Genomic analysis of a key innovation in an experimental Escherichia coli population.

Evolutionary novelties have been important in the history of life, but their origins are usually difficult to examine in detail. We previously described the evolution of a novel trait, aerobic citrate utilization (Cit(+)), in an experimental population of Escherichia coli. Here we analyse genome sequences to investigate the history and genetic basis of this trait. At least three distinct clades coexisted for more than 10,000 generations before its emergence. The Cit(+) trait originated in one clade by a tandem duplication that captured an aerobically expressed promoter for the expression of a previously silent citrate transporter. The clades varied in their propensity to evolve this novel trait, although genotypes able to do so existed in all three clades, implying that multiple potentiating mutations arose during the population's history. Our findings illustrate the importance of promoter capture and altered gene regulation in mediating the exaptation events that often underlie evolutionary innovations.

An integrated knowledge synthesis of regional ambient monitoring in Canada's oil sands.

The desire to document and understand the cumulative implications of oil sands (OS) development in the ambient environment of northeastern Alberta has motivated increased investment and release of information in the past decade. Here, we summarize the knowledge presented in the theme-based review papers in this special series, including air, surface water, terrestrial biology, and Indigenous community-based monitoring in order to (1) consolidate knowledge gained to date, (2) highlight key commonalities and gaps, and (3) leverage this knowledge to assess the state of integration in environmental monitoring efforts in the OS region and suggest next steps. Among air, water, and land studies, the individual reviews identified a clear focus on describing stressors, including primarily (1) contaminant emission, transport, transformation, deposition, and exposure, and (2) landscape disturbance. These emphases are generally partitioned by theme; air and water studies focus heavily on chemical stressors, whereas terrestrial monitoring focuses on biological change and landscape disturbance. Causal attribution is often stated as a high priority objective across all themes. However, studies often rely on spatial proximity to attribute cause to industrial activity, leaving causal attribution potentially confounded by spatial covariance of both OS- and non-OS-related stressors in the region, and by the complexity of interacting pathways between sources of environmental change and ecological receptors. Geospatial and modeling approaches are common across themes and may represent clear integration opportunities, particularly to help inform investigation-of-cause, but are not a replacement for robust field monitoring designs. Cumulative effects assessment remains a common focus of regional monitoring, but is limited in the peer-reviewed literature, potentially reflecting a lack of integration among monitoring efforts beyond narrow integrated interpretations of results. Addressing this requires greater emphasis on a priori integrated data collection and integrated analyses focused on the main residual exposure pathways, such as atmospheric deposition. Integr Environ Assess Manag 2022;18:428-441. © 2021 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

Forest health effects due to atmospheric deposition: Findings from long-term forest health monitoring in the Athabasca Oil Sands Region.

Oil sands developments release acidifying compounds (SO2 and NO2) with the potential for acidifying deposition and impacts to forest health. This article integrates the findings presented in the Oil Sands Forest Health Special Issue, which reports on the results of 20 years of forest health monitoring, and addresses the key questions asked by WBEA's Forest Health Monitoring (FHM) Program: 1) is there evidence of deposition affecting the environment?, 2) have there been changes in deposition or effects over time?, 3) do acid deposition levels require management intervention?, 4) what are major sources of deposited substances? and 5) how can the program be improved? Deposition of sulphur, nitrogen, base cations (BC), polycyclic aromatic compounds and trace elements decline exponentially with distance from sources. There is little evidence for acidification effects on forest soils or on understory plant communities or tree growth, but there is evidence of nitrogen accumulation in jack pine needles and fertilization effects on understory plant communities. Sulphur, BC and trace metal concentrations in lichens increased between 2008 and 2014. Source apportionment studies suggest fugitive dust in proximity to mining is a primary source of BC, trace element and organic compound deposition, and BC deposition may be neutralizing acidifying deposition. Sulphur accumulation in soils and nitrogen effects on vegetation may indicate early stages of acidification. Deposition estimates for sites close to emissions sources exceed proposed regulatory trigger levels, suggesting a detailed assessment of acidification risk close to the emission sources is warranted. However, there is no evidence of widespread acidification as suggested by recent modeling studies, likely due to high BC deposition. FHM Program evolution should include continued integration with modeling approaches, ongoing collection and assessment of monitoring data and testing for change over time, and addition of monitoring sites to fill gaps in regional coverage.

Chemical interactions between organisms in microbial communities.

Bacteria live almost exclusively in communities with other microorganisms, and often in association with multicellular hosts. These communities are capable of maintaining complex structural and functional stability over time, and exhibit fascinating properties of resiliency in response to environmental changes. This is a result of interactions between microbes and the environment and amongst members of the community. A multitude of chemical interactions occur in microbial communities where primary and secondary metabolites contribute to a wealth of interactions between organisms. The chemicals include a variety of nutrients, toxic or neutral metabolic byproducts, antibiotics, and cell-cell signaling molecules. These chemical and physical signals facilitate microbial relationship that can be competitive, cooperative or neutral, and thus are responsible for determining community structure. In turn, the surrounding community changes the microenvironment of individual cells who respond to chemical and environmental cues in a combinatorial manner. Current laboratory understanding of the genetics and mechanisms of interactions between microbes has the power to help us understand how complex microbial communities behave in the natural environment. In this chapter we review the current understanding of microbial communication, from the genetic and molecular aspects, to our current understanding of their ecological role.

Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age.

The upper respiratory tract (URT) is a crucial site for host defense, as it is home to bacterial communities that both modulate host immune defense and serve as a reservoir of potential pathogens. Young children are at high risk of respiratory illness, yet the composition of their URT microbiota is not well understood. Microbial profiling of the respiratory tract has traditionally focused on culturing common respiratory pathogens, whereas recent culture-independent microbiome profiling can only report the relative abundance of bacterial populations. In the current study, we used both molecular profiling of the bacterial 16S rRNA gene and laboratory culture to examine the bacterial diversity from the oropharynx and nasopharynx of 51 healthy children with a median age of 1.1 years (range 1-4.5 years) along with 19 accompanying parents. The resulting profiles suggest that in young children the nasopharyngeal microbiota, much like the gastrointestinal tract microbiome, changes from an immature state, where it is colonized by a few dominant taxa, to a more diverse state as it matures to resemble the adult microbiota. Importantly, this difference in bacterial diversity between adults and children accompanies a change in bacterial load of three orders of magnitude. This indicates that the bacterial communities in the nasopharynx of young children have a fundamentally different structure from those in adults and suggests that maturation of this community occurs sometime during the first few years of life, a period that includes ages at which children are at the highest risk for respiratory disease.

Integration of transcriptional inputs at promoters of the arabinose catabolic pathway.

BACKGROUND: Most modelling efforts of transcriptional networks involve estimations of in vivo concentrations of components, binding affinities and reaction rates, derived from in vitro biochemical assays. These assays are difficult and in vitro measurements may not approximate actual in vivo conditions. Alternatively, changes in transcription factor activity can be estimated by using partially specified models which estimate the "hidden functions" of transcription factor concentration changes; however, non-unique solutions are a potential problem. We have applied a synthetic biology approach to develop reporters that are capable of measuring transcription factor activity in vivo in real time. These synthetic reporters are comprised of a constitutive promoter with an operator site for the specific transcription factor immediately downstream. Thus, increasing transcription factor activity is measured as repression of expression of the transcription factor reporter. Measuring repression instead of activation avoids the complications of non-linear interactions between the transcription factor and RNA polymerase which differs at each promoter. RESULTS: Using these reporters, we show that a simple model is capable of determining the rules of integration for multiple transcriptional inputs at the four promoters of the arabinose catabolic pathway. Furthermore, we show that despite the complex and non-linear changes in cAMP-CRP activity in vivo during diauxic shift, the synthetic transcription factor reporters are capable of measuring real-time changes in transcription factor activity, and the simple model is capable of predicting the dynamic behaviour of the catabolic promoters. CONCLUSIONS: Using a synthetic biology approach we show that the in vivo activity of transcription factors can be quantified without the need for measuring intracellular concentrations, binding affinities and reaction rates. Using measured transcription factor activity we show how different promoters can integrate common transcriptional inputs, resulting in distinct expression patterns. The data collected show that cAMP levels in vivo are dynamic and agree with observations showing that cAMP levels show a transient pulse during diauxic shift.

Individuality in bacteria.

While traditionally microbiologists have examined bacterial behavior averaged over large populations, increasingly we are becoming aware that bacterial populations can be composed of phenotypically diverse individuals generated by a variety of mechanisms. Though the results of different mechanisms, the phenomena of bistability, persistence, variation in chemotactic response, and phase and antigenic variation are all strategies to develop population-level diversity. The understanding of individuality in bacteria requires an appreciation of their environmental and ecological context, and thus evolutionary theory regarding adaptations to time-variable environments is becoming more applicable to these problems. In particular, the application of game and information theory to bacterial individuality has addressed some interesting problems of bacterial behavior. In this review we discuss the mechanisms of generating population-level variability, and the application of evolutionary theory to problems of individuality in bacteria.

Evolutionary loss of the rdar morphotype in Salmonella as a result of high mutation rates during laboratory passage.

Rapid evolution of microbes under laboratory conditions can lead to domestication of environmental or clinical strains. In this work, we show that domestication due to laboratory passage in rich medium is extremely rapid. Passaging of wild-type Salmonella in rich medium led to diversification of genotypes contributing to the loss of a spatial phenotype, called the rdar morphotype, within days. Gene expression analysis of the rdar regulatory network demonstrated that mutations were primarily within rpoS, indicating that the selection pressure for scavenging during stationary phase had the secondary effect of impairing this highly conserved phenotype. If stationary phase was omitted from the experiment, radiation of genotypes and loss of the rdar morphotype was also demonstrated, but due to mutations within the cellulose biosynthesis pathway and also in an unknown upstream regulator. Thus regardless of the selection pressure, rapid regulatory changes can be observed on laboratory timescales. The speed of accumulation of rpoS mutations during daily passaging could not be explained by measured fitness and mutation rates. A model of mutation accumulation suggests that to generate the observed accumulation of sigma 38 mutations, this locus must experience a mutation rate of approximately 10(-4) mutations/gene/generation. Sequencing and gene expression of population isolates indicated that there were a wide variety of sigma 38 phenotypes within each population. This suggests that the rpoS locus is highly mutable by an unknown pathway, and that these mutations accumulate rapidly under common laboratory conditions.