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Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation.

Simmons SL, Dibartolo G, Denef VJ, Goltsman DS, Thelen MP, Banfield JF.

PLoS Biol. 2008 Jul 22;6(7):e177. doi: 10.1371/journal.pbio.0060177.


Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) bacteria in acid mine drainage biofilms.

Goltsman DS, Denef VJ, Singer SW, VerBerkmoes NC, Lefsrud M, Mueller RS, Dick GJ, Sun CL, Wheeler KE, Zemla A, Baker BJ, Hauser L, Land M, Shah MB, Thelen MP, Hettich RL, Banfield JF.

Appl Environ Microbiol. 2009 Jul;75(13):4599-615. doi: 10.1128/AEM.02943-08. Epub 2009 May 8.


Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation.

Denef VJ, VerBerkmoes NC, Shah MB, Abraham P, Lefsrud M, Hettich RL, Banfield JF.

Environ Microbiol. 2009 Feb;11(2):313-25. doi: 10.1111/j.1462-2920.2008.01769.x. Epub 2008 Sep 23.


Community structure and metabolism through reconstruction of microbial genomes from the environment.

Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF.

Nature. 2004 Mar 4;428(6978):37-43. Epub 2004 Feb 1.


Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities.

Denef VJ, Kalnejais LH, Mueller RS, Wilmes P, Baker BJ, Thomas BC, VerBerkmoes NC, Hettich RL, Banfield JF.

Proc Natl Acad Sci U S A. 2010 Feb 9;107(6):2383-90. doi: 10.1073/pnas.0907041107. Epub 2010 Feb 2.


New group in the Leptospirillum clade: cultivation-independent community genomics, proteomics, and transcriptomics of the new species "Leptospirillum group IV UBA BS".

Goltsman DS, Dasari M, Thomas BC, Shah MB, VerBerkmoes NC, Hettich RL, Banfield JF.

Appl Environ Microbiol. 2013 Sep;79(17):5384-93. doi: 10.1128/AEM.00202-13. Epub 2013 May 3.


Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria.

Lo I, Denef VJ, Verberkmoes NC, Shah MB, Goltsman D, DiBartolo G, Tyson GW, Allen EE, Ram RJ, Detter JC, Richardson P, Thelen MP, Hettich RL, Banfield JF.

Nature. 2007 Mar 29;446(7135):537-41. Epub 2007 Mar 7.


Strainer: software for analysis of population variation in community genomic datasets.

Eppley JM, Tyson GW, Getz WM, Banfield JF.

BMC Bioinformatics. 2007 Oct 17;8:398.


Genome dynamics in a natural archaeal population.

Allen EE, Tyson GW, Whitaker RJ, Detter JC, Richardson PM, Banfield JF.

Proc Natl Acad Sci U S A. 2007 Feb 6;104(6):1883-8. Epub 2007 Jan 31.


Genetic exchange across a species boundary in the archaeal genus ferroplasma.

Eppley JM, Tyson GW, Getz WM, Banfield JF.

Genetics. 2007 Sep;177(1):407-16. Epub 2007 Jul 1.


Genomic patterns of recombination, clonal divergence and environment in marine microbial populations.

Konstantinidis KT, DeLong EF.

ISME J. 2008 Oct;2(10):1052-65. doi: 10.1038/ismej.2008.62. Epub 2008 Jun 26.


Horizontal gene transfer regulation in bacteria as a "spandrel" of DNA repair mechanisms.

Fall S, Mercier A, Bertolla F, Calteau A, Gueguen L, Perrière G, Vogel TM, Simonet P.

PLoS One. 2007 Oct 24;2(10):e1055.


Complete genome sequence of the bioleaching bacterium Leptospirillum sp. group II strain CF-1.

Ferrer A, Bunk B, Spröer C, Biedendieck R, Valdés N, Jahn M, Jahn D, Orellana O, Levicán G.

J Biotechnol. 2016 Mar 20;222:21-2. doi: 10.1016/j.jbiotec.2016.02.008. Epub 2016 Feb 4.


In situ evolutionary rate measurements show ecological success of recently emerged bacterial hybrids.

Denef VJ, Banfield JF.

Science. 2012 Apr 27;336(6080):462-6. doi: 10.1126/science.1218389.


Quantitative proteomic analyses of the response of acidophilic microbial communities to different pH conditions.

Belnap CP, Pan C, Denef VJ, Samatova NF, Hettich RL, Banfield JF.

ISME J. 2011 Jul;5(7):1152-61. doi: 10.1038/ismej.2010.200. Epub 2011 Jan 13.


Genetic structure of marine Borrelia garinii and population admixture with the terrestrial cycle of Lyme borreliosis.

Gómez-Díaz E, Boulinier T, Sertour N, Cornet M, Ferquel E, McCoy KD.

Environ Microbiol. 2011 Sep;13(9):2453-67. doi: 10.1111/j.1462-2920.2011.02515.x. Epub 2011 Jun 8.


Genetic variation: molecular mechanisms and impact on microbial evolution.

Arber W.

FEMS Microbiol Rev. 2000 Jan;24(1):1-7. Review.


Purifying selection, sequence composition, and context-specific indel mutations shape intraspecific variation in a bacterial endosymbiont.

Williams LE, Wernegreen JJ.

Genome Biol Evol. 2012;4(1):44-51. doi: 10.1093/gbe/evr128. Epub 2011 Nov 24.


Proteome changes in the initial bacterial colonist during ecological succession in an acid mine drainage biofilm community.

Mueller RS, Dill BD, Pan C, Belnap CP, Thomas BC, VerBerkmoes NC, Hettich RL, Banfield JF.

Environ Microbiol. 2011 Aug;13(8):2279-92. doi: 10.1111/j.1462-2920.2011.02486.x. Epub 2011 Apr 25.


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