Microbial Diversity in the Phyllosphere and Rhizosphere of an Apple Orchard Managed under Prolonged “Natural Farming” Practices

Abstract

Microbial diversity in an apple orchard cultivated with natural farming practices for over 30 years was compared with conventionally farmed orchards to analyze differences in disease suppression. In this long-term naturally farmed orchard, major apple diseases were more severe than in conventional orchards but milder than in a short-term natural farming orchard. Among major fungal species in the phyllosphere, we found that Aureobasidium pullulans and Cryptococcus victoriae were significantly less abundant in long-term natural farming, while Cladosporium tenuissimum predominated. However, diversity of fungal species in the phyllosphere was not necessarily the main determinant in the disease suppression observed in natural farming; instead, the maintenance of a balanced, constant selection of fungal species under a suitable predominant species such as C. tenuissimum seemed to be the important factors. Analysis of bacteria in the phyllosphere revealed Pseudomonas graminis, a potential inducer of plant defenses, predominated in long-term natural farming in August. Rhizosphere metagenome analysis showed that Cordyceps and Arthrobotrys, fungal genera are known to include insect- or nematode-infecting species, were found only in long-term natural farming. Among soil bacteria, the genus Nitrospira was most abundant, and its level in long-term natural farming was more than double that in the conventionally farmed orchard.

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

“…In the organic samples, we identified more Sphingomonas , Burkholderia , and WD21-01 soil group than in organic mulches. Sphingomonas has been detected as one of the main genera, while Burkholderia as the top genus predominated in the apple rhizosphere [ 55 , 56 ]. The unclassified WD21-01 soil group has been determined as a hub of barley and the most frequent and differentially associated node, forming majorly negative associations in host-plant-specific interconnections.…”