The hidden world within plants: metatranscriptomics unveils the complexity of wood microbiomes

CRISPR/Cas9-driven double modification of grapevine MLO6-7 imparts powdery mildew resistance, while editing of NPR3 augments powdery and downy mildew tolerance

The implementation of genome editing strategies in grapevine is the easiest way to improve sustainability and resilience while preserving the original genotype. Among others, the Mildew Locus-O (MLO) genes have already been reported as good candidates to develop powdery mildew-immune plants. A never-explored grapevine target is NPR3, a negative regulator of the systemic acquired resistance. We report the exploitation of a cisgenic approach with the Cre-lox recombinase technology to generate grapevine-edited plants with the potential to be transgene-free while preserving their original genetic background. The characterization of three edited lines for each target demonstrated immunity development against Erysiphe necator in MLO6-7-edited plants. Concomitantly, a significant improvement of resilience, associated with increased leaf thickness and specific biochemical responses, was observed in defective NPR3 lines against E. necator and Plasmopara viticola. Transcriptomic analysis revealed that both MLO6-7 and NPR3 defective lines modulated their gene expression profiles, pointing to distinct though partially overlapping responses. Furthermore, targeted metabolite analysis highlighted an overaccumulation of stilbenes coupled with an improved oxidative scavenging potential in both editing targets, likely protecting the MLO6-7 mutants from detrimental pleiotropic effects. Finally, the Cre-loxP approach allowed the recovery of one MLO6-7 edited plant with the complete removal of transgene. Taken together, our achievements provide a comprehensive understanding of the molecular and biochemical adjustments occurring in double MLO-defective grape plants. In parallel, the potential of NPR3 mutants for multiple purposes has been demonstrated, raising new questions on its wide role in orchestrating biotic stress responses.

Conjoined partners: efficacy and side effects of grafting and dsRNA application on the microbial endophyte population of grapevine plants inoculated with two esca-related fungal pathogens

Grafting has been exploited since 7000 BC to enhance productivity, disease resistance, and adaptability of cultivated plants to stressful conditions especially in woody crops such as grapevine (Vitis spp.). In contrast, the application of sequence specific double-stranded RNAs (dsRNAs) to control fungal pathogens and insect pests has only been recently developed. The possibility of combining these approaches to enhance plant resilience, reducing reliance on pesticides, offers new perspectives for a more sustainable agriculture. In this study, we assessed the potential of utilizing dsRNAs to enhance resilience against esca-related wood fungal pathogens in grapevine, considering various rootstock-scion combinations. The results showed that the scion genotype modulates the ability of the rootstock to cope with the inoculated wood fungal pathogens, mainly by altering the efficacy of producing stilbene compounds. Additionally, we found that dsRNAs reduced the growth of two inoculated esca-related fungal pathogens but they did not completely stop their colonization. Furthermore, wood microbiome data showed that the scion genotype (always belonging to Vitis vinifera species) was also able to influence the rootstock-associated microbiota, with a major effect on the fungal community. Lastly, adverse effects on non-target microorganisms are reported, raising questions on the environmental fate of dsRNAs and how dsRNAs can directly or indirectly affect plant-associated microbial communities.

Enhancing Agricultural Sustainability Through Rhizomicrobiome: A Review

Sustainable agriculture represents the responsible utilization of natural resources while safeguarding the well-being of the natural environment. It encompasses the objectives of preserving the environment, fostering economic growth, and promoting socioeconomic equality. To achieve sustainable development for humanity, it is imperative to prioritize sustainable agriculture. One significant approach to achieving this transition is the extensive utilization of microbes, which play a crucial role due to the genetic reliance of plants on the beneficial functions provided by symbiotic microbes. This review focuses on the significance of rhizospheric microbial communities, also known as the rhizomicrobiome (RM). It is a complex community of microorganisms that live in the rhizosphere and influence the plant's growth and health. It provides its host plant with various benefits related to plant growth, including biocontrol, biofertilization, phytostimulation, rhizoremediation, stress resistance, and other advantageous properties. Yet, the mechanisms by which the RM contributes to sustainable agriculture remain largely unknown. Investigating this microbial population presents a significant opportunity to advance toward sustainable agriculture. Hence, this study aims to provide an overview of the diversity and applications of RM in sustainable agriculture practices. Lately, there has been growing momentum in various areas related to rhizobiome research and its application in agriculture. This includes rhizosphere engineering, synthetic microbiome application, agent-based modeling of the rhizobiome, and metagenomic studies. So, developing bioformulations of these beneficial microorganisms that support plant growth could serve as a promising solution for future strategies aimed at achieving a new green revolution.

Impact of the Biocontrol Product, Esquive® WP, on the Indigenous Grapevine Wood Microbiome after a 6-Year Application Period

Grapevine trunk diseases (GTDs) are currently limiting grapevine productivity in many vineyards worldwide. As no chemical treatments are registered to control GTDs, biocontrol agents are being tested against these diseases. Esquive® WP, based on the fungus Trichoderma atroviride I-1237 strain, is the first biocontrol product registered in France to control GTDs. In this study, we determine whether, following grapevine pruning wound treatments with Esquive® WP, changes occurred or not in the indigenous microbial communities that are colonizing grapevine wood. Over a 6-year period, Esquive® WP was applied annually to pruning wounds on three grapevine cultivars located in three different regions. Wood samples were collected at 2 and 10 months after the Esquive® WP treatments. Based on MiSeq high-throughput sequencing analyses, the results showed that specific microbial communities were linked to each 'region/cultivar' pairing. In certain cases, a significant modification of alpha diversity indexes and the relative abundance of some microbial taxa were observed between treated and non-treated grapevines 2 months after Esquive® WP treatment. However, these modifications disappeared over time, i.e., 10 months post-treatment. This result clearly showed that Esquive® WP pruning wood treatment did not induce significant changes in the grapevine wood's microbiome, even after 6 years of recurrent applications on the plants.

Invisible Inhabitants of Plants and a Sustainable Planet: Diversity of Bacterial Endophytes and their Potential in Sustainable Agriculture

Uncontrolled usage of chemical fertilizers, climate change due to global warming, and the ever-increasing demand for food have necessitated sustainable agricultural practices. Removal of ever-increasing environmental pollutants, treatment of life-threatening diseases, and control of drug-resistant pathogens are also the need of the present time to maintain the health and hygiene of nature, as well as human beings. Research on plant-microbe interactions is paving the way to ameliorate all these sustainably. Diverse bacterial endophytes inhabiting the internal tissues of different parts of the plants promote the growth and development of their hosts by different mechanisms, such as through nutrient acquisition, phytohormone production and modulation, protection from biotic or abiotic challenges, assisting in flowering and root development, etc. Notwithstanding, efficient exploitation of endophytes in human welfare is hindered due to scarce knowledge of the molecular aspects of their interactions, community dynamics, in-planta activities, and their actual functional potential. Modern "-omics-based" technologies and genetic manipulation tools have empowered scientists to explore the diversity, dynamics, roles, and functional potential of endophytes, ultimately empowering humans to better use them in sustainable agricultural practices, especially in future harsh environmental conditions. In this review, we have discussed the diversity of bacterial endophytes, factors (biotic as well as abiotic) affecting their diversity, and their various plant growth-promoting activities. Recent developments and technological advancements for future research, such as "-omics-based" technologies, genetic engineering, genome editing, and genome engineering tools, targeting optimal utilization of the endophytes in sustainable agricultural practices, or other purposes, have also been discussed.

Unraveling plant-microbe interactions: can integrated omics approaches offer concrete answers?

Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant-microbe interactions in a concerted way. Integrating multi-omics datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of complex crop-microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant-microbe interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis, which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness.

Pathogen Eradication in Garlic in the Phytobiome Context: Should We Aim for Complete Cleaning?

Global food production is challenged by plant pathogens that cause significant crop losses. Fungi, bacteria, and viruses have long threatened sustainable and profitable agriculture. The danger is even higher in vegetatively propagated horticultural crops, such as garlic. Currently, quarantine, rouging infected plants, and control of natural vectors are used as the main means of disease and pest control in garlic crops. Agricultural biotechnology, meristem-tip culture, and cryotherapy offer solutions for virus eradication and for the multiplication of 'clean stocks', but at the same time, impact the symbiotic and beneficial components of the garlic microbiome. Our research involves the first metatranscriptomic analysis of the microbiome of garlic bulb tissue, PCR analyses, and a biological assay of endophytes and pathogens. We have demonstrated that in vitro sanitation methods, such as shoot tip culture or cryotherapy can alter the garlic microbiome. Shoot tip culture proved ineffective in virus elimination, but reduced bacterial load and eliminated fungal infections. Conversely, cryotherapy was efficient in virus eradication but demolished other components of the garlic microbiome. Garlic plants sanitized by cryotherapy exhibited a lower survival rate, and a longer in vitro regeneration period. The question arises whether total eradication of viruses, at the expense of other microflora, is necessary, or if a partial reduction in the pathogenic load would suffice for sanitized garlic production. We explore this question from both scientific and commercial perspectives.

Opportunities and challenges for microbiomics in ecosystem restoration

Microbiomics is the science of characterizing microbial community structure, function, and dynamics. It has great potential to advance our understanding of plant-soil-microbe processes and interaction networks which can be applied to improve ecosystem restoration. However, microbiomics may be perceived as complex and the technology is not accessible to all. The opportunities of microbiomics in restoration ecology are considerable, but so are the practical challenges. Applying microbiomics in restoration must move beyond compositional assessments to incorporate tools to study the complexity of ecosystem recovery. Advances in metaomic tools provide unprecedented possibilities to aid restoration interventions. Moreover, complementary non-omic applications, such as microbial inoculants and biopriming, have the potential to improve restoration objectives by enhancing the establishment and health of vegetation communities.

Effects of fungicide application on physiological and molecular responses of grapevine (Vitis vinifera L.): a comparison between copper and sulfur fungicides applied alone and in combination with novel fungicides

BACKGROUND

Chemical products against fungi and oomycetes pose serious environmental issues. In the last decade, the use of less impacting active ingredients was encouraged to reduce chemical inputs in viticulture. In this study, the effect of different antifungal compounds on grapevine agronomic, physiological, and molecular responses in the vineyard was evaluated in addition to protection against powdery and downy mildews.

RESULTS

In 2 years and in two Vitis vinifera cultivars (Nebbiolo and Arneis), a conventional crop protection approach, based on traditional fungicides (sulfur and copper), was compared to combined strategies. A well-known resistance inducer (potassium phosphonate), Bacillus pumilus strain QST 2808 and calcium oxide, both active ingredients whose biological interaction with grapevine is poorly characterized, were applied in the combined strategies in association with chemical fungicides. Despite a genotype effect occurred, all treatments optimally controlled powdery and downy mildews, with minimal variations in physiological and molecular responses. Gas exchange, chlorophyll content and photosystem II efficiency increased in treated plants at the end of season, along with a slight improvement in the agronomic performances, and an activation of molecular defense processes linked to stilbene and jasmonate pathways.

CONCLUSION

The disease control strategies based on potassium phosphonate, Bacillus pumilus strain QST 2808 or calcium oxide combined with traditional chemical compounds did not cause severe limitations in plant ecophysiology, grape quality, and productive yields. The combination of potassium phosphonate and calcium oxide with traditional fungicides can represent a valuable strategy for reducing copper and sulfur inputs in the vineyards, including those organically managed. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota)

In April 2023, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by one new family, 14 new genera, and 140 new species. Two genera and 538 species were renamed. One species was moved, and four were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

New viruses of Cladosporium sp. expand considerably the taxonomic structure of Gammapartitivirus genus

Despite the fact that Cladosporium sp. are ubiquitous fungi, their viromes have been little studied. By analysing a collection of Cladosporium fungi, two new partitiviruses named Cladosporium cladosporioides partitivirus 1 (CcPV1) and Cladosporium cladosporioides partitivirus 2 (CcPV2) co-infecting a strain of Cladosporium cladosporioides were identified. Their complete genome consists of two monocistronic dsRNA segments (RNA1 and RNA2) with a high percentage of pairwise identity on 5' and 3' end. The RNA directed RNA polymerase (RdRp) of both viruses and the capsid protein (CP) of CcPV1 display the classic characteristics required for their assignment to the Gammapartitivirus genus. In contrast, CcPV2 RNA2 encodes for a 41 KDa CP that is unusually smaller when aligned to CPs of other viruses classified in this genus. The structural role of this protein is confirmed by electrophoresis on acrylamide gel of purified viral particles. Despite the low percentage of identity between the capsid proteins of CcPV1 and CcPV2, their three-dimensional structures predicted by AlphaFold2 show strong similarities and confirm functional proximity. Fifteen similar viral sequences of unknown function were annotated using the CcPV2 CP sequence. The phylogeny of the CP was highly consistent with the phylogeny of their corresponding RdRp, supporting the organization of Gammapartitiviruses into three distinct clades despite stretching the current demarcation criteria. It is proposed that a new subgenus be created within the genus Gammapartitivirus for this new group.

Microbial Biological Control of Fungi Associated with Grapevine Trunk Diseases: A Review of Strain Diversity, Modes of Action, and Advantages and Limits of Current Strategies

Grapevine trunk diseases (GTDs) are currently among the most important health challenges for viticulture in the world. Esca, Botryosphaeria dieback, and Eutypa dieback are the most current GTDs caused by fungi in mature vineyards. Their incidence has increased over the last two decades, mainly after the ban of sodium arsenate, carbendazim, and benomyl in the early 2000s. Since then, considerable efforts have been made to find alternative approaches to manage these diseases and limit their propagation. Biocontrol is a sustainable approach to fight against GTD-associated fungi and several microbiological control agents have been tested against at least one of the pathogens involved in these diseases. In this review, we provide an overview of the pathogens responsible, the various potential biocontrol microorganisms selected and used, and their origins, mechanisms of action, and efficiency in various experiments carried out in vitro, in greenhouses, and/or in vineyards. Lastly, we discuss the advantages and limitations of these approaches to protect grapevines against GTDs, as well as the future perspectives for their improvement.

Looking beyond Virus Detection in RNA Sequencing Data: Lessons Learned from a Community-Based Effort to Detect Cellular Plant Pathogens and Pests

High-throughput sequencing (HTS), more specifically RNA sequencing of plant tissues, has become an indispensable tool for plant virologists to detect and identify plant viruses. During the data analysis step, plant virologists typically compare the obtained sequences to reference virus databases. In this way, they are neglecting sequences without homologies to viruses, which usually represent the majority of sequencing reads. We hypothesized that traces of other pathogens might be detected in this unused sequence data. In the present study, our goal was to investigate whether total RNA-seq data, as generated for plant virus detection, is also suitable for the detection of other plant pathogens and pests. As proof of concept, we first analyzed RNA-seq datasets of plant materials with confirmed infections by cellular pathogens in order to check whether these non-viral pathogens could be easily detected in the data. Next, we set up a community effort to re-analyze existing Illumina RNA-seq datasets used for virus detection to check for the potential presence of non-viral pathogens or pests. In total, 101 datasets from 15 participants derived from 51 different plant species were re-analyzed, of which 37 were selected for subsequent in-depth analyses. In 29 of the 37 selected samples (78%), we found convincing traces of non-viral plant pathogens or pests. The organisms most frequently detected in this way were fungi (15/37 datasets), followed by insects (13/37) and mites (9/37). The presence of some of the detected pathogens was confirmed by independent (q)PCRs analyses. After communicating the results, 6 out of the 15 participants indicated that they were unaware of the possible presence of these pathogens in their sample(s). All participants indicated that they would broaden the scope of their bioinformatic analyses in future studies and thus check for the presence of non-viral pathogens. In conclusion, we show that it is possible to detect non-viral pathogens or pests from total RNA-seq datasets, in this case primarily fungi, insects, and mites. With this study, we hope to raise awareness among plant virologists that their data might be useful for fellow plant pathologists in other disciplines (mycology, entomology, bacteriology) as well.

Mycoviruses as a part of the global virome: Diversity, evolutionary links and lifestyle

Knowledge of mycovirus diversity, evolution, horizontal gene transfer and shared ancestry with viruses infecting distantly related hosts, such as plants and arthropods, has increased vastly during the last few years due to advances in the high throughput sequencing methodologies. This also has enabled the discovery of novel mycoviruses with previously unknown genome types, mainly new positive and negative single-stranded RNA mycoviruses ((+) ssRNA and (-) ssRNA) and single-stranded DNA mycoviruses (ssDNA), and has increased our knowledge of double-stranded RNA mycoviruses (dsRNA), which in the past were thought to be the most common viruses infecting fungi. Fungi and oomycetes (Stramenopila) share similar lifestyles and also have similar viromes. Hypothesis about the origin and cross-kingdom transmission events of viruses have been raised and are supported by phylogenetic analysis and by the discovery of natural exchange of viruses between different hosts during virus-fungus coinfection in planta. In this review we make a compilation of the current information on the genome organization, diversity and taxonomy of mycoviruses, discussing their possible origins. Our focus is in recent findings suggesting the expansion of the host range of many viral taxa previously considered to be exclusively fungal, but we also address factors affecting virus transmissibility and coexistence in single fungal or oomycete isolates, as well as the development of synthetic mycoviruses and their use in investigating mycovirus replication cycles and pathogenicity.

Coevolutionary legacies for plant decomposition

Coevolution has driven speciation and evolutionary novelty in functional traits across the Tree of Life. Classic coevolutionary syndromes such as plant-pollinator, plant-herbivore, and host-parasite have focused strongly on the fitness consequences during the lifetime of the interacting partners. Less is known about the consequences of coevolved traits for ecosystem-level processes, in particular their 'afterlife' legacies for litter decomposition, nutrient cycling, and the functional ecology of decomposers. We review the mechanisms by which traits resulting from coevolution between plants and their consumers, microbial symbionts, or humans, and between microbial decomposers and invertebrates, drive plant litter decomposition pathways and rates. This supports the idea that much of current global variation in the decomposition of plant material is a legacy of coevolution.

Breeding toward improved ecological plant-microbiome interactions

Domestication processes, amplified by breeding programs, have allowed the selection of more productive genotypes and more suitable crop lines capable of coping with the changing climate. Notwithstanding these advancements, the impact of plant breeding on the ecology of plant-microbiome interactions has not been adequately considered yet. This includes the possible exploitation of beneficial plant-microbe interactions to develop crops with improved performance and better adaptability to any environmental scenario. Here we discuss the exploitation of customized synthetic microbial communities in agricultural systems to develop more sustainable breeding strategies based on the implementation of multiple interactions between plants and their beneficial associated microorganisms.

The Promises, Challenges, and Opportunities of Omics for Studying the Plant Holobiont

Microorganisms are critical drivers of biological processes that contribute significantly to plant sustainability and productivity. In recent years, emerging research on plant holobiont theory and microbial invasion ecology has radically transformed how we study plant–microbe interactions. Over the last few years, we have witnessed an accelerating pace of advancements and breadth of questions answered using omic technologies. Herein, we discuss how current state-of-the-art genomics, transcriptomics, proteomics, and metabolomics techniques reliably transcend the task of studying plant–microbe interactions while acknowledging existing limitations impeding our understanding of plant holobionts.

Fungal species associated with grapevine trunk diseases in Washington wine grapes and California table grapes, with novelties in the genera Cadophora, Cytospora, and Sporocadus

Grapevine trunk diseases cause serious economic losses to grape growers worldwide. The identification of the causal fungi is critical to implementing appropriate management strategies. Through a culture-based approach, we identified the fungal species composition associated with symptomatic grapevines from wine grapes in southeastern Washington and table grapes in the southern San Joaquin Valley of California, two regions with contrasting winter climates. Species were confirmed through molecular identification, sequencing two to six gene regions per isolate. Multilocus phylogenetic analyses were used to identify novel species. We identified 36 species from 112 isolates, with a combination of species that are new to science, are known causal fungi of grapevine trunk diseases, or are known causal fungi of diseases of other woody plants. The novel species Cadophora columbiana, Cytospora macropycnidia, Cytospora yakimana, and Sporocadus incarnatus are formally described and introduced, six species are newly reported from North America, and grape is reported as a new host for three species. Six species were shared between the two regions: Cytospora viticola, Diatrype stigma, Diplodia seriata, Kalmusia variispora, Phaeoacremonium minimum, and Phaeomoniella chlamydospora. Dominating the fungal community in Washington wine grape vineyards were species in the fungal families Diatrypaceae, Cytosporaceae and Sporocadaceae, whereas in California table grape vineyards, the dominant species were in the families Diatrypaceae, Togniniaceae, Phaeomoniellaceae and Hymenochaetaceae. Pathogenicity tests demonstrated that 10 isolates caused wood discoloration similar to symptomatic wood from which they were originally isolated. Growth rates at temperatures from 5 to 35°C of 10 isolates per region, suggest that adaptation to local climate might explain their distribution.

The road to molecular identification and detection of fungal grapevine trunk diseases

Grapevine is regarded as a highly profitable culture, being well spread worldwide and mostly directed to the wine-producing industry. Practices to maintain the vineyard in healthy conditions are tenuous and are exacerbated due to abiotic and biotic stresses, where fungal grapevine trunk diseases (GTDs) play a major role. The abolishment of chemical treatments and the intensification of several management practices led to an uprise in GTD outbreaks. Symptomatology of GTDs is very similar among diseases, leading to underdevelopment of the vines and death in extreme scenarios. Disease progression is widely affected by biotic and abiotic factors, and the prevalence of the pathogens varies with country and region. In this review, the state-of-the-art regarding identification and detection of GTDs is vastly analyzed. Methods and protocols used for the identification of GTDs, which are currently rather limited, are highlighted. The main conclusion is the utter need for the development of new technologies to easily and precisely detect the presence of the pathogens related to GTDs, allowing to readily take phytosanitary measures and/or proceed to plant removal in order to establish better vineyard management practices. Moreover, new practices and methods of detection, identification, and quantification of infectious material would allow imposing greater control on nurseries and plant exportation, limiting the movement of infected vines and thus avoiding the propagation of fungal inoculum throughout wine regions.