Review of Recent EPA TERAs for Outdoor Research with Modified Microorganisms

In a recent blog post, I summarized submissions to the U.S. Environmental Protection Agency for outdoor field tests of genetically modified microorganisms under the TERA (TSCA Environmental Release Application) provisions of the Agency’s biotechnology regulations under the Toxic Substances Control Act (TSCA). In today’s post, and the ones that will follow, I’ll briefly describe the most recent TERAs, beginning with those filed with EPA since 2014.

As previously described, the commercial use of modified microorganisms for purposes subject to TSCA jurisdiction might be subject to EPA’s biotechnology regulations under TSCA. Commercial use or importation into the U.S. of certain modified microorganisms (i.e., “new organisms” containing coding nucleic acids from more than one taxonomic genus) for purposes that are within TSCA’s jurisdiction require prior submittal to EPA of a Microbial Commercial Activity Notice (MCAN). Applications potentially subject to TSCA jurisdiction include production of industrial chemicals (including biofuels and certain enzymes), as well as uses of microorganisms for environmental purposes such as bioremediation and non-pesticidal agricultural uses. The latter category might include plant inoculants to promote nitrogen fixation, soil amendments, biofertilizers and plant biostimulants. Although R&D activities are largely exempt from TSCA oversight, the biotechnology regulations require that research involving “new microorganisms” in the open environment (outside a “contained structure”) require EPA review before the research can be conducted, through the filing of a TERA.  The TERA process provides an expedited review procedure for small-scale field tests and other outdoor R&D uses of new organisms, with applicants required to submit TERAs at least 60 days in advance of the proposed activity. See my earlier blog post for more background on TERAs, their data requirements, and the review process.

As I reported in the earlier post, there has only been limited experience with TERAs since the biotechnology rule was put into place in 1997.   According to EPA’s websites, there have been about 40 TERAs submitted for open environmental use of engineered microorganisms, and all but four of these proposals were approved. I have reviewed the TERAs filed prior to 2014 in previous posts, and in today’s post I will describe three TERAs filed in 2014 and 2015.

TERAs R-15-0001 and R-15-0002 were submitted by Elemental Enzymes Ag and Turf, LLC. According to the company’s website, Elemental Enzyme creates “enzyme, peptide and natural solutions that improve plant health, performance and yield” by applying cross-disciplinary scientific solutions to complex agricultural problems. Their products and processes are “applied through seed treatment, in-furrow soil treatments, foliar applications, tree injection, fertilizer impregnation and fertigation”. These TERAs proposed a series of field tests of a technology in which select beneficial enzymes were expressed on the outermost layer (the exosporium) of spores of Bacillus thuringiensis subsp. Israelensis. The company was developing this technology in the expectation that such spores would be an efficacious way to deliver enzymes directly to crop plants. B. thuringiensis is of course a species well-known for different subspecies that express specific insect toxins, and which have been used as natural biopesticides against lepidopteran and coleopteran pests for many years. However, Elemental Enzymes was not making use of that trait, and in fact their strain of B. thuringiensis subsp. Israelensis was missing the genes needed to encode the insect toxin.

The company created multiple strains of modified B. thuringiensis subsp. Israelensis, each expressing a different plasmid-encoded enzyme. The eight enzymes expressed by these strains were endo-1,4-β-glucanase, β-1,3 glucanase, phytase, chitosanase, protease 2, alkaline phosphatase 4, lipase EstA,  and phosphatidylcholine phospholipase. The strains were to be administered either directly to seed or in-furrow, and field tests were planned in 14 states on a variety of crops including corn, squash, tomatoes and cucumber. The purpose of the trials was to determine if the enzymes imparted beneficial growth-promoting properties to any of the crop plants; monitoring of the modified strains was also contemplated.

It is not known in the public record if these tests were carried out and what the result may have been, and there were no follow-up TERAs submitted for these strains. Today, the company is selling or developing a number of products for agriculture, but spore-delivered growth-promoting enzymes do not appear to be among them.

These TERAs are unique in several ways. They are likely the only submissions to a federal agency for a field test involving spores of genetically modified microorganisms. And the proposed experiments were somewhat unusual in the use of a species known for its pesticidal properties for a purpose unrelated to such properties. These TERAs also appear to have been the first for testing of soil inocula since the nitrogen-fixing experiments under TERAs in 1999-2000, which is of interest given the recent increase in commercial activity towards developing improved seed and soil inoculants to improve crop growth and yield.

TERA R-15-0003 was submitted by the National Institute of Standards and Technology (NIST) on April 30, 2015 for a proposed field test of a modified strain of Saccharomyces cerevisiae. This proposal is also one that is unlike any other TERA that has yet been filed with EPA. The purpose of the proposed field test was to test the ability of a modified yeast strain to serve as a “reference material to support first responder training and workflow evaluation for on-site biological assessment technologies”.  In response to a 2011 report from the Department of Homeland Security, researchers at NIST were developing a program to train first responders how to deal with “suspicious white powder incidents” that might arise from terrorist activity. The goal of this project was to evaluate whether this modified S. cerevisiae strain could be used “as a qualitative and quantitative reference material for microbial abundance measurements” under conditions mimicking a field response to a white powder incident.

The NIST team modified a wild type S. cerevisiae strain to contain a 438 bp fragment from a heterologous organism, Methanocaldococcus jannaschii, a noncoding sequence selected to have minimal homology to the S. cerevisiae sequences, which could be used to detect the microorganism in PCR assays. In the proposed test under the TERA, cells of the modified strain were to be lyophilized and released to the environment in two ways: either fixed on metal coupons which would be placed at different locations around the test site, or released to the atmosphere in a plume at the site. In the first case, the plan was for the researchers to retrieve the metal coupons and obtain microbial samples using swabs, and the samples would then be quantified using qPCR and viable-cell counting. In the second case, clean metal coupons would be used to collect the microorganisms from the plume, and the coupons used as in the first experiment to obtain microbial samples for qPCR and plate counting.

NIST conducted the test in July 2015 and subsequently filed a report with EPA describing the results. The air plume experiment was not carried out due to unforeseen circumstances, but the first experiment with the metal coupons was conducted. The report concluded “Overall, the use of the yeast was a success. Of the 4 detection sites, only 3 sites reported results. One site did not report results due to technical difficulties at the time of testing. All the reporting sites successfully detected the yeast from the samples collected from coupons with yeast”.

These two proposals from several years ago are indicative of the breadth of R&D activity in exploring the uses of modified microorganisms for beneficial uses in the environment. As noted above, the Elemental Enzyme TERAs can be seen as an early harbinger of renewed commercial interest in developing improved microorganisms for non-pesticidal agricultural purposes, and the NIST proposal is an example of how the techniques of modern biotechnology can be applied in innovative and perhaps unexpected ways.

In the blog post that will follow in a few days, I’ll describe another batch of TERAs, including three successful proposals for open-pond field testing of genetically modified algae.

To conclude, I’ll reiterate my earlier comments that the TERA process is well-suited to allow the assessment of the potential risks of proposed environmental uses of modified organisms. The TERA process allows outdoor uses of modified microorganisms to take place in a stepwise fashion under appropriate monitoring and agency oversight, to enable legitimate scientific issues of environmental risk assessment to be addressed with data from actual controlled small-scale environmental use, thus facilitating subsequent risk assessments for larger-scale uses.

D. Glass Associates, Inc. is a consulting company specializing in government and regulatory affairs support for renewable fuels and industrial biotechnology. David Glass, Ph.D. is a veteran of over thirty-five years in the biotechnology industry, with expertise in industrial biotechnology regulatory affairs, U.S. and international renewable fuels regulation, patents, technology licensing, and market and technology assessments. More information on D. Glass Associates’ regulatory affairs consulting capabilities, and links to some of Dr. Glass’s prior presentations on biofuels and biotechnology regulation, are available at www.dglassassociates.com. The views expressed in this blog are those of Dr. Glass and D. Glass Associates and do not represent the views of any other organization with which Dr. Glass is affiliated.

EPA TERAs for Agricultural and Environmental R&D with Modified Microorganisms

In past years on the blog, I’ve written about various aspects of the U.S. EPA regulations under the Toxic Substances Control Act (TSCA) that cover industrial and other uses of genetically modified microorganisms, which in recent years have applied to many commercial biofuel and bio-based chemical projects. Today I’m writing about one aspect of these regulations that cover proposed outdoor research activities of certain modified microorganisms, which might affect not only the open-pond use of modified algae to produce fuels or chemicals, but also proposed field testing of certain agricultural microorganisms intended for non-pesticidal use in the open environment. This is the requirement to obtain prior EPA review and approval of field test plans through submission of a TSCA Environmental Release Application (TERA).  

As previously described, the commercial use of modified microorganisms for purposes subject to TSCA jurisdiction might be subject to EPA’s biotechnology regulations under TSCA. Commercial use of certain modified microorganisms (i.e., “new organisms” containing coding nucleic acids from more than one taxonomic genus) for purposes that are within TSCA’s jurisdiction  require prior submittal to EPA of a Microbial Commercial Activity Notice (MCAN). These rules include an exemption for R&D activities that in practice is fairly broad and which potentially covers most laboratory or pilot plant activities if conducted in a suitably contained facility or reactor.

By statute, TSCA applies only to new chemicals that are not subject to regulation by other federal agencies, and this same statutory limitation applies to EPA’s biotechnology regulations under this law. For the most part, TSCA jurisdiction includes uses of microorganisms in industrial manufacturing, such as the production of fuels, chemicals, enzymes or any other product that is not regulated as by FDA as a food or food additive, a dietary supplement of any kind, a drug, biologic, or cosmetic, or not regulated by EPA as a pesticide. The TSCA biotech regulations would also cover uses of microorganisms for environmental uses such as bioremediation as well as agricultural uses not regulated as pesticides, including plant inoculants such as those promoting nitrogen fixation, soil amendments and other biofertilizer applications. It is also likely that these regulations would also cover the testing and commercialization of plant biostimulants, a category of products which EPA considers falls outside its pesticide regulations. (EPA has just recently issued an updated draft guidance document for determining which products would be considered as biostimulants and thus not be regulated as pesticides).

Earlier blog posts have described the requirements for determining if an activity qualifies for the broad R&D exemption by virtue of taking place in a “contained structure”. Today’s post deals with EPA regulation of proposed R&D uses of new microorganisms in the open environment, such as agricultural field tests or open-pond uses of modified algae, or other activities that would be deemed not to qualify for the “contained structure” exemption. Such proposed uses would likely require EPA review before the research can be conducted, through the filing of a TERA.  

The TERA process provides an expedited review procedure for small-scale field tests and other outdoor R&D uses of new organisms. Applicants proposing such uses must file a TERA with the EPA at least 60 days in advance of the proposed activity. The data requirements for TERAs are outlined in §§725.255 and 725.260 of the regulations, and these requirements address the key issues which should be considered in environmental risk assessments, as described in the published papers mentioned in an earlier post on the blog. This includes all information in the applicant’s possession pertaining to:

  • phenotypic and ecological characteristics of the microorganism
  • a detailed description of the proposed R&D activity
  • number of microorganisms proposed to be released, and the methods proposed for the release
  • characteristics of the test site(s), including location, geographical, physical, chemical and biological features
  • target organisms (e.g., prey) of the modified microorganism (if any)
  • Information on monitoring, confinement, mitigation, and emergency termination procedures for the microorganisms to be released

EPA is required to review the submitted information and decide whether or not to approve the proposed outdoor R&D activity within 60 days, although the agency could extend the review by an additional 60 days. If EPA determines that the proposed activity does not present an unreasonable risk of injury to health or the environment, it will notify the applicant in writing that the TERA has been approved.  When a TERA is approved, the applicant must carry out the testing under the conditions and limitations described in the TERA application document, but also in accordance with any requirements or conditions included in EPA’s written approval. In most cases, it is likely that EPA will require applicants to conduct some form of monitoring, to detect the possible spread or dispersal of the microorganism from the test site, or to detect any other potential adverse environmental effects. EPA may require collection and submission of other data as well. As specified in §725.270 of the regulations, EPA’s approval is legally binding on the applicant, and violations are subject to civil and criminal penalties. EPA further has the authority to modify or revoke the approval upon receipt of evidence that raises significant questions about the potential risk of the activity.

There has only been limited experience with TERAs since the biotechnology rule was put into place in 1997.   According to EPA’s websites, there have been about 40 TERAs submitted for open environmental use of engineered microorganisms, and all but four of these proposals were approved (those four were either withdrawn or rejected by the agency: further details are not available on the website). The following is a summary of the purposes of the approved TERAS.

From 1998-2015: 30 approved, 3 withdrawn

  • Rhizobia for nitrogen fixation: 5
  • Pesticide research: 3
  • Hazardous waste detection (bioindicators): 13
  • Bioremediation: 2
  • Biofuel research (algae): 5
  • Enzyme production: 2

2016 to date: 6 approved, 1 withdrawn (details not available on the website, due to changes in EPA’s website reporting after the adoption of the 2016 TSCA amendment)

The 5 TERAs for nitrogen fixation all arose in the early 1990s, for a research program that ultimately led to EPA’s approval in September 1997 of limited commercialization of a modified strain of Sinorhizobium meliloti with improved capacity to provide fixed nitrogen to alfalfa. There have apparently been no TERAs since then for microorganisms for improved nitrogen fixation or other biofertilizer applications. It is worth noting that the regulations provided very limited exemptions from TERA reporting for small-scale field testing of modified strains of R. meliloti (now S. meliloti) and Bradyrhizobium japonicum, under 40 CFR Part 725.239, but that these exemptions are extremely narrow and would cover only those proposed tests meeting the stated requirements.

The 3 TERAs which I’ve identified as pesticide research were academic projects from the University of California Riverside in the early 2000s for research on the biology of Alcaligenes xylosoxidans, which was being investigated as a potential biopesticide to control a disease of grapes. I don’t know if this research continued, but these tests were subject to TSCA because they were basic research: if an actual candidate pesticide product had been developed, its field testing would have been subject to EPA regulations under the pesticide law FIFRA and would likely have required obtaining an Experimental Use Permit under those regulations.  

By far the largest category were the 13 TERAs for testing of bioindicators: these were generally microorganisms that had been engineered to contain reporter genes that would be expressed in the presence of hazardous compounds in the environment (e.g. in potentially contaminated soil), triggering a biochemical response that could be detected and quantified. These projects were carried out from 1998 through 2007 by academic and government scientists and one private company, Micro Systems Technologies. It does not appear that this technology has ever been commercialized.

The TERAs in the bioremediation category were submitted in 2013 by the US Army Engineer Research and Development Center and the US Army Corps of Engineers to propose the use of modified strains of Gordonia terrae and Rhodococcus jostii in a field demonstration of bioaugmentation (i.e. bioremediation) to enhance the degradation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in contaminated groundwater. As I previously discussed in the blog, these TERAs appear to be the first in which approval was granted for release of modified microorganisms into the groundwater (all previous TERAs were for introductions into soil). EPA’s approval included significant monitoring and reporting requirements.

The 5 TERAs for biofuel research constituted a single submission from Sapphire Energy for a field test of modified algae in a biofuel research program. These TERAs were the first to cover the use of modified algae in open-pond reactors, and they proposed the testing of five different intergeneric strains of Scenedesmus dimorphus that had been modified to express metabolism-related genes and a marker gene. The stated purpose of this testing, as summarized on the EPA website, was to (1) evaluate the translatability of the genetically modified strains from the laboratory to an outdoor setting, and (2) to characterize the potential ecological impact (dispersion and invasion) of the genetically-modified microalgae. I described this experiment in more detail in a December 2013 blog post, and Sapphire and their collaborators from the University of California San Diego have published the results of these field tests.

Less is publicly known about the remaining two pre-2016 TERAs, which were two applications submitted and approved in 2015 for the use of Bacillus thuringiensis subspecies Israelensis for what was characterized as “enzyme production”. Since this species is known to have pesticidal properties, this designation is curious, but the EPA website does not include a link to a decision document that might provide more information. It’s likely that this too is a basic research proposal related to the development of a biological or biochemical pesticide.

Similarly, the EPA website gives virtually no information at all about the 7 TERAs submitted after the 2016 TSCA Amendments took effect.  I am in the process of filing a FOIA request to obtain more information on these TERAs and the two 2015 TERAs for enzyme production, and I will report on my findings about these TERAs in a future blog post once I have received that information.

 As a final word, I would note that the TERA process is well-suited to allow the assessment of the potential risks of proposed environmental uses of modified organisms. There are legitimate scientific issues that most observers feel should be addressed in the assessment of such uses, and the TERA process allows outdoor uses of modified microorganisms to take place in a stepwise fashion under appropriate monitoring and agency oversight, to enable environmental risk assessment questions to be addressed with data from actual controlled small-scale environmental use, thus facilitating subsequent risk assessments for larger-scale uses.

D. Glass Associates, Inc. is a consulting company specializing in government and regulatory affairs support for renewable fuels and industrial biotechnology. David Glass, Ph.D. is a veteran of over thirty-five years in the biotechnology industry, with expertise in industrial biotechnology regulatory affairs, U.S. and international renewable fuels regulation, patents, technology licensing, and market and technology assessments. More information on D. Glass Associates’ regulatory affairs consulting capabilities, and links to some of Dr. Glass’s prior presentations on biofuels and biotechnology regulation, are available at www.dglassassociates.com. The views expressed in this blog are those of Dr. Glass and D. Glass Associates and do not represent the views of any other organization with which Dr. Glass is affiliated.