The energy spilling reactions of bacteria and other organisms

Bioenergetic characterization of hyperthermophilic archaean Methanocaldococcus sp. FS406-22

Hyperthermophilic archaean Methanocaldococcus sp. FS406-22 (hereafter FS406) is a hydrogenotrophic methanogen isolated from a deep-sea hydrothermal vent. To better understand the energetic requirements of hydrogen oxidation under extreme conditions, the thermodynamic characterization of FS406 incubations is necessary and notably underexplored. In this work, we quantified the bioenergetics of FS406 incubations at a range of temperatures (65, 76, and 85 ℃) and hydrogen concentrations (1.1, 1.4, and 2.1 mm). The biomass yields (C-mol of biomass per mol of H2 consumed) ranged from 0.02 to 0.19. Growth rates ranged from 0.4 to 1.5 h-1. Gibbs energies of incubation based on macrochemical equations of cell growth ranged from - 198 kJ/C-mol to - 1840 kJ/C-mol. Enthalpies of incubation determined from calorimetric measurements ranged from - 4150 kJ/C-mol to - 36333 kJ/C-mol. FS406 growth rates were most comparable to hyperthermophilic methanogen Methanocaldococcus jannaschii. Maintenance energy calculations from the thermodynamic parameters of FS406 and previously determined heterotrophic methanogen data revealed that temperature is a primary determinant rather than an electron donor. This work provides new insights into the thermodynamic underpinnings of a hyperthermophilic hydrothermal vent methanogen and helps to better constrain the energetic requirements of life in extreme environments.

Heparosan biosynthesis in recombinant Bacillus megaterium: Influence of N-acetylglucosamine supplementation and kinetic modeling

Heparosan, an unsulfated polysaccharide, plays a pivotal role as a primary precursor in the biosynthesis of heparin-an influential anticoagulant with diverse therapeutic applications. To enhance heparosan production, the utilization of metabolic engineering in nonpathogenic microbial strains is emerging as a secure and promising strategy. In the investigation of heparosan production by recombinant Bacillus megaterium, a kinetic modeling approach was employed to explore the impact of initial substrate concentration and the supplementation of precursor sugars. The adapted logistic model was utilized to thoroughly analyze three vital parameters: the B. megaterium growth dynamics, sucrose utilization, and heparosan formation. It was noted that at an initial sucrose concentration of 30 g L-1 (S1), it caused an inhibitory effect on both cell growth and substrate utilization. Intriguingly, the inclusion of N-acetylglucosamine (S2) resulted in a significant 1.6-fold enhancement in heparosan concentration. In addressing the complexities of the dual substrate system involving S1 and S2, a multi-substrate kinetic models, specifically the double Andrew's model was employed. This approach not only delved into the intricacies of dual substrate kinetics but also effectively described the relationships among the primary state variables. Consequently, these models not only provide a nuanced understanding of the system's behavior but also serve as a roadmap for optimizing the design and management of the heparosan production method.

Characterization and shelf life of synbiotic drink powder from porang (Amorphophallus muelleri)

Amorphophallus muelleri BI was included in the Araceae family, which is a type of tuber. It is a tuber with high potential due to its abundant bioactive compounds. Amorphophallus muelleri BI flour (AF) contains a high glucomannan and carbon compounds that serve as nutrients for probiotic bacteria. Although Amorphophallus muelleri BI thrives in Indonesia, its utilization rate in the country remains relatively low and haven't been any studies conducted regarding synbiotic powder from AF. The primary objective of this research is to develop a synergistic beverage enriched with varying concentrations of Amorphophallus muelleri BI as a prebiotic and LA as probiotic (synbiotic). The process starts with culture preparation, synbiotic drink process, synbiotic and microencapsulation, includes the examination of solubility, proximate analysis, calorie content, viability, and shelf life. Results showed that the proximate and solubility had no significant effect. Synbiotic drink powder from AF can be produced using spray dry technology. The highest LA growth was observed when augmenting the AF quantity at a 0.4% concentration, which can be seen from the viability parameter with a value of 7.29 log CFU/g. Samples shelf life at -21 and 3 °C with LA viability critical parameter was determined to be 4 days.

Impact of combined management strategies of monensin and virginiamycin in high energy diets on ruminal fermentation and nutrients utilization

Feed additives such as monensin (MON) and virginiamycin (VM) are commonly utilized in feedlot diets to enhance rumen fermentation. Nevertheless, the precise effects of combining MON and VM during specific feedlot periods and the advantages of this combination remain unclear. This study was designed to investigate the effects of withdrawal of MON when associated with VM during the adaptation and finishing periods on ruminal metabolism, feeding behavior, and nutrient digestibility in Nellore cattle. The experimental design was a 5 × 5 Latin square, where each period lasted 28 days. Five rumen-cannulated Nellore yearling bulls were used (414,86 ± 21,71 kg of body weight), which were assigned to five treatments: (1) MON during the entire feeding period; (2) VM during the entire feeding period; (3) MON + VM during the adaptation period and only VM during the finishing period 1 and 2; (4) MON + VM during the entire feeding period; (5) MON + VM during the adaptation and finishing period 1 and only VM during the finishing period 2. For the finishing period 1, animals fed T3 had improved potential degradability of dry matter (p = 0.02). Cattle fed T3 and T5 had the highest crude protein degradability when compared to animals receiving T2 (p = 0.01). Animals fed T2 and T3 had reduced the time (p < 0.01) and area under pH 6.2 (p = 0.02). Moreover, animals fed T4 had greater population of protozoa from the genus Diplodinium (p = 0.04) when compared to those from animals fed T2, T3 and T5. For the finishing period 2, animals fed T3 had greater starch degradability when compared to animals receiving T4 and T5 (p = 0.04). Animals fed T3, T4 and T5 had increased the duration of time in which pH was below 5.6 (p = 0.03). The area under the curve for ruminal pH 5.2 and pH 5.6 was higher for the animals fed T3 (p = 0.01), and the area under pH 6.2 was higher for the animals fed T3 and T5 (p < 0.01) when compared to animals receiving T2. There is no substantial improvement on the rumen fermentation parameters by the concurrent utilization of MON and VM molecules, where the higher starch and protein degradability did not improve the rumen fermentation.

Chapter 6: The Breadth and Limits of Life on Earth

Scientific ideas about the potential existence of life elsewhere in the universe are predominantly informed by knowledge about life on Earth. Over the past ∼4 billion years, life on Earth has evolved into millions of unique species. Life now inhabits nearly every environmental niche on Earth that has been explored. Despite the wide variety of species and diverse biochemistry of modern life, many features, such as energy production mechanisms and nutrient requirements, are conserved across the Tree of Life. Such conserved features help define the operational parameters required by life and therefore help direct the exploration and evaluation of habitability in extraterrestrial environments. As new diversity in the Tree of Life continues to expand, so do the known limits of life on Earth and the range of environments considered habitable elsewhere. The metabolic processes used by organisms living on the edge of habitability provide insights into the types of environments that would be most suitable to hosting extraterrestrial life, crucial for planning and developing future astrobiology missions. This chapter will introduce readers to the breadth and limits of life on Earth and show how the study of life at the extremes can inform the broader field of astrobiology.

Unique architecture of microbial snottites from a methane driven biofilm revealed by confocal microscopy

Microbial biofilms occur in many shapes and different dimensions. In natural and semi-artificial caves they are forming pendulous structures of 10 cm and more. In this study a methane driven microbial community of a former medicinal spring was investigated. The habitat was completely covered by massive biofilms and snottites with a wobbly, gelatinous appearance. By using fluorescence techniques in combination with confocal laser scanning microscopy the architecture of these so far unknown snottites was examined. The imaging approaches applied comprised reflection of geogenic and cellular origin, possible autofluorescence, nucleic acid staining for bacterial cells, protein staining for bacteria and extracellular fine structures, calcofluor white for β 1 → 3, β 1 → 4 polysaccharide staining for possible fungi as well as lectin staining for the extracellular biofilm matrix glycoconjugates. The results showed a highly complex, intricate structure with voluminous, globular, and tube-like glycoconjugates of different dimensions and densities. In addition, filamentous bacteria seem to provide additional strength to the snottites. After screening with all commercially available lectins, by means of fluorescence lectin barcoding and subsequent fluorescence lectin binding analysis, the AAL, PNA, LEA, and Ban lectins identified α-Fuc, β-Gal, β-GlcNAc, and α-Man with α-Fuc as a major component. Examination of the outer boundary with fluorescent beads revealed a potential outer layer which could not be stained by any of the fluorescent probes applied. Finally, suggestions are made to further elucidate the characteristics of these unusual microbial biofilms in form of snottites. RESEARCH HIGHLIGHTS: The gelatinous snottites revealed at the microscale a highly complex structure not seen before. The extracellular matrix of the snottite biofilm was identified as clusters of different shape and density. The matrix of snottites was examined by taking advantage of 78 fluorescently-labeled lectins. The extracellular matrix glycoconjugates of snottites identified comprised: α-Fuc, β-Gal, β-GlcNAc, and α-Man. Probing the snottite outer surface indicated an additional unknown stratum.

Impact of nicotine and cotinine on macrophage inflammatory plasticity via vesicular modifications in gastrointestinal bacteria

OBJECTIVES

This study aimed to elucidate mechanistic explanation(s) for compositional changes to enteric microbiota by determining the impacts of continuous nicotine/cotinine exposure on representative gastrointestinal bacteria and how these alterations impact innate immune cell plasticity.

METHODS

In vitro cultures of the gastrointestinal bacteria (Bacteroides fragilis 25285, Prevotella bryantii B14, and Acetoanaerobium sticklandii SR) were continuously exposed to nicotine or cotinine. Supernatant samples were collected for fermentation acid analysis. Vesicles were collected and analyzed for physiological changes in number, size, and total protein cargo. Cultured macrophages were stimulated to a tolerogenic phenotype, exposed to control or altered (nicotine or cotinine - exposed) vesicles, and inflammatory plasticity assessed via inflammatory cytokine production.

RESULTS

Nicotine/cotinine exposure differentially affected metabolism of all bacteria tested in a Gram (nicotine) and concentration-dependent (cotinine) manner. Physiological studies demonstrated changes in vesiculation number and protein cargo following nicotine/cotinine exposures. Continuous exposure to 1 μM nicotine and 10 μM cotinine concentrations reduced total protein cargo of Gram (-) - 25285 and B14 vesicles, while cotinine generally increased total protein in Gram (+) - SR vesicles. We found that theses physiological changes to the vesicles of 25285 and SR formed under nicotine and cotinine, respectively, challenged the plasticity of tolerogenic macrophages. Tolerogenic macrophages exposed to vesicles from 1 μM nicotine, and 5 or 10 μΜ cotinine cultures produced significantly less IL-12p70, TNFα, or KC/GRO, regardless of macrophage exposure to nicotine/cotinine.

CONCLUSIONS

Nicotine/cotinine exposure differentially alters bacterial metabolism and vesicle physiology, ultimately impacting the inflammatory response of tolerogenic macrophages.

Microbial carbon use efficiency in different ecosystems: A meta-analysis based on a biogeochemical equilibrium model

Soil microbial carbon use efficiency (CUE) is a crucial parameter that can be used to evaluate the partitioning of soil carbon (C) between microbial growth and respiration. However, general patterns of microbial CUE among terrestrial ecosystems (e.g., farmland, grassland, and forest) remain controversial. To address this knowledge gap, data from 41 study sites (n = 197 soil samples) including 58 farmlands, 95 forests, and 44 grasslands were collected and analyzed to estimate microbial CUEs using a biogeochemical equilibrium model. We also evaluated the metabolic limitations of microbial growth using an enzyme vector model and the drivers of CUE across different ecosystems. The CUEs obtained from soils of farmland, forest, and grassland ecosystems were significantly different with means of 0.39, 0.33, and 0.42, respectively, illustrating that grassland soils exhibited higher microbial C sequestration potentials (p < .05). Microbial metabolic limitations were also distinct in these ecosystems, and carbon limitation was dominant exhibiting strong negative effects on CUE. Exoenzyme stoichiometry played a greater role in impacting CUE values than soil elemental stoichiometry within each ecosystem. Specifically, soil exoenzymatic ratios of C:phosphorus (P) acquisition activities (EEAC:P ) and the exoenzymatic ratio of C:nitrogen (N) acquisition activities (EEAC:N ) imparted strong negative effects on soil microbial CUE in grassland and forest ecosystems, respectively. But in farmland soils, EEAC:P exhibited greater positive effects, showing that resource constraints could regulate microbial resource allocation with discriminating patterns across terrestrial ecosystems. Furthermore, mean annual temperature (MAT) rather than mean annual precipitation (MAP) was a critical climate factor affecting CUE, and soil pH as a major factor remained positive to drive the changes in microbial CUE within ecosystems. This research illustrates a conceptual framework of microbial CUEs in terrestrial ecosystems and provides the theoretical evidence to improve soil microbial C sequestration capacity in response to global change.

Functional decomposition of metabolism allows a system-level quantification of fluxes and protein allocation towards specific metabolic functions

Quantifying the contribution of individual molecular components to complex cellular processes is a grand challenge in systems biology. Here we establish a general theoretical framework (Functional Decomposition of Metabolism, FDM) to quantify the contribution of every metabolic reaction to metabolic functions, e.g. the synthesis of biomass building blocks. FDM allowed for a detailed quantification of the energy and biosynthesis budget for growing Escherichia coli cells. Surprisingly, the ATP generated during the biosynthesis of building blocks from glucose almost balances the demand from protein synthesis, the largest energy expenditure known for growing cells. This leaves the bulk of the energy generated by fermentation and respiration unaccounted for, thus challenging the common notion that energy is a key growth-limiting resource. Moreover, FDM together with proteomics enables the quantification of enzymes contributing towards each metabolic function, allowing for a first-principle formulation of a coarse-grained model of global protein allocation based on the structure of the metabolic network.

A Hitchhiker's Guide to Supplying Enzymatic Reducing Power into Synthetic Cells

The construction from scratch of synthetic cells by assembling molecular building blocks is unquestionably an ambitious goal from a scientific and technological point of view. To realize functional life-like systems, minimal enzymatic modules are required to sustain the processes underlying the out-of-equilibrium thermodynamic status hallmarking life, including the essential supply of energy in the form of electrons. The nicotinamide cofactors NAD(H) and NADP(H) are the main electron carriers fueling reductive redox reactions of the metabolic network of living cells. One way to ensure the continuous availability of reduced nicotinamide cofactors in a synthetic cell is to build a minimal enzymatic module that can oxidize an external electron donor and reduce NAD(P)+. In the diverse world of metabolism there is a plethora of potential electron donors and enzymes known from living organisms to provide reducing power to NAD(P)+ coenzymes. This perspective proposes guidelines to enable the reduction of nicotinamide cofactors enclosed in phospholipid vesicles, while avoiding high burdens of or cross-talk with other encapsulated metabolic modules. By determining key requirements, such as the feasibility of the reaction and transport of the electron donor into the cell-like compartment, we select a shortlist of potentially suitable electron donors. We review the most convenient proteins for the use of these reducing agents, highlighting their main biochemical and structural features. Noting that specificity toward either NAD(H) or NADP(H) imposes a limitation common to most of the analyzed enzymes, we discuss the need for specific enzymes─transhydrogenases─to overcome this potential bottleneck.

CBD resistant Salmonella strains are susceptible to epsilon 34 phage tailspike protein

The rise of antimicrobial resistance is a global public health crisis that threatens the effective control and prevention of infections. Due to the emergence of pandrug-resistant bacteria, most antibiotics have lost their efficacy. Bacteriophages or their components are known to target bacterial cell walls, cell membranes, and lipopolysaccharides (LPS) and hydrolyze them. Bacteriophages being the natural predators of pathogenic bacteria, are inevitably categorized as "human friends", thus fulfilling the adage that "the enemy of my enemy is my friend". Leveraging on their lethal capabilities against pathogenic bacteria, researchers are searching for more ways to overcome the current antibiotic resistance challenge. In this study, we expressed and purified epsilon 34 phage tailspike protein (E34 TSP) from the E34 TSP gene, then assessed the ability of this bacteriophage protein in the killing of two CBD-resistant strains of Salmonella spp. We also assessed the ability of the tailspike protein to cause bacteria membrane disruption, and dehydrogenase depletion. We observed that the combined treatment of CBD-resistant strains of Salmonella with CBD and E34 TSP showed poor killing ability whereas the monotreatment with E34 TSP showed considerably higher killing efficiency. This study demonstrates that the inhibition of the bacteria by E34 TSP was due in part to membrane disruption, and dehydrogenase inactivation by the protein. The results of this work provides an interesting background to highlight the crucial role phage protein such as E34 TSP could play in pathogenic bacterial control.

Heterogeneity and Evolutionary Tunability of Escherichia coli Resistance against Extreme Acid Stress

Since acidic environments often serve as an important line of defense against bacterial pathogens, it is important to fully understand how the latter manage to mount and evolve acid resistance mechanisms. Escherichia coli, a species harboring many pathovars, is typically equipped with the acid fitness island (AFI), a genomic region encoding the GadE master regulator together with several GadE-controlled functions to counter acid stress. This study reveals that gadE and consequently AFI functions are heterogeneously expressed even in the absence of any prior acid stress, thereby preemptively creating acid-resistant subpopulations within a clonal E. coli population. Directed evolution efforts selecting for modulated gadE expression confirm that a gain-of-function mutation in the EvgS sensor kinase can constitutively upregulate gadE expression and concomitant acid resistance. However, we reveal that such upregulation of EvgS also causes cross-resistance to heat stress because of SafA-mediated cross-activation of the PhoPQ regulon. Surprisingly, loss of function of the serC gene (encoding phosphoserine/phosphohydroxythreonine aminotransferase) can also significantly upregulate gadE expression, acid resistance, and heat cross-resistance, although via a currently cryptic mechanism. As such, our data reveal a noisy expression of gadE in E. coli that is functional for the survival of sudden acid stress and that can readily be genetically tuned. IMPORTANCE Acidic environments constitute one of the most important stresses for enteric bacteria and can be encountered in both natural (e.g., host gastrointestinal tract) and manmade (e.g., food processing) environments. The enteric species Escherichia coli harbors many pathovars and is well known for its ability to cope with acid stress. In this study, we uncover that E. coli's acid fitness island (AFI), a genomic region that encodes important functions to deal with acid stress, is by default expressed in a heterogeneous manner. In fact, using microfluidics-based single-cell approaches, we further demonstrate that this heterogeneity preemptively creates a clonal subpopulation that is much better equipped to survive a sudden acid shock. In addition, we reveal that environments with recurring acid stress can readily select for mutants displaying a higher fraction of AFI-expressing cells. These new insights are important to properly understand and anticipate the survival characteristics of E. coli.

Microbial fuel cell compared to a chemostat

Microbial Fuel Cells (MFCs) represent a green and sustainable energy conversion system that integrate bacterial biofilms within an electrochemical two-electrode set-up to produce electricity from organic waste. In this review, we focus on a novel exploratory model, regarding "thin" biofilms forming on highly perfusable (non-diffusible) anodes in small-scale, continuous flow MFCs due to the unique properties of the electroactive biofilm. We discuss how this type of MFC can behave as a chemostat in fulfilling common properties including steady state growth and multiple steady states within the limit of biological physicochemical conditions imposed by the external environment. With continuous steady state growth, there is also continuous metabolic rate and continuous electrical power production, which like the chemostat can be controlled. The model suggests that in addition to controlling growth rate and power output by changing the external resistive load, it will be possible instead to change the flow rate/dilution rate.

Down-regulation of the bacterial protein biosynthesis machinery in response to weeks, years, and decades of soil warming

How soil microorganisms respond to global warming is key to infer future soil-climate feedbacks, yet poorly understood. Here, we applied metatranscriptomics to investigate microbial physiological responses to medium-term (8 years) and long-term (>50 years) subarctic grassland soil warming of +6°C. Besides indications for a community-wide up-regulation of centralmetabolic pathways and cell replication, we observed a down-regulation of the bacterial protein biosynthesis machinery in the warmed soils, coinciding with a lower microbial biomass, RNA, and soil substrate content. We conclude that permanently accelerated reaction rates at higher temperatures and reduced substrate concentrations result in cellular reduction of ribosomes, the macromolecular complexes carrying out protein biosynthesis. Later efforts to test this, including a short-term warming experiment (6 weeks, +6°C), further supported our conclusion. Down-regulating the protein biosynthesis machinery liberates energy and matter, allowing soil bacteria to maintain high metabolic activities and cell division rates even after decades of warming.

Pyrophosphate and Irreversibility in Evolution, or why PPi Is Not an Energy Currency and why Nature Chose Triphosphates

The possible evolutionary significance of pyrophosphate (PPi) has been discussed since the early 1960s. Lipmann suggested that PPi could have been an ancient currency or a possible environmental source of metabolic energy at origins, while Kornberg proposed that PPi vectorializes metabolism because ubiquitous pyrophosphatases render PPi forming reactions kinetically irreversible. To test those ideas, we investigated the reactions that consume phosphoanhydride bonds among the 402 reactions of the universal biosynthetic core that generates amino acids, nucleotides, and cofactors from H2, CO2, and NH3. We find that 36% of the core's phosphoanhydride hydrolyzing reactions generate PPi, while no reactions use PPi as an energy currency. The polymerization reactions that generate ~80% of cell mass - protein, RNA, and DNA synthesis - all generate PPi, while none use PPi as an energy source. In typical prokaryotic cells, aminoacyl tRNA synthetases (AARS) underlie ~80% of PPi production. We show that the irreversibility of the AARS reaction is a kinetic, not a thermodynamic effect. The data indicate that PPi is not an ancient energy currency and probably never was. Instead, PPi hydrolysis is an ancient mechanism that imparts irreversibility, as Kornberg suggested, functioning like a ratchet's pawl to vectorialize the life process toward growth. The two anhydride bonds in nucleoside triphosphates offer ATP-cleaving enzymes an option to impart either thermodynamic control (Pi formation) or kinetic control (PPi formation) upon reactions. This dual capacity explains why nature chose the triphosphate moiety of ATP as biochemistry's universal energy currency.

Infrared thermography can detect previsual bacterial growth in a laboratory setting via metabolic heat detection

Aims

Detection of bacterial contamination in healthcare and industry takes many hours if not days. Thermal imaging, the measurement of heat by an infrared camera, was investigated as a potential noninvasive method of detecting bacterial growth.

Methods and Results

Infrared thermography can detect the presence of Escherichia coli and Staphylococcus aureus on solid growth media by an increase in temperature before they are visually observable. A heat decrease is observed after treatment with ultraviolet light and heat increased after incubation with dinitrophenol.

Conclusions

Infrared thermography can detect early growth of bacteria before they are detectable by other microbiology‐based method. The heat observed is due to the cells being viable and metabolically active, as cells killed with ultraviolet light exhibit reduced increase in temperature and treatment with dinitrophenol increases heat detected.

Significance and Impact of the Study

Infrared thermography detects bacterial growth without the need for specialized temperature control facilities. The method is statistically robust and can be undertaken in situ, thus is highly versatile. These data support the application of infrared thermography in a laboratory, clinical and industrial setting for vegetative bacteria, thus may become into an important methodology for the timely and straightforward detection of early‐stage bacterial growth.

Conditions stimulating neutral detergent fiber degradation by dosing branched-chain volatile fatty acids. III: Relation with solid passage rate and pH on prokaryotic fatty acid profile and community in continuous culture

Our objectives were to evaluate potential interactions in culture conditions that influence how exogenously dosed branched-chain VFA (BCVFA) would be recovered as elongated fatty acids (FA) or would affect bacterial populations. A 2 × 2 × 2 factorial arrangement of treatments evaluated 3 factors: (1) without versus with BCVFA (0 vs. 2 mmol/d each of isobutyrate, isovalerate, and 2-methylbutyrate; each dose was partially substituted with ¹³C-enriched tracers before and during the collection period); (2) high versus low pH (ranging diurnally from 6.3 to 6.8 vs. 5.7 to 6.2); and (3) low versus high particulate-phase passage rate (k_p; 2.5 vs. 5.0%/h) in continuous cultures administered a 50:50 forage:concentrate diet twice daily. Samples of effluent were collected and composited before harvesting bacteria from which FA and DNA were extracted. Profiles and enrichments of FA in bacteria were evaluated by gas chromatography and isotope-ratio mass spectrometry. The ¹³C enrichment in bacterial FA was calculated as percentage recovery of dosed ¹³C-labeled BCVFA. Dosing BCVFA increased the even-chain iso-FA, preventing the reduced concentration at higher k_p and potentially as a physiological response to decreased pH. However, decreasing pH decreased recovery of ¹³C in these even-chain FA, suggesting greater reliance on isobutyrate produced from degradation of dietary valine. The iso-FA were decreased, whereas anteiso-FA and 16:0 increased with decreasing pH. Thus, 2-methylbutyrate still appeared to be important as a precursor for anteiso-FA to counter the increased rigidity of bacterial membranes that had more saturated straight-chain FA when pH decreased. Provision of BCVFA stimulated the relative sequence abundance of Fibrobacter and Treponema, both of which require isobutyrate and 2-methylbutyrate. Numerous bacterial community members were shifted by low pH, including increased Prevotella and genera within the phylum Proteobacteria, at the expense of members within phylum Firmicutes. Because of relatively few interactions with pH and k_p, supplementation of BCVFA can stimulate neutral detergent fiber degradability via key fibrolytic bacteria across a range of conditions. Decreasing pH shifted bacterial populations and their FA composition, suggesting that further research is needed to distinguish pH from dietary changes.

A General Model for Biofilm-Driven Microbial Electrosynthesis of Carboxylates From CO2

Up to now, computational modeling of microbial electrosynthesis (MES) has been underexplored, but is necessary to achieve breakthrough understanding of the process-limiting steps. Here, a general framework for modeling microbial kinetics in a MES reactor is presented. A thermodynamic approach is used to link microbial metabolism to the electrochemical reduction of an intracellular mediator, allowing to predict cellular growth and current consumption. The model accounts for CO₂ reduction to acetate, and further elongation to n-butyrate and n-caproate. Simulation results were compared with experimental data obtained from different sources and proved the model is able to successfully describe microbial kinetics (growth, chain elongation, and product inhibition) and reactor performance (current density, organics titer). The capacity of the model to simulate different system configurations is also shown. Model results suggest CO₂ dissolved concentration might be limiting existing MES systems, and highlight the importance of the delivery method utilized to supply it. Simulation results also indicate that for biofilm-driven reactors, continuous mode significantly enhances microbial growth and might allow denser biofilms to be formed and higher current densities to be achieved.

Measuring and modeling energy and power consumption in living microbial cells with a synthetic ATP reporter

Background

Adenosine triphosphate (ATP) is the main energy carrier in living organisms, critical for metabolism and essential physiological processes. In humans, abnormal regulation of energy levels (ATP concentration) and power consumption (ATP consumption flux) in cells is associated with numerous diseases from cancer, to viral infection and immune dysfunction, while in microbes it influences their responses to drugs and other stresses. The measurement and modeling of ATP dynamics in cells is therefore a critical component in understanding fundamental physiology and its role in pathology. Despite the importance of ATP, our current understanding of energy dynamics and homeostasis in living cells has been limited by the lack of easy-to-use ATP sensors and the lack of models that enable accurate estimates of energy and power consumption related to these ATP dynamics. Here we describe a dynamic model and an ATP reporter that tracks ATP in E. coli over different growth phases.

Results

The reporter is made by fusing an ATP-sensing rrnB P1 promoter with a fast-folding and fast-degrading GFP. Good correlations between reporter GFP and cellular ATP were obtained in E. coli growing in both minimal and rich media and in various strains. The ATP reporter can reliably monitor bacterial ATP dynamics in response to nutrient availability. Fitting the dynamics of experimental data corresponding to cell growth, glucose, acetate, dissolved oxygen, and ATP yielded a mathematical and circuit model. This model can accurately predict cellular energy and power consumption under various conditions. We found that cellular power consumption varies significantly from approximately 0.8 and 0.2 million ATP/s for a tested strain during lag and stationary phases to 6.4 million ATP/s during exponential phase, indicating ~ 8–30-fold changes of metabolic rates among different growth phases. Bacteria turn over their cellular ATP pool a few times per second during the exponential phase and slow this rate by ~ 2–5-fold in lag and stationary phases.

Conclusion

Our rrnB P1-GFP reporter and kinetic circuit model provide a fast and simple way to monitor and predict energy and power consumption dynamics in bacterial cells, which can impact fundamental scientific studies and applied medical treatments in the future.

To What Inanimate Matter Are We Most Closely Related and Does the Origin of Life Harbor Meaning?

The question concerning the meaning of life is important, but it immediately confronts the present authors with insurmountable obstacles from a philosophical standpoint, as it would require us to define not only what we hold to be life, but what we hold to be meaning in addition, requiring us to do both in a properly researched context. We unconditionally surrender to that challenge. Instead, we offer a vernacular, armchair approach to life’s origin and meaning, with some layman’s thoughts on the meaning of origins as viewed from the biologist’s standpoint. One can observe that biologists generally approach the concept of biological meaning in the context of evolution. This is the basis for the broad resonance behind Dobzhansky’s appraisal that “Nothing in biology makes sense except in the light of evolution”. Biologists try to understand living things in the historical context of how they arose, without giving much thought to the definition of what life or living things are, which for a biologist is usually not an interesting question in the practical context of daily dealings with organisms. Do humans generally understand life’s meaning in the context of history? If we consider the problem of life’s origin, the question of what constitutes a living thing becomes somewhat more acute for the biologist, though not more answerable, because it is inescapable that there was a time when there were no organisms on Earth, followed by a time when there were, the latter time having persisted in continuity to the present. This raises the question of where, in that transition, chemicals on Earth became alive, requiring, in turn, a set of premises for how life arose in order to conceptualize the problem in relation to organisms we know today, including ourselves, which brings us to the point of this paper: In the same way that cultural narratives for origins always start with a setting, scientific narratives for origins also always start with a setting, a place on Earth or elsewhere where we can imagine what happened for the sake of structuring both the problem and the narrative for its solution. This raises the question of whether scientific origins settings convey meaning to humans in that they suggest to us from what kind of place and what kinds of chemicals we are descended, that is, to which inanimate things we are most closely related.

Conjugation dynamics depend on both the plasmid acquisition cost and the fitness cost

Plasmid conjugation is a major mechanism responsible for the spread of antibiotic resistance. Plasmid fitness costs are known to impact long-term growth dynamics of microbial populations by providing plasmid-carrying cells a relative (dis)advantage compared to plasmid-free counterparts. Separately, plasmid acquisition introduces an immediate, but transient, metabolic perturbation. However, the impact of these short-term effects on subsequent growth dynamics has not previously been established. Here, we observed that de novo transconjugants grew significantly slower and/or with overall prolonged lag times, compared to lineages that had been replicating for several generations, indicating the presence of a plasmid acquisition cost. These effects were general to diverse incompatibility groups, well-characterized and clinically captured plasmids, Gram-negative recipient strains and species, and experimental conditions. Modeling revealed that both fitness and acquisition costs modulate overall conjugation dynamics, validated with previously published data. These results suggest that the hours immediately following conjugation may play a critical role in both short- and long-term plasmid prevalence. This time frame is particularly relevant to microbiomes with high plasmid/strain diversity considered to be hot spots for conjugation.

The Autotrophic Core: An Ancient Network of 404 Reactions Converts H2, CO2, and NH3 into Amino Acids, Bases, and Cofactors

The metabolism of cells contains evidence reflecting the process by which they arose. Here, we have identified the ancient core of autotrophic metabolism encompassing 404 reactions that comprise the reaction network from H₂, CO₂, and ammonia (NH₃) to amino acids, nucleic acid monomers, and the 19 cofactors required for their synthesis. Water is the most common reactant in the autotrophic core, indicating that the core arose in an aqueous environment. Seventy-seven core reactions involve the hydrolysis of high-energy phosphate bonds, furthermore suggesting the presence of a non-enzymatic and highly exergonic chemical reaction capable of continuously synthesizing activated phosphate bonds. CO₂ is the most common carbon-containing compound in the core. An abundance of NADH and NADPH-dependent redox reactions in the autotrophic core, the central role of CO₂, and the circumstance that the core’s main products are far more reduced than CO₂ indicate that the core arose in a highly reducing environment. The chemical reactions of the autotrophic core suggest that it arose from H₂, inorganic carbon, and NH₃ in an aqueous environment marked by highly reducing and continuously far from equilibrium conditions. Such conditions are very similar to those found in serpentinizing hydrothermal systems.

Energetics of Acidianus ambivalens growth in response to oxygen availability

All life requires energy to drive metabolic reactions such as growth and cell maintenance; therefore, fluctuations in energy availability can alter microbial activity. There is a gap in our knowledge concerning how energy availability affects the growth of extreme chemolithoautotrophs. Toward this end, we investigated the growth of thermoacidophile Acidianus ambivalens during sulfur oxidation under aerobic to microaerophilic conditions. Calorimetry was used to measure enthalpy (ΔH_inc ) of microbial activity, and chemical changes in growth media were measured to calculate Gibbs energy change (ΔG_inc ) during incubation. In all experiments, Gibbs energy was primarily dissipated through the release of heat, which suggests enthalpy-driven growth. In microaerophilic conditions, growth was significantly more efficient in terms of biomass yield (defined as C-mol biomass per mole sulfur consumed) and resulted in lower ΔG_inc and ΔH_inc . ΔG_inc in oxygen-limited (OL) and oxygen- and CO₂ -limited (OCL) microaerophilic growth conditions resulted in averages of -1.44 × 10³  kJ/C-mol and -7.56 × 10²  kJ/C-mol, respectively, and average ΔH_inc values of -1.11 × 10⁵  kJ/C-mol and -4.43 × 10⁴  kJ/C-mol, respectively. High-oxygen experiments resulted in lower biomass yield values, an increase in ΔG_inc to -1.71 × 10⁴  kJ/C-mol, and more exothermic ΔH_inc values of -4.71 × 10⁵  kJ/C-mol. The observed inefficiency in high-oxygen conditions may suggest larger maintenance energy demands due to oxidative stresses and a preference for growth in microaerophilic environments.

How Thermodynamics Illuminates Population Interactions in Microbial Communities

In traditional population models of microbial ecology, there are two central players: producers and consumers (including decomposers that depend on organic carbon). Producers support surface ecosystems by generating adenosine triphosphate (ATP) from sunlight, part of which is used to build new biomass from carbon dioxide. In contrast, the productivity of subsurface ecosystems with a limited supply of sunlight must rely on bacteria and archaea that are able generate ATP solely from chemical or electric energy to fix inorganic carbon. These “light-independent producers” are frequently not included in traditional food webs, even though they are ubiquitous in nature and interact with one another through the utilization of the by-products of others. In this review, we introduce theoretical approaches based on population dynamics that incorporate thermodynamics to highlight characteristic interactions in the microbial community of subsurface ecosystems, which may link community structures and ecosystem expansion under conditions of a limited supply of sunlight. In comparison with light-dependent producers, which compete with one another for light, the use of Gibbs free energy (chemical energy) can lead cooperative interactions among light-independent producers through the effects of the relative quantities of products and reactants on the available chemical energy, which is termed abundant resource premium. The development of a population theory that incorporates thermodynamics offers fundamental ecological insights into subsurface microbial ecosystems, which may be applied to fields of study such as environmental science/engineering, astrobiology, or the microbial ecosystems of the early earth.

Effects of terrigenous organic substrates and additional phosphorus on bacterioplankton metabolism and exoenzyme stoichiometry

Bamboo, as a pioneer vegetation, often forms forests on bare lands after catastrophic landslides. Compared to evergreen forest soil, bamboo forest soil is much more labile, with a higher percentage of microbially derived organic carbon (OC), lower molecular weight, and lower humic acid content. We hypothesised that different terrigenous organic matter (tOM) sources with varying lability and phosphorus (P) availability select for bacterioplankton with distinct metabolic pathways.We incubated natural bacterioplankton assemblages with tOM leached from bamboo forest soil (BOM) and evergreen forest soil (EOM) and compared these to a lake water control. To test if microbial metabolism would be limited by OC or P availability of each tOM treatment, we used acetate as an extra labile OC source and phosphate as an inorganic P source. Bacterial metabolism was measured by analysing respiration via O2 consumption and production via tritiated thymidine (TdR) assimilation.Bacterioplankton metabolism is limited by the availability of P in BOM substrates. When using BOM, bacteria had higher enzymatic activities for phosphatase. The nutrients required for bacterial biomass seemed to be derived from organic matter. Under BOM treatment, bacterial production (BP) (0.92 ± 0.13 μg C L-1 hr-1) and cell specific TdR assimilation rates (0.015 ± 0.002 10-18 M TdR cell-1 hr-1) were low. Adding P enhanced BP (BOM+P 1.52 ± 0.31 and BOM+C+P 2.25 ± 0.37 μg C L-1 hr-1) while acetate addition had no significant effect on BOM treatment.This indicated that the bacteria switched to using added inorganic P to respire a P-limited BOM substrate, which increased total BP and abundance, resulting in even more active respiration and lower growth efficiency. We also found higher activities for chitin-degrading enzyme β-N-acetylglucosaminidase, which is associated with N mining from aminosaccharides.Microbes using EOM, however, did not change metabolic strategies with additional acetate or/and inorganic P. This is due to higher concentrations of organic P in EOM substrates and the presence of inorganic N in the EOM leachates an alternative nutrient source. Bacteria produced β-glucosidase and leucyl-aminopeptidase in order to utilise the humic substances, which sustained greater bacterial abundance, higher BP (2.64 ± 0.39 μg C L-1 hr-1), and lower cell-specific respiration. This yielded a much higher bacterial growth efficiency (15 ± 9.2%) than the lake water control.Our study demonstrated the aquatic metabolic discrepancy between tOM of different forest types. Bacterioplankton in BOM and EOM exhibit distinct metabolic responses. Bacterial metabolic strategy when using BOM implied that the supposedly stabilised biomass OM might be efficiently used by aquatic bacterioplankton. As the labile and nutrient-deficient BOM is more susceptible to the influence of additional nutrients, fertiliser residues in bamboo forest catchments might have a stronger effect on aquatic bacterial metabolic pathways. Thus, it is important to take tOM differences into consideration when building models to estimate soil carbon turnover rates along a terrestrial-aquatic continuum.

Understanding How Microorganisms Respond to Acid pH Is Central to Their Control and Successful Exploitation

Microbes from the three domains of life, Bacteria, Archaea, and Eukarya, share the need to sense and respond to changes in the external and internal concentrations of protons. When the proton concentration is high, acidic conditions prevail and cells must respond appropriately to ensure that macromolecules and metabolic processes are sufficiently protected to sustain life. While, we have learned much in recent decades about the mechanisms that microbes use to cope with acid, including the unique challenges presented by organic acids, there is still much to be gained from developing a deeper understanding of the effects and responses to acid in microbes. In this perspective article, we survey the key molecular mechanisms known to be important for microbial survival during acid stress and discuss how this knowledge might be relevant to microbe-based applications and processes that are consequential for humans. We discuss the research approaches that have been taken to investigate the problem and highlight promising new avenues. We discuss the influence of acid on pathogens during the course of infections and highlight the potential of using organic acids in treatments for some types of infection. We explore the influence of acid stress on photosynthetic microbes, and on biotechnological and industrial processes, including those needed to produce organic acids. We highlight the importance of understanding acid stress in controlling spoilage and pathogenic microbes in the food chain. Finally, we invite colleagues with an interest in microbial responses to low pH to participate in the EU-funded COST Action network called EuroMicropH and contribute to a comprehensive database of literature on this topic that we are making publicly available.

The functional development of the rumen is influenced by weaning and associated with ruminal microbiota in lambs

Rumen development is critical for the development of early lambs. This work aims to evaluate the effects of abrupt weaning at day 21 on rumen fermentation, histomorphological traits and the ruminal microbiota compared with continuous suckling. Twelve pairs of artificially reared full-sib neonatal male Hu lambs were allocated to two groups, one of which was weaned at day 21 (EW group) and the other which was not weaned (CON group). At day 26 and day 49, six lambs from each group were randomly selected and sacrificed to collect ruminal contents and rumen tissue samples. Results showed that weaning influenced the fermentation parameters in the rumen, and altered the microbial community composition on day 49 (p < 0.05). Several genera were associated with rumen fermentation parameters (p < 0.05). Volatile fatty acid (VFA) concentration is the key parameter impacting microbiota composition. Weaning influenced the expression of genes associated with VFA metabolism and regulation of cell proliferation (p < 0.05). In conclusion, weaning significantly influenced the morphological and functional development of the rumen, and bacterial community composition. The microbial community composition was strongly associated with rumen weight and fermentation profiles, but not with morphological development.

An alternative pentose phosphate pathway in human gut bacteria for the degradation of C5 sugars in dietary fibers

The microbial degradation of pentoses in the human gut is a crucial factor for the utilization of plant-based dietary fibers. A vast majority of gut microbes are able to use these C5-sugars as a carbon and energy source. However, the underlying metabolic pathways are not fully understood. Bioinformatic analysis showed that a large number of abundant gut bacteria lack genes encoding a transaldolase as a key enzyme of the pentose phosphate pathway. Among them was the important human gut microbe Prevotella copri, which was able to grow in minimal media containing xylose or hemicelluloses as the sole carbon source. Therefore, we looked for an alternative pathway for pentose conversion in P. copri using bioinformatics, enzyme activity assays, and the detection of intermediates of pentose metabolism. It became evident that the organism converted C5-sugars via the sedoheptulose-1,7-bisphosphate pathway (SBPP) to connect pentose metabolism with glycolysis. To circumvent the transaldolase reaction, P. copri uses the combined catalysis of a pyrophosphate-dependent phosphofructokinase and a fructose-bisphosphate aldolase. Furthermore, we present strong evidence that the SBPP is widely distributed in important gut bacteria, including members of the phyla Bacteroides, Firmicutes, Proteobacteria, Verrucomicrobia, and Lentisphaerae.

Fast antimicrobial susceptibility testing on Escherichia coli by metabolic heat nanocalorimetry

Fast spreading of antimicrobial resistance is now considered a major global health threat. New technologies are required, enabling rapid diagnostics of bacterial infection combined with fast antimicrobial susceptibility testing (AST) for evaluating the efficiency and dosage of antimicrobial compounds in vitro. This work presents an integrated chip-based isothermal nanocalorimetry platform for direct microbial metabolic heat measurements and evaluates its potential for fast AST. Direct detection of the bacteria-generated heat allows monitoring of metabolic activity and antimicrobial action at subinhibitory concentrations in real-time. The high heat sensitivity of the platform enables bacterial growth detection within only a few hours of incubation, whereas growth inhibition upon administration of antibiotics is revealed by a decrease or the absence of the heat signal. Antimicrobial stress results in lag phase extension and metabolic energy spilling. Oxygen consumption and optical density measurements provide a more holistic insight of the metabolic state and the evolution of bacterial biomass. As a proof-of-concept, a metabolic heat-based AST study on Escherichia coli as model organism with 3 clinically relevant antibiotics is performed and the minimum inhibitory concentrations are determined.

In silico co-factor balance estimation using constraint-based modelling informs metabolic engineering in Escherichia coli

In the growing field of metabolic engineering, where cells are treated as ‘factories’ that synthesize industrial compounds, it is essential to consider the ability of the cells’ native metabolism to accommodate the demands of synthetic pathways, as these pathways will alter the homeostasis of cellular energy and electron metabolism. From the breakdown of substrate, microorganisms activate and reduce key co-factors such as ATP and NAD(P)H, which subsequently need to be hydrolysed and oxidized, respectively, in order to restore cellular balance. A balanced supply and consumption of such co-factors, here termed co-factor balance, will influence biotechnological performance. To aid the strain selection and design process, we used stoichiometric modelling (FBA, pFBA, FVA and MOMA) and the Escherichia coli (E.coli) core stoichiometric model to investigate the network-wide effect of butanol and butanol precursor production pathways differing in energy and electron demand on product yield. An FBA-based co-factor balance assessment (CBA) algorithm was developed to track and categorise how ATP and NAD(P)H pools are affected in the presence of a new pathway. CBA was compared to the balance calculations proposed by Dugar et al. (Nature Biotechnol. 29 (12), 1074–1078). Predicted solutions were compromised by excessively underdetermined systems, displaying greater flexibility in the range of reaction fluxes than experimentally measured by ¹³C-metabolic flux analysis (MFA) and the appearance of unrealistic futile co-factor cycles. With the assumption that futile cycles are tightly regulated in reality, the FBA models were manually constrained in a step-wise manner. Solutions with minimal futile cycling diverted surplus energy and electrons towards biomass formation. As an alternative, the use of loopless FBA or constraining the models with measured flux ranges were tried but did not prevent futile co-factor cycles. The results highlight the need to account for co-factor imbalance and confirm that better-balanced pathways with minimal diversion of surplus towards biomass formation present the highest theoretical yield. The analysis also suggests that ATP and NAD(P)H balancing cannot be assessed in isolation from each other, or even from the balance of additional co-factors such as AMP and ADP. We conclude that, through revealing the source of co-factor imbalance CBA can facilitate pathway and host selection when designing new biocatalysts for implementation by metabolic engineering.

The chemicals industry is a major contributor to greenhouse gas emissions and desperately requires more sustainable alternatives. Genetically engineered microorganisms can be used as ‘bio-factories’ to manufacture chemicals, replacing those currently sourced from fossil fuels or unsustainable tropical plant agriculture. However, due to the complexity of biology, the features that render one bio-factory design more efficient than others are difficult to identify. Computational modelling of such designs can enable the selection of optimally performing designs, but it remains challenging as biology is complex and not fully understood. Microorganisms require energy for their own growth and maintenance, but also to convert molecules into desired target products. The supply and consumption of such energy is through co-factors, and the balance of such co-factors influences the performance of the engineered bio-factories. This study developed a computer-aided approach for quantification of the co-factor balance of bio-factories. Using the chemical n-butanol as a case study, our study explores the impact of variant bio-factory designs with differing co-factor balance on the potential efficiency of biomanufacturing. We provide insights into the relative balance of different designs and provide a computational framework to select the best-performing designs.

Trait-based approach to bacterial growth efficiency

Bacterial growth efficiency (BGE) is the proportion of assimilated carbon that is converted into biomass and reflects the balance between growth and energetic demands. Often measured as an aggregate property of the community, BGE is highly variable within and across ecosystems. To understand this variation, we first identified how species identity and resource type affect BGE using 20 bacterial isolates belonging to the phylum Proteobacteria that were enriched from north temperate lakes. Using a trait-based approach that incorporated genomic and phenotypic information, we characterized the metabolism of each isolate and tested for predicted trade-offs between growth rate and efficiency. A substantial amount of variation in BGE could be explained at broad (i.e., order, 20%) and fine (i.e., strain, 58%) taxonomic levels. While resource type was a relatively weak predictor across species, it explained >60% of the variation in BGE within a given species. A metabolic trade-off (between maximum growth rate and efficiency) and genomic features revealed that BGE may be a species-specific metabolic property. Our study suggests that genomic and phylogenetic information may help predict aggregate microbial community functions like BGE and the fate of carbon in ecosystems.

Older Than Genes: The Acetyl CoA Pathway and Origins

For decades, microbiologists have viewed the acetyl CoA pathway and organisms that use it for H2-dependent carbon and energy metabolism, acetogens and methanogens, as ancient. Classical evidence and newer evidence indicating the antiquity of the acetyl CoA pathway are summarized here. The acetyl CoA pathway requires approximately 10 enzymes, roughly as many organic cofactors, and more than 500 kDa of combined subunit molecular mass to catalyze the conversion of H2 and CO2 to formate, acetate, and pyruvate in acetogens and methanogens. However, a single hydrothermal vent alloy, awaruite (Ni3Fe), can convert H2 and CO2 to formate, acetate, and pyruvate under mild hydrothermal conditions on its own. The chemical reactions of H2 and CO2 to pyruvate thus have a natural tendency to occur without enzymes, given suitable inorganic catalysts. This suggests that the evolution of the enzymatic acetyl CoA pathway was preceded by-and patterned along-a route of naturally occurring exergonic reactions catalyzed by transition metal minerals that could activate H2 and CO2 by chemisorption. The principle of forward (autotrophic) pathway evolution from preexisting non-enzymatic reactions is generalized to the concept of patterned evolution of pathways. In acetogens, exergonic reduction of CO2 by H2 generates acyl phosphates by highly reactive carbonyl groups undergoing attack by inert inorganic phosphate. In that ancient reaction of biochemical energy conservation, the energy behind formation of the acyl phosphate bond resides in the carbonyl, not in phosphate. The antiquity of the acetyl CoA pathway is usually seen in light of CO2 fixation; its role in primordial energy coupling via acyl phosphates and substrate-level phosphorylation is emphasized here.

Dynamic Metabolic Analysis of Cupriavidus necator DSM545 Producing Poly(3-hydroxybutyric acid) from Glycerol

Cupriavidus necator DSM 545 can utilise glycerol to synthesise poly(3-hydroxybutyric acid) under unbalanced growth conditions, i.e., nitrogen limitation. To improve poly(3-hydroxybutyric acid) (PHB) batch production by C. necator through model-guided bioprocessing or genetic engineering, insights into the dynamic effect of the fermentation conditions on cell metabolism are crucial. In this work, we have used dynamic flux balance analysis (DFBA), a constrained-based stoichiometric modelling approach, to study the metabolic change associated with PHB synthesis during batch cultivation. The model employs the ‘minimisation of all fluxes’ as cellular objectives and measured extracellular fluxes as additional constraints. The mass balance constraints are further adjusted based on thermodynamic considerations. The resultant flux distribution profiles characterise the evolution of metabolic states due to adaptation to dynamic extracellular conditions and provide further insights towards improvements that can be implemented to enhance PHB productivity.

From sunscreens to medicines: Can a dissipation hypothesis explain the beneficial aspects of many plant compounds?

Medicine has utilised plant‐based treatments for millennia, but precisely how they work is unclear. One approach is to use a thermodynamic viewpoint that life arose by dissipating geothermal and/or solar potential. Hence, the ability to dissipate energy to maintain homeostasis is a fundamental principle in all life, which can be viewed as an accretion system where layers of complexity have built upon core abiotic molecules. Many of these compounds are chromophoric and are now involved in multiple pathways. Plants have further evolved a plethora of chromophoric compounds that can not only act as sunscreens and redox modifiers, but also have now become integrated into a generalised stress adaptive system. This could be an extension of the dissipative process. In animals, many of these compounds are hormetic, modulating mitochondria and calcium signalling. They can also display anti‐pathogen effects. They could therefore modulate bioenergetics across all life due to the conserved electron transport chain and proton gradient. In this review paper, we focus on well‐described medicinal compounds, such as salicylic acid and cannabidiol and suggest, at least in animals, their activity reflects their evolved function in plants in relation to stress adaptation, which itself evolved to maintain dissipative homeostasis.

Production of prodigiosin pigment by Serratia marcescens is negatively associated with cellular ATP levels during high-rate, low-cell-density growth

Serratia marcescens is a facultatively anaerobic bacterium and the most recognized producer of the hydrophobic pigment prodigiosin. Previous work has shown that prodigiosin both increases ATP production during population lag phase and approximately doubles the stationary-phase cell yield. Here, we employed both batch and chemostat culture methods to investigate prodigiosin's role during high rate growth at low cell density as peak cellular ATP levels decline. Batch culture experiments utilizing artificial pigment induction showed an ATP reduction during low cell density growth. In addition, pigment induction during fixed growth rate chemostat culture revealed a negative correlation between cellular levels of prodigiosin and ATP (r = -0.95). Variable growth rate chemostat experiments showed an inverse relationship between ATP per cell and prodigiosin per cell during low-density growth but a direct relationship during high-density growth. Rate modeling of chemostat data quantified the pigment's effect on cellular levels of ATP for both population growth phases. Finally, prodigiosin production in a heterologous bacterium led to ATP decline. These data with intact cells complement the established in vitro proton import function of prodigiosin pigment and may indicate an energy-spilling function during high rate, low cell density growth.

Microbial energy management-A product of three broad tradeoffs

Wherever thermodynamics allows, microbial life has evolved to transform and harness energy. Microbial life thus abounds in the most unexpected places, enabled by profound metabolic diversity. Within this diversity, energy is transformed primarily through variations on a few core mechanisms. Energy is further managed by the physiological processes of cell growth and maintenance that use energy. Some aspects of microbial physiology are streamlined for energetic efficiency while other aspects seem suboptimal or even wasteful. We propose that the energy that a microbe harnesses and devotes to growth and maintenance is a product of three broad tradeoffs: (i) economic, trading enzyme synthesis or operational cost for functional benefit, (ii) environmental, trading optimization for a single environment for adaptability to multiple environments, and (iii) thermodynamic, trading energetic yield for forward metabolic flux. Consideration of these tradeoffs allows one to reconcile features of microbial physiology that seem to opposingly promote either energetic efficiency or waste.

Anaerobic nitrate respiration in the aerobe Streptomyces coelicolor A3(2): helping maintain a proton gradient during dormancy

Respiratory nitrate reductases (Nar) catalyse the reduction of nitrate to nitrite, coupling this process to energy conservation. The obligate aerobic actinobacterium Streptomyces coelicolor synthesizes three Nar enzymes that contribute to maintenance of a membrane potential when either the mycelium or the spores become hypoxic or anoxic. No growth occurs under such conditions but the bacterium survives the lack of O₂ by remaining metabolically active; reducing nitrate is one means whereby this process is aided. Nar1 is exclusive to spores, Nar2 to vegetative mycelium and Nar3 to stationary-phase mycelium, each making a distinct contribution to energy conservation. While Nar2 and Nar3 appear to function like conventional menaquinol oxidases, unusually, Nar1 is completely dependent for its activity on a cytochrome bcc-aa ₃ oxidase supercomplex. This suggest that electrons within this supercomplex are diverted to Nar1 during O₂ limitation. Receiving electrons from this supercomplex potentially allows nitrate reduction to be coupled to the Q-cycle of the cytochrome bcc complex. This modification likely improves the efficiency of energy conservation, extending longevity of spores under O₂ limitation. Knowledge gained on the bioenergetics of NO₃ ^- respiration in the actinobacteria will aid our understanding of how many microorganisms survive under conditions of extreme nutrient and energy restriction.

Glycogen Synthesis and Metabolite Overflow Contribute to Energy Balancing in Cyanobacteria

Understanding how living cells manage high-energy metabolites such as ATP and NADPH is essential for understanding energy transformations in the biosphere. Using light as the energy input, we find that energy charge (ratio of ATP over ADP+ATP) in the cyanobacterium Synechocystis sp. PCC 6803 varies in different growth stages, with a peak upon entry into the rapid growth phase, as well as a positive correlation with light intensity. In contrast, a mutant that can no longer synthesize the main carbon storage compound glycogen showed higher energy charge. The overflow of organic acids in this mutant under nitrogen depletion could also be triggered under high light in nitrogen-replete conditions, with an energy input level dependency. These findings suggest that energy charge in cyanobacteria is tightly linked to growth and carbon partition and that energy management is of key significance for their application as photosynthetic carbon dioxide-assimilating cell factories.

Bacterial metabolic state more accurately predicts antibiotic lethality than growth rate

Growth rate and metabolic state of bacteria have been separately shown to affect antibiotic efficacy^1-3. However, the two are interrelated as bacterial growth inherently imposes a metabolic burden⁴; thus, determining individual contributions from each is challenging^5,6. Indeed, faster growth is often correlated with increased antibiotic efficacy^7,8; however, the concurrent role of metabolism in that relationship has not been well characterized. As a result, a clear understanding of the interdependence between growth and metabolism, and their implications for antibiotic efficacy, are lacking⁹. Here, we measured growth and metabolism in parallel across a broad range of coupled and uncoupled conditions to determine their relative contribution to antibiotic lethality. We show that when growth and metabolism are uncoupled, antibiotic lethality uniformly depends on the bacterial metabolic state at the time of treatment, rather than growth rate. We further reveal a critical metabolic threshold below which antibiotic lethality is negligible. These findings were general for a wide range of conditions, including nine representative bactericidal drugs and a diverse range of Gram-positive and Gram-negative species (Escherichia coli, Acinetobacter baumannii and Staphylococcus aureus). This study provides a cohesive metabolic-dependent basis for antibiotic-mediated cell death, with implications for current treatment strategies and future drug development.

Hydrogen Oxidation Influences Glycogen Accumulation in a Verrucomicrobial Methanotroph

Metabolic flexibility in aerobic methane oxidizing bacteria (methanotrophs) enhances cell growth and survival in instances where resources are variable or limiting. Examples include the production of intracellular compounds (such as glycogen or polyhydroxyalkanoates) in response to unbalanced growth conditions and the use of some energy substrates, besides methane, when available. Indeed, recent studies show that verrucomicrobial methanotrophs can grow mixotrophically through oxidation of hydrogen and methane gases via respiratory membrane-bound group 1d [NiFe] hydrogenases and methane monooxygenases, respectively. Hydrogen metabolism is particularly important for adaptation to methane and oxygen limitation, suggesting this metabolic flexibility may confer growth and survival advantages. In this work, we provide evidence that, in adopting a mixotrophic growth strategy, the thermoacidophilic methanotroph, Methylacidiphilum sp. RTK17.1 changes its growth rate, biomass yields and the production of intracellular glycogen reservoirs. Under nitrogen-fixing conditions, removal of hydrogen from the feed-gas resulted in a 14% reduction in observed growth rates and a 144% increase in cellular glycogen content. Concomitant with increases in glycogen content, the total protein content of biomass decreased following the removal of hydrogen. Transcriptome analysis of Methylacidiphilum sp. RTK17.1 revealed a 3.5-fold upregulation of the Group 1d [NiFe] hydrogenase in response to oxygen limitation and a 4-fold upregulation of nitrogenase encoding genes (nifHDKENX) in response to nitrogen limitation. Genes associated with glycogen synthesis and degradation were expressed constitutively and did not display evidence of transcriptional regulation. Collectively these data further challenge the belief that hydrogen metabolism in methanotrophic bacteria is primarily associated with energy conservation during nitrogen fixation and suggests its utilization provides a competitive growth advantage within hypoxic habitats.

Valorization of glycerol/ethanol-rich wastewater to bioflocculants: recovery, properties, and performance

Microbial extracellular polymeric substances (EPS) were produced in two membrane bioreactors, each separately treating fresh and saline synthetic wastewater (consisting of glycerol and ethanol), with the purpose of applying them as sustainable bioflocculants. The reactors were operated under nitrogen-rich (COD/N ratios of 5 and 20) and limited (COD/N ratios of 60 and 100) conditions. Under both conditions, high COD removal efficiencies of 87-96% were achieved. However, nitrogen limitation enhanced EPS production, particularly the polysaccharide fraction. The maximum EPS recovery (g EPS-COD/g COD_influent) from the fresh wastewater was 54% and 36% recovery was obtained from the saline (30 g NaCl/L) wastewater. The biopolymers had molecular weights up to 2.1 MDa and anionic charge densities of 2.3-4.7 meq/g at pH 7. Using kaolin clay suspensions, high flocculation efficiencies of 85-92% turbidity removal were achieved at EPS dosages below 0.5 mg/g clay. Interestingly, EPS produced under saline conditions proved to be better flocculants in a saline environment than the corresponding freshwater EPS in the same environment. The results demonstrate the potential of glycerol/ethanol-rich wastewater, namely biodiesel/ethanol industrial wastewater, as suitable substrates to produce EPS as effective bioflocculants.

Effects of in-feed enzymes on milk production and components, reproduction, and health in dairy cows

Our objectives were to characterize responses in the field to a mix of fibrolytic enzymes using large commercial dairy herds and sufficient study power to evaluate milk production and reproductive responses to an enzyme treatment started during the precalving period. We hypothesized that the use of the enzyme treatment would increase milk production when provided to dairy cows precalving and for approximately 200 d of lactation. The study was conducted on 7,507 cows, in 8 replicates and 16 pens, at 3 dairies in the United States. Eight pens were randomly allocated as control pens and received no enzyme, and another 8 pens received enzyme treatment at a dose of 750 mL/t of dry matter feed. Milk production and energy-corrected milk yield were increased with the enzyme treatment by 0.70 and 0.80 kg/d, respectively, across a 5-month period. Milk fat percentage was not significantly increased by enzyme treatment, but milk fat yield was significantly increased by 0.040 kg/d, compared with controls. Milk protein yield increased 0.010 kg/d with enzyme treatment despite a small reduction of 0.020 percentage units in milk protein percentage. We found no evidence of an increase in the ln somatic cell count for the enzyme-treated cows. Body weight overall was not increased for enzyme-treated cows, but we did observe a numerical increase in dry matter intake (0.20 kg/head per day) for enzyme-treated cows. Most production responses to the enzyme treatment were influenced by dairy. Compared with controls, milk yield in enzyme-treated cows was significantly higher by 3.6 kg/d in dairy 2 and numerically higher by 0.60 and 0.20 kg/d in dairies 1 and 3, respectively. Reproduction, health, and risk of removal or death were not significantly influenced by treatment, apart from a reduced time to first breeding. Production responses to the enzyme treatment varied by dairy from substantial to minor increases, but variation among dairies was not evident in differences in dry matter intake or in partitioning of body weight among enzyme-treated and control pens and cows. It appears likely that the increase in production reflected increased digestibility of feed; however, further work is needed to identify factors influencing the variation in production responses to enzymes.

Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism

Growth rate and yield are fundamental features of microbial growth. However, we lack a mechanistic and quantitative understanding of the rate-yield relationship. Studies pairing computational predictions with experiments have shown the importance of maintenance energy and proteome allocation in explaining rate-yield tradeoffs and overflow metabolism. Recently, adaptive evolution experiments of Escherichia coli reveal a phenotypic diversity beyond what has been explained using simple models of growth rate versus yield. Here, we identify a two-dimensional rate-yield tradeoff in adapted E. coli strains where the dimensions are (A) a tradeoff between growth rate and yield and (B) a tradeoff between substrate (glucose) uptake rate and growth yield. We employ a multi-scale modeling approach, combining a previously reported coarse-grained small-scale proteome allocation model with a fine-grained genome-scale model of metabolism and gene expression (ME-model), to develop a quantitative description of the full rate-yield relationship for E. coli K-12 MG1655. The multi-scale analysis resolves the complexity of ME-model which hindered its practical use in proteome complexity analysis, and provides a mechanistic explanation of the two-dimensional tradeoff. Further, the analysis identifies modifications to the P/O ratio and the flux allocation between glycolysis and pentose phosphate pathway (PPP) as potential mechanisms that enable the tradeoff between glucose uptake rate and growth yield. Thus, the rate-yield tradeoffs that govern microbial adaptation to new environments are more complex than previously reported, and they can be understood in mechanistic detail using a multi-scale modeling approach.

This study reconciles multiple existing microbial rate-yield tradeoff theories with experimental data. There is great interest in developing quantitative descriptions of the relationship between growth rate and growth yield [1]. However, some reported experiments [2–4] in the literature do not agree with existing theories [5–7]. Specifically, overflow metabolism in E. coli can either be coupled [5, 8] or decoupled [2–4] from growth rate. We found that adaptive laboratory evolution (ALE) experiments of E. coli reveal a two-dimensional rate-yield tradeoff in adapted strains where the dimensions are (i) a tradeoff between growth rate and growth yield, previously reported by [5], and (ii) a tradeoff between substrate uptake rate and growth yield. The appearance of this two-dimensional tradeoff during adaptation suggests that microorganisms adapting to new environments are subject to a more complex set of rate-yield tradeoffs than previously reported [5, 6]. In this study, the two-dimensional rate-yield tradeoff is quantitatively explained through our multi-scale modeling approach, combining a previously reported small-scale proteome allocation model [5] with a genome-scale model of metabolism and gene-expression (ME-model) [9]. The modeling approach is also instrumental to future studies.

Metabolism of sucrose in a non-fermentative Escherichia coli under oxygen limitation

Biotechnological industry strives to develop anaerobic bioprocesses fueled by abundant and cheap carbon sources, like sucrose. However, oxygen-limiting conditions often lead to by-product formation and reduced ATP yields. While by-product formation is typically decreased by gene deletion, the breakdown of oligosaccharides with inorganic phosphate instead of water could increment the ATP yield. To observe the effect of oxygen limitation during sucrose consumption, a non-fermentative Escherichia coli K-12 strain was transformed with genes enabling sucrose assimilation. It was observed that the combined deletion of the genes adhE, adhP, mhpF, ldhA, and pta abolished the anaerobic growth using sucrose. Therefore, the biomass-specific conversion rates were obtained using oxygen-limited continuous cultures. Strains performing the breakdown of the sucrose by hydrolysis (SUC-HYD) or phosphorolysis (SUC-PHOSP) were studied in such conditions. An experimentally validated in silico model, modified to account for plasmid and protein burdens, was employed to calculate carbon and electron consistent conversion rates. In both strains, the biomass yields were lower than expected and, strikingly, SUC-PHOSP showed a yield lower than SUC-HYD. Flux balance analyses indicated a significant increase in the non-growth-associated ATP expenses by comparison with the growth on glucose. The observed fructose-1,6-biphosphatase and phosphoglucomutase activities, as well as the concentrations of glycogen, suggest the operation of ATP futile cycles triggered by a combination of the oxygen limitation and the metabolites released during the sucrose breakdown.

Sustained substrate cycles between hexose phosphates and free sugars in phosphate-deficient potato (Solanum tuberosum) cell cultures

Futile cycling between free sugars and hexose phosphates occurring under phosphate deficiency could be involved in the maintenance of a threshold level of free cellular phosphate to preserve respiratory metabolism. We studied the metabolic response of potato cell cultures growing in Pi sufficient (2.5 mM, +Pi) or deficient (125 µM, -Pi) conditions. Under Pi deficiency, cellular growth was severely affected, however -Pi cells were able to maintain a low but steady level of free Pi. We surveyed the activities of 33 primary metabolic enzymes during the course of a 12 days Pi deficiency period. Our results show that many of these enzymes had higher specific activity in -Pi cells. Among these, we found typical markers of Pi deficiency such as phosphoenolpyruvate phosphatase and phosphoenolpyruvate carboxylase as well as enzymes involved in the biosynthesis of organic acids. Intriguingly, several ATP-consuming enzymes such as hexokinase (HK) and phosphofructokinase also displayed increased activity in -Pi condition. For HK, this was associated with an increase in the steady state of a specific HK polypeptide. Quantification of glycolytic intermediates showed a pronounced decrease in phosphate esters under Pi deficiency. Adenylate levels also decreased in -Pi cells, but the Adenylate Energy Charge was not affected by the treatment. To investigate the significance of HK induction under low Pi, [U-¹⁴C]-glucose tracer studies were conducted. We found in vivo evidence of futile cycling between pools of hexose phosphates and free sugars under Pi deficiency. Our study suggests that the futile cycling between hexose phosphates and free sugars which is active under +Pi conditions is sustained under Pi deficiency. The possibility that this process represents a metabolic adaptation to Pi deficiency is discussed with respect to Pi homeostasis in Pi-deficient conditions.

The Less the Better: How Suppressed Base Addition Boosts Production of Monoclonal Antibodies With Chinese Hamster Ovary Cells

Biopharmaceutical production processes strive for the optimization of economic efficiency. Among others, the maximization of volumetric productivity is a key criterion. Typical parameters such as partial pressure of CO2 (pCO2) and pH are known to influence the performance although reasons are not yet fully elucidated. In this study the effects of pCO2 and pH shifts on the phenotypic performance were linked to metabolic and energetic changes. Short peak performance of qmAb (23 pg/cell/day) was achieved by early pCO2 shifts up to 200 mbar but followed by declining intracellular ATP levels to 2.5 fmol/cell and 80% increase of qLac. On the contrary, steadily rising qmAb could be installed by slight pH down-shifts ensuring constant cell specific ATP production (qATP) of 27 pmol/cell/day and high intracellular ATP levels of about 4 fmol/cell. As a result, maximum productivity was achieved combining highest qmAb (20 pg/cell/day) with maximum cell density and no lactate formation. Our results indicate that the energy availability in form of intracellular ATP is crucial for maintaining antibody synthesis and reacts sensitive to pCO2 and pH-process parameters typically responsible for inhomogeneities after scaling up.

Effect of metabolic uncoupler, 2,4‑dinitrophenol (DNP) on sludge properties and fouling potential in ultrafiltration membrane process

Energy uncoupling technology was applied to the membrane process to control the problem of bio-fouling. Different dosages of uncoupler (2,4‑dinitrophenol, DNP) were added to the activated sludge, and a short-term ultrafiltration test was systematically investigated for analyzing membrane fouling potential and underlying mechanisms. Ultrafiltration membrane was used and made of polyether-sulfone with a molecular weight cut off (MWCO) of 150 kDa. Results indicated that low DNP concentration (15-30 mg/g VSS) aggravated membrane fouling because more soluble microbial products were released and then rejected by the membrane, which significantly increased cake layer resistance compared with the control. Conversely, a high dosage of DNP (45 mg/g VSS) retarded membrane fouling owing to the high inhibition of extracellular polymeric substances (proteins and polysaccharides) of the sludge, which effectively prevented the formation of cake layer on the membrane surface. Furthermore, analyses of fouling model revealed that a high dosage of DNP delayed the fouling model from pore blocking transition to cake filtration, whereas this transition process was accelerated in the low dosage scenario.

Do more mechanistic models increase accuracy of prediction of metabolisable protein supply in ruminants?

Ruminal microbes partially degrade dietary protein and synthesise microbial protein, which, along with undegraded true protein, contributes to metabolisable protein for the animal. Rumen models have been developed over the past several decades in an effort to better predict metabolisable protein supply for ration formulation for ruminants. These models have both empirical and mechanistic components. Separation of dietary protein into fractions that include non-protein nitrogen, true protein and unavailable protein has been a fundamental element of these models. Ruminal degradation of one or more true protein fractions is then estimated on the basis of the kinetics of digestion and passage. Some models use the same method to predict substrate supply for microbial protein production. Although mechanistic models have been extensively used in diet-formulation programs worldwide, their ability to improve accuracy of prediction of metabolisable protein over simpler empirical models is questionable. This article will address the potential of mechanistic models to better predict metabolisable protein supply in ruminants as well as their limitations.