New insights into the applications of viruses to biotechnology

Viruses are responsible for many devastating human and animal diseases, such as Ebola, rabies, HIV, smallpox, influenza, dengue, and SARS-CoV-2. The deleterious impact of viruses is also shown in agriculture, wherein plant virus diseases account for USD30 billion in annual losses globally, thereby threatening world food security. Viruses are obligate parasites, and are present in all habitats where there is life. They are the most abundant agents on Earth; the estimated number of viral particles on earth is close to 10^31. Needless to say, the vast majority of viruses are unknown; however, the breakthrough and development of new sequencing technologies such as next-generation sequencing are accelerating the discovery of new viruses. The world of technology is evolving at a rapid pace, and innovative technologies are continuously being discovered, allowing the genetic manipulation of these available simple viral systems and making them attractive tools for exploitation in different fields of science. We can go back to the 18th century to find the first application of viruses in biotechnology; when, cowpox pustules were used to combat smallpox. All subsequent scientific advances have enabled us today to use highly efficient vaccines containing genetically modified viruses to combat COVID-19. Viruses are being used in the prevention and treatment of many infectious diseases or cancer, not only through vaccines, but also as vectors to carry and deliver substances in situ, in which we can take advantage of their capacity to target specific cells. In agriculture, viruses have been studied to introduce desirable characteristics in plants, showing their potential in plant breeding and plant protection. Viruses have also been used in materials science and nanotechnology as a source of nanoparticles and as building blocks. Other industries such as pharmacology, cosmetics, electronics, are some areas that are also benefiting from the potential uses of viruses. We cannot ignore the harm viruses can cause to us, but we also cannot ignore the good they can do, and the potential they have alongside the cutting edge technologies we possess. It is clear that the more they are studied, the more possibilities they offer. In this Special Issue ‘The Application of Viruses to Biotechnology, 2022’, we have gath- ered up-to-date research on the use of viruses in biotechnology, reinforcing the contribution these extraordinary agents to significant advances in science that would not be possible without their existence.info:eu-repo/semantics/publishedVersio

An Overview of the Application of Viruses to Biotechnology

Viruses may cause devastating diseases in several organisms; however, they are simple systems that can be manipulated to be beneficial and useful for many purposes in different areas. In medicine, viruses have been used for a long time in vaccines and are now being used as vectors to carry materials for the treatment of diseases, such as cancer, being able to target specific cells. In agriculture, viruses are being studied to introduce desirable characteristics in plants or render resistance to biotic and abiotic stresses. Viruses have been exploited in nanotechnology for the deposition of specific metals and have been shown to be of great benefit to nanomaterial production. They can also be used for different applications in pharmacology, cosmetics, electronics, and other industries. Thus, viruses are no longer only seen as enemies. They have shown enormous potential, covering several important areas in our lives, and they are making our lives easier and better. Although viruses have already proven their potential, there is still a long road ahead. This prompt us to propose this theme in the Special Issue “The application of viruses to biotechnology”. We believe that the articles gathered here highlight recent significant advances in the use of viruses in several fields, contributing to the current knowledge on virus applications

Collapse of zostera noltii seagrass beds effects on nematode community structure in the Mira estuary (southwest coast of Portugal): analysis of estuarine nematodes assemblages in early recovery

This research focuses on the benthic nematode assemblages response during a natural recovery of the habitat, after a major collapse of the Zostera noltii, in Mira estuary (SW coast, Portugal). The main aim was attained by comparing nematode assemblages distribution patterns of density, diversity, trophic composition, biomass and morphometric attributes, between the stable ecological condition of the seagrass habitat and the early recovery process. During the early recovery no evident temporal patterns of the assemblages were observed, and a high density and diversity was registered. However, in comparison to the stable ecological condition, during the early recovery, the nematodes density decreased, while the diversity, biomass and morphometric attributes increased. The dual stable isotopes allowed to determine that carbon inputs associated with seagrass beds extend well beyond the vegetation boundaries. The essence of ecological functioning was maintained after the habitat loss, being possible to predict that a “good ecological state” can be achieved; ABSTRACT: Efeito do colapso da planta marinha Zostera noltii na estrutura de uma comunidade de nemátodes no Estuário do Mira (Sudoeste de Portugal): Análise de Nemátodes Marinhos no Início do Processo de Recuperação Este trabalho centra-se na resposta das comunidades de nemátodes bentónicos durante a recuperação natural do habitat, após um grande colapso de Zostera noltii, no estuário do Mira (Costa Sudoeste de Portugal). O principal objetivo foi alcançado através da comparação de padrões de distribuição das comunidades de nemátodes em termos de densidade, diversidade, composição trófica, biomassa e atributos morfométricos, entre a condição ecológica estável da pradaria marinha e o processo de recuperação inicial. Durante o início da recuperação não foram observados padrões temporais evidentes das comunidades e foi observada uma alta densidade e diversidade. No entanto, comparando com o estado ecológico estável, durante o início da recuperação, a densidade de nemátodes diminuiu, enquanto a diversidade, biomassa e atributos morfométricos aumentaram. Os isótopos estáveis permitiram determinar que as adições de carbono associados às pradarias marinhas estendem-se bem além dos limites da vegetação. A essência do funcionamento ecológico foi mantida após a perda do habitat sendo por isso possível prever que possa ser alcançado um "bom estado ecológico”

Benthic Nematode assemblages response to seagrass beds spatial heterogeneity in natural recovery process of Zostera Noltii after major colapse

After a seagrass beds (Zostera noltii) colapse in 2008 of the Mira estuary (SW coast of Portugal) symptoms of early recovery were observed. The principal goal of this study is to assess the evolution and resilience of the benthic nematodes assemblages during the natural recovery of the seagrass beds through analysis of the spatial and temporal differences in structural and functional characteristics of the communities. The horizontal macroscale (km) and small scale (m) variability was evaluate. We hypothesize that the new environmental conditions of the early recovery, with sparsely distributed and small-sized seagrass patches, will increase the spatial heterogeneity of nematode communities and significantly affect community diversity, both taxonomic and functional. The sampling design was follows: Samples were collected in five “occasions”, (February, June, September, December 2010 and February 2011), at randomly “stations” located over a distance 50 m, at two “sites”, 2km distance. To test the hypothesis that the composition of nematodes assemblages changes spatially and seasonally a two–way PERMANOVA analysis was performed. Mean nematode densities varied between 1416 ± 107 ind. 10 cm-2 (Site A) and 2611 ± 230 ind. 10 cm-2 (Site B) , and a total of 89 species were identified. The PCO ordination based on abundance and composition of nematode genera do not shown the discrimination of the two sampling sites. However densities and trophic groups showed significant differences across macroscale (sites A and B), the increase of spatial heterogeneity was clear identified in small scale. No significant differences was observed between the temporal variation. The response of the nematode assemblages after the collapse, both in terms of density and diversity, showed a substantial potential of resilience and recovery

The dual role of Plant Viruses in CRISPR

Plant viruses cause devastating diseases in many agriculture systems, being a serious threat for the provision of adequate nourishment to a continuous growing population. At the present there are no chemical products that directly target the viruses, and their control rely mainly on preventive sanitary measures to reduce viral infections that, although important, have proved to be far from enough. The current most effective and sustainable solution is the use of virusresistant varieties, which require too much work and time to obtain. In the recent years, the versatile gene editing technology known as CRISPR/Cas has simplified the engineering of crops and has successfully been used for the development of viral resistant plants. CRISPR stands for Clustered regularly interspaced short palindromic repeats and CRISPR-associated (Cas) proteins, and is based on a natural adaptive immune system that most archaeal and some bacterial species present to defend themselves against invading bacteriophages. Plant viral resistance using CRISPR/Cas technology has been achieved either through manipulation of plant genome (plant-mediated resistance), by mutating host factors required for viral infection, or through manipulation of virus genome (virus-mediated resistance), for which CRISPR/Cas systems must specifically target and cleave viral DNA or RNA. Viruses present an efficient machinery and comprehensive genome structure and, in a different perspective, they have been used as biotechnological tools in several areas such as medicine, materials industry and agriculture with several purposes. Due to all this potential, it is not surprising that viruses have also been used as vectors for CRISPR technology, namely to deliver CRISPR components into plants, a crucial step for the success of CRISPR technology. Here we discuss the basic principles of CRISPR/Cas technology, with a special focus on the advances of CRISPR/Cas to engineer plant resistance against DNA and RNA viruses. We also describe several strategies for the delivery of these systems into plant cells, focusing on the advantages and disadvantages of the use of plant viruses as vectors. We conclude by discussing the constrains faced by the application of CRISPR/Cas technology in agriculture and future prospects

Plant Viruses: From Targets to Tools for CRISPR

Plant viruses cause devastating diseases in many agriculture systems, being a serious threat for the provision of adequate nourishment to a continuous growing population. At the present, there are no chemical products that directly target the viruses, and their control rely mainly on preventive sanitary measures to reduce viral infections that, although important, have proved to be far from enough. The current most effective and sustainable solution is the use of virus-resistant varieties, but which require too much work and time to obtain. In the recent years, the versatile gene editing technology known as CRISPR/Cas has simplified the engineering of crops and has successfully been used for the development of viral resistant plants. CRISPR stands for ‘clustered regularly interspaced short palindromic repeats’ and CRISPR-associated (Cas) proteins, and is based on a natural adaptive immune system that most archaeal and some bacterial species present to defend themselves against invading bacteriophages. Plant viral resistance using CRISPR/Cas technology can been achieved either through manipulation of plant genome (plant-mediated resistance), by mutating host factors required for viral infection; or through manipulation of virus genome (virus-mediated resistance), for which CRISPR/Cas systems must specifically target and cleave viral DNA or RNA. Viruses present an efficient machinery and comprehensive genome structure and, in a different, beneficial perspective, they have been used as biotechnological tools in several areas such as medicine, materials industry, and agriculture with several purposes. Due to all this potential, it is not surprising that viruses have also been used as vectors for CRISPR technology; namely, to deliver CRISPR components into plants, a crucial step for the success of CRISPR technology. Here we discuss the basic principles of CRISPR/Cas technology, with a special focus on the advances of CRISPR/Cas to engineer plant resistance against DNA and RNA viruses. We also describe several strategies for the delivery of these systems into plant cells, focusing on the advantages and disadvantages of the use of plant viruses as vectors. We conclude by discussing some of the constrains faced by the application of CRISPR/Cas technology in agriculture and future prospects

High throughput sequencing unravels tomato- pathogen interactions towards a sustainable plant breeding

Tomato (Solanum lycopersicum) is one of the most economically important vegetables throughout the world. It is one of the best studied cultivated dicotyledonous plants, often used as a model system for plant research into classical genetics, cytogenetics, molecular genetics, and molecular biology. Tomato plants are affected by different pathogens such as viruses, viroids, fungi, oomycetes, bacteria, and nematodes, that reduce yield and affect product quality. The study of tomato as a plant-pathogen system helps to accelerate the discovery and understanding of the molecular mechanisms underlying disease resistance and offers the opportunity of improving the yield and quality of their edible products. The use of functional genomics has contributed to this purpose through both traditional and recently developed techniques, that allow the identification of plant key functional genes in susceptible and resistant responses, and the understanding of the molecular basis of compatible interactions during pathogen attack. Nextgeneration sequencing technologies (NGS), which produce massive quantities of sequencing data, have greatly accelerated research in biological sciences and offer great opportunities to better understand the molecular networks of plant–pathogen interactions. In this review, we summarize important research that used high-throughput RNA-seq technology to obtain transcriptome changes in tomato plants in response to a wide range of pathogens such as viruses, fungi, bacteria, oomycetes, and nematodes. These findings will facilitate genetic engineering efforts to incorporate new sources of resistance in tomato for protection against pathogens and are of major importance for sustainable plant-disease management, namely the ones relying on the plant’s innate immune mechanisms in view of plant breeding

Plant-Pathogen Interaction

Plant diseases result in severe losses to natural plant systems, and also cause problems for economics and production in agricultural systems. While many biotic constraints are well known and confronted with variable success, the occurrence of emerging pathogens and the progressive incidence of novel virulent strains, races, or pathotypes is evident. Plant disease management faces challenges due to the increasing incidence of emergent diseases, with a consequent decrease in the production potential of agriculture. Furthermore, the deteriorating ecology of agro-ecosystems and the depletion of natural resources, together with an increased risk of disease epidemics resulting from agricultural intensification and monocultures, should be taken into account. Moreover, the practicability of some of the currently available plant protection measures is questionable. The UE directories for commercialization withdrawal of several chemical substances used for pest and disease control, and the new rules for reducing agricultural greenhouse gas emissions contained in the 2015 Paris Agreement of the United Nations Framework Convention on Climate Change, bring new challenges to agricultural production

Spatial and temporal variation of fungal endophytic richness and diversity associated to the phyllosphere of olive cultivars

Fungal endophytes are micro-organisms that colonize healthy plant tissues without causing disease symptoms. They are described as plant growth and disease resistance promoters and have shown antimicrobial activity. The spatial-temporal distribution of endophytic communities in olive cultivars has been poorly explored. This study aims to investigate the richness and diversity of endophytic fungi in different seasons and sites, within the Alentejo region, Portugal. Additionally, and because the impact of some pathogenic fungi (e.g. Colletotrichum spp.) varies according to olive cultivars; three cultivars, Galega vulgar, Cobrançosa and Azeiteira, were sampled. 1868 fungal isolates were identified as belonging to 26 OTUs; 13 OTUs were identified to the genera level and 13 to species level. Cultivar Galega vulgar and season autumn showed significant higher values in terms of endophytic richness and diversity. At site level, Elvas showed the lowest fungal richness and diversity of fungal endophytes. This study reinforces the importance of exploring the combined spatio-temporal distribution of the endophytic biodiversity in different olive cultivars. Knowledge about endophytic communities may help to better understand their functions in plants hosts, such as their ecological dynamics with pathogenic fungi, which can be explored for their use as biocontrol agents

Co infection of OMMV and OLV-1 enhances symptoms and increases both viruses accumulation and viral derived siRNAs in plants

Previous extensive field surveys in olive orchards have revealed high levels of Olive mild mosaic virus (OMMV) and Olive latent virus 1 (OLV-1), frequently appearing in mixed infections. These viruses belong to genus Alphanecrovirus and their RNA dependent RNA polymerase (RdRp),as well as their p6 and p8 amino acid sequences share over 87% identity. Preliminary studies have shown that co infection of OMMV and OLV-1 is associated to an intensification of symptoms, as well to an increase in transmission efficiency, suggesting a synergistic effect. Single and double infections of OMMV and OLV-1 were obtained through mechanical inoculation of Nicotiana benthamiana plants and the second upper leaf from each inoculated plant was collected at different stages and used for quantitative PCR. In this study we found that the co infection of OMMV and OLV-1 causes an exacerbation of symptoms and increases the accumulation of both viruses in N. benthamiana plants. Highthroughput sequencing of siRNAs from both viruses in singly and co infected plants showed that OMMV and OLV-1 co infection increased the accumulation of siRNAs, mainly of 21 and 22 nt in length, with most non distinguishable between OMMV and OLV-1 siRNAs. Our findings suggest that siRNAs of both viruses have possible roles in the synergistic interaction between OLV-1 and OMMV in N. benthamiana plants. Whether a similar situation occurs in olive fields is not yet known and studies are being pursued