Biology subjects

Alcaraz, L. D.

Publications and source records attributed to Alcaraz, L. D..

14 recordsLinked to original sources

bioRxiv2026

Exploring protein duplication across Archaea genomes

Gene duplication is a major driver of genomic innovation, but whether paralog accumulation scales uniformly with increasing genome size across the domain Archaea remains unclear. This study presents a domain-wide analysis of 1,829 archaeal genomes and their predicted proteomes to evaluate protein family expansions, their distribution, and lineage-specific patterns of gene duplication. Protein family expansions were classified as recent (90% sequence identity), intermediate (70%), or old (40%) duplications based on sequence-identity thresholds within each family. The findings show that gene duplication content is decoupled from overall proteome size at high sequence-identity levels, indicating that recent paralog retention does not correlate with proteome expansion. Archaeal lineages exhibit contrasting gene duplication profiles. All 1,829 genomes contained paralogs at the 40% sequence identity threshold, indicating the widespread presence of ancient or divergent duplication events. In contrast, paralogs detected at the 90% identity threshold, showed substantial variation across lineages. Their proportion reached up to 16.6% in groups such as Halobacteria, whereas only 74 genomes (4.04%) completely lacked paralogs at this threshold. Highly duplicated families are enriched for membrane transport systems (ABC/MFS), central metabolic enzymes (e.g., acetyl-CoA synthetase), a high proportion of uncharacterized functions, and mobile elements, predominantly transposases. Notably, we identified 314 transposase protein families in Archaea, distributed in 161 unique families in Archaea and 153 families shared with Bacteria, suggesting mechanisms of interdomain gene transfer. Overall, paralog accumulation in Archaea is a lineage-specific phenomenon shaped by targeted functional duplications and mobile element activity, rather than a simple consequence of proteome growth.

genomics↗

bioRxiv2024

Rhizosphere Microbiome Influence on Tomato Growth under Low-Nutrient Settings

Studies have shown that reduced nutrient availability enhances microbial diversity around plant roots, positively impacting plant productivity. However, the specific contributions of rhizosphere microbiomes in nutrient-poor environments still need to be better understood. This study investigates the role of Plant Growth-Promoting Rhizobacteria (PGPR) in enhancing the growth of Solanum lycopersicum under hydroponic conditions. We hypothesised that nutrient limitation would increase the selection of beneficial bacterial communities, compensating for nutrient deficiencies. Our hydroponic system, with treatments consisting of 50% reduced fertiliser application supplemented with a soil-derived inoculum, exhibited greater bacterial diversity and biomass than controls, suggesting a successful enrichment of PGPR that compensates for nutrient deficiencies. Using 16S rRNA gene sequencing, we found a significant enrichment (p [≤] 0.001) and correlation with beneficial plant traits (p [≤] 0.05) of bacterial genera such as Luteolibacter, Sphingopyxis, and Kaistia. Shotgun metagenomics identified the critical role of Methyloversatilis in nitrogen fixation and other key taxa bacterial proteins in plant-bacteria interactions. Additionally, our findings identify core taxa across different cultivation systems. These results support the potential for microbiome engineering to enhance microbial diversity and plant productivity, offering a path to reduce fertiliser use in agriculture and improve sustainability.

genomics↗

bioRxiv2024

Microbial communities thriving in agave fermentations are locally influenced across diverse biogeographic regions

The production of traditional agave spirits in Mexico is a deeply rooted traditional process that relies on environmental microorganisms to ferment the cooked must from agave plants. Analysis of these microorganisms provides the opportunity to understand the dynamics of the microbial communities in the interface of natural and human-associated environments in a biologically and culturally rich region of the world. Here, we performed 16S and ITS amplicon sequencing of close to 100 fermentation tanks from 42 distilleries throughout Mexico. The Agave species used, production practices, climatic conditions, and biogeographic characteristics varied considerably among sites. Yet, we did find taxa present in most fermentations suggesting that there is a core of microorganisms that are hallmarks of these communities. These core taxa are represented by hundreds of OTUs showing large intra-specific variation. The only variable that was consistently associated with the composition of both bacterial and fungal communities was the distillery, suggesting that microbial composition is determined by the local production practices and unique attributes of each site. Fermentation stage, climate and producing region were also associated with the community composition, but only for prokaryotes. Analysis of microbial composition in several tanks within three distilleries also revealed taxa that were enriched in specific fermentation stages or agave species. Our work provides a comprehensive analysis of the microbiome of agave fermentations, contributing key knowledge for its management and conservation.

microbiology↗

bioRxiv2023

Unraveling the Genomic and Environmental Diversity of the Ubiquitous Solirubrobacter

2.Solirubrobacter, a genus within the Actinobacteriota phylum, is commonly found in soils and rhizospheres yet remains unexplored despite its widespread presence and diversity, as revealed through metagenomic studies. Previously recognized as a prevalent soil bacterium, our study delved into phylogenomics, pangenomics, environmental diversity, and bacterial interactions of Solirubrobacter. Analyzing the limited genomic sequences available for this genus, we uncovered a pangenome consisting of 19,645 protein families, with 2,644 constituting a strict core genome. While reported isolates do not exhibit motility, we intriguingly discovered the presence of flagellin genes, albeit with an incomplete flagellum assembly pathway. Our examination of 16S ribosomal genes unveiled a considerable diversity (3,166 operational taxonomic units OTUs) of Solirubrobacter in Mexican soils, and co-occurrence network analysis indicated its extensive connectivity with other bacterial taxa. Through phylogenomic analysis, we delved into the relatedness of sequenced strains and notably dismissed ASM999324v1 as a member of this genus. Our investigation extended to the metagenomic diversity of Solirubrobacter across various environments, affirming its pervasive presence in rhizospheres and certain soils. This broader pangenomic view revealed genes linked to transcription, signal transduction, defense mechanisms, and carbohydrate metabolism, highlighting Solirubrobacters adaptability. We observed that Solirubrobacters prevalence in rhizospheres is geographically indiscriminate, prompting intriguing questions about its potential interactions with plants and the biotic and abiotic determinants of its soil occurrence. Given its richness and diversity, Solirubrobacter might be a versatile yet overlooked keystone species in its environments, meriting further recognition and study. 3. Impact statementThis study explored the enigmatic world of Solirubrobacter, a widespread microbe commonly found in soils and plants across various regions. Despite its prevalence, little is known about its genetic diversity and functionality and how it thrives in diverse environments. Our research unveils the genetic secrets of Solirubrobacter, shedding light on its adaptability and ecological interactors and roles. We showed that Solirubrobacter environmental prevalence makes it a good candidate for studying the genetic basis of being a successful microbe associated with soil and plants. 4. Data summaryData, scripts and statistical analysis available in GitHub: https://github.com/genomica-fciencias-unam/Solirubrobacter Sequences, phylogenetic analysis, raw data structures: https://doi.org/10.6084/m9.figshare.24446521 16S rRNA gene raw data: https://www.ncbi.nlm.nih.gov/sra/PRJNA603586 https://www.ncbi.nlm.nih.gov/sra/PRJNA603590 Shotgun metagenomes: https://www.ncbi.nlm.nih.gov/bioproject/603603 All supporting data, code, and protocols are within the article, supplementary files, and described repositories.

genomics↗

bioRxiv2023

Comparative evaluation of bioinformatic tools for virus-host prediction and their application to a highly diverse community in the Cuatro Cienegas Basin, Mexico

The sheer diversity of unculturable viruses has prompted the need to describe new viruses through culture-independent techniques. The associated host is one important phenotypic feature that can be inferred from metagenomic viral contigs -- thanks to the development of various bioinformatic tools. Here we compare the performance of recently developed tools for virus-host prediction on a dataset of 1,046 virus-host pairs and then apply the best-performing tools on a metagenomic dataset derived from a highly diverse transiently hypersaline site known as Archaean Domes within the Cuatro Cienegas Basin, Coahuila, Mexico. We also introduce a virus-host prediction tool called CrisprCustomDB, which uses specific criteria to solve controversial host assignments with custom spacers databases. Host-dependent alignment-based methods showed an average precision of 83% and a sensitivity from 13.7% to 17.7%, whereas host-dependent alignment-free methods achieved an average precision of 75.7% and a sensitivity of 57.5%. RaFAH, a virus-dependent alignment-based tool, had the best performance overall (F1_score = 95.7%). However, when applied to the highly diverse metagenomic dataset, the host-dependent alignment-based (e.g., CrisprCustomDB) and alignment-free (e.g., PHP) methods showed the greatest agreement with each other, even though they are fundamentally different methods. This is because instead of depending on known hosts or viruses-with-known-host databases, they can directly relate metagenomic viral contigs and metagenome-assembled genomes from the same dataset. Such methods also showed the greatest consistency between the source environment and the predicted host taxonomy, habitat, lifestyle, or metabolism, revealing that Archaean Domes viruses likely infect halophilic Archaea as well as a variety of Bacteria which may be halophilic, halotolerant, alkaliphilic, thermophilic, oligotrophic, sulfate-reducing or marine-related. Consequently, using a combination of methods and qualitative validations relating to the source environment and the predicted host biology will increase the number of correct predictions, mainly when dealing with novel viruses.

bioinformatics↗

bioRxiv2023

A Study of Microbial Diversity in a Biofertilizer Consortium

Biofertilizers supply living microorganisms to help plants grow and maintain their health. In this study, we examine the microbiome composition of a commercial biofertilizer that has been proven to promote plant growth. Using ITS and 16S rRNA gene sequence analyses, we describe the microbial communities of the biofertilizer, with 182 fungal species and 964 bacterial genera identified. The biofertilizer contains a variety of microorganisms that had been reported to enhance nutrient uptake, phytohormone production, stress tolerance, and pathogen resistance in plants. Plant roots created a microenvironment that boosted bacterial diversity but filtered fungal communities. We propose using plant roots as bioreactors to sustain dynamic environments that promote the proliferation of microorganisms with biofertilizer potential. However, preserving the fungal-inoculated substrate is crucial to maintain fungal diversity in the root fraction. The study suggests that bacteria grow close to plant roots, while root-associated fungi may be a subset of the substrate fungi. These findings indicate that the composition of the biofertilizer may be influenced by the selection of microorganisms associated with plant roots, which could have implications for the effectiveness of the biofertilizer in promoting plant growth.

microbiology↗

bioRxiv2020

Passenger-surface microbiome interactions in the subway of Mexico City

Interaction between hands and the environment permits the interchange of microorganisms. The Mexico City subway is used daily by millions of passengers that get in contact with its surfaces. In this study, we used 16S rRNA gene sequencing to characterize the microbiomes of frequently touched surfaces, also comparing regular and women-only wagons. We also explored the effect of surface cleaning on microbial resettling. Finally, we studied passenger behavior and characterized microbial changes after traveling. Most passengers (99%), showed some type of surface interaction during a wagon trip, mostly with the hands (92%). We found microbiome differences associated with surfaces, probably reflecting diverse surface materials and usage frequency. The platform floor was the most bacterial diverse surface, while the stair handrail and pole were the least diverse ones. After pole cleaning, the resettling of microbial diversity was fast (5-30 minutes); however, it did not resemble the initial composition. After traveling, passengers significantly increased their hand microbial diversity and converged to a similar microbial composition among passengers. Additionally, passenger hand microbiomes resembled subway surfaces in diversity and also in the frequency of potentially pathogenic taxa. However, microbial fingerprints were preserved within passengers after traveling.

microbiology↗

bioRxiv2020

Testing the two-step model of plant root microbiome acquisition under multiple plant species and soil sources

The two-step model for plant root microbiomes considers soil as the primary microbial source. Active selection of the plants bacterial inhabitants results in a biodiversity decrease towards roots. We collected in situ ruderal plant roots and their soils and used these soils as the main microbial input for single genotype tomatoes grown in a greenhouse. We massively sequenced the 16S rRNA and shotgun metagenomes of the soils, in situ plants, and tomato roots. Tomato roots did follow the two-step model, while ruderal plants did not. Ruderal plants and their soils are closer than tomato and its soil, based on protein comparisons. We calculated a metagenomic tomato root core of 51 bacterial genera and 2,762 proteins, which could be the basis for microbiome-oriented plant breeding programs. The tomato and ruderal metagenomic differences are probably due to plant domestication trade-offs, impacting plant-microbe interactions.

microbiology↗

bioRxiv2019

Station and train surface microbiomes of Mexico City’s metro (subway/underground)

The metro is one of the more representative urban systems of Mexico City, and it transports approximately 4.5 million commuters every day. Large crowds promote the constant exchange of human and environmental microbes. In this study, we determined the bacterial diversity profile of the Mexico City subway by massive sequencing of the 16S rRNA gene. We identified a total of 50,197 operative taxonomic units (OTUs) and 1058 genera. The metro microbiome was dominated by the phylum Actinobacteria and by the genera Propionibacterium (15%) (P. acnes 13%), Corynebacterium (13%), Streptococcus (9%), and Staphylococcus (5%) (S. epidermidis; 4%), reflecting the microbe composition of normal human skin. The metro microbial sources were skin, dust, saliva, and vaginal, with no fecal contribution detected. A total of 420 bacterial genera were universal to the twelve metro lines tested, and they contributed to 99.10% of the abundance. The large OTUs number are probably reflecting the vast human influx, while selection from hosts and environments are constraining the genera diversity, shown by the OTUs to genus ratio. Finally, this study shows that the microbial composition of the Mexico City subway comes from a mixture of environmental and human sources and that commuters are exposed to normal human microbiota.

microbiology↗

bioRxiv2019

Genomic adaptations in information processing underpin trophic strategy in a whole-ecosystem nutrient enrichment experiment

Several universal genomic traits affect the capacity, cost, and efficiency of biochemical information processing underpinning metabolism and reproduction. We analyzed their role in mediating planktonic microbial community responses to nutrient enrichment in an oligotrophic, phosphorus-deficient pond in Cuatro Cienegas, Mexico--one of the first whole-ecosystem experiments involving replicated metagenomic assessments. As predicted assuming oligotrophy favors lower information-processing costs whereas copiotrophy favors higher processing rates, mean bacteria genome size was higher in the fertilized treatment, as were GC content, total number of tRNA genes, total number of rRNA genes and codon usage bias in ribosomal protein sequences. However, contrasting changes in trait variances also suggested differences between traits in mediating assembly under oligotrophic versus copiotrophic conditions. Tradeoffs in information-processing traits are apparently sufficiently pronounced to play a role in community assembly and all different components of metabolism-- information, energy, and nutrient requirements--are fine-tuned to an organisms growth and trophic strategy.

ecology↗

bioRxiv2019

Deep microbial community profiling along the fermentation process of pulque, a major biocultural resource of Mexico.

Some of the biggest non-three plants endemic to Mexico were called metl in the Nahua culture. During colonial times they were renamed with the antillan word maguey. This was changed again by Carl von Linne who called them Agave (a greco-latin voice for admirable). For several Mexican prehispanic cultures, Agave species were not only considered as crops, but also part of their biocultural resources and cosmovision. Among the major products obtained from some Agave spp since pre-hispanic times is the alcoholic beverage called pulque or octli. This beverage represents a precolumbian biotechnological development obtained by the natural fermentation of the mead (aguamiel) from such plants. The pulque played a central role in mexican prehispanic cultures, mainly the Mexica and the Tolteca, where it was considered as sacred. For modern Mexicans, pulque is still part of their heritage and, in recent times, there has been a renewed interest in this ancient beverage, due to its high content in nutrients such as essential amino acids. We focus this study in the microbial diversity involved in pulque fermentation process, specially because it is still produced using classic antique technologies. In this work, we report the microbiome of pulque fermentation stages, using massive sequencing of the 16S rRNA gene and the internal transcribed spacer (ITS) for describing bacterial and fungal diversity and dynamics along pulque production. In this study, we are providing the most diverse catalogue of microbes during pulque production with 57 identified bacterial genus and 94 fungal species, these findings allowed us to identify core microbes resilient during pulque production which point to be potential biomarkers exclusive to each fermentation stage.\n\nO_LIOur approach allowed the identification of a broader microbial diversity in Pulque\nC_LIO_LIWe increased 4.4 times bacteria genera and 40 times fungal species detected in mead.\nC_LIO_LINewly reported bacteria genera and fungal species associated to Pulque fermentation\nC_LI

microbiology↗

bioRxiv2019

Rhizosphere metagenomics of mine tailings colonizing plants: assembling and selecting synthetic bacterial communities to enhance in situ bioremediation

Mine tailings phytostabilization has been proposed as a bioremediation strategy to constrain the contaminants dispersion using plants to limit the effects of erosion. Rhizospheric bacteria impact plant health and facilitate plant establishment through their metabolic functions, which could be relevant in bioremediation strategies. We studied both culturable and metagenomic diversity or rhizospheric bacteria of mine tailings colonizing plants of an abandoned mine operation in Nacozari de Garcia, Sonora, Mexico. Diversity was described through amplification of the 16S rRNA gene and whole metagenome shotgun sequencing of both environmental and cultured rhizosphere associated microbes. The culturable bacteria were assembled in a synthetic community (SC; 235 bacteria genera). Subsequently, we performed an experimental evolution setup with the SC, selecting for heavy metal resistance, microbial competition, and the ability for growing in plant-derived nutrient sources. The selection experiment show that bacteria diversity decreases from the environmental culture-free microbiomes to the mine tailings rhizospheres and the experimental evolution outcome: the synthetic community (FSC; 43 bacteria genera). The rhizosphere communities shifted from the dominance of Actinobacteria in their environment to Proteobacteria in the cultivated consortia and the synthetic communities. Both environmental and cultured metagenomes contained plant-growth promotion, heavy-metal homeostasis, and antibiotic resistance predicted genes. The FSC included predicted proteins related to plant-growth promotion such as siderophore production and plant hormone regulation proteins. We reconstructed a metagenome assembled genomic sequence named Enterobacter sp., Nacozari. The recovered Enterobacter sp. Nacozari, have predicted coding genes for direct and indirect plant growth promotion along with adhesion and oxidative stress-related proteins. The metabolic potential of the FSC presents promising features that might make it useful for plant-growth promotion in tailored phytostabilization strategies for the abandoned mine-tailings of Nacozari.

genomics↗

bioRxiv2018

The lost world of Cuatro Cienegas Basin, a relictual bacterial niche in a desert oasis.

Barriers to immigration can lead to localized adaptive radiations and increased endemism. We propose that extreme oligotrophy can be a strong barrier to immigration over geological timescales, and facilitate the evolution of diverse and coevolved microbial communities. We show here that the endangered oasis of Cuatro Cienegas Basin can be a model for a lost world, where the ancient niche of extreme oligotrophy favoured survival of ancestral microorganisms that persisted due to environmental stability and low extinction rates, generating a diverse and unique bacteria diversity. Diversification/extinction rates in Bacillus showed several CCB endemic clades that diverged from the rest of Bacillus spp. in different times of the Paleozoic and Mesozoic, in contrast to more recent Bacillus, Clostridium and Bacteroidetes lineages. CCB conservation is vital to the understanding of early evolutionary and ecological processes.

evolutionary biology↗

bioRxiv2017

Marchantia liverworts as a proxy to plants basal microbiomes.

Microbiomes influence plant development, establishment, nutrient acquisition, pathogen defense, and the myriad of roles that ultimately impacts plant health. Plants microbiome are shaped through interactions between the microbes (ranging from cooperative functions to chemical warfare) and a selection process entailed by the host plants that distinguishes between pathogens, commensals, symbionts and transient bacteria. The soil is a primary source for microbes colonizing plants, along with other environmental sources including rain and interactions with other organisms. In this work, we explore the microbiomes through massive sequencing of the 16S rRNA gene in the eldest terrestrial plants: Marchantia liverworts. We compared microbiomes from M. polymorpha, and M. paleacea plants collected in the wild and their soils, all together luckily in the same geographical location (sympatric) thus reducing geographic effects; and also from plants grown in vitro and established from gemmae obtained from the same population of wild plants. Qualitative and quantitative microbiome analysis allowed us to identify microbes conserved in both native and in vitro Marchantia species. While M. polymorpha native plants microbiomes richness is reduced about M. paleacea, containing almost half of the Operative Taxonomic Units (OTUs) observed in M. paleacea, M. polymorpha grown in vitro exhibits larger OTUs. This diversity differences might be the result of impairment to recognize their microbial partners and being an open niche for opportunistic bacteria. The main OTUs in Marchantia microbiomes were assigned to the genera: Methylobacterium, Rhizobium, Paenibacillus, Lysobacter, Pirellula, Steroidobacter, and Bryobacter. The assigned genera correspond to bacteria capable of plant-growth promotion, complex exudates degradation, nitrogen fixation, methylotrophs, and disease-suppressive bacteria, all hosted in the relatively simple anatomy of the plant that provides refuge on their surfaces, rhizoids, and multiple gas chambers that work as specialized niches for different bacterial groups. Marchantia is a promising model to study not only long-term relationships between plants and their microbes but also the transgenerational impact of microbiomes because of Marchantia long 450 million years under climate change conditions testing microbiome configurations.

microbiology↗