Seasonal succession leads to habitat-dependent differentiation in ribosomal RNA:DNA ratios among freshwater lake bacteria
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 acrossmore »
- Authors:
-
- Univ. of Michigan, Ann Arbor, MI (United States)
- Publication Date:
- Research Org.:
- Univ. of Michigan, Ann Arbor, MI (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1257632
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Frontiers in Microbiology
- Additional Journal Information:
- Journal Volume: 7; Journal ID: ISSN 1664-302X
- Publisher:
- Frontiers Research Foundation
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; estuary; great lakes; potential activity; protein synthesis potential; particle-associated; free-living; 16S rRNA
Citation Formats
Denef, Vincent J., Fujimoto, Masanori, Berry, Michelle A., and Schmidt, Marian L. Seasonal succession leads to habitat-dependent differentiation in ribosomal RNA:DNA ratios among freshwater lake bacteria. United States: N. p., 2016.
Web. doi:10.3389/fmicb.2016.00606.
Denef, Vincent J., Fujimoto, Masanori, Berry, Michelle A., & Schmidt, Marian L. Seasonal succession leads to habitat-dependent differentiation in ribosomal RNA:DNA ratios among freshwater lake bacteria. United States. https://doi.org/10.3389/fmicb.2016.00606
Denef, Vincent J., Fujimoto, Masanori, Berry, Michelle A., and Schmidt, Marian L. Fri .
"Seasonal succession leads to habitat-dependent differentiation in ribosomal RNA:DNA ratios among freshwater lake bacteria". United States. https://doi.org/10.3389/fmicb.2016.00606. https://www.osti.gov/servlets/purl/1257632.
@article{osti_1257632,
title = {Seasonal succession leads to habitat-dependent differentiation in ribosomal RNA:DNA ratios among freshwater lake bacteria},
author = {Denef, Vincent J. and Fujimoto, Masanori and Berry, Michelle A. and Schmidt, Marian L.},
abstractNote = {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.},
doi = {10.3389/fmicb.2016.00606},
journal = {Frontiers in Microbiology},
number = ,
volume = 7,
place = {United States},
year = {Fri Apr 29 00:00:00 EDT 2016},
month = {Fri Apr 29 00:00:00 EDT 2016}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
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
- Lami, R.; Ghiglione, Jf; Desdevises, Y.
- Aquatic Microbial Ecology, Vol. 54
A single-cell view on the ecophysiology of anaerobic phototrophic bacteria
journal, November 2008
- Musat, N.; Halm, H.; Winterholler, B.
- Proceedings of the National Academy of Sciences, Vol. 105, Issue 46
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
- Stibal, Marek; Schostag, Morten; Cameron, Karen A.
- Environmental Microbiology Reports, Vol. 7, Issue 2
Metacommunity dynamics of bacteria in an arctic lake: the impact of species sorting and mass effects on bacterial production and biogeography
journal, March 2014
- Adams, Heather E.; Crump, Byron C.; Kling, George W.
- Frontiers in Microbiology, Vol. 5
Drivers shaping the diversity and biogeography of total and active bacterial communities in the South China Sea
journal, April 2014
- Zhang, Yao; Zhao, Zihao; Dai, Minhan
- Molecular Ecology, Vol. 23, Issue 9
Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform
journal, June 2013
- Kozich, James J.; Westcott, Sarah L.; Baxter, Nielson T.
- Applied and Environmental Microbiology, Vol. 79, Issue 17
Growth rates and rRNA content of four marine bacteria in pure cultures and in the Delaware estuary
journal, September 2015
- Lankiewicz, Thomas S.; Cottrell, Matthew T.; Kirchman, David L.
- The ISME Journal, Vol. 10, Issue 4
Responses of soil bacterial and fungal communities to extreme desiccation and rewetting
journal, July 2013
- Barnard, Romain L.; Osborne, Catherine A.; Firestone, Mary K.
- The ISME Journal, Vol. 7, Issue 11
RNA Preservation Agents and Nucleic Acid Extraction Method Bias Perceived Bacterial Community Composition
journal, March 2015
- McCarthy, Ann; Chiang, Edna; Schmidt, Marian L.
- PLOS ONE, Vol. 10, Issue 3
Active and total microbial communities in forest soil are largely different and highly stratified during decomposition
journal, July 2011
- Baldrian, Petr; Kolařík, Miroslav; Štursová, Martina
- The ISME Journal, Vol. 6, Issue 2
Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses
journal, July 2013
- Blazewicz, Steven J.; Barnard, Romain L.; Daly, Rebecca A.
- The ISME Journal, Vol. 7, Issue 11
The ecology of pelagic freshwater methylotrophs assessed by a high-resolution monitoring and isolation campaign
journal, May 2015
- Salcher, Michaela M.; Neuenschwander, Stefan M.; Posch, Thomas
- The ISME Journal, Vol. 9, Issue 11
Study of bacterial communities in Antarctic coastal waters by a combination of 16S rRNA and 16S rDNA sequencing
journal, December 2006
- Gentile, Gabriella; Giuliano, Laura; D'Auria, Giuseppe
- Environmental Microbiology, Vol. 8, Issue 12
A new method for non-parametric multivariate analysis of variance: NON-PARAMETRIC MANOVA FOR ECOLOGY
journal, February 2001
- Anderson, Marti J.
- Austral Ecology, Vol. 26, Issue 1
Reproducibility and quantitation of amplicon sequencing-based detection
journal, February 2011
- Zhou, Jizhong; Wu, Liyou; Deng, Ye
- The ISME Journal, Vol. 5, Issue 8
Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
journal, April 2014
- McMurdie, Paul J.; Holmes, Susan
- PLoS Computational Biology, Vol. 10, Issue 4
Vertical Distribution of Functional Potential and Active Microbial Communities in Meromictic Lake Kivu
journal, April 2015
- İnceoğlu, Özgul; Llirós, Marc; Crowe, Sean A.
- Microbial Ecology, Vol. 70, Issue 3
Comparison of cell-specific activity between free-living and attached bacteria using isolates and natural assemblages
journal, January 2007
- Grossart, Hans-Peter; Tang, Kam W.; Kiørboe, Thomas
- FEMS Microbiology Letters, Vol. 266, Issue 2
A Guide to the Natural History of Freshwater Lake Bacteria
journal, March 2011
- Newton, R. J.; Jones, S. E.; Eiler, A.
- Microbiology and Molecular Biology Reviews, Vol. 75, Issue 1
Phylogenetic conservatism of functional traits in microorganisms
journal, December 2012
- Martiny, Adam C.; Treseder, Kathleen; Pusch, Gordon
- The ISME Journal, Vol. 7, Issue 4
In situ substrate preferences of abundant bacterioplankton populations in a prealpine freshwater lake
journal, December 2012
- Salcher, Michaela M.; Posch, Thomas; Pernthaler, Jakob
- The ISME Journal, Vol. 7, Issue 5
Seasonal bloom dynamics and ecophysiology of the freshwater sister clade of SAR11 bacteria ‘that rule the waves’ (LD12)
journal, March 2011
- Salcher, Michaela M.; Pernthaler, Jakob; Posch, Thomas
- The ISME Journal, Vol. 5, Issue 8
Evaluation of metatranscriptomic protocols and application to the study of freshwater microbial communities: Metatranscriptomics of freshwater communities
journal, June 2014
- Tsementzi, Despina; Poretsky, Rachel; Rodriguez-R, Luis M.
- Environmental Microbiology Reports, Vol. 6, Issue 6
Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes
journal, November 2015
- Salazar, Guillem; Cornejo-Castillo, Francisco M.; Borrull, Encarna
- Molecular Ecology, Vol. 24, Issue 22
Community composition and activity state of estuarine bacterioplankton assessed using differential staining and metagenomic analysis of 16S rDNA and rRNA
journal, July 2013
- Franklin, Rb; Luria, C.; Shozo Ozaki, L.
- Aquatic Microbial Ecology, Vol. 69, Issue 3
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
journal, April 2013
- McMurdie, Paul J.; Holmes, Susan
- PLoS ONE, Vol. 8, Issue 4
Aquatic Microbiology for Ecosystem Scientists: New and Recycled Paradigms in Ecological Microbiology
journal, May 1999
- Cole, Jonathan J.
- Ecosystems, Vol. 2, Issue 3
Diel and Seasonal Variations in Abundance, Activity, and Community Structure of Particle-Attached and Free-Living Bacteria in NW Mediterranean Sea
journal, March 2007
- Ghiglione, J. F.; Mevel, G.; Pujo-Pay, M.
- Microbial Ecology, Vol. 54, Issue 2
A unique assemblage of cosmopolitan freshwater bacteria and higher community diversity differentiate an urbanized estuary from oligotrophic Lake Michigan
journal, September 2015
- Newton, Ryan J.; McLellan, Sandra L.
- Frontiers in Microbiology, Vol. 6
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
journal, November 2012
- Quast, Christian; Pruesse, Elmar; Yilmaz, Pelin
- Nucleic Acids Research, Vol. 41, Issue D1
Acidobacteria dominate the active bacterial communities of Arctic tundra with widely divergent winter-time snow accumulation and soil temperatures
journal, November 2012
- Männistö, Minna K.; Kurhela, Emilia; Tiirola, Marja
- FEMS Microbiology Ecology, Vol. 84, Issue 1
The Ecological Role of Water-Column Microbes in the Sea
journal, January 1983
- Azam, F.; Fenchel, T.; Field, Jg
- Marine Ecology Progress Series, Vol. 10
Phylogenetic conservation of freshwater lake habitat preference varies between abundant bacterioplankton phyla: Bacterial habitat preferences in freshwater lakes
journal, January 2016
- Schmidt, Marian L.; White, Jeffrey D.; Denef, Vincent J.
- Environmental Microbiology, Vol. 18, Issue 4
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
- Denef, Vincent J.; Mueller, Ryan S.; Chiang, Edna
- Applied and Environmental Microbiology, Vol. 82, Issue 5
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
- Eckert, Ester M.; Salcher, Michaela M.; Posch, Thomas
- Environmental Microbiology, Vol. 14, Issue 3
Microbial community structure and function on sinking particles in the North Pacific Subtropical Gyre
journal, May 2015
- Fontanez, Kristina M.; Eppley, John M.; Samo, Ty J.
- Frontiers in Microbiology, Vol. 6
Maximum growth rates and possible life strategies of different bacterioplankton groups in relation to phosphorus availability in a freshwater reservoir
journal, September 2006
- Šimek, Karel; Horňak, Karel; Jezbera, Jan
- Environmental Microbiology, Vol. 8, Issue 9
Major contribution of both zooplankton and protists to the top-down regulation of freshwater aerobic anoxygenic phototrophic bacteria
journal, September 2015
- Garcia-Chaves, Mc; Cottrell, Mt; Kirchman, Dl
- Aquatic Microbial Ecology, Vol. 76, Issue 1
Microbial seed banks: the ecological and evolutionary implications of dormancy
journal, January 2011
- Lennon, Jay T.; Jones, Stuart E.
- Nature Reviews Microbiology, Vol. 9, Issue 2
Activity of abundant and rare bacteria in a coastal ocean
journal, July 2011
- Campbell, B. J.; Yu, L.; Heidelberg, J. F.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 31
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
- Muttray, A. F.; Mohn, W. W.
- Microbial Ecology, Vol. 38, Issue 4
Relationship between phytoplankton cell size and the rate of orthophosphate uptake: in situ observations of an estuarine population
journal, January 1978
- Friebele, E. S.; Correll, D. L.; Faust, M. A.
- Marine Biology, Vol. 45, Issue 1
Diversity of total and active free-living vs. particle-attached bacteria in the euphotic zone of the NW Mediterranean Sea
journal, October 2009
- Ghiglione, Jean-François; Conan, Pascal; Pujo-Pay, Mireille
- FEMS Microbiology Letters, Vol. 299, Issue 1
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
journal, March 2012
- Caporaso, J. Gregory; Lauber, Christian L.; Walters, William A.
- The ISME Journal, Vol. 6, Issue 8
Intracellular Compartmentation in Planctomycetes
journal, October 2005
- Fuerst, John A.
- Annual Review of Microbiology, Vol. 59, Issue 1
Dreissena and the disappearance of the spring phytoplankton bloom in Lake Michigan
journal, January 2010
- Vanderploeg, Henry A.; Liebig, James R.; Nalepa, Thomas F.
- Journal of Great Lakes Research, Vol. 36
Comparison of bacterial communities on limnic versus coastal marine particles reveals profound differences in colonization: Marine and limnic particle-associated bacteria
journal, April 2014
- Bižić-Ionescu, Mina; Zeder, Michael; Ionescu, Danny
- Environmental Microbiology, Vol. 17, Issue 10
Metagenomic Sequencing of an In Vitro-Simulated Microbial Community
journal, April 2010
- Morgan, Jenna L.; Darling, Aaron E.; Eisen, Jonathan A.
- PLoS ONE, Vol. 5, Issue 4
Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies
journal, December 2011
- Schloss, Patrick D.; Gevers, Dirk; Westcott, Sarah L.
- PLoS ONE, Vol. 6, Issue 12
Bacterial diversity, community structure and potential growth rates along an estuarine salinity gradient
journal, August 2012
- Campbell, Barbara J.; Kirchman, David L.
- The ISME Journal, Vol. 7, Issue 1
Dormancy contributes to the maintenance of microbial diversity
journal, March 2010
- Jones, S. E.; Lennon, J. T.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 13
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014
- Love, Michael I.; Huber, Wolfgang; Anders, Simon
- Genome Biology, Vol. 15, Issue 12
Long-Term Characterization of Free-Living and Particle-Associated Bacterial Communities in Lake Tiefwaren Reveals Distinct Seasonal Patterns
journal, April 2012
- Rösel, Stefan; Allgaier, Martin; Grossart, Hans-Peter
- Microbial Ecology, Vol. 64, Issue 3
Leucine incorporation by aerobic anoxygenic phototrophic bacteria in the Delaware estuary
journal, May 2014
- Stegman, Monica R.; Cottrell, Matthew T.; Kirchman, David L.
- The ISME Journal, Vol. 8, Issue 11
Diel and Seasonal Variations in Abundance, Activity, and Community Structure of Particle-Attached and Free-Living Bacteria in NW Mediterranean Sea
journal, March 2007
- Ghiglione, J. F.; Mevel, G.; Pujo-Pay, M.
- Microbial Ecology, Vol. 54, Issue 2
Long-Term Characterization of Free-Living and Particle-Associated Bacterial Communities in Lake Tiefwaren Reveals Distinct Seasonal Patterns
journal, April 2012
- Rösel, Stefan; Allgaier, Martin; Grossart, Hans-Peter
- Microbial Ecology, Vol. 64, Issue 3
Aquatic Microbiology for Ecosystem Scientists: New and Recycled Paradigms in Ecological Microbiology
journal, May 1999
- Cole, Jonathan J.
- Ecosystems, Vol. 2, Issue 3
Dreissena and the disappearance of the spring phytoplankton bloom in Lake Michigan
journal, January 2010
- Vanderploeg, Henry A.; Liebig, James R.; Nalepa, Thomas F.
- Journal of Great Lakes Research, Vol. 36
Reproducibility and quantitation of amplicon sequencing-based detection
journal, February 2011
- Zhou, Jizhong; Wu, Liyou; Deng, Ye
- The ISME Journal, Vol. 5, Issue 8
Seasonal bloom dynamics and ecophysiology of the freshwater sister clade of SAR11 bacteria ‘that rule the waves’ (LD12)
journal, March 2011
- Salcher, Michaela M.; Pernthaler, Jakob; Posch, Thomas
- The ISME Journal, Vol. 5, Issue 8
Active and total microbial communities in forest soil are largely different and highly stratified during decomposition
journal, July 2011
- Baldrian, Petr; Kolařík, Miroslav; Štursová, Martina
- The ISME Journal, Vol. 6, Issue 2
In situ substrate preferences of abundant bacterioplankton populations in a prealpine freshwater lake
journal, December 2012
- Salcher, Michaela M.; Posch, Thomas; Pernthaler, Jakob
- The ISME Journal, Vol. 7, Issue 5
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
journal, March 2012
- Caporaso, J. Gregory; Lauber, Christian L.; Walters, William A.
- The ISME Journal, Vol. 6, Issue 8
Bacterial diversity, community structure and potential growth rates along an estuarine salinity gradient
journal, August 2012
- Campbell, Barbara J.; Kirchman, David L.
- The ISME Journal, Vol. 7, Issue 1
Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses
journal, July 2013
- Blazewicz, Steven J.; Barnard, Romain L.; Daly, Rebecca A.
- The ISME Journal, Vol. 7, Issue 11
Responses of soil bacterial and fungal communities to extreme desiccation and rewetting
journal, July 2013
- Barnard, Romain L.; Osborne, Catherine A.; Firestone, Mary K.
- The ISME Journal, Vol. 7, Issue 11
Leucine incorporation by aerobic anoxygenic phototrophic bacteria in the Delaware estuary
journal, May 2014
- Stegman, Monica R.; Cottrell, Matthew T.; Kirchman, David L.
- The ISME Journal, Vol. 8, Issue 11
Growth rates and rRNA content of four marine bacteria in pure cultures and in the Delaware estuary
journal, September 2015
- Lankiewicz, Thomas S.; Cottrell, Matthew T.; Kirchman, David L.
- The ISME Journal, Vol. 10, Issue 4
The ecology of pelagic freshwater methylotrophs assessed by a high-resolution monitoring and isolation campaign
journal, May 2015
- Salcher, Michaela M.; Neuenschwander, Stefan M.; Posch, Thomas
- The ISME Journal, Vol. 9, Issue 11
Niche partitioning of the ubiquitous and ecologically relevant NS5 marine group
journal, February 2022
- Priest, Taylor; Heins, Anneke; Harder, Jens
- The ISME Journal, Vol. 16, Issue 6
Comparative analysis of racial differences in breast tumor microbiome
journal, August 2020
- Thyagarajan, Srikantha; Zhang, Yan; Thapa, Santosh
- Scientific Reports, Vol. 10, Issue 1
A single-cell view on the ecophysiology of anaerobic phototrophic bacteria
journal, November 2008
- Musat, N.; Halm, H.; Winterholler, B.
- Proceedings of the National Academy of Sciences, Vol. 105, Issue 46
Dormancy contributes to the maintenance of microbial diversity
journal, March 2010
- Jones, S. E.; Lennon, J. T.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 13
Activity of abundant and rare bacteria in a coastal ocean
journal, July 2011
- Campbell, B. J.; Yu, L.; Heidelberg, J. F.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 31
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
journal, November 2012
- Quast, Christian; Pruesse, Elmar; Yilmaz, Pelin
- Nucleic Acids Research, Vol. 41, Issue D1
Comparison of bacterial communities on limnic versus coastal marine particles reveals profound differences in colonization: Marine and limnic particle-associated bacteria
journal, April 2014
- Bižić-Ionescu, Mina; Zeder, Michael; Ionescu, Danny
- Environmental Microbiology, Vol. 17, Issue 10
Acidobacteria dominate the active bacterial communities of Arctic tundra with widely divergent winter-time snow accumulation and soil temperatures
journal, November 2012
- Männistö, Minna K.; Kurhela, Emilia; Tiirola, Marja
- FEMS Microbiology Ecology, Vol. 84, Issue 1
Evaluation of metatranscriptomic protocols and application to the study of freshwater microbial communities: Metatranscriptomics of freshwater communities
journal, June 2014
- Tsementzi, Despina; Poretsky, Rachel; Rodriguez-R, Luis M.
- Environmental Microbiology Reports, Vol. 6, Issue 6
Maximum growth rates and possible life strategies of different bacterioplankton groups in relation to phosphorus availability in a freshwater reservoir
journal, September 2006
- Šimek, Karel; Horňak, Karel; Jezbera, Jan
- Environmental Microbiology, Vol. 8, Issue 9
Study of bacterial communities in Antarctic coastal waters by a combination of 16S rRNA and 16S rDNA sequencing
journal, December 2006
- Gentile, Gabriella; Giuliano, Laura; D'Auria, Giuseppe
- Environmental Microbiology, Vol. 8, Issue 12
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
- Eckert, Ester M.; Salcher, Michaela M.; Posch, Thomas
- Environmental Microbiology, Vol. 14, Issue 3
Comparison of cell-specific activity between free-living and attached bacteria using isolates and natural assemblages
journal, January 2007
- Grossart, Hans-Peter; Tang, Kam W.; Kiørboe, Thomas
- FEMS Microbiology Letters, Vol. 266, Issue 2
Diversity of total and active free-living vs. particle-attached bacteria in the euphotic zone of the NW Mediterranean Sea
journal, October 2009
- Ghiglione, Jean-François; Conan, Pascal; Pujo-Pay, Mireille
- FEMS Microbiology Letters, Vol. 299, Issue 1
Drivers shaping the diversity and biogeography of total and active bacterial communities in the South China Sea
journal, April 2014
- Zhang, Yao; Zhao, Zihao; Dai, Minhan
- Molecular Ecology, Vol. 23, Issue 9
Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes
journal, November 2015
- Salazar, Guillem; Cornejo-Castillo, Francisco M.; Borrull, Encarna
- Molecular Ecology, Vol. 24, Issue 22
Relationship between Abundance and Specific Activity of Bacterioplankton in Open Ocean Surface Waters
journal, October 2012
- Hunt, Dana E.; Lin, Yajuan; Church, Matthew J.
- Applied and Environmental Microbiology, Vol. 79, Issue 1
Isolation of Novel Ultramicrobacteria Classified as Actinobacteria from Five Freshwater Habitats in Europe and Asia
journal, March 2003
- Hahn, M. W.; Lunsdorf, H.; Wu, Q.
- Applied and Environmental Microbiology, Vol. 69, Issue 3
Intracellular Compartmentation in Planctomycetes
journal, October 2005
- Fuerst, John A.
- Annual Review of Microbiology, Vol. 59, Issue 1
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014
- Love, Michael I.; Huber, Wolfgang; Anders, Simon
- Genome Biology, Vol. 15, Issue 12
Metagenomic Sequencing of an In Vitro-Simulated Microbial Community
journal, April 2010
- Morgan, Jenna L.; Darling, Aaron E.; Eisen, Jonathan A.
- PLoS ONE, Vol. 5, Issue 4
Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies
journal, December 2011
- Schloss, Patrick D.; Gevers, Dirk; Westcott, Sarah L.
- PLoS ONE, Vol. 6, Issue 12
RNA Preservation Agents and Nucleic Acid Extraction Method Bias Perceived Bacterial Community Composition
journal, March 2015
- McCarthy, Ann; Chiang, Edna; Schmidt, Marian L.
- PLOS ONE, Vol. 10, Issue 3
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
- Lami, R.; Ghiglione, Jf; Desdevises, Y.
- Aquatic Microbial Ecology, Vol. 54
Community composition and activity state of estuarine bacterioplankton assessed using differential staining and metagenomic analysis of 16S rDNA and rRNA
journal, July 2013
- Franklin, Rb; Luria, C.; Shozo Ozaki, L.
- Aquatic Microbial Ecology, Vol. 69, Issue 3
Major contribution of both zooplankton and protists to the top-down regulation of freshwater aerobic anoxygenic phototrophic bacteria
journal, September 2015
- Garcia-Chaves, Mc; Cottrell, Mt; Kirchman, Dl
- Aquatic Microbial Ecology, Vol. 76, Issue 1
Metacommunity dynamics of bacteria in an arctic lake: the impact of species sorting and mass effects on bacterial production and biogeography
journal, March 2014
- Adams, Heather E.; Crump, Byron C.; Kling, George W.
- Frontiers in Microbiology, Vol. 5
Microbial community structure and function on sinking particles in the North Pacific Subtropical Gyre
journal, May 2015
- Fontanez, Kristina M.; Eppley, John M.; Samo, Ty J.
- Frontiers in Microbiology, Vol. 6
A unique assemblage of cosmopolitan freshwater bacteria and higher community diversity differentiate an urbanized estuary from oligotrophic Lake Michigan
journal, September 2015
- Newton, Ryan J.; McLellan, Sandra L.
- Frontiers in Microbiology, Vol. 6
Works referencing / citing this record:
Microbial Mat Compositional and Functional Sensitivity to Environmental Disturbance
journal, October 2016
- Preisner, Eva C.; Fichot, Erin B.; Norman, Robert S.
- Frontiers in Microbiology, Vol. 7
Illuminating the functional rare biosphere of the Greenland Ice Sheet’s Dark Zone
posted_content, June 2019
- Gokul, Jarishma K.; Cameron, Karen A.; Irvine-Fynn, Tristram D. L.
- BioRxiv
Hidden in plain sight—highly abundant and diverse planktonic freshwater Chloroflexi
text, January 2018
- Mehrshad, Maliheh; Salcher, Michaela M.; Okazaki, Yusuke
- BioMed Central
Hidden in plain sight—highly abundant and diverse planktonic freshwater Chloroflexi
journal, October 2018
- Mehrshad, Maliheh; Salcher, Michaela M.; Okazaki, Yusuke
- Microbiome, Vol. 6, Issue 1
Feather mites play a role in cleaning host feathers: New insights from DNA metabarcoding and microscopy
journal, May 2018
- Doña, Jorge; Proctor, Heather; Serrano, David
- Molecular Ecology, Vol. 28, Issue 2
Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem
journal, February 2020
- Zhu, Xinyu; Campanaro, Stefano; Treu, Laura
- Microbiome, Vol. 8, Issue 1
Microbial Mat Compositional and Functional Sensitivity to Environmental Disturbance
journal, October 2016
- Preisner, Eva C.; Fichot, Erin B.; Norman, Robert S.
- Frontiers in Microbiology, Vol. 7