The rhizosphere is a dynamic and highly interactive habitat where diverse microbial communities are established, and it plays crucial roles in plant health and disease dynamics. In this study, microbial communities and functional profiles in the rhizosphere of both asymptomatic and symptomatic apple trees were investigated through amplicon sequencing and shotgun metagenomics. The research was conducted at a location in the municipality of Cuauhtemoc, Chihuahua State, Mexico, and a total of 22 samples were collected, comprising 12 for amplicon sequencing and 10 for shotgun metagenomic sequencing. Symptomatic trees were identified based on reddish branches and internal necrosis in the trunk and root, while asymptomatic trees exhibited a healthy physiology. The findings showed that the dominant bacterial phyla included Proteobacteria, Actinobacteria, and Bacteroidetes, with prevalent genera such as Streptomyces, Pseudomonas, and Rhodanobacter. The fungal communities featured Ascomycota, Mortierellomycota, and Basidiomycota, which were dominated by Fusarium, Penicillium, and Mortierella. In the fungal communities, Mortierellomycota, notably abundant in asymptomatic trees, holds potential as a biocontrol agent, as seen in other studies on the suppression of Fusarium wilt disease. The application of shotgun metagenomic sequencing revealed significant differences in alpha and beta diversities in bacterial communities, suggesting a health-dependent change in species composition and abundance. Functional profile analysis highlighted enzymatic activities associated with lipid synthesis/degradation, amino acid biosynthesis, carbohydrate metabolism, and nucleotide synthesis, which have been documented to participate in symbiotic relationships between plants. These insights not only contribute to understanding the dynamics of rhizosphere microbial activity but also provide valuable perspectives on the potential application of microbial communities for tree health and implications for the management of apple orchards.

Heavy metal(loid) (HM) contamination in soils from smelting activities poses significant environmental and public health risks, as well as disruptions in microbial community dynamics and HM resistance gene profiles. This study investigates the microbial diversity, resistome, and physicochemical properties of soils from the abandoned Avalos smelter in Chihuahua, Mexico. Through soil analyses, we identified elevated concentrations of certain HMs, which pose serious environmental and health hazards. The metagenomic analysis of the microbial community, composed of bacteria, archaea, and fungi, was dominated by genera such as Streptomyces, Bradyrhizobium, Halobaculum, Nitrosocosmicus, Fusarium, and Aspergillus in rhizospheric soil. Furthermore, a diverse array of metal resistance genes (MRGs) were detected, associated with copper, arsenic, iron, lead, cadmium, zinc, and other HMs. Additionally, metagenome-assembled genomes (MAGs) revealed the presence of functional genes linked to HM resistance, providing deeper insights into the ecological roles and metabolic capabilities of microbial taxa. These findings highlight the significant impact of smelting-derived contamination on microbial diversity and functional potential, offering valuable insights for the development of bioremediation strategies in HM-contaminated environments.

The rhizospheric microorganisms of agricultural crops play a crucial role in plant growth and nutrient cycling. In this study, we isolated two Streptomyces strains, Streptomyces sp. LM32 and Streptomyces sp. LM65, from the rhizosphere of Vitis vinifera L. We then conducted genomic analysis by assembling, annotating, and inferring phylogenomic information from the whole genome sequences. Streptomyces sp. strain LM32 had a genome size of 8.1 Mb and a GC content of 72.14%, while Streptomyces sp. strain LM65 had a genome size of 7.3 Mb and a GC content of 71%. Through ANI results, as well as phylogenomic, pan-, and core-genome analysis, we found that strain LM32 was closely related to the species S. coelicoflavus, while strain LM65 was closely related to the species S. achromogenes subsp. achromogenes. We annotated the functional categories of genes encoded in both strains, which revealed genes involved in nitrogen and phosphorus metabolism. This suggests that these strains have the potential to enhance nutrient availability in the soil, promoting agricultural sustainability. Additionally, we identified gene clusters associated with nitrate and nitrite ammonification, nitrosative stress, allantoin utilization, ammonia assimilation, denitrifying reductase gene clusters, high-affinity phosphate transporter and control of PHO regulon, polyphosphate, and phosphate metabolism. These findings highlight the ecological roles of these strains in sustainable agriculture, particularly in grapevine and other agricultural crop systems.