Genetically modified crops for the bioeconomy: meeting public and regulatory expectations

The role of microbial partners in heavy metal metabolism in plants: a review

Heavy metal pollution threatens plant growth and development as well as ecological stability. Here, we synthesize current research on the interplay between plants and their microbial symbionts under heavy metal stress, highlighting the mechanisms employed by microbes to enhance plant tolerance and resilience. Several key strategies such as bioavailability alteration, chelation, detoxification, induced systemic tolerance, horizontal gene transfer, and methylation and demethylation, are examined, alongside the genetic and molecular basis governing these plant-microbe interactions. However, the complexity of plant-microbe interactions, coupled with our limited understanding of the associated mechanisms, presents challenges in their practical application. Thus, this review underscores the necessity of a more detailed understanding of how plants and microbes interact and the importance of using a combined approach from different scientific fields to maximize the benefits of these microbial processes. By advancing our knowledge of plant-microbe synergies in the metabolism of heavy metals, we can develop more effective bioremediation strategies to combat the contamination of soil by heavy metals.

A high solids field-to-fuel research pipeline to identify interactions between feedstocks and biofuel production

BACKGROUND

Environmental factors, such as weather extremes, have the potential to cause adverse effects on plant biomass quality and quantity. Beyond adversely affecting feedstock yield and composition, which have been extensively studied, environmental factors can have detrimental effects on saccharification and fermentation processes in biofuel production. Only a few studies have evaluated the effect of these factors on biomass deconstruction into biofuel and resulting fuel yields. This field-to-fuel evaluation of various feedstocks requires rigorous coordination of pretreatment, enzymatic hydrolysis, and fermentation experiments. A large number of biomass samples, often in limited quantity, are needed to thoroughly understand the effect of environmental conditions on biofuel production. This requires greater processing and analytical throughput of industrially relevant, high solids loading hydrolysates for fermentation, and led to the need for a laboratory-scale high solids experimentation platform.

RESULTS

A field-to-fuel platform was developed to provide sufficient volumes of high solids loading enzymatic hydrolysate for fermentation. AFEX pretreatment was conducted in custom pretreatment reactors, followed by high solids enzymatic hydrolysis. To accommodate enzymatic hydrolysis of multiple samples, roller bottles were used to overcome the bottlenecks of mixing and reduced sugar yields at high solids loading, while allowing greater sample throughput than possible in bioreactors. The roller bottle method provided 42-47% greater liquefaction compared to the batch shake flask method for the same solids loading. In fermentation experiments, hydrolysates from roller bottles were fermented more rapidly, with greater xylose consumption, but lower final ethanol yields and CO₂ production than hydrolysates generated with shake flasks. The entire platform was tested and was able to replicate patterns of fermentation inhibition previously observed for experiments conducted in larger-scale reactors and bioreactors, showing divergent fermentation patterns for drought and normal year switchgrass hydrolysates.

CONCLUSION

A pipeline of small-scale AFEX pretreatment and roller bottle enzymatic hydrolysis was able to provide adequate quantities of hydrolysate for respirometer fermentation experiments and was able to overcome hydrolysis bottlenecks at high solids loading by obtaining greater liquefaction compared to batch shake flask hydrolysis. Thus, the roller bottle method can be effectively utilized to compare divergent feedstocks and diverse process conditions.

Reviewing the interface of bioeconomy and ecosystem service research

The bioeconomy is currently being globally promoted as a sustainability avenue involving several societal actors. While the bioeconomy is broadly about the substitution of fossil resources with bio-based ones, three main (competing or complementary) bioeconomy visions are emerging in scientific literature: resource, biotechnology, and agroecology. The implementation of one or more of these visions into strategies implies changes to land use and thus ecosystem services delivery, with notable trade-offs. This review aims to explore the interdisciplinary space at the interface of these two concepts. We reviewed scientific publications explicitly referring to bioeconomy and ecosystem services in their title, abstract, or keywords, with 45 documents identified as relevant. The literature appeared to be emerging and fragmented but eight themes were discernible (in order of decreasing occurrence frequency in the literature): a. technical and economic feasibility of biomass extraction and use; b. potential and challenges of the bioeconomy; c. frameworks and tools; d. sustainability of bio-based processes, products, and services; e. environmental sustainability of the bioeconomy; f. governance of the bioeconomy; g. biosecurity; h. bioremediation. Approximately half of the documents aligned to a resource vision of the bioeconomy, with emphasis on biomass production. Agroecology and biotechnology visions were less frequently found, but multiple visions generally tended to occur in each document. The discussion highlights gaps in the current research on the topic and argues for communication between the ecosystem services and bioeconomy communities to forward both research areas in the context of sustainability science.

Regulatory Uncertainty Around New Breeding Techniques

Emerging precision breeding techniques have great potential to develop new crop varieties with specific traits that can contribute to ensuring future food security in a time of increasing climate change pressures, such as disease, insects and drought. These techniques offer options for crop trait development in both private and public sector breeding programs. Yet, the success of new breeding techniques is not guaranteed at the scientific level alone: political influences and social acceptance significantly contribute to how crops will perform in the market. Using survey data, we report results from an international panel of experts regarding the institutional and social barriers that might impede the development of new plant technologies. Survey results clearly indicate that regulatory issues, social, and environmental concerns are critical to the success of precision breeding. The cross-regional analysis shows heterogeneity between Europeans and North Americans, particularly regarding political attitudes and social perceptions of targeted breeding techniques.

Safety, Security, and Policy Considerations for Plant Genome Editing

Genome editing with engineered nucleases (GEEN) is increasingly used as a tool for gene discovery and trait development in crops through generation of targeted changes in endogenous genes. The development of the CRISPR-Cas9 system (clustered regularly interspaced short palindromic repeats with associated Cas9 protein), in particular, has enabled widespread use of genome editing. Research to date has not comprehensively addressed genome-editing specificity and off-target mismatches that may result in unintended changes within plant genomes or the potential for gene drive initiation. Governance and regulatory considerations for bioengineered crops derived from using GEEN will require greater clarity as to target specificity, the potential for mismatched edits, unanticipated downstream effects of off-target mutations, and assurance that genome reagents do not occur in finished products. Since governance and regulatory decision making involves robust standards of evidence extending from the laboratory to the postcommercial marketplace, developers of genome-edited crops must anticipate significant engagement and investment to address questions of regulators and civil society.

The Regulatory Status of Genome-edited Crops

Genome editing with engineered nucleases (GEEN) represents a highly specific and efficient tool for crop improvement with the potential to rapidly generate useful novel phenotypes/traits. Genome editing techniques initiate specifically targeted double strand breaks facilitating DNA-repair pathways that lead to base additions or deletions by non-homologous end joining as well as targeted gene replacements or transgene insertions involving homology-directed repair mechanisms. Many of these techniques and the ancillary processes they employ generate phenotypic variation that is indistinguishable from that obtained through natural means or conventional mutagenesis; and therefore, they do not readily fit current definitions of genetically engineered or genetically modified used within most regulatory regimes. Addressing ambiguities regarding the regulatory status of genome editing techniques is critical to their application for development of economically useful crop traits. Continued regulatory focus on the process used, rather than the nature of the novel phenotype developed, results in confusion on the part of regulators, product developers, and the public alike and creates uncertainty as of the use of genome engineering tools for crop improvement.

RNA interference: concept to reality in crop improvement

The phenomenon of RNA interference (RNAi) is involved in sequence-specific gene regulation driven by the introduction of dsRNA resulting in inhibition of translation or transcriptional repression. Since the discovery of RNAi and its regulatory potentials, it has become evident that RNAi has immense potential in opening a new vista for crop improvement. RNAi technology is precise, efficient, stable and better than antisense technology. It has been employed successfully to alter the gene expression in plants for better quality traits. The impact of RNAi to improve the crop plants has proved to be a novel approach in combating the biotic and abiotic stresses and the nutritional improvement in terms of bio-fortification and bio-elimination. It has been employed successfully to bring about modifications of several desired traits in different plants. These modifications include nutritional improvements, reduced content of food allergens and toxic compounds, enhanced defence against biotic and abiotic stresses, alteration in morphology, crafting male sterility, enhanced secondary metabolite synthesis and seedless plant varieties. However, crop plants developed by RNAi strategy may create biosafety risks. So, there is a need for risk assessment of GM crops in order to make RNAi a better tool to develop crops with biosafety measures. This article is an attempt to review the RNAi, its biochemistry, and the achievements attributed to the application of RNAi in crop improvement.

Maternal and fetal exposure to pesticides associated to genetically modified foods in Eastern Townships of Quebec, Canada

Pesticides associated to genetically modified foods (PAGMF), are engineered to tolerate herbicides such as glyphosate (GLYP) and gluphosinate (GLUF) or insecticides such as the bacterial toxin bacillus thuringiensis (Bt). The aim of this study was to evaluate the correlation between maternal and fetal exposure, and to determine exposure levels of GLYP and its metabolite aminomethyl phosphoric acid (AMPA), GLUF and its metabolite 3-methylphosphinicopropionic acid (3-MPPA) and Cry1Ab protein (a Bt toxin) in Eastern Townships of Quebec, Canada. Blood of thirty pregnant women (PW) and thirty-nine nonpregnant women (NPW) were studied. Serum GLYP and GLUF were detected in NPW and not detected in PW. Serum 3-MPPA and CryAb1 toxin were detected in PW, their fetuses and NPW. This is the first study to reveal the presence of circulating PAGMF in women with and without pregnancy, paving the way for a new field in reproductive toxicology including nutrition and utero-placental toxicities.

From petrochemistry to biotech: a European perspective on the bio-based economy

This paper gives an account of the issues at play in Europe with regard to the transition to a bio-based economy. Agricultural crops have always been used for the production of food, feed, fibre and fuel. The Model T Ford—the first mass produced car—originally ran on bioethanol, and wood has been in use as a source for energy ever since the discovery of fire. What is new is that the balance between agricultural uses is changing under the pressure of an increasing need for food and feed, as well as the new need for biofuels and biomaterials. At the basis of this change lie several serious issues related to the current use of bio-based feedstock to secure energy supply, the future depletion of natural resources and global climate change. Innovations in industrial biotechnology are expected to play a crucial role in dealing with these issues in biomass use.

PET imaging of thin objects: measuring the effects of positron range and partial-volume averaging in the leaf of Nicotiana tabacum

INTRODUCTION

PET imaging in plants is receiving increased interest as a new strategy to measure plant responses to environmental stimuli and as a tool for phenotyping genetically engineered plants. PET imaging in plants, however, poses new challenges. In particular, the leaves of most plants are so thin that a large fraction of positrons emitted from PET isotopes ((18)F, (11)C, (13)N) escape while even state-of-the-art PET cameras have significant partial-volume errors for such thin objects. Although these limitations are acknowledged by researchers, little data have been published on them.

METHODS

Here we measured the magnitude and distribution of escaping positrons from the leaf of Nicotiana tabacum for the radionuclides (18)F, (11)C and (13)N using a commercial small-animal PET scanner. Imaging results were compared to radionuclide concentrations measured from dissection and counting and to a Monte Carlo simulation using GATE (Geant4 Application for Tomographic Emission).

RESULTS

Simulated and experimentally determined escape fractions were consistent. The fractions of positrons (mean±S.D.) escaping the leaf parenchyma were measured to be 59±1.1%, 64±4.4% and 67±1.9% for (18)F, (11)C and (13)N, respectively. Escape fractions were lower in thicker leaf areas like the midrib. Partial-volume averaging underestimated activity concentrations in the leaf blade by a factor of 10 to 15.

CONCLUSIONS

The foregoing effects combine to yield PET images whose contrast does not reflect the actual activity concentrations. These errors can be largely corrected by integrating activity along the PET axis perpendicular to the leaf surface, including detection of escaped positrons, and calculating concentration using a measured leaf thickness.

Recent advances in plant transformation

Plant genetic engineering has become one of the most important molecular tools in the modern molecular breeding of crops. Over the last decade, significant progress has been made in the development of new and efficient transformation methods in plants. Despite a variety of available DNA delivery methods, Agrobacterium- and biolistic-mediated transformation remain the two predominantly employed approaches. In particular, progress in Agrobacterium-mediated transformation of cereals and other recalcitrant dicot species has been quite remarkable. In the meantime, other transgenic-enabling technologies have emerged, including generation of marker-free transgenics, gene targeting, and chromosomal engineering. Although transformation of some plant species or elite germplasm remains a challenge, further advancement in transformation technology is expected because the mechanisms of governing the regeneration and transformation processes are now better understood and are being creatively applied to designing improved transformation methods or to developing new enabling technologies.

Environmental risk assessments for transgenic crops producing output trait enzymes

The environmental risks from cultivating crops producing output trait enzymes can be rigorously assessed by testing conservative risk hypotheses of no harm to endpoints such as the abundance of wildlife, crop yield and the rate of degradation of crop residues in soil. These hypotheses can be tested with data from many sources, including evaluations of the agronomic performance and nutritional quality of the crop made during product development, and information from the scientific literature on the mode-of-action, taxonomic distribution and environmental fate of the enzyme. Few, if any, specific ecotoxicology or environmental fate studies are needed. The effective use of existing data means that regulatory decision-making, to which an environmental risk assessment provides essential information, is not unnecessarily complicated by evaluation of large amounts of new data that provide negligible improvement in the characterization of risk, and that may delay environmental benefits offered by transgenic crops containing output trait enzymes.

Gene flow, invasiveness, and ecological impact of genetically modified crops

The main environmental concerns about genetically modified (GM) crops are the potential weediness or invasiveness in the crop itself or in its wild or weedy relatives as a result of transgene movement. Here we briefly review evidence for pollen- and seed-mediated gene flow from GM crops to non-GM or other GM crops and to wild relatives. The report focuses on the effect of abiotic and biotic stress-tolerance traits on plant fitness and their potential to increase weedy or invasive tendencies. An evaluation of weediness and invasive traits that contribute to the success of agricultural weeds and invasive plants was of limited value in predicting the effect of biotic and abiotic stress-tolerance GM traits, suggesting context-specific evaluation rather than generalizations. Fitness data on herbicide, insect, and disease resistance, as well as cold-, drought-, and salinity-tolerance traits, are reviewed. We describe useful ecological models predicting the effects of gene flow and altered fitness in GM crops and wild/weedy relatives, as well as suitable mitigation measures. A better understanding of factors controlling population size, dynamics, and range limits in weedy volunteer GM crop and related host or target weed populations is necessary before the effect of biotic and abiotic stress-tolerance GM traits can be fully assessed.