Brian C. Thomas

A new view of the tree of life

The tree of life is one of the most important organizing principles in biology1. Gene surveys suggest the existence of an enormous number of branches2, but even an approximation of the full scale of the tree has remained elusive. Recent depictions of the tree of life have focused either on the nature of deep evolutionary relationships3–5 or on the known, well-classified diversity of life with an emphasis on eukaryotes6. These approaches overlook the dramatic change in our understanding of lifes diversity resulting from genomic sampling of previously unexamined environments. New methods to generate genome sequences illuminate the identity of organisms and their metabolic capacities, placing them in community and ecosystem contexts7,8. Here, we use new genomic data from over 1,000 uncultivated and little known organisms, together with published sequences, to infer a dramatically expanded version of the tree of life, with Bacteria, Archaea and Eukarya included. The depiction is both a global overview and a snapshot of the diversity within each major lineage. The results reveal the dominance of bacterial diversification and underline the importance of organisms lacking isolated representatives, with substantial evolution concentrated in a major radiation of such organisms. This tree highlights major lineages currently underrepresented in biogeochemical models and identifies radiations that are probably important for future evolutionary analyses.

Unusual biology across a group comprising more than 15% of domain Bacteria

A prominent feature of the bacterial domain is a radiation of major lineages that are defined as candidate phyla because they lack isolated representatives. Bacteria from these phyla occur in diverse environments and are thought to mediate carbon and hydrogen cycles. Genomic analyses of a few representatives suggested that metabolic limitations have prevented their cultivation. Here we reconstructed 8 complete and 789 draft genomes from bacteria representing >35 phyla and documented features that consistently distinguish these organisms from other bacteria. We infer that this group, which may comprise >15% of the bacterial domain, has shared evolutionary history, and describe it as the candidate phyla radiation (CPR). All CPR genomes are small and most lack numerous biosynthetic pathways. Owing to divergent 16S ribosomal RNA (rRNA) gene sequences, 50–100% of organisms sampled from specific phyla would evade detection in typical cultivation-independent surveys. CPR organisms often have self-splicing introns and proteins encoded within their rRNA genes, a feature rarely reported in bacteria. Furthermore, they have unusual ribosome compositions. All are missing a ribosomal protein often absent in symbionts, and specific lineages are missing ribosomal proteins and biogenesis factors considered universal in bacteria. This implies different ribosome structures and biogenesis mechanisms, and underlines unusual biology across a large part of the bacterial domain.

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system.

The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central to Earths biogeochemical cycles. However, little is known about how complex microbial communities in such environments are structured, and how inter-organism interactions shape ecosystem function. Here we apply terabase-scale cultivation-independent metagenomics to aquifer sediments and groundwater, and reconstruct 2,540 draft-quality, near-complete and complete strain-resolved genomes that represent the majority of known bacterial phyla as well as 47 newly discovered phylum-level lineages. Metabolic analyses spanning this vast phylogenetic diversity and representing up to 36% of organisms detected in the system are used to document the distribution of pathways in coexisting organisms. Consistent with prior findings indicating metabolic handoffs in simple consortia, we find that few organisms within the community can conduct multiple sequential redox transformations. As environmental conditions change, different assemblages of organisms are selected for, altering linkages among the major biogeochemical cycles.

Proteogenomic Monitoring of Geobacter Physiology during Stimulated Uranium Bioremediation

ABSTRACT Implementation of uranium bioremediation requires methods for monitoring the membership and activities of the subsurface microbial communities that are responsible for reduction of soluble U(VI) to insoluble U(IV). Here, we report a proteomics-based approach for simultaneously documenting the strain membership and microbial physiology of the dominant Geobacter community members during in situ acetate amendment of the U-contaminated Rifle, CO, aquifer. Three planktonic Geobacter-dominated samples were obtained from two wells down-gradient of acetate addition. Over 2,500 proteins from each of these samples were identified by matching liquid chromatography-tandem mass spectrometry spectra to peptides predicted from seven isolate Geobacter genomes. Genome-specific peptides indicate early proliferation of multiple M21 and Geobacter bemidjiensis-like strains and later possible emergence of M21 and G. bemidjiensis-like strains more closely related to Geobacter lovleyi. Throughout biostimulation, the proteome is dominated by enzymes that convert acetate to acetyl-coenzyme A and pyruvate for central metabolism, while abundant peptides matching tricarboxylic acid cycle proteins and ATP synthase subunits were also detected, indicating the importance of energy generation during the period of rapid growth following the start of biostimulation. Evolving Geobacter strain composition may be linked to changes in protein abundance over the course of biostimulation and may reflect changes in metabolic functioning. Thus, metagenomics-independent community proteogenomics can be used to diagnose the status of the subsurface consortia upon which remediation biotechnology relies.

New CRISPR-Cas systems from uncultivated microbes.

CRISPR–Cas systems provide microbes with adaptive immunity by employing short DNA sequences, termed spacers, that guide Cas proteins to cleave foreign DNA. Class 2 CRISPR–Cas systems are streamlined versions, in which a single RNA-bound Cas protein recognizes and cleaves target sequences. The programmable nature of these minimal systems has enabled researchers to repurpose them into a versatile technology that is broadly revolutionizing biological and clinical research. However, current CRISPR–Cas technologies are based solely on systems from isolated bacteria, leaving the vast majority of enzymes from organisms that have not been cultured untapped. Metagenomics, the sequencing of DNA extracted directly from natural microbial communities, provides access to the genetic material of a huge array of uncultivated organisms. Here, using genome-resolved metagenomics, we identify a number of CRISPR–Cas systems, including the first reported Cas9 in the archaeal domain of life, to our knowledge. This divergent Cas9 protein was found in little-studied nanoarchaea as part of an active CRISPR–Cas system. In bacteria, we discovered two previously unknown systems, CRISPR–CasX and CRISPR–CasY, which are among the most compact systems yet discovered. Notably, all required functional components were identified by metagenomics, enabling validation of robust in vivo RNA-guided DNA interference activity in Escherichia coli. Interrogation of environmental microbial communities combined with in vivo experiments allows us to access an unprecedented diversity of genomes, the content of which will expand the repertoire of microbe-based biotechnologies.

Diverse uncultivated ultra-small bacterial cells in groundwater

Bacteria from phyla lacking cultivated representatives are widespread in natural systems and some have very small genomes. Here we test the hypothesis that these cells are small and thus might be enriched by filtration for coupled genomic and ultrastructural characterization. Metagenomic analysis of groundwater that passed through a ~0.2-μm filter reveals a wide diversity of bacteria from the WWE3, OP11 and OD1 candidate phyla. Cryogenic transmission electron microscopy demonstrates that, despite morphological variation, cells consistently have small cell size (0.009±0.002 μm(3)). Ultrastructural features potentially related to cell and genome size minimization include tightly packed spirals inferred to be DNA, few densely packed ribosomes and a variety of pili-like structures that might enable inter-organism interactions that compensate for biosynthetic capacities inferred to be missing from genomic data. The results suggest that extremely small cell size is associated with these relatively common, yet little known organisms.

Did a gamma-ray burst initiate the late Ordovician mass extinction?

Gamma-ray bursts (GRBs) produce a flux of radiation detectable across the observable Universe. A GRB within our own galaxy could do considerable damage to the Earths biosphere; rate estimates suggest that a dangerously near GRB should occur on average two or more times per billion years. At least five times in the history of life, the Earth has experienced mass extinctions that eliminated a large percentage of the biota. Many possible causes have been documented, and GRBs may also have contributed. The late Ordovician mass extinction approximately 440 million years ago may be at least partly the result of a GRB. A special feature of GRBs in terms of terrestrial effects is a nearly impulsive energy input of the order of 10 s. Due to expected severe depletion of the ozone layer, intense solar ultraviolet radiation would result from a nearby GRB, and some of the patterns of extinction and survivorship at this time may be attributable to elevated levels of UV radiation reaching the Earth. In addition, a GRB could trigger the global cooling which occurs at the end of the Ordovician period that follows an interval of relatively warm climate. Intense rapid cooling and glaciation at that time, previously identified as the probable cause of this mass extinction, may have resulted from a GRB.

Gamma-Ray Bursts and the Earth: Exploration of Atmospheric, Biological, Climatic, and Biogeochemical Effects

Gamma-ray bursts (GRBs) are likely to have made a number of significant impacts on the Earth during the last billion years. The gamma radiation from a burst within a few kiloparsecs would quickly deplete much of the Earths protective ozone layer, allowing an increase in solar UVB radiation reaching the surface. This radiation is harmful to life, damaging DNA and causing sunburn. In addition, NO2 produced in the atmosphere would cause a decrease in visible sunlight reaching the surface and could cause global cooling. Nitric acid rain could stress portions of the biosphere, but the increased nitrate deposition could be helpful to land plants. We have used a two-dimensional atmospheric model to investigate the effects on the Earths atmosphere of GRBs delivering a range of fluences, at various latitudes, at the equinoxes and solstices, and at different times of day. We have estimated DNA damage levels caused by increased solar UVB radiation, reduction in solar visible light due to NO2 opacity, and deposition of nitrates through rainout of HNO3. For the typical nearest burst in the last billion years, we find globally averaged ozone depletion up to 38%. Localized depletion reaches as much as 74%. Significant global depletion (at least 10%) persists up to about 7 yr after the burst. Our results depend strongly on time of year and latitude over which the burst occurs. The impact scales with the total fluence of the GRB at the Earth but is insensitive to the time of day of the burst and its duration (1-1000 s). We find DNA damage of up to 16 times the normal annual global average, well above lethal levels for simple life forms such as phytoplankton. The greatest damage occurs at mid- to low latitudes. We find reductions in visible sunlight of a few percent, primarily in the polar regions. Nitrate deposition similar to or slightly greater than that currently caused by lightning is also observed, lasting several years. We discuss how these results support the hypothesis that the Late Ordovician mass extinction may have been initiated by a GRB.

Causes of an ad 774-775 14C increase

Arising from F. Miyake, K. Nagaya, K. Masuda & T. Nakamura 486, 240–242 (2012)10.1038/nature11123Atmospheric 14C production is a potential window into the energy of solar proton and other cosmic ray events. It was previously concluded that 14C results from ad 774–775 would require solar events that were orders of magnitude greater than known past events. We find that the coronal mass ejection energy based on 14C production is much smaller than claimed in ref. 1, but still substantially larger than the maximum historical Carrington Event of 1859. Such an event would cause great damage to modern technology, and in view of recent confirmation of superflares on solar-type stars, this issue merits attention.

Terrestrial effects of possible astrophysical sources of an AD 774‐775 increase in 14C production

We examine possible sources of a substantial increase in tree ring 14C measurements for the years AD 774-775. Contrary to claims regarding a coronal mass ejection (CME), the required CME energy is not several orders of magnitude greater than known solar events. We consider solar proton events (SPEs) with three different fluences and two different spectra. The data may be explained by an event with fluence about one order of magnitude beyond the October 1989 SPE. Two hard spectrum cases considered here result in moderate ozone depletion, so no mass extinction is implied, though we do predict increases in erythema and damage to plants from enhanced solar UV. We are able to rule out an event with a very soft spectrum that causes severe ozone depletion and subsequent biological impacts. Nitrate enhancements are consistent with their apparent absence in ice core data. The modern technological implications of such an event may be extreme, and considering recent confirmation of superflares on solar-type stars, this issue merits attention.