Viruses cause epidemics on all major crops of agronomic importance, and a timely and accurate identification is essential for control. High throughput sequencing (HTS) is a technology that allows the identification of all viruses without prior knowledge on the targeted pathogens. In this paper, we used HTS technique for the detection and identification of different viral species occurring in single and mixed infections in plants in Poland. We analysed various host plants representing different families. Within the 20 tested samples, we identified a total of 13 different virus species, including those whose presence has not been reported in Poland before: clover yellow mosaic virus (ClYMV) and melandrium yellow fleck virus (MYFV). Due to this new finding, the obtained sequences were compared with others retrieved from GenBank. In addition, cucurbit aphid-borne yellows virus (CABYV) was also detected, and due to the recent occurrence of this virus in Poland, a phylogenetic analysis of these new isolates was performed. The analysis revealed that CABYV population is highly diverse and the Polish isolates of CABYV belong to two different phylogenetic groups. Our results showed that HTS-based technology is a valuable diagnostic tool for the identification of different virus species originating from variable hosts, and can provide rapid information about the spectrum of plant viruses previously not detected in a region.

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In recent years, the occurrence of cucumber mosaic virus (CMV) has been noted in zucchini crops in Poland. Beside characteristic isolates, which displayed mosaics and chlorosis on infected plants, new necrotic isolates have also been identified. Here, we analysed the molecular variability of 27 isolates of CMV collected from zucchini in various regions of the country. Sequence and phylogenetic analysis based on the genes encoding the coat (CP) and movement (MP) proteins revealed that the Polish isolates belong to two subgroups: IA and II, with the prevalence of subgroup II. New recombinant variants with an IA-MP/II-CP pattern for RNA3 were also detected.

Tomato black ring virus (TBRV) infects a wide range of economically important plants, and is distributed worldwide. TBRV is transmitted by soil-inhabiting nematodes. However, a long-distance dispersion is possible via seeds and pollen. In this study, we provided evidence that virus can be efficiently transmitted through tomato seeds. Three tomato varieties (Beta Lux, Grace and Money Maker) and four genetically diverse TBRV isolates collected originally from different hosts were used in the experiments. The seedlings were grown in an insect-proof glasshouse and the presence of TBRV was verified by immunoassay (ELISA). The seed transmission was significantly dependent on tomato cultivar and virus isolate ranging from 1.69% up to 14.57%. Bioassays using Chenopodium quinoa plants confirmed the presence of infectious virus in the seeds.

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Soybean (Glycine max Willd.) is one of the most economically important crops in the world, and it’s importance continuously increasing. Routine screening of Polish soybean fields has revealed an outburst of a new disease of soybean plants, with symptoms resembling those described for the bacterial blight, caused by Pseudomonas syringae pv. glycinae, and bacterial pustule caused by Xanthomonas axonopodis pv. glycines. The symptoms were observed in the field, on the leaves of investigated plants. The goal of this paper was the identification and characterization of the causal agent of that disease. Our studies have excluded virus and fungi and pointed the bacteria as the disease causal agent. Identification based on biological (Biolog Gen III), and molecular methods (16S rDNA, and gyrB sequencing, PCR species-specific testing) revealed that the soy pathogenic bacteria is Kosakonia cowanii species. We believe that the presence of such pathogens in the environment pose a serious threat for the crops and is also a warning, that in the near future we may be faced a new type of bacterial pathogens: both epi- and endophytic, abundant in the natural environment, with huge metabolic potential, and ability of quick colonization of new ecological niches and hosts, e.g. opportunistic pathogens of plants or humans. What’s important is that the plant-pathogenic and plant-epiphytic “environmental” strains of such species can be distinguished from each other only post factum, in the pathogenicity tests. They are indistinguishable or very hard to distinguish morphologically, biochemically or molecularly.

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