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Culture-independent analysis of Pseudomonas community structures in fertilized and unfertilized agricultural soils

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Abstract

Pseudomonas community structures were investigated by analyzing 16S rRNA clone libraries derived from fertilized and unfertilized soil plots under corn–alfalfa rotation in a long-term experiment. Amplified 16S rRNA fragments derived by polymerase chain reaction (PCR) were cloned and sequenced. A total of 729 clone sequences were analyzed, of which 51 were possible chimeras and discarded. The remaining clone sequences (678) belonged to γ-proteobacteria with 61.8 % (419) classified to the genus Pseudomonas. Unclassified Gammaproteobacteria accounted for 23.4 % of total clones sequences. Rarefaction analyses showed a more diverse community structure of both Gammaproteobacteria and Pseudomonas in unfertilized than fertilized field soils irrespective of plant types under cultivation. Bacterial or Pseudomonas community structures differed significantly between fertilized and unfertilized soil plots. Clone sequences that are affiliated to Pseudomonas putida and P. oryzihabitans were more prominent in libraries from fertilized plots, while those that clustered with Pseudomonas frederiksbergensis were more often retrieved from unfertilized soil plots. A strong influence of fertilizer applications on community structure was supported by principal component analysis. We conclude that long-term use of mineral fertilizers could influence Pseudomonas community structure.

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Acknowledgement

Funding for this work was provided by Agriculture and Agri-Food Canada through project # 152. We are indebted to C. Drury, for managing the long-term experimental plots at Woodslee, Ontario, Canada. We are also grateful to T. Barasubiye for extraction of total soil DNA, and Rafik Assabgui for technical assistance in DNA sequencing.

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  1. Environmental Health Program (Biodiversity), Eastern Cereal and Oilseed research Center, Agriculture and Agri-Food Canada in Ottawa, 960 Carling avenue, Ottawa, ON, K1A 0C6, Canada

    James Tabi Tambong & Renlin Xu

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  1. James Tabi Tambong
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  2. Renlin Xu
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Correspondence to James Tabi Tambong.

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Tambong, J.T., Xu, R. Culture-independent analysis of Pseudomonas community structures in fertilized and unfertilized agricultural soils. Ann Microbiol 63, 323–333 (2013). https://doi.org/10.1007/s13213-012-0477-9

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