Genomics and evolutionary analysis of Chlorella variabilis-infecting viruses demarcate criteria for defining species of giant viruses.

Chloroviruses exhibit a close relationship with their hosts with the phenotypic aspect of their ability to form lytic plaques having primarily guided the taxonomy. However, with the isolation of viruses that are only able to complete their replication cycle in one strain of Chlorella variabilis, systematic challenges emerged. In this study, we described the genomic features of 53 new chlorovirus isolates and used them to elucidate part of the evolutionary history and taxonomy of this clade. Our analysis revealed new chloroviruses with the largest genomes to date (>400 kbp) and indicated that four genomic features are statistically different in the viruses that only infect the Syngen 2-3 strain of C. variabilis (OSy viruses). We found large regions of dissimilarity in the genomes of viruses PBCV-1 and OSy-NE5 when compared with the other genomes. These regions contained genes related to the interaction with the host cell machinery and viral capsid proteins, which provided insights into the evolution of the replicative and structural modules in these giant viruses. Phylogenetic analysis using hallmark genes of Nucleocytoviricota revealed that OSy-viruses evolved from the NC64A-viruses, possibly emerging as a result of the strict relationship with their hosts. Merging phylogenetics and nucleotide identity analyses, we propose strategies to demarcate viral species, resulting in seven new species of chloroviruses. Collectively, our results show how genomic data can be used as lines of evidence to demarcate viral species. Using the chloroviruses as a case study, we expect that similar initiatives will emerge using the basis exhibited here.IMPORTANCEChloroviruses are a group of giant viruses with long dsDNA genomes that infect different species of Chlorella-like green algae. They are host-specific, and some isolates can only replicate within a single strain of Chlorella variabilis. The genomics of these viruses is still poorly explored, and the characterization of new isolates provides important data on their genetic diversity and evolution. In this work, we describe 53 new chlorovirus genomes, including many isolated from alkaline lakes for the first time. Through comparative genomics and molecular phylogeny, we provide evidence of genomic gigantism in chloroviruses and show that a subset of viruses became highly specific for their hosts at a particular point in evolutionary history. We propose criteria to demarcate species of chloroviruses, paving the way for an update in the taxonomy of other groups of viruses. This study is a new and important piece in the complex puzzle of giant algal viruses.

Cordyceps cateniannulata: An endophyte of coffee, a parasite of coffee leaf rust and a pathogen of coffee pests.

Here, we report on a Cordyceps species entering into a multi-trophic, multi-kingdom association. Cordyceps cateniannulata, isolated from the stem of wild Coffea arabica in Ethiopia, is shown to function as an endophyte, a mycoparasite and an entomopathogen. A detailed polyphasic taxonomic study, including a multilocus phylogenetic analysis, confirmed its identity. An emended description of C. cateniannulata is provided herein. Previously, this species was known as a pathogen of various insect hosts in both the Old and New World. The endophytic status of C. cateniannulata was confirmed by re-isolating it from inoculated coffee plants. Inoculation studies have further shown that C. cateniannulata is a mycoparasite of Hemileia vastatrix, as well as an entomopathogen of major coffee pests; infecting and killing Hypothenemus hampei and Leucoptera coffeella. This is the first record of C. cateniannulata from Africa, as well as an endophyte and a mycoparasite. The implications for its use as a biocontrol agent are discussed.

Energy input, habitat heterogeneity and host specificity drive avian haemosporidian diversity at continental scales.

The correct identification of variables affecting parasite diversity and assemblage composition at different spatial scales is crucial for understanding how pathogen distribution responds to anthropogenic disturbance and climate change. Here, we used a database of avian haemosporidian parasites to test how the taxonomic and phylogenetic diversity and phylogenetic structure of the genera Plasmodium, Haemoproteus and Leucocytozoon from three zoogeographic regions are related to surrogate variables of Earth's energy input, habitat heterogeneity (climatic diversity, landscape heterogeneity, host richness and human disturbance) and ecological interactions (resource use), which was measured by a novel assemblage-level metric related to parasite niche overlap (degree of generalism). We found that different components of energy input explained variation in richness for each genus. We found that human disturbance influences the phylogenetic structure of Haemoproteus while the degree of generalism explained richness and phylogenetic structure of Plasmodium and Leucocytozoon genera. Furthermore, landscape attributes related to human disturbance (human footprint) can filter Haemoproteus assemblages by their phylogenetic relatedness. Finally, assembly processes related to resource use within parasite assemblages modify species richness and phylogenetic structure of Plasmodium and Leucocytozoon assemblages. Overall, our study highlighted the genus-specific patterns with the different components of Earth's energy budget, human disturbances and degree of generalism.

New morphological and biological contributions to adults and immature forms of Pissonotusparaguayensis (Fulgoromorpha, Delphacidae) in wetlands of Argentina.

In the search for insects as biological control agents for the water primrose, the delphacid Pissonotusparaguayensis (Delphacidae) was found on Ludwigiagrandiflorasubsp.hexapetala (Onagraceae) in a wetland of Central East Argentina. The morphology of the unknown females (brachypterous and macropterous) and immature stages are described and illustrated. Adults and nymphs were collected in wetlands of Del Plata River Basin, from Buenos Aires to the northeastern part of Argentina. A rearing methodology was developed to perform biological studies. Both winged forms and structural features of the female genitalia are described for the first time at the genus level. Eggs and immature stages are described and keyed; fifth nymphal instars may be easily recognised by the yellowish colouration, blackish on dorsal of head, thorax and abdomen with conspicuous yellowish pits, ventrally only darkened on base of frons extended to lower level of eyes and dorsal surface of antennomeres I and II, and legs with distinctive black marks at femoro-tibial joint and apex. The geographical distribution is updated, expanding its range into Argentina, making Buenos Aires the southernmost limit of the genus in America. Biological information of the species is also reported here: life cycle, fecundity, oviposition behaviour, and host plant. Field observations showed that P.paraguayensis breeds, feeds, and causes damage to L.g.subsp.hexapetala. This delphacid presents a certain degree of specificity to the Ludwigia species in the Jussiaea section in host specificity tests. More studies are required to test this species as a potential biological control agent.

Drosophila suzukii in Argentina: State of the Art and Further Perspectives.

Drosophila suzukii (Matsumura) (Diptera: Drosophilidae), commonly known as spotted-wing drosophila or SWD, is an invasive, severe, and damaging pest, which is able to inflict huge economic losses on soft thin-skinned fruits worldwide. Argentina was not excluded from the rapid invasion of this new and aggressive pest. Berries and cherries are among the most economically important fruits, showing an increasing demand from both domestic and export markets, which make necessary the application of effective and early protection measures. Although SWD is currently established almost everywhere in Argentina, the scarcity of research on and rapid regulatory actions against this pest have probably contributed to its fast spread throughout the country. In view of that, the article reviews first the current threat status of SWD in Argentina, provides summarized information on crop and non-crop host fruits, seasonal variation and population dynamics, resident natural enemy assemblages, and describes control actions implemented to date. Finally, the need to focus local control actions within an integrated national SWD management program is emphasized. The development and application of complementary eco-friendly strategies, such as Sterile Insect Technique, biological control, mass trapping, and the use of innovative lactone-derived synthetic insecticides with extremely low toxicity for SWD parasitoids, in environmentally distinguishable Argentinian regions is also highlighted.

Unlocking a Mystery: Characterizing the First Appearance of Clavibacter nebraskensis in Mexican Cornfields.

The Goss's wilt and leaf blight is a disease of maize (Zea mays) caused by Clavibacter nebraskensis, which was widespread in the last several years throughout the Midwest in the United States, south in Texas, and north to Canada. The bacterium is included within the high-risk list of quarantine pathogens by many plant protection organizations and countries including Mexico. Severe blight symptoms on maize plants were found in different provinces from Coahuila and Tlaxcala, Mexico, in 2012 and 2021, respectively. Twenty bacterial isolates with morphology similar to C. nebraskensis were obtained from the diseased maize leaves. The isolates were confirmed by phenotypic tests and 16S rRNA and gyrB sequencing. Two strains were tested for pathogenicity tests on seven hybrid sweet corn cultivars available in Mexico, and the most sensitive cultivar was tested for all the strains to fulfill Koch's postulates. The phylogenetic reconstruction based on two single loci reveals a remarkable clustering of Mexican strains to American strains reported approximately 50 years ago. The presence of this pathogen represents a risk and a significant challenge for plant protection strategies in Mexico and maize diversity.

Pectobacterium carotovorum Subsp. brasiliense Causing Soft Rot in Eggplant in Xinjiang, China.

An outbreak of stem rot in eggplants was observed in Heshuo County, Xinjiang, during winter 2021-2022 in about 12-35% of the eggplants in the region (about 40 hm2). The infected tissues yielded a total of four bacterial strains, which were subsequently subjected to physiological and biochemical assays as well as molecular identification. Based on these analyses, the pathogen was identified as Pectobacterium carotovorum subsp. brasiliense. The pathogenicity was confirmed through the fulfillment of Koch's postulates. The host range test confirmed the broad spectrum of species susceptible to infection by the strains. This study represents the first case of infection caused by P. carotovorum subsp. brasiliense resulting in stem rot in eggplant.

First Record of the Elusive Ant Parasitoid Horismenus floridensis (Hymenoptera: Eulophidae) in Mexico and New Association with an Ant Host.

Most eulophid wasps are primary parasitoids, mainly of endophytic insect larvae (Diptera, Coleoptera, Lepidoptera, Hymenoptera, Hemiptera, and Thysanoptera), but can also attack spider eggs, gall-forming mites, or nematodes. A few species are known to parasitize ants. Here we report on the occurrence of Horismenus floridensis (Schauff and Boucek) attacking Camponotus atriceps (Smith) in southern Mexico (Campeche), expanding the distribution for this eulophid species and the range of its potential hosts. We also provide an updated list of the Horismenus Walker species found in Mexico, which currently includes 21 identified species. This is the second host ant ever recorded for H. floridensis and the first reliable record of C. atriceps as a host for this eulophid wasp. The first host ant reported from Florida 35 years ago was the closely related valid species, C. floridanus (Buckley), erroneously synonymized at that time with C. atriceps (formerly, C. abdominalis (Fabricius)).

Host-parasite Interactions between a Copepod (Pharodes tortugensis) and Small Reef-associated Gobies (Coryphopterus) in the British Virgin Islands.

The effects of parasitic copepods on free-living hosts are infrequently documented, and the copepod Pharodes tortugensis has remained virtually unstudied since described. For the first time, we document its host range in the British Virgin Islands (BVI), the prevalence and intensity of infections on wild hosts, and its impacts on host morphology and performance. Infections were observed on four benthic gobies in the BVI (Coryphopterus glaucofraenum, C. venezuelae, C. dicrus and C. eidolon) but not on other host species previously reported from other parts of the western Atlantic. Infected gobies were widespread in the BVI (detected at 33 of 52 sites, prevalence from 1-25%) but extremely rare elsewhere in the Caribbean (detected at 2 of 16 sites, prevalence < 0.006%). As is typical of macroparasite infections, P. tortugensis was over-dispersed in BVI host populations (mean intensity = 4.7, range = 1-17). Infections were most common in juvenile and female hosts, and rarely found in larger male hosts. The copepods attach in the branchial chamber of the goby; female copepods show high attachment fidelity to the ventral surface of the chamber, while male copepods attached most often to the first two gill arches and in the branchial chamber adjacent to the female. Infections caused substantial damage to the host's branchial chamber and gill filaments. Parasitized gobies also had larger livers and smaller gonads than unparasitized individuals of similar length. The changes in organ mass of infected gobies were not sizeable enough to affect total body mass, and host condition (the body-length vs. body-mass relationship) was similar for gobies with and without infections. Parasitized gobies were, however, significantly smaller in body mass at a given age, reflecting slower overall growth. Effects of P. tortugensis on individual hosts were broadly similar to those of other parasitic copepods that infect fish gills and, for unknown reasons, the BVI appears to be a persistent hotspot of infections on these goby hosts.

Host range and virulence diversity of Pectobacterium carotovorum subsp. brasiliense strain RDKLR infecting radish in India, and development of a LAMP-based diagnostics.

AIM: This work aimed at determining the pathogenicity, molecular characterization, host range and rapid detection of Pectobacterium carotovorum subsp. brasiliense (Pcb) causing soft rot disease in radish. METHODS AND RESULTS: The four isolated isolates were inoculated to radish, typical soft rot symptoms were observed and Koch's postulates were proved. The most virulent strain RDKLR was morphologically and biochemically distinct. Pcb showed a positive potato soft rot test and elicited hypersensitivity response on Nicotiana tobaccum. The genes Pel2 and pmrA were used for subspecies characterization of Pcb. It has a wide host range and infection was observed on slices of carrot, tomato, radish, potato, cauliflower, cabbage, chilli, knol-khol, bell pepper and cucumber. Infectivity was also seen in seedlings under glasshouse conditions. Pcb produced cell wall degrading enzymes in semi-quantification assay and is a strong biofilm producer. The LAMP technique was standardized to help rapid detection and take prophylactic measures to manage the disease. CONCLUSION: This work reports Pcb as a new soft rot causing organism of radish in India. Pcb is highly virulent with a broad host range. The LAMP technique helps in rapid detection. SIGNIFICANCE AND IMPACT OF THE STUDY: Pcb-induced soft rot causes significant yield loss, decreased market value, damage in transit, storage and the market. Disease characterization and early identification aid in disease management and prevention in the field.

Molecular, Phenotypical, and Host-Range Characterization of Robbsia andropogonis Strains Isolated from Bougainvillea spp. in Mexico.

Characteristic leaf spot and blight symptoms caused by Robbsia andropogonis on bougainvillea plants were found in three locations in different provinces of Mexico from 2019 to 2020. Eleven bacterial isolates with morphology similar to R. andropogonis were obtained from the diseased bougainvillea leaves. The isolates were confirmed as R. andropogonis by phenotypic tests and 16S rRNA, rpoD, and gyrB gene sequencing. In addition to bougainvillea, the strains were pathogenic to 10 agriculturally significant crops, including maize (Zea mays), sorghum (Sorghum bicolor), barley (Hordeum vulgare), coffee (Coffea arabiga), carnation (Dianthus caryophilus), Mexican lime (Citrus × aurantifolia), common bean (Phaseolus vulgaris), broadbeans (Vicia faba), and pea (Pisum sativum), but not runner bean (Phaseolus coccineus). The haplotypes network reveals the genetic variability among Mexican strains and its phylogeographic relationship with Japan, the U.S.A., and China. The presence of this pathogen represents a challenge for plant protection strategies in Mexico.

Outbreak of the South American tomato leafminer, Tuta absoluta, in the Chinese mainland: geographic and potential host range expansion.

BACKGROUND: In 2017 Tuta absoluta was identified as an invasive species in China. Due to its rapid geographic expansion and the severe crop damage it causes, T. absoluta poses a serious threat to China's tomato production industry. To determine its geographic distribution and host range, intensive surveys and routine monitoring were conducted across the Chinese mainland between 2018 and 2019. The population colonization coefficient (PCC; ratio of colonized sites and prefectures) and population occurrence index (POI; ratio of infested host species and PCCs) were calculated. RESULTS: In northwestern China, T. absoluta populations established in Xinjiang exhibited a medium PCC value (~0.03). In southwestern China, populations in Yunnan and its five neighboring provinces exhibited high (~0.50 in Yunnan and Guizhou), or low (<0.02 in Guangxi, Sichuan, Hunan, and Chongqing) PCC values. In the Chinese mainland, infestations of four crop plant species (tomato, eggplant, potato, and Chinese lantern) and two wild plant species (black nightshade and Dutch eggplant) were identified; tomatoes were infested in every colonized province. Chinese lantern and Dutch eggplant are potentially novel hosts. Yunnan, Guizhou, and Xinjiang experienced the most serious damage (POI). In southwestern China, observed damage significantly decreased with increased distance from the first discovery site of T. absoluta to the farthest county of an infested province increased. CONCLUSION: T. absoluta populations are well-established and could potentially spread to other regions of China. The present study helps to inform the establishment of better pest management guidelines and strategies in China and tomato-producing regions worldwide. © 2021 Society of Chemical Industry.

Host range dynamics at different scales: host use by a hemiparasite across its geographic distribution.

The complexity of natural communities is the result of interactions among species that coexist within them. Parasitic interactions are among the most common species interaction types, and analysis of parasite-host ranges can advance understanding of how host-parasite pairs structure community interactions across their geographic distributions. Using network analysis and host preference relative index, we analysed host use by the South American mistletoe, Tristerix corymbosus (Loranthaceae), in 22 localities among two biomes: Chilean matorral and temperate forest. The total number of host species recorded was 27, and 40% of these species were non-native. The non-native Populus sp. was shared between biomes. There was a positive relationship between host range and potential host species richness at the studied localities. On average, the mistletoe parasitized each host species relative to its abundance. However, some host species in some localities are more parasitized than expected. Network structure showed a differences in host use between the two biomes: Aristotelia chilensis was central in the temperate forest, with Populus sp. in the Chilean matorral. Host use intensity in the Chilean matorral was higher for non-native species. Tristerix corymbosus has a wide host range and could be considered a generalist parasite across its full geographic distribution, but at local scales, host preferences differed among localities and are related to host coverage. Alterations in community composition, due to natural events or human activities, can modify the availability of possible hosts. Hence, the mistletoe with the described characteristics may be able to change its infection preference while maintaining the interaction functionality.

Nucleopolyhedrovirus Coocclusion Technology: A New Concept in the Development of Biological Insecticides.

Nucleopolyhedroviruses (NPV, Baculoviridae) that infect lepidopteran pests have an established record as safe and effective biological insecticides. Here, we describe a new approach for the development of NPV-based insecticides. This technology takes advantage of the unique way in which these viruses are transmitted as collective infectious units, and the genotypic diversity present in natural virus populations. A ten-step procedure is described involving genotypic variant selection, mixing, coinfection and intraspecific coocclusion of variants within viral occlusion bodies. Using two examples, we demonstrate how this approach can be used to produce highly pathogenic virus preparations for pest control. As restricted host range limits the uptake of NPV-based insecticides, this technology has recently been adapted to produce custom-designed interspecific mixtures of viruses that can be applied to control complexes of lepidopteran pests on particular crops, as long as a shared host species is available for virus production. This approach to the development of NPV-based insecticides has the potential to be applied across a broad range of NPV-pest pathosystems.

Morphologic, molecular, and pathogenic characterization of Phytophthora palmivora isolates causing flower rot on azalea.

The objective of this work was to characterize two Phytophthora palmivora isolates causing floral blight and rot in azalea plants and to evaluate the pathogenicity of this oomycete pathogen on several plant species. Azalea plants with symptoms of flower blight and rot were obtained in the municipality of Holambra-SP. After an attempt of isolation, colonies with Phytophthora characteristics grown only on selective V8 medium. Molecular identification of the isolates was done by amplification and sequencing of ITS and COX2 regions. In the phylogenetic analysis, the azalea isolates clustered with reference isolates of P. palmivora. Morphological characteristics were similar to those described for P. palmivora. Isolates were inoculated in healthy azalea plants and caused leaf blight and floral rot. The pathogen was re-isolated from symptomatic plants completing Koch's postulates. In a host range test, the azalea isolates were able to cause lesions on leaves of vinca, snapdragon, basil, and tomato, and affected both leaves and flowers of geranium. Fruit rot was observed on tomato, potato, sweet pepper, scarlet eggplant, zucchini, cucumber, maroon cucumber, onion, apple, papaya, guava, and carrot. This is the first report of the species P. palmivora causing flower blight and rot in azalea plants in Brazil and probably in the world.

Potential of native palm species in Northeast Brazil as hosts for the invasive mite Raoiella indica (Acari: Tenuipalpidae).

The red palm mite, Raoiella indica Hirst (Tenuipalpidae), has mainly been registered on palm species (Arecaceae), and its expansion in Brazil has the potential to cause significant negative impact on cultivated as well as native palms. Here, we evaluate the potential of native palms from Northeast Brazil to act as hosts of R. indica. Specifically, we used in situ free-choice and confinement tests, in which sections of palm leaves/leaflets of various species were experimentally infested with R. indica. We tested the following species: Acrocomia aculeata, Acrocomia intumescens, Allagoptera caudescens, Attalea funifera, Attalea oleifera, Bactris acanthocarpa var. acanthocarpa, Bactris ferruginea, Bactris glassmanii, Bactris hirta var. spruceana, Bactris pickelii, Copernicia prunifera, Desmoncus orthacanthos, Desmoncus polyacanthos, Syagrus coronata and Syagrus schizophylla. All of these were compared with the mite's preferred host, the coconut palm, Cocos nucifera. In the free-choice test, both male and female R. indica preferred C. nucifera in comparison to each of the native palms. In the confinement test, we observed significant differences in the survivorship between mites on native palms and those on coconut palms after the second day of infestation. By the fifth day, survivorship of mites on the native palms was almost always significantly lower than on C. nucifera (excepting for C. prunifera). We conclude that, among all the native palms evaluated, only the carnauba palm (C. prunifera) is at risk from R. indica. This result is relevant as this palm is an economically important species in the region.

Here, There, and Everywhere: The Wide Host Range and Geographic Distribution of Zoonotic Orthopoxviruses.

The global emergence of zoonotic viruses, including poxviruses, poses one of the greatest threats to human and animal health. Forty years after the eradication of smallpox, emerging zoonotic orthopoxviruses, such as monkeypox, cowpox, and vaccinia viruses continue to infect humans as well as wild and domestic animals. Currently, the geographical distribution of poxviruses in a broad range of hosts worldwide raises concerns regarding the possibility of outbreaks or viral dissemination to new geographical regions. Here, we review the global host ranges and current epidemiological understanding of zoonotic orthopoxviruses while focusing on orthopoxviruses with epidemic potential, including monkeypox, cowpox, and vaccinia viruses.

PCR and histology identify new bivalve hosts of Apicomplexan-X (APX), a common parasite of the New Zealand flat oyster Ostrea chilensis.

Apicomplexan-X (APX) is a significant pathogen of the flat oyster Ostrea chilensis in New Zealand. The life cycle and host range of this species are poorly known, with only the zoite stage identified. Here, we report the use of molecular approaches and histology to confirm the presence of APX in samples of green-lipped mussels Perna canaliculus, Mediterranean mussels Mytilus galloprovincialis and hairy mussels Modiolus areolatus collected from widely distributed locations in New Zealand. The prevalence of APX infection estimated by PCR was 22.2% (n = 99) and 50% (n = 30) in cultured green-lipped mussels from Nelson and Coromandel, respectively; 0.8% (n = 258), 3.3% (n = 150) and 35.3% (n = 17) in wild Mediterranean mussels from Nelson, Foveaux Strait and Golden Bay, respectively; and 46.7% (n = 30) in wild hairy mussels from Foveaux Strait. Histology detected all cases of PCR that were positive with APX and appeared to be more sensitive. The prevalence of APX estimated by histology in green-lipped mussels from Coromandel was 60% versus 50% by PCR, and 4.3%, 10.7% and 52.9% by histology versus 0.8%, 3.3% and 35.3% by PCR in wild Mediterranean mussels from Nelson, Foveaux Strait and Golden Bay, respectively. The specific identity of the parasite found in mussels was determined by sequencing PCR products for a portion (676 bp) of the 18S rRNA gene; the resulting sequences were 99-100% similar to APX found in flat oysters. Phylogenetic analyses also confirmed that all isolates from green-lipped, Mediterranean and hairy mussels grouped with APX isolates previously identified from flat oysters. This study indicates the wide geographical distribution of APX and highlights the potentially multi-host specific distribution of the parasite in commercially important bivalve shellfish.

Two Phages of the Genera Felixounavirus Subjected to 12 Hour Challenge on Salmonella Infantis Showed Distinct Genotypic and Phenotypic Changes.

Salmonella Infantis is considered in recent years an emerging Salmonella serovar, as it has been associated with several outbreaks and multidrug resistance phenotypes. Phages appear as a possible alternative strategy to control Salmonella Infantis (SI). The aims of this work were to characterize two phages of the Felixounavirus genus, isolated using the same strain of SI, and to expose them to interact in challenge assays to identify genetic and phenotypic changes generated from these interactions. These two phages have a shared nucleotide identity of 97% and are differentiated by their host range: one phage has a wide host range (lysing 14 serovars), and the other has a narrow host range (lysing 6 serovars). During the 12 h challenge we compared: (1) optical density of SI, (2) proportion of SI survivors from phage-infected cultures, and (3) phage titer. Isolates obtained through the assays were evaluated by efficiency of plating (EOP) and by host-range characterization. Genomic modifications were characterized by evaluation of single nucleotide polymorphisms (SNPs). The optical density (600 nm) of phage-infected SI decreased, as compared to the uninfected control, by an average of 0.7 for SI infected with the wide-host-range (WHR) phage and by 0.3 for SI infected with the narrow-host-range (NHR) phage. WHR phage reached higher phage titer (7 × 1011 PFU/mL), and a lower proportion of SI survivor was obtained from the challenge assay. In SI that interacted with phages, we identified SNPs in two genes (rfaK and rfaB), which are both involved in lipopolysaccharide (LPS) polymerization. Therefore, mutations that could impact potential phage receptors on the host surface were selected by lytic phage exposure. This work demonstrates that the interaction of Salmonella phages (WHR and NHR) with SI for 12 h in vitro leads to emergence of new phenotypic and genotypic traits in both phage and host. This information is crucial for the rational design of phage-based control strategies.

Global In-Silico Scenario of tRNA Genes and Their Organization in Virus Genomes.

Viruses are known to be highly dependent on the host translation machinery for their protein synthesis. However, tRNA genes are occasionally identified in such organisms, and in addition, few of them harbor tRNA gene clusters comprising dozens of genes. Recently, tRNA gene clusters have been shown to occur among the three domains of life. In such a scenario, the viruses could play a role in the dispersion of such structures among these organisms. Thus, in order to reveal the prevalence of tRNA genes as well as tRNA gene clusters in viruses, we performed an unbiased large-scale genome survey. Interestingly, tRNA genes were predicted in ssDNA (single-stranded DNA) and ssRNA (single-stranded RNA) viruses as well in many other dsDNA viruses of families from Caudovirales order. In the latter group, tRNA gene clusters composed of 15 to 37 tRNA genes were characterized, mainly in bacteriophages, enlarging the occurrence of such structures within viruses. These bacteriophages were from hosts that encompass five phyla and 34 genera. This in-silico study presents the current global scenario of tRNA genes and their organization in virus genomes, contributing and opening questions to be explored in further studies concerning the role of the translation apparatus in these organisms.