BUSCADOR RECOLECTA

Document S1. Figures S1–S5. Table S1. RNA-seq quality and mapping data for B16 and CT26 cells, see STAR Methods - cDNA library preparation and illumina RNA sequencing. Table S2. Normalized read counts (FPKM) for each gene in each RNA-seq assay, see STAR Methods - Gene expression quantitation and differential expression analysis. Table S3. List of 50 top upregulated genes in B16 resistant clones relative to treatment-naïve cells, related to Figure 4A. Table S4. List of 50 top downregulated genes in B16 resistant clones relative to treatment-naïve cells, related to Figure 4A. Table S5. List of the top 500 upregulated genes in B16 resistant clones (relative to naïve B16 cells) and their corresponding log2 fold change in CT26 C1 and C4 clones (relative to naïve CT26 cells), related to Figure 7E. NA: not applicable., Peer reviewed

Table S1: Bayes Factor between treatment and control of VOCs from P. chlamydosporia in rice cultures on different DAI, Table S2: Bayes Factor between treatment and control of VOCs from P. chlamydosporia in Czapek–Dox broth cultures after different times of exposure to chitosan, Figure S1: Line plots with the median values and standard deviations of the peak heights of VOCs produced by P. chlamydosporia in rice cultures, Figure S2: GC-MS chromatogram of headspace volatile compounds produced by P. chlamydosporia 15 days after inoculation with control buffer solution (BS) and with chitosan solution (CH), Figure S3: Line plots with the median values and standard deviations of the peak heights of VOCs produced by P. chlamydosporia in modified Czapek–Dox broth cultures, Figure S4: GC-MS chromatogram of headspace volatile compounds produced by P. chlamydosporia cultured in modified Czapek–Dox broth for 5 days after 24 h with control buffer solution (BS) and 24 h of exposure to chitosan (CH)., With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), Peer reviewed

El libro de códigos está disponible en español y en traducción al inglés., [ES] El objetivo del Ecobarómetro de Andalucía (EBA) es analizar la conciencia ambiental de los andaluces y cómo se relacionan con el medio ambiente. Para ello se elabora un sistema de indicadores a partir de los resultados proporcionados por una encuesta anual dirigida a la población andaluza mayor de 18 años. La encuesta tiene por finalidad medir las distintas dimensiones de la conciencia ambiental (afectiva, cognitiva, activa y conativa), analizando las percepciones, actitudes, conocimiento y comportamiento de los andaluces respecto a diversas cuestiones ambientales. Este dataset corresponde a los resultados obtenidos en la encuesta realizada a una muestra representativa de la población andaluza mayor de 18 años durante los meses de abril y mayo de 2009. El EBA presenta su novena edición desde que se iniciara en el año 2001. La estabilidad del contenido del cuestionario, así como su comparabilidad con barómetros similares empleados en estudios de ámbito estatal o internacional, lo configuran como un valioso instrumento para el estudio de la opinión pública andaluza en temas de medio ambiente, así como su evolución en el tiempo y sus peculiaridades en el contexto más amplio de las sociedades europeas., [EN] The objective of Andalusian Barometer (EBA) is to analyze the environmental awareness of Andalusians and how they relate to the environment. For this purpose, a system of indicators is elaborated from the results provide by an annual survey directed to the Andalusian population over 18 years of age. The survey aims to measure the different dimensions of environmental awareness (affective, cognitive, active and conative), analyzing the perceptions, attitudes, knowledge and behavior of Andalusians respect different environmental issues. This dataset corresponds to the results obtained in the survey carried out on a representative sample of the Andalusian population over 18 years of age during the months of April and May 2009. The EBA is in its ninth edition since it began in the year 2001. The stability of the content of questionnaire, as well as its comparability with similar barometers used in national or international studies, make it a valuable instrument for the study of Andalusian public opinion on environmental issues, as well as its evolution over time and its peculiarities in the broader context of the European societies., Investigación realizada en el marco de un convenio de colaboración suscrito entre la Consejería de Medio Ambiente y Ordenación del Territorio de la Junta de Andalucía y el Instituto de Estudios Sociales Avanzados del Consejo Superior de Investigaciones Científicas (IESA-CSIC)., BAROMETER2009_Datafile.csv BAROMETER2009_Datafile.sav BAROMETER2009_Codebook_EN.pdf BAROMETER2009_Codebook_SP.pdf BAROMETER2009_Readme_EN.pdf BAROMETER2009_Readme_SP.pdf BAROMETER2009_Survey.pdf, Peer reviewed

Supplemental information: Document S1. Figures S1–S7 and Table S5. Table S1. General features of the 46 isolated bacteriophages. Phage ID, phylogenetic classification in 13 groups, genome size and circularity, sequencing depth, GC %, CDS, putative lysogeny genes, taxonomic family, subfamily, and genus according to IGS values with the closest phage are provided. Additionally, concentration of phages for the spot assay, formation of plaque haloes, susceptible CLTs, RBP system and number of depolymerase domains (Dpos) are also shown. REP: transcription repressor/regulator, PAR: parAB genes, REC: recombinases. TSP: Tail spike protein. CBM: carbohydrate-binding module. Taxonomy ranks marked with a star can be reclassified based on relationships showed in this study. CLTs marked with a star indicate that bacteria were acapsular. Dpos marked with a star indicate putative soluble Dpos. Table S2. General features of the 138 Klebsiella clinical strains. The strain, sequencing details, virulence and antibiotic resistance scores, wzi allele, CLT and OLT inference, number of prophages, CRISPR loci, and presence of defense systems and secondary receptors are provided. The presence of a capsule was determined by visual inspection of colonies using light microscopy. Table S3. Phage-bacteria positive combinations. The strain used for phage isolation is indicated. Spotting: positive by the spot-assay. Virulent: positive by the killing planktonic or progeny assay. Table S4. Clustering of phage RBDs with putative depolymerase activity from this work and the literature. RBDs are identified by the phage name followed by the phage protein in which the domain was detected, and the positions considered after the removal of the anchor domain. Document S2. Article plus supplemental information., Peer reviewed

Bacteriophages play key roles in bacterial ecology and evolution and are potential antimicrobials. However, the determinants of phage-host specificity remain elusive. Here, we isolate 46 phages to challenge 138 representative clinical isolates of Klebsiella pneumoniae, a widespread opportunistic pathogen. Spot tests show a narrow host range for most phages, with <2% of 6,319 phage-host combinations tested yielding detectable interactions. Bacterial capsule diversity is the main factor restricting phage host range. Consequently, phage-encoded depolymerases are key determinants of host tropism, and depolymerase sequence types are associated with the ability to infect specific capsular types across phage families. However, all phages with a broader host range found do not encode canonical depolymerases, suggesting alternative modes of entry. These findings expand our knowledge of the complex interactions between bacteria and their viruses and point out the feasibility of predicting the first steps of phage infection using bacterial and phage genome sequences., Peer reviewed

Table S1: Sampling information of the Salmonella enterica isolates included in this study. Table S2: Summary of sequence read quality. Table S3: Summary of assembly results. Table S4: Serotypes and STs. Table S5: Isolates included in HSC and their features. Figure S1: Sequence and structure of the contig containing the mcr-1 gene with the Incx4 plasmid., Peer reviewed

Figure S1: PCA of genomic signatures based on hexamer frequencies of the reference bacteria; Figure S2: k4freq-based distances of the bacterial genera to the reference phages; Figure S3: ROC curves for k4freq and k14exact; Figure S4: Statistical error analysis for different k-mer options; Figure S5: k14exact-based distances of the bacterial genera to the reference phages; Figure S6: Distances of 75 Klebsiella strains to 41 Klebsiella phages; Table S1: Bacterial genomes in the reference set; Table S2: Phage genomes in the reference set; Table S3: Plasmids in the reference set; Table S4: Summary of statistical comparisons of genomic distances; Table S5: Lysogenic activity of K. pneumoniae phages; Table S6: Bacterial single-cells and phages detected in their assemblies., Peer reviewed

The 16S rRNA gene sequence of strain P4.10XT have been deposited in GenBank under the accession number MZ994596. The genomic assembly of strain P4.10XT has been deposited under the GenBank accession number ASM2156869v1., Peer reviewed

Table S1. Absolute frequencies of Hemiptera: Aphididae by sampling area and year. Table S2: Absolute frequencies of Hymenoptera: Braconidae: Aphidiinae by sampling area and year. In parentheses, the total number of tillers examined. Table S3: Absolute frequencies of hyperparasitoids by sampling area and year. In parentheses, the total number of tillers examined., Peer reviewed

Dataset of the Sensbio applications. The CSV file is used as a database of the known TF-ligand interactions. The txt file describes the headers of the csv., Peer reviewed