Biology subjects

Escalante, A. E.

Publications and source records attributed to Escalante, A. E..

7 recordsLinked to original sources

bioRxiv2025

Plant domestication does not reduce diversity in root microbiomes

O_LIDomestication has profoundly shaped the genetic makeup of numerous plant and animal species. While the effects of plant domestication at the genetic and phenotypic levels are well-documented, its impact on plant microbiome remains less understood. C_LIO_LITwo primary hypotheses have been proposed: 1) the reduction in microbial diversity resulting from the domestication process, and 2) the diminished ability of host plants to control their microbiomes. C_LIO_LIWe conducted a meta-analysis of multiple crops, comparing the root microbiomes of domesticated plants and their wild relatives. Our results indicate that the effects of domestication are species-specific and context-dependent, with most domesticated plants exhibiting increased microbial diversity and more structured communities. C_LIO_LIOverall, this study provides evidence that plant domestication does not lead to a uniform reduction in microbial diversity or a consistently diminished ability of plants to influence their microbiomes. C_LIO_LIBased on these findings, we discuss new perspectives and the need for future studies incorporating native soils and host genetic variation in such experiments, analyzing diversity and microbiome function, and considering how root morphology might affect microbiome recruitment. C_LI

ecology↗

bioRxiv2022

Variations in microbial diversity affect the stability and function of dark fermentation bioreactors

The relationship between the taxonomic diversity and the function of microbial communities is complex. Specifically, the ecological mechanisms that drive the dynamics of microbial populations and the consequences of these dynamics on functional traits have remained elusive. Among the simplest but natural microbial communities are dark fermentation consortia, a subset of the more diverse and complex microbial communities, anaerobic digestion communities. Dark fermentation consortia have been of interest as they produce biofuels such as hydrogen and different alcohols that can be used as fossil fuels alternatives. However, these hydrogen-producing communities have unresolved instability and low yield issues. We have previously proposed that instability and low yields in dark fermentation communities could be due to reduced diversity that results from aggressive pretreatments of original anaerobic digestion communities. In this work, we used dark fermentation communities to examine experimentally the effect of diversity reduction in functional traits, including stability and microbial interactions. We established two types of treatment, (i) maintaining strict culture conditions that are known to induce hydrogen production and ii) applying a heat-shock treatment known for selecting hydrogen-producing bacteria, which resulted in two types of communities, high and low diversity. Each treatment consisted of 12 replicates that were transferred to fresh medium daily (during 28 days for the non-treated bioreactors and 61 days for the heat-shock treated bioreactors). Microbial communities of the two treatments were characterized in their function as well as resistance to invasion. Microbial composition was characterized by culture-independent 16S rRNA gene amplicon sequencing. We analyzed microbial community composition and function through time, establishing statistical relationships between bacterial groups and metabolite production. Also, we inferred the potential ecological interactions that might have been established. Results show that the replicate bioreactors for each treatment predictably shifted to a similar composition and increased and stable biogas production. The non-treated bioreactors showed less susceptibility to the invasion (with the invasive bacteria establishing only in one replicate in the non-treated bioreactors vs 6 invaded replicates of the heat-shock treated bioreactors). However, the effect observed in the non-treated bioreactor replicate where the invader bacteria established was more drastic since the invasive bacteria managed to become dominant.

ecology↗

bioRxiv2021

The environment topography alters the transition from single-cell populations to multicellular structures in Myxococcus xanthus

The social soil-dwelling bacteria Myxococcus xanthus can form multicellular structures, known as fruiting bodies. Experiments in homogeneous environments have shown that this process is affected by the physico-chemical properties of the substrate, but they have largely neglected the role of complex topographies. We experimentally demonstrate that the topography alters single-cell motility and multicellular organization in M. xanthus. In topographies realized by randomly placing silica particles over agar plates, we observe that the cells interaction with particles drastically modifies the dynamics of cellular aggregation, leading to changes in the number, size and shape of the fruiting bodies, and even to arresting their formation in certain conditions. We further explore this type of cell-particle interaction in a minimal computational model. These results provide fundamental insights into how the environment topography influences the emergence of complex multicellular structures from single cells, which is a fundamental problem of biological, ecological and medical relevance.

biophysics↗

bioRxiv2021

THE UNAPPARENT EFFECT OF CLIMATE FORCING ON URBAN AMOEBIASIS IN MEXICO CITY

AO_SCPLOWBSTRACTC_SCPLOWDespite advances in the provision of sanitation infrastructure in cities, diarrheal-related illnesses continue to be a global burden. In cities of the developing world, explanations for the persistence of diarrheal-related diseases revolve around the role of sanitation, poverty, and individual behavior. Less is known about the role of climate in forcing the inter-annual variability of transmission. We quantified the contribution of rainfall to the transmission of a diarrhoeal disease caused by the protozoan Entamoeba histolytica. We formulated a process-based model of the population dynamics of Entamoeba histolytica in 6 municipalities of Mexico City, and we reconstructed the interannual variability of the observed cases of amebiasis between 2005 and 2012. Using inference methods for non-linear systems, we estimated that 10% of the susceptible individuals were infected in early 2005 and 90% of those infections were causally related to the exposure to the environmental stage of the pathogen after rainfall events. The magnitude of these results underscores the importance of considering the interaction between climate forcing and water management as ecological determinants of health in megacities.

ecology↗

bioRxiv2020

Evidence of anthropogenic perturbation in the genomic evolution of an environmental strain of Pseudomonas otitidis from Cuatro Cienegas, Coahuila, Mexico

Anthropogenic perturbations such as water overexploitation introduce novel selective pressures to the natural environments, impacting on the genomic variability of organisms and thus altering the evolutionary trajectory of its populations. Bad agricultural practices and defective policies in Cuatro Cienegas, Coahuila, Mexico, have strongly impacted its water reservoir, pushing entire hydrological systems to the brink of extinction together with their native populations. Here, we studied the effects of continuous water overexploitation on an environmental aquatic lineage of Pseudomonas otitidis, inhabitant to a particularly affected lagoon of an exhaustively studied system in the middle of the desert, over a 13 year period which encompasses three desiccation events. By comparing the genomes of a population sample from 2003 (original state) and 2015 (perturbed state), we analyzed the demographic history and evolutionary response of this bacterial lineage to the perturbation. Through coalescent simulations, we obtained a demographic model of contraction-expansion-contraction which, alongside an increment in mean Tajimas D and recombination rate, loss of genetic and nucleotidic variation and a single amino acid under positive selection, points the occurrence of an evolutionary rescue event, possibly potentiated by horizontal gene transfer, where the population nearly went extinct during the first desiccation event but sharply recovered in the second and adapted to its new environment. Furthermore, the gain of phosphorylation, DNA recombination and small-molecule metabolism and loss of biosynthetic and regulation genes on the exclusive accessory genome suggest a functional shift to a more generalist scavenger lifestyle in an environment that went from oligotrophic to nutrient-rich.

evolutionary biology↗

bioRxiv2019

Role of aggregate size, multistability and communication in determining cell fate and patterning in M. xanthus

1.The emergence of multicellular organisms that exhibit cell differentiation and stereotypic spatial arrangements has been recognized as one of the major transitions in evolution. Myxobacteria have emerged as a useful study model to investigate multicellular evolution and development. Here, we propose a multiscale model that considers cellular adhesion and movement, molecular regulatory networks (MRNs), and cell-to-cell communication to study the emergence of cell fate determination and spatial patterning of Myxococcus xanthus fruiting bodies. The model provides a dynamic accounting of the roles of MRN multistability, intercellular communication and conglomerate size in determining cell fate and patterning during M. xanthus development. It also suggests that for cell fate determination and patterning to occur, the cell aggregate must surpass a minimum size. The model also allows us to contrast alternative scenarios for the C-signal mechanism and provides stronger support for an indirect effect (as a diffusible molecule) than a direct one (as a membrane protein).

developmental biology↗

bioRxiv2018

Plastic multicellular development of Myxococcus xanthus: genotype-environment interactions in a physical gradient

In order to investigate the contribution of the physical environment to variation in multicellular development of Myxococcus xanthus, phenotypes developed by different genotypes in a gradient of substrate stiffness conditions were quantitatively characterized. Statistical analysis showed that plastic phenotypes result from the genotype, the substrate conditions and the interaction between them. Also, phenotypes were expressed with scale- and trait-specificity. Overall, the presented information highlights the constructive role of the physical context in the development of microbial multicellularity, with both ecological and evolutionary implications.

developmental biology↗