Community structure, diversity, and species dominance of bacteria, fungi, and nematodes from naturally and conventionally farmed soil: a case study on Japanese apple orchards

Yuko Matsushita, Zhihua Bao, Daisuke Kurose, Hiroaki Okada, Shuhei Takemoto, Ayumi Sawada, Haruka Nagase, Miho Takano, Hiroharu Murakami, Motoo Koitabashi, Shigenobu Yoshida, Masanori Saito, Teruo Sano, Seiya Tsushima

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

Although there has been much research on soil microbial communities in organic farming, little research has been reported on those in natural farming (no fertilizer use). Soil chemical properties and microbial and nematode communities in naturally (Orchard-N) and conventionally (Orchard-C) farmed apple orchards were compared over 3 years as a case study. The levels of nitrate nitrogen and available phosphate were significantly lower in Orchard-N than in Orchard-C. Bacterial evenness and nematode evenness and richness using denaturing gradient gel electrophoresis (DGGE) were higher in Orchard-N than in Orchard-C. All DGGE bands were identified by relative mobility values, termed relative front (Rf) values, and the Rf value of each band was classified into three dominant groups based on intensity: high, middle, and low intensities (HD, MD, and LD, respectively). Principal component analysis (PCA) on a correlation matrix showed that Orchard-N was characterized as MD/LD, corresponding to species of Alphaproteobacteria (bacteria), Actinobacteria (bacteria), Basidiomycota (fungi), Chaetomium (fungi), and Enoplea (nematodes). In contrast, Orchard-C was characterized by HD, corresponding to species of Gammaproteobacteria (bacteria), Fusarium (fungi), and Pratylenchus (nematodes), and MD/LD, similarly, Capnodiales (fungi) and Chloroflexi (bacteria). PCA on a variance–covariance matrix showed that annual changes in fungal and nematode community structures were larger in Orchard-C than in Orchard-N due to the large effect of HD. Quantitative polymerase chain reaction revealed that Orchard-N had higher bacterial and lower fungal abundance than Orchard-C. Based on these results, the relationship between the organism communities and the soil ecosystem in both orchards is discussed.

Original languageEnglish
Pages (from-to)11-28
Number of pages18
JournalOrganic Agriculture
Volume5
Issue number1
DOIs
Publication statusPublished - 2015

Keywords

  • Microbial abundance
  • Microbial community structure
  • Microbial diversity
  • Microbial dominant species
  • Natural farming
  • Soil chemical property

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)

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  • Cite this

    Matsushita, Y., Bao, Z., Kurose, D., Okada, H., Takemoto, S., Sawada, A., Nagase, H., Takano, M., Murakami, H., Koitabashi, M., Yoshida, S., Saito, M., Sano, T., & Tsushima, S. (2015). Community structure, diversity, and species dominance of bacteria, fungi, and nematodes from naturally and conventionally farmed soil: a case study on Japanese apple orchards. Organic Agriculture, 5(1), 11-28. https://doi.org/10.1007/s13165-015-0096-4