Characterization of Six Ampeloviruses Infecting Pineapple in Reunion Island Using a Combination of High-Throughput Sequencing Approaches.

The cultivation of pineapple () is threatened worldwide by mealybug wilt disease of pineapple (MWP), whose etiology is not yet fully elucidated. In this study, we characterized pineapple mealybug wilt-associated ampeloviruses (PMWaVs, family ) from a diseased pineapple plant collected from Reunion Island, using a high-throughput sequencing approach combining Illumina short reads and Nanopore long reads. Reads co-assembly resulted in complete or near-complete genomes for six distinct ampeloviruses, including the first complete genome of pineapple mealybug wilt-associated virus 5 (PMWaV5) and that of a new species tentatively named pineapple mealybug wilt-associated virus 7 (PMWaV7).

A Comprehensive Approach Combining Short-Chain Polyphosphate and Bacterial Biostimulants for Effective Nutrient Solubilization and Enhanced Wheat Growth.

Phosphorus constitutes a crucial macronutrient for crop growth, yet its availability often limits food production. Efficient phosphorus management is crucial for enhancing crop yields and ensuring food security. This study aimed to enhance the efficiency of a short-chain polyphosphate (PolyP) fertilizer by integrating it with plant growth-promoting bacteria (PGPB) to improve nutrient solubilization and wheat growth.

Biological Characterization of Physostegia Chlorotic Mottle Virus, an Emergent Virus Infecting Vegetables in Diversified Production Systems.

In 2014, Physostegia chlorotic mottle virus (PhCMoV) was discovered in Austria in . Subsequent collaborative efforts established a link between the virus and severe fruit symptoms on important crops such as tomato, eggplant, and cucumber across nine European countries. Thereafter, specific knowledge gaps, which are crucial to assess the risks PhCMoV can pose for production and how to manage it, needed to be addressed.

Correction: Haegeman et al. Looking beyond Virus Detection in RNA Sequencing Data: Lessons Learned from a Community-Based Effort to Detect Cellular Plant Pathogens and Pests. 2023, , 2139.

In the original publication [...

First report of Melon chlorotic spot virus in cultivated sorrel () in Belgium.

In 2020, symptoms of putative viral origin were observed on 7% of tomatoes in an organic vegetable farm in Belgium (deformed uneven ripened fruits, vein clearing, mosaic and purple leaves, stunted plants). The leaves of twenty symptomatic plants were collected, pooled and screened for viruses using high throughput sequencing technologies (HTS) on Illumina NextSeq500 following a virion-associated nucleic acid (VANA) protocol (Temple et al., 2021, Be_SL1).

Cont-ID: detection of sample cross-contamination in viral metagenomic data.

Background: High-throughput sequencing (HTS) technologies completed by the bioinformatic analysis of the generated data are becoming an important detection technique for virus diagnostics. They have the potential to replace or complement the current PCR-based methods thanks to their improved inclusivity and analytical sensitivity, as well as their overall good repeatability and reproducibility. Cross-contamination is a well-known phenomenon in molecular diagnostics and corresponds to the exchange of genetic material between samples.

The First Virome of a Russian Vineyard.

Among other pathogens, more than 80 viruses infect grapevine. The aim of this work was to study the virome diversity of grapevine viruses and mycoviruses of a vineyard using high-throughput sequencing technologies. The grapevine virome was studied in symptomatic vines of the Rkatsiteli cultivar () collected at the vineyards of the Krasnodar Krai in Russia.

Detection of single nucleotide polymorphisms in virus genomes assembled from high-throughput sequencing data: large-scale performance testing of sequence analysis strategies.

Recent developments in high-throughput sequencing (HTS) technologies and bioinformatics have drastically changed research in virology, especially for virus discovery. Indeed, proper monitoring of the viral population requires information on the different isolates circulating in the studied area. For this purpose, HTS has greatly facilitated the sequencing of new genomes of detected viruses and their comparison.

Diversity and Pathobiology of an Ilarvirus Unexpectedly Detected in Diverse Plants and Global Sequencing Data.

High-throughput sequencing (HTS) and sequence mining tools revolutionized virus detection and discovery in recent years, and implementing them with classical plant virology techniques results in a powerful approach to characterize viruses. An example of a virus discovered through HTS is Solanum nigrum ilarvirus 1 (SnIV1) (), which was recently reported in various solanaceous plants from France, Slovenia, Greece, and South Africa. It was likewise detected in grapevines () and several and plant species.

Impact of Two Phosphorus Fertilizer Formulations on Wheat Physiology, Rhizosphere, and Rhizoplane Microbiota.

Phosphorus (P) is the second most important macronutrient for crop growth and a limiting factor in food production. Choosing the right P fertilizer formulation is important for crop production systems because P is not mobile in soils, and placing phosphate fertilizers is a major management decision. In addition, root microorganisms play an important role in helping phosphorus fertilization management by regulating soil properties and fertility through different pathways.

Managing the deluge of newly discovered plant viruses and viroids: an optimized scientific and regulatory framework for their characterization and risk analysis.

The advances in high-throughput sequencing (HTS) technologies and bioinformatic tools have provided new opportunities for virus and viroid discovery and diagnostics. Hence, new sequences of viral origin are being discovered and published at a previously unseen rate. Therefore, a collective effort was undertaken to write and propose a framework for prioritizing the biological characterization steps needed after discovering a new plant virus to evaluate its impact at different levels.

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.

First report of lettuce ring necrosis virus in chili pepper and tomato in Belgium and The Netherlands.

Lettuce ring necrosis virus (LRNV), genus Ophiovirus, was detected by the Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP) in June and November of 2021 in two samples of chili pepper fruits (Capsicum spp.), both in mixed infection with other viruses. The first sample originated from a production site in Belgium (Sample ID: 40009704) and the second from a production site in the Netherlands (Sample ID: 41115269).

Long-Term Anthropogenic Management and Associated Loss of Plant Diversity Deeply Impact Virome Richness and Composition of Communities.

Modern agriculture has influenced plant virus emergence through ecosystem simplification, introduction of new host species, and reduction in crop genetic diversity. Therefore, it is crucial to better understand virus distributions across cultivated and uncultivated communities in agro-ecological interfaces, as well as virus exchange among them. Here, we advance fundamental understanding in this area by characterizing the virome of three co-occurring replicated community types that represent a gradient of grass species richness and management intensity, from highly managed crop monocultures to little-managed, species-rich grasslands.

Analysis of the Genetic Diversity of Two Species from China and Europe Based on Nuclear and Mitochondrial Genes.

Population genetic studies can reveal clues about the evolution of adaptive strategies of aphid species in agroecosystems and demonstrate the influence of environmental factors on the genetic diversity and gene flow among aphid populations. To investigate the genetic diversity of two aphid species from different geographical regions, 32 populations (n = 535) of the bird cherry-oat aphid ( Linnaeus) and 38 populations (n = 808) of the corn leaf aphid ( Fitch) from China and Europe were analyzed using one nuclear (elongation factor-1 alpha) and two mitochondrial (cytochrome oxidase I and II) genes. Based on the COI-COII sequencing, two obvious clades between Chinese and European populations and a low level of gene flow (Nm = 0.

Co-diet supplementation of low density polyethylene and honeybee wax did not influence the core gut bacteria and associated enzymes of Galleria mellonella larvae (Lepidoptera: Pyralidae).

The current plastic pollution throughout the world is a rising concern that demands the optimization of biodegradation processes. One avenue for this is to identify plastic-degrading bacteria and associated enzymes from the gut bacteria of insect models such as Tenebrio molitor, Plodia interpunctella or Galleria mellonella that have the ability to ingest and rapidly degrade polyethylene. Therefore, this study takes part in understanding the role of the gut bacteria by investigating G.

First Study Case of Microbial Biocontrol Agents Isolated from Aquaponics Through the Mining of High-Throughput Sequencing Data to Control Pythium aphanidermatum on Lettuce.

Aquaponics is defined as a sustainable and integrated system that combines fish aquaculture and hydroponic plant production in the same recirculated water loop. A recent study using high-throughput sequencing (HTS) technologies highlighted that microbial communities from an aquaponic system could control one of the most problematic pathogens in soilless lettuce culture, namely, Pythium aphanidermatum. Therefore, this study aims at isolating the microorganisms responsible for this biocontrol action.

The Expanding Menagerie of -Infecting Luteoviruses.

Members of the genus are responsible for economically destructive plant diseases worldwide. Over the past few years, three luteoviruses infecting trees have been characterized. However, the biological properties, prevalence, and genetic diversity of those viruses have not yet been studied.

Risk factors associated with cassava brown streak disease dissemination through seed pathways in Eastern D.R. Congo.

Vegetatively propagated crops are particularly prone to disease dissemination through their seed systems. Strict phytosanitary measures are important to limit the impact of diseases as illustrated by the potato seed system in Europe. Cassava brown streak disease (CBSD) is a devastating disease caused by two viral species collectively named cassava brown streak viruses (CBSVs).

Identification of a novel vitivirus from pineapple in Reunion Island.

We report the complete genome sequence of a novel member of the genus Vitivirus (family Betaflexiviridae, subfamily Trivirinae) infecting pineapple. The complete genome sequence of this virus was obtained from total RNA extracted from pineapple leaf samples collected in Reunion Island, using a combination of high-throughput sequencing technologies. The viral genome is 6,757 nt long, excluding the poly(A) tail, and shares all the hallmarks of vitiviruses.

Virion-Associated Nucleic Acid-Based Metagenomics: A Decade of Advances in Molecular Characterization of Plant Viruses.

Over the last decade, viral metagenomic studies have resulted in the discovery of thousands of previously unknown viruses. These studies are likely to play a pivotal role in obtaining an accurate and robust understanding of how viruses affect the stability and productivity of ecosystems. Among the metagenomics-based approaches that have been developed since the beginning of the 21st century, shotgun metagenomics applied specifically to virion-associated nucleic acids (VANA) has been used to disentangle the diversity of the viral world.

Global nature run data with realistic high-resolution carbon weather for the year of the Paris Agreement.

The CO Human Emissions project has generated realistic high-resolution 9 km global simulations for atmospheric carbon tracers referred to as nature runs to foster carbon-cycle research applications with current and planned satellite missions, as well as the surge of in situ observations. Realistic atmospheric CO, CH and CO fields can provide a reference for assessing the impact of proposed designs of new satellites and in situ networks and to study atmospheric variability of the tracers modulated by the weather. The simulations spanning 2015 are based on the Copernicus Atmosphere Monitoring Service forecasts at the European Centre for Medium Range Weather Forecasts, with improvements in various model components and input data such as anthropogenic emissions, in preparation of a CO Monitoring and Verification Support system.