Elemental and macromolecular plasticity of Chlamydomonas reinhardtii (Chlorophyta) in response to resource limitation and growth rate

With the ongoing differential disruption of the biogeochemical cycles of major elements that are essential for all life (carbon, nitrogen, and phosphorus), organisms are increasingly faced with a heterogenous supply of these elements in nature. Given that photosynthetic primary producers form the base of aquatic food webs, impacts of changed elemental supply on these organisms are particularly important. One way that phytoplankton cope with the differential availability of nutrients is through physiological changes, resulting in plasticity in macromolecular and elemental biomass composition. Here, we assessed how the green alga Chlamydomonas reinhardtii adjusts its macromolecular (e.g., carbohydrates, lipids, and proteins) and elemental (C, N, and P) biomass pools in response to changes in growth rate and the modification of resources (nutrients and light). We observed that Chlamydomonas exhibits considerable plasticity in elemental composition (e.g., molar ratios ranging from 124 to 971 for C:P, 4.5 to 25.9 for C:N, and 15.1 to 61.2 for N:P) under all tested conditions, pointing to the adaptive potential of Chlamydomonas in a changing environment. Exposure to low light modified the elemental and macromolecular composition of cells differently than limitation by nutrients. These observed differences, with potential consequences for higher trophic levels, included smaller cells, shifts in C:N and C:P ratios (due to proportionally greater N and P contents), and differential allocation of C among macromolecular pools (proportionally more lipids than carbohydrates) with different energetic value. However, substantial pools of N and P remained unaccounted for, especially at fast growth, indicating accumulation of N and P in forms we did not measure.

A novel experimental method to determine substrate uptake kinetics of gaseous substrates applied to the carbon monoxide-fermenting Clostridium autoethanogenum

Syngas fermentation has gained momentum over the last decades. The cost-efficient design of industrial-scale bioprocesses is highly dependent on quantitative microbial growth data. Kinetic and stoichiometric models for syngas-converting microbes exist, but accurate experimental validation of the derived parameters is lacking. Here, we describe a novel experimental approach for measuring substrate uptake kinetics of gas-fermenting microbes using the model microorganism Clostridium autoethanogenum. One-hour disturbances of a steady-state chemostat bioreactor with increased CO partial pressures (up to 1.2 bar) allowed for measurement of biomass-specific CO uptake- and CO2 production rates (q CO ${q}_{{CO}}$ ,q CO 2 ${q}_{{{CO}}_{2}}$ ) using off-gas analysis. At a pCO of 1.2 bar, aq CO ${q}_{{CO}}$ of -119 ± 1 mmol g-1 X h-1 was measured. This value is 1.8-3.5-fold higher than previously reported experimental and kinetic modeling results for syngas fermenters. Analysis of the catabolic flux distribution reveals a metabolic shift towards ethanol production at the expense of acetate at pCO ≥ $\ge $  0.6 atm, likely to be mediated by acetate availability and cellular redox state. We characterized this metabolic shift as acetogenic overflow metabolism. These results provide key mechanistic understanding of the factors steering the product spectrum of CO fermentation in C. autoethanogenum and emphasize the importance of dedicated experimental validation of kinetic parameters.

Microbial Primer: Bacterial growth kinetics

tGrowth of microorganisms and interpretation of growth data are core skills required by microbiologists. While science moves forward, it is of paramount importance that essential skills are not lost. The bacterial growth curve and the information that can gleaned from it is of great value to all of microbiology, whether this be a simple growth experiment, comparison of mutant strains or the establishment of conditions for a large-scale multi-omics experiment. Increasingly, the basics of plotting and interpreting growth curves and growth data are being overlooked. This primer article serves as a refresher for microbiologists on the fundamentals of microbial growth kinetics.

Quantitative Physiology and Proteome Adaptations of Bifidobacterium breve NRBB57 at Near-Zero Growth Rates

In natural environments, nutrients are usually scarce, causing microorganisms to grow slowly while staying metabolically active. These natural conditions can be simulated using retentostat cultivations. The present study describes the physiological and proteome adaptations of the probiotic Bifidobacterium breve NRBB57 from high (0.4 h-1) to near-zero growth rates. Lactose-limited retentostat cultivations were carried out for 21 days in which the bacterial growth rate progressively reduced to 0.00092 h-1, leading to a 3.4-fold reduction of the maintenance energy requirement. Lactose was mainly converted into acetate, formate, and ethanol at high growth rates, while in the retentostat, lactate production increased. Interestingly, the consumption of several amino acids (serine, aspartic acid, and glutamine/arginine) and glycerol increased over time in the retentostat. Morphological changes and viable but nonculturable cells were also observed in the retentostat. Proteomes were compared for all growth rates, revealing a downregulation of ribosomal proteins at near-zero growth rates and an upregulation of proteins involved in the catabolism of alternative energy sources. Finally, we observed induction of the stringent response and stress defense systems. Retentostat cultivations were proven useful to study the physiology of B. breve, mimicking the nutrient scarcity of its complex habitat, the human gut. IMPORTANCE In natural environments, nutrients are usually scarce, causing microorganisms to grow slowly while staying metabolically active. In this study we used retentostat cultivation to investigate how the probiotic Bifidobacterium breve adapts its physiology and proteome under severe nutrient limitation resulting in near-zero growth rates (<0.001 h-1). We showed that the nutrient limitation induced a multifaceted response including stress defense and stringent response, metabolic shifts, and the activation of novel alternative energy-producing pathways.

Deletion of genes linked to the C1-fixing gene cluster affects growth, by-products, and proteome of Clostridium autoethanogenum

Gas fermentation has emerged as a sustainable route to produce fuels and chemicals by recycling inexpensive one-carbon (C₁) feedstocks from gaseous and solid waste using gas-fermenting microbes. Currently, acetogens that utilise the Wood-Ljungdahl pathway to convert carbon oxides (CO and CO₂) into valuable products are the most advanced biocatalysts for gas fermentation. However, our understanding of the functionalities of the genes involved in the C₁-fixing gene cluster and its closely-linked genes is incomplete. Here, we investigate the role of two genes with unclear functions-hypothetical protein (hp; LABRINI_07945) and CooT nickel binding protein (nbp; LABRINI_07950)-directly adjacent and expressed at similar levels to the C₁-fixing gene cluster in the gas-fermenting model-acetogen Clostridium autoethanogenum. Targeted deletion of either the hp or nbp gene using CRISPR/nCas9, and phenotypic characterisation in heterotrophic and autotrophic batch and autotrophic bioreactor continuous cultures revealed significant growth defects and altered by-product profiles for both ∆hp and ∆nbp strains. Variable effects of gene deletion on autotrophic batch growth on rich or minimal media suggest that both genes affect the utilisation of complex nutrients. Autotrophic chemostat cultures showed lower acetate and ethanol production rates and higher carbon flux to CO₂ and biomass for both deletion strains. Additionally, proteome analysis revealed that disruption of either gene affects the expression of proteins of the C₁-fixing gene cluster and ethanol synthesis pathways. Our work contributes to a better understanding of genotype-phenotype relationships in acetogens and offers engineering targets to improve carbon fixation efficiency in gas fermentation.

Technical versus biological variability in a synthetic human gut community

Synthetic communities grown in well-controlled conditions are an important tool to decipher the mechanisms driving community dynamics. However, replicate time series of synthetic human gut communities in chemostats are rare, and it is thus still an open question to what extent stochasticity impacts gut community dynamics. Here, we address this question with a synthetic human gut bacterial community using an automated fermentation system that allows for a larger number of biological replicates. We collected six biological replicates for a community initially consisting of five common gut bacterial species that fill different metabolic niches. After an initial 12 hours in batch mode, we switched to chemostat mode and observed the community to stabilize after 2-3 days. Community profiling with 16S rRNA resulted in high variability across replicate vessels and high technical variability, while the variability across replicates was significantly lower for flow cytometric data. Both techniques agree on the decrease in the abundance of Bacteroides thetaiotaomicron, accompanied by an initial increase in Blautia hydrogenotrophica. These changes occurred together with reproducible metabolic shifts, namely a fast depletion of glucose and trehalose concentration in batch followed by a decrease in formic acid and pyruvic acid concentrations within the first 12 hours after the switch to chemostat mode. In conclusion, the observed variability in the synthetic bacterial human gut community, as assessed with 16S rRNA gene sequencing, is largely due to technical variability. The low variability seen in HPLC and flow cytometry data suggests a highly deterministic system.

Analysis of biomass productivity and physiology of Nitrososphaera viennensis grown in continuous culture

Microbial ammonia oxidation is the first and usually rate limiting step in nitrification and is therefore an important step in the global nitrogen cycle. Ammonia-oxidizing archaea (AOA) play an important role in nitrification. Here, we report a comprehensive analysis of biomass productivity and the physiological response of Nitrososphaera viennensis to different ammonium and carbon dioxide (CO₂) concentrations aiming to understand the interplay between ammonia oxidation and CO₂ fixation of N. viennensis. The experiments were performed in closed batch in serum bottles as well as in batch, fed-batch, and continuous culture in bioreactors. A reduced specific growth rate (μ) of N. viennensis was observed in batch systems in bioreactors. By increasing CO₂ gassing μ could be increased to rates comparable to that of closed batch systems. Furthermore, at a high dilution rate (D) in continuous culture (≥ 0.7 of μ_max) the biomass to ammonium yield (Y_(X/NH3)) increased up to 81.7% compared to batch cultures. In continuous culture, biofilm formation at higher D prevented the determination of D _crit. Due to changes in Y_(X/NH3) and due to biofilm, nitrite concentration becomes an unreliable proxy for the cell number in continuous cultures at D towards μ_max. Furthermore, the obscure nature of the archaeal ammonia oxidation prevents an interpretation in the context of Monod kinetics and thus the determination of K _S. Our findings indicate that the physiological response of N. viennensis might be regulated with different enzymatic make-ups, according to the ammonium catalysis rate. We reveal novel insights into the physiology of N. viennensis that are important for biomass production and the biomass yield of AOA. Moreover, our study has implications to the field of archaea biology and microbial ecology by showing that bioprocess technology and quantitative analysis can be applied to decipher environmental factors affecting the physiology and productivity of AOA.

Nutrient-Limited Operational Strategies for the Microbial Production of Biochemicals

Limiting an essential nutrient has a profound impact on microbial growth. The notion of growth under limited conditions was first described using simple Monod kinetics proposed in the 1940s. Different operational modes (chemostat, fed-batch processes) were soon developed to address questions related to microbial physiology and cell maintenance and to enhance product formation. With more recent developments of metabolic engineering and systems biology, as well as high-throughput approaches, the focus of current engineers and applied microbiologists has shifted from these fundamental biochemical processes. This review draws attention again to nutrient-limited processes. Indeed, the sophisticated gene editing tools not available to pioneers offer the prospect of metabolic engineering strategies which leverage nutrient limited processes. Thus, nutrient- limited processes continue to be very relevant to generate microbially derived biochemicals.

Effects of Nutrient Level and Growth Rate on the Conjugation Process That Transfers Mobile Antibiotic Resistance Genes in Continuous Cultures

Bacteria in the effluent of wastewater treatment plants (WWTPs) can transfer antibiotic resistance genes (ARGs) to the bacteria in receiving water through conjugation; however, there is a lack of quantitative assessment of this phenomenon in continuous cultures. Our objective was to determine the effects of background nutrient levels in river water column and growth rates of bacteria on the conjugation frequency of ARGs from effluent bacteria to river bacteria, as well as on the resulting resistance level (i.e., MICs) of the river bacteria. Chemostats were employed to simulate the discharge points of WWTPs into rivers, where effluent bacteria (donor cells) meet river bacteria (recipient cells). Both donor and recipient cells were Escherichia coli cells, and the donor cells were constructed by filter mating with bacteria in the effluent of a local WWTP. Results showed that higher bacterial growth rate (0.45 h^-1 versus 0.15 h^-1) led to higher conjugation frequencies (10^-4 versus 10^-6 transconjugant per recipient). The nutrient level also significantly affected the conjugation frequency, albeit to a lesser extent than the growth rate. The MIC against tetracycline increased from 2 mg/L in the recipient to 64 to 128 mg/L in transconjugants. In comparison, the MIC only increased to as high as 8 mg/L in mutants. Whole-genome sequencing showed that the tet-containing plasmid in both the donor and the transconjugant cells also occur in other fecal bacterial genera. The quantitative information obtained from this study can inform hazard identification related to the proliferation of wastewater-associated ARGs in surface water. IMPORTANCE WWTPs have been regarded as an important hot spot of ARGs. The discharge point of WWTP effluent, where ARGs may be horizontally transferred from bacteria of treated wastewater to bacteria of receiving water, is an important interface between the human-dominated ecosystem and the natural environment. The use of batch cultures in previous studies cannot adequately simulate the nutrient conditions and growth rates in receiving water. In this study, chemostats were employed to simulate the continuous growth of bacteria in receiving water. Furthermore, the experimental setup allowed for separate investigations on the effects of nutrient levels (i.e., simulating background nutrients in river water) and bacterial growth rates on conjugation frequencies and resulting resistance levels. The study generates statistically sound ecological data that can be used to estimate the risk of wastewater-originated ARGs as part of the One Health framework.

Linking Increased Isotope Fractionation at Low Concentrations to Enzyme Activity Regulation: 4-Cl Phenol Degradation by Arthrobacter chlorophenolicus A6

Slow microbial degradation of organic trace chemicals ("micropollutants") has been attributed to either downregulation of enzymatic turnover or rate-limiting substrate supply at low concentrations. In previous biodegradation studies, a drastic decrease in isotope fractionation of atrazine revealed a transition from rate-limiting enzyme turnover to membrane permeation as a bottleneck when concentrations fell below the Monod constant of microbial growth. With degradation of the pollutant 4-chlorophenol (4-CP) by Arthrobacter chlorophenolicus A6, this study targeted a bacterium which adapts its enzyme activity to concentrations. Unlike with atrazine degradation, isotope fractionation of 4-CP increased at lower concentrations, from ε(C) = -1.0 ± 0.5‰ in chemostats (D = 0.090 h^-1, 88 mg L^-1) and ε(C) = -2.1 ± 0.5‰ in batch (c₀ = 220 mg L^-1) to ε(C) = -4.1 ± 0.2‰ in chemostats at 90 μg L^-1. Surprisingly, fatty acid composition indicated increased cell wall permeability at high concentrations, while proteomics revealed that catabolic enzymes (CphCI and CphCII) were differentially expressed at D = 0.090 h^-1. These observations support regulation on the enzyme activity level─through either a metabolic shift between catabolic pathways or decreased enzymatic turnover at low concentrations─and, hence, reveal an alternative end-member scenario for bacterial adaptation at low concentrations. Including more degrader strains into this multidisciplinary analytical approach offers the perspective to build a knowledge base on bottlenecks of bioremediation at low concentrations that considers bacterial adaptation.

Genome-Scale Reconstruction of Microbial Dynamic Phenotype: Successes and Challenges

This review is a part of the SI 'Genome-Scale Modeling of Microorganisms in the Real World'. The goal of GEM is the accurate prediction of the phenotype from its respective genotype under specified environmental conditions. This review focuses on the dynamic phenotype; prediction of the real-life behaviors of microorganisms, such as cell proliferation, dormancy, and mortality; balanced and unbalanced growth; steady-state and transient processes; primary and secondary metabolism; stress responses; etc. Constraint-based metabolic reconstructions were successfully started two decades ago as FBA, followed by more advanced models, but this review starts from the earlier nongenomic predecessors to show that some GEMs inherited the outdated biokinetic frameworks compromising their performances. The most essential deficiencies are: (i) an inadequate account of environmental conditions, such as various degrees of nutrients limitation and other factors shaping phenotypes; (ii) a failure to simulate the adaptive changes of MMCC (MacroMolecular Cell Composition) in response to the fluctuating environment; (iii) the misinterpretation of the SGR (Specific Growth Rate) as either a fixed constant parameter of the model or independent factor affecting the conditional expression of macromolecules; (iv) neglecting stress resistance as an important objective function; and (v) inefficient experimental verification of GEM against simple growth (constant MMCC and SGR) data. Finally, we propose several ways to improve GEMs, such as replacing the outdated Monod equation with the SCM (Synthetic Chemostat Model) that establishes the quantitative relationships between primary and secondary metabolism, growth rate and stress resistance, process kinetics, and cell composition.

Exclusion of the fittest predicts microbial community diversity in fluctuating environments

Microorganisms live in environments that inevitably fluctuate between mild and harsh conditions. As harsh conditions may cause extinctions, the rate at which fluctuations occur can shape microbial communities and their diversity, but we still lack an intuition on how. Here, we build a mathematical model describing two microbial species living in an environment where substrate supplies randomly switch between abundant and scarce. We then vary the rate of switching as well as different properties of the interacting species, and measure the probability of the weaker species driving the stronger one extinct. We find that this probability increases with the strength of demographic noise under harsh conditions and peaks at either low, high, or intermediate switching rates depending on both species' ability to withstand the harsh environment. This complex relationship shows why finding patterns between environmental fluctuations and diversity has historically been difficult. In parameter ranges where the fittest species was most likely to be excluded, however, the beta diversity in larger communities also peaked. In sum, how environmental fluctuations affect interactions between a few species pairs predicts their effect on the beta diversity of the whole community.

Fluctuating Environments Maintain Genetic Diversity through Neutral Fitness Effects and Balancing Selection

Genetic variation is the raw material upon which selection acts. The majority of environmental conditions change over time and therefore may result in variable selective effects. How temporally fluctuating environments impact the distribution of fitness effects and in turn population diversity is an unresolved question in evolutionary biology. Here, we employed continuous culturing using chemostats to establish environments that switch periodically between different nutrient limitations and compared the dynamics of selection to static conditions. We used the pooled Saccharomyces cerevisiae haploid gene deletion collection as a synthetic model for populations comprising thousands of unique genotypes. Using barcode sequencing, we find that static environments are uniquely characterized by a small number of high-fitness genotypes that rapidly dominate the population leading to dramatic decreases in genetic diversity. By contrast, fluctuating environments are enriched in genotypes with neutral fitness effects and an absence of extreme fitness genotypes contributing to the maintenance of genetic diversity. We also identified a unique class of genotypes whose frequencies oscillate sinusoidally with a period matching the environmental fluctuation. Oscillatory behavior corresponds to large differences in short-term fitness that are not observed across long timescales pointing to the importance of balancing selection in maintaining genetic diversity in fluctuating environments. Our results are consistent with a high degree of environmental specificity in the distribution of fitness effects and the combined effects of reduced and balancing selection in maintaining genetic diversity in the presence of variable selection.

Multiplexing mutation rate assessment: determining pathogenicity of Msh2 variants in Saccharomyces cerevisiae

Despite the fundamental importance of mutation rate as a driving force in evolution and disease risk, common methods to assay mutation rate are time-consuming and tedious. Established methods such as fluctuation tests and mutation accumulation experiments are low-throughput and often require significant optimization to ensure accuracy. We established a new method to determine the mutation rate of many strains simultaneously by tracking mutation events in a chemostat continuous culture device and applying deep sequencing to link mutations to alleles of a DNA-repair gene. We applied this method to assay the mutation rate of hundreds of Saccharomyces cerevisiae strains carrying mutations in the gene encoding Msh2, a DNA repair enzyme in the mismatch repair pathway. Loss-of-function mutations in MSH2 are associated with hereditary nonpolyposis colorectal cancer, an inherited disorder that increases risk for many different cancers. However, the vast majority of MSH2 variants found in human populations have insufficient evidence to be classified as either pathogenic or benign. We first benchmarked our method against Luria-Delbrück fluctuation tests using a collection of published MSH2 missense variants. Our pooled screen successfully identified previously characterized nonfunctional alleles as high mutators. We then created an additional 185 human missense variants in the yeast ortholog, including both characterized and uncharacterized alleles curated from ClinVar and other clinical testing data. In a set of alleles of known pathogenicity, our assay recapitulated ClinVar's classification; we then estimated pathogenicity for 157 variants classified as uncertain or conflicting reports of significance. This method is capable of studying the mutation rate of many microbial species and can be applied to problems ranging from the generation of high-fidelity polymerases to measuring the frequency of antibiotic resistance emergence.

Pyruvate Production by Escherichia coli by Use of Pyruvate Dehydrogenase Variants

Altering metabolic flux at a key branch point in metabolism has commonly been accomplished through gene knockouts or by modulating gene expression. An alternative approach to direct metabolic flux preferentially toward a product is decreasing the activity of a key enzyme through protein engineering. In Escherichia coli, pyruvate can accumulate from glucose when carbon flux through the pyruvate dehydrogenase complex is suppressed. Based on this principle, 16 chromosomally expressed AceE variants were constructed in E. coli C and compared for growth rate and pyruvate accumulation using glucose as the sole carbon source. To prevent conversion of pyruvate to other products, the strains also contained deletions in two nonessential pathways: lactate dehydrogenase (ldhA) and pyruvate oxidase (poxB). The effect of deleting phosphoenolpyruvate synthase (ppsA) on pyruvate assimilation was also examined. The best pyruvate-accumulating strains were examined in controlled batch and continuous processes. In a nitrogen-limited chemostat process at steady-state growth rates of 0.15 to 0.28 h-1, an engineered strain expressing the AceE[H106V] variant accumulated pyruvate at a yield of 0.59 to 0.66 g pyruvate/g glucose with a specific productivity of 0.78 to 0.92 g pyruvate/g cells·h. These results provide proof of concept that pyruvate dehydrogenase complex variants can effectively shift carbon flux away from central carbon metabolism to allow pyruvate accumulation. This approach can potentially be applied to other key enzymes in metabolism to direct carbon toward a biochemical product. IMPORTANCE Microbial production of biochemicals from renewable resources has become an efficient and cost-effective alternative to traditional chemical synthesis methods. Metabolic engineering tools are important for optimizing a process to perform at an economically feasible level. This study describes an additional tool to modify central metabolism and direct metabolic flux to a product. We have shown that variants of the pyruvate dehydrogenase complex can direct metabolic flux away from cell growth to increase pyruvate production in Escherichia coli. This approach could be paired with existing strategies to optimize metabolism and create industrially relevant and economically feasible processes.

Physiological Characterization of Sulfolobus acidocaldarius in a Controlled Bioreactor Environment

The crenarchaeal model organism Sulfolobus acidocaldarius is typically cultivated in shake flasks. Although shake flasks represent the state-of-the-art for the cultivation of this microorganism, in these systems crucial process parameters, like pH or substrate availability, are only set initially, but cannot be controlled during the cultivation process. As a result, a thorough characterization of growth parameters under controlled conditions is still missing for S. acidocaldarius. In this study, we conducted chemostat cultivations at 75 °C using a growth medium containing L-glutamate and D-glucose as main carbon sources. Different pH values and dilution rates were applied with the goal to physiologically characterize the organism in a controlled bioreactor environment. Under these controlled conditions a pH optimum of 3.0 was determined. Washout of the cells occurred at a dilution rate of 0.097 h⁻¹ and the optimal productivity of biomass was observed at a dilution rate of 0.062 h⁻¹. While both carbon sources were taken up by S. acidocaldarius concomitantly, a 6.6-fold higher affinity for L-glutamate was shown. When exposed to suboptimal growth conditions, S. acidocaldarius reacted with a change in the respiratory behavior and an increased trehalose production rate in addition to a decreased growth rate.

Metabolic fluxes for nutritional flexibility of Mycobacterium tuberculosis

The co-catabolism of multiple host-derived carbon substrates is required by Mycobacterium tuberculosis (Mtb) to successfully sustain a tuberculosis infection. However, the metabolic plasticity of this pathogen and the complexity of the metabolic networks present a major obstacle in identifying those nodes most amenable to therapeutic interventions. It is therefore critical that we define the metabolic phenotypes of Mtb in different conditions. We applied metabolic flux analysis using stable isotopes and lipid fingerprinting to investigate the metabolic network of Mtb growing slowly in our steady-state chemostat system. We demonstrate that Mtb efficiently co-metabolises either cholesterol or glycerol, in combination with two-carbon generating substrates without any compartmentalisation of metabolism. We discovered that partitioning of flux between the TCA cycle and the glyoxylate shunt combined with a reversible methyl citrate cycle is the critical metabolic nodes which underlie the nutritional flexibility of Mtb. These findings provide novel insights into the metabolic architecture that affords adaptability of bacteria to divergent carbon substrates and expand our fundamental knowledge about the methyl citrate cycle and the glyoxylate shunt.

In-silico media optimization for continuous cultures using genome scale metabolic networks: The case of CHO-K1

The cell culture is the central piece of a biotechnological industrial process. It includes upstream (e.g. media preparation, fixed costs, etc.) and downstream steps (e.g. product purification, waste disposal, etc.). In the continuous mode of cell culture, a constant flow of fresh media replaces culture fluid until the system reaches a steady state. This steady state is the standard operation mode which, under very general conditions, is a function of the ratio between the cell density and the dilution rate and depends on the media supplied to the culture. To optimize the production process it is widely accepted that the concentration of the metabolites in this media should be carefully tuned. A poor media may not provide enough nutrients to the culture, while a media too rich in nutrients may be a waste of resources because, either the cells do not use all of the available nutrients, or worse, they over-consume them producing toxic byproducts. In this study, we show how an in-silico study of a genome scale metabolic network coupled to the dynamics of a chemostat could guide the strategy to optimize the media to be used in a continuous process. Given a known media we model the concentrations of the cells in a chemostat as a function of the dilution rate. Then, we cast the problem of optimizing the production process within a linear programming framework in which the goal is to minimize the cost of the media keeping fixed the cell concentration for a given dilution rate in the chemostat. We evaluate our results in two metabolic models: first a simplified model of mammalian cell metabolism, and then in a realistic genome-scale metabolic network of mammalian cells, the Chinese hamster ovary cell line. We explore the latter in more detail given specific meaning to the predictions of the concentrations of several metabolites.

glutamicum CP for L-leucine production

Most of the current industrial processes for L-leucine production are based on fermentation, usually in fed-batch operation mode. Although the culture technology has advanced in recent decades, the process still has significant drawbacks. To solve these problems, we investigated the effects of chemostat culture conditions on the production of L-leucine by Corynebacterium glutamicum CP. The dilution rate, the nitrogen source, and the carbon–nitrogen ratio of the medium were optimized. With the addition of ammonium acetate to the chemostat medium, the initial C/N ratio was adjusted to 57.6, and the L-leucine titer reached the highest level at the optimal dilution rate of 0.04 h⁻¹. Compared with fed-batch culture, the L-leucine titer was reduced (from 53.0 to 24.8 g L⁻¹), but the yield from glucose was increased by 10.0% (from 0.30 to 0.33 mol mol⁻¹) and productivity was increased by 58.3% (from 1.2 to 1.9 g L⁻¹ h⁻¹). Moreover, the titer of the by-product L-alanine was significantly reduced (from 8.9 to 0.8 g L⁻¹). In addition, gene expression levels and activity of key enzymes in the synthesis of L-leucine and L-alanine were analyzed to explain the difference of production performance between chemostat culture and fed-batch culture. The results indicate that chemostat culture has great potential to increase the industrial production of L-leucine compared to current fed-batch approaches.

Isotopic Fractionation Associated With Sulfate Import and Activation by Desulfovibrio vulgaris str. Hildenborough

The use of stable isotopes to trace biogeochemical sulfur cycling relies on an understanding of how isotopic fractionation is imposed by metabolic networks. We investigated the effects of the first two enzymatic steps in the dissimilatory sulfate reduction (DSR) network - sulfate permease and sulfate adenylyl transferase (Sat) - on the sulfur and oxygen isotopic composition of residual sulfate. Mutant strains of Desulfovibrio vulgaris str. Hildenborough (DvH) with perturbed expression of these enzymes were grown in batch culture, with a subset grown in continuous culture, to examine the impact of these enzymatic steps on growth rate, cell specific sulfate reduction rate and isotopic fractionations in comparison to the wild type strain. Deletion of several permease genes resulted in only small (∼1‰) changes in sulfur isotope fractionation, a difference that approaches the uncertainties of the measurement. Mutants that perturb Sat expression show higher fractionations than the wild type strain. This increase probably relates to an increased material flux between sulfate and APS, allowing an increase in the expressed fractionation of rate-limiting APS reductase. This work illustrates that flux through the initial steps of the DSR pathway can affect the fractionation imposed by the overall pathway, even though these steps are themselves likely to impose only small fractionations.

Controlling evolutionary dynamics to optimize microbial bioremediation

Some microbes have a fascinating ability to degrade compounds that are toxic for humans in a process called bioremediation. Although these traits help microbes survive the toxins, carrying them can be costly if the benefit of detoxification is shared by all surrounding microbes, whether they detoxify or not. Detoxification can thereby be seen as a public goods game, where nondegrading mutants can sweep through the population and collapse bioremediation. Here, we constructed an evolutionary game theoretical model to optimize bioremediation in a chemostat initially containing "cooperating" (detoxifying) microbes. We consider two types of mutants: "cheaters" that do not detoxify, and mutants that become resistant to the toxin through private mechanisms that do not benefit others. By manipulating the concentration and flow rate of a toxin into the chemostat, we identified conditions where cooperators can exclude cheaters that differ in their private resistance. However, eventually, cheaters are bound to invade. To overcome this inevitable outcome and maximize detoxification efficiency, cooperators can be periodically reinoculated into the population. Our study investigates the outcome of an evolutionary game combining both public and private goods and demonstrates how environmental parameters can be used to control evolutionary dynamics in practical applications.

The omnistat: A flexible continuous-culture system for prolonged experimental evolution

Microbial evolution experiments provide a powerful tool to unravel the molecular basis of adaptive evolution but their outcomes can be difficult to interpret, unless the selective forces that are applied during the experiment are carefully controlled. In this respect, experimental evolution in continuous cultures provides advantages over commonly used sequential batch-culture protocols because continuous cultures allow for more accurate control over the induced selective environment. However, commercial continuous-culture systems are large and expensive, while available DIY continuous-culture systems are not versatile enough to allow for multiple sensors and rigorous stirring.We present a modular continuous-culture system that adopts the commonly used GL45 glass laboratory bottle as a bioreactor vessel. Our design offers three advantages: first, it is equipped with a large head plate, fitting two sensors and seven input/output ports, enabling the customization of the system for many running modes (chemostat, auxostat, etc.). Second, the bioreactor is small (25-250 ml), which makes it feasible to run many replicates in parallel. Third, bioreactor modules can be coupled by uni- or bi-directional flows to induce spatiotemporal variation in selection. These features result in a particularly flexible culturing platform that facilitates the investigation of a broad range of evolutionary and ecological questions.To illustrate the versatility of our culturing system, we outline two evolution experiments that impose a temporally or spatially variable regime of selection. The first experiment illustrates how controlled temporal variation in resource availability can be utilized to select for anticipatory switching. The second experiment illustrates a spatially structured morbidostat setup that is designed to probe epistatic interactions between adaptive mutations. Furthermore, we demonstrate how sensor data can be used to stabilize selection pressures or track evolutionary adaptation.Evolution experiments in which populations are exposed to controlled spatiotemporal variation, are essential to gain insight into the process of adaptation and the mechanisms that constrain evolution. Continuous-culture systems, like the one presented here, offer control over key environmental parameters and establish a well-defined regime of selection. As such, they create the opportunity to expose evolutionary constraints in the form of phenotypic trade-offs, contributing to a mechanistic understanding of adaptive evolution.

Contribution of Complex I NADH Dehydrogenase to Respiratory Energy Coupling in Glucose-Grown Cultures of Ogataea parapolymorpha

The thermotolerant yeast Ogataea parapolymorpha (formerly Hansenula polymorpha) is an industrially relevant production host that exhibits a fully respiratory sugar metabolism in aerobic batch cultures. NADH-derived electrons can enter its mitochondrial respiratory chain either via a proton-translocating complex I NADH-dehydrogenase or via three putative alternative NADH dehydrogenases. This respiratory entry point affects the amount of ATP produced per NADH/O2 consumed and therefore impacts the maximum yield of biomass and/or cellular products from a given amount of substrate. To investigate the physiological importance of complex I, a wild-type O. parapolymorpha strain and a congenic complex I-deficient mutant were grown on glucose in aerobic batch, chemostat, and retentostat cultures in bioreactors. In batch cultures, the two strains exhibited a fully respiratory metabolism and showed the same growth rates and biomass yields, indicating that, under these conditions, the contribution of NADH oxidation via complex I was negligible. Both strains also exhibited a respiratory metabolism in glucose-limited chemostat cultures, but the complex I-deficient mutant showed considerably reduced biomass yields on substrate and oxygen, consistent with a lower efficiency of respiratory energy coupling. In glucose-limited retentostat cultures at specific growth rates down to ∼0.001 h-1, both O. parapolymorpha strains showed high viability. Maintenance energy requirements at these extremely low growth rates were approximately 3-fold lower than estimated from faster-growing chemostat cultures, indicating a stringent-response-like behavior. Quantitative transcriptome and proteome analyses indicated condition-dependent expression patterns of complex I subunits and of alternative NADH dehydrogenases that were consistent with physiological observations.IMPORTANCE Since popular microbial cell factories have typically not been selected for efficient respiratory energy coupling, their ATP yields from sugar catabolism are often suboptimal. In aerobic industrial processes, suboptimal energy coupling results in reduced product yields on sugar, increased process costs for oxygen transfer, and volumetric productivity limitations due to limitations in gas transfer and cooling. This study provides insights into the contribution of mechanisms of respiratory energy coupling in the yeast cell factory Ogataea parapolymorpha under different growth conditions and provides a basis for rational improvement of energy coupling in yeast cell factories. Analysis of energy metabolism of O. parapolymorpha at extremely low specific growth rates indicated that this yeast reduces its energy requirements for cellular maintenance under extreme energy limitation. Exploration of the mechanisms for this increased energetic efficiency may contribute to an optimization of the performance of industrial processes with slow-growing eukaryotic cell factories.

Genome-scale modeling for Bacillus coagulans to understand the metabolic characteristics

Lactic acid is widely used in many industries, especially in the production of poly-lactic acid. Bacillus coagulans is a promising lactic acid producer in industrial fermentation due to its thermophilic property. In this study, we developed the first genome-scale metabolic model (GEM) of B. coagulans iBag597, together with an enzyme-constrained model ec-iBag597. We measured strain-specific biomass composition and integrated the data into a biomass equation. Then, we validated iBag597 against experimental data generated in this study, including amino acid requirements and carbon source utilization, showing that simulations were generally consistent with the experimental results. Subsequently, we carried out chemostats to investigate the effects of specific growth rate and culture pH on metabolism of B. coagulans. Meanwhile, we used iBag597 to estimate the intracellular metabolic fluxes for those conditions. The results showed that B. coagulans was capable of generating ATP via multiple pathways, and switched among them in response to various conditions. With ec-iBag597, we estimated the protein cost and protein efficiency for each ATP-producing pathway to investigate the switches. Our models pave the way for systems biology of B. coagulans, and our findings suggest that maintaining a proper growth rate and selecting an optimal pH are beneficial for lactate fermentation.

Two-Stage Continuous Conversion of Carbon Monoxide to Ethylene by Whole Cells of Azotobacter vinelandii

Azotobacter vinelandii is an obligate aerobic diazotroph with a verified transient ability to reduce carbon monoxide to ethylene by its vanadium nitrogenase. In this study, we implemented an industrially relevant continuous two-stage stirred-tank system for in vivo biotransformation of a controlled supply of air enriched with 5% carbon monoxide to 302 μg ethylene g^-1 glucose consumed. To attain this value, the process required overcoming critical oxygen limitations during cell proliferation while simultaneously avoiding the A. vinelandii respiratory protection mechanism that negatively impacts in vivo nitrogenase activity. Additionally, process conditions allowed the demonstration of carbon monoxide's solubility as a reaction-limiting factor and a competitor with dinitrogen for the vanadium nitrogenase active site, implying that excess intracellular carbon monoxide could lead to a cessation of cell proliferation and ethylene formation as shown genetically using a new strain of A. vinelandii deficient in carbon monoxide dehydrogenase.IMPORTANCE Ethylene is an essential commodity feedstock used for the generation of a variety of consumer products, but its generation demands energy-intensive processes and is dependent on nonrenewable substrates. This work describes a continuous biological method for investigating the nitrogenase-mediated carbon monoxide reductive coupling involved in ethylene production using whole cells of Azotobacter vinelandii If eventually adopted by industry, this technology has the potential to significantly reduce the total energy input required and the ethylene recovery costs, as well as decreasing greenhouse gas emissions associated with current production strategies.

Fitness and Productivity Increase with Ecotypic Diversity among Escherichia coli Strains That Coevolved in a Simple, Constant Environment

Polymicrobial consortia occur in both environmental and clinical settings. In many cases, diversity and productivity correlate in these consortia, especially when sustained by positive, density-dependent interactions. However, the evolutionary history of such entities is typically obscure, making it difficult to establish the relative fitness of consortium partners and to use those data to illuminate the diversity-productivity relationship. Here, we dissect an Escherichia coli consortium that evolved under continuous glucose limitation in the laboratory from a single common ancestor. We show that a partnership consisting of cross-feeding ecotypes is better able to secure primary and secondary resources and to convert those resources to offspring than the ancestral clone. Such interactions may be a prelude to a special form of syntrophy and are likely determinants of microbial community structure in nature, including those having clinical significance such as chronic infections.

The productivity of a biological community often correlates with its diversity. In the microbial world this phenomenon can sometimes be explained by positive, density-dependent interactions such as cross-feeding and syntrophy. These metabolic interactions help account for the astonishing variety of microbial life and drive many of the biogeochemical cycles without which life as we know it could not exist. While it is difficult to recapitulate experimentally how these interactions evolved among multiple taxa, we can explore in the laboratory how they arise within one. These experiments provide insight into how different bacterial ecotypes evolve and from these, possibly new “species.” We have previously shown that in a simple, constant environment a single clone of Escherichia coli can give rise to a consortium of genetically and phenotypically differentiated strains, in effect, a set of ecotypes, that coexist by cross-feeding. We marked these different ecotypes and their shared ancestor by integrating fluorescent protein into their genomes and then used flow cytometry to show that each evolved strain is more fit than the shared ancestor, that pairs of evolved strains are fitter still, and that the entire consortium is the fittest of all. We further demonstrate that the rank order of fitness values agrees with estimates of yield, indicating that an experimentally evolved consortium more efficiently converts primary and secondary resources to offspring than its ancestor or any member acting in isolation.

IMPORTANCE Polymicrobial consortia occur in both environmental and clinical settings. In many cases, diversity and productivity correlate in these consortia, especially when sustained by positive, density-dependent interactions. However, the evolutionary history of such entities is typically obscure, making it difficult to establish the relative fitness of consortium partners and to use those data to illuminate the diversity-productivity relationship. Here, we dissect an Escherichia coli consortium that evolved under continuous glucose limitation in the laboratory from a single common ancestor. We show that a partnership consisting of cross-feeding ecotypes is better able to secure primary and secondary resources and to convert those resources to offspring than the ancestral clone. Such interactions may be a prelude to a special form of syntrophy and are likely determinants of microbial community structure in nature, including those having clinical significance such as chronic infections.

Transcriptomic Response of Nitrosomonas europaea Transitioned from Ammonia- to Oxygen-Limited Steady-State Growth

Nitrification is a ubiquitous microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments, increasing the eutrophication of downstream aquatic ecosystems, and produces the greenhouse gas nitrous oxide. As ammonia-oxidizing bacteria are the most dominant ammonia-oxidizing microbes in fertilized agricultural soils, understanding their responses to a variety of environmental conditions is essential for curbing the negative environmental effects of nitrification. Notably, oxygen limitation has been reported to significantly increase nitric oxide and nitrous oxide production during nitrification. Here, we investigate the physiology of the best-characterized ammonia-oxidizing bacterium, Nitrosomonas europaea, growing under oxygen-limited conditions.

Ammonia-oxidizing microorganisms perform the first step of nitrification, the oxidation of ammonia to nitrite. The bacterium Nitrosomonas europaea is the best-characterized ammonia oxidizer to date. Exposure to hypoxic conditions has a profound effect on the physiology of N. europaea, e.g., by inducing nitrifier denitrification, resulting in increased nitric and nitrous oxide production. This metabolic shift is of major significance in agricultural soils, as it contributes to fertilizer loss and global climate change. Previous studies investigating the effect of oxygen limitation on N. europaea have focused on the transcriptional regulation of genes involved in nitrification and nitrifier denitrification. Here, we combine steady-state cultivation with whole-genome transcriptomics to investigate the overall effect of oxygen limitation on N. europaea. Under oxygen-limited conditions, growth yield was reduced and ammonia-to-nitrite conversion was not stoichiometric, suggesting the production of nitrogenous gases. However, the transcription of the principal nitric oxide reductase (cNOR) did not change significantly during oxygen-limited growth, while the transcription of the nitrite reductase-encoding gene (nirK) was significantly lower. In contrast, both heme-copper-containing cytochrome c oxidases encoded by N. europaea were upregulated during oxygen-limited growth. Particularly striking was the significant increase in transcription of the B-type heme-copper oxidase, proposed to function as a nitric oxide reductase (sNOR) in ammonia-oxidizing bacteria. In the context of previous physiological studies, as well as the evolutionary placement of N. europaea’s sNOR with regard to other heme-copper oxidases, these results suggest sNOR may function as a high-affinity terminal oxidase in N. europaea and other ammonia-oxidizing bacteria.

IMPORTANCE Nitrification is a ubiquitous microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments, increasing the eutrophication of downstream aquatic ecosystems, and produces the greenhouse gas nitrous oxide. As ammonia-oxidizing bacteria are the most dominant ammonia-oxidizing microbes in fertilized agricultural soils, understanding their responses to a variety of environmental conditions is essential for curbing the negative environmental effects of nitrification. Notably, oxygen limitation has been reported to significantly increase nitric oxide and nitrous oxide production during nitrification. Here, we investigate the physiology of the best-characterized ammonia-oxidizing bacterium, Nitrosomonas europaea, growing under oxygen-limited conditions.

Quantifying Methane and Methanol Metabolism of "Methylotuvimicrobium buryatense" 5GB1C under Substrate Limitation

Methanotrophic metabolism has been under investigation for decades using biochemical and genetic approaches. Recently, a further step has been taken toward understanding methanotrophic metabolism in a quantitative manner by means of flux balance analysis (FBA), a mathematical approach that predicts fluxes constrained by mass balance and a few experimental measurements. However, no study has previously been undertaken to experimentally quantitate the complete methanotrophic central metabolism. The significance of this study is to fill such a gap by performing ¹³C INST-MFA on a fast-growing methanotroph. Our quantitative insights into the methanotrophic carbon and energy metabolism will pave the way for future FBA studies and set the stage for rational design of methanotrophic strains for industrial applications. Further, the experimental strategies can be applied to other methane or methanol utilizers, and the results will offer a unique and quantitative perspective of diverse methylotrophic metabolism.

Methanotrophic bacteria are a group of prokaryotes capable of using methane as their sole carbon and energy source. Although efforts have been made to simulate and elucidate their metabolism via computational approaches or ¹³C tracer analysis, major gaps still exist in our understanding of methanotrophic metabolism at the systems level. Particularly, direct measurements of system-wide fluxes are required to understand metabolic network function. Here, we quantified the central metabolic fluxes of a type I methanotroph, “Methylotuvimicrobium buryatense” 5GB1C, formerly Methylomicrobium buryatense 5GB1C, via ¹³C isotopically nonstationary metabolic flux analysis (INST-MFA). We performed labeling experiments on chemostat cultures by switching substrates from ¹²C to ¹³C input. Following the switch, we measured dynamic changes of labeling patterns and intracellular pool sizes of several intermediates, which were later used for data fitting and flux calculations. Through computational optimizations, we quantified methane and methanol metabolism at two growth rates (0.1 h⁻¹ and 0.05 h⁻¹). The resulting flux maps reveal a core consensus central metabolic flux phenotype across different growth conditions: a strong ribulose monophosphate cycle, a preference for the Embden-Meyerhof-Parnas pathway as the primary glycolytic pathway, and a tricarboxylic acid cycle showing small yet significant fluxes. This central metabolic consistency is further supported by a good linear correlation between fluxes at the two growth rates. Specific differences between methane and methanol growth observed previously are maintained under substrate limitation, albeit with smaller changes. The substrate oxidation and glycolysis pathways together contribute over 80% of total energy production, while other pathways play less important roles.

IMPORTANCE Methanotrophic metabolism has been under investigation for decades using biochemical and genetic approaches. Recently, a further step has been taken toward understanding methanotrophic metabolism in a quantitative manner by means of flux balance analysis (FBA), a mathematical approach that predicts fluxes constrained by mass balance and a few experimental measurements. However, no study has previously been undertaken to experimentally quantitate the complete methanotrophic central metabolism. The significance of this study is to fill such a gap by performing ¹³C INST-MFA on a fast-growing methanotroph. Our quantitative insights into the methanotrophic carbon and energy metabolism will pave the way for future FBA studies and set the stage for rational design of methanotrophic strains for industrial applications. Further, the experimental strategies can be applied to other methane or methanol utilizers, and the results will offer a unique and quantitative perspective of diverse methylotrophic metabolism.

Acetate formation during recombinant protein production in Escherichia coli K-12 with an elevated NAD(H) pool

Acetate formation is a disadvantage in the use of Escherichia coli for recombinant protein production, and many studies have focused on optimizing fermentation processes or altering metabolism to eliminate acetate accumulation. In this study, E. coli MEC697 (MG1655 nadR nudC mazG) maintained a larger pool of NAD(H) compared to the wild-type control, and also accumulated lower concentrations of acetate when grown in batch culture on glucose. In steady-state cultures, the elevated total NAD(H) found in MEC697 delayed the threshold dilution rate for acetate formation to a growth rate of 0.27 h^-1. Batch and fed-batch processes using MEC697 were examined for the production of β-galactosidase as a model recombinant protein. Fed-batch culture of MEC697/pTrc99A-lacZ compared to MG1655/pTrc99A-lacZ at a growth rate of 0.22 h^-1 showed only a modest increase of protein formation. However, 1 L batch growth of MEC697/pTrc99A-lacZ resulted in 50% lower acetate formation compared to MG1655/pTrc99A-lacZ and a two-fold increase in recombinant protein production.

The impact of mixtures of xylose and glucose on the microbial diversity and fermentative metabolism of sequencing-batch or continuous enrichment cultures

Efficient industrial fermentation of lignocellulosic waste containing a large part of glucose and xylose is desirable to implement a circular economy. Mixed culture biotechnologies can aid in realizing this goal. The effect of feeding equivalent substrates to a microbial community, such a xylose and glucose, is not well understood in terms of the number of dominant species and how these species compete for the substrates. We compared the metabolism and microbial community structure in a continuous-flow stirred tank reactor (CSTR) and a sequencing batch reactor (SBR) fed with a mixture of xylose and glucose, inoculated with bovine rumen at pH 8, 30°C and a hydraulic retention time of 8 h. We hypothesised that a CSTR will select for generalist species, taking up both substrates. We used 16S rRNA gene sequencing and fluorescent in situ hybridisation to accurately determine the microbial community structures. Both enrichments were stoichiometrically and kinetically characterised. The CSTR enrichment culture was dominated by Clostridium intestinale (91% ± 2%). The SBR showed an abundance of Enterobacteriaceae (75% ± 8%), dominated by Citrobacter freundii and a minor fraction of Raoultella ornithinolytica. C. freundii ferments xylose and glucose in a non-diauxic fashion. Clearly, a non-diauxic generalist outcompetes specialists and diauxic generalists in SBR environments.

A Residence Time Theory for Biodiversity

From microorganisms to the largest macroorganisms, much of Earth's biodiversity is subject to forces of physical turnover. Residence time is the ratio of an ecosystem's size to its rate of flow and provides a means for understanding the influence of physical turnover on biological systems. Despite its use across scientific disciplines, residence time has not been integrated into the broader understanding of biodiversity, life history, and the assembly of ecological communities. Here we propose a residence time theory for the growth, activity, abundance, and diversity of traits and taxa in complex ecological systems. Using thousands of stochastic individual-based models to simulate energetically constrained life-history processes, we show that our predictions are conceptually sound and mutually compatible and that they support ecological relationships that underpin much of biodiversity theory. We discuss the importance of residence time across the ecological hierarchy and propose how residence time can be integrated into theories ranging from population genetics to macroecology.

Role of Dilution Rate and Nutrient Availability in the Formation of Microbial Biofilms

We revisited the mathematical model of the chemostat and examined consequences of considerably decreasing the concentration of limiting nutrient in the inflow for the growth of both the planktonic and biofilm cells in the chemostat tank (fermenter). The model predicts a substantially lower steady-state biomass of planktonic cells in response to decreasing inflowing nutrient concentration. Contrarily, the steady-state concentration of nutrient inside the fermenter is expected to remain the same, as long as the inflowing concentration does not fall below its value. This allows the biofilm cells to grow at a rate regulated only by the exchange rate of the medium (dilution rate). We maintained a strain of Enterococcus faecalis in a chemostat of our own design with limiting nutrient in the inflow set near saturation constant at three dilution rates (0.09, 0.28, and 0.81 h^-1). The highest dilution rate was near the critical rate calculated by the model. The one-day total biofilm buildup was 21× larger and its estimated growth rate 2.4× higher at highest dilution rate than at the lowest one. This increased biofilm formation with increased dilution rates is in agreement with previously published data on pure and mixed continuous flow cultures.

Resistance and Resilience of Sulfidogenic Communities in the Face of the Specific Inhibitor Perchlorate

Hydrogen sulfide is a toxic and corrosive gas, produced by the activity of sulfate-reducing microorganisms (SRM). Owing to the environmental, economic and human-health consequences of sulfide, there is interest in developing specific inhibitors of SRM. Recent studies have identified perchlorate as a promising emerging inhibitor. The aim of this work is to quantitatively dissect the inhibitory dynamics of perchlorate. Sulfidogenic mixed continuous-flow systems were treated with perchlorate. SRM number, sulfide production and community structure were monitored pre-, during and post-treatment. The data generated was compared to a simple mathematical model, where SRM growth slows as a result of inhibition. The experimental data supports the interpretation that perchlorate largely acts to suppress SRM growth rates, rendering planktonic SRM increasingly susceptible to wash-out. Surface-attachment was identified as an important parameter preventing SRM wash-out and thus governing inhibitory dynamics. Our study confirmed the lesser depletion of surface-attached SRM as compared to planktonic SRM during perchlorate treatment. Indirect effects of perchlorate (bio-competitive exclusion of SRM by dissimilatory perchlorate-reducing bacteria, DPRB) were also assayed by amending reactors with DPRB. Indeed, low concentrations of perchlorate coupled with DRPB amendment can drive sulfide concentrations to zero. Further, inhibition in a complex community was compared to that in a pure culture, highlighting similarities and differences between the two scenarios. Finally, we quantified susceptibility to perchlorate across SRM in various culture conditions, showing that prediction of complex behavior in continuous systems from batch results is possible. This study thus provides an overview of the sensitivity of sulfidogenic communities to perchlorate, as well as mechanisms underlying these patterns.

Proteomic and Isotopic Response of Desulfovibrio vulgaris to DsrC Perturbation

Dissimilatory sulfate reduction is a microbial energy metabolism that can produce sulfur isotopic fractionations over a large range in magnitude. Calibrating sulfur isotopic fractionation in laboratory experiments allows for better interpretations of sulfur isotopes in modern sediments and ancient sedimentary rocks. The proteins involved in sulfate reduction are expressed in response to environmental conditions, and are collectively responsible for the net isotopic fractionation between sulfate and sulfide. We examined the role of DsrC, a key component of the sulfate reduction pathway, by comparing wildtype Desulfovibrio vulgaris DSM 644T to strain IPFG07, a mutant deficient in DsrC production. Both strains were cultivated in parallel chemostat reactors at identical turnover times and cell specific sulfate reduction rates. Under these conditions, sulfur isotopic fractionations between sulfate and sulfide of 17.3 ± 0.5‰ or 12.6 ± 0.5‰ were recorded for the wildtype or mutant, respectively. The enzymatic machinery that produced these different fractionations was revealed by quantitative proteomics. Results are consistent with a cellular-level response that throttled the supply of electrons and sulfur supply through the sulfate reduction pathway more in the mutant relative to the wildtype, independent of rate. We conclude that the smaller fractionation observed in the mutant strain is a consequence of sulfate reduction that proceeded at a rate that consumed a greater proportion of the strains overall capacity for sulfate reduction. These observations have consequences for models of sulfate reducer metabolism and how it yields different isotopic fractionations, notably, the role of DsrC in central energy metabolism.

Determination of Microbial Maintenance in Acetogenesis and Methanogenesis by Experimental and Modeling Techniques

For biogas-producing continuous stirred tank reactors, an increase in dilution rate increases the methane production rate as long as substrate input can be converted fully. However, higher dilution rates necessitate higher specific microbial growth rates, which are assumed to have a strong impact on the apparent microbial biomass yield due to cellular maintenance. To test this, we operated two reactors at 37°C in parallel at dilution rates of 0.18 and 0.07 days-1 (hydraulic retention times of 5.5 and 14 days, doubling times of 3.9 and 9.9 days in steady state) with identical inoculum and a mixture of volatile fatty acids as sole carbon sources. We evaluated the performance of the Anaerobic Digestion Model No. 1 (ADM1), a thermodynamic black box approach (TBA), and dynamic flux balance analysis (dFBA), to describe the experimental observations. All models overestimated the impact of dilution rate on the apparent microbial biomass yield when using default parameter values. Based on our analysis, a maintenance coefficient value below 0.2 kJ per carbon mole of microbial biomass per hour should be used for the TBA, corresponding to 0.12 mmol ATP per gram dry weight per hour for dFBA, which strongly deviates from the value of 9.8 kJ Cmol h-1 that has been suggested to apply to all anaerobic microorganisms at 37°C. We hypothesized that a decrease in dilution rate might select taxa with minimized maintenance expenditure. However, no major differences in the dominating taxa between the reactors were observed based on amplicon sequencing of 16S rRNA genes and terminal restriction fragment length polymorphism analysis of mcrA genes. Surprisingly, Methanosaeta dominated over Methanosarcina even at a dilution rate of 0.18 days-1, which contradicts previous model expectations. Furthermore, only 23-49% of the bacterial reads could be assigned to known syntrophic fatty acid oxidizers, indicating that unknown members of this functional group remain to be discovered. In conclusion, microbial maintenance was found to be much lower for acetogenesis and methanogenesis than previously assumed, likely due to the exceptionally low growth rates in anaerobic digestion. This finding might also be relevant for other microbial systems operating at similarly low growth rates.

Deconstructing the Dissimilatory Sulfate Reduction Pathway: Isotope Fractionation of a Mutant Unable of Growth on Sulfate

The sulfur isotope record provides key insight into the history of Earth's redox conditions. A detailed understanding of the metabolisms driving this cycle, and specifically microbial sulfate reduction (MSR), is crucial for accurate paleoenvironmental reconstructions. This includes a precise knowledge of the step-specific sulfur isotope effects during MSR. In this study, we aim at resolving the cellular-level fractionation factor during dissimilatory sulfite reduction to sulfide within MSR, and use this measured isotope effect as a calibration to enhance our understanding of the biochemistry of sulfite reduction. For this, we merge measured isotope effects associated with dissimilatory sulfite reduction with a quantitative model that explicitly links net fractionation, reaction reversibility, and intracellular metabolite levels. The highly targeted experimental aspect of this study was possible by virtue of the availability of a deletion mutant strain of the model sulfate reducer Desulfovibrio vulgaris (strain Hildenborough), in which the sulfite reduction step is isolated from the rest of the metabolic pathway owing to the absence of its QmoABC complex (ΔQmo). This deletion disrupts electron flux and prevents the reduction of adenosine phosphosulfate (APS) to sulfite. When grown in open-system steady-state conditions at 10% maximum growth rate in the presence of sulfite and lactate as electron donor, sulfur isotope fractionation factors averaged -15.9‰ (1 σ = 0.4), which appeared to be statistically indistinguishable from a pure enzyme study with dissimilatory sulfite reductase. We coupled these measurements with an understanding of step-specific equilibrium and kinetic isotope effects, and furthered our mechanistic understanding of the biochemistry of sulfite uptake and ensuing reduction. Our metabolically informed isotope model identifies flavodoxin as the most likely electron carrier performing the transfer of electrons to dissimilatory sulfite reductase. This is in line with previous work on metabolic strategies adopted by sulfate reducers under different energy regimes, and has implications for our understanding of the plasticity of this metabolic pathway at the center of our interpretation of modern and palaeo-environmental records.

Ammonia Inhibition of Anaerobic Volatile Fatty Acid Degrading Microbial Communities

Ammonia inhibition is an important reason for reactor failures and economic losses in anaerobic digestion. Its impact on acetic acid degradation is well-studied, while its effect on propionic and butyric acid degradation has received little attention and is consequently not considered in the Anaerobic Digestion Model No. 1 (ADM1). To compare ammonia inhibition of the degradation of these three volatile fatty acids (VFAs), we fed a mixture of them as sole carbon source to three continuous stirred tank reactors (CSTRs) and increased ammonium bicarbonate concentrations in the influent from 52 to 277 mM. The use of this synthetic substrate allowed for the determination of degradation efficiencies for the individual acids. While butyric acid degradation was hardly affected by the increase of ammonia concentration, propionic acid degradation turned out to be even more inhibited than acetic acid degradation with degradation efficiencies dropping to 31 and 65% for propionic and acetic acid, respectively. The inhibited reactors acclimatized and approximated pre-disturbance degradation efficiencies toward the end of the experiment, which was accompanied by strong microbial community shifts, as observed by amplicon sequencing of 16S rRNA genes and terminal restriction fragment length polymorphism (T-RFLP) of mcrA genes. The acetoclastic methanogen Methanosaeta was completely replaced by Methanosarcina. The propionic acid degrading genus Syntrophobacter was replaced by yet unknown propionic acid degraders. The butyric acid degrading genus Syntrophomonas and hydrogenotrophic Methanomicrobiaceae were hardly affected. We hypothesized that the ammonia sensitivity of the initially dominating taxa Methanosaeta and Syntrophobacter led to a stronger inhibition of the acetic and propionic acid degradation compared to butyric acid degradation and hydrogenotrophic methanogenesis, which were facilitated by the ammonia tolerant taxa Syntrophomonas and Methanomicrobiaceae. We implemented this hypothesis into a multi-taxa extension of ADM1, which was able to simulate the dynamics of both microbial community composition and VFA concentration in the experiment. It is thus plausible that the effect of ammonia on VFA degradation strongly depends on the ammonia sensitivity of the dominating taxa, for syntrophic propionate degraders as much as for acetoclastic methanogens.

Scaling of G1 Duration with Population Doubling Time by a Cyclin in Saccharomyces cerevisiae

The longer cells stay in particular phases of the cell cycle, the longer it will take these cell populations to increase. However, the above qualitative description has very little predictive value, unless it can be codified mathematically. A quantitative relation that defines the population doubling time (Td) as a function of the time eukaryotic cells spend in specific cell cycle phases would be instrumental for estimating rates of cell proliferation and for evaluating introduced perturbations. Here, we show that in human cells, the length of the G1 phase (TG1) regressed on Td with a slope of ≈0.75, while in the yeast Saccharomyces cerevisiae, the slope was slightly smaller, at ≈0.60. On the other hand, cell size was not strongly associated with Td or TG1 in cell cultures that were proliferating at different rates. Furthermore, we show that levels of the yeast G1 cyclin Cln3p were positively associated with rates of cell proliferation over a broad range, at least in part through translational control mediated by a short upstream ORF (uORF) in the CLN3 transcript. Cln3p was also necessary for the proper scaling between TG1 and Td In contrast, yeast lacking the Whi5p transcriptional repressor maintained the scaling between TG1 and Td These data reveal fundamental scaling relationships between the duration of eukaryotic cell cycle phases and rates of cell proliferation, point to the necessary role of Cln3p in these relationships in yeast, and provide a mechanistic basis linking Cln3p levels to proliferation rates and the scaling of G1 with doubling time.

Automated Cell Treatment for Competence and Transformation of Escherichia coli in a High-Throughput Quasi-Turbidostat Using Microtiter Plates

Metabolic engineering and genome editing strategies often lead to large strain libraries of a bacterial host. Nevertheless, the generation of competent cells is the basis for transformation and subsequent screening of these strains. While preparation of competent cells is a standard procedure in flask cultivations, parallelization becomes a challenging task when working with larger libraries and liquid handling stations as transformation efficiency depends on a distinct physiological state of the cells. We present a robust method for the preparation of competent cells and their transformation. The strength of the method is that all cells on the plate can be maintained at a high growth rate until all cultures have reached a defined cell density regardless of growth rate and lag phase variabilities. This allows sufficient transformation in automated high throughput facilities and solves important scheduling issues in wet-lab library screenings. We address the problem of different growth rates, lag phases, and initial cell densities inspired by the characteristics of continuous cultures. The method functions on a fully automated liquid handling platform including all steps from the inoculation of the liquid cultures to plating and incubation on agar plates. The key advantage of the developed method is that it enables cell harvest in 96 well plates at a predefined time by keeping fast growing cells in the exponential phase as in turbidostat cultivations. This is done by a periodic monitoring of cell growth and a controlled dilution specific for each well. With the described methodology, we were able to transform different strains in parallel. The transformants produced can be picked and used in further automated screening experiments. This method offers the possibility to transform any combination of strain- and plasmid library in an automated high-throughput system, overcoming an important bottleneck in the high-throughput screening and the overall chain of bioprocess development.

Application of Continuous Culture Methods to Recombinant Protein Production in Microorganisms

Depending on the environmental conditions, cells adapt their metabolism and specific growth rate. Rearrangements occur on many different levels such as macromolecular composition, gene and protein expression, morphology and metabolic flux patterns. As the interplay of these processes also determines the output of a recombinant protein producing system, having control over specific growth rate of the culture is advantageous. Continuous culture methods were developed to grow cells in a constant environment and have been used for decades to study basic microbial physiology in a controlled and reproducible manner. Our review summarizes the uses of continuous cultures in cell physiology studies and process development, with a focus on recombinant protein-producing microorganisms.

Effect of bacterial growth rate on bacteriophage population growth rate

It is important to understand how physiological state of the host influence propagation of bacteriophages (phages), due to the potential higher phage production needs in the future. In our study, we tried to elucidate the effect of bacterial growth rate on adsorption constant (δ), latent period (L), burst size (b), and bacteriophage population growth rate (λ). As a model system, a well-studied phage T4 and Escherichia coli K-12 as a host was used. Bacteria were grown in a continuous culture operating at dilution rates in the range between 0.06 and 0.98 hr-1 . It was found that the burst size increases linearly from 8 PFU·cell-1 to 89 PFU·cell-1 with increase in bacteria growth rate. On the other hand, adsorption constant and latent period were both decreasing from 2.6∙10-9  ml·min-1 and 80 min to reach limiting values of 0.5 × 10-9  ml·min-1 and 27 min at higher growth rates, respectively. Both trends were mathematically described with Michaelis-Menten based type of equation and reasons for such form are discussed. By applying selected equations, a mathematical equation for prediction of bacteriophage population growth rate as a function of dilution rate was derived, reaching values around 8 hr-1 at highest dilution rate. Interestingly, almost identical description can be obtained using much simpler Monod type equation and possible reasons for this finding are discussed.

Competitive resource allocation to metabolic pathways contributes to overflow metabolisms and emergent properties in cross-feeding microbial consortia

Resource scarcity is a common stress in nature and has a major impact on microbial physiology. This review highlights microbial acclimations to resource scarcity, focusing on resource investment strategies for chemoheterotrophs from the molecular level to the pathway level. Competitive resource allocation strategies often lead to a phenotype known as overflow metabolism; the resulting overflow byproducts can stabilize cooperative interactions in microbial communities and can lead to cross-feeding consortia. These consortia can exhibit emergent properties such as enhanced resource usage and biomass productivity. The literature distilled here draws parallels between in silico and laboratory studies and ties them together with ecological theories to better understand microbial stress responses and mutualistic consortia functioning.

Analysis of the Genes Involved in Thiocyanate Oxidation during Growth in Continuous Culture of the Haloalkaliphilic Sulfur-Oxidizing Bacterium Thioalkalivibrio thiocyanoxidans ARh 2T Using Transcriptomics

Thiocyanate is a moderately toxic and chemically stable sulfur compound that is produced by both natural and industrial processes. Despite its significance as a pollutant, knowledge of the microbial degradation of thiocyanate is very limited. Therefore, investigation of thiocyanate oxidation in haloalkaliphiles such as the genus Thioalkalivibrio may lead to improved biotechnological applications in wastewater remediation.

Thiocyanate (N=C−S⁻) is a moderately toxic, inorganic sulfur compound. It occurs naturally as a by-product of the degradation of glucosinolate-containing plants and is produced industrially in a number of mining processes. Currently, two pathways for the primary degradation of thiocyanate in bacteria are recognized, the carbonyl sulfide pathway and the cyanate pathway, of which only the former has been fully characterized. Use of the cyanate pathway has been shown in only 10 strains of Thioalkalivibrio, a genus of obligately haloalkaliphilic sulfur-oxidizing Gammaproteobacteria found in soda lakes. So far, only the key enzyme in this reaction, thiocyanate dehydrogenase (TcDH), has been purified and studied. To gain a better understanding of the other genes involved in the cyanate pathway, we conducted a transcriptomics experiment comparing gene expression during the growth of Thioalkalivibrio thiocyanoxidans ARh 2^T with thiosulfate with that during its growth with thiocyanate. Triplicate cultures were grown in continuous substrate-limited mode, followed by transcriptome sequencing (RNA-Seq) of the total mRNA. Differential expression analysis showed that a cluster of genes surrounding the gene for TcDH were strongly upregulated during growth with thiocyanate. This cluster includes genes for putative copper uptake systems (copCD, ABC-type transporters), a putative electron acceptor (fccAB), and a two-component regulatory system (histidine kinase and a σ⁵⁴-responsive Fis family transcriptional regulator). Additionally, we observed the increased expression of RuBisCO and some carboxysome shell genes involved in inorganic carbon fixation, as well as of aprAB, genes involved in sulfite oxidation through the reverse sulfidogenesis pathway.

IMPORTANCE Thiocyanate is a moderately toxic and chemically stable sulfur compound that is produced by both natural and industrial processes. Despite its significance as a pollutant, knowledge of the microbial degradation of thiocyanate is very limited. Therefore, investigation of thiocyanate oxidation in haloalkaliphiles such as the genus Thioalkalivibrio may lead to improved biotechnological applications in wastewater remediation.

Mathematical models of microbial growth and metabolism: a whole-organism perspective

We review the principles underpinning the development of mathematical models of the metabolic activities of micro-organisms. Such models are important to understand and chart the substantial contributions made by micro-organisms to geochemical cycles, and also to optimise the performance of bioreactors that exploit the biochemical capabilities of these organisms. We advocate an approach based on the principle of dynamic allocation. We survey the biological background that motivates this approach, including nutrient assimilation, the regulation of gene expression, and the principles of microbial growth. In addition, we discuss the classic models of microbial growth as well as contemporary approaches. The dynamic allocation theory generalises these classic models in a natural manner and is readily amenable to the additional information provided by transcriptomics and proteomics approaches. Finally, we touch upon these organising principles in the context of the transition from the free-living unicellular mode of life to multicellularity.

Evolutionary Engineering in Chemostat Cultures for Improved Maltotriose Fermentation Kinetics in Saccharomyces pastorianus Lager Brewing Yeast

The lager brewing yeast Saccharomyces pastorianus, an interspecies hybrid of S. eubayanus and S. cerevisiae, ferments maltotriose, maltose, sucrose, glucose and fructose in wort to ethanol and carbon dioxide. Complete and timely conversion ("attenuation") of maltotriose by industrial S. pastorianus strains is a key requirement for process intensification. This study explores a new evolutionary engineering strategy for improving maltotriose fermentation kinetics. Prolonged carbon-limited, anaerobic chemostat cultivation of the reference strain S. pastorianus CBS1483 on a maltotriose-enriched sugar mixture was used to select for spontaneous mutants with improved affinity for maltotriose. Evolved populations exhibited an up to 5-fold lower residual maltotriose concentration and a higher ethanol concentration than the parental strain. Uptake studies with ¹⁴C-labeled sugars revealed an up to 4.75-fold higher transport capacity for maltotriose in evolved strains. In laboratory batch cultures on wort, evolved strains showed improved attenuation and higher ethanol concentrations. These improvements were also observed in pilot fermentations at 1,000-L scale with high-gravity wort. Although the evolved strain exhibited multiple chromosomal copy number changes, analysis of beer made from pilot fermentations showed no negative effects on flavor compound profiles. These results demonstrate the potential of evolutionary engineering for strain improvement of hybrid, alloploid brewing strains.

Fermentative Bacteria Influence the Competition between Denitrifiers and DNRA Bacteria

Denitrification and dissimilatory reduction to ammonium (DNRA) are competing nitrate-reduction processes that entail important biogeochemical consequences for nitrogen retention/removal in natural and man-made ecosystems. The nature of the available carbon source and electron donor have been suggested to play an important role on the outcome of this microbial competition. In this study, the influence of lactate as fermentable carbon source on the competition for nitrate was investigated for varying ratios of lactate and nitrate in the influent (Lac/N ratio). The study was conducted in an open chemostat culture, enriched from activated sludge, under strict anoxia. The mechanistic explanation of the conversions observed was based on integration of results from specific batch tests with biomass from the chemostat, molecular analysis of the biomass enriched, and a computational model. At high Lac/N ratio (2.97 mol/mol) both fermentative and respiratory nitrate reduction to ammonium occurred, coupled to partial oxidation of lactate to acetate, and to acetate oxidation respectively. Remaining lactate was fermented to propionate and acetate. At a decreased Lac/N ratio (1.15 mol/mol), the molar percentage of nitrate reduced to ammonium decreased to 58%, even though lactate was supplied in adequate amounts for full ammonification and nitrate remained the growth limiting compound. Data evaluation at this Lac/N ratio suggested conversions were comparable to the higher Lac/N ratio, except for lactate oxidation to acetate that was coupled to denitrification instead of ammonification. Respiratory DNRA on acetate was likely catalyzed by two Geobacter species related to G. luticola and G. lovleyi. Two Clostridiales members were likely responsible for lactate fermentation and partial lactate fermentation to acetate coupled to fermentative DNRA. An organism related to Propionivibrio militaris was identified as the organism likely responsible for denitrification. The results of this study clearly show that not only the ratio of available substrates, but also the nature of the electron donor influences the outcome of competition between DNRA and denitrification. Apparently, fermentative bacteria are competitive for the electron donor and thereby alter the ratio of available substrates for nitrate reduction.

pCO2 effects on species composition and growth of an estuarine phytoplankton community

The effects of ongoing changes in ocean carbonate chemistry on plankton ecology have important implications for food webs and biogeochemical cycling. However, conflicting results have emerged regarding species-specific responses to pCO2 enrichment and thus community responses have been difficult to predict. To assess community level effects (e.g., production) of altered carbonate chemistry, studies are needed that capitalize on the benefits of controlled experiments but also retain features of intact ecosystems that may exacerbate or ameliorate the effects observed in single-species or single cohort experiments. We performed incubations of natural plankton communities from Narragansett Bay, RI, USA in winter at ambient bay temperatures (5-13 °C), light and nutrient concentrations under three levels of controlled and constant CO2 concentrations, simulating past, present and future conditions at mean pCO2 levels of 224, 361, and 724 μatm respectively. Samples for carbonate analysis, chlorophyll a, plankton size-abundance, and plankton species composition were collected daily and phytoplankton growth rates in three different size fractions (<5, 5-20, and >20 μm) were measured at the end of the 7-day incubation period. Community composition changed during the incubation period with major increases in relative diatom abundance, which were similar across pCO2 treatments. At the end of the experiment, 24-hr growth responses to pCO2 levels varied as a function of cell size. The smallest size fraction (<5 μm) grew faster at the elevated pCO2 level. In contrast, the 5-20 μm size fraction grew fastest in the Present treatment and there were no significant differences in growth rate among treatments in the > 20 μm size fraction. Cell size distribution shifted toward smaller cells in both the Past and Future treatments but remained unchanged in the Present treatment. Similarity in Past and Future treatments for cell size distribution and growth rate (5-20 μm size fraction) illustrate non-monotonic effects of increasing pCO2 on ecological indicators and may be related to opposing physiological effects of high CO2 and low pH both within and among species. Interaction of these effects with other factors (e.g., nutrients, light, temperature, grazing, initial species composition) may explain variability among published studies. The absence of clear treatment-specific effects at the community level suggest that extrapolation of species-specific responses or experiments with only present day and future pCO2 treatments levels would produce misleading predictions of ocean acidification impacts on plankton production.

An Effective Method of Continuous Production of Erythritol from Glycerol by Yarrowia lipolytica MK1

This study demonstrates the potential applicability of the UV mutant Yarrowia lipolytica MK1 for the valorisation of glycerol and erythritol production in a chemostat culture. The aim of this research is to investigate the optimal C:N ratio in the feeding medium in order to enhance erythritol production. The highest erythritol concentration, at 113.1 g/L with a volumetric erythritol production rate of 1.1 g/(L·h) and a yield of 0.57 g/g, was obtained in the feeding medium with a C:N ratio of 80:1. Moreover, no residual glycerol was observed in the culture broth during cultivation. The chemical composition of the biomass was analysed. The contents of lysine and threonine in the biomass protein amino acid profile were higher than those required by the FAO/WHO for fodder yeast.

Carbon Availability Modifies Temperature Responses of Heterotrophic Microbial Respiration, Carbon Uptake Affinity, and Stable Carbon Isotope Discrimination

Microbial transformations of organic carbon (OC) generate a large flux of CO₂ into the atmosphere and influence the C balance of terrestrial and aquatic ecosystems. Yet, inherent heterogeneity in natural environments precludes direct quantification of multiple microbial C fluxes that underlie CO₂ production. Here we used a continuous flow bioreactor coupled with a stable C isotope analyzer to determine the effects of temperature and C availability (cellobiose concentration) on C fluxes and ¹³C discrimination of a microbial population growing at steady-state in a homogeneous, well-mixed environment. We estimated C uptake affinity and C use efficiency (CUE) to characterize the physiological responses of microbes to changing environmental conditions. Temperature increased biomass-C specific respiration rate and C uptake affinity at lower C availability, but did not influence those parameters at higher C availability. CUE decreased non-linearly with increasing temperature. The non-linear, negative relationship between CUE and temperature was more pronounced under lower C availability than under relatively high C availability. We observed stable isotope fractionation between C substrate and microbial biomass C (7~12‰ depletion), and between microbial biomass and respired CO₂ (4~10‰ depletion). Microbial discrimination against ¹³C-containing cellobiose during C uptake was influenced by temperature and C availability, while discrimination during respiration was only influenced by C availability. Shifts in C uptake affinity with temperature and C availability may have modified uptake-induced ¹³C fractionation. By stressing the importance of C availability on temperature responses of microbial C fluxes, C uptake affinity, CUE, and isotopic fractionation, this study contributes to a fundamental understanding of C flow through microbes. This will help guide parameterization of microbial responses to varying temperature and C availability within Earth-system models.