Biology subjects

Forgia, M.

Publications and source records attributed to Forgia, M..

6 recordsLinked to original sources

bioRxiv2026

Viral diversity and activity in Arctic tundra soils in wintertime

Arctic soils store vast amounts of carbon and are warming faster than the rest of the globe. Still, little is known about microbe-mediated feedback responses to the ongoing environmental changes in the warming Arctic. Specifically, viral diversity, functions, and virus-host interactions remain largely unknown in northern soils outside the growing season. Here, we analyzed the diversity and activity of viruses in oroarctic tundra soils during wintertime using metatranscriptomics. Through de novo virus prediction as well as targeted searches, we identified 995 viral operational taxonomic units (vOTUs) in total. Most of these vOTUs, 93%, represented RNA viruses, part of which were presumably segments of multipartite genomes. RNA vOTUs were classified mainly within the phyla Lenarviricota (259), Kitrinoviricota (198), Pisuviricota (135), Ambiviricota (103), Negarnaviricota (79), and Duplornaviricota (42). Thirty-seven DNA vOTUs (mostly Caudoviricetes) were also detected, suggesting active viral infections. In total, 81% of all vOTUs were assigned with a putative host organism, mostly fungi (515 vOTUs). Viral communities were distinct across vegetation types, and pH and moisture contributed to the differences. Putative novel clades within Ambiviricota and Orpoviricetes were identified, expanding their known diversity. The study contributes to uncovering diverse RNA viruses and viroid-like elements in Arctic tundra soils and highlights that soil viruses remain active in wintertime.

microbiology↗

bioRxiv2026

A viroid-like RNA can be transmitted among different Trichoderma species affecting their antagonistic capacity

Viroids are small, circular non-coding RNAs that autonomously replicate in plants, exploiting host cellular machinery for replication and spread. Recent studies reveal that viroid-like agents can infect filamentous fungi, suggesting cross-kingdom interactions. In this study, we report the discovery and the characterization of TsvlRNA1 in Trichoderma spirale, a transmissible viroid-like RNA containing a hammerhead ribozyme in one polarity strand. Bioinformatic data, molecular validation, and reverse genetics experiments demonstrate that TsvlRNA1 is circular with an active ribozyme essential for replication. TsvlRNA1 replicates autonomously and transmits horizontally between Trichoderma species, eliciting 21-23 nt viroid-derived small RNAs consistent with RNA silencing targeting. The biocontrol capacity of Trichoderma against Rhizoctonia solani is variably modulated by TsvlRNA1, with effects ranging from positive to negative depending on host strain. In T. spirale, data suggests genotype-by-agent interactions influence antagonistic potential negatively. TsvlRNA1 transmission via horizontal routes is prevalent, and the viroid-like RNA fails to infect plant hosts experimentally. These results highlight so-far the underappreciated ecological and functional diversity of viroid-like agents in fungi, with implications for fungal biology, biocontrol, and genotype-phenotype relationships in eukaryotes. ImportanceSpecies of the fungal genus Trichoderma play a central role in sustainable agriculture by controlling fungal plant pathogens and supporting plant growth. For this reason, Trichoderma-based products represent a substantial share of the global market for microbial biofungicides. Viroids are the smallest known infectious agents, and their presence in filamentous fungi has only recently been discovered. Consequently, little is known about their biology, transmission, or interactions with fungal hosts. In this study, we describe TsvlRNA1, a viroid-like RNA associated with T. spirale, representing only the second viroid-like RNA to be biologically characterized in fungi. We show that TsvlRNA1 can influence the ability of Trichoderma to inhibit Rhizoctonia solani, a major plant pathogen, demonstrating its biological relevance. Unexpectedly, TsvlRNA1 can be transmitted between different Trichoderma species. This finding raises concerns about the possible transfer of genetic traits between fungi, including those related to fungicide resistance, with important implications for agricultural biocontrol. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/702247v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@1b6de6eorg.highwire.dtl.DTLVardef@c52141org.highwire.dtl.DTLVardef@a61fcorg.highwire.dtl.DTLVardef@1a6f0a4_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

Self-cleaving ribozymes conserved in RNA viruses unveil a new role in protein translation

Small self-cleaving ribozymes are catalytic RNAs originally discovered in viroid-like agents, which are replicating circular RNAs (circRNAs) postulated as relics of a prebiotic RNA world. In the last decade, however, small ribozymes have also been detected across the tree of life, from bacterial to human genomes, and more recently, in unusual circRNA viruses. Here we report the conserved occurrence of diverse small ribozymes within the linear genomes of typical double- and single-stranded RNA virus families from fungi and plants. Type I hammerhead ribozyme motifs occur in the 5-UTR regions of chrysovirids and fusarivirids, displaying self-cleaving activity in vitro and in vivo. Similar hammerhead, as well as hepatitis delta and twister ribozymes, are also found in diverse megabirna-, hypo-, fusagra-, toti-or tombus-like viruses among others. The ribozymes occur not only as isolated motifs within UTRs but also as tandem pairs that encompass small RNA segments (186-399 nt) resembling Zetavirus-like sequences. In vivo characterization of the 5-UTR with a ribozyme from a chrysovirid revealed that the RNA-cleaving activity is essential for protein translation initiation in fungi. Analogous experiments in plants with diverse ribozyme motifs indicated that just the presence of a self-cleaving activity can induce cap-independent translation. We conclude that RNA self-cleaving activity, historically linked to the rolling circle replication of viroid-like circRNAs, appears to be co-opted by linear RNA viruses for translational roles.

microbiology↗

bioRxiv2023

A collection of Trichoderma isolates from natural environments in Sardinia, a biodiversity hotspot, reveals a complex virome that includes negative-stranded mycoviruses with unprecedented genome organizations

The Trichoderma genus includes soil-inhabiting fungi that provide important ecological services in their interaction with plants and other fungi. They are exploited for biocontrol. A collection of Trichoderma isolates from the Sardinia island (a biodiversity hotspot) had been previously characterized. Here we started a characterization of the viral components associated to 113 selected Trichoderma isolates, representatives of the collection. We carried out NGS sequencing of ribosome depleted total RNA following a bioinformatic pipeline that detects virus RNA-dependent RNA polymerases (RdRP) and other conserved virus protein sequences. This pipeline detected 17 viral RdRPs. Two of them correspond to viruses already detected in other regions of the world. The remaining 15 represent isolates of new virus species: surprisingly, eight of them are from new negative stranded RNA viruses, which for the first time are reported in the genus Trichoderma. Among them is a cogu-like virus, very closely related to plant-infecting viruses. Regarding the positive strand viruses, it is noticeable the presence of an ormycovirus belonging to a recently characterized group of bi-segmented ssRNA genome viruses with still uncertain phylogenetic assignment. Finally, for the first time we report a bipartite mononegavirales-infecting fungi: the proteins encoded by the second genomic RNA were used to re-evaluate a number of viruses in the Penicillimonavirus and Plasmopamonavirus genera, here shown to be bipartite and to encode a conserved polypeptide having structural conservation with the nucleocapsid (NC) domain of members of the Rabhdoviridae. IMPORTANCE Trichoderma is a genus of fungi of great biotechnological impact in multiple industrial fields. The possibility to investigate a diverse collection of Trichoderma isolates allowed us to characterize both double-stranded and single-stranded virus genomes belonging to three of the major phyla that constitute the RNA viral kingdom, thus further increasing the taxa of viruses infecting this genus. To our knowledge here we report for the first time negative-stranded RNA viruses infecting Trichoderma spp. and through in silico structural analysis a new conserved domain of nucleocapsids common among some mymonavirids. Obtaining such a library of mycoviruses could be the basis for further development of targeted virus-induced gene silencing or gene editing (VIGS/VIGE) tools; in addition, the many biotechnological applications of this fungus, will require to assess the qualitative (commercial) stability of strains, linked to positive or negative effects caused by mycovirus infections.

microbiology↗

bioRxiv2022

Extant hybrids of RNA viruses and viroid-like elements

Earths life may have originated as self-replicating RNA. Some of the simplest current RNA replicators are RNA viruses, defined by linear RNA genomes encoding an RNA-dependent RNA polymerase (RdRP), and subviral agents with single-stranded, circular RNA genomes, such as viroids encoding paired self-cleaving ribozymes. Amongst a massive expansion of candidate viroid and viroid-like elements, we report that fungal pathogens, ambiviruses, are viroid-like elements which undergo rolling circle replication and encode their own viral RdRP, thus they are a distinct hybrid infectious agent. These findings point to a deep evolutionary history between modern RNA viruses and sub-viral elements and offer new perspectives on the evolution of primordial infectious agents, and RNA life. One-Sentence SummaryNovel infectious agents resembling self-cleaving viroid-like RNAs whilst encoding a viral RNA-dependent RNA polymerase.

microbiology↗

bioRxiv2019

A complex virome that includes two distinct emaraviruses is associated to virus-like symptoms in Camellia japonica

Camellia japonica plants manifesting a complex and variable spectrum of viral symptoms like chlorotic ringspots, necrotic rings, yellowing with necrotic rings, yellow mottle, leaves and petals deformations, flower color-breaking were studied since 1940 essentially through electron microscopic analyses; however, a strong correlation between symptoms and one or more well characterized viruses was never verified. In this work samples collected from symptomatic plants were analyzed by NGS technique and a complex virome composed by viruses members of the Betaflexiviridae and Fimoviridae families was identified. In particular, the genomic fragments typical of the emaravirus group were organized in the genomes of two new emaraviruses species, tentatively named Camellia japonica associated emaravirus 1 and 2. They are the first emaraviruses described in camellia plants and were always found solely in symptomatic plants. On the contrary, in both symptomatic and asymptomatic plants, we detected five betaflexiviruses isolates that, based on aa identitiy comparisons, can be classified in two new putative species called Camellia japonica associated betaflexivirus 1 and Camellia japonica associated betaflexivirus 2. Together with other recently identified betaflexiviruses associated to Camellia japonica disease, the betaflexiviruses characterized in this study show an unusual hyper-conservation of the coat protein at aminoacidic level.

microbiology↗