Biology subjects

Diez, B.

Publications and source records attributed to Diez, B..

3 recordsLinked to original sources

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↗