Biology subjects

Cardona, L.

Publications and source records attributed to Cardona, L..

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↗

bioRxiv2020

Integrative analyses to investigate the link between microbial activity and molecules degradation during anaerobic digestion

Anaerobic digestion (AD) is a promising biological process which converts waste into sustainable energy. To fully exploit ADs capability, we need to deepen our knowledge of the microbiota involved in this complex bioprocess. High-throughput methodologies open new perspectives to investigate AD process at the molecular level, supported by recent data integration methodologies to extract relevant information. In this study, we investigated the link between microbial activity and substrate degradation in a lab-scale anaerobic co-digestion experiment, where bioreactors were fed with 9 different mixtures of three co-substrates (fish waste, sewage sludge, and grass). Samples were profiled using 16S rRNA sequencing and untargeted metabolomics. In this article, we propose a suite of multivariate tools to statistically integrate these data and identify coordinated patterns between groups of microbial and metabolic profiles specific of each co-substrate. Five main groups of features were successfully evidenced, including cadaverine degradation found to be associated with the activity of microorganisms from the order Clostridiales and the genus Methanosarcina. This study highlights the potential of data integration towards a comprehensive understanding of AD microbiota.

bioengineering↗