A comparison of DNA- and RNA-based clone libraries from the same marine bacterioplankton community

Abstract

Clones from the same marine bacterioplankton community were sequenced, 100 clones based on DNA (16S rRNA genes) and 100 clones based on RNA (16S rRNA). This bacterioplankton community was dominated by alpha-Proteobacteria in terms of repetitive DNA clones (52%), but gamma-Proteobacteria dominated in terms of repetitive RNA clones (44%). The combined analysis led to a characterization of phylotypes otherwise uncharacterized if only the DNA or RNA libraries would have been analyzed alone. Of the DNA clones, 25.5% were found only in this library and no close relatives were detected in the RNA library. For clones from the RNA library, 21.5% of RNA clones did not indicate close relatives in the DNA library. Based on the comparisons between DNA and RNA libraries, our data indicate that the characterization of the bacterial community based on RNA has the potential to characterize distinct phylotypes from the marine environment, which remain undetected on the DNA level.

Activity profiles for marine sponge-associated bacteria obtained by 16S rRNA vs 16S rRNA gene comparisons

“…Each of these cases can be readily explained-or at least speculated upon (Moeseneder et al, 2005). First, phylotypes from the same sponge species represented in both DNA and RNA libraries are clearly present and-as indicated by the detection of their rRNA-are presumably active as well.…”

“…Activity profiles for marine sponge-associated bacteria J Kamke et al Bacterial 16S rRNA gene vs 16S rRNA comparisons in sponges Earlier studies have successfully used the 16S rRNA gene vs rRNA approach to investigate the activity of, for example, marine plankton, sediment and gas hydrate communities (Moeseneder et al, , 2005Mills et al, 2005;Gentile et al, 2006;RodriguezBlanco et al, 2009 Agelas dilatata clone AD004, EF076125 Tethya aurantium clone TAA-10-101, AM259897…”

“…The analysis of 16S rRNA genes through clone libraries and fingerprinting approaches such as denaturing gradient gel electrophoresis (DGGE) has greatly extended our knowledge about the phylogenetic richness of sponge-associated bacteria and archaea (Webster et al, 2001(Webster et al, , 2004Hentschel et al, 2002;Taylor et al, 2004Taylor et al, , 2007bHolmes and Blanch, 2006;Longford et al, 2007;Schmitt et al, 2007Schmitt et al, , 2008Thiel et al, 2007;Mohamed et al, 2008b;Zhu et al, 2008). Researchers in other systems have taken this approach one step further, yielding insights into both richness and activity by comparing 16S rRNA gene-and 16S rRNA-derived sequences, respectively (Moeseneder et al, , 2005Winter et al, 2001;Troussellier et al, 2002;Mills et al, 2005;Gentile et al, 2006;Martinez et al, 2006;Brinkmann et al, 2008;McIlroy et al, 2008;West et al, 2008;Rodriguez-Blanco et al, 2009). In general, cellular concentrations of rRNA are correlated with growth rate and activity (DeLong et al, 1989;Poulsen et al, 1993), hence-with acknowledgement of certain caveats (e.g., for ammoniaoxidizing bacteria; Morgenroth et al, 2000)-the rRNA itself can yield useful information about which community members are active.…”

Vertical Distribution of Functional Potential and Active Microbial Communities in Meromictic Lake Kivu

“…Even though potential biases can be introduced during DNA and RNA extraction, complementary DNA (cDNA) synthesis, and PCR amplification [12], parallel comparisons of DNA-and RNA-based pyrosequencing approaches can help differentiate whether abundant taxa are active or whether rare but active taxa exist. In addition, stronger evidence on the links between biogeochemical processes and microbial communities might be obtained if active communities are monitored rather than bulk communities [13][14][15][16].…”

Effects of temperature and fertilization on the structure of total versus active bacterial communities from sub-Antarctic seawater exposed to crude oil and diesel fuel

“…The importance of focusing not only on the total bacterial community (based on 16S rDNA) but also on the metabolically active fraction (based on 16S rRNA) to evaluate the influence of environmental factors on bacterial populations has been underlined in previous studies (Schafer et al 2001;Troussellier et al 2002;Moeseneder et al 2005;Gentile et al 2006;Lami et al 2009;). To our knowledge, only one study used a combined 16S rDNA/16S rRNA approach to compare dynamics of total versus metabolically active bacterial community structure of hypersaline microbial mats in the context of hydrocarbons pollution (Bordenave et al 2007).…”