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Tanja Woyke highlights a 2014 study by Kashtan et al., who applied single-cell genomics to populations of the marine cyanobacterium Prochlorococcus, revealing hundreds of subpopulations with distinct genomic backbones of this wild uncultured microorganism.

Uncultivated archaeal and bacterial cells of major uncharted branches of the tree of life are targeted and sequenced using single-cell genomics; this enables resolution of many intra- and inter-phylum-level relationships, uncovers unexpected metabolic features that challenge established boundaries between the three domains of life, and leads to the proposal of two new superphyla.

Genome-wide approaches have uncovered the vast microbial and viral diversity across ecosystems. This Review explores advances in metagenomics, single-cell sequencing and functional profiling to elucidate the evolution, biogeography and ecological dynamics of Earth’s microbiomes.

Significant gaps in our characterization of microbial diversity remain; this meta-analysis of amplicon-based rRNA studies shows that they miss approximately 10% of environmental microbial sequences, most belonging to the candidate phyla radiation.

Few aerobic hyperthermophilic microorganisms are known to degrade polysaccharides. Here, Nou et al. use genomic information to enrich and optical tweezers to isolate an aerobic hyperthermophilic bacterium that can grow at 65–87.5 °C using polysaccharides as sole carbon sources.

Bacterial microcompartments (BMCs) are organelles consisting of a protein shell in which certain metabolic reactions take place separated from the cytoplasm. Here, Sutter et al. present a comprehensive catalog of BMC loci, substantially expanding the number of known BMCs and describing distinct types and compartmentalized reactions.

CRISPR spacers in DPANN archaea target putative essential genes in their episymbionts and could be a widespread occurrence across diverse archaeal lineages.

Analysis of metagenomics data revealed that large and giant viruses are globally widely distributed and are associated with most major eukaryotic lineages.

The analysis of existing metagenomic data can lead to discovery of new microorganisms. Here, Eloe-Fadrosh et al. perform a large-scale analysis of global metagenomic data, followed by genome reconstruction and single-cell genomics, to describe a new bacterial phylum that inhabits geothermal springs.

The discovery of giant viruses, with virions as large as some bacteria and eukaryotes, megabase-range genomes, and a variety of traits typically found only in cellular organisms, was one of the most remarkable breakthroughs in biology. In this Review, Schulz, Abergel and Woyke explore insights into the biology, diversity, biogeography and ecology of giant viruses provided by culture and genomic technologies.

Little is known about viral-host interactions in the continental subsurface. Here, the authors use a combination of metagenomics, fluorescence in situ hybridization, and electron microscopy to show infections of abundant C-fixing subsurface archaea by lytic viruses.

Single-cell genome sequencing of eight uncultured fungal species provides insights into the phylogenetic placement of early-diverging lineages, highlights metabolic deficiencies and identifies gene expansions correlated with parasitism and unculturability.

Most cyanobacteria are oxygenic photoautotrophs, and fermenters under dark anoxic conditions. Here, the authors analyse genomic sequences of related uncultivated bacteria, inferring their metabolic potential, and supporting that their common ancestor was an anaerobe capable of fermentation and H₂ metabolism.

A machine learning approach was used to recover over 10,000 inovirus-like sequences from existing microbial genomes and metagenomes, consequently proposing the reclassification of the Inoviridae family to a viral order, and uncover the previously unrecognized diversity of these viruses across hosts and environments.

Current knowledge of giant virus diversity is largely based on samples from aquatic environments. Here the authors employ cultivation-independent metagenomics and mini-metagenomics on forest soil and identify 16 novel giant virus genomes, some of which representing novel lineages, including the so far largest genome in Mimiviridae.

Little is known about Marinimicrobia, a group of bacteria that are prevalent in the oceans. Here, the authors study global populations of Marinimicrobia using single-cell genomics, metagenomics and metatranscriptomics, showing potential co-metabolic interactions and participation in the sulfur and nitrogen cycles.

Bacteria of the SAR11 clade constitute up to one half of all marine microbes and are thought to require oxygen for growth; here, a subgroup of SAR11 bacteria are shown to thrive in ocean oxygen minimum zones and to encode abundant respiratory nitrate reductases.

Analysis of a CO₂-driven geyser over a complete eruption cycle showed temporal changes in microbial community composition and function, associated with eruption phase and aquifer water depth, and revealed a putative archaeal symbiosis.

Comparative genomic analysis of 3,837 bacterial genomes, including new sequences from 484 root-associated isolates, identifies plant-associated gene clusters and plant-mimicking domains.

This month’s Genome Watch highlights the use of genome-centric approaches to further our understanding of the human gut microbiome.

A computational approach to generate reference-free protein families from the sequence space in metagenomes reveals an enormously diverse functional space.

A compendium of Omnitrophota genomes is coupled with cell size and qSIP analyses to predict the physiology and lifestyle of this enigmatic phylum.

Cataloging microbial genomes from Earth’s environments expands the known phylogenetic diversity of bacteria and archaea.

Rumen microbiome biology gets a boost with the release of 410 high-quality reference genomes from the Hungate1000 project.

The Critical Assessment of Metagenome Interpretation (CAMI) community initiative presents results from its first challenge, a rigorous benchmarking of software for metagenome assembly, binning and taxonomic profiling.

Metagenomic and microbial sequence data are made easier to interpret with the addition of 1,003 genomes to the Genomic Encyclopedia of Bacteria and Archaea.

This paper presents standards and best practices for reporting genome sequences of uncultivated viruses.

Standards for sequencing the microbial 'uncultivated majority', namely bacterial and archaeal single-cell genome sequences, and genome sequences from metagenomic datasets, are proposed.

This study presents an extensive global compendium of metagenomically derived sequences that will serve as a foundation for understanding the role of viruses in soil ecosystems.

This review outlines experimental considerations, advances and challenges in microbial single-cell genome sequencing and discusses the applications and scientific questions that this approach enabled.