Insights into the phylogeny and coding potential of microbial dark matter

  title={Insights into the phylogeny and coding potential of microbial dark matter},
  author={Christian Rinke and Patrick Schwientek and Alexander Sczyrba and Natalia N. Ivanova and Iain Anderson and Jan-Fang Cheng and Aaron E. Darling and Stephanie Malfatti and Brandon K. Swan and Esther A. Gies and Jeremy A. Dodsworth and Brian P. Hedlund and George Tsiamis and Stefan M. Sievert and Wen-Tso Liu and Jonathan A. Eisen and Steven J. Hallam and Nikos C. Kyrpides and Ramunas Stepanauskas and Edward M. Rubin and P. Bernt Hugenholtz and Tanja Woyke},
Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional diversity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. We apply single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly… 

Genomic diversity, lifestyles and evolutionary origins of DPANN archaea

The current knowledge of the gene repertoires and lifestyles of members of the tentative archaeal superphylum referred to as DPANN are reviewed and their placement in the tree of life is discussed, which is the basis for the understanding of the deep microbial roots and the role of symbiosis in the evolution of life on Earth.

Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia

This study assembles draft metagenome-assembled genomes from environmental DNA extracted from two hot springs within an active volcanic ecosystem on the Kamchatka peninsula, Russia, and highlights MAGs that were taxonomically assigned to groups previously underrepresented in available genome data.

Diversity, ecology and evolution of Archaea

How genomes belonging to uncultured groups from the environment elucidate the metabolic capabilities of the Archaea and their ecological roles are discussed, while also expanding the view of the tree of life and of eukaryogenesis.

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space.

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

The recovery of 7,903 bacterial and archaeal metagenome-assembled genomes increases the phylogenetic diversity represented by public genome repositories and provides the first representatives from 20 candidate phyla.

Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes

An overview of state-of-the-art cultivation-independent genomics approaches is provided, and how these methods were used to obtain draft genome sequences of several novel members of the TACK superphylum are demonstrated, including Lokiarchaeum, two representatives of the Miscellaneous Crenarchaeotal Group (Bathyarchaeota), and a Kor Archaeum-related lineage.

Archaeal “Dark Matter” and the Origin of Eukaryotes

It is shown that a recent analysis incorporating new genomes from uncultivated Archaea recovered a strongly supported three domains tree, consistent with a number of recent studies in which improved archaeal sampling and better phylogenetic models agree in supporting the eocyte tree over the three domains hypothesis.



A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

The results strongly support the need for systematic ‘phylogenomic’ efforts to compile a phylogeny-driven ‘Genomic Encyclopedia of Bacteria and Archaea’ in order to derive maximum knowledge from existing microbial genome data as well as from genome sequences to come.

Metagenomics: Application of Genomics to Uncultured Microorganisms

  • J. Handelsman
  • Biology
    Microbiology and Molecular Biology Reviews
  • 2004
Reassembly of multiple genomes has provided insight into energy and nutrient cycling within the community, genome structure, gene function, population genetics and microheterogeneity, and lateral gene transfer among members of an uncultured community.

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

Reanalysis of published metagenomes reveals that differential coverage binning facilitates recovery of more complete and higher fidelity genome bins than other currently used methods, which are primarily based on sequence composition.

A major clade of prokaryotes with ancient adaptations to life on land.

It is shown how combined evidence from phylogenetic, cytological, and environmental data support the existence of an evolutionary group that appears to have had a common ancestor on land early in Earth's history and includes two-thirds of known prokaryote species.

Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

Bacterial PERegrinations Many branches of the bacterial domain of life are only known from sequences that turn up in metagenomic analyses and are still only named by acronym—for example, the

De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities

Reconstruction of two highly unusual archaeal genomes by de novo metagenomic assembly of multiple, deeply sequenced libraries from surface waters of Lake Tyrrell, Australia demonstrates that even historically well-characterized environments can reveal unexpected diversity when analyzed by metagenomics, and advances the understanding of the ecology of hypersaline environments and the evolutionary history of the archaea.

Unexpected Diversity and Complexity of the Guerrero Negro Hypersaline Microbial Mat

The biological complexity of the mat far exceeds that observed in other polysaccharide-rich microbial ecosystems, such as the human and mouse distal guts, and suggests that positive feedbacks exist between chemical complexity and biological diversity.

Enigmatic, ultrasmall, uncultivated Archaea

Metagenomics has provided access to genomes of as yet uncultivated microorganisms in natural environments, yet there are gaps in our knowledge—particularly for Archaea—that occur at relatively low

Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives

The relationship between 16 S rRNA gene sequence similarity and overall levels of gene conservation in four groups of species: gut specialists and cosmopolitans, each of which can be divided into pathogens and non-pathogens is characterized.

Origin of an Alternative Genetic Code in the Extremely Small and GC–Rich Genome of a Bacterial Symbiont

Using a combination of genome sequencing and high-throughput proteomics, it is shown that an α-Proteobacterial symbiont of cicadas has the unprecedented combination of an extremely small genome, a GC–biased base composition, and a coding reassignment of UGA Stop→Trp.