Biology subjects

Alonso-Reyes, D. G.

Publications and source records attributed to Alonso-Reyes, D. G..

6 recordsLinked to original sources

bioRxiv2025

Echoes of 1816: Microbial Footprints in Heritage Artifacts From Argentina's Museum of Independence

Historical artifacts preserved in museums are invaluable cultural treasures, yet they are often vulnerable to biodeterioration caused by microbial colonization. This study presents the first comprehensive investigation of microbial communities inhabiting heritage artifacts from Argentinas Museum of Independence. By integrating advanced microscopy with phenotypic and genomic characterization, we analyzed samples collected from wooden objects, textiles, architectural elements, and exterior walls. Scanning electron microscopy revealed diverse and well-structured biofilms, with intricate three-dimensional arrangements embedded in extracellular polymeric substances. A total of 49 bacterial strains were isolated and identified via VITEK MALDI-TOF mass spectrometry, with a predominance of Gram-positive genera such as Bacillus, Micrococcus, and Kocuria. Remarkably, the 19th-century albumen print photograph emerged as the most biodiverse artifact, yielding 21 distinct strains, including Streptomyces, Oceanobacillus, and thermophilic Caldibacillus thermoamylovorans. The protein-rich and halophilic environment of the albumen layer likely facilitated microbial colonization and persistence. Pseudomonas species were exclusively associated with this photographic substrate, further underscoring its niche specificity. Human-associated taxa like Staphylococcus epidermidis and Staphylococcus equorum were prevalent in high-contact areas, while exterior surfaces displayed distinct microbial signatures, including potential pathogens linked to environmental exposure. These findings reveal a complex and artifact-specific microbial landscape, emphasizing the need for tailored, bio-informed conservation strategies. This work advances the field of heritage microbiology and supports efforts to safeguard culturally significant objects through a deeper understanding of their microbial ecosystems.

microbiology↗

bioRxiv2024

From Genes to Nanotubes: Exploring the UV-Resistome in the Andean Extremophile Exiguobacterium Sp. S17

Exiguobacterium sp. S17, a polyextremophile isolated from modern stromatolites in a High-Altitude Andean Lake, exhibits a remarkable multi-resistance profile against toxic arsenic concentrations, high levels of UV radiation (UV), and elevated salinity. Here, we perform a comprehensive characterization of the mechanisms underlying the UV resistance of S17 (UV-resistome/UVres) through comparative genomics within the Exiguobacterium genus. Additionally, we describe the morphological and ultrastructural changes in the strain when exposed to different levels of UV. UVres in Exiguobacterium species ranges from 112 to 132 genes, with a median of 117. While we anticipated Exiguobacterium sp. S17 to lead the non-HAAL UVres, it ranked eleventh with 113 genes. This larger UVres in Exiguobacterium spp. aligns with their known adaptation to extreme environments. Morphological and ultrastructural analyses using Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy (TEM) demonstrated significant changes in response to UV exposure in S17 cells. We observed the formation of nanotubes (NTs), a novel finding in Exiguobacterium spp., which increased with higher UV-B doses. These NTs, confirmed to be membranous structures through sensitivity studies and SEM/TEM imaging, suggest a role in cellular communication and environmental sensing. Genomic evidence supports the presence of essential NT biogenesis genes in S17, further elucidating its adaptive capabilities. Our study highlights the complex interplay of genetic and phenotypic adaptations enabling Exiguobacterium sp. S17 to thrive in extreme UV environments. The novel discovery of NTs under UV stress presents a new avenue for understanding bacterial survival strategies in harsh conditions.

ecology↗

bioRxiv2022

ARCHE: A HIERARCHICAL, EASY TO DOWNLOAD, FUNCTIONAL-OPTIMIZED ANNOTATOR FOR MICROBIAL META(GENOMES)

The growing amount of genomic data has prompted a need for less demanding and user friendly functional annotators. At the present, its hard to find a pipeline for the annotation of multiple functional data, such as both enzyme commission numbers (E.C.) and orthologous identifiers (KEGG and eggNOG), protein names, gene names, alternative names, and descriptions. In this work, we provide a new solution which combines different algorithms (BLAST, DIAMOND, HMMER3) and databases (UniprotKB, KOfam, NCBIFAMs, TIGRFAMs, and PFAM), and also overcome data download challenges. The software framework, Arche, herein demonstrated competitive results over Escherichia coli K-12 genome, the metagenome-assembled genome of Ferrovum myxofaciens S2.4, and a freshwater metagenome when compared to other annotators. Finally, Arche provides an analysis pipeline that can accommodate advanced tools in a unique order, creating several advantages regarding to other commonly used annotators.

bioinformatics↗

bioRxiv2022

DISSECTING LIGHT SENSING AND METABOLIC PATHWAYS ON THE MILLIMETER SCALE IN HIGH-ALTITUDE MODERN STROMATOLITES

Modern non-lithifying stromatolites (STs) on the shore of the volcanic lake Socompa in the Puna are affected by several extreme conditions. Although STs were proposed as ecologic models for understanding stress response and resilience in microbial ecosystems constituting a window into the past, our knowledge of ST function is still nascent. The present study assesses for the first time light utilization and functional metabolic stratification of STs on a millimeter scale through shotgun metagenomics. In addition, a scanning-electron-microscopy approach was used to explore the community. Our results demonstrated that Bacteroidetes and Cyanobacteria play major roles as ST builders and primary producers to sustain a diverse community of heterotrophs. STs manifest a high occurrence of genes for the synthesis of UV-protecting pigments, the cryptochrome-photolyase family (CPF), and rhodopsins in the surface layers. Three different ecologic niches involving the use of light in energy production were defined. Calvin-Benson and Wood-Ljungdahl pathways were proposed as the main mechanisms for carbon fixation. Several genes account for the microelectrode chemical data and pigment measurements performed in previous publications. We also provide here an explanation for the vertical microbial mobility within the ST described previously. Finally, our study points to STs as ideal modern analogues of ancient STs.

ecology↗

bioRxiv2020

Genomic Insights of an Andean Multi-resistant Soil Actinobacterium of Biotechnological Interest

Central Andean Ecosystems (between 2000 and 6000 masl) are typical arid to semiarid environments suffering from the highest total solar and UVB radiation on the planet but displaying numerous salt flats and shallow lakes. Isolated from these environments, Andean Microbial Communities (AME) of exceptional biodiversity endures multiple severe conditions. Also, the poly-extremophilic nature of AMEs microbes indicates the potential for biotechnological applications. In this context, the presented study used genome mining and physiological characterization to reveal the multi-resistant profile of Nesterenkonia sp. Act20, an actinobacterium isolated from the soil surrounding Lake Socompa, Salta, Argentina (3570 m). UV-B, desiccation, and copper assays showed the strains exceptional resistance to all these factors. Act20s genome presented coding sequences involving antibiotics, low temperatures, UV and arsenic resistance, nutrient limiting conditions, osmotic stress response, low atmospheric oxygen pressure, heavy metal stress, and resistance to fluoride and chlorite. Act20 can also synthesize proteins and natural products such as an insecticide, bacterial cellulose, ectoine, bacterial hemoglobin, and even antibiotics like colicin V and aurachin C. We also found numerous enzymes for animal and vegetal biomass degradation and application in other industrial processes. The herein report shed light on the microbial adaptation to high-altitude environments, its possible extrapolation for studying other extreme environments of relevance, and its application to industrial and biotechnological processes. HIGHLIGHTSO_LIArid Andean Soils are attractive sources of microbial strains useful in biotechnological processes. C_LIO_LIPhysiological studies revealed the multi-resistant nature of the poly-extremophile Nesterenkonia sp. Act20. C_LIO_LIAct20s genome analysis showed a complete set of genes coding for proteins involved in resistance to multiple stresses, including extremoenzymes and extremolytes. C_LI

genomics↗

bioRxiv2019

Unveiling The Worldwide UV-Metaresistome: Metagenomic Analysis of Microbiomes Exposed to Different UV-B Regimes

During evolution, microorganisms exposed to high UV-B doses developed a fine-tuned photo-enzymes called "photolyases" to cope with DNA damage by UV-B. These photoreceptors belonging to the Cryptochrome/Photolyase Family (CPF) were well characterized at the genomic and proteomic level in bacteria isolated from a wide range of environments. In this work, we go further towards studying the abundance of CPF on aquatic microbial communities from different geographic regions across the globe. Metagenomics data combined with geo-referenced solar irradiation measurements indicated that the higher the UV-B dose suffered by the microbiomes environment, the higher the abundance of CPF genes and lower the microbial diversity. A connection between CPF abundance and radiation intensity/photoperiod was reported. Likewise, cryptochrome-like genes were found abundant in most exposed microbiomes, indicating a complementary role to standard photolyases. Also, we observed that CPFs are more likely present in dominant taxa of the highly irradiated microbiomes, suggesting an evolutionary force for survival and dominance under extreme solar exposure. Finally, this work reported three novel CPF clades not identified so far, proving the potential of global metagenomic analyses in detecting novel proteins.

molecular biology↗