Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA.
Retrieval of first genome data for rice cluster I methanogens by a combination of cultivation and molecular techniques
Article first published online: 5 JAN 2006
FEMS Microbiology Ecology
Volume 53, Issue 2, pages 187–204, July 2005
How to Cite
Erkel, C., Kemnitz, D., Kube, M., Ricke, P., Chin, K.-J., Dedysh, S., Reinhardt, R., Conrad, R. and Liesack, W. (2005), Retrieval of first genome data for rice cluster I methanogens by a combination of cultivation and molecular techniques. FEMS Microbiology Ecology, 53: 187–204. doi: 10.1016/j.femsec.2004.12.004
- Issue published online: 5 JAN 2006
- Article first published online: 5 JAN 2006
- Received 28 July 2004, Revised 5 November 2004, Accepted 9 December 2004
- Rice cluster I;
- rrn Operons;
- Informational genes;
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.