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Retrieval of first genome data for rice cluster I methanogens by a combination of cultivation and molecular techniques

MPS-Authors

Erkel,  Christoph
Max Planck Society;

Kemnitz,  Dana
Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons50397

Kube,  Michael
High Throughput Technologies, Max Planck Institute for Molecular Genetics, Max Planck Society;

Ricke,  Peter
Max Planck Society;

Chin,  Kuk-Jeong
Max Planck Society;

Dedysh,  Svetlana
Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons50488

Reinhardt,  Richard
High Throughput Technologies, Max Planck Institute for Molecular Genetics, Max Planck Society;

Conrad,  Ralf
Max Planck Society;

Liesack,  Werner
Max Planck Society;

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Citation

Erkel, C., Kemnitz, D., Kube, M., Ricke, P., Chin, K.-J., Dedysh, S., et al. (2005). Retrieval of first genome data for rice cluster I methanogens by a combination of cultivation and molecular techniques. FEMS Microbiology Ecology, 53(2), 187-204. doi:10.1016/j.femsec.2004.12.004.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0010-874E-B
Abstract
We report first insights into a representative genome of rice cluster I (RC-I), a major group of as-yet uncultured methanogens. The starting point of our study was the methanogenic consortium MRE50 that had been stably maintained for 3 years by consecutive transfers to fresh medium and anaerobic incubation at 50 °C. Process-oriented measurements provided evidence for hydrogenotrophic CO2-reducing methanogenesis. Assessment of the diversity of consortium MRE50 suggested members of the families Thermoanaerobacteriaceae and Clostridiaceae to constitute the major bacterial component, while the archaeal population was represented entirely by RC-I. The RC-I population amounted to more than 50% of total cells, as concluded from fluorescence in situ hybridization using specific probes for either Bacteria or Archaea. The high enrichment status of RC-I prompted construction of a large insert fosmid library from consortium MRE50. Comparative sequence analysis of internal transcribed spacer (ITS) regions revealed that three different RC-I rrn operon variants were present in the fosmid library. Three, approximately 40-kb genomic fragments, each representative for one of the three different rrn operon variants, were recovered and sequenced. Computational analysis of the sequence data resulted in two major findings: (i) consortium MRE50 most likely harbours only a single RC-I genotype, which is characterized by multiple rrn operon copies; (ii) seven genes were identified to possess a strong phylogenetic signal (eIF2a, dnaG, priA, pcrA, gatD, gatE, and a gene encoding a putative RNA-binding protein). Trees exemplarily computed for the deduced amino acid sequences of eIF2a, dnaG, and priA corroborated a specific phylogenetic association of RC-I with the Methanosarcinales.