Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes
Abstract
The origin of eukaryotes represents an enigmatic puzzle, which is still lacking a number of essential pieces. Whereas it is currently accepted that the process of eukaryogenesis involved an interplay between a host cell and an alphaproteobacterial endosymbiont, we currently lack detailed information regarding the identity and nature of these players. A number of studies have provided increasing support for the emergence of the eukaryotic host cell from within the archaeal domain of life, displaying a specific affiliation with the archaeal TACK superphylum. Recent studies have shown that genomic exploration of yet-uncultivated archaea, the so-called archaeal 'dark matter', is able to provide unprecedented insights into the process of eukaryogenesis. Here, we provide an overview of state-of-the-art cultivation-independent approaches, and demonstrate how these methods were used to obtain draft genome sequences of several novel members of the TACK superphylum, including Lokiarchaeum, two representatives of the Miscellaneous Crenarchaeotal Group (Bathyarchaeota), and a Korarchaeum-related lineage. In conclusion, the maturation of cultivation-independent genomics approaches, as well as future developments in next-generation sequencing technologies, will revolutionize our current view of microbial evolution and diversity, and provide profound new insights into the early evolution of life, including the enigmatic origin of the eukaryotic cell.
- Authors:
-
- Uppsala Univ., Uppsala (Sweden)
- Univ. of Nevada, Las Vegas, NV (United States); California State Univ. (CalState), San Bernardino, CA (United States)
- Univ. of Nevada, Las Vegas, NV (United States)
- Univ. of New Mexico, Albuquerque, NM (United States)
- Univ. of Nevada, Las Vegas, NV (United States). School of Life Sciences
- Publication Date:
- Research Org.:
- Univ. of Nevada, Las Vegas, NV (United States)
- Sponsoring Org.:
- USDOE; National Aeronautics and Space Administration (NASA); National Science Foundation (NSF); EU; ERC; Swedish Research Council (SRC); Marie Curie
- OSTI Identifier:
- 1343570
- Grant/Contract Number:
- SC0006771; EE-0000716; EXO-NNX11AR78G; 621-2009-4813
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences
- Additional Journal Information:
- Journal Volume: 370; Journal Issue: 1678; Journal ID: ISSN 0962-8436
- Publisher:
- The Royal Society Publishing
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Archaea; eukaryogenesis; metagenomics; microbial diversity; single-cell genomics; tree of life
Citation Formats
Saw, Jimmy H., Spang, Anja, Zaremba-Niedzwiedzka, Katarzyna, Juzokaite, Lina, Dodsworth, Jeremy A., Murugapiran, Senthil K., Colman, Dan R., Takacs-Vesbach, Cristina, Hedlund, Brian P., Guy, Lionel, and Ettema, Thijs J. G. Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes. United States: N. p., 2015.
Web. doi:10.1098/rstb.2014.0328.
Saw, Jimmy H., Spang, Anja, Zaremba-Niedzwiedzka, Katarzyna, Juzokaite, Lina, Dodsworth, Jeremy A., Murugapiran, Senthil K., Colman, Dan R., Takacs-Vesbach, Cristina, Hedlund, Brian P., Guy, Lionel, & Ettema, Thijs J. G. Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes. United States. https://doi.org/10.1098/rstb.2014.0328
Saw, Jimmy H., Spang, Anja, Zaremba-Niedzwiedzka, Katarzyna, Juzokaite, Lina, Dodsworth, Jeremy A., Murugapiran, Senthil K., Colman, Dan R., Takacs-Vesbach, Cristina, Hedlund, Brian P., Guy, Lionel, and Ettema, Thijs J. G. Mon .
"Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes". United States. https://doi.org/10.1098/rstb.2014.0328. https://www.osti.gov/servlets/purl/1343570.
@article{osti_1343570,
title = {Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes},
author = {Saw, Jimmy H. and Spang, Anja and Zaremba-Niedzwiedzka, Katarzyna and Juzokaite, Lina and Dodsworth, Jeremy A. and Murugapiran, Senthil K. and Colman, Dan R. and Takacs-Vesbach, Cristina and Hedlund, Brian P. and Guy, Lionel and Ettema, Thijs J. G.},
abstractNote = {The origin of eukaryotes represents an enigmatic puzzle, which is still lacking a number of essential pieces. Whereas it is currently accepted that the process of eukaryogenesis involved an interplay between a host cell and an alphaproteobacterial endosymbiont, we currently lack detailed information regarding the identity and nature of these players. A number of studies have provided increasing support for the emergence of the eukaryotic host cell from within the archaeal domain of life, displaying a specific affiliation with the archaeal TACK superphylum. Recent studies have shown that genomic exploration of yet-uncultivated archaea, the so-called archaeal 'dark matter', is able to provide unprecedented insights into the process of eukaryogenesis. Here, we provide an overview of state-of-the-art cultivation-independent approaches, and demonstrate how these methods were used to obtain draft genome sequences of several novel members of the TACK superphylum, including Lokiarchaeum, two representatives of the Miscellaneous Crenarchaeotal Group (Bathyarchaeota), and a Korarchaeum-related lineage. In conclusion, the maturation of cultivation-independent genomics approaches, as well as future developments in next-generation sequencing technologies, will revolutionize our current view of microbial evolution and diversity, and provide profound new insights into the early evolution of life, including the enigmatic origin of the eukaryotic cell.},
doi = {10.1098/rstb.2014.0328},
journal = {Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences},
number = 1678,
volume = 370,
place = {United States},
year = {2015},
month = {8}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 14 works
Citation information provided by
Web of Science
Web of Science
Figures / Tables:
Figure 1: Phylogenetic diversity of the TACK superphylum based on known 16S rRNA gene sequences. Maximum-likelihood phylogeny of archaeal lineages withinthe TACK superphylum was constructed based on a total of 343 16S rRNA gene sequences. Five members of Euryarchaeota were used as outgroup to root the tree.Acronyms used for somemore »
All figures and tables
(7 total)
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:
MetaCluster 4.0: A Novel Binning Algorithm for NGS Reads and Huge Number of Species
journal, February 2012
- Wang, Yi; Leung, Henry C. M.; Yiu, S. M.
- Journal of Computational Biology, Vol. 19, Issue 2
ClaMS: A Classifier for Metagenomic Sequences
journal, November 2011
- Pati, Amrita; Heath, Lenwood S.; Kyrpides, Nikos C.
- Standards in Genomic Sciences, Vol. 5, Issue 2
The Binning of Metagenomic Contigs for Microbial Physiology of Mixed Cultures
journal, January 2012
- Strous, Marc; Kraft, Beate; Bisdorf, Regina
- Frontiers in Microbiology, Vol. 3
A congruent phylogenomic signal places eukaryotes within the Archaea
journal, October 2012
- Williams, Tom A.; Foster, Peter G.; Nye, Tom M. W.
- Proceedings of the Royal Society B: Biological Sciences, Vol. 279, Issue 1749
PhymmBL expanded: confidence scores, custom databases, parallelization and more
journal, April 2011
- Brady, Arthur; Salzberg, Steven
- Nature Methods, Vol. 8, Issue 5
Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization
journal, August 2012
- Sharon, I.; Morowitz, M. J.; Thomas, B. C.
- Genome Research, Vol. 23, Issue 1
The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa.
journal, March 2002
- Cavalier-Smith, T.
- International Journal of Systematic and Evolutionary Microbiology, Vol. 52, Issue 2
Community-wide analysis of microbial genome sequence signatures
journal, January 2009
- Dick, Gregory J.; Andersson, Anders F.; Baker, Brett J.
- Genome Biology, Vol. 10, Issue 8
The archaeal ‘TACK’ superphylum and the origin of eukaryotes
journal, December 2011
- Guy, Lionel; Ettema, Thijs J. G.
- Trends in Microbiology, Vol. 19, Issue 12
Ancestral lipid biosynthesis and early membrane evolution
journal, September 2004
- Peretó, Juli; López-García, Purificación; Moreira, David
- Trends in Biochemical Sciences, Vol. 29, Issue 9
Cell division and the ESCRT complex: A surprise from the Archaea
journal, March 2009
- Ettema, Thijs J. G.; Bernander, Rolf
- Communicative & Integrative Biology, Vol. 2, Issue 2
Orthologs of the small RPB8 subunit of the eukaryotic RNA polymerases are conserved in hyperthermophilic Crenarchaeota and "Korarchaeota"
journal, January 2007
- Koonin, Eugene V.; Makarova, Kira S.; Elkins, James G.
- Biology Direct, Vol. 2, Issue 1
An Evolutionary Network of Genes Present in the Eukaryote Common Ancestor Polls Genomes on Eukaryotic and Mitochondrial Origin
journal, January 2012
- Thiergart, Thorsten; Landan, Giddy; Schenk, Marc
- Genome Biology and Evolution, Vol. 4, Issue 4
MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm
journal, August 2014
- Wu, Yu-Wei; Tang, Yung-Hsu; Tringe, Susannah G.
- Microbiome, Vol. 2, Issue 1
Archaeal chromatin and transcription: Chromatin and transcription
journal, April 2003
- Reeve, John N.
- Molecular Microbiology, Vol. 48, Issue 3
MEGAN analysis of metagenomic data
journal, February 2007
- Huson, D. H.; Auch, A. F.; Qi, J.
- Genome Research, Vol. 17, Issue 3
Transcript amplification from single bacterium for transcriptome analysis
journal, May 2011
- Kang, Y.; Norris, M. H.; Zarzycki-Siek, J.
- Genome Research, Vol. 21, Issue 6
Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments
journal, May 2012
- Kubo, Kyoko; Lloyd, Karen G.; F. Biddle, Jennifer
- The ISME Journal, Vol. 6, Issue 10
Phylogenetic classification of short environmental DNA fragments
journal, February 2008
- Krause, Lutz; Diaz, Naryttza N.; Goesmann, Alexander
- Nucleic Acids Research, Vol. 36, Issue 7
An archaeal origin for the actin cytoskeleton: Implications for eukaryogenesis
journal, November 2011
- Bernander, Rolf; Lind, Anders E.; Ettema, Thijs J. G.
- Communicative & Integrative Biology, Vol. 4, Issue 6
The Archaeal Legacy of Eukaryotes: A Phylogenomic Perspective
journal, July 2014
- Guy, L.; Saw, J. H.; Ettema, T. J. G.
- Cold Spring Harbor Perspectives in Biology, Vol. 6, Issue 10
Binning metagenomic contigs by coverage and composition
journal, September 2014
- Alneberg, Johannes; Bjarnason, Brynjar Smári; de Bruijn, Ino
- Nature Methods, Vol. 11, Issue 11
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
journal, May 2013
- Albertsen, Mads; Hugenholtz, Philip; Skarshewski, Adam
- Nature Biotechnology, Vol. 31, Issue 6
An actin-based cytoskeleton in archaea: An archaeal cytoskeleton
journal, April 2011
- Ettema, Thijs J. G.; Lindås, Ann-Christin; Bernander, Rolf
- Molecular Microbiology, Vol. 80, Issue 4
Accurate phylogenetic classification of variable-length DNA fragments
journal, December 2006
- McHardy, Alice Carolyn; Martín, Héctor García; Tsirigos, Aristotelis
- Nature Methods, Vol. 4, Issue 1
Assembling the Marine Metagenome, One Cell at a Time
journal, April 2009
- Woyke, Tanja; Xie, Gary; Copeland, Alex
- PLoS ONE, Vol. 4, Issue 4
Genome of a Low-Salinity Ammonia-Oxidizing Archaeon Determined by Single-Cell and Metagenomic Analysis
journal, February 2011
- Blainey, Paul C.; Mosier, Annika C.; Potanina, Anastasia
- PLoS ONE, Vol. 6, Issue 2
The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?
journal, September 2010
- Gribaldo, Simonetta; Poole, Anthony M.; Daubin, Vincent
- Nature Reviews Microbiology, Vol. 8, Issue 10
GroopM: an automated tool for the recovery of population genomes from related metagenomes
journal, January 2014
- Imelfort, Michael; Parks, Donovan; Woodcroft, Ben J.
- PeerJ, Vol. 2
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
Phylogenomic Test of the Hypotheses for the Evolutionary Origin of Eukaryotes
journal, January 2014
- Rochette, Nicolas C.; Brochier-Armanet, Céline; Gouy, Manolo
- Molecular Biology and Evolution, Vol. 31, Issue 4
Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group
journal, December 2010
- Nunoura, Takuro; Takaki, Yoshihiro; Kakuta, Jungo
- Nucleic Acids Research, Vol. 39, Issue 8
Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective
journal, September 2012
- Teeling, H.; Glockner, F. O.
- Briefings in Bioinformatics, Vol. 13, Issue 6
Single cell genomics: an individual look at microbes
journal, October 2012
- Stepanauskas, Ramunas
- Current Opinion in Microbiology, Vol. 15, Issue 5
Archaebacteria (Archaea) and the origin of the eukaryotic nucleus
journal, December 2005
- Martin, William
- Current Opinion in Microbiology, Vol. 8, Issue 6
Metagenomics: Application of Genomics to Uncultured Microorganisms
journal, December 2004
- Handelsman, J.
- Microbiology and Molecular Biology Reviews, Vol. 68, Issue 4
Supertrees Disentangle the Chimerical Origin of Eukaryotic Genomes
journal, May 2007
- Pisani, Davide; Cotton, James A.; McInerney, James O.
- Molecular Biology and Evolution, Vol. 24, Issue 8
Eukaryotic evolution, changes and challenges
journal, March 2006
- Embley, T. Martin; Martin, William
- Nature, Vol. 440, Issue 7084
Archaeal origin of tubulin
journal, January 2012
- Yutin, Natalya; Koonin, Eugene V.
- Biology Direct, Vol. 7, Issue 1
Genomic evidence for two functionally distinct gene classes
journal, May 1998
- Rivera, M. C.; Jain, R.; Moore, J. E.
- Proceedings of the National Academy of Sciences, Vol. 95, Issue 11
Archaea in Organic-Lean and Organic-Rich Marine Subsurface Sediments: An Environmental Gradient Reflected in Distinct Phylogenetic Lineages
journal, January 2012
- Durbin, Alan M.; Teske, Andreas
- Frontiers in Microbiology, Vol. 3
A DNA topoisomerase IB in Thaumarchaeota testifies for the presence of this enzyme in the last common ancestor of Archaea and Eucarya
journal, January 2008
- Brochier-Armanet, Céline; Gribaldo, Simonetta; Forterre, Patrick
- Biology Direct, Vol. 3, Issue 1
A Role for the ESCRT System in Cell Division in Archaea
journal, December 2008
- Samson, R. Y.; Obita, T.; Freund, S. M.
- Science, Vol. 322, Issue 5908
From archaeon to eukaryote: the evolutionary dark ages of the eukaryotic cell
journal, January 2013
- Martijn, Joran; Ettema, Thijs J. G.
- Biochemical Society Transactions, Vol. 41, Issue 1
A unique cell division machinery in the Archaea
journal, November 2008
- Lindas, A. -C.; Karlsson, E. A.; Lindgren, M. T.
- Proceedings of the National Academy of Sciences, Vol. 105, Issue 48
Discovery of a black smoker vent field and vent fauna at the Arctic Mid-Ocean Ridge
journal, November 2010
- Pedersen, Rolf B.; Rapp, Hans Tore; Thorseth, Ingunn H.
- Nature Communications, Vol. 1, Issue 1
The PhyloPythiaS Web Server for Taxonomic Assignment of Metagenome Sequences
journal, June 2012
- Patil, Kaustubh Raosaheb; Roune, Linus; McHardy, Alice Carolyn
- PLoS ONE, Vol. 7, Issue 6
The Common Ancestor of Archaea and Eukarya Was Not an Archaeon
journal, January 2013
- Forterre, Patrick
- Archaea, Vol. 2013
Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
journal, August 2009
- Brady, Arthur; Salzberg, Steven L.
- Nature Methods, Vol. 6, Issue 9
From The Cover: Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem
journal, January 2005
- Spear, J. R.; Walker, J. J.; McCollom, T. M.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 7, p. 2555-2560
An archaeal origin of eukaryotes supports only two primary domains of life
journal, December 2013
- Williams, Tom A.; Foster, Peter G.; Cox, Cymon J.
- Nature, Vol. 504, Issue 7479
Reconciling an archaeal origin of eukaryotes with engulfment: a biologically plausible update of the Eocyte hypothesis
journal, January 2011
- Poole, Anthony M.; Neumann, Nadja
- Research in Microbiology, Vol. 162, Issue 1
The global phylogeny of glycolytic enzymes
journal, April 2002
- Canback, B.; Andersson, S. G. E.; Kurland, C. G.
- Proceedings of the National Academy of Sciences, Vol. 99, Issue 9
The Dispersed Archaeal Eukaryome and the Complex Archaeal Ancestor of Eukaryotes
journal, April 2014
- Koonin, E. V.; Yutin, N.
- Cold Spring Harbor Perspectives in Biology, Vol. 6, Issue 4
Archaeal genetics — the third way
journal, January 2005
- Allers, Thorsten; Mevarech, Moshe
- Nature Reviews Genetics, Vol. 6, Issue 1
Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage
journal, May 2013
- Dodsworth, Jeremy A.; Blainey, Paul C.; Murugapiran, Senthil K.
- Nature Communications, Vol. 4, Issue 1
The origin and early evolution of eukaryotes in the light of phylogenomics
journal, January 2010
- Koonin, Eugene V.
- Genome Biology, Vol. 11, Issue 5
Genomes from Metagenomics
journal, November 2013
- Sharon, I.; Banfield, J. F.
- Science, Vol. 342, Issue 6162
Community structure and metabolism through reconstruction of microbial genomes from the environment
journal, February 2004
- Tyson, Gene W.; Chapman, Jarrod; Hugenholtz, Philip
- Nature, Vol. 428, Issue 6978
Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences.
journal, August 1996
- Barns, S. M.; Delwiche, C. F.; Palmer, J. D.
- Proceedings of the National Academy of Sciences, Vol. 93, Issue 17
Genomic Analysis at the Single-Cell Level
journal, December 2011
- Kalisky, Tomer; Blainey, Paul; Quake, Stephen R.
- Annual Review of Genetics, Vol. 45, Issue 1
Supertrees and symbiosis in eukaryote genome evolution
journal, October 2007
- Esser, Christian; Martin, William
- Trends in Microbiology, Vol. 15, Issue 10
Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment.
journal, March 1994
- Barns, S. M.; Fundyga, R. E.; Jeffries, M. W.
- Proceedings of the National Academy of Sciences, Vol. 91, Issue 5
Complex archaea that bridge the gap between prokaryotes and eukaryotes
journal, May 2015
- Spang, Anja; Saw, Jimmy H.; Jørgensen, Steffen L.
- Nature, Vol. 521, Issue 7551
Korarchaeota Diversity, Biogeography, and Abundance in Yellowstone and Great Basin Hot Springs and Ecological Niche Modeling Based on Machine Learning
journal, May 2012
- Miller-Coleman, Robin L.; Dodsworth, Jeremy A.; Ross, Christian A.
- PLoS ONE, Vol. 7, Issue 5
Microfluidics Expanding the Frontiers of Microbial Ecology
journal, May 2014
- Rusconi, Roberto; Garren, Melissa; Stocker, Roman
- Annual Review of Biophysics, Vol. 43, Issue 1
Nucleotide sequence of pig plasma gelsolin
journal, October 1988
- Way, Michael; Weeds, Alan
- Journal of Molecular Biology, Vol. 203, Issue 4
Recent advances in genomic DNA sequencing of microbial species from single cells
journal, August 2014
- Lasken, Roger S.; McLean, Jeffrey S.
- Nature Reviews Genetics, Vol. 15, Issue 9
Predominant archaea in marine sediments degrade detrital proteins
journal, March 2013
- Lloyd, Karen G.; Schreiber, Lars; Petersen, Dorthe G.
- Nature, Vol. 496, Issue 7444
Genetic and functional properties of uncultivated MCG archaea assessed by metagenome and gene expression analyses
journal, October 2013
- Meng, Jun; Xu, Jun; Qin, Dan
- The ISME Journal, Vol. 8, Issue 3
Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth
journal, July 2007
- Marcy, Y.; Ouverney, C.; Bik, E. M.
- Proceedings of the National Academy of Sciences, Vol. 104, Issue 29, p. 11889-11894
An Overview of Endosymbiotic Models for the Origins of Eukaryotes, Their ATP-Producing Organelles (Mitochondria and Hydrogenosomes), and Their Heterotrophic Lifestyle
journal, January 2001
- Martin, William; Hoffmeister, Meike; Rotte, Carmen
- Biological Chemistry, Vol. 382, Issue 11
The origins of phagocytosis and eukaryogenesis
journal, January 2009
- Yutin, Natalya; Wolf, Maxim Y.; Wolf, Yuri I.
- Biology Direct, Vol. 4, Issue 1
Ecology of Sulfur-Oxidizing Bacteria in Hot Acid Soils
journal, January 1972
- Fliermans, Carl B.; Brock, Thomas D.
- Journal of Bacteriology, Vol. 111, Issue 2
Data from: Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes
dataset, December 2015
- Saw, J. H.; Sprang, A.; Zaremba-Niedzwiedzka, K.
- Dryad, 821.0 Kb
Remarkable archaeal diversity detected in a Yellowstone national park hot spring environment
journal, June 1994
- Barns, S. M.; Fundgya, R. E.; Jeffries, M. W.
- Trends in Genetics, Vol. 10, Issue 6
Archaea in Organic-Lean and Organic-Rich Marine Subsurface Sediments: An Environmental Gradient Reflected in Distinct Phylogenetic Lineages
text, January 2012
- Andreas, Teske,; M., Durbin, Alan
- The University of North Carolina at Chapel Hill University Libraries
Discovery of a black smoker vent field and vent fauna at the Arctic Mid-Ocean Ridge
text, January 2010
- Pedersen, Rolf B.; Rapp, Hans T.; Thorseth, Ingunn H.
- ETH Zurich
Metagenomics: Application of Genomics to Uncultured Microorganisms
journal, March 2005
- Handelsman, Jo
- Microbiology and Molecular Biology Reviews, Vol. 69, Issue 1
Data from: Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes
dataset, December 2015
- Saw, J. H.; Sprang, A.; Zaremba-Niedzwiedzka, K.
- Dryad, 821.0 Kb
Works referencing / citing this record:
Metagenomic approaches: effective tools for monitoring the structure and functionality of microbiomes in anaerobic digestion systems
journal, November 2019
- Carabeo-Pérez, Annerys; Guerra-Rivera, Gilda; Ramos-Leal, Miguel
- Applied Microbiology and Biotechnology, Vol. 103, Issue 23-24
Genotyping of Bartonella bacteria and their animal hosts: current status and perspectives
journal, August 2017
- Kosoy, M.; Mckee, C.; Albayrak, L.
- Parasitology, Vol. 145, Issue 5
Asgard archaea illuminate the origin of eukaryotic cellular complexity
journal, January 2017
- Zaremba-Niedzwiedzka, Katarzyna; Caceres, Eva F.; Saw, Jimmy H.
- Nature, Vol. 541, Issue 7637
Archaea and the origin of eukaryotes
journal, November 2017
- Eme, Laura; Spang, Anja; Lombard, Jonathan
- Nature Reviews Microbiology, Vol. 15, Issue 12
Genomes of two archaeal endosymbionts show convergent adaptations to an intracellular lifestyle
journal, July 2018
- Lind, Anders E.; Lewis, William H.; Spang, Anja
- The ISME Journal, Vol. 12, Issue 11
Building de novo reference genome assemblies of complex eukaryotic microorganisms from single nuclei
journal, January 2020
- Montoliu-Nerin, Merce; Sánchez-García, Marisol; Bergin, Claudia
- Scientific Reports, Vol. 10, Issue 1
Energetics and population genetics at the root of eukaryotic cellular and genomic complexity
journal, December 2015
- Koonin, Eugene V.
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 52
Integrative modeling of gene and genome evolution roots the archaeal tree of life
journal, May 2017
- Williams, Tom A.; Szöllősi, Gergely J.; Spang, Anja
- Proceedings of the National Academy of Sciences, Vol. 114, Issue 23
Genomic diversity, lifestyles and evolutionary origins of DPANN archaea
journal, January 2019
- Dombrowski, Nina; Lee, Jun-Hoe; Williams, Tom A.
- FEMS Microbiology Letters, Vol. 366, Issue 2
Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery
journal, February 2018
- Bernard, Guillaume; Pathmanathan, Jananan S.; Lannes, Romain
- Genome Biology and Evolution, Vol. 10, Issue 3
Tracing the Archaeal Origins of Eukaryotic Membrane-Trafficking System Building Blocks
journal, February 2016
- Klinger, Christen M.; Spang, Anja; Dacks, Joel B.
- Molecular Biology and Evolution, Vol. 33, Issue 6
Changing ideas about eukaryotic origins
journal, September 2015
- Williams, Tom A.; Embley, T. Martin
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 370, Issue 1678
Assessing the viral content of uncultured picoeukaryotes in the global‐ocean by single cell genomics
journal, September 2019
- Castillo, Yaiza M.; Mangot, Jean‐François; Benites, Luiz Felipe
- Molecular Ecology, Vol. 28, Issue 18
The Physiology of Phagocytosis in the Context of Mitochondrial Origin
journal, June 2017
- Martin, William F.; Tielens, Aloysius G. M.; Mentel, Marek
- Microbiology and Molecular Biology Reviews, Vol. 81, Issue 3
Birth of Archaeal Cells: Molecular Phylogenetic Analyses of G1P Dehydrogenase, G3P Dehydrogenases, and Glycerol Kinase Suggest Derived Features of Archaeal Membranes Having G1P Polar Lipids
journal, January 2016
- Yokobori, Shin-ichi; Nakajima, Yoshiki; Akanuma, Satoshi
- Archaea, Vol. 2016
Multiple levels of the unknown in microbiome research
journal, June 2019
- Thomas, Andrew Maltez; Segata, Nicola
- BMC Biology, Vol. 17, Issue 1
Microbial Community Response to Simulated Petroleum Seepage in Caspian Sea Sediments
journal, April 2017
- Stagars, Marion H.; Mishra, Sonakshi; Treude, Tina
- Frontiers in Microbiology, Vol. 8
Cultivation and Genomic Analysis of “Candidatus Nitrosocaldus islandicus,” an Obligately Thermophilic, Ammonia-Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland
journal, February 2018
- Daebeler, Anne; Herbold, Craig W.; Vierheilig, Julia
- Frontiers in Microbiology, Vol. 9
Data from: Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes
dataset, December 2015
- Saw, J. H.; Sprang, A.; Zaremba-Niedzwiedzka, K.
- Dryad, 821.0 Kb
Figures / Tables found in this record:
Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.