The kingdom of fungi comprises some of the most mysterious, poorly studied, and diverse organisms on our planet. The pioneering DNA-based technology known as the polymerase chain reaction (PCR) is now revolutionizing our understanding of fungal taxonomy, systematics, and ecology.

Pseudomonas syringae pv. syringae (Pss) constitutes a diverse group of bacterial strains that cause canker of stone fruits, blight of cereals and red streak of sugarcane. The purpose of this study was to determine how diverse Iranian strains of Pss are when they come from different hosts. We compared a total of 32 Pss strains isolated from stone fruits, barley, wheat and sugarcane from different geographical regions of Iran based on their phenotypic and molecular properties. Strains showed some variation regarding carbon and nitrogen utilization. Pss strains were similar in their protein banding patterns. Additional bands were found in sugarcane strains. Most strains showed one indigenous plasmid DNA and a few had two and some none. The genes of syrB and syrD encoding syringomycin synthesis and secretion, respectively, were amplified using specific primers in polymerase chain reaction. Syringomycin, producing strains amplified two DNA fragments of 752 and 446 bp representing syrB and syrD genes, respectively. Primer specificity was shown for Pss using various genera. Based on the results of this study, it is suggested that Pss strains from different hosts and geographical regions show diversity in phenotypic and molecular characters. It is thought that phenotypic variation is due to adaptation to specific hosts and niches for survival and pathogenicity.

Cucumber mosaic virus (CMV; family Bromoviridae, genus Cucumovirus) is the most cosmopolitan plant virus occurring worldwide. In the present study, leaf samples showing deformations, mosaics, and chlorotic spots symptoms were collected from naturally infected Basella alba, Telfairia occidentalis and Talinum fruticosum in a home yard garden in Ibadan, Nigeria. Total nucleic acid was extracted from leaves and used as template for cDNA synthesis. RT-PCR was carried out using CMV-specific primers targeting RNA-1 segment. Samples were also tested by RT-PCR using Potyvirus and Begomovirus genusspecific primers. DNA fragments with the expected sizes of ~500 bp were amplified by using CMV-specific primers; however, the expected amplicons were not produced using specific primers used for the detection of potyviruses and begomoviruses. The nucleotide and deduced amino acid sequences obtained for the isolates studied contained 503–511 nt and 144 aa, respectively. The isolates shared 81.9–85.3% nucleotide and 74.3–77.8% amino acid sequence identities with each other. The results of BLASTN analyses showed the highest identities of the isolates (80–93%) with CMV strains from Japan, USA and South Korea. Alignment of deduced partial protein revealed multiple amino acid substitutions within the three isolates and high identities with CMV subgroup I. Phylogenetic analyses putatively categorized the isolates in close association with subgroup IB isolates. The three isolates clustered together into a separate subclade, indicating possible new CMV strains. The results provide the first molecular evidence for CMV infections of T. fruticosum and B. alba in Nigeria and seem to show the possible presence of new strain(s). These findings also add three new hosts to the list of natural host range of the virus in Nigeria.

The present study was to reflect the use of some bacteria in the treatment and removal of pollutants in three selected wastewater sites, including a vegetable oil plant (viz. Al-Etihad Food Industries), the main wastewater treatment station in the city of Hila, and Al-Hila River water from October 2019 to January 2020. The bacterial isolates identified in these three sites were Klebsiella pneumoniae, Escherichia coli, Enterobacteria cloacae, Pseudomonas aeruginosa, Thalasobacillus devorans, Acinetobacter baumannii, and Bacillus subtilis. The molecular study of the bacterial isolates involved the detection of bacterial genera using the polymerase chain reaction (PCR). The results showed that water had a variable nature, depending on the substances in it. It recorded varying chemical and physical property values, ranging between 6.36 and 7.82 for pH and from 2500 to 7100 mg∙dm–3 for total alkalinity. Additional values were 713–2051 μS∙cm–1 for electrical conductivity (EC), 5.90–9.80 mg∙dm–3 for chemical oxygen demand (COD), and 480–960 mg∙dm–3 for total hardness. The given values were also 0.20–0.65 μg∙dm–3, 0.03-0.23 μg∙dm–3, and 0–107 mg∙dm–3 for nitrite (NO2), phosphate (PO4) oils, respectively.

In this study, a SYBR Green-based real-time quantitative polymerase chain reaction (qPCR) assay was developed for rapid detection of porcine parvovirus (PPV) 6. Primer pairs targeting the conserved regions of PPV6 Capsid gene were designed. Sensitivity analyses revealed the lowest detection limit of the SYBR Green-based real-time PCR assay to be 47.8 copies/μL, which indicated it was 1000 times higher than that found in the conventional PCR investigations. This assay was specific and showed no cross-species amplification with other six porcine viruses. The assay demonstrated high repeatability and reproducibility; the intra- and inter-assay coefficients of variation were 0.79% and 0.42%, respectively. The positive detection rates of 180 clinical samples with SYBR Green-based real-time PCR and conventional PCR were 12.22% (22/180) and 4.44% (8/180), respectively. Our method is sensitive, specific, and reproducible. The use of SYBR Green-based real-time PCR may be suitable for the clinical detection and epidemiological investigation of PPV6.

Onion yellow dwarf virus (OYDV), an aphid-borne potyvirus is one of the major viral pathogens of garlic causing significant yield losses worldwide. It is found almost everywhere in the world where Allium species is grown. The aim of this study was to test the presence of OYDV infection in garlic from Ethiopia. The presence of the virus was tested by Reverse transcription polymerase chain reaction (RT-PCR). The direct sequencing of the PCR product produced a sequence of 296 bp. Sequence analysis showed 89.27% sequence homology with an isolate from Australia (HQ258894) and 89.29% with an isolate from Spain (JX429964). A phylogenetic tree constructed with MEGA 7.0 revealed high levels of homology with various isolates of OYDV from all over the world and thus further confirmed the identity of the virus.

Strawberry leaves showing leaf blight symptoms were collected from six different farms in Ismailia and Beheira Governorates in Egypt during the 2020–2021 growing season. Eight bacterial isolates, i.e., Pa₁, Pa₂, Pa₃, Pa₄ (Ismailia farms) and Pa₅, Pa₆, Pa₇ and Pa₈ (Beheira farms) were isolated. A pathogenicity test of bacterial isolates was carried out using detached strawberry leaf technique. All bacterial isolates produced leaf blight disease symptoms. Isolates Pa₂ and Pa₆ showed the highest pathogenic characteristics with clear symptoms on detached strawberry leaves. The phenotypic, biochemical and physiological characters of the highest pathogenic isolates were confirmed by PCR analysis using 16S rRNA gene. The two bacterial isolates were identified as Pantoea ananatis with similarity of 97.05% with accession number MH_127816.1 (isolate Pa₂, Ismailia), while the isolate ( Pa₆, Beheira) with similarity of 97.03% with accession number NR_026045.1. The 16S rDNA sequences were deposited in the GenBank nucleotide databases under accession numbers OM258167 and OM279507, respectively. According to the pathogenicity test, morphological and physiological characteristics as well as molecular data (16S rRNA sequencing analysis), this finding is the first report of P. ananatis as a causal agent of strawberry leaf blight disease in Egypt.

In performed experiments, insoluble polyvinylpolypyrrolidone, PVPP as an additive to the extraction buffer was used for isolation of total nucleic acids from hop plants and grapevine in order to obtain templates useful for detection ofHLVd and HSVd by means ofRT-PCR. Addition of2% of PVPP to the original GTC buffer (Chomczynski and Sacchi, 1987) appeared to be the most favorable. Due to PVPP addition, the protocol of extraction of nucleic acids was simplified by shortening of isolation time and reduction of expenses. However, application of the simplified method for obtaining of templates that guaranteed full repeatability of test results was limited to the spring and early summer season.

In the spring of 2019, many plants, mainly winter wheat, were observed to have dwarfism and leaf yellowing symptoms. These plants from several regions of Poland were collected and sent to the Plant Disease Clinic of the Institute of Plant Protection – National Research Institute in Poznań to test for the presence of viral diseases. Double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) results showed numerous cases of Wheat dwarf virus (WDV) and a few cases of plant infections caused by Barley yellow dwarf viruses (BYDVs). WDV was detected in 163 out of 236 tested winter wheat plants (69.1%), in 10 out of 27 tested winter barley plants (37%) and in 6 out of 7 triticale plants (85.7%) while BYDVs were found, respectively, in 9.7% (23 out of 236) and in 18.5% (5 out of 27) of tested winter forms of wheat and barley plants. Infected plants came mainly from the regions of Lower Silesia and Greater Poland. Furthermore, individual cases of infections were also confirmed in the following districts: Lubusz, Opole, Silesia, Kuyavia-Pomerania and Warmia-Masuria. Results of Duplex-immunocapture-polymerase chain reaction (Duplex-IC-PCR) indicated the dominance of WDV-W form in wheat and WDV-B form in barley plants. Moreover, results of reverse transcription – polymerase chain reaction (RT-PCR) connected with restriction fragment length polymorphism (RFLP) analysis, performed for 17 BYDVs samples, revealed 8 BYDV-PAS, 4 BYDV-MAV and 2 BYDVPAV as well as the presence of two mixed infections of BYDV-MAV/-PAS and one case of BYDV-MAV/-PAV. Next, RT-PCR reactions confirmed single BYDV-GAV infection and the common presence of BYDV-SGV. To the best of our knowledge, in 2020 the viruses were not a big threat to cereal crops in Poland.