Biology subjects

Barreto, E.

Publications and source records attributed to Barreto, E..

6 recordsLinked to original sources

bioRxiv2025

Genome-Resolved Metagenomics Analysis of Rice Straw Degradation Experiments Unveils MAGs with High Potential to Decompose Lignocellulosic Residues

BackgroundRice is one of the top three crops that contribute 60% of the calories consumed by humans worldwide. Nonetheless, extensive rice harvesting yields more than 800 million tons of rice straw (RS) per year globally, generating a byproduct that is often difficult for farmers to manage efficiently without burning it. As a result, millions of tons of carbon dioxide and greenhouse gases are released, causing issues such as respiratory problems, soil degradation, and global warming. In this work, we explore the biological decomposition of RS through the application of microbial consortia from a metagenomics perspective. ResultsWe applied different treatments to RS placed in a mulching setup during experiments carried out in Colombian rice fields, using various combinations of a Trichoderma-based commercial product, the bacterial strain Bacillus altitudinis IBUN2717, inorganic nitrogen, and a mixture of potassium-reducing organic acids. Before inoculation and after 30 days of treatment, we characterized the microbial community on the RS surface and from the bulk soil by performing a reference-based compositional analysis, and reconstructing and functionally annotating Metagenome-Assembled Genomes (MAGs). High-quality MAGs with great potential to decompose RS, represented by the extensive number of carbohydrate-active enzymes, were recovered. Soil MAGs taxonomic classification indicates that they may represent potential novel microbial taxa. At the same time, the main part of the RS MAGs with superior lignocellulose-degrading capacity were affiliated under Actinomycetota and Bacteroidota phyla. Moreover, {beta}-glucosidase activity measurements indicated an increased RS degradation after the application of the treatment that included inorganic nitrogen. ConclusionsThis contribution underscores the possibility of promoting RS degradation through the application of biological strategies. Further, the newly unveiled MAGs with high RS-degrading potential provide a valuable resource for exploring the functional potential of previously uncharacterized microbial diversity in Colombian agricultural ecosystems, including microorganisms that have not been previously reported as remarkable lignocellulose decomposers. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/642948v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@bc3c35org.highwire.dtl.DTLVardef@14ce6aorg.highwire.dtl.DTLVardef@1fbb30aorg.highwire.dtl.DTLVardef@1a788ce_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

A probabilistic view of forbidden links: their prevalence and their consequences for the robustness of mutualistic networks

The presence in ecological communities of unfeasible species interactions, termed forbidden links, due to physiological or morphological exploitation barriers has been long debated, but little direct evidence has been found. Forbidden links are likely to make ecological communities less robust to species extinctions, stressing the need to assess their prevalence. Here, we used a dataset of plant-hummingbird interactions, coupled with a Bayesian hierarchical model, to assess the importance of exploitation barriers in determining species interactions. We found evidence for exploitation barriers between flowers and hummingbirds across the 32 studied communities, however, the proportion of forbidden links changed drastically among communities, because of changes in trait distributions. The higher the proportion of forbidden links, the more they decreased network robustness, because of constraints on interaction rewiring. Our results suggest that exploitation barriers are not rare in plant-hummingbird communities and have the potential to limit the rescue of species experiencing partner extinction.

ecology↗

bioRxiv2023

When cheating turns into a stabilizing mechanism of mutualistic networks

Mutualistic interactions, such as plant-mycorrhizal or plant-pollinator interactions, are widespread in ecological communities and frequently exploited by cheaters, species that profit from interactions without providing benefits in return. Cheating usually negatively affects the fitness of the individuals that are cheated on, but the effects of cheating at the community level remains poorly understood. Here we describe two different kinds of cheating in mutualistic networks and use a generalized Lotka-Volterra model to show that they have very different consequences for the persistence of the community. Conservative cheating, where a species cheats on its mutualistic partners to escape the cost of mutualistic interactions, negatively affects community persistence. In contrast, innovative cheating occurs with species with whom legitimate interactions are not possible, because of a physiological or morphological barrier. Innovative cheating can enhance community persistence under some conditions: when cheaters have few mutualistic partners, cheat at low or intermediate frequency and the cost associated with mutualism is not too high. In this case, the negative effects of cheating on partner persistence are over-compensated at the community level by the positive feedback loops that arise in mutualistic networks. Using an empirical dataset of plant-bird interactions, we found that observed cheating patterns are highly consistent with theoretical cheating patterns found to increase community persistence. This result suggests that the cheating patterns observed in nature could contribute to promote species coexistence in mutualistic communities, instead of necessarily destabilizing them.

ecology↗

bioRxiv2022

A Simple Model of Cortical Intraregional Metastability

Transient synchronization of bursting activity in neural networks, which occurs in patterns of metastable phase relationships between neurons, is a notable feature of network dynamics observed in vivo. However, the mechanisms that contribute to this dynamical complexity in neural circuits are not well understood. Local circuits in cortical regions consist of populations of neurons with diverse intrinsic oscillatory features. In this study, we numerically show that the phenomenon of transient synchronization, also referred to as metastability, emerges in an inhibitory neural population when the neurons intrinsic fast-spiking dynamics are appropriately modulated by slower inputs from an excitatory neural population. Using a compact model of a mesoscopic-scale network consisting of excitatory pyramidal and inhibitory fast-spiking neurons, our work demonstrates a relationship between the frequency of neural oscillations and the features of emergent metastability. In addition, a novel metric is formulated to characterize collective transitions in metastable networks. Finally, we discuss a blueprint to model the whole-brain resting-state dynamics using our scalable representation of intraregional network metastability.

neuroscience↗

bioRxiv2020

Itinerant complexity in networks of intrinsically bursting neurons

Active neurons can be broadly classified by their intrinsic oscillation patterns into two classes characterized by periodic spiking or periodic bursting. Here we show that networks of identical bursting neurons with inhibitory pulsatory coupling exhibit itinerant dynamics. Using the relative phases of bursts between neurons, we numerically demonstrate that the network exhibits endogenous transitions among multiple modes of transient synchrony. This is true even for bursts consisting of two spikes. In contrast, our simulations reveal that identical singlet-spiking neurons do not exhibit such complexity in the network. These results suggest a role for bursting dynamics in realizing itinerant complexity in neural circuits.

neuroscience↗

bioRxiv2019

A preliminary study of the cytotoxicity of the protein extract of Chrysobalanus icaco L. and Eugenia astringens Cambess., commercialized in markets

The use of plants and their products for medical treatment is very common procedure in Brazil, especially for treatment of diabetes. In fact, several plants can demonstrate hypoglycemic effects in vitro assays. However, the use for human treatment requires the knowledge of their toxicological properties. The aim of this study was to evaluate the effect of protein extracts of Chrysobalanus icaco collected from natural habitats and of Eugenia astringens acquired from the market of Rio de Janeiro on the viability and migration of fibroblasts. E. astringens has a similar morphology as C. icaco and it is sold as Chrysobalanus in a popular market in Rio de Janeiro. Being a different plant, E. astringens expresses different proteins, and its protein extract has proved to possess higher toxic properties than C. icaco does. Cytotoxicity assays indicated that, as the protein extract concentration increases, fibroblast viability decreases. Only the E. astringens extract displayed cytotoxicity at all concentrations, in addition to reduced fibroblast migration. The results obtained in this study demonstrates that its necessary integrative policies for rational use of medicinal plants and their commercialization, since the current use of medicinal plants may be inadequate and it is of great importance for Public Health.

plant biology↗