Genetically Engineered
Soil Microbes:
Risks and Concerns

Acknowledgements

This report was written by Kendra Klein, Ph.D., deputy director of science,
Friends of the Earth and edited by Dana Perls, senior food and technology
program manager and Lisa Archer, director of food & agriculture at Friends ofthe Earth. We are grateful to Dr. Margaret Reeves, senior scientist at Pesticide
Action Network North America for her contributions and detailed review and
Dr. Steve Suppan, senior policy analyst at the Institute for Agriculture andTrade Policy for his detailed review.

About Friends of the Earth
Friends of the Earth United States, founded by David Brower in
1969, is the U.S. voice of the world’s largest federation of grassroots
environmental groups, with a presence in 75 countries. Friends of the
Earth works to defend the environment and champion a more healthy
and just world. We have provided crucial leadership in campaigns
resulting in landmark environmental laws, precedent-setting legal
victories and groundbreaking reforms of domestic and international
regulatory, corporate and financial institution policies. Visit www.foe.org
to learn more.

Any errors or omissions in this brief are the responsibility of Friends of the Earth U.S.
©Copyright August 2023 by Friends of the Earth U.S.

Table of Contents
I. Introduction

4

Ecological risks

26

A quick history of microbial inputs in agriculture 4

1. Gene containment and lack thereof

26

The booming ‘biologicals’ market		

2. Altering microbial communities

27

3. The pesticide treadmill				29

Human health risks				30

5The pending proliferation of GE microbes inagriculture

					

5

Agrichemical corporations’ false marketing claims:
From ‘feeding the world’ to ‘regenerative
agriculture’			6

Key conclusions				8

1. Novel pathogens

30

2. Antibiotic resistance30

3. Immunosuppression and opportunistic
pathogens				30

4. Consumer exposure and the humanII. Background9

The fundamental role of microbes in the soil andmicrobiome					 31Socioeconomic risks

31

VI. Policy context

32

Summary of current regulatory system

32

farm ecosystem					 9The importance of organic and agroecologicalfarming for fostering healthy soil microbiomes							 101. U.S. Environmental Protection Agency

33

2. U.S. Department of Agriculture

33

The need for a system to track the spread andIII. The growing investment ofagrichemical companies inbiological products				13Understanding how engineering techniques shape

Factors driving agrichemical corporations’potential risks				investment in biologicals			
Reductionism vs ecology

14
14

impacts of GE microbes				

33
34

1. Evaluating the potential for horizontal genetransfer					

34Independent biologicals companies and startups 17

2. Methods of transformation

34

The role of academic research

3. Nature of the engineered trait

34

17

4. Use of stabilizing chemicals and surfactants 34

IV. The rise of genetically engineered
microbes in agriculture			18

VII. Policy Recommendations

36

Types of applications of GE microbes

Appendices38

Appendix I. Methods of genetically engineering
microbes						
Appendix Il. Horizontal gene transfer		

38
39

References				40

in agriculture				19

1. Nitrogen fixation

20

2. Pest control

21

3. Making microbes ‘easier to handle’22

V. Risks and Concerns

25

Limits of our knowledge & unintended
consequences				25

I. Introduction
A handful of healthy soil contains more
microorganisms than there are people on the planet.
These tiny creatures, such as bacteria and fungi,
play a massive role in agriculture, from making
nutrients in the soil available to crops and providing
crops greater immunity to pests and diseases toregulating global carbon and nitrogen cycles. Just as
we are beginning to comprehend the fundamentalrole that the human gut microbiome plays inmaintaining our health, scientists are increasingly
recognizing the importance of agricultural
microbiomes. And yet, soil microbiomes — and theirrelationship to the crops we grow and the broader
ecosystems of which they are a part — are marked
by incredible complexity that we are only beginningto understand. Of the billions of species of microbesthat make up the living soil, only a few hundred
thousand, far less than one percent, have beenscientifically characterized in detail.1
Despite these unknowns, biotech companies havebegun to commercialize genetically engineered(GE) soil microbes for use across millions of acresof farmland. At least two products are currently
being used by U.S. farmers — a GE bacteria from
Pivot Bio called Proven® and BASF’s ‘2.0’ version of
its Poncho®/VOTiVO® seed treatment (see page 15
and 16). The U.S. Environmental Protection Agency(EPA) reports that it has registered eight GE
microbes that act as pesticides, however, it is all but
impossible to determine what they are and whether
they have been commercialized given the EPA’s
extreme lack of transparency (see page 7).2
This report provides historical context for this novel
technology, insight into future trends, a summaryof potential risks and policy recommendations thatwould ensure robust assessment and oversight as
more GE microbes move from the lab to the field.ii

A quick history of microbial
inputs in agriculture
Since ancient times, farmers have worked withmicrobes — adding organic matter to soil in theform of compost is essentially feeding the soil
microbiome. The history of applying specificmicrobes to achieve specific goals in agriculture
dates back to the late 19th century when scientists
began isolating soil bacteria and exploring their rolein key agricultural activities like nitrogen fixationand control of plant pests.3,4 In 1938, what is now
the most widely used microbial pesticide, Bacillus
thuringiensis (Bt), was first sold to farmers inFrance.5
Today, over 1,200 companies worldwide offer
agricultural products derived from naturally
occurring microbes and plants.6 In industry terms,
these are known as ‘biologicals.’ Unlike synthetic
chemical fertilizers and pesticides, which arederived largely from fossil fuels, biologicals arederived from living microorganisms and plants.
Along with microbes, they include naturally-derived
compounds like pheromones and biomolecules likeamino acids. Biologicals are typically categorized as
biostimulants to improve plant growth, biofertilizers
to improve crop nutrition, and biocontrols or
biopesticides to manage pests and diseases. They
can be applied directly to soil, to the leaves of crops
or as seed treatments.
Farmers can choose from many hundreds of
biological products. Over 600 microbial ‘fertilizers’
and 490 microbial ‘pesticides’ are approved foruse in organic production in the U.S. according to
the Organic Materials Review Institute’s catalogue.
Biological inputs are often associated with organicand other ecological forms of production because

It is important to understand that major agrichemical companies, along with a significant number of mid- and small-sized companies, already do — andwill continue to — sell biological products that are not genetically engineered. This report aims to explore potential concerns related to GE biologicals.
It is also important to understand that this report does not address genetically engineered microbes that are grown indoors in industrial conditions tomake chemicals that are then applied to crops. As one example, the company Vestaron has a pesticide product called Spear® which is created by using
genetically engineered yeast cells to produce components of spider venom. These GE yeast cells are grown in vats and then killed before being applied asa spray to control crop pests. Rather, this report focuses on current and prospective applications of living GE microbes released into agroecosystems.

4Figure 1:
Biologicals market
projected growth,
2018-2030

Source: DunhamTrimmer
International Bio Intelligence

they are non-toxic, biodegradable, and work withnatural systems. However, they are also used inconventional production, for example, 49 percent ofrespondents to an American Fruit Grower’s survey
report using biological inputs.7

The booming ‘biologicals’ market
We are at a major turning point in the use of
biologicals in agriculture. The global biologicals
market is expected to nearly triple in a span ofeight years, from $10.25 billion in 2021 to $29.31
billion by 2029.8 A major driver of the changing
landscape is the entry of the largest agrichemicalcompanies — Bayer, Syngenta (ChemChina),
Corteva (Dow-Dupont) and BASF. These companies
have spent millions acquiring biologicals companies
in recent years and now offer a range of biologicalproducts. There is also increased interest on thepart of the government, as evidenced by the U.S.
Department of Agriculture (USDA) including
the “development of microbial technologies” in
its Science and Research Strategy platform thisyear.9 And conventional growers, which, on thewhole, have historically dismissed biologicals, arealso showing increased interest. For example, theWestern Growers Association — one of the largest
agricultural trade associations in the U.S. — hosted
its first-ever ‘Biological Summit’ this year, with
Syngenta and Bayer among the sponsors.10

The pending proliferation of GE
microbes in agriculture
While many new biological products will not beengineered, we are on the verge of a proliferationof the use of GE microbes in agriculture, as
agrichemical companies and biotech startups
are investing heavily in these technologies. The
release of GE microbes directly onto millions ofacres of farmland is a new chapter in agricultural
biotechnology — GE microbes are live organismsthat can reproduce and interact with other species.
And, unlike plants and animals, microbes are able
to share genetic material with each other far more
readily, even across completely unrelated organisms
in a process known as ‘horizontal gene transfer.’ Asa result, the genetic modifications released insideengineered microbes may move across species
boundaries in unpredictable ways.
Releasing GE microbes in agriculture represents anunprecedented open-air experiment that may haveirreversible consequences. Once they are released,
microbes cannot be ‘recalled.’ The scale of releaseis far larger, and the odds of containment are far
smaller, than for GE crops. Consider the following:
just under 3 trillion corn plants are grown each year
in the United States, most of which are geneticallyengineered. An application of GE bacteria releases
the same number of modified organisms about
every half an acre.

The scale of release is far larger and theodds of containment are far smaller
than what we have come to know forgenetically engineered crops. Consider
the following: just under 3 trillion corn
plants are grown each year in the UnitedStates, most of which are geneticallyengineered. An application of geneticallyengineered bacteria releases the same
number of modified organisms about
every half an acre.
5

By their nature, biologicals — engineered or not— seek to change the microbiomes of the fields
or plants that they are applied to. Research showsthat, while many commercial biologicals have only ashort-lived effect on indigenous soil microbes or noeffect at all, others may have a long-term impact.
Changing the microbiome can result in directly
observable changes to plant growth and insect
communities, hence the interest in these productsin the first place. However, while many of thesechanges can be beneficial to farmers, there may
also be unintended consequences, such as loweringrather than improving crop yield, or increasing
rather than decreasing disease suppression.11
We urgently need a shift in agriculture from thedominant chemical paradigm to a biologicalparadigm. Use of toxic synthetic chemical
pesticides and fertilizers continues to rise,
underpinning industrial agriculture systems thatcost the world an estimated $3 trillion annuallyin environmental damage, according to the UN.12
Biologicals may be able to play a significant
role in helping farmers transition to ecologicallyregenerative and resilient systems.
At the same time, the entry of massive agrichemicalcompanies into the field of biologicals and theirinterest in genetically engineering microbes raises
critical questions about whether GE microbes will
be used in a way that further entrenches industrial
approaches to agriculture and unjust relationshipsof power within the food system or whether they
have any potential to become part of ecologicalfarming systems.
The problems that biotech companies are
purporting to solve via genetically engineering
microbes — such as pest resistance to chemical
pesticides and depleted soils lacking fertility —result from monoculture industrial farming systems
in the first place. In the long run, we cannot
engineer our way out of these problems, we must
shift to agroecological approaches that protect andregenerate the natural resources we depend on to
grow food, now and for generations to come. We
have decades of scientific data and millennia of
farmer experience demonstrating that ecologicalapproaches to farming already achieve what
GE microbes are being marketed to do, such asprovide ample nutrients for plant growth, produce
healthy plants that better resist pests and diseases,
and achieve greater soil carbon sequestrationand improve farmers’ resilience to floods anddroughts.13,14,15

Agrichemical corporations’ false
marketing claims: From ‘feeding
the world’ to ‘regenerative
agriculture’
Agrichemical companies are leaning on the
debunked trope that we need to increase yield to‘feed the world’ in their marketing of GE microbes,
as they have with GE crops. Yet, a vast body ofdata show that hunger is not primarily a problemof overall supply of food but rather of poverty,lack of democracy, and unequal access to land,
water, and other resources, especially for women.16
What’s more, these same corporations have along track record of actively working against longterm food security — blocking regulations andmanipulating science to keep their toxic pesticides,
which harm biodiversity and human health, on themarket; designing GE crops only to withstand theirproprietary pesticides rather than any humanitariangoal; and leveraging their market power to increaseprices of inputs for farmers. Expert consensus
around the globe has called for a rapid shift fromthe type of input-intensive industrial agriculturethat these companies profit from to agroecologicalfarming methods in order to address world hunger
and the biodiversity and climate crises we arefacing.17,18,19
Agrichemical companies are also citing theirinvestment in biologicals as evidence of theirleadership in ‘regenerative agriculture’ — amovement focused on improving soil health inorder to sequester carbon, restore biodiversity,
conserve water and improve farmers’ resilience inthe face of climate change. Yet, they are primarily
selling biologicals as part of ‘integrated’ platforms,
such that the biologicals cannot be obtained
separately from their engineered seeds, pesticides,
and other proprietary products that are widely
associated with significant harm to soil life andother biodiversity. Bayer plainly states this strategy
on its website, saying that biologicals “complement
traditional crop protection tools as part of an
integrated crop management system.” Thecompany sells a GE microbe as part of Poncho®/
VOTiVO® 2.0 seed treatment, which also contains
the neonicotinoid insecticide clothianidin, whichis associated with serious harm to soil organisms,
pollinators and other beneficial insects, and aquatic
ecosystems.

6Regulatory agencies’ extreme lack of transparency
The ‘green’ wall of silence
Detailed information about engineered microbes is usually hidden by a deep desire for secrecy on the partof developers and a regulatory system with serious failings in relation to transparency.20 This report goesdeep into scientific research and regulatory filings to uncover details that would be almost impossible toobtain for concerned members of the public. Despite these efforts, we could not even identify the agricultural
GE microbes that are in the pipeline of the regulatory process or that are commercialized beyond the two
described in this report, which have received press coverage. This highlights the fact that lack of transparency
is an overarching, urgent problem for how we evaluate and oversee products of biotechnology, including
genetically engineered microbes.21
For example, an EPA process known as TERA (TSCA Environmental Release Application) is used to approve
field trials of genetically engineered microbes. Someone with prior information about a specific microbe
can find brief, generic summaries of these decisions online.22 Should a member of the public want to see
the actual government documents allowing this release, they would be required to telephone the EPA tomake a request — and what they receive would be only the information that the developer of the technology
deems ‘nonconfidential.’ And that is only for GE microbes that one already knows exist. There is no way to
do a general search for agricultural GE microbes that are going through the regulatory process or that arecommercialized. Nor is there a way to use the scientific name of genetically engineered microbes as one finds
them described in the scientific literature to search for actual agricultural on-the-shelf products.
USDA has historically done better than the EPA at making detailed documents about regulatory decisions
available but allows developers of GE crops and microbes to self-designate unlimited amounts of information
as ‘Confidential Business Information’ (CBI). And, as of 2021, the process the USDA uses to review exemptions
from regulation for GE microbes and crops became significantly more opaque with the establishment of the
SECURE Rule under the Trump administration.
Below is an excerpt of a table from a letter sent by Pivot Bio to the USDA regarding its GE microbe, Proven®.
This is as it appears in the publicly accessible regulatory system — the entire 4-page table is completely
blank because the information has been deemed ‘Confidential Business Information,’ as stated in the margin
throughout. Every detail about the nature of the product has been hidden from the public. The ability fordevelopers to do this is at the discretion of the regulatory agencies that currently allow these extreme levelsof secrecy.
It is imperative that systems for far greater transparency are implemented by government agencies to allow
for robust, informed decision-making processes that include all relevant stakeholders, including independentscientists, farmers, and members of the public.

Excerpt from Pivot Bio letter submitted to USDA APHIS June 12, 2020 as it appears in the public record

7Key conclusions

�This report provides background on the importanceof microbes to soil health and agriculture, thehistory of genetic engineering of microbes, andexamples and trends of GE agricultural microbe
products reaching the market. We highlight thepotential risks and concerns related to geneticallyengineered microbes intended for use in agriculture
and explore the economic and political relationships
shaping their development. Finally, we summarize
the current U.S. regulatory system and provide
recommendations to inform the development ofrobust, science-based regulatory oversight of thisnovel technology.

Companies’ ability to patent geneticallyengineered microbes raises important questions
about how the technology may be used toreinforce relationships of power in the foodsystem that benefit corporations at the expenseof family-scale farmers, communities and theenvironment.

�

There are massive gaps in our knowledge that
impede our ability to thoroughly assess risks
and to predict the consequences of releasing
GE microbes into the environment.

�

Adoption of genetically engineered microbes
on an industrial scale will represent anunprecedented open-air experiment in therelease of GE living organisms. Any release of
GE microbes has the potential to affect theenvironment in unintended ways.

�Containment of GE microbes applied inagriculture is impossible. Fungal spores,
bacterial cells and viruses can drift long
distances on air currents, moving across national
borders. Releasing genetically engineered
microbes into the environment raises serious
new questions about containment of geneticallyengineered sequences.

�

We must consider the prospect that in rarecases, genetically engineered microbes could
become human or animal pathogens and could
impact the human microbiome.

�

A moratorium should be placed on applications
which seek to create microbes that geneticallyengineer other microbes, known as ‘guided
biotics.’ Companies are actively working on
applications for livestock feed. This systemshares properties with gene drives, which havebeen treated with far more trepidation thanother types of genetic engineering; the UN has
essentially halted the environmental release ofgene drives anywhere in the world.

�Engineered microbes have not yet shown
effects that could not have been achieved by
non-engineered microbes and agroecologicalapproaches to farming. Decades of scientific
data and millennia of farmer experienceshow that organic and other agroecologicalapproaches to farming already achieve thebenefits that proponents of GE microbes claim
for the technology.

We make the following key conclusions:
�

�

�

�

The current regulatory system is confusing,inadequate and lacks transparency and ongoingoversight. Precautionary, science-based
regulations that account for the unique featuresof genetically engineered microbes should beestablished ahead of further environmental
release and commercialization of these novel
technologies. A system of monitoring theirspread and impact once released into theenvironment and re-evaluating their safety overtime must be established.
The definition of what constitutes genetic
engineering must be defined broadly to include
both conventional genetic engineering and gene
editing techniques and should be rooted in thedefinition of modern biotechnology from the
Codex Alimentarius of the United Nations Foodand Agriculture Organization.23
Lack of transparency is an overarching, urgent
problem for how we evaluate and oversee
products of biotechnology, including geneticallyengineered microbes. It is imperative thatsystems for far greater transparency are
implemented by government agencies to allow
for robust, informed decision-making processes
that include all relevant stakeholders, including
independent scientists, farmers and members of
the public.
The companies investing in commercializing
genetically engineered microbes include major
agrichemical corporations along with startups
that have roots in those companies. In thiscontext, there is significant potential for thedevelopment and deployment of GE microbes
to further entrench an industrial approach toagriculture.

8II. Background
The fundamental role of microbes
in the soil and farm ecosystem
When you imagine a thriving ecosystem, you
might picture a forest rich with plants, roamed byherbivores that are hunted by carnivores. All of thisis biomass, living carbon. But you should know that,as a rule of thumb, there is just as much biomass
living in the soil as on it. In fact, soils represent themost biodiverse ecosystems on the planet. Vibrantsoil ecosystems are an essential part of the naturalenvironment, and they must be respected andprotected as strongly as more familiar targets ofconservation. Indeed, without healthy soil neither
the wild environment nor human needs can besustained into the future.
Soil biomass is made up mostly of two things, plantroots and microbes. Microbes are by far the mostdiverse of these two. Microbes are tiny living things
that are found all around us and are often too small
to be seen by the naked eye. They live in water, soil,
air, on plants as well as in human and other animal
bodies.
Viruses, bacteria, and protozoans are all foundin the soil microbiome, as are larger and more
complex organisms like fungi. Some microbes blurthe boundaries of the category. Most people would
not consider a mushroom a microbe, but many
mushrooms are merely temporary reproductive
structures formed by microscopic fungi below theground. Tiny animals like nematodes and water
bears that have bodies with specialized organs andshow complex behaviors are also members of thesoil microbiome.24

Figure 2: Soil microorganisms

Bacteria

Fungi

Algae

Protozoa

What are microbes?
Microbes are tiny living things that arefound all around us and are often too small
to be seen by the naked eye. They live inwater, soil, air on plants, as well as in humanand other animal bodies. Viruses, bacteria
and protozoans are all found in the soil
microbiome, as are larger and more complex
organisms like fungi. In recent years, sciencehas come to understand that microbes
are responsible for essential functions inecosystems, human health, and agriculture.

Complex interactions take place among thesemicrobes just as they do between organisms above
the ground. There is spatial variation in habitats
with different communities of microbes inhabiting
subtly different parts of the same patch of soil. The
roots of different plant species are a major sourceof this variation, and many microbes specialize ingrowing around, on, and in plant roots.
We now know that plants recruit microbes andhave a stable consortium that is specific to plantvariety. In the short term the microbes in a plant’s
root zone, or rhizosphere, have a strong influenceon how the plant experiences its environment. In
the long term, soil microbes shape the environment
itself by changing the chemistry of the soil, its
structure, and the decomposition of organisms fromabove the ground.
Agricultural crops are no exception to the effectof the soil microbiome. Some of these effects are
obvious. Bacteria that convert nitrogen gas fromthe air into a form usable by plants have symbiotic
relationships with plants like legumes, forming
nodule structures that are visible to the nakedeye.25,26 Nitrogen is a nutrient that is critical to crop
growth. For legumes like soy and peas, microbiallyfixed nitrogen can satisfy the great majority of the9plants’ needs.26,27 In agroecological farming systems,
crop rotation with plants that host these bacteria
is a key source of nitrogen. Most crops also havesymbiotic associations with mycorrhizal fungi intheir root systems that receive carbon from theplants in exchange for water, phosphorus and othernutrients.28 In this way, microbes play a central rolein soil carbon sequestration as the ‘bridge’ thatmoves carbon from the plant into the soil.
Many other effects of the microbiome, however, arejust as important but less obvious from the humanperspective. Beneficial microbes protect plantsfrom disease by signaling to the plant, secreting
protective chemicals in the soil and competingwith pathogens.29 Microbes can also make nutrients
more available to plants by releasing them from soil
particles or changing their chemical form. Crucially,
these functions often depend on the microbialcommunity as a whole, not just a single species,and can vary for different plants. This is one of thereasons that science has been slow to realize theimportance of the soil microbiome and is still justbeginning to understand how it works.

The importance of organic
and agroecological farming
for fostering healthy soil
microbiomes
Even when we don’t set out specifically to workwith microbes, by changing plant species and soil
conditions we radically alter the microbiome.30 The
microbes that live in a farmer’s field, no matter what
approach is used in cultivation, are different fromthe microbes that live in a nearby wild habitat or
the microbes that were there before the field wascleared.

Even when we don’t set out towork with microbes, by changing
plant species and soil conditions weradically alter the microbiome.
A wide range of choices we make about how tofarm dramatically shape the soil microbiome —which crop varieties we use; whether we dependon synthetic fertilizers or instead use compost andintegrate legumes and livestock into the system
for fertility; whether we grow monocultures versus
incorporate diversity through cover cropping, crop
diversification, hedgerows, silvopasture or othermeans; whether we depend on synthetic chemical
pesticides or instead holistically manage the system
to prevent pests and use least-toxic pesticides as alast resort.
A growing body of data show that it is imperativethat we rapidly transform our agricultural systems
from a reductionist, industrial paradigm that isdependent on synthetic pesticides and fertilizers
to an agroecological paradigm that is rooted in
the principles of diversity and that works withnatural systems to manage pests and provide
fertility. The basis of agroecological farming is theholistic integration of practices like cover cropping,
diversified crop rotations, intercropping, inclusionof perennial crops and hedgerows, incorporation of
livestock and composting. These practices createhigh levels of soil organic matter, a carbon andnitrogen-rich substance that is both the natural
product and the habitat of microbes.31,32

10

Figure 3: Agricultural microbiomes are shaped by choices about agricultural practices

Agroecology includes a wide range of ecologically
restorative food and farming systems, including
diversified organic production that meets orexceeds the standards of the U.S. National Organic
Program. Research has found that organic farming
can significantly enrich soil microbial abundance,
diversity and activity.33,34 Conversely, researchshows that conventional agricultural practices result
in severe impacts on the microbiome, including
reduced diversity, abundance and function.35,36,37,38
By fostering healthy, living soils, organic andother agroecological farming systems generatemany environmental benefits, including water
conservation, decreased soil erosion and greater
soil biodiversity.39,40 They also enhance farmers’
resilience in the face of climate change byimproving soil structure and water-holding capacity
which helps farmers better cope with drought andfloods.13,41 And by sequestering more carbon in thesoil than conventional practices, these methods canbe an important part of climate change mitigation
strategies.42
ii

In relation to the use of commercial biologicalproducts — engineered or not — two generalthemes that emerge from the available researchshow the importance of an ecological versus
reductionist paradigm. First, biologicals are more
efficacious when used in a holistic farming system.
Second, organic and agroecological approaches
often achieve the environmental benefits discussed
above even without the addition of biologicals.
In fact, in healthy, biologically active soils, theexisting soil microbiome tends to outcompete andoverwhelm commercial biological products.11,ii
In other words, we can’t just replace a jug ofchemicals with a jug of biologicals and think we’regoing to have a sustainable farming system — aholistic approach achieves better, more consistentand more long-lasting results than “silver bullet”
microbes that can be isolated, produced andmarketed.

Exceptions include rhizobia and mycorrhizal inoculants applied directly to seeds or root balls, disease-suppressive microbes applied to plants, seeds, orstarts, and microbes applied to roots or in root zone that induce systemic resistance in the plant.

11

We can’t replace a jug of chemicals
with a jug of biologicals and think
we’re going to have a sustainable
farming system — a holistic approachachieves better, more consistent
results than “silver bullet” microbesthat can be isolated, produced andmarketed.

An agroecological approach tonitrogen fixation for corn
Mandaamin Institute research onland races
Our choices about farming practices shape
the microbiome, which in turn shapes
farming practices. Dr. Walter Goldstein at the
Mandaamin Institute has published in-depth
research finding major differences in the
microbiomes of the root zones of traditional
land races of maize versus modern Corn Belt
hybrids. Land races are crop varieties that are
adapted to specific regions and climates andtherefore exhibit a lot of genetic diversity. The
land races support free-living nitrogen fixing
bacteria and can derive up to half of theirnitrogen requirement that way, whereas themodern hybrids host Fusarium fungi that help
them thrive in the high-input conventional
systems for which they were developed.
However, those Fusarium inhibit the nitrogen
fixing bacteria in the soil, making the modern
hybrids more dependent on external inputs ofnitrogen.43 The Mandaamin Institute is using thisknowledge to develop non-engineered cornvarieties that are extremely efficient at obtaining
nitrogen and other nutrients from the soil andeven from the air with the help of bacteria.

12III. The growing investment ofagrichemical companies inbiological products
The creation and distribution of geneticallyengineered crops has infamously been controlled
by large agrichemical corporations that have along track record of disregarding the massive
environmental and human health impacts of theirproducts, disenfranchising family-scale farmers,
obfuscating the truth about their products andobstructing regulations.44 These same companies
are now rapidly moving into the field of biologicalproducts.
Syngenta now claims to be “one of the strongest
players in the global biologicals market,” andCorteva acquired the leading biologicals andbiotechnology company Symborg and anotherfirm in this sector, the Stoller Group, in 2022.45,46
While biologicals are currently only 5 percent of the
global pesticide market, Corteva’s CEO has statedthat by 2035, “biologicals will make up 25 percent
of crop protection revenue.”47 Bayer has amassed acollection of at least 125,000 wild microbial strains
and in 2019 created an umbrella branch for related
products called ‘Biologicals by Bayer.’ The company
has rapidly expanded their activities in this area
via acquisitions.48 Between 2012 and 2014, Bayeracquired three biologicals companies and in 2022
established a strategic partnership with Ginkgo
Bioworks, a startup company which has received$15 billion in investment to develop a platform toautomate the genetic engineering of thousands ofmicrobes at once. Bayer also acquires and markets
individual microbial products from other companies.
The most prominent microbial products released by
the company to date are bacteria-based fungicides
as well as some plant growth promoting products.

Figure 4: Consolidation in the biologicals industry, 2012-2023

13

Factors driving agrichemical
corporations’ investment inbiologicals
Several factors are likely driving agrichemical
corporations’ investment in biologicals. The
discovery and commercialization of new chemical
pesticides has become increasingly difficult in
the past two decades, while the development
and launch of biopesticides is much quicker andcheaper. One analysis estimates that it takes morethan $280 million to develop one new synthetic
pesticide and nearly twelve years to launch it incontrast to $3 to $7 million and approximately four
years to get a new biopesticide to market in the
U.S.49Some other likely drivers are growing publicconcern about the enormous harm of synthetic
chemical pesticides and fertilizers on human health,biodiversity and the climate. The vast and growing
body of science detailing these harms is resulting inbans on hazardous pesticides in countries aroundthe world, lawsuits that are costing agrichemicalcompanies millions — or billions in the case of Bayerand its flagship herbicide Roundup (glyphosate),and consumer demand for organic food grownwithout toxic synthetic pesticides. Farmers arealso interested in alternative approaches as they
face increased drought and floods related toclimate change, rising costs of inputs like synthetic
fertilizers and staggering challenges from weeds
and insects that have developed resistance tosynthetic pesticides.50
Agrichemical companies have been quick to market
the sustainability potential of biologicals.
Syngenta, for example, stated that its acquisitionof one biologicals company was a move to “helpfarmers deliver a food system working in harmony
with nature.”51 And Bayer has claimed that its
development of biologicals is part of a plan
to “reduce the environmental impact of crop
protection by 30 percent without sacrificing yieldand the health of the harvest” by 2030.52

are “hard for the big companies to grasp, they likesingle compounds and narrow approaches.”53
Will ‘squeezing’ biological products into a
reductionist approach strip away some of
the factors that have historically made themenvironmentally friendly? If companies geneticallyengineer microbes to survive on a wider range ofcrops or soils than they would naturally occur on,
would it potentially make them more competitiveand more likely to overtake naturally occurring
microbes in the environment? While naturally
occurring microbial products are typically highlybiodegradeable, will companies engineer microbes
to persist longer in the environment, thereby also
increasing this likelihood?
While naturally-occurring microbes produce a
cocktail of pesticidal compounds and typically work
together in a consortium or ‘broth,’ agrichemicalcompanies are interested in engineering microbes
to express a single mode of pesticidal action(meaning a single way to kill a pest). This will
increase the likelihood of pests developing
resistance to them. Another factor driving the
likelihood of resistance is that, rather than applying
microbial pesticides sporadically in relation toactual pest pressures, agrichemical companies arelikely to sell them as seed treatments on commodity
crops like corn and soy — as we’ve already seen
with Poncho®/VOTiVO® 2.0 — making their presencein the environment ubiquitous across millions ofacres. Thus, pesticidal microbes may perpetuatethe ‘pesticide treadmill’ common to industrial
agricultural systems rather than offer a true
alternative.

Reductionism vs ecology
Research and development of GE microbes for
agricultural use is often rooted in a reductionist
mindset. As one leader in the traditional biologicals
field noted, agrichemical companies have been
more interested in innovations that are “chemicallike,” such as single peptides for crop protection
rather than microbial consortiums that containmixtures of compounds — the complex mixtures

14

Pivot Bio’s Proven®
Unproven sustainability claims
A product called Proven®, released in 2019, is the first genetically engineered microbe widely available
in agriculture. It’s produced by the biotech company Pivot Bio and is backed by hundreds of millions ininvestment funds including from the Gates Foundation and some of the world’s wealthiest individuals.
According to Pivot Bio, the product was used on 3 million acres of corn in the U.S. by 2022.54 In thatyear, the company released three related products, Proven®40 On-Seed for corn and Return® On-Seedand In-Furrow for barley, millet, oats, sorghum, sunflower and spring wheat. Pivot Bio is also working
with Bayer on a similar technology for soybeans.
Proven® consists of live Kosakonia sacchari and Klebsiella variicola bacteria that have been gene edited
to eliminate the ‘off switch’ on the microbes’ process for fixing nitrogen.55,56 Nitrogen is an elementthat plants need to grow. They can only access it with the help of bacteria that ‘fix’ it by turning
atmospheric nitrogen into a form that plants can use. Normally, when nitrogen fixing bacteria sensehigh levels of nitrogen in the soil, they stop converting it. In Proven® the bacteria are prevented fromdown-regulating their nitrogen fixing activity.
In industrial farming systems, nitrogen is typically applied as synthetic petrochemical fertilizers which
are associated with major environmental problems, from run-off that produces ‘dead zones’ in water
bodies around the world to significant greenhouse gas emissions linked to their production andapplication.57 Reducing use of synthetic nitrogen fertilizer is a critical environmental goal.
While Pivot Bio’s website for the product claims to have solved the environmental problem of “howto replace synthetic nitrogen with something better,” peer-reviewed scientific evidence has not yet
borne out those claims. In fact, Pivot Bio’s field trials of Proven® from 2019 to 2021 published in thescientific literature didn’t include any reduction of applications of synthetic nitrogen fertilizer, they
only evaluated how crop yield was impacted by adding Proven® in addition to growers’ existing useof synthetic fertilizer.58 In other trial data shared on the company website, the ‘replaced’ synthetic
nitrogen is in fact a minority fraction of what’s applied, and there are no negative control fields tosee how plants do without Proven® at all. While the internet is full of bold headlines proclaiming thebenefits of the product, there is no peer-reviewed science backing those claims.
There is evidence that we can eliminate the use of synthetic nitrogen fertilizer through entirely
different means — agroecological farming methods. As discussed in the section above, organic
farmers meet their crops’ nutrient needs without the use of any synthetic fertilizers, which areprohibited by law in organic systems. Crop rotations using nitrogen-fixing plants like legumes andapplication of compost and manure are key sources of nitrogen in organic and other ecologicalfarming systems. Also see page 12 on corn varieties that naturally form relationships with nitrogenfixing bacteria in the soil. What’s more, other companies offer naturally occurring microbes that claim
the same benefits as Proven® without the use of genetic engineering.

15

BASF’s Poncho®/VOTiVO® 2.0
Engineering false fixes
A seed treatment called Poncho®/VOTiVO®, along with its ‘2.0’ version, are examples of theincreasing use of biologicals within monoculture, industrial farming systems.
Poncho®/VOTiVO® was originally developed by Bayer and is now sold by BASF (as a result ofdivestitures forced by the U.S. government after Bayer acquired Monsanto). According to news
reports, it was used on 40 million acres of corn and soy in the U.S. by 2017.59,60 The treatment
combines the neonicotinoid insecticide clothianidin (Poncho®) with a non-engineered Bacillus
firmus bacteria with nematicidal properties (VOTiVO®).
In 2019, Poncho®/VOTiVO® 2.0 was released by Bayer and is now sold by BASF. It is one of two GE
biologicals currently known to be on the market. The ‘2.0’ version added a genetically modified Bt
bacteria to the seed treatment. It’s marketed as a novel form of crop protection, in essence aiming
to improve plant health in order to increase plants’ resistance to pests.61 Specifically, the Bt bacteria
is engineered to express a foreign protein which produces an enzyme that aids in converting deadplant residue in the soil to sugars. This encourages microbial activity in the soil with the aim ofincreasing nutrient availability and uptake by the crop.
The widespread use of these two microbes in industrial monoculture farming systems raises
certain questions. First, agrichemical companies are marketing biological pesticides like VOTiVO®
as a solution to a problem they largely created — the resistance of hundreds of pest species
to commonly used pesticides. The intensive use of pesticides in industrial farming systems is aperfect breeding ground for resistance — the ‘strongest’ of a population survive exposure to apesticide, they reproduce, and a species evolves resistance. As one example, ‘superweeds’ resistant
to glyphosate (aka Bayer-Monsanto’s Roundup) now plague over 60 million acres in the U.S.62
As a result, farmers who don’t turn toward ecological pest and weed management must sprayever more, and more toxic, pesticides to kill pests and weeds, a process often referred to as the‘pesticide treadmill.’
While a shift toward biological solutions could be a huge win for the environment and publichealth, BASF is selling this biological treatment in combination with a highly problematic
neonicotinoid insecticide, clothianidin, known for its extreme toxicity to pollinators and otherbeneficial insects and linked to a growing set of health concerns. What’s more, rather thanapplying the bacteria in response to real-time pest pressures and as part of a holistic system for
managing pests, the prophylactic, ubiquitous use of this microbial nematicide across millions ofacres annually increases the likelihood that it will only contribute to the pesticide treadmill that it isbeing marketed as a solution to.
Second, BASF is marketing the ‘2.0’ part of its product — the GE microbe meant to increasenutrient availability for the crop — as a ‘next-generation’ enhancement in plant health. But it istaking a well-known principle borne out in ecological farming systems — that healthy soils growhealthy plants that better resist pests — and applying it in a profoundly reductionist way that will
not resolve the underlying problem. In healthy soils, there is no need for an engineered bacteria
to convert plant residue to sugar, that activity is happening in abundance among complex
communities of microbes. This technology is an inadequate response to another problem theagrichemical industry has largely created — a farming system marked by depleted soils withvastly diminished microbial communities. What’s more, other companies offer naturally-occurring
microbes that claim the same benefit that the ‘2.0’ GE microbe promises without the potential
risks associated with releasing engineered bacteria into the environment.

16

Independent biologicals
companies and startups
Most biologicals specialists engage in the discoveryof naturally occurring microbes rather than in
microbe engineering. However, some companies
have openly indicated an interest in using genetic
engineering techniques. For example, AgBiome, aprominent and recently founded biologicals startup,
used its library of bacterial strains to develop
its own gene editing platform that it intends
to incorporate alongside its non-engineering
activities in development of new biologicals.
Other companies like BioConsortia, Robigo,
Switch Bioworks and Quorum Bio are working on
genetically engineered microbes for agriculture.
It is important to understand there is a great dealof overlap between large agrichemical corporations
and many of these startups. For example, AgBiome
was founded by two public university professors
alongside three ex-executives from Bayer, including
its past CEO. Its first investor was the venture
capital arm of Monsanto. Large chemical companies
are also increasingly handling the marketingand distribution of biologicals made by smaller
companies as they seek to expand their presence inthis arena.
If we already know that the people staffing andfunding independent companies have been
trained inside agribusiness corporations whose
track records on the use of genetic engineering is
associated with myriad social and environmental
harms, we should not take their claims about thepotential benefits of their products at face value.
At the same time, the lower cost and technology
barriers for development of genetically engineered

microbes as compared to engineered crops could
enable smaller companies, startups, academics, or
nonprofits to make products that reach the market.
Some of these new players could have genuineinterests in sustainability and in creating productsthat displace chemical treatments and challenge
harmful business practices.

The role of academic research
Academic work on GE microbes in agricultureintersects with major biotechnology corporations.
As the trade group Biotechnology Innovation
Organization describes, “on the academic side, in
addition to maintaining the spirit of research forthe common good, there is also a growing trend
in support of the commercialization of discoveries.
. .and for industry’s part, sponsored researchwith academic partners broadens the search forinnovative R&D.”63,iii For promising commercial
technologies, the intellectual property owned
by universities is often licensed to establishedcompanies like those described above forcommercialization. This includes innovations thatemerge from research funded by federal grants.
These publicly funded developments should be
subject to conditions of use for the public good,
although they currently are not.
Research by academic labs has contributed to
the largest number of environmental releases ofengineered microbes so far. Seventy-eight of all 128
environmental release permits ever issued throughthe EPA’s TERA program for genetically engineered
microbes were provided to universities. These were
for diverse types of work, often in limited areas andintended only for study, not direct application inagriculture.

iii While this report focuses on medical innovation, the intersections between corporate and academic research also reflects the agricultural sphere.

17IV. The rise of geneticallyengineered microbes in agriculture

The concept of genetically engineered microbes
as agricultural treatments is not new; suchtechnologies have been proposed and tested
at small scale since the 1980s (see call-out box
6 on Ice-minus) but have never gained traction
for availability to the public.64 Since the mid1990s, the primary focus of genetic engineeringin agriculture has been crops. However, microbes
are far easier to engineer. And the advent of gene
editing techniques — in which DNA is modified
but not moved between species — is driving a
new set of discoveries as well as new investments
in edited microbes just as it is in other types ofbiotechnology.65,66
This has made GE microbes essential tools forbasic science — tens of thousands of researchstudies using engineered microbes are publishedevery year. Whereas the generation of a geneticallyengineered plant or animal requires specialized
equipment, expensive chemicals, and accessto sterile conditions and can take years before
reaching a point where the effect can be assessed,
for tractable organisms like brewer’s yeast and E.
coli bacteria, a gene may be permanently inserted
and its effect observed within a single day.67,68
Tools and reagents for this process are cheap andaccessible, to an extent that microbial genetic
engineering is readily performed by high school
students.69,70 (Note — this does not mean that theresults are predictable or precise, see page 25 formore on unintended outcomes.)
A much wider range of engineered microbes can befound in academic work and field trials than thosethat have advanced to commercialization. These
include more complex engineered systems and useof transgenes from distant sources. Giving microbes
completely new traits is the most extreme form ofgenetic engineering. In general, this is done whena microbe that lives on or in a certain part of aplant or habitat can be used to deliver a useful traitfrom a different microbe. Industry work for nearfuture applications appears to emphasize the useof gene editing rather than transgenic engineering(when genes are moved across species) due tothe lower regulatory burden for products of thosetechnologies in the U.S., particularly following the
adoption of the 2020 SECURE rule at the USDA. It
is possible that, in addition to the factors mentioned
above, the trend toward deregulation of agricultural
biotechnologies in the U.S. is contributing tocompanies’ interest in development of GE microbes.

18

The first GE microbe to be field tested - ‘Ice-minus’
The first engineered microbe to be field tested, in the early 1980s, was ‘ice-minus’ Pseudomonas, anyof several strains of engineered bacteria in this genus. They were developed for commercial use under
the name Frostban but never made available to farmers.
The presence of wild Pseudomonas bacteria on plant surfaces enables damaging ice to form attemperatures about 7 degrees higher than in plants that are completely free of bacteria (30.2 vs. 23
degrees Fahrenheit). The wild bacteria were therefore found to result in frost damage for crops in thefield, limiting the growing season.71,72
The engineered Pseudomonas had an alteration in their surface structure that removes their ability toform ice crystals, and they were able to outcompete the natural ice-forming bacteria for space.73 In
a test with strawberries, the engineered Pseudomonas were sprayed on crops where they displaced
their wild relatives. As predicted, the majority of plants treated with the engineered bacteria avoided
frost damage at temperatures as low as 23 degrees while the majority of plants covered in wild
bacteria were frozen by the time temperatures reached 30 degrees.64,74 Evidence from the field also
showed the engineered Pseudomonas could protect pears and potatoes from similar damage.73,75
Proponents argued that enabling plants to withstand lower temperatures would protect fruit
production from weather extremes. Opponents of ice-minus bacteria were concerned that its
application could alter rain and snow patterns because bacteria serve as a natural source of ice crystal
formation in the atmosphere.76,77
However, within a few years the scientist who originated ice-minus bacteria and the company
attempting to commercialize it had both moved on to working with a naturally-occurring mutant
strain with identical benefits.64 The non-engineered microbial products are in use on a variety of crops
today. The research with engineered surface proteins continues, however, for different applications
such as disease prevention in fruits and tomatoes.

Types of applications of GE microbes in agriculture
Bacteria, viruses and fungi have been targeted for
agricultural genetic engineering, with bacteria being
the most commonly used.
�

Bacteria: To many people in the field“microbiome,” and especially “microbiome
engineering,” are synonymous with “bacteria.”
The GE microbes now available for commercial
use are bacteria. Bacteria are prokaryotes,
meaning they have no nucleus and a simpler
genetic system than eukaryotes—organisms
whose cells have a nucleus, including fungi,
algae, plants and animals. It can be easier toinsert genes and control how they functionin prokaryotes. Most beneficial microbes arebacteria that are found to naturally live in avery tight relationship with plants (Figure 6).78,79
These beneficial bacteria make up most of thespecies that are targeted for engineering. For
example, Pseudomonas is a large and diverse
family of bacteria which are tractable to workwith in the lab and contain members with
important roles in plant growth.
�Fungi: In general, engineering of fungi foruse as live microbes in agriculture lags behindengineering of bacteria because their complex
genome structure and biology makes many
fungi difficult to apply genetic engineering
methods to. It can be harder to insert genes
into eukaryotes and to control how theyfunction in a new organism. The technologies
described below pertaining to fungi are notcurrently commercialized or on a clear path tocommercialization.

�

Viruses: Work with genetically modified

viruses has been subject to concern about thepersistence and potentially wide host range ofviruses, and no engineered virus has nearedcommercialization for agriculture.

19

Figure 6:
Most engineered microbes are species that have intimate relationships with plants. The bacteria in this figure are growing
between plant cells on the leaf surface as well as on and into the pores that allow the plant to take up CO2 for photosynthesis;
Pseudomonas, right, and Burkholderia, left & center.

Nitrogen fixation
Plants need nitrogen to grow — it is a major
component of chlorophyll, the compound by whichplants use sunlight energy to produce sugars fromwater and carbon dioxide (i.e. photosynthesis), and
it is a major component of the building blocks ofproteins, without which plants wither and die. Somecrops, such as lentils and other legumes, naturally
form symbiotic relationships with nitrogen-fixing
soil bacteria called rhizobia, while others such as
corn, wheat and rice do not. Despite years of trying,
researchers have failed to successfully engineer
crops that do not naturally fix nitrogen to do so,either by engineering nitrogen-fixing bacteria tocreate relationships with crops or by attempting
to put genes for nitrogen fixation directly into thecrops.80,81,82,83
Over the past decade, a growing number of
researchers have taken interest in engineering
nitrogen fixation into microbes themselves.81 Recent
work is focused on bacteria that do not form adeep symbiosis with plants but which can be used
to make nitrogen available to crops other thanlegumes.84,85 Prominent examples of this approveare Pivot Bio’s Proven® product (see page 15) andthe research of a group at Shangdong Academy ofAgricultural Sciences in China.58,86

Pest control
Pesticides
The most widely used insecticidal bacteria inagriculture is Bacillus thuringiensis (Bt), which
naturally lives in the soil and on plants. It produces
proteins that kill insects, including plant-eating crop
pests. Non-engineered Bt concentrate is allowed inorganic production as an insecticide.
For decades, researchers have applied genetic
engineering techniques to try to expand the ways
Bt bacteria can be used as a pesticide. In fieldtrials beginning in the 1980s and continuing to thepresent, Bt proteins have been moved into othertypes of microbes, including bacteria that live
on different plant species and different parts ofplants than Bt, which would expand the scope of
application.87 Some of these engineered bacteria
are more durable than Bt, better surviving contact
with UV light, temperature and other organisms
in the field.88,89,90,91 In field tests on corn, cabbage,
cotton and legumes, the engineered bacteria
achieved 40-80 percent control of a wide range ofpests that could not effectively be targeted withnatural Bt treatments.92,93,94 Bt strains were also
genetically engineered to have additional toxinsfrom other subspecies of Bt in order to target
a wider variety of insects, and even to make Bteffective against fungi.95,96,97,98,99 This academic
work has been successful in producing functional
Bt toxins in a variety of organisms. However, there
are no documented attempts to commercialize thistype of engineered microbe.

Figure 7:
Bacteria targeted
for genetic
engineering
The white mass isthe fungus Beauveria
bassiana, which infects
and kills insects suchas this stinkbug,
and is used as abioinsecticide in organicand conventional agriculture. Scientists have tested anengineered strain of the fungus with Bt toxin to augment its
pesticidal effect.
20

Within a few years of the first experiments withengineered Bt microbes, researchers, including
those at major pesticide companies, turned toward
genetically engineering crops to express Bt toxin
throughout their tissues. Genetically engineered
Bt corn and cotton were introduced in 1996 by
Novartis and Monsanto, respectively. Today, 80
percent of corn and 85 percent of cotton grownin the U.S. are genetically engineered to express
Bt. While these GE crops were associated with an
initial decrease in the use of insecticides, data show
populations of key pests developed resistance,
undercutting the initial success and contributing
to the ‘pesticide treadmill’ discussed above.100
This result is not surprising given that planting
GE Bt crops in vast monocultures increases pests’
exposure to the toxin, speeding the development ofresistance; scientists warned of this outcome at theadvent of this technology.101
Wild fungi are a common component of
biopesticides that do not involve genetic
engineering. Beauveria bassiana is a fungus which
naturally attacks insects and is used as a popularbiopesticide in its natural form. Researchers haveattempted on many separate occasions to engineer
Beauveria by adding genes for environmental
durability, insect toxicity and degradation ofmolecules in the insect’s shell.102,103
There has also been research on engineeringviruses to act as delivery systems for proteinsor molecules that could kill agricultural pests.
The most prominent such example is the use of
baculoviruses that specifically infect insects but
not vertebrates or crustaceans. Researchers added
genes to attempt to make these viruses more
toxic to their target pests, such as arachnid venom
proteins or genes that affect insect developmental
hormones, so that pest insects that feed on a plant
treated with the virus quickly die.104 As mentioned
above, concerns have been raised about geneticallyengineering viruses given their potential persistence
and ability to infect a wide range of hosts, and noengineered virus has neared commercialization.

Making pathogens less harmfulSome research focuses on genetically engineering
plant pathogens in attempts to make them lessharmful or even beneficial. Pseudomonas syringae,
unlike its beneficial relatives, is a plant pathogen
which has been the subject of engineering to
produce less-harmful strains that can displace thewild population of P. syringae.
Another application sought to address a fruit tree
disease called fireblight. Researchers from the

University of Pennsylvania produced a less virulent
mutant of the bacterium that causes the disease
through gene deletion. In 2018, they inquired
to the USDA whether coating trees with the
mutant to suppress colonization by its pathogenic
wild relative would be subject to government
regulation.105,106 The USDA determined that theengineered bacterium was subject to regulation notbecause of the genetic modification, but because
the weakened pathogen was nevertheless still apathogen. The modified bacterium has been thesubject of continued academic work but there havebeen no further attempts at application.107,108
In the early 2000s, researchers made a geneticallymodified microbe system to control a diseasein grapes called Pierce’s Disease that occurs
when insects transmit a pathogenic bacterium
to the vascular system of plants. The researchers
added a protein which targets and suppresses
the pathogenic bacterium to a different speciesof benign bacteria that naturally lives inside plantveins. When the insects fed on plants treated withthe engineered bacteria, instead of transmitting
the disease to the plants, as the engineeredbacteria that were inside the plant were eaten, they
prevented the pathogen from being transmitted
by suppressing it within the insects’ digestivesystems. Small-scale field studies of this microbe
were approved by EPA, but it was not specificallyintended for commercialization and has never been
publicly available.109,110,111 Pierce’s Disease remains amajor problem in grape farming and is controlled
primarily by spraying insecticides to kill the insects
that carry the disease.
Pathogenic fungi have been engineered to makeharmless or less harmful strains that could displace
their wild relatives. This has been done, notably,with the chestnut blight fungus through both directengineering and use of a virus that infects thefungus.112,113
In another example, researchers at the Universityof Kentucky gene-edited Epichloe coenophiala,a beneficial fungus that lives inside the tissuesof grasses. The fungus protects grass fromenvironmental stress but also produces protective
chemicals called ergot alkaloids. These chemicals
can damage livestock that eat grass containing
the fungus. The engineered fungus cannot create
alkaloids, and the goal of the research was toinoculate pasture grass with it in order to gain
growth benefits while preventing colonization by
the wild, toxic strain that would harm grazing farmanimals. USDA determined that the edited fungus
was not subject to regulation, but it has not beencommercialized.
21

Making microbes ‘easier to handle’
Industry actors have also expressed significant
interest in using genetic engineering to makebiologicals “easier to handle.”114,115 This means finding
ways to produce them in large volumes, package
them and add them to tank mixes of pesticides andfertilizers.116,117,118,119 This can include providing genesthat enable microbes to grow on a wider range offeedstocks or tolerate a higher density of culture.
This is already commonly done with industrial
microbes outside agriculture (e.g. for medicine,
biofuels, synthetic chemicals) and in academic
research, though no microbe carrying this typeof modification has yet reached the public as an
agricultural product.120,121,122

Table 1: Commercially available GE microbes in agriculture
Developer
Pivot Bio

Product
Proven®
Applied infurrow during
planting.
Available forcorn, wheat
and sorghum.
In 2022,three related
products werereleased.

BASF(originallydevelopedby Bayer)

Poncho® /Votivo® 2.0
Appliedas a seedtreatment.
Available forcorn, soybeans,sorghum andcottonMicrobeGoal

Regulation

Kosakonia
sacchari andKlebsiellavariicola

Nitrogen fixation — thecompany gene editedsoil bacteria to eliminate
the ‘off switch’ on the
microbes’ process for
fixing nitrogen; thus they
continue to fix nitrogeneven in high-nitrogen soil
conditions.

In 2020, the USDA
determined that the
product is not regulatedby the agency because
the wild form of thebacterium is not aplant pathogen andthe engineered form
contains no foreign DNA.
The publicly available
form of the USDA letteris heavily redacted.

Bacillusthuringiensis

Plant protection — thecompany engineereda bacteria to express a
foreign protein which
produces an enzymethat aids in converting
dead plant residues inthe soil to sugars toencourage soil microbialactivity with the aimof increasing nutrient
availability for plants.

As a ‘biostimulant’ thegenetically engineered
component of Poncho®
/ Votivo® 2.0 faces
far less oversight andtransparency thana biopesticide. Few
documents on theregulatory history are
publicly available.

22

Table 2: Examples of GE microbe research & development in agriculture
Applications submitted to USDA
Developer

MicrobeSummary

Regulation

West
Virginia
University

Cryphonectria
parasitica –invasive fungal
pathogen
responsible forchestnut blight

Researchers engineered
an invasive chestnut blightpathogen to be less virulent
and less harmful to wild native
American chestnut trees.

In 2020, the USDA* determinedthat although the engineered
fungus is less pathogenic thanits wild parent, it remains aplant pathogen and is therefore
subject to regulation.

FoliumScienceE. coli bacteria

The company engineered
E. coli to transfer DNA topathogenic Salmonella bacteria
containing instructions for
CRISPR gene editing that cause
the Salmonella to destroy its
own cells. Chickens fed theengineered E. coli were clearedof the pathogen in this way.

In 2020, the USDA determinedthat this product is not
regulated by the agency
because it is not a plant
pathogen, but the product issubject to regulation by FDA
and EPA.

UniversityofKentuckyEpichloecoenophiala –beneficial fungus
that lives inside
tissues of grasses

Scientists gene-edited a fungus
which helps grass grow sothat it was unable to produce
chemicals that can harm grazing
animals that eat the grass.

In 2020, the USDA determinedthat the edited fungus was not
subject to regulation.

Penn
State
University

Erwinia amylovora– pathogenic
bacteria
responsible forfruit tree disease
fireblight

Researchers deleted a genefrom a fruit tree pathogen. The
engineered bacterium was lesspathogenic than its wild relative
and was intended to prevent
disease by displacing its wild
relative.

In 2018, the USDA determinedthat the engineered bacteria
remained a plant pathogen
for regulatory purposes andthe researchers would be
required to submit a full permit
application to conduct the fieldtrial.

Researchers used gene editing
to create mushrooms thatbrown less when cut and last
longer in storage.

In 2016, the USDA determinedthat the engineered mushroom
was not subject to regulation
because its wild form is not aplant pathogen, and although
genetic components of plantpests were used transiently inthe engineering process, noforeign DNA remained in the
final product.

Penn
State
University

23

Applications submitted to EPA
University
of Florida,
Southern
Gardens
CitrusCitrus tristeza
virus

Researchers collaborating witha private orange company
engineered the Citrus Tristeza
Virus to deliver antimicrobial
genes to orange trees which
they hoped would protect thetrees from bacterial diseases.

In 2011, the EPA under FIFRA**
Determined that the researchers
were permitted to conduct fieldtrials.

Universityof Maryland

Metarhizium
anisopliae –fungus that
attacks insects

Researchers engineereda fungus which attacks
insects and is already used
for biocontrol of plant pests
to produce a component ofscorpion venom.

In 2007, the EPA determined
under FIFRA that the
researchers were permitted to
conduct field trials.

UniversityofCalifornia
Riverside

Alcaligenes
xlyosoxidans– bacteria thatcoexists withplantsResearchers inserted a red
fluorescent protein into thebacterium. The goal of the redcolor was to be able to detect
the engineered organism in
the environment if it was usedin future applications to help
control disease.

In 2005, the EPA under TSCA**
determined that the researchers
were permitted to conduct fieldtrials.

MycogenPseudomonas
fluorescens –plant bacteria

The company engineereda bacterium to produce
insecticidal Bt toxins derived
from Bacillus thuringiensis. Theirgoal was to use the engineered
cells to produce larger amountsof Bt toxin in the lab than B.
thuringiensis can itself produce,then kill the bacteria and apply
it to plants as a more convenientand effective form of Bt.

In 1992, the EPA, under TSCA
determined that the researchers
were permitted to conduct
field trials with the productcontaining the dead GE
bacteria.

* The U.S. Department of Agriculture (USDA) Am I Regulated (AIR) program which reviewed all of these applications was terminated in
2021 and replaced with the Sustainable, Ecological, Consistent, Uniform, Responsible, Efficient (SECURE) rule.)** U.S. Environmental Protection Agency (EPA) Federal Insecticide, Fungicide and Rodenticide Act (FIFRA) and Toxic Substances Control
Act (TSCA)

24

V. Risks and Concerns

Genetically engineered microbes were one of
the earliest topics of debate and risk analysis forengineered organisms before trends in agriculture
moved mostly to engineered crops. Some of therisks raised for these products were very specificand based on underlying knowledge of theindividual microbes. For example, opponents of iceminus bacteria were concerned that its application
could alter rain and snow patterns because bacteria
serve as a natural source of ice crystal formationin the atmosphere (see page 19).76,77 Engineeredbacteria with Bt toxin concerned scientists whoworried the microbes would affect non-target
organisms, such as pollinators, in their new areas ofapplication.123 Neither of these concerns were borne
out, but they illustrate an overarching unique risk inregard to engineered microbes: we fundamentallyknow less about their biology in the wild than we
do about the plants they cohabitate with.

When we attempt to intentionallyalter the microbiome by applying
chemical treatments or inoculatinga field with a new strain of microbe,
there is no guarantee that things will
go as intended. The fine details of
the existing microbial community,
other treatments, and environmental
factors all affect how microbial
treatments work, often in ways westill don’t understand.
When we attempt to intentionally alter the
microbiome by applying chemical treatments or
inoculating a field with a new strain of microbe,
there is no guarantee that things will go asintended. The fine details of the existing microbialcommunity, other treatments being applied, andenvironmental factors all affect how microbial

treatments work, often in ways we still don’t
understand.
It’s possible that widely distributing microbes with‘useful’ functions could enable new and unintended
associations to form with weed or pest species with
unintended consequences for agriculture.
Adoption of biologicals on a scale that matches
the chemical products they compete with will
represent an unprecedented free-air experimentin the release of living organisms. Engineered
microbes will not suddenly turn into virulent
pathogens because they are engineered, but bothengineered and non-engineered microbes may
behave in unexpected ways when they encounternew environments. Although it is not likely thatsuch unexpected behavior will be common either inengineered or non-engineered microbes, we must
understand that “rare events” are real, and their
number is meaningful when we are discussing vast
applications.

Limits of our knowledge &unintended consequences
The gaps in our knowledge and limitations of ourability to predict or control the outcomes of thisnovel technology are profound and varied. The ideathat genetic engineering of organisms is ‘precise’,as manufacturers claim, is not founded in the latest
understanding of genes. The genetic structure oforganisms is now understood to be considerably
more complex than previously thought, and wehave only just begun to explore and understandthe expanse of relationships that regulate genomic
activities.124 A cascade of activities involving a vast
number of cellular processes and multiple stretchesof DNA located both near and far from a particulargene may be involved for a particular action
to take place or to result in a particular trait.125
This complexity is reflected in Pivot Bio’s patentapplication for Proven®40, which lists at least 29
different genes and myriad proteins and enzymes
that can be manipulated to result in changes to thetargeted bacteria’s ability to fix nitrogen.126

25

The patent details methods to “disrupt” and “shortcircuit” the cellular nitrogen sensing cascade and“trick” the cells into perceiving a nitrogen-limited
state. That we can tinker with genetic regulatory
processes does not mean we understand the fullcomplexity of the system or what might happen asa result of our intervention. As an example, a study
published by the developers of Proven® showsthat they were surprised to find that knocking out
two genes (GlnD and GlnE) — which normally playdouble roles of enhancing nitrogen fixation understarvation (soil conditions with little nitrogen) but
repressing it under sufficiency — clearly enhanced
nitrogen fixation, as it could just as easily haveended up reducing it due to the genes’ dual role.56
This suggests that there is more going on than they
understand.

That we can tinker with genetic
regulatory processes does not mean
we understand the full complexity ofthe system or what might happen asa result of our intervention. Genetic
engineering can result in an arrayof unintended genetic consequences,including insertions, deletions,inversions and translocations thatwere not expected.
Genetic engineering (including gene editing
techniques like CRISPR which are often claimed
to be more ‘precise’) can result in an array ofunintended genetic consequences, including
insertions, deletions, inversions and translocations
that were not expected.127,128,129
Further, we have only scientifically characterized asmall fraction of the microbes living in the soil. Of
the billions of species of bacteria, archaea, fungi,
viruses and microeukaryotes below ground, only
a few hundred thousand have been characterized
in detail.1 We have only scratched the surface ofunderstanding the complexity of how they function,interact with plants and shape agricultural and wild
ecosystems.

We have only scratched the surfaceof understanding the complexity of
how microbes function, interact withplants and shape agricultural andwild ecosystems. We do not haveenough knowledge to meaningfully
assess the possible ecologicalramifications of releasing GE
microbes into the environment.
In the case of Proven®, what might be therepercussions of releasing billions of microbes thatno longer have the ability to down-regulate nitrogenproduction across millions of acres? Consider thatplants and bacteria have sophisticated responses
to environmental conditions and to each other — ifyou swamp a legume with nitrogen, it will downregulate colonization of bacteria that fix nitrogenso that it can focus energy on other relationships
and processes. When an organism is engineered
to do something that nature has not designed it
to do — and when that ability may spread to othermicrobes via horizontal gene transfer — we do nothave enough knowledge to meaningfully assess thepossible ecological ramifications.

Ecological risks
Gene containment and lack thereof
Releasing genetically engineered microbes into theenvironment raises serious new questions about
containment of the engineered sequences. This is
for three reasons.

The scale of release
First, the sheer number of organisms released in
an application of genetically engineered microbes
is orders of magnitude larger than our current
experiences with genetically engineered crops.
A field of corn contains about 35,000 plants per
acre.130 A typical application of a bacteria-based
biological will use 1 to 5 kilograms of material
containing a billion cells per gram.131,132 This equates
to the release of up to 5,000,000,000,000
genetically engineered organisms on each acre ofcropland, greater than a hundred million times thenumber we are used to seeing with crops. If every

26acre of corn on earth was genetically engineered,that would be about 17,143,496,298,999 plants.133 A
typical application of a bacteria-based biologicalwould release the same number of geneticallyengineered organisms about every four acres. The
huge difference in scale means we must treat theprobability of rare events differently.

Releasing genetically engineered
microbes into the environment
raises serious new questions about
containment of the engineeredsequences. The genetic modifications
released inside engineered microbes
may move across species boundaries
in unpredictable ways.
Containment is impossible
Second, the complete containment of microbes
to the area of application is impossible. Fungal
spores, bacterial cells and viruses can drift long
distances on air currents, moving across national
borders in a single year.134,135,136 Microbes also
move in groundwater and are transported by the
movement of animals and insects.137 Unlike plants,
microbes are not limited in time or space by sexual
reproduction because they can reproduce clonally.
The spread of individual microbes also cannot be
detected directly even by the most vigilant farmer
or scientist, requiring technological methods tospot and confirm their identity.
On one hand, the scale and ability of microbes
to spread when applied in agriculture is not
because they are genetically engineered — it isbecause they are microbes, and applications of
nonengineered microbes with these properties havelong been accepted. On the other hand, geneticallyengineered microbes will be no easier to containthan their non-engineered relatives, which pastexperience shows is nearly impossible.

Horizontal gene transfer
Third, microbes are capable of horizontal genetransfer — DNA from one organism can beincorporated into the genome of another organism,
sometimes completely unrelated, without sexual
reproduction (see Appendix II).138 As a result, thegenetic modifications released inside engineered

microbes may move across species boundaries
in unpredictable ways. Horizontal gene transfer
can enable genes to move between completely
unrelated organisms and is more likely to occur inorganisms that engage in pathogenic and symbiotic
relationships — the same categories that are ofhighest interest as targets of genetic engineering.139
The question of horizontal transfer is most pressing
for bacteria, which are the greatest target fordevelopment of biologicals and very active inhorizontal transfer. Microbes have key biologicaldifferences that increase the frequency with which
they undergo horizontal transfer.

Tan spot fungus – a cautionary
tale of horizontal genetransfer
Horizontal gene transfer in microbes has
been documented to rapidly change thenature of their interactions with plants. For
example, tan spot fungus disease of wheat,one of the most important diseases in thiscrop, causes yield losses of up to 50 percent
but was not a significant problem prior to1941.140,141 Naturally occurring transfer of asingle gene from the fungus Pheosphaeria
nodorum to its relative Pyrenophora triticirepentis happened around this time andcaused P. tritici-repentis to transformovernight from a neutral member of the
microbiome to the aggressive pathogen thatcauses tan spot disease.142 The pathogenic
strain spread rapidly to become a worldwide
issue within ten years and remains a serious
challenge for wheat agriculture. Cases ofhorizontal transfer like this are gaining
increasing recognition for their role in
the evolutionary history of agriculturally
important microbes.143,144,145,146

Altering microbial communities
The currently available research shows that mostmicrobial treatments in agriculture don’t persist
long-term because they don’t overcome the balanceof local factors that shape the existing microbialcommunity composition. However, research on
non-GE biologicals has shown the possibility for
persistent impacts on microbial communities. Even
when microbial inoculants die off relatively quicky,

27

their application can significantly alter the plant andsoil microbiome by changing the overall diversityof bacterial and fungal species.35,147 This inevitably
disrupts an existing, complex community.148
Most experiments with microbial treatments inagriculture fail to assess the impact and length ofeffect on the native microbiome as a whole.149 Thosethat do show that the effect on other microbes cansometimes be long term, taking months or years
for the native microbial community to return to its
original state after a single treatment.150,151,152 While
this can be desirable for the application, the effecton native microbes cannot be neglected and is not
limited to microbes themselves. Changes to themicrobiome can snowball into directly observablechanges to plant growth and insect communities —and again, these may be different from the intended
effects of the inoculum.153,154
Effects on plant-microbe-insect relationships
are particularly important. Symbiotic microbes
enable many plant-eating insects to survive byparticipating in amino acid synthesis, or enable
them to digest difficult molecules like cellulose fromplant cell walls.155 A beneficial microbe in one areaof agriculture might function differently if it shows
up in the wrong place — for example, bacteria canprotect insect pests from fungal disease in the same
way they protect plants, ultimately increasing pest
populations.155 Or, for example, altered microbialcommunities can degrade agricultural chemicals
like pesticides, therefore enabling pest insects tosurvive.156
Some of the effects of microbiome changes alterfeatures of plant growth that could have major
impacts on wild plants and the communities they
support. Microbe treatments can cause Arabidopsis
and related plants to flower a week sooner in thelab.157,158 A similar effect was seen in field-grown
genetically identical poplar trees, where differencesin the microbiome caused flowering up to ten days
earlier in response to climate change.159 In othercontexts, earlier flowering time has been identified
as a major crisis point for effects of climate change
because it can cause a mismatch between when
flowers form and when pollinators are available
to fertilize them, and consequently when andhow much ripe fruits and nuts of wild plants areavailable. These effects trickle up into how many
insects, birds and mammals can be supported by
the ecosystem. 160
Microbiome treatments can affect the growthof trees and other long-lived plants just as they
do crops and annuals. Just as in other cases, theeffect of microbe treatment can last long after the

microbiome has returned to normal, and this canbe magnified in trees and perennial ecosystems:
an effect that changes which seedlings survive to
become established over a few early months oflife could be sustained for hundreds of years — thewhole lifetime of those trees.

Invasive species provide a
cautionary tale
The plant microbiome is already known asa warfront in the establishment of invasive
species that should provide cautionary
examples for the power of the microbiome
to drive environmental harms as well as
benefits.161 The invasive plant garlic mustard(Alliara petiolata) secretes chemicals thatkill off or repel the mycorrhizal symbionts
of native plants.162,163,164 This not only harms
the native plants by reducing their accessto nutrients, it increases the availabilityof soil nutrients to nonmycorrhizal plants
like garlic mustard, providing a double
competitive advantage in taking over native
ecosystems.165,166,167 Another invasive plantin desert habitats of the Americas andAustralia, buffelgrass (Cenchus ciliaris) does
the opposite: it shapes its own specialized
microbiome with many beneficial bacteria
and fungi and uses these associations tooutperform and outgrow native species.
168
Even the nitrogen-fixing symbiosis
of legumes considered so beneficial insustainable agriculture is, in other contexts,
a way for weeds from this family to better
invade new areas.169

Finally, the wild microbiome itself deservesconservation. Even if there are no ‘aboveground’
effects, altering the structure of a community
with thousands of native, potentially rare or even
undiscovered species, should not be taken lightly
just because these organisms are small. Even therare chance of a foreign, agriculturally applied
microbe becoming permanently established in thewild environment is a serious concern due to theways it may then influence other relationships andeven the structure of whole ecosystems. While
such effects might be counteracted in the heavily
managed agricultural context, there will be little
ability to do so in wild systems.

28

The pesticide treadmill
As with chemical pesticides, pest resistance is a
critical concern. Since the advent of widespreaduse of chemical pesticides, hundreds of insect andweed species have developed resistance. In thehistory of chemical pesticides, social pressure andeconomic profit-seeking have driven their use inways that reduce, rather than prolong, their useful
lifespan and lead to higher doses, additional toxic
pesticides and combinations of toxic pesticides tomanage resistant pests, in a process often referred
to as the ‘pesticide treadmill’.50,170 Geneticallyengineered crops have played a massive role inentrenching the pesticide treadmill. Currently, 98.2
percent of all genetically engineered crop acreagein the U.S. is devoted to herbicide-tolerant crops,
primarily Roundup Ready corn and soy that areengineered to withstand the application of BayerMonsanto’s Roundup (aka glyphosate) and otherharmful herbicides.171 As noted above, ‘superweeds’
resistant to Roundup now plague over 60 million
acres in the U.S.
If microbes are used within industrial monoculture
agriculture systems to suppress insects or otherplant-pathogenic microbes, there is no reason
to think that the same concerns of resistancedevelopment that apply to chemical pesticides
would not apply (see page 16). Some microbial
products with multiple modes of action may beprotected from resistance for longer than chemicaltreatments but are not otherwise unique. If we are
driven to adopt engineered microbes as a resultof the chemical pesticide treadmill, we should notassume new, biological technology will produce
better outcomes unless we learn the lessons of thepast and shift toward ecological, systems-based
approaches to managing pests.

Action needed – A moratoriumon ‘guided biotics’
While there are reasons to be concerned
about unintended horizontal gene transfer,developers are also exploring technologythat intentionally increases the horizontaltransfer of transgenes. In essence, thisconstitutes an organism that indiscriminately
genetically engineers other organisms.
For example, the ‘guided biotics’ systemdeveloped by Folium Bioscience usesbacteria that are designed to widelytransmit DNA encoding a CRISPR-Cas
system to other bacteria. When the system
is transmitted to a specified harmful
microbe, the target bacterium expresses a
CRISPR construct that destroys an essential
piece of its own DNA, killing it. The safety ofthe technology relies on the assumption thatwhen transmitted to non-target species thesystem will neither persist nor create geneedits. However, there is a significant historyof off-target editing in CRISPR that indicatesthe specificity of this system is unlikely tobe perfect, especially when used at large
scale. This system shares properties withgene drives, which have been treated withmuch more trepidation than other types ofgenetic engineering. The UN Convention on
Biological Diversity has essentially imposeda moratorium on release of any gene drives
worldwide.172 A similar moratorium should beplaced on guided biotics.

If we are driven to adopt engineered microbes as a result of the chemical
pesticide treadmill, we should not assume new, biological technology willproduce better outcomes unless we learn the lessons of the past and shift
toward ecological, systems-based approaches to managing pests.

29

Human health risks
Novel pathogens
Microbes, like sprays of agricultural chemicals, cantravel long distances quickly. While agrichemicals
raise serious health concerns when they do this,they cannot reproduce or become infectious. We
should consider the prospect that in rare cases,
genetically engineered microbes could become
human or animal pathogens. Opportunistic
infections occur from microbes that are notnormally considered pathogens when certain
conditions are met — such as encountering
immunocompromised individuals or co-infection
with specific other microbes. The soil microbiome
is a known source of some of these pathogens,including members of genera that are targeted
for use in agbiotech, such as Pseudomonas andOchrobactrum.173 Engineering these organisms forfaster growth may make them more able to growpathogenically.174

Figure 8: A human eye infected with
Beauveria bassiana
Beauveria bassiana is the agriculturally beneficial
fungus shown attacking a stinkbug in Figure 7. The
patient was a 76-year-old farmer with a number ofunderlying conditions.

Antibiotic resistance
Antibiotic resistance — when germs, bacteria andfungi have developed the ability to withstandthe drugs applied to treat them — is an urgent
worldwide public health crisis. Antibiotic resistancemarkers are commonly used in the developmentof transgenic organisms. Scientists often add
genes that code for resistance to antibiotics liketetracycline, ampicillin and others during genetic
modification so that the GE organisms and cells canbe distinguished from non-GE ones. While the riskof antibiotic resistance from transgenic organisms
resulting in resistance in human pathogens has
been substantially investigated and found to be low,
the use of antibiotic markers in microbes that might
directly become human pathogens casts theirpresence in GE microbes in a new light. Figure 8,
for example, shows a rare incidence of infection of ahuman by Beauveria bassiana, a fungus that is used
as a biocontrol and has been used for engineeringexperiments.175,176,177 This patient’s infection was
susceptible to only two of nine tested antibiotics.178
Had this been a genetically engineered fungus
expressing an antibiotic resistance marker, theoutcome of the case may have been affected. The
same would be true if the fungus were engineered
to express spider venom to increase its effectagainst insects, as has been tried before.

Immunosuppression andopportunistic pathogens
Given that the present trend in GE biologicals
development involves co-integration with synthetic
chemicals rather than complete elimination,
the real-world scenario of application includes
a potentially grim intersection of factors. First,
multiple pesticides that are in active use today
have been noted to have immunosuppressive
effects on wildlife, livestock and humans near
farms.179,180,181,182,183,184 Thus, we should not rule out
the possibility that deployment of biologicals inthe same locations as chronic pesticide use could
be a very real intersection of microbes that might
become opportunistic animal pathogens and thetypes of individuals that are susceptible to such
infections. A special factor for people living in
agricultural communities is that, subsequent to
the epidemiological incidence of high cancer rates
among pesticide applicators, the same people
who apply and live near potential sites of microbe
application are more likely than the rest of the
population to have medically suppressed immune
systems due to treatment for cancer.185,186,187,188,189,190
Evaluation of pathogenicity is not currently an
explicit aspect of approval for GE or non-GE
biologicals, but should be included in future
regulation as microbial products become morecommon.

30

Consumer exposure and the humanmicrobiome
Separate from the question of pathogenicity, it
should be assumed that while most microbial
treatments are transient and die off while crops
are still in the field, as use of GE biologicals grow,some amount of engineered bacteria will come into
contact with consumers via the food supply. The
overall risks of these live bacteria causing healthproblems is very low relative to food processing andanimal factory farming, which are dominant sourcesof foodborne illness.191,192 However, the obvious
concern is for impacts on the human microbiome.
Some companies like Folium and Pebble aredeveloping engineered microbes explicitly intended
for animal feed to alter the animal microbiome byproducing CRISPR-Cas or RNAi constructs thattarget harmful bacteria (see page 29). It should
be assumed that if they come in contact withhumans, these microbes will continue to live andcarry out their intended job, but with potentiallyunknown effects on new species of bacteria orbacteria that play different roles in the humanmicrobiome compared to animals. Evaluation of
low-level exposures from food residue in humancell and microbiome models would be an essentialconsideration to guard against risks from this typeof exposure.

Socioeconomic risks
Since the commercial release of geneticallyengineered microbes in agriculture is so new,
we don’t yet know how companies’ intellectual
property rights to these products might impact
farmers and other stakeholders in the food system.
However, the history of agrichemical giants’ use of
intellectual property rights related to GE crops topursue predatory lawsuits against hundreds of small
farmers should raise important red flags.193

evidence of genetic engineering. Companies could
potentially engineer genetic ‘tags’ into GE microbesthat could allow them to screen for them without
trespassing on farmers’ fields, for example showing
up under UV light. Microbes are prolific and readilytransfer genetic material with each other, making the
likelihood that they will rapidly spread to neighbor’s
fields nearly guaranteed. Would a company be able
to legally enforce their intellectual property rights
to the microbes or genetic constructs that havedrifted or that remain in a farmer’s field long after
application? Although it seems far-fetched, weshould not rule it out as a possibility.
Of note, the high likelihood of genetic drift also
poses a threat to organic farming systems, whichby law prohibit the use of GE organisms. As theorganic farming community has argued in the caseof genetically engineered crops, the burden for
dealing with the outcomes of genetic contaminationof organic fields should be on the manufacturers of
GE organisms.194
Another socioeconomic concern is the way
consolidation within the industry may shapeinnovation.195 In addition to patenting GE microbes,
companies can also patent the methods ofproducing a genetically engineered organism.
For example, Corteva holds a patent for aprocess modifying the genome of a cell using
CRISPR techniques and claims the intellectual
property rights to any cells, seeds and plants that
include the same genetic information, whether
in broccoli, maize, soy, rice, wheat, cotton, barleyor sunflower.196 The already apparent trend of
consolidation with the biologicals market, as major
agrichemical companies buy up smaller biotech
companies and acquire patents on research anddiscovery processes, may narrow the scope ofinnovation in this sphere, further entrenching the
economic interests of powerful corporations overthe public good.

In the U.S., microbes cannot be patented unlessthey are genetically engineered. Companies canpatent products containing non-engineered
microbes if they demonstrate that the formulation,
as a whole, meets the criteria for a patent (suchas novelty, usefulness, and being a compositionof matter that does not occur naturally without
human intervention). But the microbes in thoseformulations are not patented.
Thus, companies patenting engineered microbes
potentially have different opportunities to enforce
their intellectual property rights. In theory, it would
be possible for a company to test a farmers’ soil
for the presence of one of their GE microbes in thesame way that they have tested farmers’ crops for31VI. Policy context

The regulations, norms and strategic alignmentsthat we have developed over decades of debate
about genetically engineered crops must be
reexamined and supplemented for application to
genetically engineered microbes. GE microbes do
not fit neatly into past experience with genetic
engineering. While their usage involves releasing
tremendous numbers — trillions — of GE organisms,
they are mostly invisible. Unlike engineered crops,
they include species that have only recently
become known to science. GE microbes areunlikely to be contained in any meaningful senseand cannot be tracked except by methods that
require laboratory analysis. In addition to a robust
regulatory process governing all GE microbes
developed for use in agriculture, case by caseconsideration of the unique features of each new
GE microbe proposed for use in agriculture should
be required.

Summary of current regulatory
systemThe current regulatory system for GE microbes is
confusing and inadequate. We must make sure thatapplications of engineered microbes aren’t assumed
to be acceptable — let alone beneficial — simply
because they are approved faster than we canunderstand them.
All of the systems described below have extremely
poor transparency (see page 7). Submitting entities
are able to redact almost all details from public viewin most regulatory filings under the self-designationof ‘Confidential Business Information.’ This may
include the engineered gene and even the type oforganism. Even these redacted records are difficult
to access and not clearly identified with the end
products in which they appear.

U.S. Environmental Protection Agency
Pesticidal microbes
Any microbe that acts as a ‘biopesticide’ must be
approved by the U.S. Environmental Protection
Agency under the Federal Insecticide, Fungicide,and Rodenticide Act (FIFRA). The EPA Office ofPesticides Programs has a specific division that is
responsible for all regulatory activities related tobiologically-based pesticides, the Biopesticides and
Pollution Prevention Division. Of note, the EPA’s
definition of ‘biopesticides’ does not align with thecommon use of it to refer to biologicals, it includes
gene-silencing RNAi pesticides and crops that havebeen genetically engineered to incorporate a ‘plant
protectant’ (the most prominent being Bt).
The EPA does not have specific regulations
that take into account the unique properties ofgenetically engineered microbes. First, the samegeneral authority and standards used for chemical
pesticides apply to microbes with pesticidal
qualities, both GE and non-GE. Second, theEPA makes clear that it does not have specificregulations pertaining to GE microbes. The agency
states that, aside from requiring data on the genetic
engineering process used and the results of thatprocess, GE microbial pesticides are regulatedusing “essentially the same data requirements
used for naturally occurring microbial pesticides.”Under FIFRA, the EPA approves field trials andExperimental Use Permits of any scale for any sortof pesticide, including microbes. Unlike regulators inmost countries, the EPA does not ask for field data
demonstrating the efficacy of any new pesticides
before approving them.

32Unlike regulators in most countries,
the EPA does not ask for field data
demonstrating the efficacy of new
pesticides before approving them.

GE microbes that contain foreign DNA(transgenic) and may or may not bebiopesticides
The EPA also has authority under the Toxic
Substances Control Act (TSCA) to regulate any“new substance” which has been applied to include
GE microbes that contain a gene from a different
genus of microbe, regardless of their function. GE
microbes that function to improve plant growthor perform other non-pesticidal functions are
regulated through TSCA. The components of TSCA
review, however, are vague and include no specificstandards or required information.

U.S. Department of Agriculture
GE microbes that do not contain foreign
DNA (i.e. gene-edited) and are notbiopesticides
Many microbial products are not used as
biopesticides or have a function that is hard toplace under a single category. Many such microbes
fall through the cracks of current regulation. For
gene-edited microbes that are non-pesticidal,
neither FIRFA nor TSCA apply.
In the past, some gene-edited microbes wereconsidered by the U.S. Department of Agriculture(USDA) under the Plant Pest Act through a process
called “Am I Regulated” (AIR). Those reviews almost
always concluded that the edited microbes were
exempt from regulation due to the nature of theengineering method.20 As of 2021, the AIR program
was terminated and replaced with the Sustainable,
Ecological, Consistent, Uniform, Responsible,
Efficient (SECURE) rule, which exemplifies thefederal government’s deregulatory trend toward
biotechnology. SECURE codified several exemptions
from regulation that could apply to geneticallyengineered microbes. One such exemption
for certain gene-edited organisms is such thatdevelopers can self-determine exempt status andcommercialize a microbe without any oversight(though USDA still provides a voluntary exemptionconfirmation process).208 USDA retains the ability
to regulate microbes that it deems a plant pestrisk, but under SECURE, the agency moves
from applying default data-based review of any
genetically engineered organisms to making ad hoc
decisions about the need and scope of examination
required for any product.209

The need for a system to track
the spread and impacts of GE
microbes
Each application of genetically engineered microbes
in the field essentially constitutes an uncontained
environmental release. Once GE microbes are usedin field trials or released commercially, there is no
program dedicated to surveilling the extent of theiruse or re-evaluating their safety over time. However,methods to evaluate changes to the microbiome are
effective and accessible within the scientific system,
including metagenomics and metabolic profilingnow offered as off-the-shelf services by universities
and commercial scientific providers.149,197,198,199 Making
use of these methods would involve mandating
their inclusion in safety studies for regulatory
agencies.200
In the absence of federal action, scientists, farmers
or members of the public may be able to submit
samples of soil and track changes caused by new
treatments. State-level programs and citizen sciencestudies have already been designed which enable
members of the public to collect microbiome
samples which are analyzed and made available inpublished research.201,202,203 Such programs could
analyze DNA sequences against a genetic database
containing known genetic engineering tools or
screen microbes for inserted genes that are often
used in laboratory research, such as antibiotic
resistance markers.204,205 However, the efficacy ofsuch efforts will be severely limited in the absenceof formal coordination and transparent standards.
Each environmental microbiome sample is a single
snapshot of a jumble of all microbial genes present
at that place and time; special analysis tools areused to identify the species and genes of interest
that are there.206 Some genes and mutations, likecommon laboratory markers, are cataloged in public
databases and are easy to find, but proprietarychanges that developers have not shared are
extremely hard to find without advance knowledgeof what they are.207 Even when a particular modified
microbe can be confidently identified, actuallyknowing where it is in the world requires constantsampling of even unexpected locations in order tofollow its spread.
33

A system for monitoring the spread and impact of
GE microbes once released into the environmentand re-evaluating their safety over time must be
established.

Understanding how engineering
techniques shape potential risks
Evaluating the potential for horizontal
gene transfer
Not every type of genetic engineering will affectwhether a microbe is likely to undergo horizontaltransfer when it leaves the lab, but some might.
Key factors that affect the likelihood of transfer are
the method of transformation, the nature of theengineered trait and whether stabilizing chemicals
or surfactants are used. Regulators could use thesecriteria to help determine potential risks on a caseby-case basis.

Methods of transformation
Biotechnology often uses plasmids, small circularmolecules of DNA, to move transgenes around.
Genes contained on plasmids are more likely tocontinue undergoing horizontal transfer than thosein the main genome.139,208 Genetic engineering may
also make use of transposons or recombinaserecognition sites to assemble and insert DNA
as desired. These are short DNA sequences thatflank a gene of interest and make it easier tomove in and out of the genome. However, via thesame mechanisms that make them useful, thesesequences can make the genes associated withthem more likely to undergo horizontal transfer
later on.209,210,211,212

Nature of the engineered trait
The nature of the engineered trait can also be an
important predictor of whether a modified geneis likely to have a biological effect in other species
and/or spread through a population following
horizontal transfer. If the modification enhances
the natural tendencies of a microbe that carries
out a rare function, moving any one gene fromthat microbe into another is not likely to have ameaningful biological effect because the function
is dependent on interaction with the rest of thenative genetic context. Consider the analogy oftaking a spring from a fancy watch and putting it ina toaster; outside its interaction with all the othercomponents of the watch, the spring does not
move the toaster towards being able to tell time inany way.
An example of an engineered microbe withmultiple features that lessen its risks as a sourceof horizontal transfer is a gene edited fungus
Epichloë coenophiala produced by researchers at
the University of Kentucky. Epichloë naturally lives
inside grasses that belong to the fescue family
commonly found in pastures and residential lawns.
Epichloë has many benefits for the grass, making
it resistant to pests, drought and stress. However,this beneficial fungus also produces toxic chemicals
called ergot alkaloids. In nature the alkaloids
probably help protect the grass from herbivores,
but in agriculture they can have serious toxic effects
on animals that graze on the grass. The researchers
gene-edited the fungus to delete two regions of
the genome containing several genes that enable itto produce the alkaloids, rendering it and the grass
it lives in nontoxic to livestock while keeping the
growth benefits. Because the organism is a fungus,
it is overall less likely to undergo horizontal transfer.
Because the modification made was a complete
deletion, there is no new protein-coding sequencethat could be transferred to another organism. Even
if the developers made an error in characterizing
the engineered fungus or if some of the remaining
sequence retained an effect related to alkaloids,
the transferred gene would be unlikely to bebiologically relevant in most of the organisms that
could receive it via horizontal transfer, including its
host grasses, because they lack the other biologicalmechanisms of alkaloid synthesis that would put
the transferred gene in a functional context.213

Use of stabilizing chemicals andsurfactants
The use of stabilizing chemicals and surfactants(agents that reduce surface tension) cansignificantly change the likelihood of horizontaltransfer. Biological products that are mixed together
before, during, or by sequential application are
also prime opportunities for horizontal transfer tooccur. For example, in a universally used laboratory
method, the plant pathogen Agrobacterium is able
to transfer its DNA to the ovules of Arabidopsis
at high levels upon contact with its flowers — but
only in the presence of Silwet L-77, a surfactant
which is also commonly used as a wetting agent inagricultural sprays.214

34

Figure 9: Factors influencing the likelihood of horizontal gene transfer in genetically 		
modified microbes

35VII. Policy Recommendations

The information in this report supports adopting
the following principles in policy, advocacy andregulation of genetically engineered microbes
intended for use in agriculture.

1: Recognize that engineered microbes
are novel
GE microbes for use in agriculture do not fit neatly
into past experience with genetic engineering.
Unlike GE microbes used in industrial processes,
they are not contained. Unlike GE crops,
they include species that have only recently
become known to science. GE microbes foruse in agriculture are unlikely to be contained
and cannot be thoroughly tracked except byadvanced laboratory methods combined withsystematic environmental sampling of public andprivate land. The norms, regulations and strategicalignments that we have developed over decadesof debate about GE crops must be reexamined andsupplemented for application to microbes.

2: Distinguish genetic engineering from
biologicals in general
GE microbes are a small fraction of microbial
applications in agriculture. There is no general
requirement to use genetic engineering for
microbes to be useful, and some microbial
technologies are ancient and grounded in
traditional agricultural knowledge. Geneticallyengineered microbes should be evaluated in a
way that assesses the specific contribution ofengineering.

3: Define genetically engineered
microbes inclusively
In the realm of GE crops, there is a history of
exemptions for certain types of genetic engineering,such as gene editing. Even if the reasons given forthese exemptions are accepted, they do not apply
equally to microbes. Microbes engage in a widearray of genetic functions that are not found inplants and animals. Legalistic exemptions based onwhether the outcome of genetic engineering could
conceivably be ‘natural’ should not be permitted.
Any microbe that has been subjected to direct

manipulation of its DNA should be subject toregulatory review.

4: Initiate a rulemaking on field trials vs.
contained testing
The EPA and any other potential regulators should
initiate a rulemaking on the extent to which
field trials of genetically engineered microbes
constitute an irrevocable environmental release. In
acknowledging that full containment is unlikely to
impossible, agencies should develop protocols for
rigorous monitoring of the spread and effects of GE
microbes.

5: Prevent containment failure from being
used as a weapon of economic coercion
The tendency of genetically engineered crops
to escape their fields and show up elsewhereis nothing compared to microbes that cancross national boundaries on an air current.
Acknowledging that full containment is essentially
impossible, developers and users of GE microbes
must not allow escaped self-replicating microbes toharm others’ crops or, worse, to force adoption of
the technology.

6. Place a moratorium on any field testingof ‘guided biotics’ applications
Guided biotics refers to the development of
GE microbes that are intended to propagate
and transmit engineered DNA — organismsthat indiscriminately genetically engineer otherorganisms. This system shares properties with gene
drives, which have been treated with much more
trepidation than other types of genetic engineeringand should be subject to similar concern.

7: Require greater transparency
Lack of transparency on the part of federal
regulatory agencies is an overarching, urgent
problem for how we evaluate and oversee productsof biotechnology, including GE microbes. Far
greater transparency is fundamental to our ability
to grapple, as a society, with the potential risks andbenefits of this novel technology.
36

8: Use a precautionary approach
Regulatory bodies should use the Precautionary
Principle to guide action, meaning that
precautionary measures to minimize or avoid
threats to human health or the environment should
be taken based on the weight of the available
scientific evidence rather than waiting for fullscientific certainty about cause and effect, which
can take years or decades while harm accrues.
The Precautionary Principle also elevates theimportance of a full evaluation of safer approaches
before moving ahead with a potentially risky newtechnology. Oversight should include independent
assessment for public health and environmental
safety, and long-term impacts should be assessed
before products are released onto the market or
into the environment. The Precautionary Principle
also guides the incorporation of public input into
decision-making processes, as the impacts of newtechnologies such as GE microbes in agriculture
will be borne by society as a whole. In addition,socioeconomic concerns arising from the expansionof corporate property rights over microbes must be
incorporated into decision-making before products
are commercialized.

37

Appendices
Appendix I. Methods ofgenetically engineering microbes
A. Gene insertion
Gene insertion is the process of adding a pieceof DNA to a microbe. The genetically engineered
herbicide tolerant (e.g. Roundup Ready) and insect
resistant (Bt) crop plants that make up the majority
of corn and soy acreage in the US are mostly the
result of gene insertion. Usually, the new DNA
contains instructions for one or more proteins. The
proteins may have a direct function — for example,
the Cry proteins found in Bacillus thuringiensis are
responsible for its insecticidal activity — or may
carry out chemical reactions, such as nitrogen
fixation. In microbes, unlike plants, the DNA may
be inserted as part of a plasmid, a piece of circular
DNA that is permanently incorporated into themicrobe but stays separate from its genome. DNA
may also be inserted directly into the genome, as
has been done with engineered plants.
When DNA is integrated into the genome,
processes called site-specific recombinationand homology-directed repair are commonlyused to try to control the precise location of thetransgene. The use of these methods are much
more common and effective in microbes than inplants. Genes must also be inserted with (or in asite containing) promoter and terminator DNA
sequences; these are responsible for directing when
the gene is expressed and are extremely importantto successful applications of transgenic microbes.
Promoter activity is generally lost or changed
across organisms as they become less closely
related to the one where the promoter originated.
A former barrier to moving genes across unrelatedorganisms was access to the donor sequence, as well
as something called codon optimization. The versionof the genetic code (or ‘codon usage’) varies acrossspecies, and genes may not be made into proteinsif there are large differences between the donor andhost organisms. In even the recent past, obtaining
a specific DNA sequence from an organism, andaltering its codon optimization, were both significant
undertakings that required access to quality samplesof the organism and a lot of time in the lab.

However, gene synthesis has now become widely
available. In gene synthesis a DNA sequence ismade from raw materials by a lab or company
rather than extracted from the donor organism.
This effectively allows genetic engineers to order
up any gene sequence from any organism on
demand, with codon optimization for any target
organism. Gene synthesis also makes genetic
components more accessible; a piece of DNA
encoding the fairly large Cry1a protein from Bt thatis found in many transgenic plants, can be obtained
for about $250 from any of several synthesis
companies, with a production time of about 1 week.
Gene synthesis is now an integral component ofindustry R&D programs, where large numbers ofgene-promoter combinations go directly fromcomputational design to synthesis and insertion
into microbes, without requiring individual designand construction.

B. Gene editing
Gene editing is the process of targeting a sequenceof DNA in the microbe and altering or removing it.
This process uses CRISPR-Cas complexes or othersequence-specific enzymes that cut DNA. Editing
can cause random mutations at the targeted site,or it can lead to a prespecified small change inthe DNA there, depending how it is done. Editing
is now a prominent method in biotechnology. To
edit a gene, the machinery of the editing system
is introduced into the microbe as either DNA orprotein, then removed once the targeted edit has
been achieved.
Editing does not necessarily mean that the targeted
gene is removed. A common tactic, for example
used in the construction of Pivot Bio’s nitrogenfixing bacteria, is to edit a gene’s promoter orproteins that interfere with its expression, rather
than the protein-coding sequence itself. The
expression of the target gene can be increased bythis type of editing as well as decreased. Editing
can also change the function of a gene rather
than destroying it. For example, it is possible
to make glyphosate-resistant corn by editing asingle base pair of an enzyme found in the plant,
which changes the structure of the protein madeby that gene so that it is no longer sensitive toglyphosate.215

38

Appendix II. Horizontal genetransfer
Horizontal transfer does not just mean that foreign
DNA is present inside an organism. In fact, all living
things interact with foreign DNA all the time. The
DNA of any organism you consume will be present
in your body for a period of time, as is the DNA of
all the microbes in your personal microbiome. A
few fragments of foreign DNA from these sources
will enter the cells of your body in the course of
normal life, and the same is true for microbes andplants in the environment. Most of these events will
be quickly eliminated, either because the DNA isdegraded by enzymes as soon as it enters the cell,
is lost when the cell divides because it does notstably integrate into the cell’s genome, or it is lostwhen the cell that contains the DNA dies without
replicating.

Bacteria readily engage in transformation andconjugation and very commonly maintainplasmids, small pieces of DNA that can bephysically exported from the cell and exchanged
with other organisms.217Bacteria are targeted bybacteriophages, a common and rapidly evolving
type of virus that are well known to transmit genes
across species. The genome of a bacterium is notcontained inside a nucleus and is therefore morechemically accessible for integration of foreign
DNA. Likely due to this underlying fact, a range ofother processes can lead to horizontal transfer intoand out of bacteria even when one of the wellknown mechanisms is not in place. The presence of
these ‘non-canonical’ mechanisms that have yet to
be understood are a further illustration of the factthat complete containment of genetically modified
sequences released within engineered microbes is
impossible.

Horizontal transfer in the meaningful sense occurs
in rare events where foreign DNA becomes apermanent part of the host genome, in a form
that is biochemically stable and heritable acrossgenerations. Horizontal transfer is not necessarily
harmful or helpful to the receiving organism, butsometimes confers important new functions. Whenthe transferred DNA also confers a meaningful
biological advantage, it can spread through thereal-world population as was the case for tan spot
disease (see call-out box 7). Any organism canprovide or receive DNA for horizontal transfer, andthere are traces of it in the evolutionary historyof all species. The human genome contains about
1,500 regions that clearly result from horizontaltransfer, and likely many others that have yet
to be identified.216 These events happen on theevolutionary, not day-to-day, timescale — but bearin mind that for microbes whose generation time
is between minutes and days, the evolutionary
timescale can be as short as a few months.
Microbes have key biological differences that
increase the frequency with which they undergohorizontal transfer. For all categories of microbes, a
tremendously important difference from transgenic
GE crops is that the microbes are able to reproduce
asexually. In plants and animals, a horizontallytransferred gene will only be heritable if it happens
to affect one of the small number of cells in a
reproductive organ. In microbes that are unicellularor that can reproduce from any fragment of theirbodies, any transformed cell has the potential toinitiate the spread of a population-wide transfer
event.

39

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