Over the past few years, symptoms akin to late blight disease have been reported on a variety of crop plants in South America. Despite the economic importance of these crops, the causal agents of the diseases belonging to the genus Phytophthora have not been completely characterized. In this study, a new Phytophthora species was described in Colombia from tree tomato (Solanum betaceum), a semi-domesticated fruit grown in northern South America. Comprehensive phylogenetic, morphological, population genetic analyses, and infection assays to characterize this new species, were conducted. All data support the description of the new species, Phytophthora betacei sp. nov. Phylogenetic analyses suggest that this new species belongs to clade 1c of the genus Phytophthora and is a close relative of the potato late blight pathogen, P. infestans. Furthermore, it appeared as the sister group of the P. andina strains collected from wild Solanaceae (clonal lineage EC-2). Analyses of morphological and physiological characters as well as host specificity showed high support for the differentiation of these species. Based on these results, a complete description of the new species is provided and the species boundaries within Phytophthora clade 1c in northern South America are discussed.

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Here we present the physiological features of Pseudomonas extremaustralis strain USBA-GBX-515 (CMPUJU 515), isolated from soils in Superparamo ecosystems, > 4000 m.a.s.l, in the northern Andes of South America, as well as the thorough analysis of the draft genome. Strain USBA-GBX-515 is a Gram-negative rod shaped bacterium of 1.0-3. 0 μm × 0.5-1 μm, motile and unable to form spores, it grows aerobically and cells show one single flagellum. Several genetic indices, the phylogenetic analysis of the 16S rRNA gene sequence and the phenotypic characterization confirmed that USBA-GBX-515 is a member of Pseudomonas genus and, the similarity of the 16S rDNA sequence was 100% with P. extremaustralis strain CT14-3 T . The draft genome of P. extremaustralis strain USBA-GBX-515 consisted of 6,143,638 Mb with a G + C content of 60.9 mol%. A total of 5665 genes were predicted and of those, 5544 were protein coding genes and 121 were RNA genes. The distribution of genes into COG functional categories showed that most genes were classified in the category of amino acid transport and metabolism (10.5%) followed by transcription (8.4%) and signal transduction mechanisms (7.3%). We performed experimental analyses of the lipolytic activity and results showed activity mainly on short chain fatty acids. The genome analysis demonstrated the existence of two genes, lip515A and est515A, related to a triacylglycerol lipase and carboxylesterase, respectively. Ammonification genes were also observed, mainly nitrate reductase genes. Genes related with synthesis of poly-hydroxyalkanoates (PHAs), especially poly-hydroxybutyrates (PHBs), were detected. The phaABC and phbABC operons also appeared complete in the genome. P. extremaustralis strain USBA-GBX-515 conserves the same gene organization of the type strain CT14-3 T . We also thoroughly analyzed the potential for production of secondary metabolites finding close to 400 genes in 32 biosynthetic gene clusters involved in their production.

Three morphologically similar thermo-acidophilic strains, USBA-GBX-501, USBA-GBX-502 and USBA-GBX-503, were isolated from acidic thermal springs at the National Natural Park Los Nevados (Colombia). All isolates were spore-forming, Gram-stain-positive and motile, growing aerobically at 25-55 °C (optimum ~45 °C) and at pH 1.5-4.5 (optimum pH ~3.0). Phylogenetic analysis of the 16S rRNA gene sequences of these isolates showed an almost identical sequence (99.0 % similarity) and they formed a robust cluster with the closest relative Alicyclobacillus tolerans DSM 16297 with a sequence similarity of 99.0 %. Average similarity to other species of the genus Alicyclobacillus was 93.0 % and average similarity to species of the genus Effusibacillus was 90 %. In addition, the level of DNA-DNA hybridization between strain USBA-GBX-503 and Alicyclobacillus tolerans DSM 16297 was 31.7 %. The genomic DNA G+C content of strain USBA-GBX-503 was 44.6 mol%. The only menaquinone was MK-7 (100.0 %). No ω-alicyclic fatty acids were detected in strain USBA-GBX-503, and the major cellular fatty acids were C18 : 1ω7c, anteiso-C17 : 0 and iso-C17 : 0. Based on phenotypic and chemotaxonomic characteristics, phylogenetic analysis and DNA-DNA relatedness values, along with low levels of identity at the whole genome level (ANIb and ANIm values of <67.0 and <91.0 %, respectively), it can be concluded that strain USBA-GBX-503 represents a novel species of the genus Alicyclobacillus, for which the name Alicyclobacillus montanus sp. nov. is proposed. The type strain is USBA-GBX-503 (=CMPUJ UGB U503=CBMAI1927).

A free-living, nitrogen-fixing, mesophilic and facultative aerobe, designated strain USBA 369, was isolated from a terrestrial saline spring of the Colombian Andes. The non-sporulating rods (1.5×0.8 µm) with rounded ends stained Gram-negative and were motile by means of lophotrichous flagella. The strain grew optimally at 30 °C, at pH 6.9-7.5 and with 1.5 % (w/v) NaCl. The major fatty acids detected were C18 : 1ω7c and C19 : 0 cyclo ω8c, and the respiratory lipoquinone ubiquinone 10 (Q-10) was present. The genome consisted of 4.65 Mb with a DNA G+C content of 64.3 mol%. A total of 4371 genes were predicted and, of those, 4300 were protein coding genes and 71 were RNA genes. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain USBA 369 formed a different lineage within the class Alphaproteobacteria, order Rhizobiales, and DNA homology studies with the most closely related genera, Aurantimonas, Aureimonas and Rhizobium (95 % 16S rRNA gene sequence similarity), showed values of <15 %. The phylogenomic analysis provided evidence for clear phylogenetic divergence between strain USBA 369 and the closely related genera. On the basis of the phenotypic, chemotaxonomic and phylogenomic evidence, strain USBA 369 is considered to represent a novel genus and a novel species for which the name Consotaella salsifontis gen. nov., sp. nov. is proposed. The type strain is USBA 369 (=KCTC 22549=CMPUJ U369).

ImportanceA transdiagnostic treatment, the Unified Protocol, is as effective as single diagnostic protocols in comorbid emotional disorders in clinical populations. However, its effects on posttraumatic stress disorder and other emotional disorders in individuals living in war and armed conflict contexts have not been studied.ObjectiveTo evaluate the efficacy of a cultural and contextual adaptation of the Unified Protocol (CXA-UP) on posttraumatic stress disorder, anxiety, and depression compared to waitlist control in individuals exposed to armed conflict in Colombia.Design, Setting, and ParticipantsFrom April 2017 to March 2020, 200 participants 18 years and older were randomly assigned to the CXA-UP or to a waitlist condition. CXA-UP consisted of 12 to 14 twice-a-week or weekly individual 90-minute face-to-face sessions. Outcomes were assessed at baseline, posttreatment, and 3 months following treatment. Analyses were performed and compared for all randomly allocated participants (intent-to-treat [ITT]) and for participants who completed all sessions and posttreatment measures (per protocol [PP]). The study took place at an outpatient university center and included individuals who were registered in the Colombian Victims Unit meeting DSM-5 diagnostic criteria for posttraumatic stress disorder, anxiety, or depression or were severely impaired by anxiety or depression. Individuals who were receiving psychological therapy, were dependent on alcohol or drugs, were actively suicidal or had attempted suicide in the previous 2 months, had psychosis or bipolar disorder, or were cognitively impaired were excluded.InterventionCXA-UP or waitlist.Main Outcomes and MeasuresPrimary outcomes were changes in anxiety, depression, and somatic scores on the Patient Health Questionnaire and Posttraumatic Stress Disorder Checklist for DSM-5.ResultsAmong the 200 participants (160 women [80.0%]; 40 men [20.0%]; mean [SD] age, 43.1 [11.9] years), 120 were randomized to treatment and 80 to waitlist. Results for primary outcomes in the ITT analysis showed a significant pretreatment-to-posttreatment reduction when comparing treatment and waitlist on the posttraumatic stress disorder checklist for DSM-5 scores (slope [SE], −31.12 [3.00]; P &amp;lt; .001; Cohen d, 0.90; 90% CI, 0.63-1.19), 9-item Patient Health Questionnaire (PHQ-9) (slope [SE],−11.94 [1.30]; P &amp;lt; .001; Cohen d, 0.77; 90% CI, 0.52-1.06), PHQ-anxiety (slope [SE], −6.52 [0.67]; P &amp;lt; .001; Cohen d, 0.82; 90% CI, 0.49-1.15), and PHQ-somatic (slope [SE], −8.31 [0.92]; P &amp;lt; .001; Cohen d, 0.75; 90% CI, 0.47-1.04).Conclusions and RelevanceIn this study, significant reductions and large effect sizes in all measures of different emotional disorders showed efficacy of a single transdiagnostic intervention in individuals exposed to armed conflicts.Trial RegistrationClinicalTrials.gov Identifier: NCT03127982

PremiseTransposable elements (TEs) make up more than half of the genomes of complex plant species and can modulate the expression of neighboring genes, producing significant variability of agronomically relevant traits. The availability of long‐read sequencing technologies allows the building of genome assemblies for plant species with large and complex genomes. Unfortunately, TE annotation currently represents a bottleneck in the annotation of genome assemblies.Methods and ResultsWe present a new functionality of the Next‐Generation Sequencing Experience Platform (NGSEP) to perform efficient homology‐based TE annotation. Sequences in a reference library are treated as long reads and mapped to an input genome assembly. A hierarchical annotation is then assigned by homology using the annotation of the reference library. We tested the performance of our algorithm on genome assemblies of different plant species, including Arabidopsis thaliana, Oryza sativa, Coffea humblotiana, and Triticum aestivum (bread wheat). Our algorithm outperforms traditional homology‐based annotation tools in speed by a factor of three to >20, reducing the annotation time of the T. aestivum genome from months to hours, and recovering up to 80% of TEs annotated with RepeatMasker with a precision of up to 0.95.ConclusionsNGSEP allows rapid analysis of TEs, especially in very large and TE‐rich plant genomes.

Over the past few years, symptoms akin to late blight disease have been reported on a variety of crop plants in South America. Despite the economic importance of these crops, the causal agents of the diseases belonging to the genus Phytophthora have not been completely characterized. In this study, we used an integrative approach that leveraged morphological, ecological, and genetic approaches to explore cryptic speciation within P. infestans sensu lato. We described a new Phytophthora species collected in Colombia from tree tomato (Solanum betaceum), a semi-domesticated fruit. All morphological traits and population genetic analyses, using microsatellite data and a reduced representation of single nucleotide polymorphism (SNP) data, support the description of the new species, Phytophthora betacei sp. nov. We have demonstrated that ecological differences are important in the persistence of P. infestans and P. betacei as genetically isolated units across an overlapping area in the northern Andes.