Biology subjects

Barajas, H. R.

Publications and source records attributed to Barajas, H. R..

3 recordsLinked to original sources

bioRxiv2026

Programmed strain tagging and gene disruption throughout a diverse bacterial genus

Transposons are a convenient vehicle for inserting DNA into a bacterial genome, but widely-used transposons such as Tn7, Tn5, and Mariner do not hit custom targets. Recently, CRISPR-associated transposons (CASTs) have been developed as tools to direct the insertion of a transposon to a chosen site with a short guide sequence. We adapted this system for use in the widespread plant-associated genus Sphingomonas, uniquely tagging genetically diverse strains in several different sites, and we demonstrate the utility of the tags for quantitative strain tracking in complex bacterial populations. Although we initially targeted the conserved site into which Tn7 integrates as a benign transposition location, a genomics search revealed insertions at this site would frequently disrupt genes not only in Sphingomonas but also in widely studied Pseudomonas. Therefore we identified improved genus-wide conserved sites between convergently terminating genes as alternatives. We experimentally validated an improved neutral site in Sphingomonas, and then targeted this site in a heterogeneous uncharacterized Sphingomonas population. Using a tagIM seq, a novel rapid transposon mapping method introduced here, we screened resulting transformant colonies for off-target transposon insertions. This enabled prioritization of correctly tagged novel strains, accelerating the creation of fully tagged synthetic communities for the high-throughput study of fine-scale bacterial natural variation.

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

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↗