Y H Zeng1, X H Chen, N Z Jiao. 1. State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, PR China.
Abstract
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.
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.
Authors: Thomas Riedel; Jürgen Tomasch; Ina Buchholz; Jenny Jacobs; Mario Kollenberg; Gunnar Gerdts; Antje Wichels; Thorsten Brinkhoff; Heribert Cypionka; Irene Wagner-Döbler Journal: Appl Environ Microbiol Date: 2010-03-19 Impact factor: 4.792