Ecology and exploration of the rare biosphere

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Ecology and exploration of the rare biosphere

Michael D.J.Lynch and Josh D.Neufeld

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.

For most of the twentieth century, our understanding of microbial diversity relied on microscopy, cultivation and experimentation to identify the genetic and phenotypic characteristics of isolated microorganisms. Although these approaches led to many foundational discoveries, the magnitude of microbial diversity and the phylogenetic relationships among microorganisms were poorly understood. Extending from the groundbreaking work of researchers such as Woese and Fox1, small subunit ribosomal RNA (SSU rRNA) was established as a marker to survey the diversity of natural microbial communities2,3,

originally by a comparison to ~25 published fulllength reference sequences4. This new molecular view of the microbial world led Norman Pace to recommend that we undertake a representative survey of microbial diversity in the environment (REF.5) on the grounds that this would answer many questions about the microbial biosphere.

Cost and labour considerations limited the scope of early molecular studies of microbial communities

(FIG.1), and the sample sizes involved were inadequate6. Nevertheless, traditional assessments of microbial diversity were identified as being analogous to sampling of community members in traditional (macro)ecological analyses7, enabling the adoption of nonparametric estimators of diversity. This provided an empirical target for the sequencing effort that was required to evaluate and compare community diversity, which was well timed for the introduction of Sangerbased tag sequencing810

and the subsequent advent of highthroughput sequencing (HTS) technologies.

The initial discovery of vast sequence diversity at low relative abundance involved an analysis of marine water

column and sediment samples by Sogin et al.11. They generated thousands of short rRNA gene sequences (tags) and showed that even when these reads were clustered into broad categories, grouping sequences...