Limited metagenomic analysis of the hot spring microbial communities first provided us a glimpse into the mosaic genomes of Synechococcus sp. (). To explore this further we used novel statistical analytical methods in combination with deep sequencing, and discovered a high degree of intragenic recombination. We predicted that this gives rise to mosaic genomes, which is not consistent with the mainstream idea of well-delineated ecotypes [26023139, 30427861]. It is possible that such micro- diversity is common in many natural environments and may be linked to adaptation to specific environmental niches. This can be pursued by carrying out metagenomic studies in other extreme environments or by mining the large databases already available, including our own. By using data generated from an ongoing DOE-Joint Genome Institute, large-scale community sequencing project (CSP) we propose to test some of these ideas. We know almost nothing about how such diversity is maintained (e.g. recombination processes; transposon activity [21666019]). This detailed data-based approach will be used to test hypotheses about microbial evolution and recombination.

Select Publications

Bhaya, D. (2019). Diversity, dynamics and defense in microbial communities. In APS March Meeting Abstracts (Vol. 2019, pp. C36-002).

Rosen, M. J., Davison, M., Fisher, D. S., & Bhaya, D. (2018). Probing the ecological and evolutionary history of a thermophilic cyanobacterial population via statistical properties of its microdiversity. PloS one, 13(11), e0205396. https://doi.org/10.1371/journal.pone.0205396

Silas, S., Makarova, K. S., Shmakov, S., Páez-Espino, D., Mohr, G., Liu, Y., ... & Fire, A. Z. (2017). On the origin of reverse transcriptase-using CRISPR-Cas systems and their hyperdiverse, enigmatic spacer repertoires. MBio, 8(4), e00897-17. https://doi.org/10.1128/mBio.00897-17

Davison, M., Treangen, T. J., Koren, S., Pop, M., & Bhaya, D. (2016). Diversity in a polymicrobial community revealed by analysis of viromes, endolysins and CRISPR spacers. PloS one, 11(9). https://doi.org/10.1371/journal.pone.0160574

Davison, M., Hall, E., Zare, R., & Bhaya, D. (2015). Challenges of metagenomics and single-cell genomics approaches for exploring cyanobacterial diversity. Photosynthesis research, 126(1), 135-146. https://doi.org/10.1007/s11120-014-0066-9

Rosen, M. J., Davison, M., Bhaya, D., & Fisher, D. S. (2015). Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche. Science, 348(6238), 1019-1023. http://doi.org/10.1126/science.aaa4456

Held, N. L., Childs, L. M., Davison, M., Weitz, J. S., Whitaker, R. J., & Bhaya, D. (2013). CRISPR-Cas systems to probe ecological diversity and host–viral interactions. In CRISPR-Cas systems (pp. 221-250). Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-34657-6_9

Bhaya, D. (2012). Probing functional diversity of thermophilic cyanobacteria in microbial mats. In Functional genomics and evolution of photosynthetic systems (pp. 17-46). Springer, Dordrecht. https://doi.org/10.1007/978-94-007-1533-2_2

Bhaya, D. (2011). Approaches to Understanding Population Level Functional Diversity in a Microbial Community. Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats, 341-354.

Bhaya, D., Grossman, A. R., Steunou, A.-S., Khuri, N., Cohan, F. M., Hamamura, N., Melendrez, M. C., Bateson, M. M., Ward, D. M., & Heidelberg, J. F. (2007). Population level functional diversity in a microbial community revealed by comparative genomic and metagenomic analyses. The ISME Journal, 1(8), 703–713. https://doi.org/10.1038/ismej.2007.46