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Mykytczuk, N. C., Foote, S. J., Omelon, C. R., Southam, G., Greer, C. W., & Whyte, L. G. (2013). Bacterial growth at −15 °C; molecular insights from the permafrost bacterium Planococcus halocryophilus Or1. The ISME Journal, 1–16. doi:10.1038/ismej.2013.8 Planococcus halocryophilus strain Or1, isolated from high Arctic permafrost, grows and divides at ~15 °C, the lowest…
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Meyer, F., Paarmann, D., D’Souza, M., Olson, R., Glass, E. M., Kubal, M., Paczian, T., et al. (2008).The metagenomics RAST server a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC bioinformatics, 9, 386. doi:10.1186/1471-2105-9-386 BACKGROUND: Random community genomes (metagenomes) are now commonly used to study microbes in different environments. Over the…
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Teeling, H., & Glöckner, F. O. (2012). Current opportunities and challenges in microbial metagenome analysis–a bioinformatic perspective. Briefings in bioinformatics, 13(6), 728–742. doi:10.1093/bib/bbs039 Metagenomics has become an indispensable tool for studying the diversity and metabolic potential of environmental microbes, whose bulk is as yet non-cultivable. Continual progress in next-generation sequencing allows for generating increasingly large…
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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…