Biology subjects

Vazquez-Rosas-Landa, M.

Publications and source records attributed to Vazquez-Rosas-Landa, M..

4 recordsLinked to original sources

bioRxiv2026

Global biogeography of mangrove sediment microbiomes is structured by a conserved core and environmental selection

Mangrove sediments are globally important biogeochemical hotspots, yet the large-scale organization and assembly of their microbiomes remain poorly resolved. Here, we compiled and analysed 390 shotgun metagenomes from mangrove sediments across 43 sites worldwide to quantify how diversity, spatial turnover, and ecological processes structure microbial communities across environmental and geographic gradients. We identify a striking dual architecture in mangrove sediment microbiomes. A remarkably small and ubiquitous taxonomic core, representing a minor fraction of total richness but dominating community abundance, persists across continents, climatic regimes, and marine realms. This core is composed primarily of anaerobic microbial lineages associated with carbon, nitrogen, and sulfur cycling and shows limited spatial and environmental turnover. In contrast, the non-core fraction is highly diverse, responds strongly to climatic and edaphic gradients, and drives most biogeographic differentiation. Assembly-process modelling reveals that deterministic selection dominates global taxonomic turnover, with homogeneous selection stabilizing shared community components and heterogeneous selection promoting regional differentiation, while dispersal limitation plays a secondary role. Network analyses further show that core taxa occupy structurally central positions in microbial co-occurrence networks, supporting overall connectivity despite pronounced regional variation in peripheral community composition. Together, these results demonstrate that mangrove sediment microbiomes combine a conserved functional backbone with an environmentally responsive periphery. This organization reconciles global functional continuity with strong regional differentiation and provides a basis for anticipating microbiome responses to environmental change in mangrove ecosystems.

ecology↗

bioRxiv2024

CAMDA 2023: finding patterns in urban microbiomes

The Critical Assessment of Massive Data Analysis (CAMDA) addresses the challenge of effectively utilizing Big Data in life science. Serving as both a conference and a catalyst for research groups, CAMDA annually presents challenges that foster innovative solutions. For the Forensics CAMDA 2023 challenge, we analyzed 365 metagenomic samples from 16 cities worldwide to characterize their origin. The forensic challenge was addressed from two perspectives: using the reduced abundance OTU tables and employing functional annotations. To identify the most informative Operational Taxonomic Units, we fit negative binomial models ultimately reducing variables to 294. After OTU selection, we implemented supervised models and conducted 5-fold cross-validation (CV) with a 4:1 training-to-validation ratio in each scenario. Support vector classification (SVC) achieved the highest F1 score (0.96) for the abundance tables, accurately classifying most cities, although New York City (NYC) posed a challenge. Via functional profiles with Mifaser at level 4, we achieved the best functional classification using the Neural Network (NN) model. Additionally, to gain insight into further associations between bacterial distribution with other covariates, we applied Dirichlet regression over Escherichia, Enterobacter, and Klebsiella bacteria abundances. We considered climatic and demographic variables of the cities, observing that population increase is indeed associated with a rise in the mean of Escherichia while decreasing temperature is linked to higher proportions of Klebsiella. For replicability of the scripts, a Docker container and a Conda environment are available at the repository: GitHub:github.com/ccm-bioinfo/cambda2023.

bioinformatics↗

bioRxiv2024

Flooding patterns shape microbial community in mangrove sediments

BackgroundMangrove ecosystems located in the tropics and subtropics, are crucial for regulating global weather patterns and sequestering carbon. However, they face threats from human activities like altered water flow and deforestation. While the symbiotic relationship between mangrove trees and surrounding microbes are essential for their survival, the impact of human activity on these microbial communities remains incompletely understood. We investigated how microbial communities change in degraded mangrove ecosystems due to loss of hydrologic connectivity, aiming to elucidate consequences and inform restoration strategies. MethodsEmploying 16S rRNA sequencing, we analyzed samples of sediment cores from conserved, moderately degraded, and degraded mangrove sites across dry and flood seasons at three sediment depths. ResultsOur analysis identified 11,469 Amplicon Single Variant (ASVs), revealing diversity loss correlated with degradation levels. Notably, we observed shifts in microbial diversity within sediment layers, with conserved sites dominated by Vibrionaceae in upper layers, potentially indicating urban contamination. In moderate-degradation sites, seasonal patterns emerged, with Halomonas and Marinomonas dominating the dry season and Exiguobacterium thriving during flooding. Interestingly, a community mainly composed of Firmicutes persisted across all degradation scenarios in deeper sediment layers, suggesting potential for ecosystem restoration. Our findings provide insights into microbial responses to human-induced stressors and highlight the role of core microbial communities in guiding restoration efforts for degraded mangrove ecosystems.

microbiology↗

bioRxiv2019

Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation.

BackgroundIn bacteria, pan-genomes are the result of the evolutionary \"tug of war\" between selection and horizontal gene transfer (HGT). High rates of HGT increase the genetic pool and the effective population size, resulting in open pan-genomes. In contrast, selective pressures can lead to local adaptation by purging the variation introduced by HGT, resulting in closed pan-genomes and clonal lineages. In this study, we explored both hypotheses elucidating the pan-genome of Vibrionaceae isolates after a perturbation event in the endangered oasis of Cuatro Cienegas Basin (CCB), Mexico, and looking for signals of adaptation to the environments in their genomes.\n\nResultsWe obtained 42 genomes of Vibrionaceae distributed in six lineages, two of them did not showed any close reference strain in databases. Five of the lineages showed closed pan-genomes and were associated to either water or sediment environment; their high effective population size (Ne) estimates suggest that these lineages are not from a recent origin. The only clade with an open pan-genome was found in both environments and was formed by ten genetic groups with low Ne, suggesting a recent origin. The recombination and mutation estimators (r/m) ranged from 0.0052 to 2.7249, which are similar to oceanic Vibrionaceae estimations; however, we identified 367 gene families with signals of positive selection, most of them found in the core genome; suggesting that despite recombination, natural selection moves the Vibrionaceae CCB lineages to local adaptation purging the genomes and keeping closed pan-genome patterns. Moreover, we identify 598 SNPs associated with an unstructured environment; some of the genes under this SNPs were related to sodium transport.\n\nConclusionsDifferent lines of evidence suggest that the sampled Vibrionaceae, are part of the rare biosphere usually living under famine conditions. Two of these lineages were reported by the first time. Most Vibrionaceae lineages of CCB are adapted to their microhabitats rather than to the sampled environments. This pattern of adaptation agrees with the association of closed pan-genomes and local adaptation.

evolutionary biology↗