title: Effect of organic, conventional and mixed cultivation practices on soil microbial community structure and nematode abundance in a cultivated onion crop.
abstract: BACKGROUND
  Responses of the soil microbial and nematode community to organic and conventional agricultural practices were studied using the Teagasc Kinsealy Systems Comparison trial as the experimental system. The trial is a long-term field experiment which divides conventional and organic agriculture into component pest-control and soil treatment practices. We hypothesised that management practices would affect soil ecology and used community level physiological profiles, microbial and nematode counts, and denaturing gradient gel electrophoresis (DGGE) to characterise soil microbial communities in plots used for onion (Allium cepa L.) cultivation.
  
  
  RESULTS
  Microbial activity and culturable bacterial counts were significantly higher under fully organic management. Culturable fungi, actinomycete and nematode counts showed a consistent trend towards higher numbers under fully organic management but these data were not statistically significant. No differences were found in the fungal/bacterial ratio. DGGE banding patterns and sequencing of excised bands showed clear differences between treatments. Putative onion fungal pathogens were predominantly sequenced under conventional soil treatment practices whilst putative soil suppressive bacterial species were predominantly sequenced from the organic pest-control treatment plots.
  
  
  CONCLUSIONS
  Organic management increased microbial activity and diversity. Sequence data was indicative of differences in functional groups and warrants further investigation.
authors: Teagasc Kinsealy Research Centre, Dublin, 17, Ireland; Horticulture Development Department, TFRCA, Ashtown, Dublin, 15, Ireland.
authors: Kim
authors: K
authors: Reilly
authors: Eileen
authors: E
authors: Cullen
authors: Theodora
authors: T
authors: Lola-Luz
authors: Dorothy
authors: D
authors: Stone
authors: Juan
authors: J
authors: Valverde
authors: Michael
authors: M
authors: Gaffney
authors: Nigel
authors: N
authors: Brunton
authors: James
authors: J
authors: Grant
authors: Bryan S
authors: BS
authors: Griffiths
mesh_terms: D000383:Agriculture / Q000379:methods*; D000818:Animals; D001419:Bacteria; D004269:DNA, Bacterial; D004271:DNA, Fungal; D058645:Denaturing Gradient Gel Electrophoresis; D017753:Ecosystem; D005658:Fungi; D009348:Nematoda; D019697:Onions; D058871:Organic Agriculture / Q000379:methods; D012987:Soil; D012988:Soil Microbiology
chemical_list: D004269:DNA, Bacterial; D004271:DNA, Fungal; D012987:Soil
keywords: Biolog Eco-plates; community level physiological profile; denaturing gradient gel electrophoresis; microbial diversity; organic agriculture