Microbial Biocontrol Agents: Developing Effective Biopesticides

By Abhishek Anand, Marc Bardin, Ana Bejarano and 30 more

The negative impact of chemical pesticides on human wellbeing and the environment has encouraged the development of eco-friendly alternatives for the management of plant pathogens. However, only a small number of microbial biocontrol agents (mBCAs) have been developed, registered and used in the management of plant diseases. This book analyses the deployment of mBCAs for the development of novel microbial biopesticides, considering the main plant-beneficial traits, procedures needed for effective formulations and the processes used for their validation. To guide the readers through the world of microbial biopesticides, the book starts with a chapter dedicated to the regulations that need to be followed for the development of final products. Readers will understand the importance of formulation and mode of action of mBCAs in developing microbial biopesticides. They will become familiar with key mBCAs such as Ampelomyces quisqualis, Bacillus spp., Trichoderma spp., and Pseudomonas spp., understanding the importance of formulation for their application in the field. This book explains the use of mBCAs to control post-harvest diseases and the potential of endophytic microorganisms as next-generation microbial biopesticides. A final chapter provides a useful workflow for the selection of new mBCAs and describes microbial species including promising mBCAs that might be developed as new microbial biopesticides.
- Gives useful insights into the practicalities of regulation of mBCAs
- Describes the underlying biology that it is critical to developing mBCAs
- Provides case studies for key mBCA species
- Indicates microbial species exploitable for the development of new microbial biopesticides
For students and researchers involved in crop protection and biological control

• Language: English
• Publisher: CAB International
• Release date: Nov 22, 2022
• ISBN: 9781789249200

Book preview

1Registration or the Sword of Damocles over the Development of Biopesticides

LARS HUBER

* AND CARLA S. LORENZ

SCC, Scientific Consulting Company, Department for Agrochemicals and Biorationals, Bad Kreuznach, Germany

*Corresponding author: [e-mail]

©CAB International 2023. Microbial Biocontrol Agents: Developing Effective Biopesticides (ed. G. Puopolo)

DOI: 10.1079/9781789249200.0001

Abstract

The general principles for registration of plant protection products (PPPs), including biopesticides, are essentially quite similar worldwide. For biopesticides, differences mainly exist in regard to administrative and regulatory handling as well as public perception. Especially in view of the latter, the registration procedure for biopesticides in the European Union (EU) is one of the most criticized. However, EU laws and regulations on human, animal and environmental health and safety are among the first established and most elaborated worldwide. Therefore, to understand the current and future requirements and pitfalls in biopesticide registration this chapter mainly focuses on the conditions in the EU.

1.1  How Regulations on the Development of Biopesticides Changed During the Past Decades

The registration process for active substances (AS) and plant protection products (PPPs) is based on two main processes. The first represents scientifically related topics with respect to the AS and PPP specific characteristics as well as technical methods and possibilities for obtaining data relevant for registration. The second process focuses on legal and political (in other words, regulatory) requirements and conditions to be observed and to be complied with, in order to achieve registrations and thus bringing a PPP onto the market, augmenting the farmers’ toolbox.

As agricultural practice shows, in some cases these two processes are in line, complementing each other. However, there are also many examples highlighting huge discrepancies, especially in the registration of biopesticides. Therefore, it is of utmost importance to align both operational processes from research and development (R&D) to commercialization of AS and PPPs. On the one hand, streamlining both operational processes significantly reduces the risk for a PPP to get stuck in the valley of death. On the other hand, this allows for exploiting all opportunities, benefits and incentives provided for in the registration process for biopesticides.

To understand the registration process for biopesticides, one has to look at the historical developments on which the current and future rules are based (Table 1.1).

This is of special importance since the registration process for PPPs is not a stand-alone procedure but is linked with and interrelated to many other regulatory and legal EU frameworks. Thinking about biopesticides, especially the thematic strategies and frameworks on human, animal or environmental safety, sustainability or greening come to mind as this type of legislation substantially influences the transition from a chemically oriented agriculture to a sustainable, integrated approach and hence also paving the way for biopesticides.

The oldest EU act of law on the environment is the Birds Directive, adopted in 1979. As one of the cornerstones of EU environmental legislation, the Birds Directive was last amended in 2009, thus highlighting the constant development of legislation, often continuing over decades. In addition to this, the example of the Birds Directive shows another characteristic of EU legislation: the interrelatedness of legislative frameworks. Habitat loss and degradation were identified as one of the most serious threats to the conservation of wild birds. Therefore, in 1992 the so-called Habitats Directive was adopted, establishing for example the Natura 2000 ecological network. These legislative acts not only triggered the inclusion of certain ecotoxicological data requirements in the respective legislative framework for PPP registration. They also set the basis for ongoing and future developments and changes in the registration of PPPs. One of the main respective legislative acts is the Sustainable Use Directive (SUD) (Directive 2009/128), establishing, for example, integrated pest management (IPM) as a mandatory obligation for all professional farmers from 2014 onwards. Similar interrelations and developmental processes are constantly triggered. Further examples are the Water Framework Directive and the General Food Law.

The previous examples are mainly related to general human, animal and environmental health and safety developments in PPP regulations, data requirements and risk assessment. However, they represent only one part of the registration process. Other important parts are administrative, legal and regulatory aspects, for which the same characteristics, interrelatedness and continued development of legislative frameworks apply. Two main examples in this regard are based on even older legislative acts. The first is the EU-wide harmonization of legislation and registration rules based on the oldest piece of EU legislation, the 1957 Treaty on the Functioning of the European Union (TFEU) (Treaty of Rome) and subsequently the Treaty on European Union (TEU 1992) (Treaty of Maastricht). Whereas the AS approval process is handled on an EU level, PPP authorizations are the responsibility of national authorities. To guarantee that only safe PPPs are made available to end-users in all EU Member States (MS), each PPP in the EU has to be evaluated according to the so-called Uniform Principles. In conjunction with another principle of TFEU and TEU, the free movement of goods in the EU, the uniform and harmonized registration process for PPPs allows for several administrative procedures simplifying registrations and bringing PPPs onto the market in EU countries. A valuable tool also for biocontrol companies based on these legal acts is the so-called mutual recognition procedure. Mutual recognition allows for a stepwise approach for PPP registrations, to split registration costs and workloads and thus to better tackle the burden of investments. For many low-risk AS and PPPs, including some biopesticides, harmonized rules allow for further incentives such as reduced numbers of PPP studies or reduced registration costs. Nevertheless, it is argued sometimes that such procedures could be avoided if PPP registration were not to be a national process but also to be handled on an EU level. However, considering the many differences between MS in respect of geographical, environmental, climatic and agricultural conditions, it becomes clear that one-for-all PPP registration is not feasible. In addition, conditions of use of most products have to be adapted to climatic or agricultural conditions. National authorizations allow for this and consequently are also in the interest of manufacturers and applicants. Therefore, national PPP registration procedures are not the sword of Damocles or an unnecessary and outdated legal procedure, as is often claimed, but a scientific and technical necessity.

Table 1.1. Overview on main legislative acts and timelines (excerpt) relevant for registration and implementation of biopesticides. The table contains only major regulations and major amendments without referring to guidelines, guidance documents, communication from Commission or similar documents. For a more detailed summary of historical developments in the EU see Huber (2019).

In addition to the basic implementations of EU legal frameworks on the AS and PPP registration process as described above, there are several other important legislative procedures with an even more direct impact on the current registration procedures. With entry into force of the first specific PPP authorization regulation, Directive 91/414, the basis for registration of PPPs was established. Many of the provisions introduced by this directive are still in use, such as the AS renewal or PPP re-authorization processes. Other parts of Directive 91/414 had a more feeble and transient character, as for example the introduction of the IPM principles, and thus the basis for a broader use of biopesticides. As experience shows, inclusion of IPM in Directive 91/414 had no significant impact on biopesticide use or registration for many years, leading to deficiencies in the development of IPM strategies and consequently also in improving sustainability. After the introduction of Directive 91/414 many amendments and guidance documents were published, but these were mainly focused on administrative procedures and requirements for chemical PPPs, as for example regulations on the maximum residue limits (MRLs) of pesticides. The neglect of biopesticides became especially evident with the entry into force of Directive 2001/36 in 2001, establishing the data requirements for AS and PPPs. As was obvious from the beginning, these data requirements were not suitable for most biopesticides and especially microorganisms, since they were designed for the evaluation and registration of chemical pesticides. Unfortunately, for biopesticides based on microorganisms this situation again did not change with the revision and update of the data requirements for pesticides in 2013. Data requirements for microorganisms provided for in the respective Regulation 283/2013 for AS and Regulation 284/2013 for PPPs stayed unaltered, again using a ‘copy and paste’ approach from chemical pesticide requirements. Currently, decades after establishing the framework for PPP evaluation by Directive 91/414, the status quo of data requirements for microorganisms is more or less still unaltered. At least, entry into force of Regulation 1107/2009 in 2011 established a new concept, deemed to be beneficial to many biopesticide registrations, i.e., the separation of the so-called basic substances and low-risk substances from conventional chemical AS. For substances with a respective low-risk profile with regard to human, animal and environmental health and safety, this should simplify the registration process and provide certain incentives for industry to register low-risk products, such as reduced registration costs or longer approval periods of up to 15 years. As with the general data requirements, for biopesticides based on microorganisms, introduction of the low-risk category again did not profoundly change the registration process for several years. This is particularly evident in the fact that the criteria for classification of low-risk substances were published only in 2017. In addition, the low-risk criteria established by Regulation 2017/1432 for microorganisms are incomplete and final criteria are currently still under development. However, for other, non-microbial biopesticides such as botanicals, introduction of the low-risk category by Regulation 1107/2009 and 2017/1432 are a significant improvement in the registration process. From end of 2022 onwards, new data requirements for MBCAs will apply. In general, the upcoming data requirements shall better reflect the special characteristics of microorganisms. For example, for environmental fate the focus is restricted now to surface and groundwater only and a microorganism persisting in concentrations considerably higher than the natural background levels is not excluded from registration per se anymore. Moreover, the new regulations enable registration holders, at least theoretically, to register microbial consortia.

As is obvious from the description of the historical developments, the EU’s PPP legal framework is only seldom proactive but mainly responds to other, more reactive legal frameworks, often with a significant delay. However, Regulation 1107/2009 was not published as a single legislative act but in conjunction with three other acts, namely regulations on the statistics on pesticides, on the machinery for pesticide application and especially the SUD. An example for the interplay between these regulations is the subsequent adoption of the so-called harmonized risk indicators to estimate the risks from pesticide use. Calculations are based on the quantities of AS brought onto the market, the number of authorizations granted for PPPs for emergency use and the hazard weighting of AS. Whereas low-risk active substances have a weighting factor of one, candidates for substitution have a weighting factor of 16 and any other AS a weighting factor of eight. The regulation obliges MS to calculate annually the Harmonized Risk Indicators. The results of these evaluations have to be made available to the EU’s Commission (EC), MS and the public. Hence, this additional legal triple pack was designed to set the framework for the current registration process and future developments, and aligns PPP registration processes with other EU legal frameworks. Indeed, in the recent past SUD allowed for implementation of accompanying human, animal and environmental health and safety initiatives, especially the EU’s Green Deal and the revised General Food Law. Fostered by several motions and initiatives of the European Parliament, the Green Deal was introduced as a roadmap for the transition to a sustainable, fair EU economy by converting the current climatic and environmental challenges to innovations across all policy areas. Central pillars of this roadmap are the first European Climate Law, a Biodiversity Strategy, a new Industrial Strategy and Circular Economy Action Plan and a Farm to Fork Strategy to boost sustainable food and to make proposals for a pollution-free Europe. To name only a few, key actions targeted by the Green Deal include the reduction of the use and risk of chemical pesticides by 50% by 2030, the revision of the SUD, and the development of the EU organic farming area. The EU organic farming strategy aims at conversion of 25% of total farmland to organic rules, also by 2030. The initiatives of the Green Deal package affect PPPs in every aspect, from R&D to production, registration and sales, as PPPs have to comply with all the requirements of the Green Deal. Indeed, biopesticides and their use, especially in IPM and organic farming, are regarded as a major tool to achieve this transition. The revision of the General Food Law, particularly Regulation 2019/1381 on the transparency and sustainability of the EU risk assessment in the food chain, adopted in June 2019 and applicable from March 2021 onwards, causes significant changes for PPPs. In general, this regulation partly implements some of the EU Green Deal and sustainability goals, as it introduces several requirements and tools in the registration process for PPPs to achieve a higher transparency. This is accomplished by making information on AS and respective studies available to the public and allowing for public participation in the registration process at a very early stage. As is evident, this affects not only the registration process itself, but of course also R&D, registration and business strategies for all PPPs, including biopesticides.

As well as all the requirements, developments, innovations and opportunities already in place or ongoing at an EU level, national regulations, laws and aspects are not to be neglected. On the one hand, this applies for the often very different national requirements for PPP authorization. On the other hand, the business and registration strategies, national legal and regulatory terms and conditions are of high importance. In the case of biopesticides, this is particularly evident in the national programmes that offer incentives to promote the authorization and use of biopesticides, which are mainly anchored in the so-called National Action Plans, based on the SUD. Reduced registration fees, funding programmes or preferential handling of applications for low-risk PPPs and biopesticides are examples for such incentives. Consequently, national measures may offer several opportunities and possibilities for low-risk and biopesticide AS and PPPs.

The aim of this historical view on developments and conditions is to provide a basic overview on current and future PPP rules. However, it should also highlight that consideration and knowledge of legal and regulatory aspects are key elements and the sine qua non for the development of business and registration strategies for biopesticides. Hence, their incorporation at the AS/PPP-specific level as early as possible is crucial.

The previous paragraphs focused on the legal and regulatory frameworks for the registration of AS and PPPs in the EU, as this topic is too complex and diverse to consider additionally developments for other countries in this chapter. However, the developments in PPP regulations are triggered by similar circumstances and conditions and their economic impacts worldwide: climate change, increase in world population, soil erosion and degradation, water protection, safe food, sustainability and greening, etc. In addition, globalization and consequently the global food trade also influence national country-specific rules and vice versa, for example in regard to import and export of food and feed treated with PPPs. Thus, frameworks and rules for PPP use and registration become even more harmonized on a global level. One of the many examples in this regard is the recently published Green Food System Strategy for Japan, which more or less follows the established EU rules. Incorporating global developments in AS and PPP-specific business and registration strategies therefore is challenging but prudent.

1.2  Procedures to be Followed for the Registration of a Biopesticide

Active substances of PPPs, defined by Regulation 1107/2009, have to be approved at an EU level before national PPP authorizations are possible. The general procedure for an AS approval is the provision of detailed information on the AS by the applicant (Fig. 1.1).

An illustration of regulatory steps for the approval of a new active substance.

Fig. 1.1. Simplified scheme and approximate timelines of the regulatory steps for the approval of a new active substances according to Regulation 1107/2009. The scheme does not consider regulatory requirements such as study notification or pre-submission advice. Detailed information on these regulatory processes is published in Regulation 1107/2009 or Regulation 2019/1381. COM, European Commission; DAR, Draft Assessment Report; EFSA, European Food Safety Authority; m, months.

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Information and data are presented in the form of a dossier, including all information required by Regulation 283/2013 and 284/2013 in respect of the AS and a representative PPP. Subsequently, the dossier is evaluated by an MS, the so-called Rapporteur member state (RMS), which assesses whether a dossier is admissible and, if yes, will use the information provided in the applicant’s dossier to evaluate the substance and to write an Assessment Report. This Assessment Report will be further commented by the other MS, the public and the European Food Safety Authority (EFSA). The final scientific evaluation of the assessment report is conducted by EFSA, which can request further data from the applicant, to be provided within a certain time frame. At this stage, it is not possible for the applicant to provide additional information or data without specific requests from authority. Afterwards, EFSA will publish its conclusion and set a list of endpoints derived from the studies and data evaluated. The final decision whether a substance will be approved or not, maybe even as low-risk substance, is made by the European Commission. For this decision, the Commission reviews the EFSA conclusion and drafts a review report and a draft Implementing Regulation. Later on, the Standing Committee on Plants, Animals, Food and Feed (PAFF Committee) will take the respective vote. The final Implementing Regulation is published a few months after the final vote. The Commission will also decide for which AS type an approval is granted, resulting in an approval period up to 10 years for the first approval of conventional AS and 15 years for low-risk AS. Therefore, the approval of an AS must be renewed at regular intervals to keep the substance available for use in PPPs. For the renewal, more or less the same procedure as described above applies. The whole procedure for AS approval is quite time consuming and takes at least 30 months for evaluation by authorities. However, authorities often lag behind their deadlines, which can lead to significant delays.

Food safety and also the safety of PPPs are generally of very high interest for the European Union and its citizens. To guarantee a transparent insight on the scientific and regulatory evaluation of substances used in food production, and to strengthen the trust of the public in the safety of food, the Transparency Regulation 2019/1381 was adopted. The implementation of the Transparency Regulation has major impacts on the regulatory procedures, making more information available to the public. In this context, all studies that are conducted for a submission at EU level have to be notified centrally before the study starts. Studies carried out after 27 March 2021 that were not notified will not be accepted. Moreover, applicants have to provide information on each notified study and studies have to be either integrated in the dossier, or a justification for not using the study should be provided. Additionally, a rationale has to be provided if studies are terminated before being completed. If an applicant does not meet these obligations, the dossier will be considered as non-admissible and even if data or justifications are submitted later, there will be a penalty delay of 6 months in the assessment. Transparency is further increased by the mandatory use of the electronic data submission platform IUCLID (International Uniform ChemicaL Information Database) from March 2021 onwards, which makes the complete dossier, including studies, available to the public.

The procedures are similar for all AS or representative PPPs regardless of whether for a biopesticide or for a conventional chemical. Fast-track procedures for biologicals, possible in several countries outside the EU, are not foreseen. Instead, the EU differentiates between conventional and low-risk AS and PPPs. A substance must meet several criteria, listed in Regulation 2017/1432, to qualify as a low-risk substance. Substances, other than microorganisms, shall not, for example, be cancerogenic, mutagenic or cause serious eye damage. A microorganism that is intended to act as an AS may be considered as being low-risk unless at strain level it has demonstrated multiple resistance to antimicrobials used in human or veterinary medicine. However, even if this is the only criterion for microbial AS to comply with at the moment, several microbial active substances are not considered low-risk, due to for example the possible formation of secondary metabolites in situ. Additional criteria for microorganisms are currently under development.

The only derogation from the procedures described above is the approval for so-called basic substances. Basic substances, according to Regulation 1107/2009, are not regarded as typical AS. Requirements concerning safety and harmlessness are even stricter than for low-risk substances; thus, mainly substances used as food or feed are eligible for approval. In addition, it is required that the substance is not predominantly used for plant protection purposes and is not already placed on the market as a PPP. The basis of the basic substance idea is that a basic substance is not of economic interest for the plant protection industry; hence, MS or interested parties (e.g., grower associations) can apply for the approval of such substances. Considering the harmless nature of these substances, only a reduced data package needs to be submitted for the assessment. Moreover, for basic substances no renewal procedure is foreseen, as they are approved for an unlimited period of time. Nevertheless, the Commission is free to review basic substance approvals at any time, which might lead to a withdrawal if the prerequisites defining a basic substance are no longer met.

Except for basic substances, applicants must address all data requirements according to Regulation 283/2013 for AS and Regulation 284/2013 for PPPs. Both Regulations have to be considered for AS approval, since the information to be provided for the approval process consists of AS data and data on a representative PPP formulation. By providing data also for a representative PPP, authorities can assess the suitability of an AS, for example by reviewing the conditions of use for a representative PPP and by evaluating respective risks. The uses of a PPP are generally summarized in the ‘GAP table of intended uses’, where GAP stands for ‘good agricultural practice’. GAP was defined by the Food and Agriculture Organization (FAO) as a practice that ‘applies available knowledge to addressing environmental, economic and social sustainability for on-farm production and post-production processes resulting in safe and healthy food and non-food agricultural products’ (FAO, 2003). The data requirements cover different scientific information in separate sections, including identity, physical–chemical properties and biological properties, function, use and efficacy, analytical methods, toxicology, residues of the AS in or on treated crops, fate and behaviour in the environment and ecotoxicity. These data requirements were originally developed and designed for classical chemical substances. The special characteristics of biopesticides, which form a very heterogeneous group with only their natural origin in common, are not specifically considered in these regulations, but for some cases data requirements are further elucidated by guidance documents. Nevertheless, inappropriate data requirements cannot simply be ignored and applicants have to provide data or information for each point requested. However, this does not necessarily mean that studies have to be conducted. This is of special importance because also testing guidelines are often not suitable for the various biopesticides, e.g., microorganisms. Instead of using studies or even customized (and, as such, potentially expensive) studies, more effort in addressing data requirements by scientific argumentation and use of peer-reviewed literature is needed. This is generally true for all AS, but has to be emphasized for biopesticides. Scientific argumentation for addressing data requirements for biopesticides is often provided by the natural occurrence of the substance. Humans, other organisms and the environment are naturally exposed and therefore various publications on the substance or related substances or organisms might already be available. Moreover, due to the natural occurrence, MRLs are often not required for biopesticides. However, information on the residue situation of a substance must also be provided in the dossier for these cases, but a scientific justification based on natural occurrence and exposure of humans, animals and the environment is often considered sufficient.

Nevertheless, the use of biological PPPs is an artificial and additional input into the environment and all consequences must be assessed as far as possible. Effects of a substance or organism can be very different, depending on the environmental compartment or target organism. This is particularly evident for the example of plant oils used as AS. Although some oils are foodstuff without relevant toxicological effects on humans, they cannot be considered as safe in general, since they are potentially toxic for non-target species such as aquatic organisms. Moreover, the environmental fate of a substance might be very different, depending on the environmental compartment in which it is released. Therefore, data on the environmental fate of a substance in soil, water and sediment as well as air has to be assessed in a dossier. As a consequence of this, some uses of a PPP might be more critical in one dossier section compared with another. To meet all these conditions, the risk assessment can be targeted to the worst-case scenario uses by the so-called risk envelop approach. These uses are presented section-specifically in the so-called ‘critical GAP’ or ‘worst-case GAP’.

After the approval of the AS at EU level, it is possible to register respective PPPs, whereas registrations are granted on national level (Fig. 1.2).

For administrative and regulatory purposes, national PPP authorizations are handled via a so-called zonal approach, partly to account for implementation of the mutual recognition principle and the free movement of goods as well as to reduce the administrative burden for industry and MS. Regulation 1107/2009 therefore divides the EU territory into three zones with comparable conditions: the Northern European Zone (NEZ), Central European Zone (CEZ) and Southern European Zone (SEZ). For each zone wherein a PPP is intended to be authorized, a zonal Rapporteur Member State (zRMS) is assigned, taking on the main responsibility for the evaluation process. If, besides the country which acts as zRMS, authorizations are applied for in additional countries of the respective zone (denominated as so-called concerned MS (cMS)), these authorizations are mainly based on the previous evaluation of the zRMS. However, the main data requirements for PPP registration are also determined at the EU level and are listed in Regulation 284/2013. Moreover, the evaluation of PPPs is also in line with the Uniform Principles and the EU Precautionary Principles, which allows the withdrawal of a PPP registration at European level if unacceptable risks occur. This should guarantee that only safe PPPs are available on the European market.

An illustration of regulatory steps for plant protection product registration.

Fig. 1.2. Simplified scheme and approximate timelines of the regulatory steps for a plant protection product registration according to Regulation 1107/2009. Detailed information on these regulatory processes is published in Regulation 1107/2009. cMS, concerned Member State; dRR, draft Registration Report; m, months; MS, Member State; w, weeks; zRMS, zonal Rapporteur Member State.

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Depending on the AS and product characteristics, the strategy for addressing the above-mentioned data requirements has to be very substance-specific. However, performance and efficacy issues of a PPP, which are part of the AS approval, as well as the PPP authorization process (with more importance in the second procedure), also strongly depend on individual business and registration strategies. The respective study package often comprises one of the major investments in a PPP authorization venture. In the scope of the evaluation, proof of effectiveness is the main but not the only part. In addition to effectiveness, other PPP performance parameters such as selectivity and phytotoxicity, influence of a PPP on food-processing processes or food-quality traits such as taint testing also have to be addressed. In Europe, efficacy and PPP performance testing and evaluation are mainly based on standards and guidance