Microorganisms (Sep 2021)

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

  • Ying-Hong He,
  • Charith Raj Adkar-Purushothama,
  • Tsutae Ito,
  • Asuka Shirakawa,
  • Hideki Yamamoto,
  • Akiko Kashiwagi,
  • Ayumu Tatewaki,
  • Misato Fujibayashi,
  • Shuichi Sugiyama,
  • Katsuhiko Yaginuma,
  • Tomoya Akahira,
  • Shingen Yamamoto,
  • Seiya Tsushima,
  • Yuko Matsushita,
  • Teruo Sano

DOI
https://doi.org/10.3390/microorganisms9102056
Journal volume & issue
Vol. 9, no. 10
p. 2056

Abstract

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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.

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