Rommel Thiago Jucá Ramos

The ability of the rhizosphere to recruit beneficial microorganisms is central to the sustainable management of crops. Here, we investigated, through shotgun metagenomic sequencing and mass spectrometry techniques, the microbial composition, antimicrobial resistance (AMRs), and metabolomic profiles of Piper nigrum cultivated under two support systems: living Gliricidia sepium support (SL/RL) and dead wooden support (SD/RD). Bulk and rhizosphere soils were sequenced to assess taxonomic structure and ARGs, with emphasis on Actinobacteria due to their relevance in antibiotic production. Actinobacteria were highly represented across the samples (~ 35%). Dead-support rhizospheres exhibited a broader ARG repertoire and greater abundance of taxa known to include antibiotic-producing members, whereas living-support rhizospheres showed reduced ARG diversity. Metabolomic analysis further revealed support-dependent physiological responses in the host plant. PLS-DA distinguished the two cultivation systems, and three defense-related flavonoids, such as sakuranetin, isovitexin, and orientin, which were enriched in fruits of plants grown with dead support, indicating activation of stress – and defense – associated metabolic pathways. Their low abundance in living-support plants suggests reduced physiological stress, likely linked to improved nutrient cycling and rhizosphere stability provided by G. sepium . However, the volatile and total phenolic profile did not display significant chemical alterations in the samples. Together, these results suggest that support type influences both microbial functions and plant secondary metabolism. Dead support creates a more stressful ecological context that enriches antimicrobial resistance genes ARGs and defense metabolites, whereas living support promotes a more balanced soil-plant-microbe environment, supporting the use of G. sepium as a sustainable and biologically advantageous cultivation strategy for black pepper.

Background: The spread of multidrug-resistant bacteria in water bodies poses a significant public health concern. Efflux pumps represent critical mechanisms of antimicrobial resistance, regulated by genetic repressors that aid bacterial adaptation to environmental stress. This study profiles the diversity of efflux pump genes and genetic repressors in the surface waters of the Cereja (Bragança) and Uraim (Paragominas) rivers in the Amazon region of Brazil. Methods and Results: Surface water samples were collected along a gradient of anthropogenic impact, and environmental DNA was sequenced on the Illumina platform. The resulting sequencing data were subsequently subjected to metagenomic analysis, which identified a higher abundance of efflux pump genes in the Cereja River compared to the Uraim River, dominated by the RND and SMR families. Additionally, two-component system (TCS) repressor genes, particularly cbrB , were successfully recovered and modeled using Swiss-Model homology modeling. Conclusions: The higher coverage of the cbrB repressor gene in anthropogenically impacted sites underscores its regulatory role in bacterial stress responses, suggesting its potential application as a novel biomarker of environmental pollution and antibiotic resistance spread in aquatic ecosystems.

Environmental monitoring of contaminated freshwater systems still lacks curated genomic resources tailored to bioremediation‐oriented screening. In this study, we developed a curated catalogue of 546 genes from 80 microbial species associated with heavy‐metal resistance, hydrocarbon degradation, detoxification and related functions and applied it to river metagenomes from four municipalities in Pará, Brazilian Amazon: Altamira, Bragança, Marabá and Paragominas. Functional annotation was performed using eggNOG‐mapper and metagenomic reads were aligned against the curated catalogue with Bowtie2. Mercury‐ and copper‐related genes were the most frequently represented functional categories across all river systems, a pattern that may reflect both sequence representation in the metagenomes and the unequal composition of the curated reference catalogue. Bragança showed the largest detected gene repertoire, whereas diversity, Jaccard, UpSet and Dunn‐based analyses revealed marked spatial heterogeneity and sites of localized functional enrichment. Recurrently associated bacterial taxa included Acinetobacter , Enterobacter , Pseudomonas , Stenotrophomonas , Cupriavidus and Sphingopyxis . These findings indicate that the catalogue provides a targeted genomic reference for environmental screening and bioprospecting, although metagenomic detection represents functional potential rather than experimentally confirmed remediation activity.

The environmental dissemination of antimicrobial resistance (AMR) through livestock waste represents a growing concern for human, environmental, and animal health. This study investigated how swine waste stabilization ponds (WSPs), and subsequent manure application to agricultural soils, influence bacterial community structure, antimicrobial resistance genes (ARGs), and mobile genetic elements (MGEs). Using shotgun metagenomics, we analyzed 80 samples from 20 swine farms, including waste collected before and after WSP treatment and soils with and without a history of manure application. Distinct microbial profiles were observed between waste and soil environments. Waste samples were dominated by Bacillota , Bacteroidota , and Pseudomonadota , whereas soils were enriched in Actinomycetota , particularly Streptomyces . WSP significantly reduced microbial diversity and caused shifts toward stress-tolerant taxa, indicating selective pressures during the process. Manure-fertilized soils exhibited altered community composition and enrichment of clinically relevant ARGs, including the fluoroquinolone resistance gene adeF . Waste management practices influenced resistome composition, with treated waste showing increased relative abundance of macrolide resistance genes ( ermB and mefA ). In soils, ARG profiles were associated with distinct MGE patterns, suggesting environment-specific mechanisms of gene mobility. Phage-associated elements were more prevalent in waste samples, whereas transposons were more prominent in soils, where ARG-MGE co-occurrence patterns indicated potential for horizontal gene transfer. Overall, our findings demonstrate that WSP management and soil application of swine manure shape both microbial communities and resistome configurations. These results underscore the importance of integrating waste treatment strategies into AMR surveillance frameworks and support a One Health approach to mitigate its dissemination in agroecosystems.

The Amazon rainforest represents nearly 40% of the world’s tropical forests and has undergone extensive conversion to pasture, profoundly altering soil microbial communities. Given that bacteriophage-driven selective pressure shapes bacterial defense systems (the defensome) as well as mobile genetic elements (MGEs), we examined the diversity and distribution of these genetic components in native forest soils and in pasture soils under two management regimes (with and without fertilization) in the Brazilian Amazon. Metagenomic sequencing revealed pronounced differences in bacterial community structure between forest and pasture sites ( R = 0.942), whereas phages communities exhibited no significant variation. Pasture soils—particularly those under fertilization—showed higher abundances of functional genes and mobile genetic elements, including conjugative plasmid-associated genes and insertion sequences. Defensome analyses indicated an increased prevalence of retrons and Pycsar systems in managed soils, while a greater diversity of defense genes was observed in non-fertilized pastures. A strong positive correlation was observed between defensome diversity and MGE diversity, suggesting coordinated dynamics between viral selective pressure and horizontal gene transfer. These findings indicate that forest-to-pasture conversion reshapes microbial functional potential and amplifies genetic mechanisms linked to phage defense and gene mobility, with potential consequences for ecosystem functioning and the dissemination of antimicrobial resistance.

Sargassum seaweed is increasingly abundant in the Caribbean, creating ecological disruption but also providing biomass for agricultural inputs. This study compares the microbial diversity and safety of a Sargassum ‐based liquid biofertilizer (SBLB‐INTEC) with those of a conventional product (LB‐BANELINO) using 16S rRNA amplicon sequencing, rather than culture‐dependent methods. Both formulations contained key nutrients (K, Ca, and Mg) and low levels of heavy metals. They harbored dense but relatively simple bacterial communities dominated by Firmicutes, particularly Bacilli, with Proteobacteria and other phyla at lower abundances. Staphylococcus (Staphylococcaceae) was highly abundant in both products, while SBLB‐INTEC showed a somewhat more balanced community, including Delftia and other Comamonadaceae. Shannon diversity tended to be higher in SBLB‐INTEC, but differences in alpha‐ and beta‐diversity between formulations were not statistically significant. Because 16S data cannot distinguish viable from nonviable cells or resolve strain‐level pathogenicity, these results do not prove the absence of pathogens; instead, they provide a genus‐level baseline to guide targeted culture, qPCR, and functional assays. Overall, the combination of a favorable chemical profile and microbial groups commonly associated with nutrient cycling and plant‐associated functions suggests that SBLB‐INTEC could become a valuable component of integrated nutrient management in tropical agriculture, offering hope for a more sustainable future pending confirmatory plant‐response and biosafety studies. We recommend integrating these microbial data into a national biofertilizer monitoring framework, combining metagenomic surveys with targeted qPCR and resistance gene screening.

This short communication presents novel molecular tools designed for the endangered species Brycon orbignyanus. In conservation studies, the development of population-specific markers tailored to particular geographic regions is essential. In this study, the prevalence of imperfect microsatellites highlights a evolution of this type of microsatellite in a population of Pelotas, Rio Grande do Sul. Therefore, the methodology used can serve as a guideline for genetic variability analysis even before conducting in vitro or in situ tests. These findings contribute significantly to technological prospecting and hold promise for applications in conservation programs. Additionally, they provide a basis for in vitro assays, such as PCR, to support species monitoring efforts.

This study investigated bacterial diversity in soils from six cacao-producing islands in Mocajuba, Pará, Brazil. Using next generation sequencing shotgun metagenomic DNA, we characterized the microbial composition and ecological structure of floodplain soils cultivated with Theobroma cacao. Taxonomic classification revealed a rich bacterial community encompassing 21 phyla, 54 classes, 121 orders, 240 families, 604 genera, and 2,289 species. The dominant phyla, Actinomycetota and Pseudomonadota, are known for their ecological roles in organic matter decomposition, antibiotic production, nitrogen cycling, and plant growth promotion. Alpha diversity metrics varied among samples, with P3 showing the highest species richness and P5 exhibiting the highest Shannon, Simpson, and evenness indices, suggesting a more balanced community. Beta diversity analysis based on Bray–Curtis dissimilarity under Total Sum Scaling (TSS) normalization revealed ecological gradients ranging from 0.228 to 0.527. Spatial ordination and hierarchical clustering indicated gradual shifts in community composition, supporting the concept of a compositional continuum shaped by environmental gradients. Functionally, Burkholderia lata was dominant in P1, reflecting its role in potassium solubilization, while Streptomyces species—detected in five of the six samples—contribute to biogeochemical cycling and pathogen suppression. Bradyrhizobium and Paraburkholderia, identified in P3, P5, and P6, are associated with nitrogen fixation and plant hormone regulation. These findings reveal the ecological complexity and functional potential of cacao soil microbiomes, providing insights for sustainable management of Amazonian floodplain agroecosystems.

The present study characterized the complete mitochondrial genome of Cynoscion acoupa, commonly referred to as the “pescada amarela”, being a member of the Sciaenidae family. C. acoupa are exploited for food consumption, and this causes a big impact in the populations. We used a NovaSeq Illumina sequencing to access the complete mitogenome of C. acoupa and perform a comparative investigation in molecular evolution. The mitogenome has 16,506pb, containing 13 protein-coding, 22tRNAs, and 2 rRNA genes. The average of the composition in the mitogenome was A: 26.56%, T: 29.46%, G: 33.26%, and C: 10.72%, with an AT content of 56.02%. Our phylogenetic analyses based on the 13 concatenated protein-coding genes of the mitogenome indicate that Cynoscion acoupa belongs to the family Sciaenidae and is positioned near the basal region of the phylogenetic tree, suggesting a shared ancestry among the analyzed taxa. These results confirm that the combined mitochondrial gene set serves as a reliable molecular marker for elucidating phylogenetic relationships within Sciaenidae.

Klebsiella variicola strain YSP4_INTEC was isolated from a Dominican Republic River and had its genome sequenced (size: 5,611,899 bp and GC content: 57.19%). The genomic analysis identified various genes involved in plant colonization mechanisms, plus a wide array of multi-drug, biocide, and multi-metal resistance genes.