This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Supplemental material
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Google Scholar
Right arrow Articles by Davis, J. P.
Right arrow Articles by Elshahed, M. S.
PubMed
Right arrow PubMed Citation
Right arrow Articles by Davis, J. P.
Right arrow Articles by Elshahed, M. S.
Agricola
Right arrow Articles by Davis, J. P.
Right arrow Articles by Elshahed, M. S.

 Previous Article  |  Next Article 

Applied and Environmental Microbiology, June 2009, p. 4139-4148, Vol. 75, No. 12
0099-2240/09/$08.00+0     doi:10.1128/AEM.00137-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Assessment of the Diversity, Abundance, and Ecological Distribution of Members of Candidate Division SR1 Reveals a High Level of Phylogenetic Diversity but Limited Morphotypic Diversity{triangledown} ,{dagger}

James P. Davis, Noha H. Youssef, and Mostafa S. Elshahed*

Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74074

Received 20 January 2009/ Accepted 20 April 2009

We used a combination of 16S rRNA gene clone library surveys, quantitative PCR (qPCR) analysis, and fluorescent in situ hybridization to investigate the diversity, abundance, and distribution of members of candidate division SR1 in multiple habitats. Using SR1-specific 16S rRNA gene primers, we identified multiple novel SR1 lineages in four different anaerobic environments: sediments from Zodletone Spring, a sulfide- and sulfur-rich spring in southwestern Oklahoma; inner layers of microbial mats obtained from Sperm Pool, a high-temperature, low-pH pool (55°C, pH 2.5) in Yellowstone National Park; fresh bovine ruminal contents; and anaerobic freshwater pond sediments (Duck Pond) in Norman, Oklahoma. qPCR analysis indicated that SR1 members constitute a small fraction (<0.01%) of the microbial communities in Duck Pond and ruminal samples but constitute a significant fraction (11.6 and 48.7%) of the total number of bacterial 16S rRNA genes in Zodletone Spring and the inner layers of Sperm Pool microbial mat samples, respectively. By using SR1-specific fluorescent probes, filamentous cells were identified as the sole SR1 morphotype in all environments examined, with the exception of Sperm Pool, where a second bacillus morphotype was also identified. Using a full-cycle 16S rRNA approach, we show that each of these two morphotypes corresponds to a specific phylogenetic lineage identified in the Sperm Pool clone library. This work greatly expands the intralineage phylogenetic diversity within candidate division SR1 and provides valuable quantification and visualization tools that could be used for investigating the ecological roles, dynamics, and genomics of this as-yet-uncultured bacterial phylum.

* Corresponding author. Mailing address: Department of Microbiology and Molecular Genetics, Oklahoma State University, 1110 S. Innovation Way, Stillwater, OK 74074. Phone: (405) 744-3005. Fax: (405) 744-1112. E-mail: Mostafa{at}Okstate.edu

{triangledown} Published ahead of print on 24 April 2009.

{dagger} Supplemental material for this article may be found at http://aem.asm.org/.

Applied and Environmental Microbiology, June 2009, p. 4139-4148, Vol. 75, No. 12
0099-2240/09/$08.00+0     doi:10.1128/AEM.00137-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.





Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»