Broad Host Range Research Articles

Biocontrol of Salmonella Typhimurium in milk, lettuce, raw pork meat and ready-to-eat steamed-chicken breast by using a novel bacteriophage with broad host range

Salmonella spp., one of the most frequently reported bacteria, causes foodborne illness and economic losses. Due to the threat of increasing antibiotic resistant foodborne pathogens, application of bacteriophages as novel antibacterial agents in food matrices has become an emerging strategy. In this study, a novel Salmonella phage PS3-1 with high lytic activity against Salmonella Typhimurium was identified from previously isolated phages. PS3-1 belonged to the class Caudoviricetes with a broad host range, and had relatively short latent period (15 min), large burst size (92 PFU/cell), high pH stability (pH 3.0–11.0) and thermal tolerance (4–60 °C). Genome sequencing analysis showed that PS3-1 genome consisted of 107,110 bp DNA, without antibiotic resistance and virulence related genes. The results of growth curve and time-kill assay showed that PS3-1 not only inhibited the growth of S. Typhimurium, but also effectively decreased the viable cell counts (0.30–4.72 log) after 24-h incubation at 7, 25 and 37 °C (P < 0.05). Moreover, >1.28 log of established biofilm cells were effectively removed after 24-h treatment with PS3-1. Besides, PS3-1 significantly reduced the viability of S. Typhimurium in milk, lettuce, raw pork meat and ready-to-eat steamed-chicken breast at different temperatures (P < 0.05). These results demonstrated that PS3-1 may be an excellent antibacterial agent for controlling S. Typhimurium in food industry.

Subtyping of Nonhuman Primate-Adapted Cryptosporidium hominis in Macaca Fascicularis and Macaca mulatta in Yunnan Province, Southwestern China.

Background: Cryptosporidium spp. are a type of protozoan parasite responsible for causing diarrheal illness worldwide. They infect a broad range of vertebrate hosts, including both non-human primates (NHPs) and humans. In fact, zoonotic transmission of cryptosporidiosis from NHPs to humans is frequently facilitated by direct contact between the two groups. However, there is a need to enhance the information available on the subtyping of Cryptosporidium spp. in NHPs in the Yunnan province of China. Materials and Methods: Thus, the study investigated the molecular prevalence and species of Cryptosporidium spp. from 392 stool samples of Macaca fascicularis (n = 335) and Macaca mulatta (n = 57) by using nested PCR targeting the large subunit of nuclear ribosomal RNA (LSU) gene. Of the 392 samples, 42 (10.71%) were tested Cryptosporidium-positive. Results: All the samples were identified as Cryptosporidium hominis. Further, the statistical analysis revealed that age is a risk factor for the infection of C. hominis. The probability of detecting C. hominis was found to be higher (odds ratio = 6.23, 95% confidence interval 1.73-22.38) in NHPs aged between 2 and 3 years, as compared with those younger than 2 years. Sequence analysis of the 60 kDa glycoprotein (gp60) identified six (IbA9 n = 4, IiA17 n = 5, InA23 n = 1, InA24 n = 2, InA25 n = 3, and InA26 n = 18) C. hominis subtypes with "TCA" repeats. Among these subtypes, it has been previously reported that the Ib family subtypes are also capable of infecting humans. Conclusion: The findings of this study highlight the genetic diversity of C. hominis infection among M. fascicularis and M. mulatta in Yunnan province. Further, the results confirm that both these NHPs are susceptible to C. hominis infection, posing a potential threat to humans.

Characterizing conjugative plasmids from an antibiotic-resistant dataset for use as broad-host delivery vectors.

Human microbiome engineering is increasingly proposed as a way to modulate health outcomes. However, one of the current limitations to engineering microbial communities in situ is delivery of a genetic payload for introducing or modifying genes. Indeed, there is a need to identify novel broad-host delivery vectors for microbiome engineering. Therefore, in this study, we characterized conjugative plasmids from a publicly available dataset of antibiotic-resistant isolate genomes in order to identify potential broad-host vectors for further applications. From the 199 closed genomes available in the CDC & FDA AR Isolate Bank, we identified 439 plasmids, of which 126 were predicted to be mobilizable and 206 conjugative. Various characteristics of the conjugative plasmids, such as size, replication origin, conjugation machinery, host defense mechanisms, and plasmid stability proteins, were analyzed to determine these plasmids' potential host-range. Following this analysis, we clustered plasmid sequences and chose 22 unique, broad-host range plasmids that would be suitable for use as delivery vectors. This novel set of plasmids will provide a valuable resource for engineering microbial communities.

Rodents as Sentinels for Toxoplasma gondii in Rural Ecosystems in Slovakia-Seroprevalence Study.

Toxoplasma gondii is a ubiquitous intracellular parasite with felids as definitive hosts and a broad range of intermediate hosts. Rodents are considered suitable sentinels for prevalence studies of many infections, including toxoplasmosis. This study aimed to estimate the seroprevalence of T. gondii in rodents from different localities of Slovakia and investigate the correlation between the seropositivity and the species, age, sex, and sexual activity of animals. Altogether, 1009 wild rodents belonging to 9 species were trapped in 2015 and 2019, and antibodies to T. gondii were detected in 6.7% of the animals. Seropositivity was detected in seven species, ranging from 0.0% in Micromys minutus and Apodemus sylvaticus to 7.7% in A. flavicollis. The females reached significantly higher seropositivity (9.7%) than the males (3.8%), and the adults were positive significantly more often (9.2%) than the subadults (4.9%). The seropositivity differed also among localities, with significantly higher positivity detected in suburban and touristic areas (12.2%) than in localities with a lower level of human activities (5.5%). This study showed that the occurrence of T. gondii varies significantly in rodent species and habitats with various environmental conditions and different levels of anthropic use. Several biological and ecological factors, e.g., soil contamination, soil conditions, the susceptibility of rodent species etc., may influence this variability.

Field surveys indicate taxonomically diverse Pectobacterium species inducing soft rot of vegetables and annual crops in Iran

AbstractSoft rot‐inducing bacterial pathogens are considered among the main biotic constraints on vegetables and annual crops. Most of the bacterial soft rot pathogens are members of Pectobacterium spp. and Dickeya, with the former genus encompassing a continuously increasing number of species varying in geographic distribution and host of isolation. In Iran, Pectobacterium species have rarely been investigated using high‐throughput nucleotide sequence‐based techniques, leaving the genetic diversity of these pathogens mostly undetermined. During 2021, vegetables and annual crops with symptoms of soft rot and maceration were collected from Fars, Hamedan, Isfahan, Khuzestan and Kohgiluyeh‐Boyer‐Ahmad provinces of Iran. Forty‐four pectinolytic bacterial strains were isolated from symptomatic tissues of bell pepper, cabbage, carrot, lettuce, potato and zucchini. The bacterial strains were subjected to pathogenicity and host range assays, specific PCR tests and phylogenetic analysis of three housekeeping genes (dnaX, gapA and leuS). All strains were pathogenic on their host of isolation. Among the 44 pectinolytic strains, 26 strains were identified as members of Pectobacterium based on PCR using the primer pair Y1/Y2. Multilocus sequence analysis confirmed the latter bacterial strains belonging to the genus Pectobacterium and revealed that the strains scattered into four species: P. brasiliense (five strains), P. carotovorum (eight strains), P. polaris (five strains) and P. versatile (eight strains). P. polaris and P. versatile have not previously been reported in the country. Host range assays showed that P. brasiliense and P. carotovorum have a broader host range than the other two species.

Systematic Part Transfer by Extending a Modular Toolkit to Diverse Bacteria.

It is impractical to develop a new parts collection for every potential host organism. It is well-established that gene expression parts, like genes, are qualitatively transferable, but there is little quantitative information defining transferability. Here, we systematically quantified the behavior of a parts set across multiple hosts. To do this, we developed a broad host range (BHR) plasmid system compatible with the large, modular CIDAR parts collection for E.coli, which we named openCIDAR. This enabled testing of a library of DNA constructs across the Pseudomonadota─Escherichia coli, Pseudomonas putida, Cupriavidus necator, and Komagataeibacter nataicola. Part performance was evaluated with a standardized characterization procedure that quantified expression in terms of molecules of equivalent fluorescein (MEFL), an objective unit of measure. The results showed that the CIDAR parts enable graded gene expression across all organisms─meaning that the same parts can be used to program E.coli, P.putida, C.necator, and K.nataicola. Most parts had a similar expression trend across hosts, although each organism had a different average gene expression level. The variability is enough that to achieve the same MEFL in a different organism, a lookup table is required to translate a design from one host to another. To identify truly divergent parts, we applied linear regression to a combinatorial set of promoters and ribosome binding sites, finding that the promoter J23100 behaves very differently in K.nataicola than in the other hosts. Thus, it is now possible to evaluate any CIDAR compatible part in three other hosts of interest, and the diversity of these hosts implies that the collection will also be compatible with many other Proteobacteria (Pseudomonadota). Furthermore, this work defines an approach to generalize modular synthetic biology parts sets beyond a single host, implying that only a few parts sets may be needed to span the tree of life. This will accelerate current efforts to engineer diverse species for environmental, biotechnological, and health applications.

Fungal effectors versus defense-related genes of B. juncea and the status of resistant transgenics against fungal pathogens.

Oilseed brassica has become instrumental in securing global food and nutritional security. B. juncea, colloquially known as Indian mustard, is cultivated across tropics and subtropics including Indian subcontinent. The production of Indian mustard is severely hampered by fungal pathogens which necessitates human interventions. Chemicals are often resorted to as they are quick and effective, but due to their economic and ecological unsustainability, there is a need to explore their alternatives. The B. juncea-fungal pathosystem is quite diverse as it covers broad-host range necrotrophs (Sclerotinia sclerotiorum), narrow-host range necrotrophs (Alternaria brassicae and A. brassicicola) and biotrophic oomycetes (Albugo candida and Hyaloperonospora brassica). Plants ward off fungal pathogens through two-step resistance mechanism; PTI which involves recognition of elicitors and ETI where the resistance gene (R gene) interacts with the fungal effectors. The hormonal signalling is also found to play a vital role in defense as the JA/ET pathway is initiated at the time of necrotroph infection and SA pathway is induced when the biotrophs attack plants. The review discuss the prevalence of fungal pathogens of Indian mustard and the studies conducted on effectoromics. It covers both pathogenicity conferring genes and host-specific toxins (HSTs) that can be used for a variety of purposes such as identifying cognate R genes, understanding pathogenicity and virulence mechanisms, and establishing the phylogeny of fungal pathogens. It further encompasses the studies on identifying resistant sources and characterisation of R genes/quantitative trait loci and defense-related genes identified in Brassicaceae and unrelated species which, upon introgression or overexpression, confer resistance. Finally, the studies conducted on developing resistant transgenics in Brassicaceae have been covered in which chitinase and glucanase genes are mostly used. The knowledge gained from this review can further be used for imparting resistance against major fungal pathogens.

Global transmission of broad-host-range plasmids derived from the human gut microbiome.

Broad-host-range (BHR) plasmids in human gut bacteria are of considerable interest for their ability to mediate horizontal gene transfer (HGT) across large phylogenetic distance. However, the human gut plasmids, especially the BHR plasmids, remain largely unknown. Here, we identified the plasmids in the draft genomes of gut bacterial isolates from Chinese and American donors, resulting in 5372 plasmid-like clusters (PLCs), of which, 820 PLCs (comPLCs) were estimated with>60% completeness genomes and only 155 (18.9%) were classified to known replicon types (n=37). We observed that 175 comPLCs had a broad host range across distinct bacterial genera, of which, 71 were detected in at least two human populations of Chinese, American, Spanish, and Danish, and 13 were highly prevalent (>10%) in at least one human population. Haplotype analyses of two widespread PLCs demonstrated their spreading and evolutionary trajectory, suggesting frequent and recent exchanges of the BHR plasmids in environments. In conclusion, we obtained a large collection of plasmid sequences in human gut bacteria and demonstrated that a subset of the BHR plasmids can be transmitted globally, thus facilitating extensive HGT (e.g. antibiotic resistance genes) events. This study highlights the potential implications of the plasmids for global human health.

Flagella-mediated cytosolic motility of Salmonella enterica Paratyphi A aids in evasion of xenophagy but does not impact egress from host cells.

Salmonella enterica is a common foodborne, facultative intracellular enteropathogen. Typhoidal serovars like Paratyphi A (SPA) are human restricted and cause severe systemic diseases, while many serovars like Typhimurium (STM) have a broad host range, and usually lead to self-limiting gastroenteritis. There are key differences between typhoidal and non-typhoidal Salmonella in pathogenesis, but underlying mechanisms remain largely unknown. Transcriptomes and phenotypes in epithelial cells revealed induction of motility, flagella and chemotaxis genes for SPA but not STM. SPA exhibited cytosolic motility mediated by flagella. In this study, we applied single-cell microscopy to analyze triggers and cellular consequences of cytosolic motility. Live-cell imaging (LCI) revealed that SPA invades host cells in a highly cooperative manner. Extensive membrane ruffling at invasion sites led to increased membrane damage in nascent Salmonella-containing vacuole, and subsequent cytosolic release. After release into the cytosol, motile bacteria showed the same velocity as under culture conditions in media. Reduced capture of SPA by autophagosomal membranes was observed by LCI and electron microscopy. Prior work showed that SPA does not use flagella-mediated motility for cell exit via the intercellular spread. However, cytosolic motile SPA was invasion-primed if released from host cells. Our results reveal flagella-mediated cytosolic motility as a possible xenophagy evasion mechanism that could drive disease progression and contributes to the dissemination of systemic infection.

The son-killer microbe Arsenophonus nasoniae is a widespread associate of the parasitic wasp Nasonia vitripennis in Europe

Heritable microbes that exhibit reproductive parasitism are common in insects. One class of these are the male-killing bacteria, which are found in a broad range of insect hosts. Commonly, our knowledge of the incidence of these microbes is based on one or a few sampling sites, and the degree and causes of spatial variation are unclear. In this paper, we examine the incidence of the son-killer microbe Arsenophonus nasoniae across European populations of its wasp host, Nasonia vitripennis. In preliminary work, we noticed two female N. vitripennis producing highly female biased sex ratios in a field study from the Netherlands and Germany. When tested, the brood from Germany was revealed to be infected with A. nasoniae. We then completed a broad survey in 2012, in which fly pupal hosts of N. vitripennis were collected from vacated birds’ nests from four European populations, N. vitripennis wasps allowed to emerge and then tested for A. nasoniae presence through PCR assay. We then developed a new screening methodology based on direct PCR assays of fly pupae and applied this to ethanol-preserved material collected from great tit (Parus major) nests in Portugal. These data show A. nasoniae is found widely in European N. vitripennis, being present in Germany, the UK, Finland, Switzerland and Portugal. Samples varied in the frequency with which they carry A. nasoniae, from being rare to being present in 50% of the pupae parasitised by N. vitripennis. Direct screening of ethanol-preserved fly pupae was an effective method for revealing both wasp and A. nasoniae infection, and will facilitate sample transport across national boundaries. Future research should examine the causes of variation in frequency, in particular testing the hypothesis that N. vitripennis superparasitism rates drive the variation in A. nasoniae frequency through providing opportunities for infectious transmission.

Identification of an immunodominant neutralizing epitope of porcine Deltacoronavirus spike protein

Porcine deltacoronavirus (PDCoV) is a novel swine enteropathogenic coronavirus that, because of its broad host range, poses a potential threat to public health. Here, to identify the neutralizing B-cell epitopes within the S1-CTD protein, we generated three anti-PDCoV monoclonal antibodies (mAbs). Of these, the antibody designated 4E-3 effectively neutralized PDCoV with an IC50 of 3.155 μg/mL. mAb 4E-3 and one other, mAb 2A-12, recognized different linear B-cell epitopes. The minimal fragment recognized by mAb 4E-3 was mapped to 280FYSDPKSAV288 and designated S280–288, the minimal fragment recognized by mAb 2A-12 was mapped to 506TENNRFTT513, and designated S506–513. Subsequently, alanine (A)-scanning mutagenesis indicated that Asp283, Lys285, and Val288 were the critical residues recognized by mAb 4E-3. The S280–288 epitope induces PDCoV specific neutralizing antibodies in mice, demonstrating that it is a neutralizing epitope. Of note, the S280–288 coupled to Keyhole Limpet Hemocyanin (KLH) produces PDCoV neutralizing antibodies in vitro and in vivo, in challenged piglets it potentiates interferon-γ responses and provides partial protection against disease. This is the first report about the PDCoV S protein neutralizing epitope, which will contribute to research of PDCoV-related pathogenic mechanism, vaccine design and antiviral drug development.

Evaluation of the host specificity of Eimeria uekii and Eimeria raichoi for Japanese rock ptarmigans by oocyst transfer to taxonomically related birds.

Eimeria spp. are protozoan parasites that are commonly found in a broad range of vertebrate hosts. These parasites generally exhibit strict host specificity, but some Eimeria spp. can infect groups of closely related species such as species within a genus or family. Compared with Eimeria spp. that infect livestock, limited information is available about such infections in wild animals including data on host specificity, virulence, and prevalence. The Japanese rock ptarmigan, Lagopus muta japonica, is an endangered bird belonging to the family Phasianidae, order Galliformes, and inhabits only alpine areas of Japan. In conservation efforts for these birds, two Eimeria spp., E. uekii and E. raichoi, were frequently detected. Here, we examined cross-transmission of the parasites to other bird species to characterize their infectivity as well as the development of experimental bird models to contribute to conservation programs by the oocyst transfer. Consequently, among the examined eight bird species (chickens, Japanese pheasants, turkeys, chukar partridges, quails, helmeted guineafowls and ducks), only turkeys (family Phasianidae, order Galliformes) could be infected with E. raichoi. However, the number of oocysts per feces was relatively low, and few parasites in the intestinal mucosa could be found by histopathological analyses. These results might indicate that E. uekii and E. raichoi are highly adapted to Japanese rock ptarmigans that inhabit the alpine zone although further studies are anticipated.

Production status and research advancement on root rot disease of faba bean (Vicia faba L.) in China.

China is the largest producer of faba bean with a total harvested area of 8.11×105 ha and a total production of 1.69 ×106 tons (dry beans) in 2020, accounting for 30% of the world production. Faba bean is grown in China for both fresh pods and dry seed. East China cultivates large seed cultivars for food processing and fresh vegetables, while northwestern and southwestern China grow cultivars for dry seeds, with an increased production of fresh green pods. Most of the faba bean is consumed domestically, with limited exports. The absence of unified quality control measures and simple traditional cultivation practices contributes to the lower competitiveness of the faba bean industry in international markets. Recently, new cultivation methods have emerged with improved weed control, as well as better water and drainage management, resulting in higher quality and income for producers. Root rot disease in faba bean is caused by multiple pathogens, including Fusarium spp., Rhizoctonia spp., and Pythium spp. Fusarium spp. is the most prevalent species causing root rot in faba bean crops and is responsible for severe yield loss, with different species causing the disease in different regions in China. The yield loss ranges from 5% to 30%, up to 100% in severely infected fields. The management of faba bean root rot disease in China involves a combination of physical, chemical, and bio-control methods, including intercropping with non-host crops, applying rational nitrogen, and treating seeds with chemical or bio-seed treatments. However, the effectiveness of these methods is limited due to the high cost, the broad host range of the pathogens, and potential negative impacts on the environment and non-targeted soil organisms. Intercropping is the most widely utilized and economically friendly control method to date. This review provides an overview of the current status of faba bean production in China, the challenges faced by the industry due to root rot disease, and the progress in identifying and managing this disease. This information is critical for developing integrated management strategies to effectively control root rot in faba bean cultivation and facilitating the high-quality development of the faba bean industry.

Continuous surveillance and viral discovery in animals and humans are a core component of a one-health approach to address recent viral reverse zoonoses.

Contemporary human and animal viruses have a broad or narrow host range-those with a broad host range are potentially transmitted from animals to humans (ie, zoonosis) or humans to animals (ie, reverse zoonosis). This Currents in One Health article reviews the recent reverse zoonoses involving Coronaviridae, Poxviridae, arboviruses, and, for nonhuman primate species, the human respiratory viruses. The prevention and control of reverse zoonoses are also reviewed. Coronaviruses continue to emerge as new zoonotic agents, including a canine coronavirus, CCoV-HuPn-2018, circulating in people at low levels, and a pangolin coronavirus, MjHKU4r-CoV-1, circulating in Malayan pangolins. Moreover, the risk for SARS-CoV-2 variants to mutate in animal reservoirs and reinfect humans is ongoing. In the case of mpox, the risk of reverse zoonosis is low and there are vaccines for use in humans at risk. The situation with arboviruses is as varied as the number of human arboviruses, and only yellow fever virus and dengue virus have licensed vaccines in the Americas. As for reverse zoonoses in endangered species, solutions require changing human behavior and policies at all levels impacting wildlife. Overall, continuous surveillance and viral discovery in humans and animals remain core components of a one-health approach to reduce and, where possible, eliminate zoonotic and reverse zoonotic diseases. Viral zoonosis and viral reverse zoonosis focusing on recent influenza A virus disease events in humans and other species are the subjects of the companion Currents in One Health by Kibenge, AJVR, June 2023.

Endemism and Reemergence Potential of the Ipomovirus Sweet Potato Mild Mottle Virus (FamilyPotyviridae) in Eastern Africa: Half a Century of Mystery

Viruses have the ability to frequently colonize new hosts and ecological niches because of their inherently high genetic and evolutionary plasticity. However, a virus may emerge and remain of no or less economic importance until changes in viral or environmental factors dictate its epidemiological status. An example is sweet potato mild mottle virus (SPMMV), which was first reported in the 1970s on sweetpotato in eastern Africa. SPMMV has remained endemic in the region and poorly understood, yet accounting for 60 to 95% of losses, especially in mixed infections. Unlike other sweetpotato viruses which have global incidences, SPMMV has never been confirmed outside eastern Africa. This implicates the region as its center of origin but does not fully account for SPMMV's exclusive geographic delimitation to eastern Africa. Despite its importance, several mysteries and research gaps surround SPMMV, which decelerate efforts for effective virus disease management in sweetpotato. The aim of this review is to articulate research gaps, propose pivotal scientific directions, and stimulate knowledge generation for better management of virus diseases in sweetpotato. Vector-mediated transmission of SPMMV remains enigmatic. Here, we postulate testable hypotheses to explain SPMMV transmission. Comparisons between SPMMV and cassava brown streak ipomoviruses demonstrate epidemiological “hallmarks” for monitoring SPMMV. Evolutionary forces on SPMMV coupled with the virus' broad host range imply a “silent build up” of more fit variants in a changing climate, and this could explode into a worse disease conundrum. These information gaps need urgent filling to ease future management of virus disease emergences in sweetpotato.[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

The in planta gene expression of Austropuccinia psidii in resistant and susceptible Eucalyptus grandis.

Austropuccinia psidii, commonly known as myrtle rust, is an obligate, biotrophic rust pathogen that causes rust disease on a broad host range of Myrtaceae species. Eucalyptus grandis, a widely cultivated hardwood Myrtaceae species, is susceptible to A. psidii infection, with this pathogen threatening both their natural range and various forest plantations across the world. This study aimed to investigate the A. psidii transcriptomic responses in resistant and susceptible E. grandis at four time points. RNA-seq reads were mapped to the A. psidii reference genome to quantify expressed genes at 12-hours post inoculation (hpi), 1-, 2- and 5-days post inoculation (dpi). A total of eight hundred and ninety expressed genes were found, of which forty-three were candidate effector proteins. These included a rust transferred protein (RTP1) gene, expressed in susceptible hosts at 5-dpi and a hydrolase protein gene expressed in both resistant and susceptible hosts over time. Functional categorisation of expressed genes revealed processes enriched in susceptible hosts, including malate metabolic and malate dehydrogenase activity, implicating oxalic acid in disease susceptibility. These results highlight putative virulence or pathogenicity mechanisms employed by A. psidii to cause disease and provides the first insight into the molecular responses of A. psidii in E. grandis over time.

The Type IV Secretion System (T4SS) Mediates Symbiosis between Bradyrhizobium sp. SUTN9-2 and Legumes.

There has been little study of the type IV secretion system (T4SS) of bradyrhizobia and its role in legume symbiosis. Therefore, broad host range Bradyrhizobium sp. SUTN9-2 was selected for study. The chromosome of Bradyrhizobium sp. SUTN9-2 contains two copies of the T4SS gene, homologous with the tra/trb operons. A phylogenetic tree of the T4SS gene traG was constructed, which exemplified its horizontal transfer among Bradyrhizobium and Mesorhizobium genera. They also showed similar gene arrangements for the tra/trb operons. However, the virD2 gene was not observed in Mesorhizobium, except M. oppotunistum WSM2075. Interestingly, the orientation of copG, traG, and virD2 cluster was unique to the Bradyrhizobium genus. The phylogenetic tree of copG, traG, and virD2 demonstrated that copies 1 and 2 of these genes were grouped in different clades. In addition, the derived mutant and complementation strains of T4SS were investigated in representative legumes Genistoids, Dalbergioids, and Millettiods. When T4SS copy 1 (T4SS1) was deleted, the nodule number and nitrogenase activity decreased. This supports a positive effect of T4SS1 on symbiosis. In addition, delayed nodulation was observed 7 dpi, which was restored by the complementation of T4SS1. Therefore, T4SS plays an important role in the symbiotic interaction between Bradyrhizobium sp. SUTN9-2 and its leguminous hosts. IMPORTANCE SUTN9-2 is a broad host range strain capable of symbiosis with several legumes. Two copies of T4SS clusters belonging to the tra/trb operon are observed on chromosomes with different gene arrangements. We use phylogenetic tree and gene annotation analysis to predict the evolution of the tra/trb operon of rhizobia. Our finding suggests that the gene encoding the T4SS gene among Bradyrhizobium and Mesorhizobium may have coevolution. In addition, Bradyrhizobium has a uniquely arranged copG, traG, and virD2 gene cluster. The results of T4SS1 gene deletion and complementation revealed its positive effect on nodulation. Therefore, T4SS seems to be another determinant for symbiosis. This is the first report on the role of T4SS in Bradyrhizobium symbiosis.

Restriction-modification systems have shaped the evolution and distribution of plasmids across bacteria.

Many novel traits such as antibiotic resistance are spread by plasmids between species. Yet plasmids have different host ranges. Restriction-modification systems (R-M systems) are by far the most abundant bacterial defense system and therefore represent one of the key barriers to plasmid spread. However, their effect on plasmid evolution and host range has been neglected. Here we analyse the avoidance of targets of the most abundant R-M systems (Type II) for complete genomes and plasmids across bacterial diversity. For the most common target length (6 bp) we show that target avoidance is strongly correlated with the taxonomic distribution of R-M systems and is greater in plasmid genes than core genes. We find stronger avoidance of R-M targets in plasmids which are smaller and have a broader host range. Our results suggest two different evolutionary strategies for plasmids: small plasmids primarily adapt to R-M systems by tuning their sequence composition, and large plasmids primarily adapt through the carriage of additional genes protecting from restriction. Our work provides systematic evidence that R-M systems are important barriers to plasmid transfer and have left their mark on plasmids over long evolutionary time.

Phytophthora capsici: Recent Progress on Fundamental Biology and Disease Management 100 Years After Its Description.

Phytophthora capsici is a destructive oomycete pathogen of vegetable, ornamental, and tropical crops. First described by L.H. Leonian in 1922 as a pathogen of pepper in New Mexico, USA, P. capsici is now widespread in temperate and tropical countries alike. Phytophthora capsici is notorious for its capability to evade disease management strategies. High genetic diversity allows P. capsici populations to overcome fungicides and host resistance, the formation of oospores results in long-term persistence in soils, zoospore differentiation in the presence of water increases epidemic potential, and a broad host range maximizes economic losses and limits the effectiveness of crop rotation. The severity of disease caused by P. capsici and management challenges have led to numerous research efforts in the past 100 years. Here, we discuss recent findings regarding the biology, genetic diversity, disease management, fungicide resistance, host resistance, genomics, and effector biology of P. capsici.

Paramicrosphaeropsis eriobotryae sp. nov., a new agent of loquat canker in Iran

AbstractLoquat (Eriobotrya japonica) is a subtropical evergreen plant, important in terms of both horticulture and green space in the urban environment. In recent years, symptoms of branch and trunk canker, dieback and decline have been observed in the main cultivation areas of this tree in Iran. To study the aetiology of loquat canker in Fars Province, branches and trunks of loquat trees with disease symptoms were sampled from 2018 to 2019. Several isolates of an unknown Paramicrosphaeropsis species (Didymellaceae, Pleosporales, Dothideomycetes) were recovered from the trunks and branches of infected loquat trees. Phylogenetic analysis of the isolates based on a multigene phylogeny of the ribosomal internal transcribed spacer (ITS), partial β‐tubulin gene (tub2) and the second‐largest subunit of RNA polymerase II (rpb2) loci revealed that the isolates belonged to a new taxon, Paramicrosphaeropsis eriobotryae sp. nov. Pathogenicity tests revealed that this species was able to cause canker, trunk flaking, dieback, decline, leaf yellowing, defoliation and growth reduction in loquat trees. A host range evaluation on detached branches of some important horticultural trees occurring adjacent to loquat tree orchards of Fars Province showed that P. eriobotryae might have a broader host range, as it was also able to infect almond and olive trees.