TY - JOUR
T1 - Community structure, diversity, and species dominance of bacteria, fungi, and nematodes from naturally and conventionally farmed soil
T2 - a case study on Japanese apple orchards
AU - Matsushita, Yuko
AU - Bao, Zhihua
AU - Kurose, Daisuke
AU - Okada, Hiroaki
AU - Takemoto, Shuhei
AU - Sawada, Ayumi
AU - Nagase, Haruka
AU - Takano, Miho
AU - Murakami, Hiroharu
AU - Koitabashi, Motoo
AU - Yoshida, Shigenobu
AU - Saito, Masanori
AU - Sano, Teruo
AU - Tsushima, Seiya
N1 - Funding Information:
The authors are grateful to the owners of the Orchard-N and the Orchard-C. The authors are also grateful to Sho Morimoto, Yoriko Sakai, and Yumi Shimomura in qPCR analysis and Sunao Kikuchi in the analysis of total C, total N, and available PO-P. This study was supported by a Grant-in-Aid (Soil eDNA project) from the Ministry of Agriculture, Forestry and Fisheries of Japan. 4
Publisher Copyright:
© 2015, Springer Science+Business Media Dordrecht.
PY - 2015/3
Y1 - 2015/3
N2 - 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.
AB - 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.
KW - Microbial abundance
KW - Microbial community structure
KW - Microbial diversity
KW - Microbial dominant species
KW - Natural farming
KW - Soil chemical property
UR - http://www.scopus.com/inward/record.url?scp=84923774688&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84923774688&partnerID=8YFLogxK
U2 - 10.1007/s13165-015-0096-4
DO - 10.1007/s13165-015-0096-4
M3 - Article
AN - SCOPUS:84923774688
VL - 5
SP - 11
EP - 28
JO - Organic Agriculture
JF - Organic Agriculture
SN - 1879-4238
IS - 1
ER -