Genetic diversity assessment of anoxygenic photosynthetic bacteria by distance-based grouping analysis of pufM sequences
Article first published online: 8 OCT 2007
Letters in Applied Microbiology
Volume 45, Issue 6, pages 639–645, December 2007
How to Cite
Zeng, Y.H., Chen, X.H. and Jiao, N.Z. (2007), Genetic diversity assessment of anoxygenic photosynthetic bacteria by distance-based grouping analysis of pufM sequences. Letters in Applied Microbiology, 45: 639–645. doi: 10.1111/j.1472-765X.2007.02247.x
- Issue published online: 8 OCT 2007
- Article first published online: 8 OCT 2007
- 2007/0778: received 18 May 2007, revised 18 July 2007 and accepted 19 July 2007
- anoxygenic photosynthetic bacteria;
- genetic diversity;
- natural environments;
- sequence distance;
- statistical analysis
Aim: To assess how completely the diversity of anoxygenic phototrophic bacteria (APB) was sampled in natural environments.
Methods and Results: All nucleotide sequences of the APB marker gene pufM from cultures and environmental clones were retrieved from the GenBank database. A set of cutoff values (sequence distances 0·06, 0·15 and 0·48 for species, genus, and (sub)phylum levels, respectively) was established using a distance-based grouping program. Analysis of the environmental clones revealed that current efforts on APB isolation and sampling in natural environments are largely inadequate. Analysis of the average distance between each identified genus and an uncultured environmental pufM sequence indicated that the majority of cultured APB genera lack environmental representatives.
Conclusions: The distance-based grouping method is fast and efficient for bulk functional gene sequences analysis. The results clearly show that we are at a relatively early stage in sampling the global richness of APB species. Periodical assessment will undoubtedly facilitate in-depth analysis of potential biogeographical distribution pattern of APB.
Significance and Impact of the Study: This is the first attempt to assess the present understanding of APB diversity in natural environments. The method used is also useful for assessing the diversity of other functional genes.