Alteration of the genetic code of the targeted gene can produce mutant forms of the protein it encodes for, new RNA, and new protein products[28].

Unlike naturally occurring genetic changes, gene editing makes the whole genome accessible for changes[29].

After CRISPR cuts the genome, the cell repairs the break. In the process, it can unexpectedly integrate DNA that was used in the gene editing mechanism, or DNA present in the petri dish. This extraneous DNA may introduce new gene functions and/or disrupt the function of host genes[30] [31] [32].

Sometimes gene editing causes large-scale shattering and rearrangement of genomes, call chromothripsis[33].

GM microbes may adapt to environments that they are exposed to in the genetic engineering lab, that can create unintended changes in their genome. Without thorough whole-genome sequencing, the nature of these modifications can remain undetected[34].

USDA Relies on Applicants’ Faulty Evaluations of Gene Edited Organisms

It is important to note that most of the mutations and collateral damage in the references above were discovered using techniques that are not typically employed by most people who use gene editing.

The most famous example of this lack of oversight comes from the producers of gene edited cattle engineered to be born without horns[35]. In 2016, the CEO of Recombinetics described its new hornless invention as “precision breeding.” They declared it a complete success, and tried  to lobby the White House to remove FDA’s required review of gene edited animals[36].

In 2019, however, an FDA employee was testing some new bioinformatics software and needed data to test it. She happened to have access to the genome data from the hornless cattle, so she used the software to analyze it. This happenstance test revealed that bacterial genes that were used in the gene editing process had inadvertently integrated into the cow’s genome. Although there is no way to predict what dangers this new GMO cow/bacteria hybrid might pose, the bacterial sequences now found in every cell of the animal’s body contained multiple antibiotic resistant genes. These might theoretically transfer to bacteria, exacerbating the presence of resistance pathogens.

Although the USDA did not have jurisdiction over this cattle, the highly publicized mistake should have informed them that developers of GMOs can not be trusted to do the research needed to protect human, animal, or environmental health. USDA must require such comprehensive testing.

Their failure to do so in 2016 might have resulted in serious health impacts. That year, USDA decided it would not regulate edible mushrooms engineered to not turn brown when sliced. It was produced by Penn State University scientists who used CRISPR to “knock out” the browning gene. But three years later, a study in Nature showed that CRISPR gene knockouts fail about one-third of the time. Moreover, it can result in the production of potentially allergenic or toxic truncated proteins[37].

There was no indication that the mushroom developers did any tests that would rule out this dangerous outcome. USDA’s baseless insistence on the safety and predictability of gene editing could have been fatal.

It is time that USDA abandon their dangerous policy and fully regulate gene editing in all its forms.

USDA Ignores Dangers From “Non-Agricultural” GM Microbes

The system that APHIS uses for permitting GM microbes largely targets companies and researchers who are planning to release their microorganisms into an agricultural setting.

GM microbes not intended for use in agriculture, however, may travel to these areas via the air and water, and on people, animals, insects, birds, equipment, and vehicles. They may be consumed by animals and found in their manure, or present in wastewater spread on fields. The variety of GM microbes that inadvertently enter plant and animal production locations will ultimately be far greater than those intentionally released there.[a]

USDA must widen its reviews and regulatory requirements to keep our food supply safe.

USDA Ignores Most Risks Related to Gene Transfer from GM Microbes

Microbes share genetic information with other microbes. This ongoing interactive exchange of genes helps them individually and collectively survive, thrive, and adapt to the ecosystems they inhabit.

The risks from GM microbes, therefore, are not limited just to the biological activity of those that enter the agricultural ecosystem. GM microbes present in soil, for example, may transfer altered genes into natural soil microbes, changing their nature and activity.

Similarly, GM microbes created elsewhere might transfer genes into other microorganisms, which then make their way into the agricultural ecosystem. There, they may interfere directly, or pass their genes onto natural microbes that cause problems.

Altered genetic material may pass between many types of microbes. Custom sequences created for one strain of GM bacteria, for example, may end up in many other types. Some genetic alterations might also be shared with algae, fungi, or even plants. The impact on agriculture may be impossible to predict and may result from the collective effect of single altered genes present in multiple organisms, or from multiple altered genes present in one ecosystem.

Although the APHIS draft document acknowledges the principle of horizontal gene transfer between microorganisms, it asks developers:

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?

It is clear that this simple yes/no question allows developers to ignore most of the complexities and unpredictable nature of gene transfer to and from GM microbes.

For example, certain bacteria are not killed by amoeba, but rather survive inside of them. The environment within the amoeba enhances horizontal gene transfer. Bacteria and viruses that acquire new genes may then escape. If an applicant claims that they have discounted gene transfer, this is one of many plausible scenarios they overlooked[38].

USDA Ignores the Most Plentiful and Dangerous Sources of GM Microbes

Having established that GM microbes can enter agricultural ecosystems both directly and indirectly, it’s important to assess possible sources of the microorganisms. We look at three.

1.         USDA is primarily focused on companies that create commercial GM microbes specifically for release in agricultural settings. For example, bacteria that fixes nitrogen is being added to cornfields. Such direct applications are subject to the most scrutiny by USDA, and will introduce large numbers of the same GM microbes into targeted agricultural ecosystems.

2.         GM microbes may escape from facilities designed to contain them. The organisms, or their genes via horizontal gene transfer, may then travel to agricultural settings. USDA ignores most of these facilities.

3.         GM microbes may be created in experiments by students, home hobbyists, businesses, and others, where they may spread through the environment unabated. USDA ignores these GM microbes, which will ultimately provide the greatest diversity of genetic alterations and microorganisms introduced into the biosphere.

CRISPR Technology Will Flood the Environment with GM Microbes

CRISPR can create GMOs at a fraction of the cost and with far less training than before. CRISPR labs can be purchased for less than $2000, and are used by tinkerers at home, in businesses, college labs, and more and more in high schools—where they may become standard equipment.

A search of online biology supply companies reveals that virtually anyone can order from over 10,000 microorganisms. People can also collect microbes in the wild.

CRISPR users can also choose from over 100,000 target sequences, which informs the gene editing mechanism where in the genome to make a cut. Many online stores also allow people to custom design their own target sequence.

As more people create gene edited microorganisms, a vast number and variety of novel GM microbes will flood the environment. With each release, the probability that they will damage plants, livestock, aquaculture, or any product or system within the jurisdiction of the USDA, increases.

The Department ignores this growing risk by not establishing any oversight, evaluations, or safety requirements.

Synthetic Biology Factories May Contaminate Via Accidental Release and Poor Filtration

There are thousands of facilities that use synthetic biology to produce gene products such as proteins. They insert genes from a variety of sources into microbes such as bacteria, yeast, and algae. Inside contained fermentation vats, these GM microbes produce proteins and other byproducts that are collected, purified, and used in food, agriculture, manufacturing, and medicine.

These “gene products” are exempt from USDA review. They are not themselves living GM microorganisms. However, scientists have verified that many of the products of synbio, such as supplements for humans or animals, contain fragments of DNA.

One of the ways that microbes acquire new genes is by picking up “naked DNA” fragments and integrating them into their genomes. The products of synbio, if they contain DNA from GM microbes, puts us at risk.

Such risks grow with the amount of exposure. For example, livestock being continually fed synbio products that are filled with the same type of gene fragments increases the danger.

Risks are also increased if the gene that is integrated was the one used to produce the targeted protein. In such a case, livestock might be given a prescribed dosage of a medicine created by GM bacteria. Suppose the gene that produces that medicine was also consumed and then integrated into the genomes of the animals’ gut bacteria. Their own intestinal flora might then produce this medicine nonstop.  Of course the same risks apply to humans, but that should be the FDA’s concern. They ignore it.

USDA is responsible for the health of the nation’s livestock. They ignore it too.

Another risk from synbio factories is accidental escape of the GM microbes into the environment. If these organisms survive and establish niches within agricultural settings, the impacts could be severe.

Consider that synbio factories are producing insulin, CBD and THC, flavors, industrial enzymes, supplements, medicines, and more. While many may have robust security, containment, and destruction protocols, many do not. And even the highly funded facilities acknowledge that they pose a significant risk.

Gingko Bioworks, one of the larger synbio labs, is a platform where other companies can commission custom GM microbes for protein production. They acknowledge in their SEC filings:

We cannot eliminate the risk of . . . contamination from these materials or wastes, which could expose us to liability.

The release of GMOs or Genetically Modified Materials, whether inadvertent or purposeful, into uncontrolled environments could have unintended consequences. . . The genetically engineered organisms and materials that we develop may have significantly altered characteristics compared to those found in the wild, and the full effects of deployment or release of our genetically engineered organisms and materials into uncontrolled environments may be unknown. In particular, such deployment or release, including an unauthorized release, could impact the environment or community generally . . .

USDA must regulate all such facilities that might impact agriculture.

Lack of Complete Understanding is No Excuse for Abdicating Responsibility

We are coming off a pandemic where a single mutating microbe wreaked havoc. Whether COVID was genetically modified or not, GM microbes do have the theoretical capacity to wreak havoc, both on human health and the environment. The fact that this next generation is set to release millions of varieties should sound alarms.

Science is at an early stage of understanding the immense complexity of microbiomes and microbial interactions. Only about 1% of the estimated trillion microbes on earth have been identified, let alone characterized.

Our lack of understanding, however, is not an excuse to institutionalize our ignorance. No one can predict the impacts that all the varied combinations of genetic sequences will have on human and environmental health or our food system. But there is a high degree of certainty that some combinations not currently under the narrow focus of USDA (even those that can be produced in high school CRISPR labs) could devastate food safety and food security. Further, it is not possible to recall GM microbes once released. And our ability to intervene once damage is detected is limited.

It is critically important that USDA expand its jurisdiction and regulatory authority, apply the science we do know, and contribute to furthering scientific knowledge as it compiles more data.

The current USDA version of “Don’t ask, don’t tell” endangers us all.

Conclusion: The USDA Ignores Most GM Microbes, Most Threats, and Up-to-date Science

The USDA seeks to regulate modified microorganisms that “can directly or indirectly injure, cause damage to, or cause disease in a plant or plant product.”

By narrowly defining their definition of “plant pest,” ignoring risks from gene editing and the frequent side effects from all methods of genetic engineering, insisting that risks only arise from GMOs with inserted foreign DNA (from potentially pathogenic sources,) pretending that the millions of GM microbes released from schools and synbio facilities will not threaten agricultural systems, overlooking the potential impacts from horizontal gene transfer in all but a tiny fraction of interactions, and by ignoring some of the most exciting research on microbiomes and soil microbiology that show how fundamental microbes are to a healthy food supply, the USDA ignores all but a tiny fraction of the GM microbes that “can directly or indirectly injure, cause damage to, or cause disease in a plant or plant product.” At a time when genetic engineering technology is being widely adapted, the USDA’s refusal to integrate up-to-date science puts food safety, food security, and human and environmental health at significant risk.

USDA Must Step Up and Protect Us

We understand that the USDA, along with the EPA and FDA, are part of the Coordinated Framework, worked out in the 1990s to regulate GMOs. The mandate from the White House at the time was for the agencies to use existing laws as a basis for their requirements. In this way, Congress was not involved and GMOs could be brought to market quickly.

The existing laws at the time, however, were crafted before GMOs were an issue. The laws were not designed to take into consideration the biological characteristics of GMOs, their tendency towards side effects, instability once released, capacity to create new allergens and toxins, and their tendency to spread and contaminate other crops and the environment.

USDA has used the misaligned mandates of these inappropriate old laws as excuses for their dangerous hands off policy. But advancements in biotechnology demand more vision and more responsible governance.

Humanity has arrived at a time when virtually anyone with access to a simple lab can redirect the streams of evolution for all time—on purpose or by accident. Everything containing DNA is up for grabs.

Of all types of species, the ones most dangerous to genetically engineer are microbes. If the widespread introduction of GM microbes interferes with critical microbiomes, it could damage or collapse ecosystems.

Who will step up to protect us?

The wording of the APHIS mandate actually invites USDA to exert its authority and bring regulatory sanity to this field. If they are truly going to protect agriculture from modified microbes, the only scientifically justifiable way forward is to acknowledge the disruptive potential of virtually all GM microbes released into the environment. Policies must immediately address this expanding threat.

If there is fear to overstep, consider that plausible worst-case scenarios include widespread loss of livestock and food crops. If such a catastrophe were to occur, no one would give a pass to the USDA if they used the excuse that it wasn’t in their job description.

While we believe that the only scientifically responsible way forward is to prevent release of any GM microbes into the environment, we understand that USDA would unlikely approve of this precautionary approach. At a minimum, however, the USDA must assess the full range of GM microbes, wherever they are created and used, and create regulations commensurate with the enormous unprecedented risks that this technology brings.

Only a comprehensive approach to such a comprehensive threat will suffice.

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