Significance: In many infections, multiple microbial species are present simultaneously. Such polymicrobial infections can be viewed as small microbial ecosystems. Do bacteria in these communities interact with each other? If so, do these interactions affect the stability of the ecosystem, in particular, when antibiotics are present? We focus on urinary tract infections and demonstrate that there are ample ecological interactions between different bacterial species, both in the presence and absence of antibiotics. We further show that they crucially affect ecosystem stability and resilience to environmental perturbations such as antibiotics. Understanding the nature of these polymicrobial communities can point toward ways of disrupting infection ecosystems, which could potentially be used as a new strategy to eradicate infective communities.

The diversity of nitrogen-fixing bacteria was assessed in the rhizospheres of two cultivars of sorghum (IS 5322-C and IPA 1011) sown in Cerrado soil

The pentose metabolism of Archaea is largely unknown. Here, we have employed an integrated genomics approach including DNA microarray and proteomics analyses to elucidate the catabolic pathway for d-arabinose in Sulfolobus solfataricus. During growth on this sugar, a small set of genes appeared to be differentially expressed compared with growth on d-glucose. These genes were heterologously overexpressed in Escherichia coli, and the recombinant proteins were purified and biochemically studied. This showed that d-arabinose is oxidized to 2-oxoglutarate by the consecutive action of a number of previously uncharacterized enzymes, including a d-arabinose dehydrogenase, a d-arabinonate dehydratase, a novel 2-keto-3-deoxy-d-arabinonate dehydratase, and a 2,5-dioxopentanoate dehydrogenase. Promoter analysis of these genes revealed a palindromic sequence upstream of the TATA box, which is likely to be involved in their concerted transcriptional control. Integration of the obtained biochemical data with genomic context analysis strongly suggests the occurrence of pentose oxidation pathways in both Archaea and Bacteria, and predicts the involvement of additional enzyme components. Moreover, it revealed striking genetic similarities between the catabolic pathways for pentoses, hexaric acids, and hydroxyproline degradation, which support the theory of metabolic pathway genesis by enzyme recruitment.

The epistatic interactions that underlie evolutionary constraint have mainly been studied for constant external conditions. However, environmental changes may modulate epistasis and hence affect genetic constraints. Here we investigate genetic constraints in the adaptive evolution of a novel regulatory function in variable environments, using the lac repressor, LacI, as a model system. We have systematically reconstructed mutational trajectories from wild type LacI to three different variants that each exhibit an inverse response to the inducing ligand IPTG, and analyzed the higher-order interactions between genetic and environmental changes. We find epistasis to depend strongly on the environment. As a result, mutational steps essential to inversion but inaccessible by positive selection in one environment, become accessible in another. We present a graphical method to analyze the observed complex higher-order interactions between multiple mutations and environmental change, and show how the interactions can be explained by a combination of mutational effects on allostery and thermodynamic stability. This dependency of genetic constraint on the environment should fundamentally affect evolutionary dynamics and affects the interpretation of phylogenetic data. Epistatic interactions limit the number of adaptive trajectories to peaks on evolutionary fitness landscapes, and may therefore hamper the progress of evolution. Recent research has focused on adaptive landscapes in one constant environment. However, adaptive evolution is generally known to occur in variable, heterogeneous environments. Here, we have constructed fitness landscapes of three inverse lac repressor variants in two contrasting environments. We find that the epistatic interactions between the pairs of mutations are profoundly altered upon an environmental change. We develop a new graphical method to analyze the underlying higher-order interactions between genetic changes and the environment, and explain the complex environmental dependencies in terms of simple molecular mechanisms. Our results show that the information about epistatic interactions acquired in one environment does not inform on the true limitations of adaptive evolution. We argue that this dependency of genetic constraints on the environment will have important effects on the progress of adaptation in heterogeneous environments, and will affect our ability to establish realistic genealogies from the phylogenic record.

Epistatic interactions can frustrate and shape evolutionary change. Indeed, phenotypes may fail to evolve when essential mutations are only accessible through positive selection if they are fixed simultaneously. How environmental variability affects such constraints is poorly understood. Here, we studied genetic constraints in fixed and fluctuating environments using the Escherichia coli lac operon as a model system for genotype–environment interactions. We found that, in different fixed environments, all trajectories that were reconstructed by applying point mutations within the transcription factor–operator interface became trapped at suboptima, where no additional improvements were possible. Paradoxically, repeated switching between these same environments allows unconstrained adaptation by continuous improvements. This evolutionary mode is explained by pervasive cross-environmental tradeoffs that reposition the peaks in such a way that trapped genotypes can repeatedly climb ascending slopes and hence, escape adaptive stasis. Using a Markov approach, we developed a mathematical framework to quantify the landscape-crossing rates and show that this ratchet-like adaptive mechanism is robust in a wide spectrum of fluctuating environments. Overall, this study shows that genetic constraints can be overcome by environmental change and that cross-environmental tradeoffs do not necessarily impede but also, can facilitate adaptive evolution. Because tradeoffs and environmental variability are ubiquitous in nature, we speculate this evolutionary mode to be of general relevance.