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A genomic view of Earth’s biomes

Nature Reviews Genetics (2025)Cite this article

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Abstract

Microorganisms are essential to all life on Earth through critical roles in key biological processes and diverse interactions with other organisms that shape ecosystems, drive biogeochemical cycles and influence both human health and environmental health. High-throughput sequencing from environmental samples has revolutionized the understanding of microbial diversity and functions. With vast amounts of genomes now available across Earth’s biomes, these data provide a blueprint of microbial life that can be harnessed for a more holistic understanding of microbiome structure and function across the various ecosystems on Earth. Here we review the application of genome-centric approaches, including recent advances in single-cell sequencing and functional profiling, to survey microbial and viral diversity. We highlight some of the most impactful evolutionary and functional discoveries, explore the spatial diversity and temporal dynamics of microorganisms across diverse environments, and discuss genome-enabled insights into host-associated microorganisms.

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Fig. 1: A historical timeline of gene-centric and genome-centric microbial investigations from the first tree of life enabled by Sanger sequencing of ribosomal RNA genes to genome-resolved phylogenomic analyses.
Fig. 2: Primary approaches to study the genomic make-up of microbial systems.
Fig. 3: The number of isolates, metagenome-assembled and single-cell genomes per bacterial and archaeal phyla in the Genome Taxonomy Database (release 226).
Fig. 4: Distribution and scale (Mb) of metagenomic data sets in the NCBI Sequence Read Archive database with geographic information.
Fig. 5: Different levels of genome reduction among Arsenophonus symbionts of insects.

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Acknowledgements

G.S., E.A.E.-F. and T.W. were funded by the US Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility supported by the Office of Science of the US Department of Energy operated under Contract No. DE-AC02-05CH11231. J.P.-R. was supported by the US Department of Energy, Office of Biological and Environmental Research, Genomic Science Program ‘Microbes Persist’ Scientific Focus Area (award no. SCW1632) and under the auspices of the US Department of Energy under contract DE-AC52-07NA27344. The authors thank S. Roux (Joint Genome Institute) for assistance in compiling the Sequence Read Archive metadata shown in Fig. 4.

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Authors and Affiliations

  1. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA

    Gitta Szabó, Emiley A. Eloe-Fadrosh & Tanja Woyke

  2. Lawrence Livermore National Laboratory, Livermore, CA, USA

    Jennifer Pett-Ridge

  3. University of California Merced, Life and Environmental Sciences, Merced, CA, USA

    Jennifer Pett-Ridge & Tanja Woyke

  4. Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA

    Jennifer Pett-Ridge

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  1. Gitta Szabó
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  2. Emiley A. Eloe-Fadrosh
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  3. Jennifer Pett-Ridge
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  4. Tanja Woyke
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The authors contributed equally to all aspects of the article.

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Correspondence to Gitta Szabó or Tanja Woyke.

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Related links

BUSCO: https://busco.ezlab.org/

EukCC: https://github.com/EBI-Metagenomics/EukCC

geNomad: https://portal.nersc.gov/genomad/

Genome Taxonomy Database: https://gtdb.ecogenomic.org

GTDB release 226: https://gtdb.ecogenomic.org/stats/r226

GVClass: https://github.com/NeLLi-team/gvclass

Integrated Microbial Genomes and Microbiomes: https://img.jgi.doe.gov/

MGnify: https://www.ebi.ac.uk/metagenomics

National Center for Biotechnology Information: https://www.ncbi.nlm.nih.gov/

Glossary

Binning

The process of categorizing genomic DNA sequences (contigs and scaffolds) assembled from metagenomic sequencing data into groups that represent individual or highly similar genomes.

Biofilm

A structured biological layer formed on surfaces by microorganisms embedded in a matrix of secreted polymers that enables close microbial interactions and enhanced survival under harsh conditions.

Biogeochemical cycling

The natural transformation and flow of elements (for example, carbon, nitrogen and phosphorus) among the biological, geological and chemical components of Earth, which greatly influence nutrient availability and ecosystem functioning.

DPANN

A superphylum of ultra-small, often symbiotic archaea with reduced genomes and diverse environmental distributions. The name derives from the groups Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaeota.

Droplet microfluidics

A high-throughput technology that encapsulates single cells within a water-in-oil emulsion, which creates miniature reaction chambers that can be used for sorting and manipulation of individual cells.

Giant virus

Nucleo-cytoplasmic large DNA viruses within the phylum Nucleocytoviricota have large, often megabase-sized genomes with complex translation machinery and other genes involved in diverse cellular functions and virions comparable in size to bacterial cells.

Hi-C

A methodology that crosslinks and ligates DNA molecules and regions that are in close physical proximity, thereby improving genome assembly, binning and the assignment of mobile genetic elements to genomic bins.

Horizontal gene transfer

(HGT). The transfer of extrachromosomal or integrative mobile genetic elements between organisms, which can be neutral, detrimental or beneficial to the recipient cell by conferring novel functions and therefore have a profound influence on microbial evolution.

Metagenome-assembled genomes

(MAGs). Population-level microbial genomes reconstructed from community-level metagenomic data obtained from an environmental or host-associated sample.

Metagenomics

The sequencing and analysis of DNA directly extracted from the environment, providing insights into microbiome diversity and functional potential.

Metatranscriptomics

An RNA-sequencing approach that aims to capture the collective mRNA in a microbial community to study the diversity and expression levels of microbial genes of the transcriptionally active community members within natural environments.

Microbial guilds

Groups of microorganisms that perform similar ecological functions or use similar resources.

Mobile genetic elements

(MGEs). Genetic elements such as plasmids, transposons, prophages, phages and other viruses that facilitate gene transfer within and between microbial populations.

Pangenome

The set of genes found within a species or clade, which encompasses core genes present in all individuals and dispensable genes that vary between individuals.

Patescibacteria

A ubiquitous bacterial phylum consisting of members with reduced genomes, predicted to have limited metabolic capabilities and symbiotic relationship with other microorganisms. Also referred to as the Candidate Phyla Radiation and recently named Patescibacteriota based on SeqCode and Minisyncoccota according to ICNP (Internal Code of Nomenclature of Prokaryotes), a nomenclature framework for bacteria and archaea that requires a viable cultured representative as type material.

Phylogenetic tree

A graphical diagram representation displaying evolutionary relationships between organisms or groups of organisms based on genetic similarities.

SeqCode

A framework for the nomenclature of bacteria and archaea regardless of cultivation, based on high-quality sequence data.

Single amplified genomes

(SAGs). Genomes obtained from individually isolated microbial cells using single-cell whole-genome amplification before sequencing.

Stable isotope probing

(SIP). A method that uses isotopically labelled substrates to trace microbial water, carbon or nutrient uptake in environmental samples.

Sympatric speciation

The evolution of new species from a common ancestor within the same environment.

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Szabó, G., Eloe-Fadrosh, E.A., Pett-Ridge, J. et al. A genomic view of Earth’s biomes. Nat Rev Genet (2025). https://doi.org/10.1038/s41576-025-00888-1

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