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Microbial diversity in extreme environments


A wide array of microorganisms, including many novel, phylogenetically deeply rooted taxa, survive and thrive in extreme environments. These unique and reduced-complexity ecosystems offer a tremendous opportunity for studying the structure, function and evolution of natural microbial communities. Marker gene surveys have resolved patterns and ecological drivers of these extremophile assemblages, revealing a vast uncultured microbial diversity and the often predominance of archaea in the most extreme conditions. New omics studies have uncovered linkages between community function and environmental variables, and have enabled discovery and genomic characterization of major new lineages that substantially expand microbial diversity and change the structure of the tree of life. These efforts have significantly advanced our understanding of the diversity, ecology and evolution of microorganisms populating Earth’s extreme environments, and have facilitated the exploration of microbiota and processes in more complex ecosystems.

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Fig. 1: Global distribution of representative extreme environments.
Fig. 2: Microbial community composition of different extreme environments.
Fig. 3: Genomic tree of the domain Archaea showing currently proposed major lineages (phyla).
Fig. 4: Compositional and functional shifts of the microbial community along specific environmental gradients.


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Support was received from the National Natural Science Foundation of China (grant no. 41830318 to W.-S.S. and grant nos 31570500 and 31870111 to L.-N.H.). The contributions of Z. Luo and other students and postdoctoral scientists in the authors’ team are gratefully acknowledged. The authors thank Z. Hua and Z. Luo for helpful discussions, and K. Anantharaman and J. F. Banfield for providing metagenome-derived taxon abundance data for the analysis of the microbial composition of the Colorado River aquifer communities (Fig. 2).

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Correspondence to Wen-Sheng Shu or Li-Nan Huang.

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16S ribosomal RNA (rRNA) gene clone library analysis

The cloning and Sanger sequencing of 16S ribosomal RNA (rRNA) genes PCR-amplified from total DNA extracted from an environmental sample, resolving the composition and diversity of the microbial community.

Metagenomic analysis

The sequencing and genomic analysis of total community DNA directly recovered from the environment.

16S rRNA amplicon sequencing

High-throughput (next-generation) sequencing of 16S ribosomal RNA (rRNA) gene fragments PCR-amplified from total community genomic DNAs, allowing sampling and analysis of microbial diversity on an unprecedented scale.


The ability of a microorganism (that is, a thermophile) to grow at a high temperature.

Whole-genome shotgun sequencing

A process in which the genomic DNA from a pure culture is randomly fragmented and sequenced, and the sequences obtained are then assembled through bioinformatics to a whole microbial genome.

Genome bins

The population genomes (also called ‘metagenome-assembled genomes’) assembled from metagenomic sequence data based on G+C content, k-mer frequency and/or read coverage.


Near neutral.

Cryoconite holes

Small holes on the surface of a glacier. The deposited cryoconite (windblown dust comprising both mineral and biological material, including microorganisms) absorbs solar radiation, melting the snow and ice beneath.

Ectosymbiotic lifestyle

A form of symbiotic behaviour in which an ectosymbiont lives on the surface of its host.

Thalassohaline salt lake

Hypersaline lake of marine origin where salt ratios are similar to those of seawater and pH is near neutral to slightly alkaline.


The application of microorganisms to recover metals from ores or mining waste.


The finely ground residues from mined ores after extraction of valuable minerals and metals.


The combined loss of water from the land both by evaporation from the soil surface and by transpiration from the plants growing thereon.

Diel cycle

A 24-h period comprising a day and a consecutive night, or a regular day–night cycle of physiology or behaviour of an organism.

Multilocus sequence typing

A molecular typing technique in which multiple targeted housekeeping genes (loci) are sequenced, often partially.

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Shu, WS., Huang, LN. Microbial diversity in extreme environments. Nat Rev Microbiol (2021).

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