Exploring Microbial Rhizosphere Communities in Asymptomatic and Symptomatic Apple Trees Using Amplicon Sequencing and Shotgun Metagenomics

Abstract

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.

Whole Genome Analysis of Streptomyces spp. Strains Isolated from the Rhizosphere of Vitis vinifera L. Reveals Their Role in Nitrogen and Phosphorus Metabolism

“…Library concentration was quantified with Qubit dsDNA HS Assay kit (Thermo Fisher Scientific, Waltham, MA, USA) and the integrity of DNA libraries was assessed with the Bioanalyzer 2100 Agilent (NGS 1-6000 kit). Libraries were sequenced in an S4 flow cell in a 2 × 150 bp strategy on an Illumina NovaSeq 6000 sequencer (Illumina Inc., San Diego, CA, USA) [19].…”

Metagenomic Analysis for Unveiling Agricultural Microbiome

“…Disease Dynamics and Plant Health: In the research by Muñoz-Ramírez et al [15], the dynamics of microbial communities in the rhizosphere of both symptomatic and asymptomatic apple trees are explored, highlighting how shifts in microbial populations can influence plant health and disease outcomes. The interplay between fungal communities and pathogen suppression is presented in the study on soybean and maize intercropping by Cheng et al [16], where increased nitrogen-fixing bacterial diversity correlates with improved plant health.…”