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DGGE and T-RFLP Analysis of Bacterial Succession during Mushroom Compost Production and Sequence-aided T-RFLP Profile of Mature Compost

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Abstract

The amount of button mushroom (Agaricus bisporus) harvested from compost is largely affected by the microbial processes taking place during composting and the microbes inhabiting the mature compost. In this study, the microbial changes during the stages of this specific composting process were monitored, and the dominant bacteria of the mature compost were identified to reveal the microbiological background of the favorable properties of the heat-treated phase II mushroom compost. 16S ribosomal deoxyribonucleic acid (rDNA)-based denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) molecular fingerprinting methods were used to track the succession of microbial communities in summer and winter composting cycles. DNA from individual DGGE bands were reamplified and subjected to sequence analysis. Principal component analysis of fingerprints of the composting processes showed intensive changes in bacterial community during the 22-day procedure. Peak temperature samples grouped together and were dominated by Thermus thermophilus. Mature compost patterns were almost identical by both methods (DGGE, T-RFLP). To get an in-depth analysis of the mature compost bacterial community, the sequence data from cultivation of the bacteria and cloning of environmental 16S rDNA were uniquely coupled with the output of the environmental T-RFLP fingerprints (sequence-aided T-RFLP). This method revealed the dominance of a supposedly cellulose-degrading consortium composed of phylotypes related to Pseudoxanthomonas, Thermobifida, and Thermomonospora.

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Acknowledgments

We are thankful to the staff of Quality Champignons, Korona Spawn Factory, and Mr. László Bujdosó for sampling and operating the compost system. This work was supported by grant BIO 0029/2002 from the Ministry of Agriculture and Rural Development.

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  1. Anna J. Székely

    Present address: Department of Microbiology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117, Budapest, Hungary

Authors and Affiliations

  1. Department of Microbiology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117, Budapest, Hungary

    Rita Sipos, Brigitta Berta, Balázs Vajna & Károly Márialigeti

  2. Strain Research and Molecular Biological Laboratory, Korona Spawn Factory, 3395, Demjén, Hungary

    Csaba Hajdú

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  1. Anna J. Székely
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Correspondence to Anna J. Székely.

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Székely, A.J., Sipos, R., Berta, B. et al. DGGE and T-RFLP Analysis of Bacterial Succession during Mushroom Compost Production and Sequence-aided T-RFLP Profile of Mature Compost. Microb Ecol 57, 522–533 (2009). https://doi.org/10.1007/s00248-008-9424-5

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