Abstract
Relative abundance profiles of bacterial populations measured by sequencing DNA or RNA of marker genes can widely differ. These differences, made apparent when calculating ribosomal RNA:DNA ratios, have been interpreted as variable activities of bacterial populations. However, inconsistent correlations between ribosomal RNA:DNA ratios and metabolic activity or growth rates have led to a more conservative interpretation of this metric as the cellular protein synthesis potential (PSP). Little is known, particularly in freshwater systems, about how PSP varies for specific taxa across temporal and spatial environmental gradients and how conserved PSP is across bacterial phylogeny. Here, we generated 16S rRNA gene sequencing data using simultaneously extracted DNA and RNA from fractionated (free-living and particulate) water samples taken seasonally along a eutrophic freshwater estuary to oligotrophic pelagic transect in Lake Michigan. In contrast to previous reports, we observed frequent clustering of DNA and RNA data from the same sample. Analysis of the overlap in taxa detected at the RNA and DNA level indicated that microbial dormancy may be more common in the estuary, the particulate fraction, and during the stratified period. Across spatiotemporal gradients, PSP was often conserved at the phylum and class levels. PSPs for specific taxa were more similar across habitats in spring than in summer and fall. This was most notable for PSPs of the same taxa when located in the free-living or particulate fractions, but also when contrasting surface to deep, and estuary to Lake Michigan communities. Our results show that community composition assessed by RNA and DNA measurements are more similar than previously assumed in freshwater systems. However, the similarity between RNA and DNA measurements and taxa-specific PSPs that drive community-level similarities are conditional on spatiotemporal factors.
Highlights
High-throughput sequencing of conserved marker genes, the small subunit ribosomal RNA gene, allows for rapid and affordable censuses of microbial life (Caporaso et al, 2012; Kozich et al, 2013)
In line with the clustering of spring PA and FL samples across seasons, we identified a series of OTUs that display similar ribosomal RNA:DNA ratios in spring PA and FL and summer and fall FL fractions, but significantly different ratios in PA summer and fall communities (Figure 7)
This study builds on previous findings in aquatic and terrestrial systems regarding discrepancies in bacterial community composition observed when using matching environmental DNA and RNA extracts
Summary
High-throughput sequencing of conserved marker genes, the small subunit ribosomal RNA gene, allows for rapid and affordable censuses of microbial life (Caporaso et al, 2012; Kozich et al, 2013). RNA:DNA ratio data better reflect active community members (e.g., Muttray and Mohn, 1999; Gentile et al, 2006; Jones and Lennon, 2010; Männistö et al, 2013; Zhang et al, 2014; Stibal et al, 2015). This is supported by better correspondence between key environmental drivers and RNA or RNA:DNA ratio marker gene data than DNA data (Hunt et al, 2013). A recent critical perspective has suggested to interpret the ribosomal RNA:DNA ratio of a bacterial population as the potential activity or even more conservatively, the protein synthesis potential (PSP) of a population (Blazewicz et al, 2013)
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
