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Applied and Environmental Microbiology, March 2009, p. 1658-1666, Vol. 75, No. 6
0099-2240/09/$08.00+0     doi:10.1128/AEM.01304-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Biogeographic Patterns in Genomic Diversity among a Large Collection of Vibrio cholerae Isolates{triangledown} ,{dagger}

Daniel P. Keymer,* Lilian H. Lam, and Alexandria B. Boehm

Department of Civil & Environmental Engineering, Stanford University, Stanford, California 94305

Received 11 June 2008/ Accepted 6 January 2009

Vibrio cholerae strains are capable of inhabiting multiple niches in the aquatic environment and in some cases cause disease in humans. However, the ecology and biodiversity of these bacteria in environmental settings remains poorly understood. We used the genomic fingerprinting technique enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR) to profile 835 environmental isolates from waters and sediments obtained at nine sites along the central California coast. We identified 115 ERIC-PCR genotypes from 998 fingerprints, with a reproducibility of 98.5% and a discriminatory power of 0.971. When the temporal dynamics at a subset of sampling sites were explored, several genotypes provided evidence for cosmopolitan or geographically restricted distributions, and other genotypes displayed nonrandom patterns of cooccurrence. Partial Mantel tests confirmed that genotypic similarity of isolates across all sampling events was correlated with environmental similarity (0.04 ≤ r ≤ 0.05), temporal proximity (r = 0.09), and geographic distance (r = 0.09). A neutral community model for all sampling events explained 61% of the variation in genotype abundance. Cooccurrence indices (C-score, C-board, and Combo) were significantly different than expected by chance, suggesting that the V. cholerae population may have a competitive structure, especially at the regional scale. Even though stochastic processes are undoubtedly important in generating biogeographic patterns in diversity, deterministic factors appear to play a significant, albeit small, role in shaping the V. cholerae population structure in this system.

* Corresponding author. Mailing address: Jerry Yang & Akiko Yamazaki Environment & Energy Building #M-16, 473 Via Ortega, MC: 4020, Stanford, CA 94305. Phone: (650) 725-5948. Fax: (650) 723-7058. E-mail: dkeymer{at}stanford.edu

{triangledown} Published ahead of print on 9 January 2009.

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

Applied and Environmental Microbiology, March 2009, p. 1658-1666, Vol. 75, No. 6
0099-2240/09/$08.00+0     doi:10.1128/AEM.01304-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.





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