Genome-Based Microbial Taxonomy Coming of Age

Abstract

Reconstructing the complete evolutionary history of extant life on our planet will be one of the most fundamental accomplishments of scientific endeavor, akin to the completion of the periodic table, which revolutionized chemistry. The road to this goal is via comparative genomics because genomes are our most comprehensive and objective evolutionary documents. The genomes of plant and animal species have been systematically targeted over the past decade to provide coverage of the tree of life. However, multicellular organisms only emerged in the last 550 million years of more than three billion years of biological evolution and thus comprise a small fraction of total biological diversity. The bulk of biodiversity, both past and present, is microbial. We have only scratched the surface in our understanding of the microbial world, as most microorganisms cannot be readily grown in the laboratory and remain unknown to science. Ground-breaking, culture-independent molecular techniques developed over the past 30 years have opened the door to this so-called microbial dark matter with an accelerating momentum driven by exponential increases in sequencing capacity. We are on the verge of obtaining representative genomes across all life for the first time. However, historical use of morphology, biochemical properties, behavioral traits, and single-marker genes to infer organismal relationships mean that the existing highly incomplete tree is riddled with taxonomic errors. Concerted efforts are now needed to synthesize and integrate the burgeoning genomic data resources into a coherent universal tree of life and genome-based taxonomy.

Figure 1.

Two representations of the tree of life. The first (A) based on phenotypic comparisons resulting in lumping of microorganisms into a single undifferentiated mass at the base of the tree (circled in red), and the second (B) based on genotypic (rRNA genes) comparisons revealing that most diversity (including the Eucarya) is actually microbial with multicellular life forms only emerging relatively recently in evolutionary history (circled in red). (Panel A is reproduced from Haekcel 1866, and is freely available in the public domain and free of known restrictions under copyright law. Panel B is based on Figure 2 in Barns et al. 1996.)

Figure 2.

Increase in recognized phylogenetic diversity as measured by rRNA sequence novelty (y-axis) over time (x-axis). Recognized diversity has increased by an order of magnitude in the past 10 years, most of which (∼80%) is a result of newly identified uncultured lineages (microbial dark matter). Note that the apparent leveling off of novel phylogenetic diversity discovery in 2013 is likely a consequence of the recent move from full-length 16S rRNA sequencing to partial gene sequencing on next-generation sequencing platforms, which are not included in this estimate (adapted from Rinke et al. 2013).

Figure 3.

A tree of isolate genomes belonging to the class Gammaproteobacteria inferred from a concatenated alignment of 83 single-copy marker genes. Lineages are collapsed at the order level showing that some are monophyletic (in black), but many others are polyphyletic (colored), the most extreme case in this instance being the Alteromonadales. Renaming of orders to remove polyphyly is shown in parentheses. Numbers inside collapsed groups indicate the number of genomes comprising a given order.

Figure 4.

A histogram of pairwise average amino acid identities (AAI) between 290 archaeal and 5582 bacterial reference genomes colored by rank affiliation showing the uneveness of current taxonomic classifications. Extreme outliers include isolates classified in the same species (red) with only 68% AAI (Bdellovibrio bacteriovorus) and others classified in different genera (green) sharing as high as 94% AAI (e.g., Tannerella and Coprobacter) (adapted from Konstantinidis and Tiedje 2005).