Biology subjects

Rinaldo, A.

Publications and source records attributed to Rinaldo, A..

7 recordsLinked to original sources

bioRxiv2025

Reactive persistence of riverine metapopulations

Understanding the conditions that favor the persistence of metapopulations inhabiting riverine landscapes (riverscapes) is critical to guiding conservation and restoration efforts aimed at preserving biodiversity and ecological integrity in freshwater environments. In this study, we present a modeling framework to examine the transient persistence of fluvial metapopulations---the temporary occupation of riverscape patches by a metapopulation expected to become extinct in the long run. Our approach is theoretically grounded in the concept of ecological reactivity, which effectively complements asymptotic stability analysis in the study of the short-term response of ecological systems to impulsive perturbations of otherwise stable steady states. Our results suggest that, under ecohydrological conditions conducive to reactive metapopulation extinction equilibria, a metapopulation asymptotically bound to extinction can still colonize parts of the riverscape for significant periods of time. We also find that, in the presence of repeated positive perturbations of the extinction equilibrium, the temporal scales associated with these transient phenomena may allow for reactive pseudo-persistence. This phenomenon involves an arbitrarily long delay in the eventual extinction of the metapopulation, which may occur well below the deterministic extinction threshold. Identifying the ecohydrological drivers of reactivity-driven metapopulation persistence and the riverscape patches that contribute most to transient metapopulation dynamics over different temporal scales may provide valuable suggestions for the spatial prioritization of conservation and restoration efforts.

ecology↗

bioRxiv2024

Impact of redox fluctuations on the spatial distribution of the microbial community in a forest soil: A lysimeter experiment

Climate change is expected to affect precipitation intensity and soil temperature and indirectly impact the release of leached dissolved organic carbon (LDOC) from leaf litter during the early stages of its decomposition, which could affect the health and function of forest soil ecosystem. Here, we experimentally investigate the spatially-explicit impact of LDOC on the forest soil microbiome and the associated biogeochemical processes. Homogenized soil columns were subjected to realistic artificial precipitation for 3 months with the initial level of LDOC adjusted by the number of times the leaf litter was flushed in preparation for the experiment. Hydrological and geochemical parameters (redox potential, pH, dissolved oxygen, soil moisture, matric potential, chemical speciation) were measured continuously as a function of time and depth. The same initial microbial community developed into distinct communities under different LDOC and above and below the water table. The LDOC from leaf litter increased the availability of carbon (C) and nitrogen (N) in porewater four-fold and two-fold respectively in the first two weeks. This resulted in the expansion of the anoxic zone above the water table and a decrease in the soil microbial metabolic potential for cellulolysis and N2 fixation in unsaturated soil along with an increase of soil microbial metabolic potential for fermentation at all depths. Finally, increased LDOC decreased the stability, phylogenetic diversity, and complexity of the soil microbiome, limiting its functional diversity. Thus, management of leaf litter should receive more attention due to its indirect role in the impact of climate change on the soil microbiome. HighlightsO_LIDecreased microbiome diversity and stability due to enhanced leaf litter leaching C_LIO_LIExpansion of the anoxic zone into the unsaturated zone due to increased organic carbon supply C_LIO_LIDecreased soil microbiome metabolic potential for cellulolysis and N2 fixation in unsaturated soil C_LIO_LIDepth-dependent response of microbial community to increased organic carbon availability C_LIO_LIImplications for soil response to climate change C_LI

microbiology↗

bioRxiv2023

Variability in single-cell oxygen consumption kinetics

We combined microfabricated devices with multiparameter identification algorithms to probe the variability in size-dependent oxygen consumption parameters of single human hepatic cells. We demonstrate that single cells exhibit an oxygen-dependent metabolic rate, typical of Michaelis-Menten kinetics, and that their maximal oxygen consumption is significantly lower than that of monolayers or 3D hepatic cell aggregates. Notably, we found that clusters of two or more cells competing for a limited oxygen supply reduced their maximal single-cell consumption rate, highlighting their ability to adapt to local resource availability and the presence of nearby cells. Next, we used our high-throughput approach to characterize the covariance of size and oxygen consumption within a cell population. The results show that cooperative behaviour emerges in cell clusters, and that single-cell size and metabolism can be described by a lognormal joint probability density. Our study thus serves as a foundation to connect the metabolic activity of single human hepatocytes to their tissue-or organ-level metabolism as well as describe its size-related variability through scaling laws.

bioengineering↗

bioRxiv2023

Emergent Ecological Patterns and Modelling of Gut Microbiomes in Health and in Disease

Recent advancements in next-generation sequencing have revolutionized our understanding of the human microbiome. Despite this progress, challenges persist in comprehending the microbiomes influence on disease, hindered by technical complexities in species classification, abundance estimation, and data compositionality. At the same time, recently the existence of macroecological laws describing the variation and diversity in microbial communities irrespective of their environment has been proposed using 16s data and explained by a simple phenomenological model of population dynamics. We here investigate the relationship between dysbiosis, i.e. in unhealthy individuals there are deviations from the "regular" composition of the gut microbial community, and the existence of macro-ecological emergent law in microbial communities. We first quantitatively reconstruct these patterns at the species level using shotgun data, offering a more biologically interpretable approach, and addressing the consequences of sampling effects and false positives on ecological patterns. We then ask if such patterns can discriminate between healthy and unhealthy cohorts. Concomitantly, we evaluate the efficacy of different population models, which incorporate sampling and different ecological and statistical principles (e.g., the Taylors law and environmental noise) to describe such patterns. A critical aspect of our analysis is understanding the relationship between model parameters, which have clear ecological interpretations, and the state of the gut microbiome, thereby enabling the generation of synthetic compositional data that distinctively represent healthy and unhealthy individuals. Our approach, grounded in theoretical ecology and statistical physics, allows for a robust comparison of these models with empirical data, enhancing our understanding of the strengths and limitations of simple microbial models of population dynamics. Author summaryIn this study, we explore emerging ecological properties in gut microbiomes. Our aim here is to determine whether these patterns can be informative of the gut microbiome (healthy or diseased) and unveil essential ingredients driving its population dynamics. Leveraging on phenomenological models of species abundance fluctuations and metagenomics data, we highlight the pivotal role of Taylors law, a straightforward mathematical relation, in constructing theoretical models for the human gut microbiome. We thus explore such a general theoretical framework for investigating microbiome composition and show that not all ecological patterns are informative to characterize its states, while few are (e.g., species diversity). Eventually, thanks to the ecological interpretability of the inferred models parameters, our analysis provides insights into the role of environmental fluctuations and carrying capacities of the gut microbiomes in both health and disease. This study offers valuable knowledge, bridging theoretical concepts with practical implications for human health.

ecology↗

bioRxiv2020

Generation and application of river network analogues for use in ecology and evolution

O_LISeveral key processes in freshwater ecology and evolution are governed by the connectivity inherent to dendritic river networks. These networks have extensively been analyzed from a geomorphological and hydrological viewpoint, yet network structures classically used in modelling have only been partially representative of the structure of real river basins, and have often failed to capture well known scaling features of real river networks. Pioneering work has identified optimal channel networks (OCNs) as spanning trees that reproduce all scaling features characteristic of real, natural stream networks worldwide. While these networks have been used to generate landscapes for studies on metapopulations, biodiversity and epidemiology, their generation has not been generally accessible. C_LIO_LIGiven the increasing interest in dendritic riverine networks by ecologists and evolutionary biologists, we here present a method to generate OCNs and, to facilitate its application, we also provide the R-package OCNet. Owing to the random search process that generates OCNs, multiple network replicas spanning the same surface can be built, allowing one to perform computational experiments whose results do not depend on the particular shape of a single river network. The OCN construct also enables the generation of elevational gradients derived from the optimal network configuration, which can constitute three-dimensional landscapes for spatial studies in both terrestrial and freshwater realms. Moreover, the OCNet package provides functions that aggregate the OCN into an arbitrary number of nodes, calculate several metrics and descriptors of river networks, and draw relevant features of the network. C_LIO_LIWe describe the main functionalities of the package and present how it can be integrated into other R-packages commonly used in spatial ecology. Moreover, we exemplify the generation of OCNs and discuss an application to a metapopulation model for an invasive riverine species. C_LIO_LIIn conclusion, OCNet provides a powerful tool to generate and use realistic river network analogues for various applications. It thereby allows the design of spatially realistic studies in increasingly impacted ecosystems, and enhances our knowledge on spatial processes in freshwater ecology in general. C_LI

ecology↗

bioRxiv2019

Allometric Scaling of physiologically-relevant organoids

The functional and structural resemblance of organoids to mammalian organs suggests that they might follow the same allometric scaling rules. However, despite their remarkable likeness to downscaled organs, non-luminal organoids are often reported to possess necrotic cores due to oxygen diffusion limits. To assess their potential as physiologically relevant in vitro models, we determined the range of organoid masses in which quarter power scaling as well as a minimum threshold oxygen concentration is maintained. Using data on brain organoids as a reference, computational models were developed to estimate oxygen consumption and diffusion at different stages of growth. The results show that mature brain (or other non-luminal) organoids generated using current protocols must lie within a narrow range of masses to maintain both quarter power scaling and viable cores. However, micro-fluidic oxygen delivery methods could be designed to widen this range, ensuring a minimum viable oxygen threshold throughout the constructs and mass dependent metabolic scaling. The results provide new insights into the significance of the allometric exponent in systems without a resource-supplying network and may be used to guide the design of more predictive and physiologically relevant in vitro models, providing an effective alternative to animals in research.

bioengineering↗

bioRxiv2018

Prawn aquaculture as a method for schistosomiasis control and poverty alleviation: a win-win approach to address a critical infectious disease of poverty

Recent evidence suggests crustacean snail predators may aid schistosomiasis control programs by targeting the environmental component of the parasites life cycle through predation of the snail species that serve as intermediate hosts of the parasite. We evaluate costs, benefits, and potential synergies between schistosomiasis control and aquaculture of giant prawns using an integrated bio-economic-epidemiologic model. We identified combinations of stocking density and aquaculture cycle length that maximize profit and offer disease control benefits for sustainable schistosomiasis control. We consider two prawn species in sub-Saharan Africa: the endemic, non-domesticated Macrobrachium vollenhovenii, and the non-native, domesticated Macrobrachium rosenbergii. We find that, at profit-optimal densities, both M. rosenbergii and M. vollenhovenii can complement conventional control approaches (mass drug treatment of people) and lead to sustainable schistosomiasis control. We conclude that integrated aquaculture strategies can be a win-win strategy in terms of health and sustainable development in schistosomiasis endemic regions of the world.

epidemiology↗