Effect of organic, conventional and mixed cultivation practices on soil microbial community structure and nematode abundance in a cultivated onion crop

K Reilly, E Cullen, T Lola-Luz, D Stone, J Valverde, M Gaffney, N Brunton, J Grant, BS Griffiths

Research output: Contribution to journalArticle

19 Citations (Scopus)

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. CONCLUSION: Organic management increased microbial activity and diversity. Sequence data was indicative of differences in functional groups and warrants further investigation. c 2013 Society of Chemical Industry
Original languageEnglish
Pages (from-to)3700 - 3709
Number of pages10
JournalJournal of the Science of Food and Agriculture
Volume93
Issue number15
Early online date30 Apr 2013
DOIs
Publication statusPrint publication - Dec 2013

Fingerprint

onions
microbial communities
community structure
Nematoda
pest control
soil treatment
microbial activity
crops
soil ecology
soil
Actinobacteria
denaturing gradient gel electrophoresis
Allium cepa
organic production
plate count
fungi

Keywords

  • Biolog eco-plates
  • Community level physiological profile
  • Denaturing gradient gel electrophoresis
  • Microbial diversity
  • Organic agriculture

Cite this

Reilly, K ; Cullen, E ; Lola-Luz, T ; Stone, D ; Valverde, J ; Gaffney, M ; Brunton, N ; Grant, J ; Griffiths, BS. / Effect of organic, conventional and mixed cultivation practices on soil microbial community structure and nematode abundance in a cultivated onion crop. In: Journal of the Science of Food and Agriculture. 2013 ; Vol. 93, No. 15. pp. 3700 - 3709.
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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. CONCLUSION: Organic management increased microbial activity and diversity. Sequence data was indicative of differences in functional groups and warrants further investigation. c 2013 Society of Chemical Industry",
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Effect of organic, conventional and mixed cultivation practices on soil microbial community structure and nematode abundance in a cultivated onion crop. / Reilly, K; Cullen, E; Lola-Luz, T; Stone, D; Valverde, J; Gaffney, M; Brunton, N; Grant, J; Griffiths, BS.

In: Journal of the Science of Food and Agriculture, Vol. 93, No. 15, 12.2013, p. 3700 - 3709.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Effect of organic, conventional and mixed cultivation practices on soil microbial community structure and nematode abundance in a cultivated onion crop

AU - Reilly, K

AU - Cullen, E

AU - Lola-Luz, T

AU - Stone, D

AU - Valverde, J

AU - Gaffney, M

AU - Brunton, N

AU - Grant, J

AU - Griffiths, BS

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N2 - 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. CONCLUSION: Organic management increased microbial activity and diversity. Sequence data was indicative of differences in functional groups and warrants further investigation. c 2013 Society of Chemical Industry

AB - 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. CONCLUSION: Organic management increased microbial activity and diversity. Sequence data was indicative of differences in functional groups and warrants further investigation. c 2013 Society of Chemical Industry

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