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

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• 作者：Yuko Matsushita ; Zhihua Bao ; Daisuke Kurose ; Hiroaki Okada…
• 关键词：Natural farming ; Microbial community structure ; Microbial diversity ; Microbial dominant species ; Microbial abundance ; Soil chemical property
• 刊名：Organic Agriculture
• 出版年：2015
• 出版时间：March 2015
• 年：2015
• 卷：5
• 期：1
• 页码：11-28
• 全文大小：1,297 KB
• 参考文献：1. Acosta-Martinez, V, Dowd, S, Sun, Y, Allen, V (2008) Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biol Biochem 40: pp. 2762-2770 CrossRef
  2. Bissett, A, Richardson, A, Baker, G, Thrall, P (2011) Long-term land use effects on soil microbial community structure and function. Appl Soil Ecol 51: pp. 66-78 CrossRef
  3. Blaxter, ML, Ley, P, Garey, JR, Liu, LX, Scheldeman, P, Vierstraete, A, Vanfleteren, JR, Mackey, LY, Dorris, M, Frisse, LM, Vida, JT, Thomas, WK (1998) A molecular evolutionary framework for the phylum Nematoda. Nature 392: pp. 71-75 CrossRef
  4. Bongers, T (1999) The maturity index, the evolution of nematode life history traits, adaptive radiation and cp-scaling. Plant Soil 212: pp. 13-22 CrossRef
  5. Briar, S, Grewal, P, Somasekhar, N, Stinner, D, Miller, S (2007) Soil nematode community, organic matter, microbial biomass and nitrogen dynamics in field plots transitioning from conventional to organic management. Appl Soil Ecol 37: pp. 256-266 CrossRef
  6. Brussaard, L, Ruiter, P, Brown, G (2007) Soil biodiversity for agricultural sustainability. Agric Ecosyst Environ 121: pp. 233-244 CrossRef
  7. Buchan, D, Gebremikael, M, Ameloot, N, Sleutel, S, Neve, S (2013) The effect of free-living nematodes on nitrogen mineralisation in undisturbed and disturbed soil cores. Soil Biol Biochem 60: pp. 142-155 CrossRef
  8. Buee, M, Reich, M, Murat, C, Morin, E, Nilsson, R, Uroz, S, Martin, F (2009) 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytol 184: pp. 449-456 CrossRef
  9. Bulluck, L, Brosius, M, Evanylo, G, Ristaino, J (2002) Organic and synthetic fertility amendments influence soil microbial, physical and chemical properties on organic and conventional farms. Appl Soil Ecol 19: pp. 147-160 CrossRef
  10. Chapin, F, Zavaleta, E, Eviner, V, Naylor, R, Vitousek, P, Reynolds, H, Hooper, D, Lavorel, S, Sala, O, Hobbie, S, Mack, M, Diaz, S (2000) Consequences of changing biodiversity. Nature 405: pp. 234-242 CrossRef
  11. Crowder, DW, Northfield, TD, Strand, MR, Snyder, WE (2010) Organic agriculture promotes evenness and natural pest control. Nature 466: pp. 109-112 CrossRef
  12. Deruiter, P, Vanveen, J, Moore, J, Brussaard, L, Hunt, H (1993) Calculation of nitrogen mineralization in soil food webs. Plant Soil 157: pp. 263-273 CrossRef
  13. Ding, G, Piceno, Y, Heuer, H, Weinert, N, Dohrmann, A, Carrillo, A, Andersen, G, Castellanos, T, Tebbe, C, Smalla, K (2013) Changes of soil bacterial diversity as a consequence of agricultural land use in a semi-arid ecosystem. Plos One 8: pp. e59497 CrossRef
  14. Doran, J, Sarrantonio, M, Liebig, M, Sparks, D (1996) Soil health and sustainability. Adv Agron 56: pp. 1-54 CrossRef
  15. Drinkwater, LE, Letourneau, DK, Workneh, F, Bruggen, AHC, Shennan, C (1995) Fundamental differences between conventional and organic tomato agroecosystems in California. Ecol Appl 5: pp. 1098-1112 CrossRef
  16. Esperschuetz, J, Gattinger, A, Mader, P, Schloter, M, Fliessbach, A (2007) Response of soil microbial biomass
• 刊物主题：Agriculture; Life Sciences, general; Sustainable Development; Environment, general; Plant Sciences;
• 出版者：Springer Netherlands
• ISSN：1879-4246

文摘

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.