Dr Aimeric Blaud A.Blaud@napier.ac.uk
Lecturer
Analysing the effect of soil organic matter on bacterial communities using T-RFLP fingerprinting: different methods, different stories?
Blaud, A.; Diouf, F.; Herrmann, A. M.; Lerch, T. Z.
Authors
F. Diouf
A. M. Herrmann
T. Z. Lerch
Abstract
Soil microbial ecology needs robust tools to elucidate ecological questions, such as the impact of fertilisation on soil microbial communities. However, the methods and data analysis used can directly affect the biological conclusions. In this study, the sensitivity of terminal-restriction fragment length polyphorism (T-RFLP) to four restriction enzymes (RE), six peak area thresholds (PAT) from 0 to 10 % and two matrices (presence/absence and relative abundance) was assessed on soils subjected to eight different long-term amendments. The T-RFLP profiles were analysed using a three-step multivariate analysis approach: (i) cluster analysis and non-metric multi-dimensional scaling, (ii) ANOSIM and PERMANOVA and (iii) correlations. The application of organic and mineral fertilisers over 53 years changed the bacterial community composition regardless if the RE, PAT and matrix were used. However, the clustering of the community, the strength of these differences, the correlations with environmental variables and, subsequently, the biological conclusions varied with the use of RE, PAT and matrix. Hence, the bacterial community composition was found to be either highly sensitive to any changes in soil organic matter strongly correlated to C and N concentration, or only affected by large inputs of C or soil management. Different REs can reveal different bacterial populations affected by different drivers, but PATs 0.5 and 1 % should be used especially when using presence/absence matrix. This study also shows the complexity of the effect of organic and mineral amendment on bacterial community composition and stresses the importance to inform on methodological and data analysis parameters.
Citation
Blaud, A., Diouf, F., Herrmann, A. M., & Lerch, T. Z. (2015). Analysing the effect of soil organic matter on bacterial communities using T-RFLP fingerprinting: different methods, different stories?. Biology and Fertility of Soils, 51(8), 959-971. https://doi.org/10.1007/s00374-015-1041-0
Journal Article Type | Article |
---|---|
Acceptance Date | Jul 10, 2015 |
Online Publication Date | Jul 24, 2015 |
Publication Date | 2015-11 |
Deposit Date | Nov 30, 2018 |
Publicly Available Date | Dec 4, 2018 |
Journal | Biology and Fertility of Soils |
Print ISSN | 0178-2762 |
Electronic ISSN | 1432-0789 |
Publisher | BMC |
Peer Reviewed | Peer Reviewed |
Volume | 51 |
Issue | 8 |
Pages | 959-971 |
DOI | https://doi.org/10.1007/s00374-015-1041-0 |
Keywords | Bacterial community composition, Soil organic matter, T-RFLP, ANOSIM, PERMANOVA RELATE , |
Public URL | http://researchrepository.napier.ac.uk/Output/1348541 |
Publisher URL | https://link.springer.com/article/10.1007/s00374-015-1041-0 |
Contract Date | Nov 30, 2018 |
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Analysing the effect of soil organic matter on bacterial communities
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Copyright Statement
This is a post-peer-review, pre-copyedit version of an article published in Biology and Fertility of Soils. The final authenticated version is available online at: https://doi.org/10.1007/s00374-015-1041-0
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