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KEY POINTS * Microbial-community abundance distributions have a long 'tail' of low-abundance organisms, referred to as the rare biosphere, which often comprises the large majority

of species. * Rare-biosphere microorganisms display specific and sometimes unique ecology and biogeography that can differ substantially from that of more abundant representatives. * The

rare biosphere contributes to a persistent microbial seed bank, contrasting the influence of local microbial extinction and immigration. * Recruitment from the rare biosphere provides a

broad reservoir of ecological function and resiliency (redundancy and flexibility). * Broad time-series studies with rich metadata will improve the study of rare-biosphere dynamics and

conditionally rare taxa. * Study of the rare biosphere is prone to experimental artefacts (sequencing noise) and biological artefacts (dormancy and taphonomic gradients). * The majority of

microbial diversity exists, at least transiently, in the rare biosphere. * Novel rare-biosphere members can be studied through cultivation, targeted phylogenetic mining and single-cell

genomics. ABSTRACT The profound influence of microorganisms on human life and global biogeochemical cycles underlines the value of studying the biogeography of microorganisms, exploring

microbial genomes and expanding our understanding of most microbial species on Earth: that is, those present at low relative abundance. The detection and subsequent analysis of low-abundance

microbial populations — the 'rare biosphere' — have demonstrated the persistence, population dynamics, dispersion and predation of these microbial species. We discuss the ecology

of rare microbial populations, and highlight molecular and computational methods for targeting taxonomic 'blind spots' within the rare biosphere of complex microbial communities.

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support SIMILAR CONTENT BEING VIEWED BY OTHERS MICROBIAL DIVERSITY IN EXTREME ENVIRONMENTS Article 09 November 2021 DEFINITION OF THE MICROBIAL RARE BIOSPHERE THROUGH UNSUPERVISED MACHINE

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Scholar  Download references ACKNOWLEDGEMENTS The authors appreciate comments provided by M. L. Sogin and B. J. Butler during the preparation of this manuscript. They acknowledge support

from an Early Researcher Award (Government of Ontario), the Canadian Institutes of Health Research (CIHR) and the Natural Sciences and Engineering Research Council of Canada (NSERC). AUTHOR

INFORMATION AUTHORS AND AFFILIATIONS * Department of Biology, University of Waterloo, Waterloo, N2L 3G1, Ontario, Canada Michael D. J. Lynch & Josh D. Neufeld Authors * Michael D. J.

Lynch View author publications You can also search for this author inPubMed Google Scholar * Josh D. Neufeld View author publications You can also search for this author inPubMed Google

Scholar CORRESPONDING AUTHOR Correspondence to Josh D. Neufeld. ETHICS DECLARATIONS COMPETING INTERESTS The authors declare no competing financial interests. RELATED LINKS FURTHER

INFORMATION Comparative RNA Web Site International Census of Marine Microbes POWERPOINT SLIDES POWERPOINT SLIDE FOR FIG. 1 POWERPOINT SLIDE FOR FIG. 2 GLOSSARY * Rare biosphere Although this

has been an arbitrarily defined term, subject to variable abundance thresholds (for example, <0.1% of total community relative abundance), the rare biosphere may be considered as the

collective of rare viable or dormant microbial taxa that are found in a given environmental sample at a specific time point. * Bioprospecting The screening of biological systems (for

example, genomes or ecosystems) for novel components of industrial, commercial or scientific value. * Conditionally rare taxa Species that are rare under some conditions but can become

abundant when provided with optimal growth conditions. * Resilience The ability of a community to regain functionality following a disturbance event. This ability is linked to role

redundancy conferred through species diversity. * Operational taxonomic units (OTUs). Commonly used theoretical framework for relating sequence differences to discrete taxonomic entities.

The OTU remains a surrogate for a taxonomic rank (for example, species) and is typically based on a specified nucleotide identity (for example, 97% for small subunit ribosomal RNA

marker-gene studies). * Biogeography The study of species distribution through geographic space and time. * Copiotrophic Microorganisms that grow optimally in nutrient-rich environments and

are generally adapted to rapidly exploit available resources. * Killing-the-winner hypothesis A negative frequency-dependent selection, in which abundant or active bacterial types are

affected by viral pressure. This mechanism would promote the survival and viability of rare types of microorganisms, maintaining high diversity. * Taphonomic gradient A temporal gradient

involving decay and fossilization of cells. In the context of studying the rare biosphere, the term refers to the detection of nucleic acids from deceased organisms. * Microbial seed bank A

collection of dormant microorganisms that can respond to favourable environmental conditions. * _r_-selected growth Growth strategy favouring rapid reproduction and exponential population

size increase. It is common in organisms such as bacteria, insects and weeds. * _K_-selected growth Growth strategy in which abundance tends to be stable and close to the maximum capacity in

an environment. Populations undergoing _K_-selected growth often have larger body sizes, slower growth rates and longer life cycles. * Epilimnion Top layer in a thermally stratified lake,

typically with increased dissolved oxygen concentrations. * Hypolimnion Dense bottom layer of a thermally stratified lake (below the epilimnion). * Black Queen hypothesis A theory explaining

reductive evolution in free-living organisms and dependence on co-occurring microorganisms. Natural selection favours the loss of costly biological functions ('leaky' functions)

as long as the function is retained by a subset of the community and provides an indispensable public good. * Synapomorphic A derived characteristic shared by two or more taxa and their most

recent common ancestor. RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Lynch, M., Neufeld, J. Ecology and exploration of the rare biosphere. _Nat Rev

Microbiol_ 13, 217–229 (2015). https://doi.org/10.1038/nrmicro3400 Download citation * Published: 02 March 2015 * Issue Date: April 2015 * DOI: https://doi.org/10.1038/nrmicro3400 SHARE THIS

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