Investigating the eco-evolutionary tunnels for establishing cooperative communities.

Diversity is abundant among microbial communities. Understanding the assembly of diverse microbial communities is a significant challenge. One of the recent plausible explanations for the assembly involves eco-evolutionary tunnels, where species interact in the same timescale with the mutational rate.

Multi-stable bacterial communities exhibit extreme sensitivity to initial conditions.

Microbial communities can have dramatically different compositions even among similar environments. This might be due to the existence of multiple alternative stable states, yet there exists little experimental evidence supporting this possibility. Here, we gathered a large collection of absolute population abundances capturing population dynamics in one- to four-strain communities of soil bacteria with a complex life cycle in a feast-or-famine environment.

Chemical Ecosystem Selection on Mineral Surfaces Reveals Long-Term Dynamics Consistent with the Spontaneous Emergence of Mutual Catalysis.

How did chemicals first become organized into systems capable of self-propagation and adaptive evolution? One possibility is that the first evolvers were chemical ecosystems localized on mineral surfaces and composed of sets of molecular species that could catalyze each other's formation. We used a bottom-up experimental framework, chemical ecosystem selection (CES), to evaluate this perspective and search for surface-associated and mutually catalytic chemical systems based on the changes in chemistry that they are expected to induce. Here, we report the results of preliminary CES experiments conducted using a synthetic "prebiotic soup" and pyrite grains, which yielded dynamical patterns that are suggestive of the emergence of mutual catalysis.

Stochastic exits from dormancy give rise to heavy-tailed distributions of descendants in bacterial populations.

Variance in reproductive success is a major determinant of the degree of genetic drift in a population. While many plants and animals exhibit high variance in their number of progeny, far less is known about these distributions for microorganisms. Here, we used a strain barcoding approach to quantify variability in offspring number among replicate bacterial populations and developed a Bayesian method to infer the distribution of descendants from this variability.

Emergence of evolutionarily stable communities through eco-evolutionary tunnelling.

Ecological and evolutionary dynamics of communities are inexorably intertwined. The ecological state determines the fate of newly arising mutants, and mutations that increase in frequency can reshape the ecological dynamics. Evolutionary game theory and its extensions within adaptive dynamics have been the mathematical frameworks for understanding this interplay, leading to notions such as evolutionarily stable states (ESS) in which no mutations are favoured, and evolutionary branching points near which the population diversifies.

Phenotypic variability and community interactions of germinating Streptomyces spores.

A case can be made for stochastic germination and interactions among germinating spores as beneficial germination strategies in uncertain environments. However, there is little data on how widespread, species-specific or diverse such phenomena are. Focusing on Streptomycetes, a platform was developed for quantification of germination and early growth within communities of spores.

An Experimental Framework for Generating Evolvable Chemical Systems in the Laboratory.

Most experimental work on the origin of life has focused on either characterizing the chemical synthesis of particular biochemicals and their precursors or on designing simple chemical systems that manifest life-like properties such as self-propagation or adaptive evolution. Here we propose a new class of experiments, analogous to artificial ecosystem selection, where we select for spontaneously forming self-propagating chemical assemblages in the lab and then seek evidence of a response to that selection as a key indicator that life-like chemical systems have arisen. Since surfaces and surface metabolism likely played an important role in the origin of life, a key experimental challenge is to find conditions that foster nucleation and spread of chemical consortia on surfaces.

Quality filtering of Illumina index reads mitigates sample cross-talk.

Background: Multiplexing multiple samples during Illumina sequencing is a common practice and is rapidly growing in importance as the throughput of the platform increases. Misassignments during de-multiplexing, where sequences are associated with the wrong sample, are an overlooked error mode on the Illumina sequencing platform. This results in a low rate of cross-talk among multiplexed samples and can cause detrimental effects in studies requiring the detection of rare variants or when multiplexing a large number of samples.

Inhibitory interactions promote frequent bistability among competing bacteria.

It is largely unknown how the process of microbial community assembly is affected by the order of species arrival, initial species abundances and interactions between species. A minimal way of capturing competitive abilities in a frequency-dependent manner is with an invasibility network specifying whether a species at low abundance can increase in frequency in an environment dominated by another species. Here, using a panel of prolific small-molecule producers and a habitat with feast-and-famine cycles, we show that the most abundant strain can often exclude other strains--resulting in bistability between pairs of strains.

DesignSignatures: a tool for designing primers that yields amplicons with distinct signatures.

Unlabelled: For numerous experimental applications, PCR primers must be designed to efficiently amplify a set of homologous DNA sequences while giving rise to amplicons with maximally diverse signatures. We developed DesignSignatures to automate the process of designing primers for high-resolution melting (HRM), fragment length polymorphism (FLP) and sequencing experiments. The program also finds the best restriction enzyme to further diversify HRM or FLP signatures.

Counteraction of antibiotic production and degradation stabilizes microbial communities.

A major challenge in theoretical ecology is understanding how natural microbial communities support species diversity, and in particular how antibiotic-producing, -sensitive and -resistant species coexist. While cyclic ‘rock–paper–scissors’ interactions can stabilize communities in spatial environments, coexistence in unstructured environments remains unexplained. Here, using simulations and analytical models, we show that the opposing actions of antibiotic production and degradation enable coexistence even in well-mixed environments.

Structure and evolution of Streptomyces interaction networks in soil and in silico.

Soil grains harbor an astonishing diversity of Streptomyces strains producing diverse secondary metabolites. However, it is not understood how this genotypic and chemical diversity is ecologically maintained. While secondary metabolites are known to mediate signaling and warfare among strains, no systematic measurement of the resulting interaction networks has been available.

Genome rhetoric and the emergence of compositional bias.

Genomes exhibit diverse patterns of species-specific GC content, GC and AT skews, codon bias, and mutation bias. Despite intensive investigations and the rapid accumulation of sequence data, the causes of these a priori different genome biases have not been agreed on and seem multifactorial and idiosyncratic. We show that these biases can arise generically from an instability of the coevolutionary dynamics between genome composition and resource allocation for translation, transcription, and replication.

Exposing the fitness contribution of duplicated genes.

Duplicate genes from the whole-genome duplication (WGD) in yeast are often dispensable--removing one copy has little or no phenotypic consequence. It is unknown, however, whether such dispensability reflects insignificance of the ancestral function or compensation from paralogs. Here, using precise competition-based measurements of the fitness cost of single and double deletions, we estimate the exposed fitness contribution of WGD duplicate genes in metabolism and bound the importance of their ancestral pre-duplication function.

Evolution and multilevel optimization of the genetic code.

The discovery of the genetic code was one of the most important advances of modern biology. But there is more to a DNA code than protein sequence; DNA carries signals for splicing, localization, folding, and regulation that are often embedded within the protein-coding sequence. In this issue, Itzkovitz and Alon show that the specific 64-to-20 mapping found in the genetic code may have been optimized for permitting protein-coding regions to carry this extra information and suggest that this property may have evolved as a side benefit of selection to minimize the negative effects of frameshift errors.

Collective evolution and the genetic code.

A dynamical theory for the evolution of the genetic code is presented, which accounts for its universality and optimality. The central concept is that a variety of collective, but non-Darwinian, mechanisms likely to be present in early communal life generically lead to refinement and selection of innovation-sharing protocols, such as the genetic code. Our proposal is illustrated by using a simplified computer model and placed within the context of a sequence of transitions that early life may have made, before the emergence of vertical descent.

Global divergence of microbial genome sequences mediated by propagating fronts.

We model the competition between homologous recombination and point mutation in microbial genomes, and present evidence for two distinct phases, one uniform, the other genetically diverse. Depending on the specifics of homologous recombination, we find that global sequence divergence can be mediated by fronts propagating along the genome, whose characteristic signature on genome structure is elucidated, and apparently observed in closely related Bacillus strains. Front propagation provides an emergent, generic mechanism for microbial "speciation," and suggests a classification of microorganisms on the basis of their propensity to support propagating fronts.

Computationally efficient phase-field models with interface kinetics.

We present a phase-field model of solidification which allows efficient computations in the regime when interface kinetic effects dominate over capillary effects. The asymptotic analysis required to relate the parameters in the phase field with those of the original sharp-interface model is straightforward, and the resultant phase-field model can be used for a wide range of material parameters.