Biology subjects

Paez-Watson, T.

Publications and source records attributed to Paez-Watson, T..

3 recordsLinked to original sources

bioRxiv2025

Stoichiometric analysis of microbial communities: interrelating community function, structure and biomass carrying capacity

Microbial communities carry out important ecological functions. Their activities emerge from complex interactions between species, often potentiated by metabolic traits. We lack a quantitative understanding of how these traits shape community properties. Here, we present the theory for microbial communities, leveraging concepts from quantitative microbial physiology. We derive formal conditions for the steady states of microbial communities. We express the relative abundances of species (living and dead), the net metabolic conversion of a community, and the biomass carrying capacity in terms of the metabolic stoichiometry of the species and their growth and death rates. We show how niche creation can emerge from stoichiometric imbalances in cross-feeding communities. Finally, we discuss how relative species abundances depend on the ATP stoichiometries of intracellular metabolism.

ecology↗

bioRxiv2025

Measuring Temporal Variations of Nucleotide Pools in Microbial Granular Biofilm Performing Enhanced Biological Phosphorous Removal

Microbial communities often face environmental fluctuations that occur on timescales much shorter than their growth rate or proteome turnover. In such cases, cellular responses are likely driven by rapid changes in metabolite pools, particularly energy nucleotides including ATP, ADP, and AMP. However, robust methods to quantify these metabolites in biofilm-forming microbial communities are lacking. Here, we developed and systematically evaluated a metabolomics workflow for a granular biofilm enrichment, which performs Enhanced Biological Phosphorous Removal (EBPR). We combined fast quenching in liquid nitrogen and a boiling water extraction, followed by high resolution mass spectrometry, using porous graphitic carbon chromatography and 13C-labeled internal reference standards. Among tested procedures, a boiling water extraction was most suitable for extraction of nucleotides, as indicated by stable adenylate energy charge (AEC) and isotopic ratios. Applied to an anaerobic-aerobic cycle of a lab scale EBPR system, the method revealed dynamic changes in AEC and uridylate energy charge (UEC) during acetate uptake and polyphosphate degradation. These results demonstrate that energy pool imbalances underlie rapid metabolic switching observed in EBPR systems. Moreover, the established method provides a foundation for performing metabolomic studies of microbial biofilms in general.

systems biology↗

bioRxiv2025

Metabolic implications for dual substrate growth in "Candidatus Accumulibacter"

This study explores the metabolic implications of dual substrate uptake in "Candidatus Accumulibacter", focusing on the co-consumption of volatile fatty acids and amino acids under conditions typical of enhanced biological phosphorus removal (EBPR) systems. Combining batch tests from highly enriched "Ca. Accumulibacter" cultures with conditional flux balance analysis (cFBA) predictions, we demonstrated that co-consumption of acetate and aspartate leads to synergistic metabolic interactions, lowering ATP loss compared to individual substrate consumption. The metabolic synergy arises from the complementary roles of acetate and aspartate uptake: acetate uptake provides acetyl-CoA to support aspartate metabolism, while aspartate conversion generates NADH, reducing the need for glycogen degradation during acetate uptake. We termed this type of metabolic interaction as reciprocal synergy. We further expanded our predictions to uncover three types of interactions between catabolic pathways when substrates are co-consumed by "Ca. Accumulibacter": (i) neutral, (ii) one-way synergistic and (iii) reciprocal synergistic interactions. Our results highlight the importance of network topology in determining metabolic interactions and optimizing resource use. These findings provide new insights into the metabolism "Ca. Accumulibacter" and suggest strategies for improving EBPR performance in wastewater treatment plants, where the influent typically contains a mixture of organic carbon compounds. SynopsisThis research demonstrates how dual substrate uptake by "Ca. Accumulibacter" enhances metabolic efficiency in EBPR by reducing global ATP losses through optimization of storage polymer usage.

systems biology↗