Biology subjects

Morales, L. D.

Publications and source records attributed to Morales, L. D..

5 recordsLinked to original sources

bioRxiv2026

Freshwater Microbiomes Shape Viral Inactivation in Continuous Cultures

The high stability of enteric viruses in freshwater increases their risk of waterborne transmission. In aquatic environments, bacteria are known to enhance viral removal and inactivation. However, the differences in viral inactivation across freshwater ecosystems and the influence of community diversity on this process remains poorly understood. Here, we used dilution-to-extinction to generate 64 distinct freshwater communities from three lakes and three aquifers. After establishing freshwater communities in chemostat cultures, each community was challenged with two viruses, coxsackievirus B5 and human adenovirus 2. Both viruses were inactivated more rapidly in lake-derived than in groundwater-derived communities, and adenovirus was inactivated faster than coxsackievirus in both freshwater types. Community-level parameters (cell numbers, richness, evenness) were not significant predictors of viral inactivation. In contrast, differential abundance analyses identified bacterial OTUs associated with inactivation: Acidovorax sp. were associated across sources and Brevundimonas sp., Sphingopyxis sp., and Hydrogenophaga sp. showed source-specific associations. Together, these findings provide new insights into the ecological drivers of viral stability and suggest that viral inactivation may depend more strongly on specific microbial taxa and their ecological context than on overall community diversity. Identifying these associations improves our understanding of the factors governing viral persistence in freshwater environments.

microbiology↗

bioRxiv2026

Distinct kinetics and mechanisms of microbial inactivation of enteric virus revealed by capsid and genome integrity

Enteric viruses are important contaminants of surface waters and a significant burden on public health. In aquatic ecosystems, the stability of these pathogens is differentially impacted by abiotic and biotic stressors, which can exert inactivating effects. Here, we investigated the fate of two enteroviruses, echovirus 11 (E11) and coxsackievirus B5 (CVB5), and one adenovirus, human adenovirus 2 (HAdV2), in lakewater and explored the mechanisms underlying their microbial inactivation. By combining infectivity assays, genome quantification, and capsid integrity analysis, we characterized virus-specific inactivation kinetics and mechanisms and examined the relationship between infectivity loss and capsid structural integrity. We observed rapid, intermediate, and negligible decay for HAdV2, E11, and CVB5, respectively, and confirmed that microbial proteases contribute to their inactivation. In addition, we revealed that loss of capsid structural integrity drives E11 inactivation, but not HAdV2 inactivation. Genome decay did not consistently correlate with loss of infectivity, highlighting the limitations of genome-based detection for assessing the presence of infectious viruses. These findings provide new insights into the mechanisms governing virus inactivation in aquatic environments and emphasize the importance of understanding viral fate when interpreting molecular detection data to assess virus-associated microbial risks.

microbiology↗

bioRxiv2026

Burkholderia cenocepacia physiology and molecular adaptations to the acidic pH of the CF nutritional environment

Burkholderia cenocepacia is an opportunistic pathogen associated with increased disease severity and mortality in cystic fibrosis (CF) patients. We have previously shown that elevated iron and acidic pH in the CF nutritional environment increases B. cenocepacia growth rate and decreases its susceptibility to some of the antimicrobials used clinically to treat CF infections. Here, we aimed to characterize B. cenocepacia physiology and its molecular response under acidic pH and increased zinc and iron concentrations using a modified synthetic CF sputum media (SCFM-FeZn). By investigating B. cenocepacia internal pH homeostasis, we found that it maintains a neutral internal pH when exposed to mildly acidic media at pH 5.5. We also assessed the effect of B. cenocepacia growth on the pH of SCFM-FeZn. When cultured at pH 6.8, B. cenocepacia maintained a media pH of [~]6.5. In contrast, when the culture pH value was initially 5.5, it increased to 6.5 during growth. Using comparative transcriptomics and metabolomics analysis, we identified 990 differentially expressed genes, and 23 differentially abundant metabolites in supernatants at acidic compared to neutral pH. Some of these genes and metabolites were involved in aromatic amino acid metabolism including the upregulated trpE gene, encoding a tryptophan biosynthetic enzyme. A tryptophan auxotrophic trpE deletion strain grew slower in SCFM-FeZn. Overall, this work identifies mechanisms involved in B. cenocepacia adaptation to acidic pH under conditions to model the CF nutritional environment. Some of these mechanisms are also associated with pathogenicity and virulence. ImportancePathogenic bacteria can be exposed to acidic pH inside and outside the host. Their ability to adapt to pH fluctuations contributes to success in host colonization. B. cenocepacia can grow at acidic pH ([~]3.5) and has been recovered from intracellular acidic compartments of amoebas and macrophages. Adaptation to acidic pH depends on molecular mechanisms that maintain a near optimal pH inside the cell for the function of vital processes. A few mechanisms that contribute to its adaptation to acidic pH have been described, but not in conditions reflecting the CF nutritional environment. Here, we identified multiple differentially-regulated systems that are associated with bacterial susceptibility to antimicrobials and pathogenesis. This research provides a better understanding of the role of acidic pH on B. cenocepacia physiology in the CF nutritional context and highlights possible systems that should be further characterized.

microbiology↗

bioRxiv2026

A Capsid Tyrosine Residue Governs the Proteolytic Inactivation of Echovirus 11 in Lakewater

Enteroviruses are environmentally transmissible human pathogens whose stability in natural waters varies widely, yet the molecular determinants underlying this variability remain largely unknown. Echovirus 11 (E11), a re-emerging cause of severe neonatal infections, is efficiently transmitted via contaminated water, making its environmental stability a critical factor in infection risk. Here we identify a single viral capsid residue that governs E11 susceptibility to inactivation by extracellular microbial proteases in freshwater. By combining virus decay measurements in lakewater with proteolytic-cleavage profiling, viral capsid structural analyses, and reverse genetics, we show that the presence of VP2.Y97 renders E11 highly sensitive to microbially-mediated proteolytic decay. Strikingly, this residue is absent from multiple enteroviruses with greater environmental stability, indicating that substitution at a single capsid position is sufficient to shift virus fate in natural waters. These findings reveal that fine-scale capsid architecture controls virus-microbe interactions in aquatic environments and establish a molecular mechanism linking capsid variation to environmental transmission potential among enteroviruses.

microbiology↗

bioRxiv2023

Functional characterization of the disease-associated CCL2 rs1024611G-rs13900T haplotype: The role of the RNA-binding protein HuR

CC-chemokine ligand 2 (CCL2) is involved in the pathogenesis of several diseases associated with monocyte/macrophage recruitment, such as HIV-associated neurocognitive disorder (HAND), tuberculosis, and atherosclerosis. The rs1024611 (alleles: A>G; G is the risk allele) polymorphism in the CCL2 cis-regulatory region is associated with increased CCL2 expression in vitro and ex vivo, leukocyte mobilization in vivo, and deleterious disease outcomes. However, the molecular basis for the rs1024611-associated differential CCL2 expression remains poorly characterized. It is conceivable that genetic variant(s) in linkage disequilibrium (LD) with rs1024611 could mediate such effects. Previously, we used rs13900 (alleles: C>T) in the CCL2 3 untranslated region (3 UTR) that is in perfect LD with rs1024611 to demonstrate allelic expression imbalance (AEI) of CCL2 in heterozygous individuals. Here we tested the hypothesis that the rs13900 could modulate CCL2 expression by altering mRNA turnover and/or translatability. The rs13900 T allele conferred greater stability to the CCL2 transcript when compared to the rs13900 C allele. The rs13900 T allele also had increased binding to Human Antigen R (HuR), an RNA-binding protein, in vitro and ex vivo. The rs13900 alleles imparted differential activity to reporter vectors and influenced the translatability of the reporter transcript. We further demonstrated the role of HuR in mediating allele-specific effects on CCL2 expression in overexpression and silencing studies. Our studies suggest that the differential interactions of HuR with rs13900 could modulate CCL2 expression and could in part explain the interindividual differences in CCL2-mediated disease susceptibility.

genomics↗