Biology subjects

Rosado, A. S.

Publications and source records attributed to Rosado, A. S..

4 recordsLinked to original sources

bioRxiv2026

Leaf and root microbiome signatures of gray mangrove trees in the Red Sea

Mangroves persist under strong environmental constraints with support from microbes. Although microbial communities differ among mangrove compartments, their assembly mechanisms and compartment-specific functional signatures remain poorly resolved. Here, we combine peptide nucleic acid-clamping coupled with 16S rRNA gene amplicon sequencing and genome-resolved metagenomics to investigate the microbial communities associated with the leaves and roots of gray mangrove trees in the Red Sea. Our results suggest homogeneous selection and homogenizing dispersal as key processes of microbial community assembly in leaves. This phyllosphere hosts novel prokaryotic lineages, with some of its members probably synthesizing rhodopsins, plant polysaccharide-degrading enzymes, and gamma-aminobutyric acid, a metabolite that increase tolerance to salinity stress. Genomes affiliated with Desulfobacterales and Sedimenticolaceae taxa are abundant belowground, suggesting complementary sulfur- and nitrogen-cycling capacities similar as occur in other blue-carbon ecosystems. Comparison with root-derived genomes from cordgrass revealed a host-driven selection of Sedimenticolaceae species with convergent metabolic profiles. Overall, this study provides an integrative view about the microbial biology of gray mangrove trees, offering foundational insights into the diversity, ecology, and predictive functionality of their aboveground-belowground microbiomes.

microbiology↗

bioRxiv2025

Plasmidome, resistome, and virulence-associated genes characterization of Acinetobacter johnsonii in NASA cleanrooms and a clinical setting.

Evidence shows persistence of non-spore-forming Acinetobacter johnsonii in high-stakes controlled and nutrient-limited environments. This study aims to explore the mechanisms underpinning such adaptability through a comprehensive genomic analysis of 22 isolates of A. johnsonii from NASAs Payload Hazardous Servicing Facility (PHSF) and one carbapenem-resistant strain (E154408A) from patient colonization in Ireland. Core-genome phylogeny revealed clustering of PHSF-originating isolates in a monophyletic clade divergent from the main species lineage. Species-wide virulence-associated genes and metabolic profiling indicated the unique presence in PHSF-originating isolates of two complete efflux pumps and of a conserved allantoin racemase, suggesting adaptability for multiple environmental stresses. Observed ubiquity of blaOXA in investigated genomes (n=112) and phenotypically-validated multidrug-resistant profile of E154408A strain highlight A. johnsoniis potential as antimicrobial resistance (AMR) reservoir. Plasmidome analysis suggested gain/loss events across the monophyletic population and potential AMR acquisition pathways. Genome-to-metagenome mapping identified genomic signatures of A. johnsonii in PHSF >10 years post initial isolation. ImportanceAcinetobacter johnsonii is increasingly recognized as an emerging human pathogen, with growing evidence of its ability to persist in controlled, high-stakes environments, posing risks as both persisting environmental contaminant and antimicrobial resistance (AMR) reservoir. Yet, gaps remain in our understanding of its AMR profile and the mechanisms that enable its enhanced environmental adaptability. This knowledge is necessary in contexts where biological cleanliness is a priority such as clinical settings and spacecraft assembly facilities cleanrooms, where contamination of hardware with terrestrial microorganisms is concerning. In this study, we aim to address some of key knowledge gaps by providing genomic insights into a rare multi-drug resistant clinical isolate and 22 NASA cleanroom isolates that persisted for over a decade in extremely clean conditions. Our findings will help evaluate the contamination risk of A. johnsonii in high-stakes environments and ultimately strengthen our ability to manage this microbial contaminant across terrestrial and extraterrestrial settings. HighlightsO_LICleanrooms-derived A. johnsonii genomes show favorable traits for increased adaptability C_LIO_LIGenomic signatures of A. johnsonii persisted in the cleanrooms for >10 years C_LIO_LIblaOXA is ubiquitously found in the genome of all A. johnsonii C_LIO_LIE154408A is the first patient colonization by carbapenem-resistant A. johnsonii in Europe C_LI

genomics↗

bioRxiv2025

Probiotic and postbiotic treatment in situ during a marine heat wave improves coral health and promotes specific metabolic and microbiome changes

Microbial therapies are emerging as promising tools for coral protection against heat stress, yet such application was not tested in situ. We tested two coral-derived probiotic consortia and their heat-killed counterparts (postbiotics) on bleaching Acropora cf. valida in the Red Sea during a marine heatwave. Over 15 days, both live and one of the heat-killed treatments maintained photosynthetic efficiency (Fv/Fm), whereas placebo-treated corals exhibited significant thermal stress-induced decline. 16S rRNA gene sequencing profiling showed enrichment of putatively beneficial genera (e.g., Terasakiispira spp., Pseudoalteromonas spp.), and untargeted metabolomics resolved treatment-specific metabolic signatures that differed among consortia and between live and inactivated formulations. These molecular fingerprints illuminate specific underlying protective mechanisms and host-microbiome interactions under heat stress. Together, our results position microbial therapies (probiotics and specific postbiotics) as field-validated, mechanism-informed interventions capable of minimizing impacts on corals during real-world thermal extremes and provide design cues for scalable deployment.

microbiology↗

bioRxiv2024

Bacterial inoculation manipulates the coral epigenome

Environmental shifts can cause epigenetic modifications in corals, which are associated with changes in gene expression and physiology, though it remains unclear if associated bacteria can also induce such changes. Here, we inoculated nubbins of the coral Pocillopora verrucosa with an opportunistic pathogen, Vibrio coralliilyticus, and/or a coral probiotic, Cobetia sp., and subjected the nubbins to heat stress. We show that pathogen exposure led to distinct DNA methylation changes compared to the control, probiotic, and co-inoculation groups. We also demonstrate that DNA methylation correlates with coral gene expression and highlight genes altered by pathogen inoculation that showed similar responses in their expression and methylation. Notably, the coral probiotic was able to mitigate specific epigenetic changes, which correlated with increased stress resilience and higher coral survival rates. Thus, bacterial-induced changes to the coral epigenome may instigate long-term changes in host resilience.

molecular biology↗