Sun, 27 Jul 2008 09:19:21 BST CiteULike: vrich's Klepac-Ceraj http://www.citeulike.org/user/vrich/author/Klepac-Ceraj CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/vrich/article/556231 <i>Appl Environ Microbiol, Vol. 71, No. 12. (December 2005), pp. 8966-8969.</i><br /><br />The contribution of PCR artifacts to 16S rRNA gene sequence diversity from a complex bacterioplankton sample was estimated. Taq DNA polymerase errors were found to be the dominant sequence artifact but could be constrained by clustering the sequences into 99% sequence similarity groups. Other artifacts (chimeras and heteroduplex molecules) were significantly reduced by employing modified amplification protocols. Surprisingly, no skew in sequence types was detected in the two libraries constructed from PCR products amplified for different numbers of cycles. Recommendations for modification of amplification protocols and for reporting diversity estimates at 99% sequence similarity as a standard are given. PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. SG Acinas R Sarma-Rupavtarm V Klepac-Ceraj MF Polz doi:10.1128/AEM.71.12.8966-8969.2005 Appl Environ Microbiol, Vol. 71, No. 12. (December 2005), pp. 8966-8969. 2006-03-17T19:55:57-00:00 2005 Appl Environ Microbiol 0099-2240 71 12 8966 8969 pcr pcr_bias http://www.citeulike.org/user/vrich/article/2776593 <i>Science, Vol. 307, No. 5713. (25 February 2005), pp. 1311-1313.</i><br /><br />The genomic diversity and relative importance of distinct genotypes within natural bacterial populations have remained largely unknown. Here, we analyze the diversity and annual dynamics of a group of coastal bacterioplankton (greater than 99% 16S ribosomal RNA identity to Vibrio splendidus). We show that this group consists of at least a thousand distinct genotypes, each occurring at extremely low environmental concentrations (on average less than one cell per milliliter). Overall, the genomes show extensive allelic diversity and size variation. Individual genotypes rarely recurred in samples, and allelic distribution did not show spatial or temporal substructure. Ecological considerations suggest that much genotypic and possibly phenotypic variation within natural populations should be considered neutral. 10.1126/science.1106028 Genotypic Diversity Within a Natural Coastal Bacterioplankton Population Janelle Thompson Sarah Pacocha Chanathip Pharino Vanja Klepac-Ceraj Dana Hunt Jennifer Benoit Ramahi Sarma-Rupavtarm Daniel Distel Martin Polz doi:10.1126/science.1106028 Science, Vol. 307, No. 5713. (25 February 2005), pp. 1311-1313. 2008-05-09T20:41:29-00:00 2005 Science 307 5713 1311 1313 vibrios