https://hdl.handle.net/11000/423 Tue, 28 Apr 2026 14:39:01 GMT 2026-04-28T14:39:01Z https://hdl.handle.net/11000/39807 Título : The hidden genetic reservoir: structural variants as drivers of marine microbial and viral microdiversity Autor : Haro-Moreno, Jose M.; Roda-Garcia, Juan J.; Molina Pardines, Carmen; López-Pérez, Mario Resumen : Background Intraspecific genetic diversity is fundamental to understanding microbial adaptation, evolution, and contributions to ecosystem stability. However, traditional short-read metagenomics often underrepresents this diversity, particularly structural variants (SVs), due to assembly limitations in complex natural populations. To overcome these constraints, we employed third-generation (long-read) metagenomics to investigate the ecoevolutionary role of SVs in microbial and viral marine populations. Our analysis focused on the cellular metagenome fraction (0.22–5 μm size range) across distinct ecological niches within the photic zone of the marine water column. Results Insertions and deletions emerged as the predominant SVs in the marine microbiome, occurring at similar frequencies across genomes. These SVs were not only found within the core genome but also in the flexible genome, serving as a source of genetic variability within genomic islands. Insertions were significantly larger, reaching more than 2 Kb, in streamlined microbes such as Pelagibacter (SAR11 clade) or the archaeon Nitrosopumilus. In contrast, SVs in viral populations were smaller and more uniform in size (~ 430 bp). Functionally, SVs were enriched in genes linked to nutrient uptake, amino acid metabolism, and regulatory networks due to the presence of non-coding RNAs. These SVs often encompassed entire genes or operons, acting as an important reservoir of niche-specific diversity that supports the emergence of ecological lineages better adapted to environmental gradients, such as rhodopsin-containing subpopulations in shallower waters. In viruses, SV-driven genetic plasticity facilitated host range adaptation and the evolution of mechanisms modulating host metabolism. We identified long-term genetically stable populations of cyanophages and pelagiphages, wherein SVs represented the primary source of genomic diversification. Notably, certain subpopulations of pelagimyophages carry SVs encoding a pstS gene, which enhances host phosphate uptake and increases viral replication efficiency—a beneficial adaptation in phosphate-depleted environments such as the oligotrophic Mediterranean Sea. Conclusions By capturing SVs directly from natural populations, this study provides new insights into microbial evolution, phage-host interactions, and the broader implications of genomic plasticity for ecosystem resilience in marine environments. Furthermore, these results highlight the transformative potential of third-generation sequencing to unveil previously hidden layers of microbial and viral diversity. Thu, 23 Apr 2026 15:41:08 GMT https://hdl.handle.net/11000/39807 2026-04-23T15:41:08Z https://hdl.handle.net/11000/39800 Título : Bridging clinical and environmental reservoirs: antimicrobial resistance in the emerging pathogen Shewanella algae Autor : García-Rivera, Celia; Roda-García, Juan J.; Rodríguez, Juan Carlos; Molina-Pardines, Carmen; Tyshkovska, Iryna; Haro-Moreno, Jose M.; Martínez-Murcia, Antonio; Paz-Ventero, Maria; López-Pérez, Mario Resumen : The emergence of antimicrobial resistance in environmental bacteriathreatens therapeutic efficacy in clinical settings. Shewanella algae, historically regarded as a marine saprophyte, is increasingly recognized as an emerging opportunisticpathogen. In this study, we analyzed 86 S. algae isolates from Spain (19 clinical and 67environmental) and integrated them with 178 publicly available genomes to exploreantimicrobial susceptibility patterns and genomic diversity. Penicillins and fosfomycinconsistently showed poor activity, whereas piperacillin/tazobactam, third- and fourth-generation cephalosporins, aminoglycosides, ciprofloxacin, trimethoprim–sulfamethoxazole and several novel β-lactam–inhibitor combinations exhibited low MIC distributions.Recently introduced agents, including ceftazidime/avibactam, ceftolozane/tazobactam,and cefiderocol, also demonstrated strong in vitro activity. Carbapenems displayedan unusual intraclass pattern, with imipenem showing markedly higher MICs thanmeropenem and ertapenem. When interpreted using CLSI’s “Other Non-Enterobacterales” criteria, clinical and environmental isolates exhibited largely overlapping susceptibility profiles, highlighting the potential role of environmental strains as reservoirsof resistance-related traits. Genomic profiling revealed a conserved intrinsic resistome(OXA-type β-lactamases, qnrA variants, ugd, and efflux regulators) together withhorizontally acquired determinants. A 29 kb genomic island carrying multiple resistance genes was identified in a clinical isolate, with homologous structures detectedin Vibrio and Proteus, suggesting interspecies transfer. Furthermore, plasmids harboringclass 1 integrons (mobile integrons) were widespread, shared with Enterobacterales andVibrionaceae across clinical and environmental settings. Overall, these findings highlightS. algae as both a clinically relevant pathogen and a reservoir of mobile AMR determinants and underscore the urgent need for species-specific antimicrobial susceptibilityinterpretive criteria to improve clinical decision-making for this emerging pathogen. Wed, 22 Apr 2026 17:53:52 GMT https://hdl.handle.net/11000/39800 2026-04-22T17:53:52Z https://hdl.handle.net/11000/39420 Título : Effect of deficit irrigation strategies on the elemental composition of “Mirlo Rojo” apricot cultivated in Spain Autor : Rodríguez-Estrada, Marcos; Carbonell-Barrachina, Ángel A.; Andreu-Coll, Lucía; Hernández, Francisca; Signes-Pastor, Antonio J. Resumen : Background: Deficit irrigation (DI) is a key strategy for optimizing water use in agriculture, particularly in regions affected by climate change. This study evaluates the effects of four DI regimes (100 %, 66 %, 33 %, and 0 % of crop evapotranspiration) on the elemental profile of "Mirlo Rojo" apricots (Prunus armeniaca L.) cultivated in southeastern Spain. Methodology: Essential (B, Ca, Cu, Fe, K, Mg, Mn, Na, P, and Zn) and non-essential elements (As, Cr, Pb, and Rb) were quantified by ICP MS following microwave-assisted acid digestion. Data analysis employed Kruskal-Wallis test and Spearman’s rank correlation (bivariate analysis). Method validity was confirmed by 80 %-120 % recovery rates. Results: Seven elements varied significantly (B, Cu, Fe, Na, P, Pb, Rb), while major elements (K, Ca, Mg), Mn and Zn remained stable. K, the most abundant element, peaked at 18,200 mg/kg (33 % DI). As was undetectable and Pb (0.11–0.13 mg/kg) remained below current European regulatory limits, regardless of DI. Non-monotonic responses and significant element correlations were observed, suggesting complex soil-plant interactions. Conclusion: DI did not appear to compromise fruit safety or nutritional value. The element stability under water stress supports the potential of DI as a sustainable water management practice without increasing potentially toxic elements. Wed, 25 Feb 2026 14:31:28 GMT https://hdl.handle.net/11000/39420 2026-02-25T14:31:28Z https://hdl.handle.net/11000/39419 Título : Deficit Irrigation and Preharvest Chitosan Sprays Enhance Fruit Quality and Postharvest Performance in Peach Autor : Andreu Coll, Lucía; Blaya Ros, Pedro J; García Castellanos, Begoña; Vigueras Fernández, Jesús; Morales Guevara, Donaldo; García García, José; García Brunton, Jesús; Calín Sánchez, Ángel; Hernández, Francisca; Galindo, Alejandro Resumen : Water scarcity in Mediterranean environments has driven the search for sustainable strategies to improve water-use efficiency while maintaining fruit quality. This study evaluated the combined effect of sustained deficit irrigation and preharvest chitosan sprays on fruit quality, bioactive compounds, mineral composition, and postharvest behaviour in two late-season peach cultivars (“Tiétar” and “Duero”) grown under semi-arid Mediterranean conditions. Sustained deficit irrigation was applied throughout the season, together with preharvest chitosan applications during fruit development, to assess individual and interactive effects. Deficit irrigation caused only slight reductions in fruit size while increasing total soluble solids (TSS) concentration and the maturity index (TSS/titratable acidity). Chitosan application increased fruit firmness and modified titratable acidity depending on the irrigation regime (full irrigation or deficit irrigation). The combined treatment (chitosan + deficit irrigation) promoted the accumulation of phenolic compounds and antioxidant activity, particularly in “Tiétar”, increased calcium and iron contents, and showed a longer shelf life. These results indicate that integrating deficit irrigation with preharvest chitosan sprays can mitigate the impact of water scarcity while improving functional and postharvest quality of peaches under Mediterranean conditions. Wed, 25 Feb 2026 14:24:16 GMT https://hdl.handle.net/11000/39419 2026-02-25T14:24:16Z https://hdl.handle.net/11000/39418 Título : Profile of Sugars, Organic Acids, and Antioxidant Activity inMoroccan Figs from Oases and Atlas Regions Autor : Mardoume, Ibtissam; Teruel Andreu, Candela; Martínez, Rafael; Bouda, Said; Khachtib, Youssef; Hernández, Francisca; Haddioui, Abdelmajid Resumen : Figs are consumed fresh, dried, or processed into confectionery, compotes, and candies. Key consumer criteria include taste, nutritional value, and functional properties. The study focused on characterizing the biochemical and antioxidant properties of 51 Moroccan fig cultivars from oases and Atlas regions. The following determinations were assessed sugars (glucose, fructose, sucrose, and total sugars), organic acids (malic acid, citric acid, and total organic acids), total polyphenols and antioxidant activity. The results reveal significant variation among studied cultivars. Total sugars, glucose, fructose, and antioxidant activity (ABTS, FRAP) are the most discriminating parameters. Additionally, the cultivars from oases ‘Mrotchi’ (MR2), ‘Mrotchi’ (MR4) and ‘Tabkhant’ (TB1) exhibit the highest total polyphenols content (610.07, 681.43, and 582.76 mg GAE/100 g dw, respectively) and exceptionally high antioxidant activities (11.03, 13.88, and 11.37 mmol Trolox/kg, respectively). Additionally, the cultivars ‘Ain Hajla’ (AH5) and ‘Tazizawt’ (TZ) from southeastern oases, as well as the cultivar ‘Beida’ (BD1) from the Atlas Mountain, exhibit high levels of glucose and fructose. This study highlights the substantial biochemical diversity in Moroccan fig cultivars, providing valuable insights for the selection of genetic pools with desirable chemotypes, ultimately benefiting consumer health. Wed, 25 Feb 2026 14:19:47 GMT https://hdl.handle.net/11000/39418 2026-02-25T14:19:47Z https://hdl.handle.net/11000/39417 Título : In Vitro Techniques for Seed Potato (Solanum tuberosum L.) Tuber Production: A Systematic Review Autor : Jácome Sarchi, Guillermo Alexander; Coronel Montesdeoca, Nataly Tatiana; Hernández, Francisca; Martínez, Rafael Todos Santos Resumen : In vitro culture has become a key tool to produce seed potato (Solanum tuberosum L.) tubers, a crop of great global importance. This systematic review, based on the PRISMA-ScR methodology, analyzes the main biotechnological strategies used to obtain high-quality, healthy, and pathogen-free seeds, overcoming the limitations of traditional propagation methods. A comprehensive search was conducted in Scopus, Web of Science, and ScienceDirect (June 2025), prioritizing 65 experimental studies published between 2010 and 2025 in indexed journals. Techniques such as meristem culture, micropropagation, microtuber production, the use of temporary immersion bioreactor systems (TIBs), and synthetic seed generation were examined. These methodologies offer advantages such as accelerated propagation, higher yields, reduced use of agrochemicals, germplasm conservation, and economic efficiency. TIBs stand out for improving the survival and productivity of basic seed. This review is organized around four axes: applied techniques, key procedures, economic impact and sustainability, and future perspectives. This work constitutes a useful guide for optimizing seed tuber production using plant biotechnology. Wed, 25 Feb 2026 14:13:50 GMT https://hdl.handle.net/11000/39417 2026-02-25T14:13:50Z https://hdl.handle.net/11000/38889 Título : Cryptococcus bacillisporus causing cryptococcoma of the beak of an African grey parrot (Psittacus erithacus), Portugal Autor : Silva, Carolina; Juan-Sallés, Carles; Mendes, Joana; Mendes, Ana ; Ruivo, Mariana; Abad, Juan L; Hagen, Ferry; Colom Valiente, María Francisca Resumen : We report a severe case of rhinothecal cryptococcoma in a 13-year-old female African Grey Parrot (Psittacus erithacus). The bird was born and bred in captivity in Portugal. The beak was deformed and showed several round soft masses, and microscopic examination revealed the presence of cells suggestive for Cryptococcus. Phenotypic and molecular analyses identified the obtained yeast culture as C. bacillisporus (AFLP5/VGIII). By phylogenetic analysis the parrot strain clustered with clinical C. bacillisporus strains from Mexico. Fri, 16 Jan 2026 09:26:54 GMT https://hdl.handle.net/11000/38889 2026-01-16T09:26:54Z https://hdl.handle.net/11000/38806 Título : Unlocking the Microbial World: A Global Initiative for Education and Sustainability Autor : Ramos, Juan L.; Lal, Rup; Colom Valiente, María Francisca; Chavarria, Max; Huang, Wei; Wang, Yun; Udaondo, Zulema; Timmis, Kenneth Resumen : Microbes govern our planet! The International Microbial Literacy Initiative (IMiLI) promotes global microbial literacy with free, open-access resources in multiple languages. Understanding microbes is key to sustainability and informed decision-making. Mon, 15 Dec 2025 17:05:11 GMT https://hdl.handle.net/11000/38806 2025-12-15T17:05:11Z https://hdl.handle.net/11000/38789 Título : Don’t Fear The Science. Learning Biotechnology with Dinosaurs, Zombies, Mad Doctors and Monsters. Autor : Sánchez Angulo, Manuel Fri, 12 Dec 2025 11:07:35 GMT https://hdl.handle.net/11000/38789 2025-12-12T11:07:35Z https://hdl.handle.net/11000/38767 Título : Risk of exposure to bioaerosols in clinical environments: bronchoscopy Autor : Gómez Sánchez, Noelia; Alcalde, Lorena; Sancho Chust, José N; Boira, Ignacio; Gálvez, Beatriz; Esteban, Violeta; Chiner, Eusebi; Yubero, Eduardo; Colom, María Francisca; Ferrer, Consuelo Resumen : Healthcare professionals face a heightened risk of occupational infections, with procedures such as bronchoscopy further increasing this risk by generating aerosols containing diverse microorganisms. This study quantified bioaerosol concentrations during bronchoscopy to evaluate occupational exposure. Wed, 10 Dec 2025 08:52:44 GMT https://hdl.handle.net/11000/38767 2025-12-10T08:52:44Z