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A novel molecular approach for rapid assessment of soil nematode assemblages – variation, validation and potential applications
Article first published online: 19 AUG 2011
© 2011 The Authors. Methods in Ecology and Evolution © 2011 British Ecological Society
Methods in Ecology and Evolution
Volume 3, Issue 1, pages 12–23, February 2012
How to Cite
Donn, S., Neilson, R., Griffiths, B. S. and Daniell, T. J. (2012), A novel molecular approach for rapid assessment of soil nematode assemblages – variation, validation and potential applications. Methods in Ecology and Evolution, 3: 12–23. doi: 10.1111/j.2041-210X.2011.00145.x
- Issue published online: 1 FEB 2012
- Article first published online: 19 AUG 2011
- Received 5 April 2011; accepted 27 June 2011Handling Editor: Robert Freckleton
- soil monitoring;
- terminal-restriction fragment length polymorphism
1. Nematode assemblages are commonly used as an indicator of ecosystem health; however, conventional approaches to assemblage analyses are restricted by time-consuming processing and declining availability of expertise. Molecular methods offer a rapid and cost-effective alternative.
2. We have designed a molecular profiling system, using directed terminal-restriction fragment length polymorphism (dT-RFLP), to characterise nematode assemblages by relative abundance of feeding guilds.
3. An arable soil was first characterised by cloning and sequencing of small subunit ribosomal DNA, and an enzyme digest selected to discriminate between feeding guilds. This yielded 14 different terminal-restriction fragments (T-RFs) from the sequence set, assigned to five nematode feeding guilds.
4. Robustness of the dT-RFLP methodology was tested. The greatest amount of variation between replicates occurred at the PCR stage, with little variability between replicate digests from the same PCR product or capillary runs.
5. dT-RFLP revealed changes in assemblage composition owing to organic amendments of dairy-cattle slurry and municipal green compost. The proportion of microbial feeding nematodes was higher in compost and slurry plots than in the no amendment control in the first sampling after organic amendment. Plant feeding nematodes composed a significantly greater proportion of the control assemblage during the growing season and post-harvest.
6. The increased throughput of molecular analysis compared with microscopy increases the feasibility of studies involving large-scale sampling and makes nematode assemblage analysis more attractive as an indicator of soil health for environmental assessment.