Search Results (3)

High-throughput sequencing (HTS) has revolutionized phytopathology by overcoming many limitations of traditional diagnostic methods, as it permits precise pathogen monitoring, identification, and control, with ribosomal DNA (rDNA) regions serving as reliable markers for fungal classification. In this study, next-generation sequencing (NGS) was used, targeting the ITS1 and ITS2 regions to explore fungal diversity and pathogen presence in winter wheat grain samples and identifying 183 OTU sequences across 115 taxa. The ITS1 analysis yielded 249,743 reads, with Fusarium sp. (61%) as the dominant pathogenic taxon, followed by Sporobolomyces sp. (14%), Cladosporium sp. (3%), and other yeast-like or saprotrophic fungi, such as Cryptoccocus spp., F. wieringae, and B. alba. Sequencing of ITS1 also permitted the detection of F. acuminatum and the quarantine-regulated pathogens T. caries and T. triticoides. The ITS2 analysis produced 179,675 reads, with F. culmorum (47%) as the most abundant taxon, confirming significant grain contamination with this pathogen. Other frequently detected taxa included yeast-like fungi such as C. tephrensis (21%) and V. victoriae (13%), along with saprotrophic species like S. roseus and Davidella sp. ITS2 provided better resolution for the identification of Fusarium species by the detection of more pathogenic taxa associated with cereal diseases, including F. culmorum, as well as F. cerealis, F. poae, and F. tricinctum. The analysis revealed a diverse fungal community, including other pathogens such as A. porri, B. cinerea, and C. herbarum, as well as various non-pathogenic and saprotrophic fungal taxa. These findings underscore the complementary utility of ITS1 and ITS2 in profiling fungal diversity and detecting critical pathogens using HTS, highlighting the potential of these DNA regions for monitoring and managing cereal crop health. Full article

Microbial water quality is of vital importance for human, animal, and environmental health. Notably, pathogenically contaminated water can result in serious health problems, such as waterborne outbreaks, which have caused huge economic and social losses. In this context, the prompt detection of microbial contamination becomes essential to enable early warning and timely reaction with proper interventions. Recently, molecular diagnostics have been increasingly employed for the rapid and robust assessment of microbial water quality implicated by various microbial pollutants, e.g., waterborne pathogens and antibiotic-resistance genes (ARGs), imposing the most critical health threats to humans and the environment. Continuous technological advances have led to constant improvements and expansions of molecular methods, such as conventional end-point PCR, DNA microarray, real-time quantitative PCR (qPCR), multiplex qPCR (mqPCR), loop-mediated isothermal amplification (LAMP), digital droplet PCR (ddPCR), and high-throughput next-generation DNA sequencing (HT-NGS). These state-of-the-art molecular approaches largely facilitate the surveillance of microbial water quality in diverse aquatic systems and wastewater. This review provides an up-to-date overview of the advancement of the key molecular tools frequently employed for microbial water quality assessment, with future perspectives on their applications. Full article