A5083572087- Bacteriophages and microbial interactions
- Plant Virus Research Studies
- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Plant and Fungal Interactions Research
- Animal Virus Infections Studies
- Environmental DNA in Biodiversity Studies
- Climate change and permafrost
- Polar Research and Ecology
- Plant Disease Resistance and Genetics
- Viral gastroenteritis research and epidemiology
- CRISPR and Genetic Engineering
- Viral Infections and Vectors
- Virology and Viral Diseases
- Evolution and Genetic Dynamics
The Ohio State University
2019-2024
Centro Oceanográfico de Málaga
2024
Instituto Español de Oceanografía
2024
Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora"
2018
Consejo Superior de Investigaciones Científicas
2018
Universidad de Málaga
2018
Viruses are a significant player in many biosphere and human ecosystems, but most signals remain "hidden" metagenomic/metatranscriptomic sequence datasets due to the lack of universal gene markers, database representatives, insufficiently advanced identification tools.Here, we introduce VirSorter2, DNA RNA virus tool that leverages genome-informed advances across collection customized automatic classifiers improve accuracy range detection. When benchmarked against genomes from both isolated...
Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA insufficiently studied outside disease settings. In this study, we analyzed ≈28 terabases of Global Ocean sequences expand Earth's virus catalogs their taxonomy, investigate evolutionary origins, assess marine biogeography from pole pole. Using new approaches optimize discovery classification, identified that necessitate substantive revisions taxonomy (doubling phyla adding >50% classes)...
DNA viruses are increasingly recognized as influencing marine microbes and microbe-mediated biogeochemical cycling. However, little is known about global RNA virus diversity, ecology, ecosystem roles. In this study, we uncover patterns predictors of community- “species”-level diversity contextualize their ecological impacts from pole to pole. Our analyses revealed four zones, latitudinal depth patterns, environmental correlates for viruses. findings only partially parallel those cosampled...
Abstract Viruses, despite their great abundance and significance in biological systems, remain largely mysterious. Indeed, the vast majority of perhaps hundreds millions viral species on planet undiscovered. Additionally, many viruses deposited central databases like GenBank RefSeq are littered with genes annotated as ‘hypothetical protein’ or equivalent. Cenote-Taker 2, a virus discovery annotation tool available command line graphical user interface free high-performance computation...
Prokaryotic microbes have impacted marine biogeochemical cycles for billions of years. Viruses also impact these cycles, through lysis, horizontal gene transfer, and encoding expressing genes that contribute to metabolic reprogramming prokaryotic cells. While this is difficult quantify in nature, we hypothesized it can be examined by surveying virus-encoded auxiliary (AMGs) assessing their ecological context.
Improved RNA virus understanding is critical to studying animal and plant health, environmental processes. However, the continuous rapid evolution makes their identification characterization challenging. While recent sequence-based advances have led extensive discovery, there growing variation in how viruses are identified, analyzed, characterized, reported. To this end, an RdRp Summit was organized a hybrid meeting took place Valencia, Spain May 2023 convene leading experts with emphasis on...
Microbiomes shape ecosystems through functional profiles influenced by gene gains and losses. While culture-based experiments demonstrate that mobile genetic elements (MGEs) can mediate flux, quantitative field data remains scarce. Here we leverage large-scale soil meta-omic to develop apply analytics for studying MGEs. In our model permafrost-thaw ecosystem, Stordalen Mire, identify ~2.1 million MGE recombinases across 89 microbial phyla assess ecological distributions, functions impacted,...
Climate change thaws permafrost, which releases greenhouse gases partly from dormant microorganisms awakening and metabolizing organic matter. Though DNA viruses that infect these soil microbes have been studied, little is known on RNA viruses, typically microeukaryotes. Here we identify characterize 2,651 a 4-year time series of bulk metatranscriptomes derived the climatically fragile Stordalen Mire ecosystem - long-studied permafrost peatland. virus diversity was structured by habitat...
Geminiviruses (family Geminiviridae) possess single-stranded circular DNA genomes that are replicated by cellular polymerases in plant host cell nuclei. In their hosts, geminivirus populations behave as ensembles of mutant and recombinant genomes, known viral quasispecies. This favors the emergence new geminiviruses with altered range, facilitating or more severe diseases overcoming resistance traits. warm temperate areas several whitefly-transmitted genus Begomovirus cause tomato yellow...
Viruses play crucial roles in the ecology of microbial communities, yet they remain relatively understudied their native environments. Despite many advancements high-throughput whole-genome sequencing (WGS), sequence assembly, and annotation viruses, reconstruction full-length viral genomes directly from metagenomic is possible only for most abundant phages requires long-read technologies. Additionally, prediction cellular hosts remains difficult conventional alone. To address these gaps...
RNA viruses play crucial roles in modulating host communities, but their diversity and ecological the cryosphere are poorly understood. We investigated virome from of Tibetan Plateau (TPC), largest area mid-low latitude regions, which includes 79 metatranscriptomes ecosystems including glaciers, proglacial lake sediments, permafrost wetland upland soils. obtained 8,799 RNA-dependent polymerase encoding contigs, clustered into 5,333 viral species, adding more than 4,900 new species to global...
Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow metabolic outputs. However, ecosystem-level impacts of viral community diversity remains difficult to assess due classification issues few reference genomes. Here we establish a ~12-fold expanded global ocean DNA virome dataset 195,728 populations, now including the Arctic Ocean, validate these populations form discrete genotypic clusters. Meta-community analyses revealed five ecological zones...
Lethal mutagenesis is an antiviral therapy that relies on increasing the viral mutation rate with mutagenic nucleoside or base analogues. Currently, molecular mechanisms lead to virus extinction through enhanced are not fully understood. Increasing experimental evidence supports lethal defection model of RNA viruses, where replication-competent-defectors drive infective towards extinction. Here, we address in vivo using 5-fluorouracil (5-FU) during establishment tobacco mosaic (TMV) systemic...
Abstract Viruses, despite their great abundance and significance in biological systems, remain largely mysterious. Indeed, the vast majority of perhaps hundreds millions viral species on planet undiscovered. Additionally, many viruses deposited central databases like GenBank RefSeq are littered with genes annotated as “hypothetical protein” or equivalent. Cenote-Taker2, a virus discovery annotation tool available command line graphical user interface free high-performance computation access,...