To assess the potential of protein function prediction in environmental genomics data, we analyzed shotgun sequences from four diverse and complex habitats. Using homology searches as well as customized gene neighborhood methods that incorporate intergenic and evolutionary distances, we inferred specific functions for 76% of the 1.4 million predicted ORFs in these samples (83% when nonspecific functions are considered). Surprisingly, these fractions are only slightly smaller than the corresponding ones in completely sequenced genomes (83% and 86%, respectively, by using the same methodology) and considerably higher than previously thought. For as many as 75,448 ORFs (5% of the total), only neighborhood methods can assign functions, illustrated here by a previously undescribed gene associated with the well characterized heme biosynthesis operon and a potential transcription factor that might regulate a coupling between fatty acid biosynthesis and degradation. Our results further suggest that, although functions can be inferred for most proteins on earth, many functions remain to be discovered in numerous small, rare protein families.fatty acid ͉ heme ͉ neighborhood ͉ environmental genomics ͉ metagenome annotation

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Why is motility so common in bacteria? An obvious answer to this ecological and evolutionary question is that in almost all habitats, bacteria need to go someplace and particularly in the direction of food. Although the machinery required for motility and chemotaxis (acquiring and processing the information needed to direct movement toward nutrients) are functionally coupled in contemporary bacteria, they are coded for by different sets of genes. Moreover, information that resources are more abundant elsewhere in a habitat would be of no value to a bacterium unless it already had the means to get there. Thus, motility must have evolved before chemotaxis, and bacteria with flagella and other machinery for propulsion in random directions must have an advantage over bacteria relegated to moving at the whim of external forces alone. However, what are the selection pressures responsible for the evolution and maintenance of undirected motility in bacteria? Here we use a combination of mathematical modeling and experiments with Escherichia coli to generate and test a parsimonious and ecologically general hypothesis for the existence of undirected motility in bacteria: it enables bacteria to move away from each other and thereby obtain greater individual shares of resources in physically structured environments. The results of our experiments not only support this hypothesis, but are quantitatively and qualitatively consistent with the predictions of our model. experimental evolution | population dynamics | partial differential equations I f we accept that the presence of genes coding for flagella indicates the phenotype of self-propulsion, motility is an ancient and almost ubiquitous character in the eubacteria. Flagellar genes are significantly overrepresented in environmental samples of DNA (1, 2), and almost two-thirds of sequenced bacteria with phenotypic annotations are motile (3). Why is motility so widespread? At a qualitative level the obvious answer is almost certainly true: In most of the habitats in which bacteria reside, nutrients are not evenly dispersed. Cells with the facility to propel themselves have more access to resources than those that move solely at the whim of external forces. This qualitative answer, however, raises a number of quantitative questions that have to be addressed for a comprehensive understanding of the ecological conditions under which natural selection will favor the evolution and maintenance of motility. Under what conditions will the relatively weak propulsion ability of a bacterium enable it to overcome the viscosity (resistance to flow or gumminess) of its environment for its movement to be effective? Under what conditions will movement in random directions provide a bacterium with an edge in the acquisition of resources when competing with bacteria that are nonmotile or less motile? In contemporary bacteria, motility is commonly coupled with chemotaxis, i.e., the sensory and signaling machinery needed to direct their motion toward nutrients (4-6). Logic, retrospective eviden...

The emerging coverage of diverse habitats by metagenomic shotgun data opens new avenues of discovering functional novelty using computational tools. Here, we apply three different concepts for predicting novel functions within light-mediated microbial pathways in five diverse environments. Using phylogenetic approaches, we discovered two novel deep-branching subfamilies of photolyases (involved in light-mediated repair) distributed abundantly in high-UV environments. Using neighborhood approaches, we were able to assign seven novel functional partners in luciferase synthesis, nitrogen metabolism, and quorum sensing to BLUF domain-containing proteins (involved in light sensing). Finally, by domain analysis, for RcaE proteins (involved in chromatic adaptation), we predict 16 novel domain architectures that indicate novel functionalities in habitats with little or no light. Quantification of protein abundance in the various environments supports our findings that bacteria utilize light for sensing, repair, and adaptation far more widely than previously thought. While the discoveries illustrate the opportunities in function discovery, we also discuss the immense conceptual and practical challenges that come along with this new type of data.One of the central questions in biology, starting from the time of Charles Darwin, has been the extent and distribution of biological diversity (68). The recent sequencing of several hundred bacterial and archaeal genomes and metagenomes, along with the discovery of large-scale lateral gene transfer (10) and recombination (25) in bacterial evolution, has not only renewed interest in the question of diversity but also confounded it. The sequencing projects reveal that contrary to previous estimates, it is microbes that account for the vast majority of diversity in phenotype and genotype on earth (44, 47). Underlying this dazzling diversity in species and habitat is molecular diversity. Indeed, we are just beginning to scratch the surface of this molecular diversity (50). Even though our understanding of how the living world functions at the molecular level is far from complete, the discovery of novel molecules has important applications to medicine, agriculture, industry, and environmental conservation and remediation.But how are we to discover functional novelty in the exponentially increasing amounts of sequenced genes and habitats (Fig.