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Investigating the Diversity of Pseudomonas spp. in Soil Using Culture Dependent and Independent Techniques

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Abstract

Less than 1 % of bacterial populations present in environmental samples are culturable, meaning that cultivation will lead to an underestimation of total cell counts and total diversity. However, it is less clear whether this is also true for specific well-defined groups of bacteria for which selective culture media is available. In this study, we use culture dependent and independent techniques to describe whether isolation of Pseudomonas spp. on selective nutrient-poor NAA 1:100 agar-medium can reflect the full diversity, found by pyrosequencing, of the total soil Pseudomonas community in an urban waste field trial experiment. Approximately 3,600 bacterial colonies were isolated using nutrient-poor NAA 1:100 medium from soils treated with different fertilizers; (i) high N-level sewage sludge (SA), (ii) high N-level cattle manure (CMA), and (iii) unfertilized control soil (U). Based on Pseudomonas specific quantitative-PCR and Pseudomonas CFU counts, less than 4 % of Pseudomonas spp. were culturable using NAA 1:100 medium. The Pseudomonas selectivity and specificity of the culture medium were evaluated by 454 pyrosequencing of 16S rRNA gene amplicons generated using Bacteria- and Pseudomonas-specific primers. Pyrosequencing results showed that most isolates were Pseudomonas and that the culturable fraction of Pseudomonas spp. reflects most clusters of the total Pseudomonas diversity in soil. This indicates that NAA 1:100 medium is highly selective for Pseudomonas species, and reveals the ability of NAA 1:100 medium to culture mostly the dominant Pseudomonas species in soil.

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Acknowledgments

We thank Annelise Kjøller for proofreading of the manuscript and technician Karin Vestberg for excellent help with laboratory work. The authors thank the Danish Research Centre for Organic Food and Farming (DARCOF), for supporting the project CRUCIAL (Closing the Rural Urban Nutrient Cycle), and the Center for Environmental and Agricultural Microbiology (CREAM), funded by The Villum Foundation.

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Authors and Affiliations

  1. Section for Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, Bygning 1, 2100, Copenhagen, Denmark

    Lili Li, Waleed Abu Al-Soud, Lasse Bergmark, Leise Riber, Lars H. Hansen & Søren J. Sørensen

  2. Department of Agriculture and Ecology, Faculty of Life Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark

    Jakob Magid

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  1. Lili Li
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  2. Waleed Abu Al-Soud
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  3. Lasse Bergmark
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  4. Leise Riber
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  5. Lars H. Hansen
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  7. Søren J. Sørensen
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Correspondence to Søren J. Sørensen.

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Lili Li and Waleed Abu Al-Soud contributed equally to this study.

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Li, L., Abu Al-Soud, W., Bergmark, L. et al. Investigating the Diversity of Pseudomonas spp. in Soil Using Culture Dependent and Independent Techniques. Curr Microbiol 67, 423–430 (2013). https://doi.org/10.1007/s00284-013-0382-x

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  • DOI: https://doi.org/10.1007/s00284-013-0382-x

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