Tree Root-Associated Microbial Communities Depend on Various Floor Management Systems in an Intensive Apple (Malus × domestica Borkh.) Orchard

Abstract

Regenerative 3agriculture prioritizes soil health to build up organic soil carbon and nitrogen stocks while supporting the active and diverse soil biota that is a prerequisite for maintaining crop productivity and quality in sustainable food production. This study aimed at unravelling the impact of organic and inorganic soil maintenance systems in a ‘Red Jonaprince’ apple (Malus × domestica Borkh.) orchard on soil microbiota biodiversity and soil physico-chemical properties. During our study, we compared seven floor management systems in terms of microbial community diversity. Fungal and bacterial communities on all taxonomic levels differed largely between systems that augmented organic matter (organic) and other tested inorganic regimes. The dominant phylum of the soil in all management systems was Ascomycota. The operational taxonomic units (OTUs) within the Ascomycota were largely identified as members of Sordariomycetes, followed by Agaricomycetes, and both dominated in organic systems versus inorganic. The most prominent phyla, Proteobacteria, accounted for 43% of all assigned bacteria OTUs. Gammaproteobacteria, Bacteroidia, and Alphaproteobacteria were predominant in organic samples, while Acidobacteriae, Verrucomicrobiae, and Gemmatimonadetes were more abundant in inorganic mulches.

Stochastic Processes Shape Bacterial Community Diversity Patterns along Plant Niche Gradients

“…In our study, changes in community assembly were influenced by the strength of stochastic processes rather than by deterministic processes (Figures 7 and 8). This contradicts the results of a previous study, in which community assembly across ecological niche gradients was strongly influenced by the degree of deterministic processes [43]. One possible explanation is that under extreme soil pH conditions, changes in soil nutrients do not dominate the community assembly process [44][45][46][47].…”

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

“…The apple tree (Malus domestica), a fruit species of great economic and agricultural importance, heavily relies on the interaction between tree roots and the microbial communities present in the rhizosphere. This microbial diversity and its functions have been the subject of increasing interest in the rhizosphere of several agricultural crops [4][5][6][7][8]. For instance, certain bacterial species can fix atmospheric nitrogen, making it available to plants, while others produce phytohormones that stimulate root development and enhance nutrient uptake [9][10][11].…”