title: Genetic diversity assessment of anoxygenic photosynthetic bacteria by distance-based grouping analysis of pufM sequences.
abstract: OBJECTIVE
  To assess how completely the diversity of anoxygenic phototrophic bacteria (APB) was sampled in natural environments.
  
  
  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.
  
  
  CONCLUSIONS
  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.affiliation: State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, PR China.
authors.forename: Y H
authors.initials: YH
authors.lastname: Zeng
authors.forename: X H
authors.initials: XH
authors.lastname: Chen
authors.forename: N Z
authors.initials: NZ
authors.lastname: Jiao
mesh_terms: D001421:Bacteria, Anaerobic / Q000145:classification* / Q000235:genetics* / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics*; D044822:Biodiversity; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000235:genetics; D004783:Environmental Microbiology; D010788:Photosynthesis; D045322:Photosynthetic Reaction Center Complex Proteins / Q000235:genetics*; D017422:Sequence Analysis, DNA; D017385:Sequence Homology
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D045322:Photosynthetic Reaction Center Complex Proteins; C098543:PufM protein, Bacteria