Global physiological analysis of carbon- and energy-limited growing Escherichia coli confirms a high degree of catabolic flexibility and preparedness for mixed substrate utilization

Sampling-free investigation of microbial carbon source preferences on renewable feedstocks via online monitoring of oxygen transfer rate

The transition towards sustainable bioprocesses requires renewable feedstocks to reduce dependency on finite resources. While plant-based feedstocks offer significant potential, their complex composition poses new challenges. The microorganisms often exhibit polyauxic growth when presented with multiple carbon sources simultaneously, consuming them in a distinct order according to their carbon source preferences. The traditional investigation of polyauxic growth involves laborious sampling and offline analysis, hindering high-throughput screenings. This study introduces an efficient method for identifying carbon source consumption and their order of metabolization by various microorganisms using the respiration activity monitoring system (RAMOS) in shake flasks. As aerobic carbon metabolization and oxygen consumption are strictly correlated, the characteristic phases of polyauxic growth are visible in the oxygen transfer rate (OTR) and can be assigned to the respective carbon sources. An extended 16-flask RAMOS enables real-time monitoring of microbial respiration on up to seven carbon sources and one reference cultivation simultaneously, thus providing crucial insights into their metabolization without extensive sampling and offline analysis. The method's accuracy was validated against traditional high-performance liquid chromatography (HPLC). Its applicability to both fast-growing Escherichia coli (investigated carbon sources: glucose, arabinose, sorbitol, xylose, and glycerol) and slow-growing Ustilago trichophora (glucose, glycerol, xylose, sorbitol, rhamnose, galacturonic acid, and lactic acid) was demonstrated. Additionally, it was successfully applied to the plant-based second-generation feedstock corn leaf hydrolysate, revealing the bioavailability of the included carbon sources (glucose, sucrose, arabinose, xylose, and galactose) and their order of metabolization by Ustilago maydis.

Nutrition of Escherichia coli within the intestinal microbiome

In this chapter, we update our 2004 review of "The Life of Commensal Escherichia coli in the Mammalian Intestine" (https://doi.org/10.1128/ecosalplus.8.3.1.2), with a change of title that reflects the current focus on "Nutrition of E. coli within the Intestinal Microbiome." The earlier part of the previous two decades saw incremental improvements in understanding the carbon and energy sources that E. coli and Salmonella use to support intestinal colonization. Along with these investigations of electron donors came a better understanding of the electron acceptors that support the respiration of these facultative anaerobes in the gastrointestinal tract. Hundreds of recent papers add to what was known about the nutrition of commensal and pathogenic enteric bacteria. The fact that each biotype or pathotype grows on a different subset of the available nutrients suggested a mechanism for succession of commensal colonizers and invasion by enteric pathogens. Competition for nutrients in the intestine has also come to be recognized as one basis for colonization resistance, in which colonized strain(s) prevent colonization by a challenger. In the past decade, detailed investigations of fiber- and mucin-degrading anaerobes added greatly to our understanding of how complex polysaccharides support the hundreds of intestinal microbiome species. It is now clear that facultative anaerobes, which usually cannot degrade complex polysaccharides, live in symbiosis with the anaerobic degraders. This concept led to the "restaurant hypothesis," which emphasizes that facultative bacteria, such as E. coli, colonize the intestine as members of mixed biofilms and obtain the sugars they need for growth locally through cross-feeding from polysaccharide-degrading anaerobes. Each restaurant represents an intestinal niche. Competition for those niches determines whether or not invaders are able to overcome colonization resistance and become established. Topics centered on the nutritional basis of intestinal colonization and gastrointestinal health are explored here in detail.

The hierarchy of sugar catabolization in Lactococcus cremoris

IMPORTANCE

The availability of nutrients to microorganisms varies considerably between different environments, and changes can occur rapidly. As a general rule, a fast growth rate-typically growth on glucose-is associated with the repression of other carbohydrate utilization genes, but it is not clear to what extent catabolite repression is exerted by other sugars. We investigated the hierarchy of sugar utilization after substrate transitions in Lactococcus cremoris. For this, we determined the proteome and carbohydrate utilization capacity after growth on different sugars. The results show that the preparedness of cells for the utilization of "slower" sugars is not strictly determined by the growth rate. The data point to individual proteins relevant for various sugar transitions and suggest that the evolutionary history of the organism might be responsible for deviations from a strictly growth rate-related sugar catabolization hierarchy.

Whole-cell metabolic control analysis

Since its conception some fifty years ago, metabolic control analysis (MCA) aims to understand how cells control their metabolism by adjusting the activity of their enzymes. Here we extend its scope to a whole-cell context. We consider metabolism in the evolutionary context of growth-rate maximisation by optimisation of protein concentrations. This framework allows for the prediction of flux control coefficients from proteomics data or stoichiometric modelling. Since genes compete for finite biosynthetic resources, we treat all protein concentrations as interdependent. We show that elementary flux modes (EFMs) emerge naturally as the optimal metabolic networks in the whole-cell context and we derive their control properties. In the evolutionary optimum, the number of expressed EFMs is determined by the number of protein-concentration constraints that limit growth rate. We use published glucose-limited chemostat data of S. cerevisiae to illustrate that it uses only two EFMs prior to the onset of fermentation and that it uses four EFMs during fermentation. We discuss published enzyme-titration data to show that S. cerevisiae and E. coli indeed can express proteins at growth-rate maximising concentrations. Accordingly, we extend MCA to elementary flux modes operating at an optimal state. We find that the expression of growth-unassociated proteins changes results from classical metabolic control analysis. Finally, we show how flux control coefficients can be estimated from proteomics and ribosome-profiling data. We analyse published proteomics data of E. coli to provide a whole-cell perspective of the control of metabolic enzymes on growth rate. We hope that this paper stimulates a renewed interest in metabolic control analysis, so that it can serve again the purpose it once had: to identify general principles that emerge from the biochemistry of the cell and are conserved across biological species.

Trade-offs between the instantaneous growth rate and long-term fitness: Consequences for microbial physiology and predictive computational models

Microbial systems biology has made enormous advances in relating microbial physiology to the underlying biochemistry and molecular biology. By meticulously studying model microorganisms, in particular Escherichia coli and Saccharomyces cerevisiae, increasingly comprehensive computational models predict metabolic fluxes, protein expression, and growth. The modeling rationale is that cells are constrained by a limited pool of resources that they allocate optimally to maximize fitness. As a consequence, the expression of particular proteins is at the expense of others, causing trade-offs between cellular objectives such as instantaneous growth, stress tolerance, and capacity to adapt to new environments. While current computational models are remarkably predictive for E. coli and S. cerevisiae when grown in laboratory environments, this may not hold for other growth conditions and other microorganisms. In this contribution, we therefore discuss the relationship between the instantaneous growth rate, limited resources, and long-term fitness. We discuss uses and limitations of current computational models, in particular for rapidly changing and adverse environments, and propose to classify microbial growth strategies based on Grimes's CSR framework.

Nutrients and flow shape the cyclic dominance games between Escherichia coli strains

Evolutionary game theory has provided various models to explain the coexistence of competing strategies, one of which is the rock-paper-scissors (RPS) game. A system of three Escherichia coli strains-a toxin-producer, a resistant and a sensitive-has become a classic experimental model for studying RPS games. Previous experimental and theoretical studies, however, often ignored the influence of ecological factors such as nutrients and toxin dynamics on the evolutionary game dynamics. In this work, we combine experiments and modelling to study how these factors affect competition dynamics. Using three-dimensional printed mini-bioreactors, we tracked the frequency of the three strains in different culturing media and under different flow regimes. Although our experimental system fulfilled the requirements of cyclic dominance, we did not observe clear cycles or long-term coexistence between strains. We found that both nutrients and flow rates strongly impacted population dynamics. In our simulations, we explicitly modelled the release, removal and diffusion of toxin. We showed that the amount of toxin that is retained in the system is a simple indicator that can predict competition outcomes across broad parameter space. Moreover, our simulation results suggest that high rates of toxin diffusion might have prevented cyclic patterns from emerging in our experimental system. This article is part of the theme issue 'Half a century of evolutionary games: a synthesis of theory, application and future directions'.

Integrative biology of persister cell formation: molecular circuitry, phenotypic diversification and fitness effects

Microbial populations often contain persister cells, which reduce the extinction risk upon sudden stresses. Persister cell formation is deeply intertwined with physiology. Due to this complexity, it cannot be satisfactorily understood by focusing only on mechanistic, physiological or evolutionary aspects. In this review, we take an integrative biology perspective to identify common principles of persister cell formation, which might be applicable across evolutionary-distinct microbes. Persister cells probably evolved to cope with a fundamental trade-off between cellular stress and growth tasks, as any biosynthetic resource investment in growth-supporting proteins is at the expense of stress tasks and vice versa. Natural selection probably favours persister cell subpopulation formation over a single-phenotype strategy, where each cell is prepared for growth and stress to a suboptimal extent, since persister cells can withstand harsher environments and their coexistence with growing cells leads to a higher fitness. The formation of coexisting phenotypes requires bistable molecular circuitry. Bistability probably emerges from growth-modulated, positive feedback loops in the cell's growth versus stress control network, involving interactions between sigma factors, guanosine pentaphosphate and toxin-antitoxin (TA) systems. We conclude that persister cell formation is most likely a response to a sudden reduction in growth rate, which can be achieved by antibiotic addition, nutrient starvation, sudden stresses, nutrient transitions or activation of a TA system.

Metabolic patterns reveal enhanced anammox activity at low nitrogen conditions in the integrated I-ABR

Substrate concentrations greatly influence bacterial growth and metabolism. However, optimal nitrogen concentrations for anammox bacteria in nitrogen-limited environments remain unclear. Here, we observed enhanced nitrogen metabolism and anabolism of anammox bacteria at low nitrogen conditions. Efficient nitrogen removal was achieved at ammonium and nitrite influent concentration of 30 mg/L under HRT of 1 hr, with an average nitrogen removal rate (NRR) of 0.73 kg N/(m³ ·day) in I-ABR composed of four compartments. The highest anammox activity of 6.25 mmol N/ (gVSS·hr) was observed in the fourth compartment (C4) with the lowest substrate levels (ammonium and nitrite of 11.6 mg/L and 7 mg/L). This could be resulted from the highest expression level of genes involved in nitrogen metabolism in C4, which was 1.49-1.67 times higher than that in other compartments. Besides, the second compartment (C2) exhibited the most active anabolism at ammonium and nitrite of 17 mg/L and 13 mg/L, respectively, which contributed to the most active amino acid synthesis and thus the highest EPS (1.35 times higher) in C2. This enhanced amino acid auxotrophy between anammox bacteria with heterotrophs, and consequently, heterotrophs thrived and competed for nitrite. These results hint at the potential application of anammox process in micro-polluted water. PRACTITIONER POINTS: High nitrogen removal and efficient biomass retention at low nitrogen concentrations under short HRT was achieved in I-ABR. Optimal concentrations for anammox nitrogen removal and anabolism were discussed under low nitrogen concentrations. More active anabolism contributed to enhanced amino acid synthesis and thus higher EPS contents. Low substrate levels led to enhanced expression of genes involved in nitrogen metabolism and thus high anammox activity.

Searching for principles of microbial physiology

Why do evolutionarily distinct microorganisms display similar physiological behaviours? Why are transitions from high-ATP yield to low(er)-ATP yield metabolisms so widespread across species? Why is fast growth generally accompanied with low stress tolerance? Do these regularities occur because most microbial species are subject to the same selective pressures and physicochemical constraints? If so, a broadly-applicable theory might be developed that predicts common microbiological behaviours. Microbial systems biologists have been working out the contours of this theory for the last two decades, guided by experimental data. At its foundations lie basic principles from evolutionary biology, enzyme biochemistry, metabolism, cell composition and steady-state growth. The theory makes predictions about fitness costs and benefits of protein expression, physicochemical constraints on cell growth and characteristics of optimal metabolisms that maximise growth rate. Comparisons of the theory with experimental data indicates that microorganisms often aim for maximisation of growth rate, also in the presence of stresses; they often express optimal metabolisms and metabolic proteins at optimal concentrations. This review explains the current status of the theory for microbiologists; its roots, predictions, experimental evidence and future directions.

Tailoring the distribution of microbial communities and gene expressions to achieve integrating nitrogen transformation in a gravity-driven submerged membrane bioreactor

A pilot-scale upgraded gravity-driven submerged membrane (GDSM) reactor was constructed to enhance nitrogen removal. It was artificially formed multiple stratified environments (dissolved oxygen (DO) and substrate supply (TOC, TN, COD, NH₄⁺-N, NO₂^--N, and NO₃^--N)) by embedding moving water baffles to control water-flow process in bulk liquid with slow-flowing liquid state. Significant diversity and relative abundance of microorganisms associated with nitrogen transformation paths (i.e., ammonia-oxidizing archaea, ammonia-oxidizing bacteria, nitrite oxidizing bacteria, and denitrifying bacteria) were tailored to distribute on different spatial and temporal regions, and performed their dominant functions. The process simultaneously integrated diverse and effective nitrogen transformation paths (i.e., nitrification, partial nitrification, denitrification, anammox, and dissimilatory nitrate reduction) to achieve high nitrogen removal, with NH₄⁺-N, TN, and COD eliminated by 94.68 ± 2.55%, 55.16 ± 5.53%, and 80.17 ± 6.75%, respectively. Gene expressions involved in the nitrogen transformations were estimated by qPCR to explore the shifts of dominant nitrogen transforming bioreactions in multiple stratified environments. Pearson correlation coefficients supported that the functional genes had more stable and active ability by complementing each other. As a result, an endogenous integration of diverse nitrogen transformation paths was achieved in a single system by artificially tailoring the distributions of microbial communities and gene expressions with enhanced nitrogen removal.

Impact of substrate and growth conditions on microbial protein production and composition

Production of microbial protein (MP) from recovered resources - e.g. CO₂-sourced formate and acetate - could provide protein while enabling CO₂ capture. To assess the protein quality obtained from this process, pure cultures and enriched communities were selected and characterized kinetically, stoichiometrically and nutritionally. Growth on acetate resulted in up to 5.3 times higher maximum specific growth rate (μ_max) than formate (i.e. 0.15-0.41 h^-1 for acetate compared to 0.061-0.29 h^-1 for formate at pH = 7). The protein content was a function of the growth phase, with the highest values during stationary phase, ranging between 18 and 82%_CDW protein depending on the organism and substrate. The negative correlation between biomass productivity and protein content indicated a trade-off between production rate and product quality. The final product (i.e. dried MP) quality was in most cases superior to soybean and all cultures were rich in threonine, phenylalanine and tyrosine, regardless of the carbon source.

Competition for growth substrates in river water between Escherichia coli and indigenous bacteria illustrated by high-resolution mass spectrometry

Escherichia coli normally cannot grow in the environment. One environmental stress that prevents E. coli growth may be the competition for growth substrates with co-existing micro-organisms. In this study, the growth substrates of E. coli were screened by high-resolution mass spectrometry and compared with those of indigenous bacteria in river water. In an incubation experiment, E. coli multiplied in sterilized river water, but did not multiply when indigenous micro-organisms were present in the water. By analysing dissolved organic matter in the river water before and after E. coli growth, 35 compounds were identified as putative growth substrates of E. coli. Among them, 33 compounds were also identified as putative growth substrates of indigenous bacteria. These results indicate that E. coli and indigenous bacteria compete for organic substrates in river water, which could suppress the growth of E. coli.

Adaptation of Carbon Source Utilization Patterns of Geobacter metallireducens During Sessile Growth

There are two main strategies known how microorganisms regulate substrate utilization: specialization on one preferred substrate at high concentrations in batch cultures or simultaneous utilization of many substrates at low concentrations in chemostats. However, it remains unclear how microorganisms utilize substrates at low concentrations in the subsurface: do they focus on a single substrate and exhibit catabolite repression or do they de-repress regulation of all catabolic pathways? Here, we investigated the readiness of Geobacter metallireducens to degrade organic substrates under sessile growth in sediment columns in the presence of a mixed community as a model for aquifers. Three parallel columns were filled with sand and flushed with anoxic medium at a constant inflow (18 ml h-1) of the substrate benzoate (1 mM) with non-limiting nitrate concentrations (30 mM) as electron acceptor. Columns were inoculated with the anaerobic benzoate degrader G. metallireducens. Microbial degradation produced concentration gradients of benzoate toward the column outlet. Metagenomics and label-free metaproteomics were used to detect and quantify the protein expression of G. metallireducens. Bulk benzoate concentrations below 0.2 mM led to increased abundance of catabolic proteins involved in utilization of fermentation products and aromatic compounds including the complete upregulation of the toluene-degrading pathway although toluene was not added to the medium. We propose that under sessile conditions and low substrate concentrations G. metallireducens expresses a specific set of catabolic pathways for preferred substrates, even when these substrates are not present.

The legacy of bacterial invasions on soil native communities

Soil microbial communities are often not resistant to the impact caused by microbial invasions, both in terms of structure and functionality, but it remains unclear whether these changes persist over time. Here, we used three strains of Escherichia coli O157:H7 (E. coli O157:H7), a species used for modelling bacterial invasions, to evaluate the resilience of the bacterial communities from four Chinese soils to invasion. The impact of E. coli O157:H7 strains on soil native communities was tracked for 120 days by analysing bacterial community composition as well as their metabolic potential. We showed that soil native communities were not resistant to invasion, as demonstrated by a decline in bacterial diversity and shifts in bacterial composition in all treatments. The resilience of native bacterial communities (diversity and composition) was inversely correlated with invader's persistence in soils (R² = 0.487, p < 0.001). Microbial invasions also impacted the functionality of the soil communities (niche breadth and community niche), the degree of resilience being dependent on soil or native community diversity. Collectively, our results indicate that bacteria invasions can potentially leave a footprint in the structure and functionality of soil communities, indicating the need of assessing the legacy of introducing exotic species in soil environments.

Ampicillin-treated Lactococcus lactis MG1363 populations contain persisters as well as viable but non-culturable cells

Lactococcus lactis is used as cell-factory and strain selections are regularly performed to improve production processes. When selection regimes only allow desired phenotypes to survive, for instance by using antibiotics to select for cells that do not grow in a specific condition, the presence of more resistant subpopulations with a wildtype genotype severely slows down the procedure. While the food grade organism L. lactis is not often exposed to antibiotics we characterized its response to ampicillin in more detail, to better understand emerging population heterogeneity and how this might affect strain selection procedures. Using growth-dependent viability assays we identified persister subpopulations in stationary and exponential phase. Growth-independent viability assays revealed a 100 times larger subpopulation that did not grow on plates or in liquid medium, but had an intact membrane and could maintain a pH gradient. Over one third of these cells restored their intracellular pH when we induced a temporary collapse, indicating that this subpopulation was metabolically active and in a viable but non-culturable state. Exposure of L. lactis MG1363 to ampicillin therefore results in a heterogeneous population response with different dormancy states. These dormant cells should be considered in survival-based strain selection procedures.

The number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates

Growth rate is a near-universal selective pressure across microbial species. High growth rates require hundreds of metabolic enzymes, each with different nonlinear kinetics, to be precisely tuned within the bounds set by physicochemical constraints. Yet, the metabolic behaviour of many species is characterized by simple relations between growth rate, enzyme expression levels and metabolic rates. We asked if this simplicity could be the outcome of optimisation by evolution. Indeed, when the growth rate is maximized-in a static environment under mass-conservation and enzyme expression constraints-we prove mathematically that the resulting optimal metabolic flux distribution is described by a limited number of subnetworks, known as Elementary Flux Modes (EFMs). We show that, because EFMs are the minimal subnetworks leading to growth, a small active number automatically leads to the simple relations that are measured. We find that the maximal number of flux-carrying EFMs is determined only by the number of imposed constraints on enzyme expression, not by the size, kinetics or topology of the network. This minimal-EFM extremum principle is illustrated in a graphical framework, which explains qualitative changes in microbial behaviours, such as overflow metabolism and co-consumption, and provides a method for identification of the enzyme expression constraints that limit growth under the prevalent conditions. The extremum principle applies to all microorganisms that are selected for maximal growth rates under protein concentration constraints, for example the solvent capacities of cytosol, membrane or periplasmic space.

A metabolomic view of how low nitrogen strength favors anammox biomass yield and nitrogen removal capability

The low yield of anaerobic ammonium oxidation (anammox) biomass has attracted great attention because of its difficulty to be abundantly enriched. Patterns of substrate supply greatly influence microbial metabolism and behavior. The present study proposed that low nitrogen strength was beneficial to anammox biomass yield and nitrogen removal when comparing a membrane bioreactor (MBR) operated at low nitrogen strength with short hydraulic retention time (HRT) (R-low; influent: fixed at 100 mg-N L^-1) and one operated at high nitrogen strength with long HRT (R-stepwise; influent: 100-700 mg-N L^-1). Different nitrite concentrations in the two MBRs would indicate discrepant environments, and inevitably resulted in the discrepant microbial responses for anammox community. In particular, we found that at low nitrogen strength, increased activities of purine and pyrimidine metabolism pathways provided more abundant nucleic acids for bacterial proliferation. More active reaction of lipid and protein synthesis favored the synthesis of cellular structure. Importantly, the metabolism of cheaper amino acids was more active under low nitrogen strength, which was coupled with higher metabolic flux and potentially more active exchange of costly amino acids as public goods. In this way, more energy could be saved and applied to biomass yield. Higher active bacterial diversity and more positive interactions among bacterial species in R-low further favored biomass yield and nitrogen removal. The present study highlighted the significant effect of substrate supply patterns on anammox, which is meaningful to overcome the current bottleneck of deficient anammox biomass for application in wastewater treatment.

Heterotrophic substrate specificity in the aquatic environment: The role of microscale patchiness investigated using modelling

Recent observations of natural bacterial communities show high genetic diversity in organic carbon uptake systems (microdiversity) and specificity in substrate species taken up. This seemingly contradicts a large body of literature from laboratory experiments under nutrient-limiting conditions, where mixed substrate use is the rule. This apparent discrepancy can be resolved by realizing that bacteria in the natural aquatic environment encounter nutrients as high-concentration patches. They may live in an ecologically nutrient-limiting environment, but they are rarely in a biologically nutrient-limited state. Rather they switch between non-growing and nutrient-replete states. During nutrient-replete growth the metabolism is saturated and assimilating additional substrates does not increase the growth rate, but carrying the assimilation system constitutes a cost. Consequently, the specialist strategy is beneficial, which is consistent with observations from laboratory experiments. When the bacteria are not growing, the added cost also reduces the fitness of the generalist species. A simple mathematical model encompassing the relevant mechanisms is developed and parameterized realistically based on the literature. The model predicts that, under pulsed conditions, specialization is beneficial when the metabolic cost of an additional uptake system is more than ~0.5% of the total metabolic cost, which is a reasonable estimate and illustrates that this is a plausible hypothesis.

Evolution of a Dominant Natural Isolate of Escherichia coli in the Human Gut over the Course of a Year Suggests a Neutral Evolution with Reduced Effective Population Size

In vitro and in vivo evolution experiments on Escherichia coli revealed several principles of bacterial adaptation. However, few data are available in the literature describing the behavior of E. coli in its natural environment. We attempted here to study the evolution in the human gut of a commensal dominant E. coli clone, ED1a belonging to the B2 phylogroup, through a longitudinal genomic study. We sequenced 24 isolates sampled at three different time points within a healthy individual over almost a year. We computed a mutation rate of 6.90 × 10^-7 mutations per base per year of the chromosome for E. coli ED1a in healthy human gut. We observed very limited genomic diversity and could not detect any evidence of selection, in contrast to what is observed in experimental evolution over a similar length of time. We therefore suggest that ED1a, being well adapted to the healthy human gut, evolves mostly neutrally with a low effective population size (N_e of ≈500 to 1,700).IMPORTANCE In this study, we follow the genomic fate of a dominant clone of Escherichia coli in the human gut of a healthy individual over about a year. We could compute a low annual mutation rate that supports low diversity, and we could not retrieve any clear signature of selection. These observations support a neutral evolution of E. coli in the human gut, compatible with a very limited effective population size that deviates drastically with the observations made previously in experimental evolution.

Mycobacterium tuberculosis in the Face of Host-Imposed Nutrient Limitation

Coevolution of pathogens and host has led to many metabolic strategies employed by intracellular pathogens to deal with the immune response and the scarcity of food during infection. Simply put, bacterial pathogens are just looking for food. As a consequence, the host has developed strategies to limit nutrients for the bacterium by containment of the intruder in a pathogen-containing vacuole and/or by actively depleting nutrients from the intracellular space, a process called nutritional immunity. Since metabolism is a prerequisite for virulence, such pathways could potentially be good targets for antimicrobial therapies. In this chapter, we review the current knowledge about the in vivo diet of Mycobacterium tuberculosis, with a focus on amino acid and cofactors, discuss evidence for the bacilli's nutritionally independent lifestyle in the host, and evaluate strategies for new chemotherapeutic interventions.

Competition and niche separation of pelagic bacteria in freshwater habitats

Freshwater bacterioplankton assemblages are composed of sympatric populations that can be delineated, for example, by ribosomal RNA gene relatedness and that differ in key ecophysiological properties. They may be free-living or attached, specialized for particular concentrations or subsets of substrates, or invest a variable amount of their resources in defence traits against protistan predators and viruses. Some may be motile and tactic whereas others are not, with far-reaching implications for their respective life styles and niche partitioning. The co-occurrence of competitors with overlapping growth requirements has profound consequences for the stability of community functions; it can to some extent be explained by habitat factors such as the microscale complexity and spatiotemporal variability of the lacustrine environments. On the other hand, the composition and diversity of freshwater microbial assemblages also reflects non-equilibrium states, dispersal and the stochasticity of community assembly processes. This review synoptically discusses the competition and niche separation of heterotrophic bacterial populations (defined at various levels of phylogenetic resolution) in the pelagic zone of inland surface waters from a variety of angles, focusing on habitat heterogeneity and the resulting biogeographic distribution patterns, the ecophysiological adaptations to the substrate field and the interactions of prokaryotes with predators and viruses.

Removal of Antibiotics in Biological Wastewater Treatment Systems-A Critical Assessment Using the Activated Sludge Modeling Framework for Xenobiotics (ASM-X)

Many scientific studies present removal efficiencies for pharmaceuticals in laboratory-, pilot-, and full-scale wastewater treatment plants, based on observations that may be impacted by theoretical and methodological approaches used. In this Critical Review, we evaluated factors influencing observed removal efficiencies of three antibiotics (sulfamethoxazole, ciprofloxacin, tetracycline) in pilot- and full-scale biological treatment systems. Factors assessed include (i) retransformation to parent pharmaceuticals from e.g., conjugated metabolites and analogues, (ii) solid retention time (SRT), (iii) fractions sorbed onto solids, and (iv) dynamics in influent and effluent loading. A recently developed methodology was used, relying on the comparison of removal efficiency predictions (obtained with the Activated Sludge Model for Xenobiotics (ASM-X)) with representative measured data from literature. By applying this methodology, we demonstrated that (a) the elimination of sulfamethoxazole may be significantly underestimated when not considering retransformation from conjugated metabolites, depending on the type (urban or hospital) and size of upstream catchments; (b) operation at extended SRT may enhance antibiotic removal, as shown for sulfamethoxazole; (c) not accounting for fractions sorbed in influent and effluent solids may cause slight underestimation of ciprofloxacin removal efficiency. Using tetracycline as example substance, we ultimately evaluated implications of effluent dynamics and retransformation on environmental exposure and risk prediction.

FlexFlux: combining metabolic flux and regulatory network analyses

BACKGROUND

Expression of cell phenotypes highly depends on metabolism that supplies matter and energy. To achieve proper utilisation of the different metabolic pathways, metabolism is tightly regulated by a complex regulatory network composed of diverse biological entities (genes, transcripts, proteins, signalling molecules…). The integrated analysis of both regulatory and metabolic networks appears very insightful but is not straightforward because of the distinct characteristics of both networks. The classical method used for metabolic flux analysis is Flux Balance Analysis (FBA), which is constraint-based and relies on the assumption of steady-state metabolite concentrations throughout the network. Regarding regulatory networks, a broad spectrum of methods are dedicated to their analysis although logical modelling remains the major method to take charge of large-scale networks.

RESULTS

We present FlexFlux, an application implementing a new way to combine the analysis of both metabolic and regulatory networks, based on simulations that do not require kinetic parameters and can be applied to genome-scale networks. FlexFlux is based on seeking regulatory network steady-states by performing synchronous updates of multi-state qualitative initial values. FlexFlux is then able to use the calculated steady-state values as constraints for metabolic flux analyses using FBA. As input, FlexFlux uses the standards Systems Biology Markup Language (SBML) and SBML Qualitative Models Package ("qual") extension (SBML-qual) file formats and provides a set of FBA based functions.

CONCLUSIONS

FlexFlux is an open-source java software with executables and full documentation available online at http://lipm-bioinfo.toulouse.inra.fr/flexflux/. It can be defined as a research tool that enables a better understanding of both regulatory and metabolic networks based on steady-state simulations. FlexFlux integrates well in the flux analysis ecosystem thanks to the support of standard file formats and can thus be used as a complementary tool to existing software featuring other types of analyses.

Slow-growing cells within isogenic populations have increased RNA polymerase error rates and DNA damage

Isogenic cells show a large degree of variability in growth rate, even when cultured in the same environment. Such cell-to-cell variability in growth can alter sensitivity to antibiotics, chemotherapy and environmental stress. To characterize transcriptional differences associated with this variability, we have developed a method—FitFlow—that enables the sorting of subpopulations by growth rate. The slow-growing subpopulation shows a transcriptional stress response, but, more surprisingly, these cells have reduced RNA polymerase fidelity and exhibit a DNA damage response. As DNA damage is often caused by oxidative stress, we test the addition of an antioxidant, and find that it reduces the size of the slow-growing population. More generally, we find a significantly altered transcriptome in the slow-growing subpopulation that only partially resembles that of cells growing slowly due to environmental and culture conditions. Slow-growing cells upregulate transposons and express more chromosomal, viral and plasmid-borne transcripts, and thus explore a larger genotypic—and so phenotypic — space.

Isogenic cells growing in the same environment show a large degree of variability. Here, by sorting yeast cells based on growth rate, the authors show that the slow-growing subpopulation exhibits stress responses, a high level of transcriptional diversity, and decreased RNA polymerase fidelity.

Effect of Global Regulators RpoS and Cyclic-AMP/CRP on the Catabolome and Transcriptome of Escherichia coli K12 during Carbon- and Energy-Limited Growth

For heterotrophic microbes, limited availability of carbon and energy sources is one of the major nutritional factors restricting the rate of growth in most ecosystems. Physiological adaptation to this hunger state requires metabolic versatility which usually involves expression of a wide range of different catabolic pathways and of high-affinity carbon transporters; together, this allows for simultaneous utilization of mixtures of carbonaceous compounds at low concentrations. In Escherichia coli the stationary phase sigma factor RpoS and the signal molecule cAMP are the major players in the regulation of transcription under such conditions; however, their interaction is still not fully understood. Therefore, during growth of E. coli in carbon-limited chemostat culture at different dilution rates, the transcriptomes, expression of periplasmic proteins and catabolomes of strains lacking one of these global regulators, either rpoS or adenylate cyclase (cya), were compared to those of the wild-type strain. The inability to synthesize cAMP exerted a strong negative influence on the expression of alternative carbon source uptake and degradation systems. In contrast, absence of RpoS increased the transcription of genes belonging to high-affinity uptake systems and central metabolism, presumably due to reduced competition of σ^D with σ^S. Phenotypical analysis confirmed this observation: The ability to respire alternative carbon substrates and to express periplasmic high-affinity binding proteins was eliminated in cya and crp mutants, while these properties were not affected in the rpoS mutant. As expected, transcription of numerous stress defence genes was negatively affected by the rpoS knock-out mutation. Interestingly, several genes of the RpoS stress response regulon were also down-regulated in the cAMP-negative strain indicating a coordinated global regulation. The results demonstrate that cAMP is crucial for catabolic flexibility during slow, carbon-limited growth, whereas RpoS is primarily involved in the regulation of stress response systems necessary for the survival of this bacterium under hunger conditions.

Biodegradation: Updating the concepts of control for microbial cleanup in contaminated aquifers

Biodegradation is one of the most favored and sustainable means of removing organic pollutants from contaminated aquifers but the major steering factors are still surprisingly poorly understood. Growing evidence questions some of the established concepts for control of biodegradation. Here, we critically discuss classical concepts such as the thermodynamic redox zonation, or the use of steady state transport scenarios for assessing biodegradation rates. Furthermore, we discuss if the absence of specific degrader populations can explain poor biodegradation. We propose updated perspectives on the controls of biodegradation in contaminant plumes. These include the plume fringe concept, transport limitations, and transient conditions as currently underestimated processes affecting biodegradation.

Commensal and Pathogenic Escherichia coli Metabolism in the Gut

E. coli is a ubiquitous member of the intestinal microbiome. This organism resides in a biofilm comprised of a complex microbial community within the mucus layer where it must compete for the limiting nutrients that it needs to grow fast enough to stably colonize. In this article we discuss the nutritional basis of intestinal colonization. Beginning with basic ecological principles we describe what is known about the metabolism that makes E. coli such a remarkably successful member of the intestinal microbiota. To obtain the simple sugars and amino acids that it requires, E. coli depends on degradation of complex glycoproteins by strict anaerobes. Despite having essentially the same core genome and hence the same metabolism when grown in the laboratory, different E. coli strains display considerable catabolic diversity when colonized in mice. To explain why some E. coli mutants do not grow as well on mucus in vitro as their wild type parents yet are better colonizers, we postulate that each one resides in a distinct "Restaurant" where it is served different nutrients because it interacts physically and metabolically with different species of anaerobes. Since enteric pathogens that fail to compete successfully for nutrients cannot colonize, a basic understanding of the nutritional basis of intestinal colonization will inform efforts to develop prebiotics and probiotics to combat infection.

Soil Conditions That Can Alter Natural Suppression of Escherichia coli O157:H7 in Ohio Specialty Crop Soils

Food-borne pathogen persistence in soil fundamentally affects the production of safe vegetables and small fruits. Interventions that reduce pathogen survival in soil would have positive impacts on food safety by minimizing preharvest contamination entering the food chain. Laboratory-controlled studies determined the effects of soil pH, moisture content, and soil organic matter (SOM) on the survivability of this pathogen through the creation of single-parameter gradients. Longitudinal field-based studies were conducted in Ohio to quantify the extent to which field soils suppressed Escherichia coli O157:H7 survival. In all experiments, heat-sensitive microorganisms were responsible for the suppression of E. coli O157 in soil regardless of the chemical composition of the soil. In laboratory-based studies, soil pH and moisture content were primary drivers of E. coli O157 survival, with increases in pH after 48 h (P = 0.02) and decreases in moisture content after 48 h (P = 0.007) significantly increasing the log reduction of E. coli O157 numbers. In field-based experiments, E. coli O157 counts from both heated and unheated samples were sensitive to both season (P = 0.004 for heated samples and P = 0.001 for unheated samples) and region (P = 0.002 for heated samples and P = 0.001 for unheated samples). SOM was observed to be a more significant driver of pathogen suppression than the other two factors after 48 h at both planting and harvest (P = 0.002 at planting and P = 0.058 at harvest). This research reinforces the need for both laboratory-controlled experiments and longitudinal field-based experiments to unravel the complex relationships controlling the survival of introduced organisms in soil.

Substrate use of Pseudovibrio sp. growing in ultra-oligotrophic seawater

Marine planktonic bacteria often live in habitats with extremely low concentrations of dissolved organic matter (DOM). To study the use of trace amounts of DOM by the facultatively oligotrophic Pseudovibrio sp. FO-BEG1, we investigated the composition of artificial and natural seawater before and after growth. We determined the concentrations of dissolved organic carbon (DOC), total dissolved nitrogen (TDN), free and hydrolysable amino acids, and the molecular composition of DOM by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR-MS). The DOC concentration of the artificial seawater we used for cultivation was 4.4 μmol C L(-1), which was eight times lower compared to the natural oligotrophic seawater we used for parallel experiments (36 μmol C L(-1)). During the three-week duration of the experiment, cell numbers increased from 40 cells mL(-1) to 2x10(4) cells mL(-1) in artificial and to 3x10(5) cells mL(-1) in natural seawater. No nitrogen fixation and minor CO2 fixation (< 1% of cellular carbon) was observed. Our data show that in both media, amino acids were not the main substrate for growth. Instead, FT-ICR-MS analysis revealed usage of a variety of different dissolved organic molecules, belonging to a wide range of chemical compound groups, also containing nitrogen. The present study shows that marine heterotrophic bacteria are able to proliferate with even lower DOC concentrations than available in natural ultra-oligotrophic seawater, using unexpected organic compounds to fuel their energy, carbon and nitrogen requirements.

Bioremediation of pesticide-contaminated water resources: the challenge of low concentrations

The use of pesticides in agricultural and urban environments has improved quality of life around the world. However, the resulting accumulation of pesticide residues in fresh water resources has negative effects on aquatic ecosystem and human health. Bioremediation has been proposed as an environmentally sound alternative for the remediation of pesticide-contaminated water resources, though full-scale implementation has thus far been limited. One major challenge that has impeded progress is the occurrence of pesticides at low concentrations. Recent research has improved our fundamental understanding of pesticide biodegradation processes occurring at low concentrations under a variety of environmental scenarios and is expected to contribute to the development of applied bioremediation strategies for pesticide-contaminated water resources.

A model framework to describe growth-linked biodegradation of trace-level pollutants in the presence of coincidental carbon substrates and microbes

Pollutants such as pesticides and their degradation products occur ubiquitously in natural aquatic environments at trace concentrations (μg L(-1) and lower). Microbial biodegradation processes have long been known to contribute to the attenuation of pesticides in contaminated environments. However, challenges remain in developing engineered remediation strategies for pesticide-contaminated environments because the fundamental processes that regulate growth-linked biodegradation of pesticides in natural environments remain poorly understood. In this research, we developed a model framework to describe growth-linked biodegradation of pesticides at trace concentrations. We used experimental data reported in the literature or novel simulations to explore three fundamental kinetic processes in isolation. We then combine these kinetic processes into a unified model framework. The three kinetic processes described were: the growth-linked biodegradation of micropollutant at environmentally relevant concentrations; the effect of coincidental assimilable organic carbon substrates; and the effect of coincidental microbes that compete for assimilable organic carbon substrates. We used Monod kinetic models to describe substrate utilization and microbial growth rates for specific pesticide and degrader pairs. We then extended the model to include terms for utilization of assimilable organic carbon substrates by the specific degrader and coincidental microbes, growth on assimilable organic carbon substrates by the specific degrader and coincidental microbes, and endogenous metabolism. The proposed model framework enables interpretation and description of a range of experimental observations on micropollutant biodegradation. The model provides a useful tool to identify environmental conditions with respect to the occurrence of assimilable organic carbon and coincidental microbes that may result in enhanced or reduced micropollutant biodegradation.

Gene expression analysis of E. coli strains provides insights into the role of gene regulation in diversification

Escherichia coli spans a genetic continuum from enteric strains to several phylogenetically distinct, atypical lineages that are rare in humans, but more common in extra-intestinal environments. To investigate the link between gene regulation, phylogeny and diversification in this species, we analyzed global gene expression profiles of four strains representing distinct evolutionary lineages, including a well-studied laboratory strain, a typical commensal (enteric) strain and two environmental strains. RNA-Seq was employed to compare the whole transcriptomes of strains grown under batch, chemostat and starvation conditions. Highly differentially expressed genes showed a significantly lower nucleotide sequence identity compared with other genes, indicating that gene regulation and coding sequence conservation are directly connected. Overall, distances between the strains based on gene expression profiles were largely dependent on the culture condition and did not reflect phylogenetic relatedness. Expression differences of commonly shared genes (all four strains) and E. coli core genes were consistently smaller between strains characterized by more similar primary habitats. For instance, environmental strains exhibited increased expression of stress defense genes under carbon-limited growth and entered a more pronounced survival-like phenotype during starvation compared with other strains, which stayed more alert for substrate scavenging and catabolism during no-growth conditions. Since those environmental strains show similar genetic distance to each other and to the other two strains, these findings cannot be simply attributed to genetic relatedness but suggest physiological adaptations. Our study provides new insights into ecologically relevant gene-expression and underscores the role of (differential) gene regulation for the diversification of the model bacterial species.

Black and white with some shades of grey: the diverse responses of inducible metabolic pathways in Escherichia coli

The metabolic pathways for many sugars are inducible. This process has been extensively studied in the case of Escherichia coli lactose metabolism. It has long been known that gratuitous induction of the lac operon with non-metabolizable lactose analogues generates an all-or-nothing response, where some cells express the lac genes at a maximal rate and others not at all. However, the response to lactose itself is graded, where all cells express the lac genes in proportion to lactose concentrations. The mechanisms generating these distinct behaviours in lactose metabolism have been a topic of many studies. Despite this large body of work, little is known about how other pathways respond to their cognate sugars. An article of Molecular Microbiology investigated the response of eight metabolic pathways in E. coli to their cognate sugars at single-cell resolution. The authors demonstrate that these pathways exhibit diverse responses, ranging from graded to all-or-nothing responses and combinations thereof. Remarkably, they were able to interpret these responses using a simple mathematical model and identify the mechanisms likely giving rise to each.

Proteome adaptation of Saccharomyces cerevisiae to severe calorie restriction in Retentostat cultures

Stationary-phase, carbon-starved shake-flask cultures of Saccharomyces cerevisiae are popular models for studying eukaryotic chronological aging. However, their nutrient-starved physiological status differs substantially from that of postmitotic metazoan cells. Retentostat cultures offer an attractive alternative model system in which yeast cells, maintained under continuous calorie restriction, hardly divide but retain high metabolic activity and viability for prolonged periods of time. Using TMT labeling and UHPLC-MS/MS, the present study explores the proteome of yeast cultures during transition from exponential growth to near-zero growth in severely calorie-restricted retentostats. This transition elicited protein level changes in 20% of the yeast proteome. Increased abundance of heat shock-related proteins correlated with increased transcript levels of the corresponding genes and was consistent with a strongly increased heat shock tolerance of retentostat-grown cells. A sizable fraction (43%) of the proteins with increased abundance under calorie restriction was involved in oxidative phosphorylation and in various mitochondrial functions that, under the anaerobic, nongrowing conditions used, have a very limited role. Although it may seem surprising that yeast cells confronted with severe calorie restriction invest in the synthesis of proteins that, under those conditions, do not contribute to fitness, these responses may confer metabolic flexibility and thereby a selective advantage in fluctuating natural habitats.

Physiological and proteomic analysis of Escherichia coli iron-limited chemostat growth

Iron bioavailability is a major limiter of bacterial growth in mammalian host tissue and thus represents an important area of study. Escherichia coli K-12 metabolism was studied at four levels of iron limitation in chemostats using physiological and proteomic analyses. The data documented an E. coli acclimation gradient where progressively more severe iron scarcity resulted in a larger percentage of substrate carbon being directed into an overflow metabolism accompanied by a decrease in biomass yield on glucose. Acetate was the primary secreted organic by-product for moderate levels of iron limitation, but as stress increased, the metabolism shifted to secrete primarily lactate (∼70% of catabolized glucose carbon). Proteomic analysis reinforced the physiological data and quantified relative increases in glycolysis enzyme abundance and decreases in tricarboxylic acid (TCA) cycle enzyme abundance with increasing iron limitation stress. The combined data indicated that E. coli responds to limiting iron by investing the scarce resource in essential enzymes, at the cost of catabolic efficiency (i.e., downregulating high-ATP-yielding pathways containing enzymes with large iron requirements, like the TCA cycle). Acclimation to iron-limited growth was contrasted experimentally with acclimation to glucose-limited growth to identify both general and nutrient-specific acclimation strategies. While the iron-limited cultures maximized biomass yields on iron and increased expression of iron acquisition strategies, the glucose-limited cultures maximized biomass yields on glucose and increased expression of carbon acquisition strategies. This study quantified ecologically competitive acclimations to nutrient limitations, yielding knowledge essential for understanding medically relevant bacterial responses to host and to developing intervention strategies.

Capacity of the bovine intestinal mucus and its components to support growth of Escherichia coli O157:H7

Colonization of the gastrointestinal tract of cattle by Shiga toxin-producing Escherichia coli increases the risk of contamination of food products at slaughter. Our study aimed to shed more light on the mechanisms used by E. coli O157:H7 to thrive and compete with other bacteria in the gastrointestinal tract of cattle. We evaluated, in vitro, bovine intestinal mucus and its constituents in terms of their capacity to support growth of E. coli O157:H7 in presence or absence of fecal inoculum, with and without various enzymes. Growth of E. coli O157:H7 and total anaerobic bacteria were proportionate to the amount of mucus added as substrate. Growth of E. coli O157:H7 was similar for small and large intestinal mucus as substrate, and was partially inhibited with addition of fecal inoculum to cultures, presumably due to competition from other organisms. Whole mucus stimulated growth to the greatest degree compared with other compounds evaluated, but the pathogen was capable of utilizing all substrates to some extent. Addition of enzymes to cultures failed to impact growth of E. coli O157:H7 except for neuraminidase, which resulted in greater growth of E. coli O157 when combined with sialic acid as substrate. In conclusion, E. coli O157 has capacity to utilize small or large intestinal mucus, and growth is greatest with whole mucus compared with individual mucus components. There are two possible explanations for these findings (i) multiple substrates are needed to optimize growth, or alternatively, (ii) a component of mucus not evaluated in this experiment is a key ingredient for optimal growth of E. coli O157:H7.

Towards habitat-oriented systems biology of "Aromatoleum aromaticum" EbN1: chemical sensing, catabolic network modulation and growth control in anaerobic aromatic compound degradation

The denitrifying betaproteobacterium "Aromatoleum aromaticum" EbN1 is a well-studied model organism for anaerobic degradation of aromatic compounds. Following publication of its genome in 2005, comprehensive physiological-proteomic studies were conducted to deduce functional understanding from the genomic blueprint. A catabolic network (85 predicted, 65 identified proteins) for anaerobic degradation of 24 aromatic growth substrates (including 11 newly recognized) was established. Newly elucidated pathways include those for 4-ethylphenol and plant-derived 3-phenylpropanoids, involving functional assignment of several paralogous genes. The substrate-specific regulation of individual peripheral degradation pathways is probably initiated by highly specific chemical sensing via dedicated sensory/regulatory proteins, e.g. three different σ⁵⁴-dependent one-component sensory/regulatory proteins are predicted to discriminate between three phenolic substrates (phenol, p-cresol and 4-ethylphenol) and two different two-component systems are assumed to differentiate between two alkylbenzenes (toluene, ethylbenzene). Investigations under in situ relevant growth conditions revealed (a) preferred utilization of benzoate from a mixture with succinate results from repressed synthesis of a C₄-dicarboxylate TRAP transporter; (b) response to alkylbenzene-induced solvent stress comprises metabolic re-routing of acetyl-CoA and reducing equivalents to poly(3-hydroxybutyrate) synthesis, alteration of cellular membrane composition and formation of putative solvent efflux systems; and (c) multifaceted adaptation to slow growth includes adjustment of energy demand for maintenance and preparedness for future nutritional opportunities, i.e. provision of uptake systems and catabolic enzymes for multiple aromatic substrates despite their absence. This broad knowledge base taken together with the recent development of a genetic system will facilitate future functional, biotechnological (stereospecific dehydrogenases) and habitat re-enacting ("eco-"systems biology) studies with "A. aromaticum" EbN1.

Is biological treatment a viable alternative for micropollutant removal in drinking water treatment processes?

In western societies, clean and safe drinking water is often taken for granted, but there are threats to drinking water resources that should not be underestimated. Contamination of drinking water sources by anthropogenic chemicals is one threat that is particularly widespread in industrialized nations. Recently, a significant amount of attention has been given to the occurrence of micropollutants in the urban water cycle. Micropollutants are bioactive and/or persistent chemicals originating from diverse sources that are frequently detected in water resources in the pg/L to μg/L range. The aim of this review is to critically evaluate the viability of biological treatment processes as a means to remove micropollutants from drinking water resources. We first place the micropollutant problem in context by providing a comprehensive summary of the reported occurrence of micropollutants in raw water used directly for drinking water production and in finished drinking water. We then present a critical discussion on conventional and advanced drinking water treatment processes and their contribution to micropollutant removal. Finally, we propose biological treatment and bioaugmentation as a potential targeted, cost-effective, and sustainable alternative to existing processes while critically examining the technical limitations and scientific challenges that need to be addressed prior to implementation. This review will serve as a valuable source of data and literature for water utilities, water researchers, policy makers, and environmental consultants. Meanwhile this review will open the door to meaningful discussion on the feasibility and application of biological treatment and bioaugmentation in drinking water treatment processes to protect the public from exposure to micropollutants.

Assessment of anaerobic toluene biodegradation activity by bssA transcript/gene ratios

Benzylsuccinate synthase (bssA) genes associated with toluene degradation were profiled across a groundwater contaminant plume under nitrate-reducing conditions and were detected in significant numbers throughout the plume. However, differences between groundwater and core sediment samples suggested that microbial transport, rather than local activity, was the underlying cause of the high copy numbers within the downgradient plume. Both gene transcript and reactant concentrations were consistent with this hypothesis. Expression of bssA genes from denitrifying toluene degraders was induced by toluene but only in the presence of nitrate, and transcript abundance dropped rapidly following the removal of either toluene or nitrate. The drop in bssA transcripts following the removal of toluene could be described by an exponential decay function with a half-life on the order of 1 h. Interestingly, bssA transcripts never disappeared completely but were always detected at some level if either inducer was present. Therefore, the detection of transcripts alone may not be sufficient evidence for contaminant degradation. To avoid mistakenly associating basal-level gene expression with actively degrading microbial populations, an integrated approach using the ratio of functional gene transcripts to gene copies is recommended. This approach minimizes the impact of microbial transport on activity assessment and allows reliable assessments of microbial activity to be obtained from water samples.

Occurrence and dynamics of micropollutants in a karst aquifer

Karst systems represent important yet vulnerable drinking water resources. A wide spectrum of pollutants may be released into karst groundwater from agriculture, livestock farming, private households, and industry. This work provides an overview on the occurrence and dynamics of micropollutants in a karst system of the Swiss Jura. Ten months of intensive monitoring for micropollutants confirmed that the swallow hole draining an agricultural plain was the main entry path for pesticides into the karst system and the two connected springs. Elevated fungicide concentrations in winter and occasional quantification of pharmaceuticals suggested wood- or façade treatment and domestic sewer as additional sources of contamination. A continuous atrazine signal in the low ng/L range might affect the autochthonous endokarst microbial community and represents a potential risk for the human population through karst groundwater.

High and stable substrate specificities of microorganisms in enhanced biological phosphorus removal plants

Microbial communities are typically characterized by conditions of nutrient limitation so the availability of the resources is likely a key factor in the niche differentiation across all species and in the regulation of the community structure. In this study we have investigated whether four species exhibit any in situ short-term changes in substrate uptake pattern when exposed to variations in substrate and growth conditions. Microautoradiography was combined with fluorescence in situ hybridization to investigate in situ cell-specific substrate uptake profiles of four probe-defined coexisting species in a wastewater treatment plant with enhanced biological phosphorus removal. These were the filamentous 'Candidatus Microthrix' and Caldilinea (type 0803), the polyphosphate-accumulating organism 'Candidatus Accumulibacter', and the denitrifying Azoarcus. The experimental conditions mimicked the conditions potentially encountered in the respective environment (starvation, high/low substrate concentration, induction with specific substrates, and single/multiple substrates). The results showed that each probe-defined species exhibited very distinct and constant substrate uptake profile in time and space, which hardly changed under any of the conditions tested. Such niche partitioning implies that a significant change in substrate composition will be reflected in a changed community structure rather than the substrate uptake response from the different species.

Bacterial growth rate reflects a bottleneck in resource allocation

BACKGROUND

Growth rate management in fast-growing bacteria is currently an active research area. In spite of the huge progress made in our understanding of the molecular mechanisms controlling the growth rate, fundamental questions concerning its intrinsic limitations are still relevant today. In parallel, systems biology claims that mathematical models could shed light on these questions.

METHODS

This review explores some possible reasons for the limitation of the growth rate in fast-growing bacteria, using a systems biology approach based on constraint-based modeling methods.

RESULTS

Recent experimental results and a new constraint-based modelling method named Resource Balance Analysis (RBA) reveal the existence of constraints on resource allocation between biological processes in bacterial cells. In this context, the distribution of a finite amount of resources between the metabolic network and the ribosomes limits the growth rate, which implies the existence of a bottleneck between these two processes. Any mechanism for saving resources increases the growth rate.

GENERAL SIGNIFICANCE

Consequently, the emergence of genetic regulation of metabolic pathways, e.g. catabolite repression, could then arise as a means to minimise the protein cost, i.e. maximising growth performance while minimising the resource allocation. This article is part of a Special Issue entitled Systems Biology of Microorganisms.

Influence of sewage and pharmaceuticals on soil microbial function

Although sewage effluent application to land is a common approach to recycle water and provide nutrients to plants, bioactive pharmaceuticals contained in sewage may change soil quality by affecting soil microbial communities. Establishing causal effects, however, is difficult, because trace levels of pharmaceuticals are confounded with other effluent constituents. Therefore, two originally similar soil microbial communities, one irrigated in situ with sewage effluent for 12 years and another nonirrigated, were exposed to high levels of acetaminophen, aspirin, carbamazepine, chlorpromazine, and tetracycline. The objectives of the current study were to determine the influence of high levels of pharmaceuticals on several soil microbial properties, the effect that prolonged effluent irrigation with ambient levels of pharmaceuticals had on soil microbial function, and how this effect would change in response to pharmaceutical exposure. Several pharmaceuticals, at high exposure levels, imposed stress on the soil microbial community as judged by increased CO(2) respiration, decreased biomass carbon, and altered substrate utilization affinities. Prolonged effluent irrigation, which altered the genetic fingerprint of the microbial community, also mitigated the response that exposure to pharmaceuticals had on the microbial community and enabled degradation of the antimicrobial salicylic acid after aspirin exposure. In conclusion, prolonged irrigation with sewage effluent containing pharmaceuticals at ambient levels influenced the microbial community so that they were able to better cope with sudden exposure to high levels of pharmaceuticals.

Genotype and phenotypes of an intestine-adapted Escherichia coli K-12 mutant selected by animal passage for superior colonization

We previously isolated a spontaneous mutant of Escherichia coli K-12, strain MG1655, following passage through the streptomycin-treated mouse intestine, that has colonization traits superior to the wild-type parent strain (M. P. Leatham et al., Infect. Immun. 73:8039-8049, 2005). This intestine-adapted strain (E. coli MG1655*) grew faster on several different carbon sources than the wild type and was nonmotile due to deletion of the flhD gene. We now report the results of several high-throughput genomic analysis approaches to further characterize E. coli MG1655*. Whole-genome pyrosequencing did not reveal any changes on its genome, aside from the deletion at the flhDC locus, that could explain the colonization advantage of E. coli MG1655*. Microarray analysis revealed modest yet significant induction of catabolic gene systems across the genome in both E. coli MG1655* and an isogenic flhD mutant constructed in the laboratory. Catabolome analysis with Biolog GN2 microplates revealed an enhanced ability of both E. coli MG1655* and the isogenic flhD mutant to oxidize a variety of carbon sources. The results show that intestine-adapted E. coli MG1655* is more fit than the wild type for intestinal colonization, because loss of FlhD results in elevated expression of genes involved in carbon and energy metabolism, resulting in more efficient carbon source utilization and a higher intestinal population. Hence, mutations that enhance metabolic efficiency confer a colonization advantage.