Open Access Highly Accessed Research article

Detection and quantification of a mycorrhization helper bacterium and a mycorrhizal fungus in plant-soil microcosms at different levels of complexity

Florence Kurth1*, Katharina Zeitler1, Lasse Feldhahn1, Thomas R Neu2, Tilmann Weber3, Václav Krištůfek4, Tesfaye Wubet15, Sylvie Herrmann56, François Buscot157 and Mika T Tarkka157

Author Affiliations

1 Department Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle/Saale, Germany

2 Department River Ecology, UFZ - Helmholtz Centre for Environmental Research, Brückstraße 3a, 39114 Magdeburg, Germany

3 Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, Tübingen, Germany

4 Biology Centre AS CR, v. v. i. - Institute of Soil Biology, Na Sádkách 7, 370 05 České Budějovice, Czech Republic

5 German Centre for Integrative Biodiversity Research, University of Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany

6 Department of Community Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle/Saale, Germany

7 Institute of Biology, University of Leipzig, Johannisallee 21-23, 04103 Leipzig, Germany

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BMC Microbiology 2013, 13:205  doi:10.1186/1471-2180-13-205

Published: 11 September 2013



Host plant roots, mycorrhizal mycelium and microbes are important and potentially interacting factors shaping the performance of mycorrhization helper bacteria (MHB). We investigated the impact of a soil microbial community on the interaction between the extraradical mycelium of the ectomycorrhizal fungus Piloderma croceum and the MHB Streptomyces sp. AcH 505 in both the presence and the absence of pedunculate oak microcuttings.


Specific primers were designed to target the internal transcribed spacer of the rDNA and an intergenic region between two protein encoding genes of P. croceum and the intergenic region between the gyrA and gyrB genes of AcH 505. These primers were used to perform real-time PCR with DNA extracted from soil samples. With a sensitivity of 10 genome copies and a linear range of 6 orders of magnitude, these real-time PCR assays enabled the quantification of purified DNA from P. croceum and AcH 505, respectively. In soil microcosms, the fungal PCR signal was not affected by AcH 505 in the absence of the host plant. However, the fungal signal became weaker in the presence of the plant. This decrease was only observed in microbial filtrate amended microcosms. In contrast, the PCR signal of AcH 505 increased in the presence of P. croceum. The increase was not significant in sterile microcosms that contained plant roots.


Real-time quantitative PCR assays provide a method for directly detecting and quantifying MHB and mycorrhizal fungi in plant microcosms. Our study indicates that the presence of microorganisms and plant roots can both affect the nature of MHB-fungus interactions, and that mycorrhizal fungi may enhance MHB growth.

Streptomycetes; Oak; Real-time PCR; Rhizosphere; Microbial community