Key issues in the deliberate release of genetically-manipulated bacteria

Abstract The deliberate release of a genetically engineered bacterium often requires that a complex pathway be travelled through scientific and regulatory questions. It is important to consider the scientific aim of the release and the nature of the modification (deletion or insertion, site of insertion, level of expression) and its likely effect on survival of the organism and the possibility of gene transfer. In Australia, the Genetic Manipulation Advisory Committee assesses applications and makes recommendations about pre-release testing and procedures for conducting field release. Two examples of field release of genetically manipulated bacteria in Australia are considered. Firstly, the commercial product Agrobacterium strain K1026 (‘NoGall’^TM), a genetically engineered biological control agent for crown gall disease of stone fruits and roses. Secondly, a lacZY -marked derivative of a strain of Pseudomonas corrugata , that can act as a biological control agent against take-all disease of wheat. Prior to release, bacterial survival and competition was tested in soil microcosms. The distribution and survival of the organism were monitored after field release. Since 1992 the marked bacteria have been recovered only after enrichment. Assessment of risk should consider the survival and spread of the genetically manipulated bacterium and its foreign DNA and the impact of the inoculated bacteria on other (‘non-target’) organisms.     

Not all GMOs are crop plants: non-plant GMO applications in agriculture

Since tools of modern biotechnology have become available, the most commonly applied and often discussed genetically modified organisms are genetically modified crop plants, although genetic engineering is also being used successfully in organisms other than plants, including bacteria, fungi, insects, and viruses. Many of these organisms, as with crop plants, are being engineered for applications in agriculture, to control plant insect pests or diseases. This paper reviews the genetically modified non-plant organisms that have been the subject of permit approvals for environmental release by the United States Department of Agriculture/Animal and Plant Health Inspection Service since the US began regulating genetically modified organisms. This is an indication of the breadth and progress of research in the area of non-plant genetically modified organisms. This review includes three examples of promising research on non-plant genetically modified organisms for application in agriculture: (1) insects for insect pest control using improved vector systems; (2) fungal pathogens of insects to control insect pests; and (3) virus for use as transient-expression vectors for disease control in plants.     

Environmental risks from the release of genetically modified organisms (GMOs)–the need for molecular ecology

Applications to release genetically modified organisms (GMOs) into the environment, usually the agricultural environment, are increasing exponentially. Many involve crop plants that are also weeds. Studies of biological invasions and of biological control show that the probability that a genetically new organism establishing itself is small; it is also unpredictable and in some cases could have severe ecological effects. GMOs pose risks both because they will be released in large numbers and because the greater the genetic novelty the greater the possibility of ecological novelty. Molecular ecology is an essential ingredient in ensuring that risks are assessed efficiently.     

U.S. regulatory framework for genetic biocontrol of invasive fish

This paper provides an overview of the U.S. regulatory framework governing genetic biocontrol efforts for invasive fish. Genetic biocontrol refers to the intentional release of genetically modified organisms (GMOs) into the environment to control a target population of a non-native species. The terms “genetically modified” and “genetically engineered” are often used interchangeably, despite the scientific distinctions. A GMO is an organism that has had its genetic material altered or modified by humans through any method, including conventional breeding. Genetic engineering, as defined by the Food and Drug Administration (FDA), is the use of recombinant DNA techniques to introduce new characteristics or traits into an organism. GE organisms are therefore a subset of GMOs. As this paper will discuss, existing laws focus on GE organisms raising significant questions as to whether organisms modified without utilizing rDNA techniques fall within the jurisdiction of any federal agency. Under the 1986 Coordinated Framework for Regulation of Biotechnology, three federal agencies have primary responsibility over biotechnology—the Environmental Protection Agency (EPA), the U.S. Department of Agriculture, and the FDA. Because the EPA has exempted biological control agents from regulation as pesticides and no fish species are currently considered plant pests, the FDA is the agency responsible for approving the use of genetically engineered fish for biocontrol. FDA regulates genetically engineered animals through its New Animal Drug Application (NADA) process. The NADA process presents several challenges to effective and transparent regulation of genetic biocontrol, including the FDA’s focus on drug safety, secrecy provisions potentially limiting disclosure of the results of environmental reviews, and the secondary role of the Fish and Wildlife Service, the federal agency with the most experience with invasive species management. In addition, relying on the NADA process creates a significant regulatory gap as NADA approval is only required for GE organisms. The regulatory framework for GMOs created for genetic biocontrol without rDNA technology is unclear and primary responsibility may fall to the states. Given its extensive experience with hatcheries, invasive fish species control, and environmental reviews, the Fish and Wildlife Service (FWS) is the more appropriate agency to review applications for genetic biocontrol. Efforts should be undertaken now, while genetic biocontrol is still in the theoretical stages, to increase the role of the FWS in the permitting process either through formal regulations or more informal mechanisms such as memorandum of understanding.     

Conjugal transfer of R68.45 and FP5 between Pseudomonas aeruginosa strains in a freshwater environment

Recent concern over the release of genetically engineered organisms has resulted in a need for information about the potential for gene transfer in the environment. In this study, the conjugal transfer in Pseudomonas aeruginosa of the plasmids R68.45 and FP5 was demonstrated in the freshwater environment of Fort Loudoun Resevoir, Knoxville, Tenn. When genetically well defined plasmid donor and recipient strains were introduced into test chambers suspended in Fort Loudoun Lake, transfer of both plasmids was observed. Conjugation occurred in both the presence and absence of the natural microbial community. The number of transconjugants recovered was lower when the natural community was present. Transfer of the broad-host-range plasmid R68.45 to organisms other than the introduced recipient was not observed in these chambers but was observed in laboratory simulations when an organism isolated from lakewater was used as the recipient strain. Although the plasmids transferred in laboratory studies were genetically and physically stable, a significant number of transconjugants recovered from the field trials contained deletions and other genetic rearrangements, suggesting that factors which increase gene instability are operating in the environment. The potential for conjugal transfer of genetic material must be considered in evaluating the release of any genetically engineered microorganism into a freshwater environment.     

Conjugal transfer of R68.45 and FP5 between Pseudomonas aeruginosa strains in a freshwater environment.

Recent concern over the release of genetically engineered organisms has resulted in a need for information about the potential for gene transfer in the environment. In this study, the conjugal transfer in Pseudomonas aeruginosa of the plasmids R68.45 and FP5 was demonstrated in the freshwater environment of Fort Loudoun Resevoir, Knoxville, Tenn. When genetically well defined plasmid donor and recipient strains were introduced into test chambers suspended in Fort Loudoun Lake, transfer of both plasmids was observed. Conjugation occurred in both the presence and absence of the natural microbial community. The number of transconjugants recovered was lower when the natural community was present. Transfer of the broad-host-range plasmid R68.45 to organisms other than the introduced recipient was not observed in these chambers but was observed in laboratory simulations when an organism isolated from lakewater was used as the recipient strain. Although the plasmids transferred in laboratory studies were genetically and physically stable, a significant number of transconjugants recovered from the field trials contained deletions and other genetic rearrangements, suggesting that factors which increase gene instability are operating in the environment. The potential for conjugal transfer of genetic material must be considered in evaluating the release of any genetically engineered microorganism into a freshwater environment.     

A functional abc for biotechnology and the dissemination of its progeny

In this paper we present a functional analysis of biotechnology and identify the particular status that genetic engineering has relative to other biotechnological techniques such as domestication. The analysis builds on work by Dan Sperber and characterises biotechnology in primarily technical and biological functional terms as symbiotic interactions in which humans modify other organisms. We identify three main routes by which these interactions are established in biotechnology. We argue that two of these routes have in-built mechanisms for preventing an uncontrolled dissemination of the modified organisms, and that one has an in-built mechanism for promoting such dissemination. The three routes are available to traditional forms of biotechnology as to state-of-the-art genetic engineering. Drawing now on work by Alfred Nordmann on the uncanniness of modern technologies, we show that genetic engineering is set apart by the epistemic consequences of the microscopic size of its progeny: genetically modified organisms, when disseminating, do so beyond our perceptual and conceptual control. Existing strategies against unwanted dissemination of organisms modified in traditional biotechnology are therefore typically not adequate against possible unwanted dissemination of genetically modified organisms, giving this dissemination a status similar to that of untraceable natural disasters.     

A public goods approach to major evolutionary innovations

The history of life is marked by a small number of major transitions, whether viewed from a genetic, ecological, or geological perspective. Specialists from various disciplines have focused on the packaging of information to generate new evolutionary individuals, on the expansion of ecological opportunity, or the abiotic drivers of environmental change to which organisms respond as the major drivers of these episodes. But the critical issue for understanding these major evolutionary transitions (METs) lies in the interactions between environmental, ecologic, and genetic change. Here, I propose that public goods may serve as one currency of such interactions: biological products that are non‐excludable and non‐rivalrous. Such biological public goods may be involved in either the generation of new evolutionary variation, as with genetic sequences that are easily transferred between different microbial lineages, or in the construction of new ecological niches, as with the progressive oxygenation of the oceans and atmosphere. Attention to public goods emphasizes the processes by which organisms actively construct their own evolutionary opportunities. Such public goods may have facilitated some METs.     

EvoluZion: a computer simulator for teaching genetic and evolutionary concepts

EvoluZion is a forward-in-time genetic simulator developed in Java and designed to perform real time simulations on the evolutionary history of virtual organisms. These model organisms harbour a set of 13 genes that codify an equal number of phenotypic features. These genes change randomly during replication, and mutant genes can have null, positive or negative effects on the organisms’ fitness, allowing to model effects of both selection pressures and drift on gene evolution. There are two versions of this program: version 1.6.x_haploid; focused on macroevolutionary events and depicting prokaryote-like organisms, and version 2.3.x_diploid that simulate diploid, sexually reproducing organisms, and it is more adequate to teach micro-evolution as well as key genetic concepts such as Mendel’s laws, epistasis, genetic linkage, genetic mapping among others. Different data sets can be collected periodically during running in order to perform further analyses. In addition, the complete genealogy of extant as well as extinct organisms can be recorded. EvoluZion is well suited for teaching evolutionary biology concepts to students of all levels in a pedagogic way. This is mainly due to three main program features: (i) its intuitive and simple graphical interface (ii) a visualisation similar to videogames (iii) flexible integration of a wide range of biological phenomena into a single simulation.     

Field Releases of the Predatory Mite Neoseiulus fallacis (Acari: Phytoseiidae) in Canada, Monitored by Pyrethroid Resistance and Allozyme Markers

The predacious phytoseiid mite Neoseiulus fallacis (Garman) is an important agent for the biological control of spider mites in deciduous fruit orchards in North America and Canada. It would be helpful to monitor the fate of released individuals to improve the results of introductions of the predators in biological control trials. We have used two types of genetic markers, pyrethroid resistance and allozymes, for indirect estimation of the survival of N. fallacis introduced in an apple orchard in Ontario, Canada. Mite samples were submitted to toxicological tests. The polymorphism of four enzymes was studied in individual females using an isoelectric focusing technique. A mite sample was taken from the field, mass-reared in the laboratory, and selected for permethrin resistance. This strain was released on several apple trees treated with permethrin, and mite samples were collected from the same trees 10 to 90 days later. The genetic composition and the insecticide resistance level of this sample were compared to those of two other samples from trees where mites had not previously been released, either in the same orchard or in a neighboring block. A control susceptible strain was compared using mites collected earlier from trees on the same site but outside the present experiment. The mites collected from the release trees and those from the strain used for the releases were found to be genetically closely related, as judged from a small genetic distance, and from similar levels of insecticide resistance in both samples. The control samples from the nonrelease trees were genetically distant from these and displayed low resistance levels. These results indicate that the released genotypes established and persisted in the release trees for the period of the experiment. The utility of the two approaches in assessing the fate of released natural enemies is discussed.     

A generalization of Pontryagin's maximum principle for dynamic evolutionary games among relatives

We present two theorems that generalize Pontryagin's maximum principle to the setting of dynamic evolutionary games between genetically related individuals. The two theorems correspond to two types of interactions among individuals: patch-structured populations in which individuals locally "play the field" and pairwise interactions. These generalizations can be used in the same way that Pontryagin's maximum principle is used and they are valid for diploid organisms under a single locus, diallelic genetic model. These generalizations involve an interesting, dynamic version of Hamilton's Rule from inclusive fitness theory. We illustrate how these theoretical results can be applied by modeling the evolution of lifetime resource allocation to growth and reproduction in an annual plant when there is competition for resources among related individuals.     

Challenges for identifying functionally important genetic variation: the promise of combining complementary research strategies

Strategies for the identification of functional genetic variation underlying phenotypic traits of ecological and evolutionary importance have received considerable attention in the literature recently. This paper aims to bring together and compare the relative strengths and limitations of various potentially useful research strategies for dissecting functionally important genetic variation in a wide range of organisms. We briefly explore the relative strengths and limitations of traditional and emerging approaches and evaluate their potential use in free-living populations. While it is likely that much of the progress in functional genetic analyses will rely on progress in traditional model species, it is clear that with prudent choices of methods and appropriate sampling designs, much headway can be also made in a diverse range of species. We suggest that combining research approaches targeting different functional and biological levels can potentially increase understanding the genetic basis of ecological and evolutionary processes both in model and non-model organisms.     

Widespread genetic mosaicism in the marine angiosperm <Emphasis Type="Italic">Zostera marina</Emphasis> is correlated with clonal reproduction

Somatic mutations are an underappreciated source of genetic variation within multi-cellular organisms. The resulting genetic mosaicism should be particularly abundant in large clones of vegetatively propagating angiosperms. Little is known on the abundance and ecological correlates of genetic mosaicism in field populations, despite its potential evolutionary significance. Because sexual reproduction restores genetic homogeneity, we predicted that in facultatively clonally reproducing organisms, the prevalence of genetic mosaicism increases with increasing clonality. This was tested among 33 coastal locations colonized by the ecologically important marine angiosperm Zostera marina, ranging from Portugal to Finland. Genetic mosaics were detectable as complex microsatellite genotypes at two hypervariable loci that revealed additional mosaic alleles, suggesting the presence of one or more divergent cell lineages within the same ramet. The proportions of non-mosaic genotypes in a population sharply decreased below a clonal richness of 0.2. Accordingly, more genetic mosaics were found at the southern and northern limit of the distribution of Z. marina in Europe where sexual reproduction is rare or absent. The genetic mosaics observed at neutral microsatellite markers suggest the possibility of within-clone variation at selectively relevant loci and supports the notion that members of clones are seldom genetically identical.     

Understanding the establishment success of non-indigenous fishes: lessons from population genetics

During the last 10 years, an increasing number of studies have explored evolutionary aspects of biological invasions. It is becoming increasingly clear that evolutionary processes play an important role during the establishment of non-native species. Genetic drift during the colonization process followed by strong selection imposed through a change in biotic conditions and co-evolutionary disequilibrium set the conditions for rapid evolutionary change in introduced populations. Different hypotheses, which have been proposed to explain how evolutionary and genetic processes, can facilitate invasiveness are explored and their relevance for fish invasions is discussed. Empirical evidence increasingly suggests that admixture after multiple introductions, hybridization between native and non-native species and enemy release can all catalyse the evolution of invasiveness. A number of studies also suggest that genetic bottlenecks might represent less of genetic paradox than previously thought. Much of the theoretical developments and empirical evidence concerning the importance of evolution during biological invasions has been provided from studies on invasive plants. Despite their prominence, fish invasions have received little attention from evolutionary biologists. Recent advances in population genetic analysis such as non-equilibrium methods and genomic techniques such as microarray technology provide suitable tools to address such issues.     

Release of transgenic bacterial inoculants - rhizobia as a case study

The current debate on the release of genetically modified organisms to the environment must be informed by scientific data obtained from field studies. Many of the microorganisms that have potential applications outside the laboratory, especially in agriculture and horticulture, could be improved by genetic modification. Rhizobia, the bacteria that form N₂-fixing symbioses with leguminous plants, have a long history of safe use as seed inoculants, their biology is relatively well known, and they represent a relevant model system. There have been several field releases of genetically modified (GM) rhizobia in the USA and Europe, which provide information on various aspects of their ecology and efficacy. This review summarises the rationale for each release, details of the methods used for monitoring, and the results. Novel properties of rhizobia did not always have the predicted effects. Most studies revealed that rhizobial numbers dropped rapidly after application to soil or seeds but then numbers stabilised for months or years. The monitoring of survival and spread of rhizobia was greatly improved by the presence of novel marker genes. Tagging of rhizobia with marker genes provided more accurate information compared to the use of conventional strains, illustrating an important application of genetic modification, for tracking bacteria in the environment.     

Deciphering host migrations and origins by means of their microbes

Mitochondrial DNA and microsatellite sequences are powerful genetic markers for inferring the genealogy and the population genetic structure of animals but they have only limited resolution for organisms that display low genetic variability due to recent strong bottlenecks. An alternative source of data for deciphering migrations and origins in genetically uniform hosts can be provided by some of their microbes, if their evolutionary history correlates closely with that of the host. In this review, we first discuss how a variety of viruses, and the bacterium Helicobacter pylori, can be used as genetic tracers for one of the most intensively studied species, Homo sapiens. Then, we review statistical problems and limitations that affect the calculation of particular population genetic parameters for these microbes, such as mutation rates, with particular emphasis on the effects of recombination, selection and mode of transmission. Finally, we extend the discussion to other host-parasite systems and advocate the adoption of an integrative approach to both sampling and analysis.     

Mapping unexplored genomes: a genetic linkage map of the Hawaiian cricket Laupala

As with many organisms of evolutionary interest, the Hawaiian cricket Laupala genome is not well characterized genetically. Mapping such an unexplored genome therefore presents challenges not often faced in model genetic organisms and not well covered in the literature. We discuss the evolutionary merits of Laupala as a model for speciation studies involving prezygotic change, our choice of marker system for detecting genetic variation, and the initial genetic expectations pertaining to the construction of any unknown genomic map in general and to the Laupala linkage map construction in particular. We used the technique of amplified fragment length polymorphism (AFLP) to develop a linkage map of Laupala. We utilized both EcoRI/MseI- and EcoRI/PstI-digested genomic DNA to generate AFLP bands and identified 309 markers that segregated among F(2) interspecific hybrid individuals. The map is composed of 231 markers distributed over 11 and 7 species-specific autosomal groups together with a number of putative X chromosome linkage groups. The integration of codominant markers enabled the identification of five homologous linkage groups corresponding to five of the seven autosomal chromosomal pairs found in Laupala.     

High genetic variance in life-history strategies within invasive populations by way of multiple introductions

Biological invasions represent major threats to biodiversity as well as large-scale evolutionary experiments. Invasive populations have provided some of the best known examples of contemporary evolution [3-6], challenging the classical view that invasive species are genetically depauperate because of founder effects. Yet the origin of trait genetic variance in invasive populations largely remains a mystery, precluding a clear understanding of how evolution proceeds. In particular, despite the emerging molecular evidence that multiple introductions commonly occur in the same place, their contribution to the evolutionary potential of invasives remains unclear. Here, by using a long-term field survey, mtDNA sequences, and a large-scale quantitative genetic experiment on freshwater snails, we document how a spectacular adaptive potential for key ecological traits can be accumulated in invasive populations. We provide the first direct evidence that multiple introductions are primarily responsible for such an accumulation and that sexual reproduction amplifies this effect by generating novel trait combinations. Thus bioinvasions, destructive as they may be, are not synonyms of genetic uniformity and can be hotspots of evolutionary novelty.     

Safety of Microorganisms Intended for Pest and Plant Disease Control: A Framework for Scientific Evaluation

Microorganisms are enormous but largely untapped natural resources for biological control of pests and diseases. There are two primary reasons for their underployment for pest or disease control: (1) the technical difficulties of using microorganisms for biological control, owing to a lack of fundamental information on them and their ecology, and (2) the costs of product development and regulatory approvals required for each strain, formulation, and use. Agriculture and forestry benefit greatly from the resident communities of microorganisms responsible for naturally occurring biological control of pest species, but additional benefits are achieved by introducing/applying them when or where needed. This can be done as (1) an inoculative release, (2) an augmentative application, or (3) an inundative application. Because of their specificity, different microbial biocontrol agents typically are needed to control different pests or the same pest in different environments. Four potential adverse effects are identified as safety issues (hazards) associated with the use of microorganisms for the biological control of plant pests and diseases. These are: (1) displacement of nontarget microorganisms, (2) allergenicity to humans and other animals, (3) toxigenicity to nontarget organisms, and (4) pathogenicity to nontarget organisms. Except for allergenicity, these are the same attributes that contribute to the efficacy of microbial biocontrol agents toward the target pest species. The probability of occurrence of a particular adverse nontarget effect of a microbial biocontrol agent may be a function of geographic origin or a specific trait genetically added or modified, but the safety issues are the still the same, including whether the microorganism intended for pest or disease control is indigenous, nonindigenous (imported and released), or genetically modified by traditional or recombinant DNA (rDNA) technology. Likewise, the probability of occurrence of a particular adverse nontarget effect may vary with method of application, e.g., whether as an aerosol, soil treatment, baits, or seed treatment, and may increase with increased scale of use, but the safety issues are still the same, including whether the microorganism is used for an inoculative release or augmentative or inundative application. Existing practices for managing microorganisms in the environment (e.g., plant pathogens,Rhizobium,plant inoculants) provide experience and options for managing the risks of microorganisms applied for pest and disease control. Moreover, experience to date indicates that any adverse nontarget effects, should they occur, are likely to be short-term or transitory effects that can, if significant, be eliminated by terminating use of the microbial biocontrol agent. In contrast, production agriculture as currently practiced, such as the use of tillage and crop rotations, has significant and long-term effects on nontarget organisms, including the intentional and unintentional displacement of microorganisms. Even the decision to leave plant pests and diseases unmanaged could have significant long-term environmental effects on nontarget organisms. Potential safety issues associated with the use of microbial biocontrol must therefore be properly identified and compared with the impact of other options for managing the pest or leaving the pest unmanaged. This paper provides a scientific framework for this process.