Genomes to Life Contractor-Grantee Workshop III
February 6-9, 2005, Washington, D.C.
Environmental Genomics
67 Environmental Bacterial Diversity from Communities to Genomes
Janelle R. Thompson1,2*, Silvia G. Acinas1, Vanja Klepac-Ceraj1,2, Sarah Pacocha1,2, Chanathip Pharino1, Dana E. Hunt1, Luisa A. Marcelino1, Jennifer Benoit1,2, Ramahi Sarma-Rupavtarm1, Daniel L. Distel3, and Martin F. Polz1 (mpolz@mit.edu)
1Massachusetts Institute of Technology, Cambridge, MA; 2Woods Hole Oceanographic Institution, Woods Hole, MA; and 3New England Biolabs, Beverly, MA
We are studying the patterns of diversity among co-occurring coastal bacterioplankton from the level of the entire community to the individual genome. Our goal is to advance the understanding of structure-function relationships in microbial assemblages addressing questions including: What is the range of genomic diversity encompassed by functionally similar populations in specific environmental contexts? What mechanisms govern selection and diversification of natural microbial populations? Using environmental 16S ribosomal RNA gene sequences (ribotypes) as a proxy for bacteria, we have shown that despite a high diversity in the environment, the majority of organisms fall into closely related clusters (<1% 16S rRNA divergence) (1). Such microdiverse sequence clusters are hypothesized to represent functionally-differentiated populations, which arise by selective sweeps (2) and persist because competitive mechanisms are too weak to purge diversity from within them (1).
To examine this hypothesis we quantitatively estimated the genomic diversity within one 16S rRNA microdiversity cluster (Vibrio splendidus). Quantitative PCR analysis (3) over an annual cycle indicated that V. splendidus was consistently present as a member of the coastal bacterioplankton community. Vibrio strains were isolated from representative months and the majority were identified as V. splendidus. Determination of sequence diversity of a universally distributed protein-coding gene (Hsp60) among all Vibrio isolates showed high heterogeneity but confirmed the monophyly of the V. splendidus strains. Still greater heterogeneity was revealed when the number of unique genotypes among strains was assayed by pulse field gel electrophoresis (PFGE), moreover, the PFGE analysis provided evidence that a large proportion of genotypes are differentiated by insertions and deletions of large genome fragments. In a set of 12 V. splendidus strains genome sizes ranged from 4.5 to 5.6 Mb with only weak correlation of genome size difference to Hsp60 sequence divergence (R = 0.37).
The high degree of heterogeneity among the V. splendidus genomes suggest that the average environmental concentration of individual genotypes is astoundingly small. To illustrate this, we divided the QPCR-based estimates of population size of V. splendidus in samples taken in Aug 03, Sept 03, and Oct 03 (1,890, 600, and 640 cells/ml, respectively) by the Chao-1 statistical estimates (4) for the number of Hsp60 alleles (125, 94 and 279) and genotypes (465, 553 and 901) in those same samples. The result suggests that unique Hsp60 alleles occurred in the monthly samples at average concentrations of 2 to 15 cells per ml (or at a frequency of 0.3 to 1%) while unique genotypes were present at ~10-fold lower frequency (average concentration for all samples estimated at <1 cell per ml).
The observed pattern of co-existing diversity suggests that purging of genotypes from the population is rare compared to processes introducing variation and that therefore variation persists because it is either favored (e.g., by balancing selection or resource specialization) or neutral. We present ecological considerations to suggest much of the observed diversity may in fact be neutral in an environmental context. Such observations of extreme genomic heterogeneity among closely related individuals have significant implications for the assembly of genome sequences from environmental samples. In addition, if similar patterns of diversity are common to other bacterial populations caution should be exercised in interpreting the extent to which gene complements or even metabolic traits of individual isolates may reflect the overall properties of populations. Indeed our results suggest that not only the gene content, but also quantitative abundance and dynamics of individual traits should be considered when evaluating the ecological significance of differences among coexisting genotypes.
References
- S. G. Acinas et al., Nature 430, 551-554 (2004).
- F. M. Cohan, Annu. Rev. Microbiol. 56, 457–487 (2002).
- J. R. Thompson et al., Appl. Environ. Microbiol. 70, 4103-4110 (2004).
- J. B. Hughes, J. J. Hellmann, T. H. Ricketts, B. J. M. Bohannan, Appl. Environ. Microbiol. 67, 4399-4406 (2001).
* Presenting author
