Biology subjects

Diez, B.

Publications and source records attributed to Diez, B..

7 recordsLinked to original sources

bioRxiv2026

Polar Marine Microbial Communities as Reservoirs of Polyester Degrading Enzymes

BackgroundPolyethylene terephthalate (PET) is one of the most widely used plastics and a major contributor to marine pollution. While the diversity of PET hydrolases (PETases), which degrade PET into mono(2-hydroxyethyl) terephthalate (MHET), terephthalate (TPA) and ethylene glycol, has been documented in temperate and tropical waters, their potential presence in polar oceans remain unascertained. ResultsHere, we systematically screened polar and non-polar marine metagenomes using Hidden Markov models (HMM) generated using experimentally validated PETases. We identified >680 putative PETase-like sequences, with Antarctic and Arctic candidates enriched in high-fidelity motifs associated with PETase-like activity. Phylogenetic and structural analyses defined a high-confidence PETase-like clade comprising both Type I and Type II enzymes, differing in thermostability-related features and PET-binding motifs. Experimental assays confirmed polyesterase activity in 5/9 candidates from this clade, including polar-derived variants active at 14-25{degrees}C. Downstream enzymes for PET consumption were also widespread, detecting 209 putative MHET hydrolases and 442 TPA-catabolyzing enzymes. Further, we reconstructed 112 metagenome-assembled genomes (MAGs) carrying at least one PETase-like gene, more than half from polar datasets. Notably, 15 MAGs encoded multiple PETase-like enzymes, and 1 Antarctic MAG harbored a complete PETase-MHETase-TPA pathway, evidencing a fully integrated degradation potential in cold-adapted taxa. ConclusionsTogether, these results demonstrate that polar oceans act as previously overlooked reservoirs of taxonomically and functionally diverse plastic-degrading enzymes. The enrichment of PETase-like enzymes and downstream pathways in polar microbial communities expands the global biogeography of plastic biodegradation and highlights cold-active enzymes as promising candidates for developing low-temperature plastic bioremediation strategies.

bioinformatics↗

bioRxiv2025

Metabolic ecology, microbial community structure, and gene-centric metagenomics

Metabolic ecology includes predictions for biological rates from molecules to ecosystems, but despite the broad range of its scope, its applicability to metagenomes remains an open question. Here, we integrate metabolic ecology with principles of DNA shotgun sequencing to generate specific testable predictions for the metagenomic structure of microbial communities. We start by predicting a scaling relationship between population and assemblage abundance with genome size. This allows us to simplify DNA shotgun sequencing equations for the reads of a population and a gene. Then we derive the temperature dependence of population and assemblage abundance using the volume-temperature and abundance-volume rules and integrate them with simplified DNA sequencing equations to show that these predictions are compatible with a metagenomic framework. In addition, we derive predictions for the temperature dependence of the structure (abundance and richness) of genes and groups of related genes (e.g., metabolic pathways). To test our model, we provide some example data from human, aquatic, and terrestrial microbiomes from recent global projects. All predictions were supported by the observed data. Our model, derived from the integration of first principles, provides a mechanistic basis for variation in the structure of microbial community genomes in environmental and host-associated ecosystems.

ecology↗

bioRxiv2025

Global patterns of taxonomic and functional diversity in hot springs microbiomes

A reformulation of the metabolic theory of ecology has been proposed based on a derivation of the Eyring-Polanyi equation, leading to a reduced model with the form of a power-law with exponential cut-off (PLECO). Moreover, the recent integration of this new model and metagenomic DNA sequencing theory has led to the hypothesis that, given that temperature affects cell size and assemblage abundance, it should also affect the number of genes, metabolisms, and populations in a microbial community. In particular, for microbial communities, the model predicts that the diversity of taxa, their genes, and metabolisms should respond to temperature according to the PLECO model, and after scaling the data using the estimated parameters, all data should collapse into a single curve. To test these predictions, we use global hot springs microbial communities; geothermally heated environments that include aquatic and terrestrial habitats with large temperature gradients. We analyzed a global database (five continents) of 19 hot springs metagenomes covering a wide gradient of temperature (32-90{degrees}C). We found that the alpha diversity of taxa, genes, and their metabolisms decreases with temperature, in agreement with the predictions of the PLECO model. Further, after non-dimensionalization of the model, we derive a single nondimensional curve for taxa and functions. Finally, using general linear models, we analyzed the effects of pH, latitude, and substrate (soil, water, or both), in addition to temperature, to explain the observed diversity pattern. We find that they explain a lower proportion of the variance, but pH can explain up to half of the variance in global diversity in these ecosystems, indicating the need to include pH in the theory. Our study supports the hypothesis that temperature regulates the structure of community genomes.

ecology↗

bioRxiv2025

Temperature and pH universally govern protein diversity in hydrothermal spring communities, but they do so differently

A general understanding of how extreme temperature and pH might universally shape the evolution of protein variants is lacking. Importantly, while pH is differentially regulated in microbial compartments, temperature is not. We hypothesise that these variables may partly explain the within-genome variability in protein rates of single-celled organisms, since genes encode proteins allocated to different compartments. To test this hypothesis, we examine the number of unique sequence contributors assigned to a KEGG across species as a coarse proxy for accumulated evolutionary divergence. Under a naive null expectation, orthologs of equal abundance should be represented by a similar number of variants. We examine sequence diversity in 17 metagenomes from El Tatio geothermal field (Chile), spanning temperatures of 45-62 {degrees}C, and pH values of 7.2-9.3. At equal abundance, warmer temperature is weakly associated to more ortholog variants, while alkaline pH is associated to fewer (in the ranges examined). The inclusion of these variables in the model robustly improved the prediction of the community-level within-KO unique sequence contributors from metagenomic abundance. KO variant diversity in the periplasm was only significantly affected by pH increases, providing partial support to the compartment hypothesis.

evolutionary biology↗

bioRxiv2025

Plasmidome-defensome interactions drive adaptation of 'Fervidacidithiobacillus caldus' in natural and industrial extreme acidic environments

Plasmids are major drivers of microbial evolution, enabling horizontal gene transfer (HGT) and facilitating adaptation through the dissemination of relevant functional genes and traits. However, little is known about plasmid diversity and function in extremophiles. Fervidacidithiobacillus caldus, a meso-thermo-acidophilic sulfur oxidizer, is a key player in sulfur cycling in natural and industrially engineered acidic environments. Here, we present a comprehensive analysis of the plasmidome, and associated anti-mobile genetic element (anti-MGE) defense systems (defensome), across genomes of this species and metagenomes from diverse natural and industrial settings harboring F. caldus. We identified >30 distinct plasmids, representing five consistent replication-mobilization families. Plasmids ranged in size between 2.5-65 kb, with gene content and plasmid modularity scaling with element size and copy numbers inversely correlating with size. Plasmids carried variable numbers of hypothetical proteins and transposases, with annotated cargo genes reflecting functional differentiation by habitat. Defensome profiling revealed over 50 anti-MGE systems in sequenced F. caldus isolates, including diverse restriction-modification systems, CRISPR-Cas types IV-A and V-F, and widespread abortive infection and composite defense systems such as Wadjet, Gabija, and Zorya. In environmental populations, an inverse relationship was observed between defensome complexity and plasmidome abundance and diversity, underscoring a pivotal role of the host defensome in modulating persistence, compatibility, and overall plasmid diversity across F. caldus populations. Yet, other plasmids appeared decoupled from both host abundance and defensome complexity, suggesting potential host shifts, environmental persistence, or differential replication under suboptimal growth conditions for the host. Altogether, these findings reveal a modular, adaptive plasmidome shaped by selective pressures and host-plasmid-defensome interactions and positions plasmids as key contributors to adaptation, gene flow, and functional innovation in this extreme acidophile. ImportancePlasmids are key vehicles of gene exchange and adaptation in bacteria, yet their roles in extremophilic systems remain poorly understood. This study provides the first integrated view of the plasmidome and defense systems in Fervidacidithiobacillus caldus, a sulfur-oxidizing acidophile relevant to both natural biogeochemical cycling and industrial bioleaching. We uncover a rich plasmid diversity structured into modular families with variable cargo and backbone features and reveal their coexistence with complex anti-MGE defense repertoires. By combining genomic and metagenomic approaches, we expose principles of plasmid compatibility, persistence, and habitat-specific adaptation. These insights expand current knowledge of mobile genetic elements in extreme environments and provide a foundation for plasmid-based vector design and synthetic biology in acidophiles, with direct implications for biomining and environmental remediation in extreme environments.

genomics↗

bioRxiv2025

Fine-scale spatial patterns in hot springs mat bacterial communities

Some of the most widely recognized spatial scaling relationships in ecology include the species-area, the abundance-occupancy, and the community compositional similarity-geographic distance relationships. These patterns have been shown to emerge from common mechanisms, such as habitat heterogeneity and colonization-extinction dynamics, and are predicted by various ecological models and theories, including Island Biogeography, Metapopulation theory, and Neutral Theory of Biodiversity and Biogeography. These patterns have been studied in microbial communities at large-scale, but studies at fine grain and small extent are rare, despite at a fine-scale, emerging patterns can be tested with a higher resolution. In this study, we explored these macroecological patterns in bacterial communities inhabiting hot springs mats, which have been shown to exhibit fine-scale spatial heterogeneity in fundamental environmental parameters such as temperature. In three different localities, we sampled a grid with a heterogeneous temperature at a fine-scale, a small extent (approximately 150 cm2), and fine grain (each containing 30 cells spaced about 1 or 2 cm apart). Our findings revealed sublinear scaling for the species-area relationship, with similar parameters across localities, indicating a low rate of spatial species turnover. For the abundance-occupancy relationship, we observed increasing trends, meaning that species that occupied more patches were, on average, more abundant. Additionally, we identified a decay in community compositional similarity with distance in two of the localities, though with low parameter values, indicating minimal geographic isolation at this scale. These results are consistent with different models that predict that spatial ecological patterns arise from spatial heterogeneity, as different species can partition their niches in space and constitute an example of predictable spatial patterns at a fine scale.

ecology↗

bioRxiv2021

A general model for temperature-dependence in biology

At present, there is no simple, complete, and first principles-based model for quantitatively describing the full range of observed biological temperature responses. Here, we derive a theory exhibiting these features based on the Eyring-Evans-Polanyi theory governing chemical reaction rates, and which is applicable across all scales from the micro to the macro. Assuming only that the conformational entropy of molecules changes with temperature, we derive a theory for the temperature dependence which takes the form of an exponential function modified by a power-law. Our framework leads to six deductions applicable to any biological trait that depends on temperature, and elucidates novel aspects of universal temperature responses across the tree of life, from quantum to classical scales. All predictions are well supported by data for a wide variety of biological rates and steady states, from molecular to ecological scales and across multiple taxonomic groups. In addition, we provide novel explanations of several empirical relationships including optimal values in temperature response curves. One-Sentence SummaryWe derive a simple and universal formulae to characterize temperature responses of biological processes across the tree of life.

ecology↗