Plant-Pathogenic Fusarium Species

Molecular Identification and Pathogenicity of Fusarium Species Associated with Wood Canker, Root and Basal Rot in Turkish Grapevine Nurseries

Fusarium species are agriculturally important fungi with a broad host range and can be found as endophytic, pathogenic, or opportunistic parasites in many crop plants. This study aimed to identify Fusarium species in bare-rooted, dormant plants in Turkish grapevine nurseries using molecular identification methods and assess their pathogenicity. Asymptomatic dormant plants were sampled from grapevine nurseries (43) in different regions of the country, and fungi were isolated from plant roots and internal basal tissues. The Fusarium strains were identified by performing gene sequencing (TEF1-α, RPB2) and phylogenetic analyses. Pathogenicity tests were carried out by inoculating mycelial agar pieces of strains onto the stem or conidial suspensions into the rhizosphere of vines (1103 Paulsen rootstock). Laboratory tests revealed that Fusarium species were highly prevalent in Turkish grapevine nurseries (41 out of 43). Gene sequencing and phylogenetic analyses unraveled that 12 Fusarium species (F. annulatum, F. brachygibbosum, F. clavum, F. curvatum, F. falciforme, F. fredkrugeri, F. glycines, F. nanum, F. nematophilum, F. nirenbergiae, F. solani, and Fusarium spp.) existed in the ready-to-sale plants. Some of these species (F. annulatum, F. curvatum and F. nirenbergiae) consistently caused wood necrosis of seedling stems, rotting of the basal zone and roots, and reduced root biomass. Although the other nine species also caused some root rot and root reduction, their virulence was not as severe as the pathogenic ones, and they were considered opportunistic parasites or endophytic species. This study suggests that Fusarium species might play an important role in root-basal rot, wood canker symptoms, and young vine decline in Turkish grapevine nurseries and that these species need to be considered for healthy seedling production.

Microbial Pathogens in Aquaponics Potentially Hazardous for Human Health

The union of aquaculture and hydroponics is named aquaponics-a system where microorganisms, fish and plants coexist in a water environment. Bacteria are essential in processes which are fundamental for the functioning and equilibrium of aquaponic systems. Such processes are nitrification, extraction of various macro- and micronutrients from the feed leftovers and feces, etc. However, in aquaponics there are not only beneficial, but also potentially hazardous microorganisms of fish, human, and plant origin. It is important to establish the presence of human pathogens, their way of entering the aforementioned systems, and their control in order to assess the risk to human health when consuming plants and fish grown in aquaponics. Literature analysis shows that aquaponic bacteria and yeasts are mainly pathogenic to fish and humans but rarely to plants, while most of the molds are pathogenic to humans, plants, and fish. Since the various human pathogenic bacteria and fungi found in aquaponics enter the water when proper hygiene practices are not applied and followed, if these requirements are met, aquaponic systems are a good choice for growing healthy fish and plants safe for human consumption. However, many of the aquaponic pathogens are listed in the WHO list of drug-resistant bacteria for which new antibiotics are urgently needed, making disease control by antibiotics a real challenge. Because pathogen control by conventional physical methods, chemical methods, and antibiotic treatment is potentially harmful to humans, fish, plants, and beneficial microorganisms, a biological control with antagonistic microorganisms, phytotherapy, bacteriophage therapy, and nanomedicine are potential alternatives to these methods.

Genomic and Metabolomic Analysis of the Endophytic Fungus Fusarium sp. VM-40 Isolated from the Medicinal Plant Vinca minor

The genus Fusarium is well-known to comprise many pathogenic fungi that affect cereal crops worldwide, causing severe damage to agriculture and the economy. In this study, an endophytic fungus designated Fusarium sp. VM-40 was isolated from a healthy specimen of the traditional European medicinal plant Vinca minor. Our morphological characterization and phylogenetic analysis reveal that Fusarium sp. VM-40 is closely related to Fusarium paeoniae, belonging to the F. tricinctum species complex (FTSC), the genomic architecture and secondary metabolite profile of which have not been investigated. Thus, we sequenced the whole genome of Fusarium sp. VM-40 with the new Oxford Nanopore R10.4 flowcells. The assembled genome is 40 Mb in size with a GC content of 47.72%, 15 contigs (≥50,000 bp; N 50~4.3 Mb), and 13,546 protein-coding genes, 691 of which are carbohydrate-active enzyme (CAZyme)-encoding genes. We furthermore predicted a total of 56 biosynthetic gene clusters (BGCs) with antiSMASH, 25 of which showed similarity with known BGCs. In addition, we explored the potential of this fungus to produce secondary metabolites through untargeted metabolomics. Our analyses reveal that this fungus produces structurally diverse secondary metabolites of potential pharmacological relevance (alkaloids, peptides, amides, terpenoids, and quinones). We also employed an epigenetic manipulation method to activate cryptic BGCs, which led to an increased abundance of several known compounds and the identification of several putative new compounds. Taken together, this study provides systematic research on the whole genome sequence, biosynthetic potential, and metabolome of the endophytic fungus Fusarium sp. VM-40.