Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes.
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. 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.
Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
Jimmy H
JH
Saw
Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
Anja
A
Spang
Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
Katarzyna
K
Zaremba-Niedzwiedzka
Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
Lina
L
Juzokaite
School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA.
Jeremy A
JA
Dodsworth
School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA.
Senthil K
SK
Murugapiran
Department of Biology, University of New Mexico, Albuquerque, NM, USA.
Dan R
DR
Colman
Department of Biology, University of New Mexico, Albuquerque, NM, USA.
Cristina
C
Takacs-Vesbach
School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA.
Brian P
BP
Hedlund
Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
Lionel
L
Guy
Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden thijs.ettema@icm.uu.se.
Thijs J G
TJ
Ettema
D001105:Archaea / Q000145:classification / Q000235:genetics*; D005057:Eukaryotic Cells / Q000145:classification* / Q000166:cytology*; D019848:Gene Expression Regulation, Archaeal / Q000502:physiology; D014644:Genetic Variation; D020745:Genome, Archaeal; D056186:Metagenomics / Q000379:methods*; D010802:Phylogeny; D019642:RNA, Archaeal / Q000235:genetics / Q000378:metabolism; D012336:RNA, Ribosomal, 16S / Q000235:genetics
D019642:RNA, Archaeal; D012336:RNA, Ribosomal, 16S
Archaea; eukaryogenesis; metagenomics; microbial diversity; single-cell genomics; tree of life