https://hdl.handle.net/11000/423 2026-05-07T17:41:47Z https://hdl.handle.net/11000/39840 Título : The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics Autor : Cabello Yeves, Pedro J.; Callieri, Cristiana; Picazo, Antonio; Mehrshad, Maliheh; Haro Moreno, Jose M.; Roda García, Juan J.; Dzhembekova, Nina; Slabakova, Violeta; Slabakova, Nataliya; Moncheva, Snejana; Rodríguez Valera, Francisco Resumen : Background: The Black Sea is the largest brackish water body in the world, although it is connected to the Mediterranean Sea and presents an upper water layer similar to some regions of the former, albeit with lower salinity and temperature. Despite its well-known hydrology and physicochemical features, this enormous water mass remains poorly studied at the microbial genomics level. Results: We have sampled its different water masses and analyzed the microbiome by shotgun and genomeresolved metagenomics, generating a large number of metagenome-assembled genomes (MAGs) from them. We found various similarities with previously described Black Sea metagenomic datasets, that show remarkable stability in its microbiome. Our datasets are also comparable to other marine anoxic water columns like the Cariaco Basin. The oxic zone resembles to standard marine (e.g. Mediterranean) photic zones, with Cyanobacteria (Synechococcus but a conspicuously absent Prochlorococcus), and photoheterotrophs domination (largely again with marine relatives). The chemocline presents very different characteristics from the oxic surface with many examples of chemolithotrophic metabolism (Thioglobus) and facultatively anaerobic microbes. The euxinic anaerobic zone presents, as expected, features in common with the bottom of meromictic lakes with a massive dominance of sulfate reduction as energy-generating metabolism, a few (but detectable) methanogenesis marker genes, and a large number of “dark matter” streamlined genomes of largely unpredictable ecology. Conclusions: The Black Sea oxic zone presents many similarities to the global ocean while the redoxcline and euxinic water masses have similarities to other similar aquatic environments of marine (Cariaco Basin or other Black Sea regions) or freshwater (meromictic monimolimnion strata) origin. The MAG collection represents very well the different types of metabolisms expected in this kind of environment. We are adding critical information about this unique and important ecosystem and its microbiome 2026-05-05T11:39:01Z https://hdl.handle.net/11000/39839 Título : Microbiome of the deep Lake Baikal, a unique oxic bathypelagic habitat Autor : Cabello Yeves, Pedro J.; Zemskaya, Tamara I.; Zakharenko, Alexandra S.; Sakirko, Mariya V.; Ivanov, Vyacheslav G.; Ghai, Rohit; Rodríguez Valera, Francisco Resumen : Lake Baikal is the deepest lake in the world. Its depth provides the only bathypelagic (> 1000 m deep) freshwaterhabitat on Earth and its oxic, ultra-oligotrophic features make it a freshwater counterpart of the deep ocean. Herewe have analyzed metagenomes from 1250 and 1350 m deep samples and built 231 metagenome-assembledgenomes (MAGs). We detected high fractions of Thaumarchaeota (ca. 20% of 16S rRNA reads) and members of thecandidate phyla radiation (CPR) (3–4.5%). Among the MAGs, we obtained ammonia-oxidizing archaea (AOA,Nitrosopumilaceae) and bacteria (AOB, Nitrosomonadaceae), and nitrite-oxidizers (Nitrospirae) indicating veryactive nitrification. A new clade of freshwater SAR202 Chloroflexi and methanotrophs (Methyloglobulus) were alsoremarkably abundant, the latter reflecting a possible role of methane oxidation as well. Novel species of streamlinedand cosmopolitan bacteria such as Ca. Fonsibacter or acI Actinobacteria were more abundant at the surface but alsopresent in deep waters. Conversely, CPRs, Myxococcales, Chloroflexi, DPANN (Diapherotrites, Parvarchaeota,Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaeota) archaea, or Gammaproteobacteria were found only inbathypelagic samples. We noted various important taxonomic and metabolic differences between deep aphoticregion of Lake Baikal and marine waters of similar depth: Betaproteobacteriales, CPR, and DPANN superphylumwere only found in bathypelagic Baikal, while Deltaproteobacteria, Gammaproteobacteria, or Alphaproteobacteriaprevailed in oceanic samples. The genes mediating ammonia and methane oxidation, aromatic compound degra-dation, or alkane/methanesulfonate monooxygenases were detected in higher numbers in deep Baikal compared totheir oceanic counterparts or its own surface. Overall, depth seems to be less relevant than salinity in configuringthe microbial community. 2026-05-05T11:37:17Z https://hdl.handle.net/11000/39838 Título : Marine-freshwater prokaryotic transitions require extensive changes in the predicted proteome Autor : Cabello Yeves, Pedro J.; Rodríguez Valera, Francisco Resumen : Background: The adaptation of a marine prokaryote to live in freshwater environments or vice versa is generally believed to be an unusual and evolutionary demanding process. However, the reasons are not obvious given the similarity of both kinds of habitats. Results: We have found major differences at the level of the predicted metaproteomes of marine and freshwater habitats with more acidic values of the isoelectric points (pI) in marine microbes. Furthermore, by comparing genomes of marine-freshwater phylogenetic relatives, we have found higher pI values (basic shift) in the freshwater ones. This difference was sharper in secreted > cytoplasmic > membrane proteins. The changes are concentrated on the surface of soluble proteins. It is also detectable at the level of total amino acid composition and involves similarly core and flexible genome- encoded proteins. Conclusions: The marked changes at the level of protein amino acid composition and pI provide a tool to predict the preferred habitat of a culture or a metagenome-assembled genome (MAG). The exact physiological explanation for such variations in the pIs and electrostatic surface potentials is not known yet. However, these changes might reflect differences in membrane bioenergetics derived from the absence of significant Na+ concentrations in most freshwater habitats. In any case, the changes in amino acid composition in most proteins imply that a long evolutionary time is required to adapt from one type of habitat to the other. 2026-05-05T11:29:44Z https://hdl.handle.net/11000/39837 Título : Genomes of Novel Microbial Lineages Assembled from the Sub-Ice Waters of Lake Baikal Autor : Cabello Yeves, Pedro J.; Zemskaya, Tamara I.; Rosselli, Riccardo; Coutinho, Felipe H.; Zakharenko, Alexandra S.; Blinov, Vadim V.; Rodriguez-Valera, Francisco Resumen : We present a metagenomic study of Lake Baikal (East Siberia). Twosamples obtained from the water column under the ice cover (5 and 20 m deep)in March 2016 have been deep sequenced and the reads assembled to generatemetagenome-assembled genomes (MAGs) that are representative of the microbes liv-ing in this special environment. Compared with freshwater bodies studied around theworld, Lake Baikal had an unusually high fraction of Verrucomicrobia. Other groups, suchas Actinobacteria and Proteobacteria, were in proportions similar to those found in otherlakes. The genomes (and probably cells) tended to be small, presumably reflecting theextremely oligotrophic and cold prevalent conditions. Baikal microbes are novel lineagesrecruiting very little from other water bodies and are distantly related to other freshwa-ter microbes. Despite their novelty, they showed the closest relationship to genomesdiscovered by similar approaches from other freshwater lakes and reservoirs. Some ofthem were particularly similar to MAGs from the Baltic Sea, which, although it is brack-ish, connected to the ocean, and much more eutrophic, has similar climatological condi-tions. Many of the microbes contained rhodopsin genes, indicating that, in spite of thedecreased light penetration allowed by the thick ice/snow cover, photoheterotrophycould be widespread in the water column, either because enough light penetrates orbecause the microbes are already adapted to the summer ice-less conditions. We havefound a freshwater SAR11 subtype I/II representative showing striking synteny with Pe-lagibacter ubique strains, as well as a phage infecting the widespread freshwater bacte-rium Polynucleobacter. 2026-05-05T11:28:27Z 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. 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. 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. 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. 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. 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. 2026-02-25T14:13:50Z