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Title: Seasonal succession leads to habitat-dependent differentiation in ribosomal RNA:DNA ratios among freshwater lake bacteria

Journal Article · · Frontiers in Microbiology
 [1];  [1];  [1];  [1]
  1. Univ. of Michigan, Ann Arbor, MI (United States)
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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. Furthermore, the similarity between RNA and DNA measurements and taxa-specific PSPs that drive community-level similarities are conditional on spatiotemporal factors.

Research Organization:
Univ. of Michigan, Ann Arbor, MI (United States)
Sponsoring Organization:
USDOE Office of Science (SC)
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1257632
Journal Information:
Frontiers in Microbiology, Vol. 7; ISSN 1664-302X
Publisher:
Frontiers Research FoundationCopyright Statement
Country of Publication:
United States
Language:
English

References (59)

Annual patterns of presence and activity of marine bacteria monitored by 16S rDNA–16S rRNA fingerprints in the coastal NW Mediterranean Sea journal February 2009
A single-cell view on the ecophysiology of anaerobic phototrophic bacteria journal November 2008
Different bulk and active bacterial communities in cryoconite from the margin and interior of the Greenland ice sheet: Bulk and active bacteria in Greenland cryoconite journal January 2015
ggplot2 book January 2009
Metacommunity dynamics of bacteria in an arctic lake: the impact of species sorting and mass effects on bacterial production and biogeography journal March 2014
Drivers shaping the diversity and biogeography of total and active bacterial communities in the South China Sea journal April 2014
Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform journal June 2013
Growth rates and rRNA content of four marine bacteria in pure cultures and in the Delaware estuary journal September 2015
Responses of soil bacterial and fungal communities to extreme desiccation and rewetting journal July 2013
RNA Preservation Agents and Nucleic Acid Extraction Method Bias Perceived Bacterial Community Composition journal March 2015
Active and total microbial communities in forest soil are largely different and highly stratified during decomposition journal July 2011
Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses journal July 2013
The ecology of pelagic freshwater methylotrophs assessed by a high-resolution monitoring and isolation campaign journal May 2015
Study of bacterial communities in Antarctic coastal waters by a combination of 16S rRNA and 16S rDNA sequencing journal December 2006
A new method for non-parametric multivariate analysis of variance: NON-PARAMETRIC MANOVA FOR ECOLOGY journal February 2001
Reproducibility and quantitation of amplicon sequencing-based detection journal February 2011
Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible journal April 2014
Vertical Distribution of Functional Potential and Active Microbial Communities in Meromictic Lake Kivu journal April 2015
Comparison of cell-specific activity between free-living and attached bacteria using isolates and natural assemblages journal January 2007
A Guide to the Natural History of Freshwater Lake Bacteria journal March 2011
Phylogenetic conservatism of functional traits in microorganisms journal December 2012
In situ substrate preferences of abundant bacterioplankton populations in a prealpine freshwater lake journal December 2012
Seasonal bloom dynamics and ecophysiology of the freshwater sister clade of SAR11 bacteria ‘that rule the waves’ (LD12) journal March 2011
Evaluation of metatranscriptomic protocols and application to the study of freshwater microbial communities: Metatranscriptomics of freshwater communities journal June 2014
Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes journal November 2015
Community composition and activity state of estuarine bacterioplankton assessed using differential staining and metagenomic analysis of 16S rDNA and rRNA journal July 2013
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data journal April 2013
Aquatic Microbiology for Ecosystem Scientists: New and Recycled Paradigms in Ecological Microbiology journal May 1999
Diel and Seasonal Variations in Abundance, Activity, and Community Structure of Particle-Attached and Free-Living Bacteria in NW Mediterranean Sea journal March 2007
A unique assemblage of cosmopolitan freshwater bacteria and higher community diversity differentiate an urbanized estuary from oligotrophic Lake Michigan journal September 2015
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools journal November 2012
Acidobacteria dominate the active bacterial communities of Arctic tundra with widely divergent winter-time snow accumulation and soil temperatures journal November 2012
The Ecological Role of Water-Column Microbes in the Sea journal January 1983
Phylogenetic conservation of freshwater lake habitat preference varies between abundant bacterioplankton phyla: Bacterial habitat preferences in freshwater lakes journal January 2016
Chloroflexi CL500-11 Populations That Predominate Deep-Lake Hypolimnion Bacterioplankton Rely on Nitrogen-Rich Dissolved Organic Matter Metabolism and C 1 Compound Oxidation journal December 2015
Rapid successions affect microbial N-acetyl-glucosamine uptake patterns during a lacustrine spring phytoplankton bloom: Succession of NAG-consuming bacteria in a lake journal November 2011
Microbial community structure and function on sinking particles in the North Pacific Subtropical Gyre journal May 2015
Maximum growth rates and possible life strategies of different bacterioplankton groups in relation to phosphorus availability in a freshwater reservoir journal September 2006
Major contribution of both zooplankton and protists to the top-down regulation of freshwater aerobic anoxygenic phototrophic bacteria journal September 2015
Microbial seed banks: the ecological and evolutionary implications of dormancy journal January 2011
Activity of abundant and rare bacteria in a coastal ocean journal July 2011
Quantitation of the Population Size and Metabolic Activity of a Resin Acid Degrading Bacterium in Activated Sludge Using Slot-Blot Hybridization to Measure the rRNA:rDNA Ratio journal November 1999
Relationship between phytoplankton cell size and the rate of orthophosphate uptake: in situ observations of an estuarine population journal January 1978
Diversity of total and active free-living vs. particle-attached bacteria in the euphotic zone of the NW Mediterranean Sea journal October 2009
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms journal March 2012
Intracellular Compartmentation in Planctomycetes journal October 2005
Dreissena and the disappearance of the spring phytoplankton bloom in Lake Michigan journal January 2010
Comparison of bacterial communities on limnic versus coastal marine particles reveals profound differences in colonization: Marine and limnic particle-associated bacteria journal April 2014
Metagenomic Sequencing of an In Vitro-Simulated Microbial Community journal April 2010
Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies journal December 2011
Bacterial diversity, community structure and potential growth rates along an estuarine salinity gradient journal August 2012
Dormancy contributes to the maintenance of microbial diversity journal March 2010
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 journal December 2014
Long-Term Characterization of Free-Living and Particle-Associated Bacterial Communities in Lake Tiefwaren Reveals Distinct Seasonal Patterns journal April 2012
Leucine incorporation by aerobic anoxygenic phototrophic bacteria in the Delaware estuary journal May 2014
Niche partitioning of the ubiquitous and ecologically relevant NS5 marine group journal February 2022
Comparative analysis of racial differences in breast tumor microbiome journal August 2020
Relationship between Abundance and Specific Activity of Bacterioplankton in Open Ocean Surface Waters journal October 2012
Isolation of Novel Ultramicrobacteria Classified as Actinobacteria from Five Freshwater Habitats in Europe and Asia journal March 2003

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59 BASIC BIOLOGICAL SCIENCES
estuary
great lakes
potential activity
protein synthesis potential
particle-associated
free-living
16S rRNA