Biology subjects

Rodilla Ramirez, P. N.

Publications and source records attributed to Rodilla Ramirez, P. N..

3 recordsLinked to original sources

bioRxiv2026

From dynamic transcripts to stable proteins: multi-omics revealed regulatory buffering of Candidatus Accumulibacter under cyclic conditions

Enhanced biological phosphorus removal (EBPR) relies on polyphosphate-accumulating organisms that experience dynamic fluctuations in redox conditions and substrate availability. How these organisms regulate metabolism across molecular layers under cyclic operation remains incompletely understood. Here, we investigated molecular regulation in a long-term, stable aerobic granular sludge system dominated by Candidatus Accumulibacter. We combined metagenomics, time-resolved metatranscriptomics, and matched metaproteomics across three consecutive operational cycles. Genome-resolved metagenomics revealed an Accumulibacter-dominated community encoding canonical EBPR functions. Time-resolved metatranscriptomics revealed extensive and reproducible transcriptional dynamics affecting hundreds of genes. These dynamics did not align with discrete EBPR phases or instantaneous environmental transitions, but instead unfolded gradually over the cycle. Despite pronounced transcript-level heterogeneity, aggregation at the functional level revealed strong consolidation, with only a limited number of KEGG orthologs exhibiting coherent temporal regulation. Quantitative metaproteomics revealed a stable proteome across EBPR cycles, with no individual proteins or functional categories showing significant differential abundance despite direct transcript-protein mapping and time-matched sampling. This indicated that transcriptional dynamics did not translate into measurable changes in protein pool size on the time scale of individual cycles, consistent with slow, growth-coupled proteome turnover relative to cycle duration. Together, these results support a hierarchical model of regulation in Candidatus Accumulibacter, in which dynamic transcriptional responses are buffered at both the functional and protein levels. This organization provides a plausible basis for stable EBPR performance under predictable cyclic operation and demonstrates how time-resolved multi-omics can be used to resolve regulatory dynamics across molecular layers in engineered microbial ecosystems.

microbiology↗

bioRxiv2024

Multiple extracellular polymeric substances pathways expressed by Accumulibacter and the flanking community during aerobic granule formation and after influent modification

Aerobic granular sludge is a biological wastewater treatment process in which a microbial community forms a granular biofilm. The role of Candidatus Accumulibacter in the production of a biofilm matrix composed of extracellular polymeric substances was studied in a sequencing batch reactor enriched with polyphosphate-accumulating organisms. The metabolisms of the microbial populations were investigated using de novo metatranscriptomics analysis. Finally, the effect of decreasing the influent phosphate concentration was investigated. A few weeks after the reactor start-up, the microbial community was dominated by Accumulibacter. Up to nine species were active in parallel. However, the most active species differed according to sampling time. Reducing the phosphate concentration led to a dominance of the glycogen-accumulating organism Propionivibrio, with some Accumulibacter species still abundant. De novo metatranscriptomic analysis indicated a high diversity of potential extracellular substances produced mainly by Azonexus, Accumulibacter, Candidatus Contendobacter, and Propionivibrio. Moreover, the results suggest that Azonexus, Contendobacter and Propionivibrio recycle the neuraminic acid produced by Accumulibacter. Changes in the microbial community did not cause the granules to disintegrate, indicating that a Propionivibrio-dominated community can maintain stable granules.

microbiology↗

bioRxiv2021

The expression of virulence increases outer-membrane permeability and sensitivity to envelope stress in Salmonella Typhimurium

Environmental cues modulate the expression of virulence in bacterial pathogens. However, while cues that upregulate virulence are often intuitive and mechanistically well understood, this is less so for cues that downregulate virulence. In this study, we noticed that upregulation of the HilD virulence regulon in Salmonella Typhimurium (S.Tm) sensitized cells to membrane stress mediated by cholate, Tris/EDTA or heat. Further monitoring of membrane status and stress resistance of S.Tm cells in relation to virulence expression, revealed that co-expressed virulence factors embedded in the envelope (including the Type Three Secretion System 1 and the flagella) increased permeability, and stress sensitivity of the membrane. Importantly, pretreating the bacteria by sublethal stress inhibited virulence expression and restored stress resistance. As such, these results demonstrate a trade-off between virulence and stress resistance, which explains the downregulation of virulence expression in response to harsh environments in S.Tm.

microbiology↗