Insights into the phylogeny and coding potential of microbial dark matter

By Christian Rinke, P. Schwientek, A. Sczyrba, Natalia N. Ivanova, I. Anderson, Jan-Fang Cheng, Aaron E. Darling, S. Malfatti, B. Swan, E. Gies and 12 more. 2013

2,164 citations recorded by the source corpus.

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 uncharted branches of the tree of life, so-called ‘microbial dark matter’. With this additional genomic information, we are able to resolve many intra- and inter-phylum-level relationships and to propose two new superphyla. We uncover unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20% of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. This study greatly expands the genomic representation of the tree of life and provides a systematic step towards a better understanding of biological evolution on our planet.

Subfields: Ecology, Molecular Biology

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Citations in the corpus

MGnify: the microbiome analysis resource in 2020 (2019, background): “Metagenomics has started to provide the scientific community with access to the ∼99% of organisms that are yet to be cultured (50).”
Ecology and exploration of the rare biosphere (2015, background): “…we discuss approaches for identifying and studying the ‘truffles’ of microbial ecology — namely, rarebiosphere species that represent unexplored branches of microbial life (‘dark matter’) 105 , taxonomic blind spots (specific taxonomic novelty) 45 , 46 and the potential fourth domain of life 106 .”
A standardized archaeal taxonomy for the Genome Taxonomy Database (2021, background): “According to its RED-based rank and concatenated protein phylog-eny, the Aigarchaeota constitutes an order-level lineage within the Nitrososphaeria, for which we propose the order Caldarchaeales ord. nov. ( Supplementary Tables 15 and 18), derived from the species Ca .”
Computational approaches to predict bacteriophage–host relationships (2015, background): “…genome space is increasingly sampled by sequencing cultured strains, single cells and assembling metagenomes, we still lack genome sequences for most host strains of naturally occurring phages (Wu et al. 2009; Rinke et al. 2013; Dutilh et al. 2014; Brown et al. 2015; Garza and Dutilh 2015).”
MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis (2018, background): “These metrics can be estimated by counting universal single-copy genes within each bin [22, 23].”
25 years of serving the community with ribosomal RNA gene reference databases and tools. (2017, background): “The numbers of bacterial and archaeal phyla are currently under a dramatic expansion (Hug et al., 2016; Rinke et al., 2013; Seitz et al., 2016; Zaremba-Niedzwiedzka et al., 2017).”
Gut microbiome of the Hadza hunter-gatherers (2014, background): “This finding also underscores the importance of increasing our reference phylogenies and resolving deep taxonomic relationships between bacteria by sampling a wider variety of environments and extreme ecological zones (Rinke et al., 2013).”
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life (2017, background): “Aquificae (1) Deferribacteres (5) Fusobacteria (8) Dependentiae (1) Latescibacteria (4) 0.”