The global nematicides market is expected to continue growing. With an increasing demand for synthetic chemical-free organic foods, botanical nematicides are taking the lead as replacements. Consequently, in the recent years, there have been vigorous efforts towards identification of the active secondary metabolites from various plants. These include mostly glucosinolates and their hydrolysis products such as isothiocyanates; flavonoids, alkaloids, limonoids, quassinoids, saponins, and the more recently probed essential oils, among others. And despite their overwhelming potential, variabilities in quality, efficacy, potency and composition continue to persist, and commercialization of new botanical nematicides is still lagging. Herein, we have reviewed the history of botanical nematicides and regional progresses, the potency of the identified phytochemicals from the key important plant families, and deciphered some of the impediments involved in standardization of the active compounds in addition to the concerns over the safety of the purified compounds to non-target microbial communities.

Phaeosphaeria species are pathogenic on wheat, barley and a wide range of wild grasses. To analyze mating type loci of the Phaeosphaeria species and investigate mating type distribution in Iran, we sequenced mating type loci of 273 Phaeosphaeria isolates including 67 isolates obtained from symptomatic leaves and ears of wheat, barley, and wild grasses from two wheat growing region in Iran as well as 206 isolates from our collection from other regions in Iran which were isolated in our previous studies. Mating type genes phylogeny was successfully used to determine the species identity and relationships among isolates within the Phaeosphaeria spp. complex. In this study, we reported seven new host records for Phaeosphaeria species and the Phaeosphaeria avenaria f. sp. tritici 3 group was first reported from Iran in this study. Mating type distribution among Phaeosphaeria species was determined. Both mating types were present in all sampling regions from Iran. We observed skewed distribution of mating types in one region (Kohgiluyeh va Boyer-Ahmad) and equal distribution in the other region (Bushehr). However, when considering our entire dataset of 273 Iranian Phaeosphaeria isolates, the ratio of mating types was not deviated significantly from 1:1 suggesting possibilities for isolates of opposite mating type to interact and reproduce sexually, although the sexual cycle may infrequently occur in some regions especially when the climatic conditions are unfavorable for teleomorph development.

Pathogenicity of eight Bacillus strains to seedlings of four cotton cultivars was evaluated under greenhouse conditions. Each of the tested cultivars was individually treated with powdered inoculum of each bacterial strain. Untreated seeds were planted as control treatments in autoclaved soil. Effects of the tested strains on levels and activities of some biochemical components of the infected seedlings were also assayed. The biochemical components included total soluble sugars, total soluble proteins, total free amino acids, peroxidase, polyphenol oxidase, phenols, and lipid peroxidation. ANOVA showed that Bacillus strain (B) was a very highly significant source of variation in damping-off and dry weight. Cotton cultivar (V) was a nonsignificant source of variation in damping-off while it was a significant source of variation in dry weight. B × V interaction was a significant source of variation in damping-off and a nonsignificant source of variation in dry weight. Bacillus strain was the most important source of variation as it accounted for 59.36 and 64.99% of the explained (model) variation in damping-off and dry weight, respectively. The lack of significant correlation between levels and activities of the assayed biochemical components and incidence of damping-off clearly demonstrated that these biochemical components were not involved in the pathogenicity of the tested strains. Therefore, it was hypothesized that the pathogenicity of the tested strains could be due to the effect of cell wall degrading enzymes of pathogenic toxins. Based on the results of the present study, Bacillus strains should be considered in studying the etiology of cotton seedling damping-off.

Pectobacterium carotovorum subsp. carotovorum (Pcc) is a gram-negative, broad host range bacterial pathogen which causes soft rot disease in potatoes as well as other vegetables worldwide. While Pectobacterium infection relies on the production of major cell wall degrading enzymes, other virulence factors and the mechanism of genetic adaptation of this pathogen is not yet clear. In the present study, we have performed an in-depth genome-wide characterization of Pcc strain ICMP5702 isolated from potato and compared it with other pathogenic bacteria from the Pectobacterium genus to identify key virulent determinants. The draft genome of Pcc ICMP5702 contains 4,774,457 bp with a G + C content of 51.90% and 4,520 open reading frames. Genome annotation revealed prominent genes encoding key virulence factors such as plant cell wall degrading enzymes, flagella-based motility, phage proteins, cell membrane structures, and secretion systems. Whereas, a majority of determinants were conserved among the Pectobacterium strains, few notable genes encoding AvrE-family type III secretion system effectors, pectate lyase and metalloprotease in addition to the CRISPR-Cas based adaptive immune system were uniquely represented. Overall, the information generated through this study will contribute to decipher the mechanism of infection and adaptive immunity in Pcc.

Though information exists regarding the pathogenesis of the shot-hole disease (SH) in flowering cherry (FC), there has been a lack of research focusing on SH management. Therefore, here, we investigated the inhibitory activities of antagonistic bacteria against SH pathogens both in vitro and in vivo as well as their biochemical characteristics and bioactive compounds. Two biosurfactant-producing bacterial antagonists, identified as Bacillus velezensis strains JCK-1618 and JCK-1696, exhibited the best effects against the growth of both bacterial and fungal SH pathogens in vitro through their cell-free culture filtrates (CFCFs). These two strains also strongly inhibited the growth of the pathogens via the action of their antimicrobial diffusible compounds and antimicrobial volatile organic compounds (VOCs). Crude enzymes, solvent extracts, and biosurfactants of the two strains exhibited antimicrobial activities. Liquid chromatography/electrospray ionization time-of-flight mass spectrometric analysis of the partially purified active fractions revealed that the two antagonists produced three cyclic lipopeptides, including iturin A, fengycin A, and surfactin, and a polyketide, oxydifficidin. In a detached leaf assay, pre-treatment and co-treatment of FC leaves with the CFCFs led to a large reduction in the severity of the leaf spots caused by Epicoccum tobaicum and Bukholderia contaminans, respectively. In addition, the two antagonists produced indole-3-acetic acid, siderophore, and a series of hydrolytic enzymes, along with the formation of a substantial biofilm. To our knowledge, this is the first report of the antimicrobial activities of the diffusible compounds and VOCs of B. velezensis against the SH pathogens and their efficiency in the biocontrol of SH.

Ceratocystis wilt disease has caused significant mortality in duku (Lansium domesticum) since 2014 and has now spread to all districts in South Sumatra, Indonesia. Recently, 16 isolates from duku representing populations from various districts in South Sumatra were isolated. Analysis for the morphological characteristic of the isolate showed that the population has a uniform morphology. Genetic analysis based on internal transcribed spacer (ITS) and β-tubulin sequences verified that the population has being dominated by the ITS5 haplotype of Ceratocystis fimbriata and a new ITS group, the ITS7b haplotype that was localized in Musi Banyuasin. Both haplotypes were highly pathogenic to duku. Inoculation tests on various forest and agroforestry plant hosts showed that both haplotypes were highly pathogenic to Acacia mangium, moderately pathogenic to Acacia carsicarpa, Eucalyptus urophylla, and Melaleuca cajuputi, but weakly pathogenic to Dyera costulata, Hevea brasiliensis, and Alstonia scholaris. Therefore, this pathogen becomes a serious threat to Indonesia's biodiversity due to its ability to infect forest and agroforestry plants, especially the indigenous ones.

Changes in physiological and biochemical patterns in lucerne plants caused by the presence of 'Candidatus Phytoplasma australasia', which is one of the significant pathogens causing yield losses in lucerne plants, were investigated. Significant differences were evident in total chlorophyll, chlorophyll a, chlorophyll b, and protein amounts between 'Ca. Phytoplasma australasia'-positive and negative lucerne plants. Stress-related metabolites such as phenol, malondialdehyde, and proline accumulations in 'Ca. Phytoplasma australasia'-positive plants were remarkably higher than those of phytoplasma-negative plants. As a response to disease attack, phytoplasma-positive plants exhibited higher antioxidant enzymes (peroxidase and catalase) and nonenzymatic metabolite responses such as jasmonic and salicylic acids. We state that partial disease responses were revealed for the first time to breed resistant lucerne lines infected by 'Ca. Phytoplasma australasia'.

Barley yellow dwarf virus (BYDV) has been a major viral pathogen causing significant losses of cereal crops including oats worldwide. It spreads naturally through aphids, and a rapid, specific, and reliable diagnostic method is imperative for disease monitoring and management. Here, we established a rapid and reliable method for isothermal reverse transcription recombinase polymerase amplification (RT-RPA) combined with a lateral flow strips (LFS) assay for the detection of BYDV-infected oat samples based on the conserved sequences of the BYDV coat protein gene. Specific primers and a probe for RT-RPA reacted and optimally incubated at 42℃ for 10 min, and the end-labeled amplification products were visualized on LFS within 10 min. The RT-RPA-LFS assay showed no cross-reactivity with other major cereal viruses, including barley mild mosaic virus, barley yellow mosaic virus, and rice black streaked dwarf virus, indicating high specificity of the assay. The sensitivity of the RT-RPA-LFS assay was similar to that of reverse transcription polymerase chain reaction, and it was successfully validated to detect BYDV in oat samples from six different regions and in individual aphids. These results confirm the outstanding potential of the RT-RPA-LFS assay for rapid detection of BYDV.

Pseudomonas amygdali is a hemibiotrophic phytopathogen that causes disease in woody and herbaceous plants. Complete genomes of four P. amygdali pathovars were comparatively analyzed to decipher the impact of genomic diversity on host colonization. The pan-genome indicated that 3,928 core genes are conserved among pathovars, while 504-1,009 are unique to specific pathovars. The unique genome contained many mobile elements and exhibited a functional distribution different from the core genome. Genes involved in O-antigen biosynthesis and antimicrobial peptide resistance were significantly enriched for adaptation to hostile environments. While the type III secretion system was distributed in the core genome, unique genomes revealed a different organization of secretion systems as follows: type I in pv. tabaci, type II in pv. japonicus, type IV in pv. morsprunorum, and type VI in pv. lachrymans. These findings provide genetic insight into the dynamic interactions of the bacteria with plant hosts.