Biology subjects

Bustos, P.

Publications and source records attributed to Bustos, P..

6 recordsLinked to original sources

bioRxiv2026

Effects of neem extract on Artemia franciscana: insights from high-throughput transcriptomics and phenotypic analysis

Neem-derived biopesticides are increasingly applied in agriculture and have been tested in aquaculture research, yet their effects on non-target aquatic invertebrates remain insufficiently characterized. We evaluated the effect of neem extract on the brine shrimp Artemia franciscana using an integrated ecotoxicological approach combining phenotypic, transcriptomic, and histological analyses. Juvenile A. franciscana exhibited dose-dependent mortality and sublethal abnormalities, with a 24 h median lethal concentration of 292.48 mg/L (95% confidence interval, 257.75- 331.89) for mortality and a median effective concentration of 146.36 mg/L (95% confidence interval, 113.04-189.50) for the combined endpoint "abnormal + dead". In adults, males showed greater mortality than females after extended exposure. High-throughput RNA sequencing revealed broad treatment-associated differences in transcript abundance, with juveniles displaying downregulation of detoxification enzymes and chitin biosynthesis genes, alongside enrichment of immune- and cuticle-related gene ontologies. Adults showed transcriptional signatures of stress, including upregulation of heat shock proteins and cytoskeletal components, and suppression of genes involved in energy metabolism. Chitin precursor enzymes were selectively downregulated in males, and altered carbohydrate metabolism was observed in females. Histological analyses revealed structural deterioration of the brood sac cuticle and reduced ovarian area in treated females, consistent with transcriptomic evidence of impaired exoskeletal and reproductive processes. Overall, neem exposure was associated with phenotypic, histological, and transcriptomic changes in A. franciscana. These results support the use of combined transcriptomic and histopathological endpoints to characterize responses to plant-derived biopesticides in aquatic arthropods.

pharmacology and toxicology↗

bioRxiv2026

Stenotrophomonas oleivorans sp. nov. A polycyclic aromatic hydrocarbon-degrading strain isolated from crude oil contaminated soil

ASS1 was isolated as a motile Stenotrophomonas strain from crude oil-contaminated soils in Tabasco, Mexico. We characterized this strain using physiological and biochemical traits. ASS1 grew at temperature 25-37 (optimally at 37 {degrees} C) and at pH 6 to 8 (optimally at pH 7 to 8). The assembled genome has a total length of 4.56MB with a G + C content of 66.6%. The 16S rRNA gene sequence analysis confirmed that this strain belongs to the genus Stenotrophomonas. Based on the 16S rRNA analysis, Stenotrophomonas geniculata ATCC 19374 is the closest species, and it shares 99.86% similarity with ASS1. Similarly, a phylogenomic tree based on core genome sequence revealed that the closest species to ASS1 is Stenotrophomonas geniculata ATCC 19374. The major fatty acids in ASS1 are C16:0, antesio C15:0, iso C12:0, iso C15:0, iso C17:0 and C18:0. The genome of ASS1 consists of 4,373,402 bp. The Average Nucleotide Identity (ANI) values for ASS1 which it shared with its closest phylogenetic neighbors, are Stenotrophomonas geniculata ATCC 19374 = JCM 13324 [T] 92.66 %, Stenotrophomonas maltophilia 13637[T] 92.15%, Stenotrophomonas maltophilia K279a 92.13% Stenotrophomonas maltophilia R551-3 92.15% Stenotrophomonas maltophilia MTCC 434 [T] 92.08% and Pseudomonas hibisicicola ATCC [T] 91.66%. ASS1 possesses genes that are essential for the degradation of Polycyclic Aromatic hydrocarbon. Genes such as 1, 2 dihydroxyl 1, 2 dihydronaphthalene dehydrogenase; MG068 17425, homologous to 2 hydroxyl chromene 2 carboxylate isomerases; MG 18055, homologous to salicylaldehyde dehydrogenase and MG068 20095, homologous to naphthalene 1, 2 dioxygenases were identified in ASS1. The dDDH value between ASS1 and its closest neighbor Stenotrophomonas geniculata ATCC 19374 = JCM 13324 [T] is 50%, which is the highest for all the typed species and as such we proposed that ASS1 is a novel species with the name Stenotrophomonas oleivorans sp. nov. sp. nov. and ASS1T as the typed strain

microbiology↗

bioRxiv2025

Prophage and SaPI diversity in local clinical Staphylococcus aureus reveal hidden drivers of virulence.

Prophages are key drivers of bacterial evolution, genomic variability, virulence, and ecological adaptation. Here, we examined the prophage diversity of 109 Staphylococcus aureus clinical isolates from four tertiary care hospitals in Mexico City, integrating comparative analyses with 993 international genomes. Prophages were detected in 97% of the local strains, mirroring the near-ubiquitous presence (99%) observed globally. We identified 216 genomic regions encoding putative prophage functional elements. Using Mitomycin C induction, we recovered 17 temperate phages, 12 of which were functionally active and capable of lysogeny-lysis switching and reinfection. Induced phages lacked virulence or antibiotic resistance genes, in contrast to 55% of the predicted prophages in local S. aureus isolates that harbored known virulence factors. Moreover, 19% of the predicted prophages were phage-inducible chromosomal islands (PICIs) related to SaPI1, SaPI2, and SaPIpt1028. These PICIs encode anti-phage defense systems (63%) and virulence genes (27%), such as tsst-1 and hlb. Our findings reveal a complex prophage and PICI landscape in S. aureus circulating in Mexican hospitals, with implications for phage- host dynamics, horizontal gene transfer, and the evolution of pathogenic potential across geographically diverse populations. ImportanceStaphylococcus aureus is a major hospital pathogen whose evolution is driven by mobile genetic elements including prophages and phage-inducible chromosomal islands (PICIs). Although computational analyses predict prophages in nearly all S. aureus genomes, we demonstrate that only a small fraction is functionally active. Through experimental induction of clinical isolates from Mexican hospitals, we recovered active prophages that surprisingly lacked virulence genes, in contrast to the predicted prophages that frequently harbor virulence factors. Importantly, we discovered that many predicted "prophages" are PICIs carrying anti-phage defenses and toxins. These findings challenge the current prophage prediction methods and reveal the complex prophage-PICI landscape that shapes horizontal gene transfer and pathogenic evolution in clinical S. aureus populations.

microbiology↗

bioRxiv2025

Major antigenic differences in Aeromonas salmonicida isolates correlate with the emergence of a new strain causing furunculosis in Chilean salmon farms

Aeromonas salmonicida is the etiological agent of furunculosis, a septicemic disease with high mortality rates affecting salmonids and other teleost species worldwide. Reviewing molecular diagnostic protocols for routine diagnostics, we realized that the amplification of the vapA target gene failed in some cases of furunculosis. Therefore, we hypothesized that the emergence of a new strain may be involved in recent outbreaks. In this work, we demonstrate that the vapA locus is absent in the new strain, which explains why it lacks the major membrane component VapA protein, a critical virulence factor. In addition, we found that the vapA-absent strain differs from its counterparts in outer membrane protein and lipopolysaccharide profiles, suggesting profound changes at the membrane structure level and in antigenic properties. These features along with sequence analysis information allowed us to infer that a complex genomic rearrangement, probably an indel encompassing the entire vapA locus, gave rise to this membrane phenotype. Although the causes for pathogen evolution and emergence were not fully elucidated, our results strongly suggest that the vapA-absent strain is responsible for a raising proportion of recent furunculosis cases, and that it may be related to a less virulent disease and a low serological response upon vaccination with the A. salmonicida antigen formulation currently used in Chile.

microbiology↗

bioRxiv2023

The elite common bean Phaseolus vulgaris cultivar Pinto Saltillo hosts a rich and diverse array of plant-growth promoting bacteria in its rhizosphere.

The rhizosphere of crop plants is a nutrient-rich niche that is inhabited by many microorganisms. Root-associated microorganisms play a crucial role in crop yields in agriculture. Given the ample diversity of varieties and cultivars of the common bean (Phaseolus vulgaris) used in agriculture, it is important to characterize their bacterial communities. In this study, we analyzed the bacterial rhizosphere components of the bean cultivar Pinto Saltillo, which is widely produced and consumed in Mexico. Bulk soil and rhizosphere samples from the P. vulgaris cultivar Pinto Saltillo were collected in situ from plots with and without cultivation history. Metagenomic analysis revealed that in both plots, the bacterial diversity in the bulk soil exceeded that in the rhizosphere. Moreover, diversity and taxonomic composition analysis confirmed the dominance of Proteobacteria in the rhizosphere. Comparisons with pairs of bulk soil-rhizosphere metagenomes of other cultivated plants (maize, wheat, tomato, cucumber, and the model plant Arabidopsis) indicated a pronounced rhizosphere effect of the cultivar Pinto Saltillo, particularly regarding the presence of bacterial genera already known as plant growth promoters, including Rhizobium. Metagenome-assembled genomes (MAGs) reconstructed from metagenomes confirmed a diverse set of species at the OTU level, closely related to this group of microorganisms. Our analysis underscores the association of R. sophoriradicis strains as the primary nodulating agent of common beans in the sampled agricultural fields. These findings imply that the success of common bean crops relies on microbial species that are still inadequately characterized beyond the established role of nitrogen-fixing bacteria. ImportanceSustainable agriculture is a long-term goal aimed at mitigating the impact of modern intensive and polluting agricultural technologies. Significant efforts are underway to understand the contributions of microorganisms to the health and productivity of crop plants. The common bean (Phaseolus vulgaris) is a domesticated leguminous plant native to Mesoamerica, that whose seeds provide sustenance for millions of people in America and Africa. Previous studies have illuminated the bacterial diversity of the rhizosphere microbiome in relation to plant resistance to pathogens and in the domestication process. These findings underscore the importance of investigating the bacterial rhizosphere communities in successful cultivars of the common bean. In this study, we demonstrate that the common bean cultivar Pinto Saltillo hosts a diverse array of plant-growth promoting bacteria in its rhizosphere. These findings suggest that the agricultural success of common bean cultivars could be attributed to the interplay between the plant and its rhizosphere bacterial community, rather than solely relying on nitrogen-fixing symbiosis.

microbiology↗

bioRxiv2020

Spatial patterns in phage-Rhizobium coevolutionary interactions across regions of common bean domestication

Bacteriophages play significant roles in the composition, diversity, and evolution of bacterial communities. Despite their importance, it remains unclear how phage diversity and phage-host interactions are spatially structured. Local adaptation may play a key role. Nitrogen-fixing symbiotic bacteria, known as rhizobia, have been shown to locally adapt to domesticated common bean at its Mesoamerican and Andean sites of origin. This may affect phage-rhizobium interactions. However, knowledge about the diversity and coevolution of phages with their respective Rhizobium populations is lacking. Here, through the study of four phage-Rhizobium communities in Mexico and Argentina, we show that both phage and host diversity is spatially structured. Cross-infection experiments demonstrated that phage infection rates were higher overall in sympatric rhizobia than in allopatric rhizobia except for one Argentinean community, indicating phage local adaptation and host maladaptation. Phage-host interactions were shaped by the genetic identity and geographic origin of both the phage and the host. The phages ranged from specialists to generalists, revealing a nested network of interactions. Our results suggest a key role of local adaptation to resident host bacterial communities in shaping the phage genetic and phenotypic composition, following a similar spatial pattern of diversity and coevolution to that in the host.

microbiology↗