EPA TERAs for Open-Pond Research with Modified Algae

Today’s post continues a series of analyses of recent 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). Today’s entry will describe two TERAs for research use of modified algae strains in open-ponds, as part of research programs ultimately aimed at developing commercial processes for production of fuels or high value chemicals.

As previously described, EPA’s TERA regulations were created to provide Agency overview over proposed outdoor experimentation using genetically modified microorganisms, within industrial sectors not regulated by other federal agencies. The requirement for prior EPA approval for such testing allows the Agency to review the potential environmental effects of the proposed activity, but on a shorter (60-day) timeframe compared to requirements for review of proposed commercial activities. The TERA process is well-suited to allow the assessment of the potential risks of proposed environmental uses of modified organisms, while also allowing 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.

Today’s post discusses two TERAs submitted by Arizona State University on behalf of the Producing Algae for Coproducts and Energy Consortium (PACE). Both applications proposed small-scale experiments entitled “Evaluation of Genetically‐Modified Chlorella sorokiniana in Open Ponds for Production of Biofuel Feedstock and High Value Co‐products”. Chlorella sorokiniana is a unicellular green alga that was described as a well-studied model organism that has long been used in research on photosynthesis and other R&D or industrial applications, including as a food additive. These applications were proposed to take place at the Arizona Center for Algae Technology and Innovation (AzCATI) test bed facility, a 4 acre site in Mesa, Arizona that features laboratories, greenhouses, a number of raceways and miniponds and a photobioreactor array for experimentation with algae technologies.

TERA R-17-0002 was submitted by ASU in May 2016. It proposed the testing of two modified strains of Chlorella sorokiniana. One strain was engineered to express pyrroline‐5‐carboxylate synthase from Vigna aconitifolia (mothbean), which is said to improve stress tolerance, and the other to express AHL‐lactonase from Bacillus sp. strain 240B1, which may play a role in disrupting quorum sensing in algae. Both genes were codon-optimized, and introduced into the recipient algae strain on a plasmid, for expression under the control of native Chlorella regulatory sequences. The goals of the study were to evaluate how well laboratory findings translated to performance in the open environment, and to compare the modified strains to wild type for resistance to environmental factors. The study also aimed to characterize the potential risks and environmental impacts of this open-environment use of modified algae, such as the possibility of dispersal beyond the test site.

TERA R-18-0001 was submitted by ASU in August 2017. It proposed the testing of one modified strain of Chlorella sorokiniana, engineered to express SNRK 2 (SNF related kinase) from the green alga Picochlorum soloecismus, an enzyme involved in sugar metabolism, with the goal of improving photosynthetic efficiency and biomass production. This gene was not codon-optimized, and was also expressed on a plasmid under the control of native Chlorella regulatory sequences. This study had the same goals as the testing proposed in the first TERA. Interestingly, the modified strain described in this application was first tested in a 50 L indoor minipond inside a greenhouse, and was found to have significantly increased carbohydrate accumulation compared to wild type.

These TERAs proposed outdoor experimentation under essentially identical conditions and procedures. Each test was proposed to take place in a total of 6 miniponds, each of which had a working volume of between 800 and 1,000 liters and a surface area of approximately 4.2 m². The miniponds were set on raised stands and were placed within secondary containment constructed of a wooden frame acting as a berm that was overlaid with an industrial liner. The miniponds were also said to be contained within a 9m x 11m perimeter that was underlined by a mesh‐reinforced, puncture‐resistant, UV‐resistant pond liner. Each test was planned to last for 60 days, during which time samples were to be taken from the miniponds to evaluate biomass accumulation of the modified strains compared to the wild type controls. The experiments also featured monitoring protocols, using water traps at various distances from the miniponds to detect any possible spread from the experimental ponds: sampling was to take place weekly, with more frequent monitoring and other mitigation steps to be taken if any dispersal was detected.

I don’t know if these tests were carried out, but since they were to be conducted by an academic group, results would likely be published eventually. Overall, these TERAs represent a sound, thoughtful approach to proposals for outdoor testing of genetically modified algae, with plans for monitoring that should produce useful data on the environmental impacts of such testing. The submissions themselves were thorough in providing the necessary information for EPA to conduct its risk assessment.

There have been other recent TERAs for outdoor experimentation using modified microalgae, which is hopefully indicative of increased interest in developing industrial uses of geneticaly-improved algae strains, as well as evidence that the tools to improve such strains are becoming more accessible. I hope to discuss these other algae TERAs in future blog posts.

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.

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.

European Commission Impact Assessment on Algae

It was recently reported in Biofuels Digest that the European Commission has published an online consultation on its roadmap aimed at promoting a strong and sustainable EU algae sector. This online portal is entitled “Consultation – your view on promoting EU algae production,” and can be accessed here. This effort is an “Inception Impact Assessment,” which in general are aimed at informing citizens and stakeholders about the Commission’s plans for certain initiatives, to seek public feedback and participation in future consultation activities. These Assessments are said to be ways in which citizens and stakeholders can provide views on the Commission’s understanding of a given problem and possible solutions and to provide any relevant information that they may have.

The document summarizing the Assessment can be downloaded as a PDF document here, although the site was somewhat balky today (please contact me if you cannot access this document, and I can send the PDF). The inquiry encompasses a broad scope of potential uses both of microalgae and macroalgae (e.g. seaweed), for uses including food, fuel and specialty chemical production, and the document states that “the initiative aims at increasing sustainable production, ensure safe consumption and boost innovative use of algae and algae-based products”. The document states that the Commission is considering at least three options: the first would be “no policy change”, the second would be what are called “targeted activities to support the sustainable growth of the algae sector” and would include measures to improve applicable regulatory frameworks, improving the business environment for algae products, increasing social awareness and also closing knowledge and research gaps. A third option would include all of the activities under the second option but would also include mandated incentives and quotas for algae products. Public input is sought on a wide range of relevant topics, as the first phase of a process that will culminate in the issuance of reports and recommendations by the fourth quarter of 2021.

The Commission opened a 4-week comment period on December 21, 2020, with January 18, 2021 as the deadline for submissions. Comments can be submitted at this site, or from the “Have your say” link at the portal page.

EPA Issues Updated Guidance for TSCA Submissions for Genetically Modified Algae

In October of this year, EPA posted on its website, apparently with little fanfare or public notice, an updated and presumably final document entitled the “Algae Supplement to the Guidance Document Points to Consider in the Preparation of TSCA Biotechnology Submissions for Microorganisms.” The website indicates that this document supplements the original 1997 TSCA “Points to Consider” document for biotechnology notices under TSCA by addressing submissions involving R&D or commercial use of genetically engineered algae.

This guidance document is the culmination of a process that EPA first began in 2015. When the Agency issued its biotechnology regulations in 1997, it finalized an earlier-prepared document called “Points to Consider in the Preparation of TSCA Biotechnology Submissions for Microorganisms“, and this document has remained unchanged since that year, and has been used by submitters of Microbial Commercial Activities Notices (MCANs), TSCA Environmental Release Applications (TERAs) and other biotechnology filings under TSCA. Its guidance largely remains relevant, although it was written well before the advent of advanced genetic technologies now in widespread use such as synthetic biology and gene-editing tools, as well as before advances in nucleic acid sequencing technology made it routine to be able to provide detailed sequence information for all the introduced genetic modifications. I believe EPA has for some time been planning a general update of this document, but to my knowledge the “Algae” supplement is the only effort where proposed new guidance has been made available to the public.

The Points to Consider document, while applicable to all biotech submissions under TSCA, was heavily biased towards information needs for applications involving the most common industrially-used heterotrophic microorganisms, primarily including bacteria, yeast and other fungal species. In 2015, EPA first announced its intention to provide a companion document that would provide additional guidance for submissions involving genetically modified algae and cyanobacteria, which, as photosynthetic organisms, were anticipated to be used in ways different from traditional microbial fermentation. Earlier blog posts described the initial public meeting on this topic that EPA held in September 2015 and the follow-up meeting in October 2016. EPA issued a draft algae guidance document in conjunction with the 2016 public meeting, and the present document is an update to the 2016 version, and incorporates the information and feedback EPA received at that open meeting and from the public records docket that was open for comment at that time.

After some introductory sections, the main body of the guidance document is a detailed, comprehensive list of the types of data that EPA would potentially like to see in submissions for uses of algae or cyanobacteria under TSCA. It follows the framework of the 1997 Points to Consider document, in providing lists of the types of data that might be required in EPA submissions, within a series of broad categories. The algae document first asks for information about the recipient microorganism (i.e. the strain that is the starting point for the genetic manipulations) and the genetic changes introduced, information about the potential health and environmental effects (including the environmental fate) of the alga, and information about the proposed use of the modified alga, whether a small-scale field test proposed in a TERA or a manufacturing use proposed in an MCAN. The document provides additional details about information specific for algae or cyanobacteria that would be important for EPA’s risk assessment of proposed use of modified algae in manufacturing, whether in open ponds, enclosed photobioreactors, or heterotrophic fermentation, as well as proposed open pond R&D activities. As with the original Points to Consider document, the algae guidance document provides a comprehensive list of issues to be considered, with the expectation that not every topic identified would be applicable to every submission. In addition, it should be noted that TSCA itself does not impose specific testing requirements on applicants, but only that notices under the Act include all data relevant to health and safety that is known to the applicants.

After brief review of the final document, it appears that EPA made only some minor revisions to the detailed information section as it appeared in the 2016 draft. I found only about 3 or 4 places where the 2020 version included a bullet point for a new topic of information or data not found in the 2016 draft, which were presumably added in response to specific comments from interested parties. This speaks to the thorough job EPA did in creating the original draft, which was so comprehensive in listing potential data needs that there really wasn’t much that needed to be added.

To date, EPA has received very few TSCA submissions for uses of algae or cyanobacteria, some of which I have described in previous blog posts. For example, discussion of MCANs from Joule and Solazyme (now known as TerraVia) posted in 2014, a brief mention of Algenol’s Consolidated MCAN for cyanobacteria posted in 2015, and discussion of the TERA submitted by Sapphire posted in 2013. Presumably this new guidance document will be of value to companies and academic groups planning MCAN or TERA submissions for modified algae or cyanobacteria species in the months and years to come.

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).

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.

GAO Report on Cell-Cultured Meat Regulation

In 2018, I wrote several posts about the emerging field of cell-based meats and federal government regulatory issues relating to this new field. Although much of the public and industry debate over this technology has quieted down a bit since that time, there have been some developments since my last post on this topic in December 2018.

As outlined in my previous posts, many observers, particularly in the industry, were concerned that jurisdictional disputes may arise between the two federal agencies having regulatory responsibilities that might apply to meat, poultry and fish products produced by cellular agriculture. These fears were somewhat abated when, in March 2019, the U.S. Department of Agriculture and the Food and Drug Administration entered into a Memorandum of Understanding outlining how they intended to work together to create a workable regulatory framework for cell-based meat products. This MOU, announced on March 7, 2019, applied only to meat and poultry products, and it stated that FDA would retain authority over cell-based fish production (other than catfish, which are currently under USDA jurisdiction). Under the MOU, the agencies agreed that, for the anticipated development of cell-based meat and poultry products, FDA would oversee activities relating to cell collection and proliferation, e.g. cell banks and cell culturing facilities, while USDA would oversee processing, packaging and labeling of cell-based meat products, including facility and product inspection. The MOU further identified areas where the agencies would work together, and it indicated that any emerging regulatory framework would likely rely on existing regulations, but that the agencies would review the possible need for new rules.

The issuance of the MOU seemed to quiet the debate somewhat, and in the months since then there has not been much activity in the public eye regarding an appropriate regulatory framework. To some extent this may be because the technology is still emerging, and aside from the well-publicized (and rapid) growth and public acceptance of plant-based products from companies like Impossible Foods and Beyond Meat, there doesn’t seem that any company is close to wanting to introduce a cell-based meat, poultry or fish product. To my knowledge, there has only been one product in this space which has successfully cleared the U.S. regulatory system, and that is the GRAS Notice submitted by Impossible Foods for the soy leghemoglobin from genetically modified microorganisms that it uses to provide texture to its plant-based meat products, which received FDA’s “no questions” letter in July 2018.

The latest development in this story came on April 7, 2020, when the U.S. General Accountability Office (GAO) released a report it prepared on federal oversight of cell-cultured meat. The GAO is an independent arm of the government that carries out nonpartisan studies of various topics, generally at the request of Members of Congress or other federal officials. This report, entitled “Food Safety: FDA and USDA Could Strengthen Existing Efforts to Prepare for Oversight of Cell-Cultured Meat” was carried out at the request of Representative Rosa DeLauro, who is the Chairwoman of the Subcommittee on Labor, Health and Human Services, Education, and Related Agencies of the House of Representatives Committee on Appropriations. The full report can be downloaded from this site.

Although this report does not break any new ground or move the public debate forward, it offers a fairly complete current overview of the situation. Much of the report is devoted to a detailed summary of the science behind cell-cultured meats, including a discussion of several areas where technological details are unknown or are still being worked out (e.g. will the process make use of genetically modified cells? What types of materials will be used as the scaffolds to grow animal cells into the desired shape and texture?). And the report summarizes the developments on the federal regulatory front since 2018, including the joint meetings and other activities that preceded the March 2019 MOU. The document reports on one development that I had not previously seen reported publicly, which is that In June 2019, FDA and USDA created three working groups to carry out the terms of the interagency MOU. The working groups are comprised of FDA and USDA officials, and were described in the GAO report as follows:

Pre-market assessment working group. Led by FDA, this group was created to clarify the process FDA will use for pre-market reviews of cell-cultured meat.
Labeling working group. Led by USDA, this group will focus on developing joint principles for product labeling and claims.
Transfer of jurisdiction working group. Co-led by FDA and USDA, this group will develop procedures for the transfer of inspection at harvest, among other things.

The GAO report indicates that the work of these groups is still in the early stages, although two of the working groups held meetings in December 2019.

The main recommendation of the report is that, while the March 2019 MOU represents a good start, and that interagency cooperation is essential, both agencies should better incorporate certain “leading practices to enhance and sustain interagency collaboration”. These are seven principles that the GAO had previously developed to guide federal agencies towards more effective collaboration. I won’t attempt to summarize these here – although they doubtlessly provide important and useful guidance to federal agencies, to the layperson they read like common sense advice for conducting effective collaborations that would also be applicable in the corporate world.

Historically, the GAO and its reports have often proven useful in guiding federal policy and public debate on questions of how best to regulate emerging technologies: this has particularly been true at various critical stages in the early growth of the biotechnology industry. Although this report doesn’t provide any new technological insights or make any substantive recommendations for policy or regulation, it does provide a comprehensive overview of many of the issues that have been discussed to date, and will hopefully serve to continue to move regulatory discussions forward.

D. Glass Associates, Inc. is a consulting company specializing in government and regulatory affairs support for renewable fuels, industrial biotechnology and related field. David Glass, Ph.D. is a veteran of over thirty 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 copies of some of Dr. Glass’s prior presentations on biofuels and biotechnology regulation, are available at www.slideshare.net/djglass99and 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.

Book chapter published on regulation of bio-based fuels and chemicals

Last year, I was asked to contribute a chapter for a book entitled “Biobased Products and Industries”, being edited by Charis M. Galanakis. This book was published by Elsevier earlier this year. My chapter, “Government Regulation of Bio-based Fuels and Chemicals”, provides a comprehensive overview of the regulations that might affect the biological production of fuels, chemicals or other specialty products, with emphasis on the U.S. and select other jurisdictions. The chapter covers the following regulatory programs in the U.S., Europe and elsewhere:

Industrial Chemicals: US regulation under TSCA, EU regulation under REACH.
Fuel Certification: Standards and registration requirements for civilian, military and aviation fuels in the US and Europe.
Promotion of Renewable, Bio-Based Products: The US Renewable Fuel Standard and state Low Carbon Fuel Standards, similar programs in Europe.
Use of Genetically Modified Microorganisms: Regulation of the use of modified microorganisms to produce fuels and chemicals under US EPA TSCA regulations and biosafety regulations elsewhere in the world.
Use of Genetically Modified Plants as Feedstocks: Regulation of the use of transgenic plants to produce fuels and chemicals under US Department of Agriculture regulations and biosafety regulations elsewhere in the world.
Other Regulations, including facility registration requirements, use of microbial biomass in animal feed, and others.

A description of the book along with a Table of Contents and other information can be accessed here. I would be happy to answer any questions you may have on this chapter or the topics discussed.

EPA revises TSCA biotechnology rule to expand the list of microorganisms eligible for tiered exemptions

EPA recently issued a Final Rule that is the first major amendment or revision to its biotechnology regulations under the Toxic Substances Control Act (TSCA) since the rules were first issued in 1997. These regulations, found at 40 CFR Part 725, cover certain commercial uses of microorganisms that have been modified to contain coding nucleic acid sequences from more than one taxonomic genus (so-called “intergeneric” microorganisms). The new Final Rule, issued on March 10, 2020, adds two species of microorganism to the list of host (“recipient”) microorganisms that are eligible to qualify for the tiered exemptions from commercial reporting under the biotechnology rule.

As previously reported in this blog, EPA published a Proposed Rule back in 2012 in which it proposed adding these two microbial species, Trichoderma reesei and Bacillus amyloliquefaciens subspecies amyloliquefaciens, to the list of microorganisms in 40 CFR 725.420 that may qualify for the Tier I and Tier II exemptions from full notification and reporting. Under the biotechnology regulations, companies planning commercial use or importation of an intergeneric microorganism, other than for purposes regulated as pesticides or by the Food and Drug Administration, must file a Microbial Commercial Activity Notice (MCAN) at least 90 days in advance of the proposed use or importation. The regulations provide several exemptions from MCAN reporting, particularly these tiered exemptions that may be available for those intergeneric microorganisms where well-characterized genetic changes have been made to one of several starting species of recipient organism. These exemptions were described in detail in one of my 2010 blog posts, and the list of the original ten eligible recipient species was included in another 2010 post. Briefly, if the company can certify that it can use a qualifying organism at a particular location in conformance with certain equipment, facilities and procedural requirements specified in the regulations to minimize potential release of the organism from the production facility, it can proceed under the Tier I exemption without prior EPA review, merely upon 10 days advance notice to EPA. If instead the company wishes to use the organism under different containment conditions that it considers to be equivalent or appropriate for the proposed use, it can submit a Tier II exemption application to EPA at least 45 days before commercial use, but must wait for EPA approval before proceeding.

The Part 725 biotechnology rule provides a process by which interested parties could file petitions proposing that additional microorganisms be added to the list of species eligible for the tiered exemptions. In response to two such petitions, on September 5, 2012, EPA published a notice in the Federal Register announcing the issuance of a Proposed Rule that would add two microbial species to the list of recipient organisms potentially eligible for the tiered exemptions. Trichoderma reesei and Bacillus amyloliquefaciens are both well-studied species that have historically been used quite frequently in industrial fermentations and which have been used to produce biofuel-processing enzymes or for production of industrial enzymes. The March 2020 action issuing the Final Rule represents the final stage of this process, so that, effective April 9, 2020, the following two species have been added to the list of qualifying organisms in 40 CFR Part 725.420.

(k) Trichoderma reesei strain QM6a and its derivatives used only in submerged standard industrial fermentation operations as defined at 40 CFR 725.3.

(l) Bacillus amyloliquefaciens subsp. amyloliquefaciens.

The eventual final rule followed the proposed rule closely, except that, in response to comments on the proposed rule submitted by industry trade groups, EPA decided to modify the qualifying language for T. reesei strains, to read as shown above. In the Federal Register notice announcing the new rule, EPA noted that it “has reviewed 48 MCANs involving intergeneric T. reesei production organisms used to manufacture a number of industrial enzymes, including amylases, glucosidases, proteases, phytase, laccase, and numerous cellulolytic enzyme preparations”. The notice did not indicate how many MCANs EPA had received for B. amylolquefaciens, but noted that the species has been widely studied and used for many years in a variety of commercial fermentations and production processes. The March 10 Federal Register notice included a detailed summary of the scientific risk assessment EPA carried out to support this final rulemaking.

The direct impact of this ruling will largely be limited to the small number of companies that have submitted MCANs for production of industrial enzymes or other products using these microorganisms. And it is curious that it took EPA over 7 years to finalize the proposed rule, although I’d note that the TSCA biotechnology team has always been understaffed, and in recent years has had to deal with an increasing number of MCAN and other submissions, so this rulemaking may not have been a major priority for the agency. It is, however, a good sign that EPA is willing to learn from its 20-plus years of experience under the biotech rule to consider ways in which the regulations can be revised and the burden on the regulated community eased in specific ways, supported by appropriate science.

D. Glass Associates, Inc.is a consulting company specializing in government and regulatory affairs support for renewable fuels, industrial biotechnology and related field. David Glass, Ph.D. is a veteran of over thirty 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 copies of some of Dr. Glass’s prior presentations on biofuels and biotechnology regulation, are available at www.slideshare.net/djglass99and 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.

Regulation of Cell-Based Meats: update on some new developments

As 2018 ends, I’m writing with a brief update on recent activity regarding the emerging field of cell-based meats and efforts by the U.S. government to establish a framework for regulation of such food products.

As I have previously reported, on September 13, 2018, the USDA published a notice in the Federal Register announcing that it and FDA would jointly hold a two-day public meeting October 23-24 entitled “The Use of Cell Culture Technology to Develop Products Derived from Livestock and Poultry”. The goals of the meeting were to focus on several specific questions relating to jurisdiction, potential risks posed by the manufacturing process, provisions for facility inspection and product labeling, among others.

I attended the first day of this public meeting, which was devoted to “Oversight, Hazards and Controls”. The second day, held on October 24, focused on “Labelling” issues, but due to a prior commitment, I was not able to stay in Washington for the second day of the meeting. This two-day session followed a sparsely-attended meeting on October 22 of FDA’s Science Advisory Board with an agenda largely addressing these issues: although I did not attend that meeting, it and the topics discussed at that meeting were frequently mentioned during the October 23 joint meeting.

I wasn’t able to post any detailed observations or comments on the meeting in its immediate aftermath, but I’ll offer a few brief comments here. First, I think all attendees where glad to see the FDA and USDA cooperating on this meeting and in their efforts to oversee the industry (more on that below). But I was also struck by the fact that neither agency seemed inclined to propose new regulations to cover this industry, and in fact most of the discussion about possible regulatory programs focused on “downstream” programs for facility inspection rather than “upstream” or pre-market review and approval of proposed food products.

Predictably, there was also discussion about potential risks, most of which were brought up by the environmental or public interest groups in attendance. Several of these commenters mentioned potential risks that to my knowledge had not previously been suggested in the public debate, such as the risk that cell-based products that originated from animal stem cell cultures might contain cancer tissue or other mutations that might have harmful effects in the food product. In general, I feel that some of those risks are overstated or don’t go much beyond the hypothetical, and that those risks which can be foreseen with a better level of probability can be managed by known techniques, such as well-established protocols for biological containment and aseptic technique.

My thoughts on such hypothetical risks and other issues can be found in the comments I submitted to the public docket before the close of the comment period on December 26, 2018. You can find my comments here; and the page for the entire public docket can be found here. As of this writing, 315 comments were received in the public docket, from a range of commenters including industry, agricultural trade groups, public interest groups and private citizens.

Following the October public meeting, and before the comment period was even closed, USDA and FDA issued a statement on November 16, 2018 to announce that the agencies would work together to develop a regulatory framework for cell-based meats. The statement said:

“Drawing on the expertise of both USDA and FDA, the Agencies are today announcing agreement on a joint regulatory framework wherein FDA oversees cell collection, cell banks, and cell growth and differentiation. A transition from FDA to USDA oversight will occur during the cell harvest stage. USDA will then oversee the production and labeling of food products derived from the cells of livestock and poultry.”

The details of this cooperative effort, and what it means for the cell-based meat industry, of course remain to be seen. However, it is certainly a positive development to see the agencies working together, so that a divisive turf battle, which would adversely affect all stake-holders, will not develop.

I’ll continue to follow this emerging field in the new year, and comment in new blog posts as appropriate.

D. Glass Associates, Inc. is a consulting company specializing in government and regulatory affairs support for renewable fuels, industrial biotechnology and related fields. David Glass, Ph.D. is a veteran of over thirty 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 copies of some of Dr. Glass’s prior presentations on biofuels and biotechnology regulation, are available at www.slideshare.net/djglass99 and 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.

Regulation of Cell-Based Meats: Follow-up and New Developments

This post continues the series of discussions, beginning with an August 20, 2018 entry, on regulatory issues relating to the anticipated introduction of human food products produced from cultured animal cells (“cell-based meat” products), as replacements for traditional meat, poultry or fish. I submitted comments to the U.S. FDA on September 24, 2018, during the open-comment period that followed the Agency’s July 12, 2018 public meeting on this topic. My comments were based on, and expanded on, the themes discussed in the previous posts. You can access a copy of my complete comments here, but the following is a summary of the points I raised:

Production of foods from animal cell culture can be carried out using well-established, reproducible and predictable methods, that can lead to safe, sanitary production of nutritious foods for U.S. consumers, that could even be safer than existing practice.
There is a long history of the safe use of animal cell culture for research and other purposes, which provides a sound basis for adoption of safe techniques for producing human food through cell culture.
If a premarket review program is to be established, I recommended that it be based on existing law and regulations to the greatest extent possible. FDA should be the lead agency for any program, and the agency should utilize the existing GRAS Notice program, which has worked extremely well to allow reviews of innovative new food ingredients, or to establish a parallel, but similar program for cell-based meats. Any such program should primarily focus on the composition, safety and nutritive value of the end product, although information about manufacturing methods must be part of the technical review.
I recommended that FDA should coordinate its efforts with the U.S. Department of Agriculture, to be sure that USDA’s scientific expertise is utilized in any reviews carried out by FDA, and that cell-based meats are subject to existing or amended USDA regulations for sanitary production, facility inspection and labeling, for those foods (meats, poultry and catfish) that are within current FSIS jurisdiction. Both agencies should strive to avoid any jurisdictional battles that would create uncertainty that could stifle an innovative, emerging industry.

As of this writing, FDA received 477 comments on regulations.gov in response to this request. I have not studied these in detail, except to note that they were submitted by a broad range of commenters from industry, academia, NGOs and public interest groups, and also from private citizens. A number of private citizens submitted comments in favor of the development of “clean meat” and for FDA’s role in regulation, while there were also a good number of letters from private citizens opposing a regulatory scheme where FDA was the sole agency, and advocating for a role for the USDA. These latter submissions were all identical, as is often the case with agency public comments, and likely originated from the beef industry. Among the public interest group submissions were comments from animal rights groups, favoring the development of cell-based meats as an alternative to the consumption of animals.

In another related development, on September 13, 2018, the USDA published a notice in the Federal Register announcing that it and FDA will jointly hold a two-day public meeting October 23-24 on cell-based meats. This meeting will focus on several specific questions relating to jurisdiction, potential risks posed by the manufacturing process, provisions for facility inspection and product labeling, among others. Public comments on these topics will be accepted through November 26, 2018. I am making plans to attend the first day of this meeting, which will feature discussion of issues pertaining to potential risks and agency oversight, and afterwards I hope to report on the outcome of the meeting.

Finally, there was an interesting article in Monday’s New York Times about the efforts to develop cell-based production processes to manufacture kosher pork products. No mention of regulatory issues, but interesting speculation about what would be needed for a cell-based meat product or its production process to be certified to be meat-free and therefore “pareve” under Jewish kosher law.

D. Glass Associates, Inc. is a consulting company specializing in government and regulatory affairs support for renewable fuels, industrial biotechnology and related field. David Glass, Ph.D. is a veteran of over thirty 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 copies of some of Dr. Glass’s prior presentations on biofuels and biotechnology regulation, are available at www.slideshare.net/djglass99 and 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.

Bio-Based Chemicals and Fuels: Business, Policy and Regulation

Discussing how advanced biotechnology is being used to improve the production of bio-based chemicals, renewable fuels and other industrial biotech products