Metagenomic analysis of plant viruses in tropical fresh and wastewater

Abstract

Due to considerable losses in the agricultural sector, phytopathogenic viruses are of significant economic importance. Several phytopathogenic viruses have been detected in water bodies. These can be transmitted to their hosts through water contact. However, relatively few studies concentrate on the presence and impact of plant‐infecting viruses in water environments. In the present study, we used a metagenomic approach to determine viral phytopathogen diversity in wastewater, freshwater, and sludge from the southernmost tropical region in Mexico. We detected 15 different phytopathogenic viruses that belonged to the family Virgaviridae, genus Tobamovirus. Pepper mild mottle virus, tomato brown rugose fruit virus, and tropical soda apple mosaic virus had the highest number of reads. Phylogenetic analysis of the coat protein (CP) amino acid sequence revealed a close relationship between the solanaceous plant‐infecting viruses and the reference sequences found in GenBank. On the other hand, the CP amino acid sequence of Fabaceae and Cucurbitaceae‐infecting viruses did not show such a close relationship when compared with GenBank reference sequences. These results suggested that detected viral sequences could originate from new strains or species of local viruses likely from the consumption of locally cultivated produce, whereas those infecting solanaceous plants might come from consumption of processed or imported food to Mexico. The prevalence of a high diversity of plant viruses in wastewater and rivers and their potential infectivity raise concerns about the use of contaminated freshwater and wastewater in agriculture in Mexico.

Virome analysis of irrigation water sources provides extensive insights into the diversity and distribution of plant viruses in agroecosystems

“…Shotgun HTS analysis, that was applied to water samples, shed light on the viral abundance and diversity within the samples. Viral reads accounted for around 1% of all reads, comparable to previously reported results [4], [9]. Although the sample preparation used here aimed at concentrating RNA sequences, we observed all possible variations of viral genome types within each sample.…”

“…Although the research of plant viruses in environmental waters has been gradually developing, there are still relatively few studies focusing on this topic. There are even fewer studies that focused on irrigation water and/or surface water near farms [9]- [11].…”

“…Many studies addressed diversity of viruses (e.g., bacteriophages) in oceans [14], [15], however, less attention has been given to freshwater bodies [16]. Virome studies of freshwater bodies, specifically focusing on plant viruses are sparse [9], [17], even though this aspect is important in the view of the possible detrimental effects of plant viruses in agriculture, if such waters are used for irrigation of plants [3], [8]. To better understand the potential risks associated with the presence of plant viruses in irrigation waters, baseline virome studies are first needed to provide information about the presence of viruses in such samples.…”

Biological Exploration and Physicochemical Characteristics of Tomato Brown Rugose Fruit Virus in Several Host Crops

“…Also, it has become apparent that the presence of YTMMV in hydroponic systems could trigger epidemics via infection of the roots of healthy plants [56]. The persistence of these viruses in water contributes to their dissemination in agricultural systems, demonstrating the presence of infectious ToBRFV viral particles in wastewater located at some distance from production areas [56,57]. Lately, the persistence of ToBRFV viral particles has become apparent in conventionally treated wastewater, and these particles maintain their infectious capacity even after treatment [58].…”

Introduction to special issue: Advancing disease ecology through eDNA monitoring of infectious agents

“…Lopez‐Roblero et al. (2023) used a metabarcoding approach to determine the diversity of viral phytopathogens in freshwater, wastewater, and sludge in a southern tropical region of Mexico. They detected 15 different phytopathogenic viruses within the family Virgaviridae and the genus Tobamovirus .…”