Freshwater carbon and nutrient cycles revealed through reconstructed population genomes
Abstract
Although microbes mediate much of the biogeochemical cycling in freshwater, the categories of carbon and nutrients currently used in models of freshwater biogeochemical cycling are too broad to be relevant on a microbial scale. One way to improve these models is to incorporate microbial data. Here, we analyze both genes and genomes from three metagenomic time series and propose specific roles for microbial taxa in freshwater biogeochemical cycles. Our metagenomic time series span multiple years and originate from a eutrophic lake (Lake Mendota) and a humic lake (Trout Bog Lake) with contrasting water chemistry. Our analysis highlights the role of polyamines in the nitrogen cycle, the diversity of diazotrophs between lake types, the balance of assimilatory vs. dissimilatory sulfate reduction in freshwater, the various associations between types of phototrophy and carbon fixation, and the density and diversity of glycoside hydrolases in freshwater microbes. We also investigated aspects of central metabolism such as hydrogen metabolism, oxidative phosphorylation, methylotrophy, and sugar degradation. Finally, by analyzing the dynamics over time in nitrogen fixation genes and Cyanobacteria genomes, we show that the potential for nitrogen fixation is linked to specific populations in Lake Mendota. This work represents an important step towards incorporating microbial datamore »
- Authors:
-
[1];
[1];
[1];
- Univ. of Wisconsin-Madison, Madison, WI (United States)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Uppsala Univ., Uppsala (Sweden)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1510750
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- PeerJ
- Additional Journal Information:
- Journal Volume: 6; Journal Issue: 12; Journal ID: ISSN 2167-8359
- Publisher:
- PeerJ Inc.
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 58 GEOSCIENCES; Freshwater; Metabolism; Carbon cycling; Nutrient cycling; Microbial communities
Citation Formats
Linz, Alexandra M., He, Shaomei, Stevens, Sarah L. R., Anantharaman, Karthik, Rohwer, Robin R., Malmstrom, Rex R., Bertilsson, Stefan, and McMahon, Katherine D. Freshwater carbon and nutrient cycles revealed through reconstructed population genomes. United States: N. p., 2018.
Web. doi:10.7717/peerj.6075.
Linz, Alexandra M., He, Shaomei, Stevens, Sarah L. R., Anantharaman, Karthik, Rohwer, Robin R., Malmstrom, Rex R., Bertilsson, Stefan, & McMahon, Katherine D. Freshwater carbon and nutrient cycles revealed through reconstructed population genomes. United States. https://doi.org/10.7717/peerj.6075
Linz, Alexandra M., He, Shaomei, Stevens, Sarah L. R., Anantharaman, Karthik, Rohwer, Robin R., Malmstrom, Rex R., Bertilsson, Stefan, and McMahon, Katherine D. Mon .
"Freshwater carbon and nutrient cycles revealed through reconstructed population genomes". United States. https://doi.org/10.7717/peerj.6075. https://www.osti.gov/servlets/purl/1510750.
@article{osti_1510750,
title = {Freshwater carbon and nutrient cycles revealed through reconstructed population genomes},
author = {Linz, Alexandra M. and He, Shaomei and Stevens, Sarah L. R. and Anantharaman, Karthik and Rohwer, Robin R. and Malmstrom, Rex R. and Bertilsson, Stefan and McMahon, Katherine D.},
abstractNote = {Although microbes mediate much of the biogeochemical cycling in freshwater, the categories of carbon and nutrients currently used in models of freshwater biogeochemical cycling are too broad to be relevant on a microbial scale. One way to improve these models is to incorporate microbial data. Here, we analyze both genes and genomes from three metagenomic time series and propose specific roles for microbial taxa in freshwater biogeochemical cycles. Our metagenomic time series span multiple years and originate from a eutrophic lake (Lake Mendota) and a humic lake (Trout Bog Lake) with contrasting water chemistry. Our analysis highlights the role of polyamines in the nitrogen cycle, the diversity of diazotrophs between lake types, the balance of assimilatory vs. dissimilatory sulfate reduction in freshwater, the various associations between types of phototrophy and carbon fixation, and the density and diversity of glycoside hydrolases in freshwater microbes. We also investigated aspects of central metabolism such as hydrogen metabolism, oxidative phosphorylation, methylotrophy, and sugar degradation. Finally, by analyzing the dynamics over time in nitrogen fixation genes and Cyanobacteria genomes, we show that the potential for nitrogen fixation is linked to specific populations in Lake Mendota. This work represents an important step towards incorporating microbial data into ecosystem models and provides a better understanding of how microbes may participate in freshwater biogeochemical cycling.},
doi = {10.7717/peerj.6075},
journal = {PeerJ},
number = 12,
volume = 6,
place = {United States},
year = {Mon Dec 10 00:00:00 EST 2018},
month = {Mon Dec 10 00:00:00 EST 2018}
}
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Works referenced in this record:
Polyamine transport in bacteria and yeast
journal, December 1999
- Igarashi, Kazuei; Kashiwagi, Keiko
- Biochemical Journal, Vol. 344, Issue 3
Ananke: temporal clustering reveals ecological dynamics of microbial communities
journal, January 2017
- Hall, Michael W.; Rohwer, Robin R.; Perrie, Jonathan
- PeerJ, Vol. 5
Green sulphur bacteria as a component of the photosynthetic plankton community in small dimictic humic lakes with an anoxic hypolimnion
journal, March 2013
- Karhunen, J.; Arvola, L.; Peura, S.
- Aquatic Microbial Ecology, Vol. 68, Issue 3
Both Forward and Reverse TCA Cycles Operate in Green Sulfur Bacteria
journal, July 2010
- Tang, Kuo-Hsiang; Blankenship, Robert E.
- Journal of Biological Chemistry, Vol. 285, Issue 46
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
journal, July 2006
- DeSantis, T. Z.; Hugenholtz, P.; Larsen, N.
- Applied and Environmental Microbiology, Vol. 72, Issue 7, p. 5069-5072
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
journal, August 2017
- Bowers, Robert M.; Kyrpides, Nikos C.; Stepanauskas, Ramunas
- Nature Biotechnology, Vol. 35, Issue 8
A ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO)-like protein from Chlorobium tepidum that is involved with sulfur metabolism and the response to oxidative stress
journal, April 2001
- Hanson, T. E.; Tabita, F. R.
- Proceedings of the National Academy of Sciences, Vol. 98, Issue 8
Whole-lake mineralization of allochthonous and autochthonous organic carbon in a large humic lake (örträsket, N. Sweden)
journal, November 2001
- Jonsson, Anders; Meili, Markus; Bergström, Ann-Kristin
- Limnology and Oceanography, Vol. 46, Issue 7
dbCAN2: a meta server for automated carbohydrate-active enzyme annotation
journal, May 2018
- Zhang, Han; Yohe, Tanner; Huang, Le
- Nucleic Acids Research, Vol. 46, Issue W1
[FeFe]- and [NiFe]-hydrogenase diversity, mechanism, and maturation
journal, June 2015
- Peters, John W.; Schut, Gerrit J.; Boyd, Eric S.
- Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, Vol. 1853, Issue 6
Interannual dynamics and phenology of bacterial communities in a eutrophic lake
journal, March 2007
- Shade, Ashley; Kent, Angela D.; Jones, Stuart E.
- Limnology and Oceanography, Vol. 52, Issue 2
Lakes and streams as sentinels of environmental change in terrestrial and atmospheric processes
journal, June 2008
- Williamson, Craig E.; Dodds, Walter; Kratz, Timothy K.
- Frontiers in Ecology and the Environment, Vol. 6, Issue 5
Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes
journal, December 2004
- Eiler, Alexander; Bertilsson, Stefan
- Environmental Microbiology, Vol. 6, Issue 12
Distinct and diverse anaerobic bacterial communities in boreal lakes dominated by candidate division OD1
journal, March 2012
- Peura, Sari; Eiler, Alexander; Bertilsson, Stefan
- The ISME Journal, Vol. 6, Issue 9
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
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
journal, March 2010
- Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P.
- PLoS ONE, Vol. 5, Issue 3
Methylotrophy in Methylobacterium extorquens AM1 from a Genomic Point of View
journal, May 2003
- Chistoserdova, L.; Chen, S. -W.; Lapidus, A.
- Journal of Bacteriology, Vol. 185, Issue 10
Algae–bacteria interactions: Evolution, ecology and emerging applications
journal, January 2016
- Ramanan, Rishiram; Kim, Byung-Hyuk; Cho, Dae-Hyun
- Biotechnology Advances, Vol. 34, Issue 1
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
Minimus: a fast, lightweight genome assembler
journal, January 2007
- Sommer, Daniel D.; Delcher, Arthur L.; Salzberg, Steven L.
- BMC Bioinformatics, Vol. 8, Issue 1
The Role of Nitrogen Fixation in Cyanobacterial Bloom Toxicity in a Temperate, Eutrophic Lake
journal, February 2013
- Beversdorf, Lucas J.; Miller, Todd R.; McMahon, Katherine D.
- PLoS ONE, Vol. 8, Issue 2
IMG: the integrated microbial genomes database and comparative analysis system
journal, December 2011
- Markowitz, V. M.; Chen, I. -M. A.; Palaniappan, K.
- Nucleic Acids Research, Vol. 40, Issue D1
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
Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010
- Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F.
- BMC Bioinformatics, Vol. 11, Issue 1
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
journal, January 2015
- Kang, Dongwan D.; Froula, Jeff; Egan, Rob
- PeerJ, Vol. 3
Investigation of XoxF methanol dehydrogenases reveals new methylotrophic bacteria in pelagic marine and freshwater ecosystems
journal, August 2015
- Ramachandran, Arthi; Walsh, David A.
- FEMS Microbiology Ecology, Vol. 91, Issue 10
Autochthonous versus allochthonous carbon sources of bacteria: Results from whole-lake 13 C addition experiments
journal, March 2004
- Kritzberg, Emma S.; Cole, Jonathan J.; Pace, Michael L.
- Limnology and Oceanography, Vol. 49, Issue 2
Microbial species delineation using whole genome sequences
journal, July 2015
- Varghese, Neha J.; Mukherjee, Supratim; Ivanova, Natalia
- Nucleic Acids Research, Vol. 43, Issue 14
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
journal, May 2015
- Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T.
- Genome Research, Vol. 25, Issue 7
Fast and accurate long-read alignment with Burrows–Wheeler transform
journal, January 2010
- Li, Heng; Durbin, Richard
- Bioinformatics, Vol. 26, Issue 5
FLASH: fast length adjustment of short reads to improve genome assemblies
journal, September 2011
- Magoc, T.; Salzberg, S. L.
- Bioinformatics, Vol. 27, Issue 21
Reshaping Data with the reshape Package
journal, January 2007
- Wickham, Hadley
- Journal of Statistical Software, Vol. 21, Issue 12
Ray Meta: scalable de novo metagenome assembly and profiling
journal, January 2012
- Boisvert, Sébastien; Raymond, Frédéric; Godzaridis, Élénie
- Genome Biology, Vol. 13, Issue 12
Metatranscriptomic signature of exogenous polyamine utilization by coastal bacterioplankton: Polyamine-transforming genes in marine bacterial communities
journal, September 2011
- Mou, Xiaozhen; Vila-Costa, Maria; Sun, Shulei
- Environmental Microbiology Reports, Vol. 3, Issue 6
Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria
journal, January 2016
- Eiler, Alexander; Mondav, Rhiannon; Sinclair, Lucas
- The ISME Journal, Vol. 10, Issue 8
Reconstructing the various facets of dissolved organic carbon bioavailability in freshwater ecosystems
journal, March 2011
- Guillemette, François; del Giorgio, Paul A.
- Limnology and Oceanography, Vol. 56, Issue 2
Experimental factors affecting PCR-based estimates of microbial species richness and evenness
journal, January 2010
- Engelbrektson, Anna; Kunin, Victor; Wrighton, Kelly C.
- The ISME Journal, Vol. 4, Issue 5
Heterotrophic Bacterial Growth Efficiency and Community Structure at Different Natural Organic Carbon Concentrations
journal, July 2003
- Eiler, A.; Langenheder, S.; Bertilsson, S.
- Applied and Environmental Microbiology, Vol. 69, Issue 7
Plumbing the Global Carbon Cycle: Integrating Inland Waters into the Terrestrial Carbon Budget
journal, February 2007
- Cole, J. J.; Prairie, Y. T.; Caraco, N. F.
- Ecosystems, Vol. 10, Issue 1
Temporal Patterns in Glycolate-Utilizing Bacterial Community Composition Correlate with Phytoplankton Population Dynamics in Humic Lakes
journal, July 2010
- Paver, Sara F.; Kent, Angela D.
- Microbial Ecology, Vol. 60, Issue 2
Metagenomic insights into strategies of aerobic and anaerobic carbon and nitrogen transformation in boreal lakes
journal, July 2015
- Peura, Sari; Sinclair, Lucas; Bertilsson, Stefan
- Scientific Reports, Vol. 5, Issue 1
Capturing Single Cell Genomes of Active Polysaccharide Degraders: An Unexpected Contribution of Verrucomicrobia
journal, April 2012
- Martinez-Garcia, Manuel; Brazel, David M.; Swan, Brandon K.
- PLoS ONE, Vol. 7, Issue 4
VSEARCH: a versatile open source tool for metagenomics
journal, January 2016
- Rognes, Torbjørn; Flouri, Tomáš; Nichols, Ben
- PeerJ, Vol. 4
Microcystin mcyA and mcyE Gene Abundances Are Not Appropriate Indicators of Microcystin Concentrations in Lakes
journal, May 2015
- Beversdorf, Lucas J.; Chaston, Sheena D.; Miller, Todd R.
- PLOS ONE, Vol. 10, Issue 5
Molecular Characterization of Methanotrophic Isolates from Freshwater Lake Sediment
journal, December 2000
- Auman, A. J.; Stolyar, S.; Costello, A. M.
- Applied and Environmental Microbiology, Vol. 66, Issue 12
Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics
journal, October 2017
- Roux, Simon; Chan, Leong-Keat; Egan, Rob
- Nature Communications, Vol. 8, Issue 1
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
journal, October 2009
- Schloss, P. D.; Westcott, S. L.; Ryabin, T.
- Applied and Environmental Microbiology, Vol. 75, Issue 23, p. 7537-7541
BLAST+: architecture and applications
journal, January 2009
- Camacho, Christiam; Coulouris, George; Avagyan, Vahram
- BMC Bioinformatics, Vol. 10, Issue 1
Sulfur globule oxidation in green sulfur bacteria is dependent on the dissimilatory sulfite reductase system
journal, January 2011
- Holkenbrink, C.; Barbas, S. O.; Mellerup, A.
- Microbiology, Vol. 157, Issue 4
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
journal, December 2012
- Luo, Ruibang; Liu, Binghang; Xie, Yinlong
- GigaScience, Vol. 1, Issue 1
Characterization of isocitrate dehydrogenase from the green sulfur bacterium Chlorobium limicola. A carbon dioxide-fixing enzyme in the reductive tricarboxylic acid cycle
journal, April 2002
- Kanao, Tadayoshi; Kawamura, Mineko; Fukui, Toshiaki
- European Journal of Biochemistry, Vol. 269, Issue 7
Biogenic Amines in Fish: Roles in Intoxication, Spoilage, and Nitrosamine Formation—A Review
journal, February 2009
- Bulushi, Ismail Al; Poole, Susan; Deeth, Hilton C.
- Critical Reviews in Food Science and Nutrition, Vol. 49, Issue 4
Polymeric and free sugars released by three phytoplanktonic species from a freshwater tropical eutrophic reservoir
journal, July 2005
- Giroldo, Danilo; Vieira, Armando Augusto Henriques
- Journal of Plankton Research, Vol. 27, Issue 7
TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution
journal, September 2018
- Rohwer, Robin R.; Hamilton, Joshua J.; Newton, Ryan J.
- mSphere, Vol. 3, Issue 5
Aquatic carbon cycling in the conterminous United States and implications for terrestrial carbon accounting
journal, December 2015
- Butman, David; Stackpoole, Sarah; Stets, Edward
- Proceedings of the National Academy of Sciences, Vol. 113, Issue 1
PhyloSift: phylogenetic analysis of genomes and metagenomes
journal, January 2014
- Darling, Aaron E.; Jospin, Guillaume; Lowe, Eric
- PeerJ, Vol. 2
The Phylogenetic Position of the Family Methylococcaceae
journal, July 1995
- Bowman, J. P.; Sly, L. I.; Stackebrandt, E.
- International Journal of Systematic Bacteriology, Vol. 45, Issue 3
Denitrification Across Landscapes and Waterscapes: a Synthesis
journal, December 2006
- Seitzinger, S.; Harrison, J. A.; Böhlke, J. K.
- Ecological Applications, Vol. 16, Issue 6
The Passive Yet Successful Way of Planktonic Life: Genomic and Experimental Analysis of the Ecology of a Free-Living Polynucleobacter Population
journal, March 2012
- Hahn, Martin W.; Scheuerl, Thomas; Jezberová, Jitka
- PLoS ONE, Vol. 7, Issue 3
APE: Analyses of Phylogenetics and Evolution in R language
journal, January 2004
- Paradis, E.; Claude, J.; Strimmer, K.
- Bioinformatics, Vol. 20, Issue 2
Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage
journal, August 2014
- Ghylin, Trevor W.; Garcia, Sarahi L.; Moya, Francisco
- The ISME Journal, Vol. 8, Issue 12
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system
journal, October 2016
- Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A.
- Nature Communications, Vol. 7, Issue 1
Insights into the phylogeny and coding potential of microbial dark matter
journal, July 2013
- Rinke, Christian; Schwientek, Patrick; Sczyrba, Alexander
- Nature, Vol. 499, Issue 7459
Structural and sequence-based classification of glycoside hydrolases
journal, October 1997
- Henrissat, Bernard; Davies, Gideon
- Current Opinion in Structural Biology, Vol. 7, Issue 5, p. 637-644
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
Eutrophication of freshwater and coastal marine ecosystems a global problem
journal, March 2003
- Smith, Val H.
- Environmental Science and Pollution Research, Vol. 10, Issue 2
Whole-Genome Analysis of the Methyl tert-Butyl Ether-Degrading Beta-Proteobacterium Methylibium petroleiphilum PM1
journal, December 2006
- Kane, S. R.; Chakicherla, A. Y.; Chain, P. S. G.
- Journal of Bacteriology, Vol. 189, Issue 5
Global rates of marine sulfate reduction and implications for sub-sea-floor metabolic activities
journal, May 2014
- Bowles, M. W.; Mogollon, J. M.; Kasten, S.
- Science, Vol. 344, Issue 6186
Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations
journal, January 2016
- Bendall, Matthew L.; Stevens, Sarah LR; Chan, Leong-Keat
- The ISME Journal, Vol. 10, Issue 7
High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton
journal, June 2011
- Martinez-Garcia, Manuel; Swan, Brandon K.; Poulton, Nicole J.
- The ISME Journal, Vol. 6, Issue 1
Novel methylotrophic isolates from lake sediment, description of Methylotenera versatilis sp. nov. and emended description of the genus Methylotenera
journal, February 2011
- Kalyuzhnaya, M. G.; Beck, D. A. C.; Vorobev, A.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 62, Issue 1
Mesobacillus aurantius sp. nov., isolated from an orange-colored pond near a solar saltern
journal, January 2021
- Rai, Anusha; Smita, N.; Shabbir, A.
- Archives of Microbiology, Vol. 203, Issue 4
Coriander Genomics Database: a genomic, transcriptomic, and metabolic database for coriander
journal, April 2020
- Song, Xiaoming; Nie, Fulei; Chen, Wei
- Horticulture Research, Vol. 7, Issue 1
Production of viable chicken by allogeneic transplantation of primordial germ cells induced from somatic cells
journal, May 2021
- Zhao, Ruifeng; Zuo, Qisheng; Yuan, Xia
- Nature Communications, Vol. 12, Issue 1
Microbial Dysbiosis During Simian Immunodeficiency Virus Infection is Partially Reverted with Combination Anti-retroviral Therapy
journal, April 2020
- Blum, Faith C.; Hardy, Britney L.; Bishop-Lilly, Kimberly A.
- Scientific Reports, Vol. 10, Issue 1
The ecology of pelagic freshwater methylotrophs assessed by a high-resolution monitoring and isolation campaign
text, January 2015
- Salcher, Michaela M.; Neuenschwander, Stefan M.; Posch, Thomas
- Nature Publishing Group
VSEARCH: a versatile open source tool for metagenomics
text, January 2016
- Rognes, Torbjorn; Flouri, Tomas; Nichols, Ben
- Karlsruhe
Polyamine transport in bacteria and yeast
journal, December 1999
- Igarashi, Kazuei; Kashiwagi, Keiko
- Biochemical Journal, Vol. 344, Issue 3
Whole-Genome Analysis of the Methyl tert -Butyl Ether-Degrading Beta-Proteobacterium Methylibium petroleiphilum PM1
journal, July 2007
- Kane, Staci R.; Chakicherla, Anu Y.; Chain, Patrick S. G.
- Journal of Bacteriology, Vol. 189, Issue 13
Capturing Single Cell Genomes of Active Polysaccharide Degraders: An Unexpected Contribution of Verrucomicrobia
text, January 2012
- Gary, Xie,; K., Swan, Brandon; G., Chain, Patrick S.
- The University of North Carolina at Chapel Hill University Libraries
In situ substrate preferences of abundant bacterioplankton populations in a prealpine freshwater lake
text, January 2013
- M., Salcher, Michaela; Thomas, Posch,; Jakob, Pernthaler,
- Nature Publishing Group
The Phylogenetic Position of the Family Methylococcaceae
journal, January 1995
- Bowman, J. P.; Sly, L. I.; Stackebrandt, E.
- International Journal of Systematic Bacteriology, Vol. 45, Issue 1
Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes
journal, March 2007
- Eiler, Alexander; Bertilsson, Stefan
- Environmental Microbiology, Vol. 9, Issue 3
PhyloSift: Phylogenetic analysis of genomes and metagenomes
dataset, January 2013
- Bik, Holly; Matsen, Erick; Lowe, Eric
- figshare
Microbial Observatory at North Temperate Lakes LTER High-resolution temporal and spatial dynamics of microbial community structure in freshwater bog lakes 2005 - 2009 original format
dataset, January 2017
- McMahon, Katherine; Jones, Stuart; Shade, Ashley
- Environmental Data Initiative
PhyloSift: Phylogenetic analysis of genomes and metagenomes
dataset, January 2013
- Bik, Holly; Matsen, Erick; Lowe, Eric
- Figshare
Microbial Observatory at North Temperate Lakes LTER High-resolution temporal and spatial dynamics of microbial community structure in freshwater bog lakes 2005 - 2009 original format
dataset, January 2017
- McMahon, Katherine; Jones, Stuart; Shade, Ashley
- Environmental Data Initiative
Microbial Observatory at North Temperate Lakes LTER High-resolution temporal and spatial dynamics of microbial community structure in freshwater bog lakes 2005 - 2009 original format
dataset, January 2019
- McMahon, Katherine; Jones, Stuart; Shade, Ashley
- Environmental Data Initiative
Temporal Patterns in Glycolate-Utilizing Bacterial Community Composition Correlate with Phytoplankton Population Dynamics in Humic Lakes
journal, July 2010
- Paver, Sara F.; Kent, Angela D.
- Microbial Ecology, Vol. 60, Issue 2
Salinimonas marina sp. nov. Isolated from Jeju Island Marine Sediment
journal, June 2021
- Kim, Minji; Lee, Ki-Eun; Cha, In-Tae
- Current Microbiology, Vol. 78, Issue 8
Plumbing the Global Carbon Cycle: Integrating Inland Waters into the Terrestrial Carbon Budget
journal, February 2007
- Cole, J. J.; Prairie, Y. T.; Caraco, N. F.
- Ecosystems, Vol. 10, Issue 1
Lysobacter ciconiae sp. nov., and Lysobacter avium sp. nov., isolated from the faeces of an Oriental stork
journal, March 2022
- Lee, So-Yeon; Kim, Pil Soo; Sung, Hojun
- Journal of Microbiology, Vol. 60, Issue 5
[FeFe]- and [NiFe]-hydrogenase diversity, mechanism, and maturation
journal, June 2015
- Peters, John W.; Schut, Gerrit J.; Boyd, Eric S.
- Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, Vol. 1853, Issue 6
Algae–bacteria interactions: Evolution, ecology and emerging applications
journal, January 2016
- Ramanan, Rishiram; Kim, Byung-Hyuk; Cho, Dae-Hyun
- Biotechnology Advances, Vol. 34, Issue 1
Experimental factors affecting PCR-based estimates of microbial species richness and evenness
journal, January 2010
- Engelbrektson, Anna; Kunin, Victor; Wrighton, Kelly C.
- The ISME Journal, Vol. 4, Issue 5
High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton
journal, June 2011
- Martinez-Garcia, Manuel; Swan, Brandon K.; Poulton, Nicole J.
- The ISME Journal, Vol. 6, Issue 1
Distinct and diverse anaerobic bacterial communities in boreal lakes dominated by candidate division OD1
journal, March 2012
- Peura, Sari; Eiler, Alexander; Bertilsson, Stefan
- The ISME Journal, Vol. 6, Issue 9
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
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
Insights into the phylogeny and coding potential of microbial dark matter
journal, July 2013
- Rinke, Christian; Schwientek, Patrick; Sczyrba, Alexander
- Nature, Vol. 499, Issue 7459
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
journal, August 2017
- Bowers, Robert M.; Kyrpides, Nikos C.; Stepanauskas, Ramunas
- Nature Biotechnology, Vol. 35, Issue 8
Erratum: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
journal, July 2018
- Bowers, Robert M.; Kyrpides, Nikos C.; Stepanauskas, Ramunas
- Nature Biotechnology, Vol. 36, Issue 7
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system
journal, October 2016
- Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A.
- Nature Communications, Vol. 7, Issue 1
Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics
journal, October 2017
- Roux, Simon; Chan, Leong-Keat; Egan, Rob
- Nature Communications, Vol. 8, Issue 1
Horizontal gene transfer enables programmable gene stability in synthetic microbiota
journal, September 2022
- Wang, Teng; Weiss, Andrea; Aqeel, Ammara
- Nature Chemical Biology, Vol. 18, Issue 11
Metagenomic insights into strategies of aerobic and anaerobic carbon and nitrogen transformation in boreal lakes
journal, July 2015
- Peura, Sari; Sinclair, Lucas; Bertilsson, Stefan
- Scientific Reports, Vol. 5, Issue 1
Polyamine transport in bacteria and yeast
journal, December 1999
- Igarashi, Kazuei; Kashiwagi, Keiko
- Biochemical Journal, Vol. 344, Issue 3
Characterization of isocitrate dehydrogenase from the green sulfur bacterium Chlorobium limicola: A carbon dioxide-fixing enzyme in the reductive tricarboxylic acid cycle
journal, April 2002
- Kanao, Tadayoshi; Kawamura, Mineko; Fukui, Toshiaki
- European Journal of Biochemistry, Vol. 269, Issue 7, p. 1926-1931
Eutrophication of freshwater and coastal marine ecosystems a global problem
journal, March 2003
- Smith, Val H.
- Environmental Science and Pollution Research, Vol. 10, Issue 2
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journal, April 2001
- Hanson, T. E.; Tabita, F. R.
- Proceedings of the National Academy of Sciences, Vol. 98, Issue 8
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journal, December 2015
- Butman, David; Stackpoole, Sarah; Stets, Edward
- Proceedings of the National Academy of Sciences, Vol. 113, Issue 1
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journal, February 2009
- Bulushi, Ismail Al; Poole, Susan; Deeth, Hilton C.
- Critical Reviews in Food Science and Nutrition, Vol. 49, Issue 4
APE: Analyses of Phylogenetics and Evolution in R language
journal, January 2004
- Paradis, E.; Claude, J.; Strimmer, K.
- Bioinformatics, Vol. 20, Issue 2
Fast and accurate long-read alignment with Burrows–Wheeler transform
journal, January 2010
- Li, Heng; Durbin, Richard
- Bioinformatics, Vol. 26, Issue 5
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journal, August 2015
- Ramachandran, Arthi; Walsh, David A.
- FEMS Microbiology Ecology, Vol. 91, Issue 10
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journal, July 2015
- Varghese, Neha J.; Mukherjee, Supratim; Ivanova, Natalia
- Nucleic Acids Research, Vol. 43, Issue 14
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journal, January 1995
- Bowman, J. P.; Sly, L. I.; Stackebrandt, E.
- International Journal of Systematic Bacteriology, Vol. 45, Issue 1
Novel methylotrophic isolates from lake sediment, description of Methylotenera versatilis sp. nov. and emended description of the genus Methylotenera
journal, February 2011
- Kalyuzhnaya, M. G.; Beck, D. A. C.; Vorobev, A.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 62, Issue 1
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journal, January 2011
- Holkenbrink, C.; Barbas, S. O.; Mellerup, A.
- Microbiology, Vol. 157, Issue 4
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journal, March 2007
- Eiler, Alexander; Bertilsson, Stefan
- Environmental Microbiology, Vol. 9, Issue 3
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journal, September 2011
- Mou, Xiaozhen; Vila-Costa, Maria; Sun, Shulei
- Environmental Microbiology Reports, Vol. 3, Issue 6
Global rates of marine sulfate reduction and implications for sub-sea-floor metabolic activities
journal, May 2014
- Bowles, M. W.; Mogollon, J. M.; Kasten, S.
- Science, Vol. 344, Issue 6186
Whole-Genome Analysis of the Methyl tert -Butyl Ether-Degrading Beta-Proteobacterium Methylibium petroleiphilum PM1
journal, July 2007
- Kane, Staci R.; Chakicherla, Anu Y.; Chain, Patrick S. G.
- Journal of Bacteriology, Vol. 189, Issue 13
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journal, September 2017
- He, Shaomei; Stevens, Sarah L. R.; Chan, Leong-Keat
- mSphere, Vol. 2, Issue 5
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journal, August 2017
- Hamilton, Joshua J.; Garcia, Sarahi L.; Brown, Brittany S.
- mSystems, Vol. 2, Issue 4
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journal, January 2009
- Camacho, Christiam; Coulouris, George; Avagyan, Vahram
- BMC Bioinformatics, Vol. 10, Issue 1
Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010
- Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F.
- BMC Bioinformatics, Vol. 11, Issue 1
Minimus: a fast, lightweight genome assembler
journal, January 2007
- Sommer, Daniel D.; Delcher, Arthur L.; Salzberg, Steven L.
- BMC Bioinformatics, Vol. 8, Issue 1
Large and linked in scientific publishing
journal, July 2012
- Goodman, Laurie; Edmunds, Scott C.; Basford, Alexandra T.
- GigaScience, Vol. 1, Issue 1
Ray Meta: scalable de novo metagenome assembly and profiling
journal, January 2012
- Boisvert, Sébastien; Raymond, Frédéric; Godzaridis, Élénie
- Genome Biology, Vol. 13, Issue 12
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journal, March 2012
- Hahn, Martin W.; Scheuerl, Thomas; Jezberová, Jitka
- PLoS ONE, Vol. 7, Issue 3
Capturing Single Cell Genomes of Active Polysaccharide Degraders: An Unexpected Contribution of Verrucomicrobia
journal, April 2012
- Martinez-Garcia, Manuel; Brazel, David M.; Swan, Brandon K.
- PLoS ONE, Vol. 7, Issue 4
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journal, May 2015
- Beversdorf, Lucas J.; Chaston, Sheena D.; Miller, Todd R.
- PLOS ONE, Vol. 10, Issue 5
Lakes and streams as sentinels of environmental change in terrestrial and atmospheric processes
journal, June 2008
- Williamson, Craig E.; Dodds, Walter; Kratz, Timothy K.
- Frontiers in Ecology and the Environment, Vol. 6, Issue 5
Green sulphur bacteria as a component of the photosynthetic plankton community in small dimictic humic lakes with an anoxic hypolimnion
journal, March 2013
- Karhunen, J.; Arvola, L.; Peura, S.
- Aquatic Microbial Ecology, Vol. 68, Issue 3
Whole-lake mineralization of allochthonous and autochthonous organic carbon in a large humic lake (örträsket, N. Sweden)
journal, November 2001
- Jonsson, Anders; Meili, Markus; Bergström, Ann-Kristin
- Limnology and Oceanography, Vol. 46, Issue 7
Autochthonous versus allochthonous carbon sources of bacteria: Results from whole-lake 13 C addition experiments
journal, March 2004
- Kritzberg, Emma S.; Cole, Jonathan J.; Pace, Michael L.
- Limnology and Oceanography, Vol. 49, Issue 2
Reconstructing the various facets of dissolved organic carbon bioavailability in freshwater ecosystems
journal, March 2011
- Guillemette, François; del Giorgio, Paul A.
- Limnology and Oceanography, Vol. 56, Issue 2
PhyloSift: phylogenetic analysis of genomes and metagenomes
journal, January 2014
- Darling, Aaron E.; Jospin, Guillaume; Lowe, Eric
- PeerJ, Vol. 2
Microbial Observatory at North Temperate Lakes LTER High-resolution temporal and spatial dynamics of microbial community structure in freshwater bog lakes 2005 - 2009 original format
dataset, January 2019
- McMahon, Katherine; Jones, Stuart; Shade, Ashley
- Environmental Data Initiative
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