Biology subjects

Ayala-Ortiz, C. O.

Publications and source records attributed to Ayala-Ortiz, C. O..

4 recordsLinked to original sources

bioRxiv2026

Genome-scale metabolic models reveal phylogenetic conservation of amino acid fermentation-linked metabolic traits in soil bacteria

Soil microorganisms drive biogeochemical cycling of carbon, nitrogen, and other elements, but the partitioning of metabolic fluxes among taxa remains poorly understood, limiting our ability to link community composition to ecosystem function. Genome-scale metabolic models (GEMs) offer a mechanistic framework to connect taxa and their metabolic pathways to these fluxes. However, heterogeneity of soil communities has hampered recovery of high-quality metagenome-assembled genomes (MAGs), constraining application of flux balance analysis (FBA) to soil metagenomes and skewing available GEMs towards cultured model organisms. This gap limits our understanding of soil microbial physiology and responses to disturbance. Here, we present a collection of GEMs for 550 MAGs (497 bacterial, 53 archaeal) recovered from 94 soil samples across the continental United States. As an example application, we used FBA to estimate uptake and secretion of 44 commonly exchanged metabolites and tested whether these fluxes are phylogenetically conserved. While the overall bacterial phylogenetic signal was weak (median r = 0.029), eight metabolites showed significant conservation: amino acids (L-methionine, L-leucine, L-isoleucine), fermentation intermediates (pyruvate, acetaldehyde, ethanol), and amino acid degradation by-products NH and CO2. Most bacterial MAGs were predicted to import branched-chain amino acids, and a subset also secreted pyruvate and ethanol, identifying candidate cross-feeding interactions. Thus, fermentation-linked traits may be phylogenetically conserved and predictable from community composition, whereas most other metabolites showed no detectable signal. Ultimately, this resource enables genome-resolved prediction of soil microbial metabolisms, from cross-feeding and carbon-use efficiency to community responses to disturbance, providing a mechanistic bridge between microbial taxonomy and ecosystem-scale biogeochemistry.

bioinformatics↗

bioRxiv2026

Phytoplankton Dynamics and Urbanization Gradients Reshape Dissolved Organic Matter and Microbial Networks across a Freshwater Estuary

Freshwater estuaries process contaminants, cycle nutrients, and support biodiversity. However, watershed development degrades water quality, alters organic matter (OM) composition, and reshapes microbial and phytoplankton communities. Understanding how anthropogenic land use shapes estuarine ecosystem function remains a key challenge. We evaluated relationships among benthic and pelagic biogeochemistry, algal, and microbial communities across six sites along an urbanization gradient, combining FTICRMS characterization of water and sediment OM, with 16S and 18S rRNA gene amplicon sequencing of bacterial/archaeal and algal assemblages, alongside measurements of nutrients, ions, turbidity, temperature, phytoplankton biovolume, and land use. Pelagic OM and microbial variation tracked seasonal gradients and transient phytoplankton dynamics modulated by urban inputs, whereas sediments responded directly to urbanization: urban sediments were N-rich with protein, and amino-sugar-like OM, while rural sediments carried aromatic, terrestrial, plant-derived signatures. Both compartments showed non-linear responses, with microbial, algal, and OM abundances shifting abruptly across urbanization thresholds. Strong associations between sediment microbial dissimilarity and phytoplankton biovolume indicate benthic-pelagic coupling, whereby urban nutrients putatively stimulate phytoplankton growth and subsequent OM deposition restructures benthic assemblages. Thus, pelagic communities capture transient urban effects mediated by phytoplankton, whereas benthic communities integrate chronic impacts, highlighting the value of compartment-specific monitoring in estuarine ecosystems.

ecology↗

bioRxiv2025

Stochastic Assembly and Metabolic Network Reorganization Drive Microbial Resilience in Arid Soils

Microbial resilience plays a pivotal role in ecosystems as environmental fluctuations impact community functioning and stability. Despite resilience emerging from both individual adaptations and community-level processes, integration of these mechanisms remains enigmatic, particularly in arid environments. These extreme ecosystems, spanning over 45% of Earths terrestrial surface, provide a natural laboratory for understanding microbial survival under harsh conditions. Here, we use time-resolved multi-omics to show that resilience results from dynamic microbial network reorganization enabling the coordination between stochastic processes that maintain community stability, and individual stress responses. Additionally, Thermoproteota emerged as a keystone taxon maintaining nitrogen cycling and fostering cross- feeding networks. Its ecological prominence highlights its central role in arid ecosystems, making it an ideal model organism for understanding microbial adaptation to environmental extremes. Our findings bridge the gap between individual adaptations and community-wide resilience, offering a framework for understanding microbial responses to environmental fluctuations and their implications for ecosystem function.

microbiology↗

bioRxiv2022

MetaboDirect: An Analytical Pipeline for the processing of FTICR-MS-based Metabolomics Data

BackgroundMicrobiomes are now recognized as main drivers of ecosystem function ranging from the oceans and soils to humans and bioreactors. However, a grand challenge in microbiome science is to characterize and quantify the chemical currencies of organic matter (i.e. metabolites) that microbes respond to and alter. Critical to this has been the development of Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), which has drastically increased molecular characterization of complex organic matter samples, but challenges users with hundreds of millions of data points where readily available, user-friendly, and customizable software tools are lacking. ResultsHere, we build on years of analytical experience with diverse sample types to develop MetaboDirect, an open-source, command-line based pipeline for the analysis, visualization, and presentation of metabolomics data by direct injection FTICR-MS after molecular formula assignment has been performed. When compared to all other available FTICR software, MetaboDirect is superior with respect to its compute time as it only requires a single line of code that launches a fully automated framework for the generation and visualization of a wide range of plots, with minimal coding experience required. Among the tools evaluated, MetaboDirect is also uniquely able to automatically generate biochemical transformation networks (ab initio) based on mass differences that provide a comprehensive experimental assessment of metabolite connectives within a given sample or a complex metabolic system, thereby providing important information about the nature of the samples and the set of the microbial reactions or pathways that gave rise to them. Finally, for more experienced users, MetaboDirect allows users to customize plots, outputs, and analyses. ConclusionApplication of MetaboDirect to FTICR-MS-based metabolomics datasets from a marine phage-bacterial infection experiment and a Sphagnum leachate microbiome incubation experiment showcase the exploration capabilities of the pipeline that will enable the FTICR-MS research community to evaluate and interpret their data in greater depth and in less time. It will further advance our knowledge of how microbial communities influence and are influenced by the chemical makeup of the surrounding system. Source code and Users guide of MetaboDirect are freely available through (https://github.com/Coayala/MetaboDirect) and (https://metabodirect.readthedocs.io/en/latest/) respectively.

bioinformatics↗