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Loman, N. J., Constantinidou, C., Chan, J. Z. M., Halachev, M., Sergeant, M., Penn, C. W., Robinson, E. R., et al. (2012). High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity. Nature reviews. Microbiology, 10(9), 599–606. doi:10.1038/nrmicro2850 Here, we take a snapshot of the high-throughput sequencing platforms, together with the relevant analytical…
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Mira, A., Pushker, R., & Rodriguez-Valera, F. (2006). The Neolithic revolution of bacterial genomes. Trends Microbiol, 14(5), 200–206. Retrieved from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16569502 Current human activities undoubtedly impact natural ecosystems. However, the influence of Homo sapiens on living organisms must have also occurred in the past. Certain genomic characteristics of prokaryotes can be used to study the…
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Mira, A., Ochman, H., & Moran, N. A. (2001). Deletional bias and the evolution of bacterial genomes, 17(10), 589–596. Retrieved from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11585665 Although bacteria increase their DNA content through horizontal transfer and gene duplication, their genomes remain small and, in particular, lack nonfunctional sequences. This pattern is most readily explained by a pervasive bias towards…
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Pushker, R., Mira, A., & Rodriguez-Valera, F. (2004). Comparative genomics of gene-family size in closely related bacteria. Genome Biol, 5(4), 0. Retrieved from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15059260 BACKGROUND: The wealth of genomic data in bacteria is helping microbiologists understand the factors involved in gene innovation. Among these, the expansion and reduction of gene families appears to have a…
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Soberón, J., & Nakamura, M. (2009). Niches and distributional areas: concepts, methods, and assumptions. Proceedings of the National …. Retrieved from http://www.pnas.org/content/106/suppl.2/19644.short Abstract: Estimating actual and potential areas of distribution of species via ecological niche modeling has become a very active field of research, yet important conceptual issues in this field remain confused. We argue…
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Naeem, S. (2009). Gini in the bottle. Nature, 458(April), 2–3. An elaborate microcosm study has a message for the wider world: declining distributional equity among species, where the rare become rarer, and the dominant become more dominant, can put ecosystems at risk…

Konopka, A. (2009). The ISME journal, 3(11), 1223–30. doi:10.1038/ismej.2009.88 The activities of complex communities of microbes affect biogeochemical transformations in natural, managed and engineered ecosystems. Meaningfully defining what constitutes a community of interacting microbial populations is not trivial, but is important for rigorous progress in the field. Important elements of research in microbial community ecology…
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