In search of a thermodynamic description of biomass yields for the chemotrophic growth of microorganisms

Novel isolates of hydrogen-oxidizing chemolithoautotrophic Sulfurospirillum provide insight to the functions and adaptation mechanisms of Campylobacteria in shallow-water hydrothermal vents

Enhancing the availability of representative isolates from hydrothermal vents (HTVs) is imperative for comprehending the microbial processes that propel the vent ecosystem. In recent years, Campylobacteria have emerged as the predominant and ubiquitous taxon across both shallow and deep-sea vent systems. Nevertheless, only a few isolates have been cultured, primarily originating from deep-sea HTVs. Presently, no cultivable isolates of Campylobacteria are accessible in shallow water vent systems (<200 m), which exhibit markedly distinct environmental conditions from their deep-sea counterparts. In this study, we enriched a novel isolate (genus Sulfurospirillum, Campylobacteria) from shallow-water HTVs of Kueishan Island. Genomic and physiological analysis revealed that this novel Campylobacteria species grows on a variety of substrate and carbon/energy sources. The pan-genome and phenotypic comparisons with 12 previously isolated Sulfurospirillum species from different environments supported the identification of functional features in Sulfurospirillum genomes crucial for adaptation to vent environments, such as sulfur oxidation, carbon fixation, biofilm formation, and benzoate/toluene degradation, as well as diverse genes related with signal transportation. To conclude, the metabolic characteristics of this novel Campylobacteria augment our understanding of Campylobacteria spanning from deep-sea to shallow-water vent systems.IMPORTANCECampylobacteria emerge as the dominant and ubiquitous taxa within vent systems, playing important roles in the vent ecosystems. However, isolated representatives of Campylobacteria have been mainly from the deep-sea hydrothermal fields, leaving a significant knowledge gap regarding the functions, activities, and adaptation strategies of the vent microorganisms in shallow-water hydrothermal vents (HTVs). This study bridges this gap by providing insights into the phenomics and genomic diversity of genus Sulfurospirillum (order Campylobacterales, class Campylobacteria) based on data derived from a novel isolate obtained from shallow-water HTVs. Our mesophilic isolate of Sulfurospirillum not only augments the genus diversity of Campylobacteria pure cultures derived from vent systems but also serves as the inaugural reference isolate for Campylobacteria in shallow-water environments.

Arcobacteraceae are ubiquitous mixotrophic bacteria playing important roles in carbon, nitrogen, and sulfur cycling in global oceans

Mixotrophy is an important trophic strategy for bacterial survival in the ocean. However, the global relevance and identity of the major mixotrophic taxa remain largely elusive. Here, we combined phylogenetic, metagenomic, and metatranscriptomic analyses to characterize ubiquitous Arcobacteraceae based on our deep-sea in situ incubations and the global data. The phylogenomic tree of Arcobacteraceae is divided into three large clades, among which members of clades A and B are almost all from terrestrial environments, while those of clade C are widely distributed in various marine habitats in addition to some terrestrial origins. All clades harbor genes putatively involved in chitin degradation, sulfide oxidation, hydrogen oxidation, thiosulfate oxidation, denitrification, dissimilatory nitrate reduction to ammonium, microaerophilic respiration, and metal (iron/manganese) reduction. Additionally, in clade C, more unique pathways were retrieved, including thiosulfate disproportionation, ethanol fermentation, methane oxidation, fatty acid oxidation, cobalamin synthesis, and dissimilatory reductions of sulfate, perchlorate, and arsenate. Within this clade, two mixotrophic Candidatus genera represented by UBA6211 and CAIJNA01 harbor genes putatively involved in the reverse tricarboxylic acid pathway for carbon fixation. Moreover, the metatranscriptomic data in deep-sea in situ incubations indicated that the latter genus is a mixotroph that conducts carbon fixation by coupling sulfur oxidation and denitrification and metabolizing organic matter. Furthermore, global metatranscriptomic data confirmed the ubiquitous distribution and global relevance of Arcobacteraceae in the expression of those corresponding genes across all oceanic regions and depths. Overall, these results highlight the contribution of previously unrecognized Arcobacteraceae to carbon, nitrogen, and sulfur cycling in global oceans.IMPORTANCEMarine microorganisms exert a profound influence on global carbon cycling and ecological relationships. Mixotrophy, characterized by the simultaneous utilization of both autotrophic and heterotrophic nutrition, has a significant impact on the global carbon cycling. This report characterizes a group of uncultivated bacteria Arcobacteraceae that thrived on the "hot time" of bulky particulate organic matter and exhibited mixotrophic strategy during the in situ organic mineralization. Compared with clades A and B, more unique metabolic pathways were retrieved in clade C, including the reverse tricarboxylic acid pathway for carbon fixation, thiosulfate disproportionation, methane oxidation, and fatty acid oxidation. Global metatranscriptomic data from the Tara Oceans expeditions confirmed the ubiquitous distribution and extensive transcriptional activity of Arcobacteraceae with the expression of genes putatively involved in carbon fixation, methane oxidation, multiple sulfur compound oxidation, and denitrification across all oceanic regions and depths.

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.

Thermodynamics of Growth in Open Chemical Reaction Networks

We identify the thermodynamic conditions necessary to observe indefinite growth in homogeneous open chemical reaction networks (CRNs) satisfying mass action kinetics. We also characterize the thermodynamic efficiency of growth by considering the fraction of the chemical work supplied from the surroundings that is converted into CRN free energy. We find that indefinite growth cannot arise in CRNs chemostatted by fixing the concentration of some species at constant values, or in continuous-flow stirred tank reactors. Indefinite growth requires a constant net influx from the surroundings of at least one species. In this case, unimolecular CRNs always generate equilibrium linear growth, i.e., a continuous linear accumulation of species with equilibrium concentrations and efficiency one. Multimolecular CRNs are necessary to generate nonequilibrium growth, i.e., the continuous accumulation of species with nonequilibrium concentrations. Pseudounimolecular CRNs-a subclass of multimolecular CRNs-always generate asymptotic linear growth with zero efficiency. Our findings demonstrate the importance of the CRN topology and the chemostatting procedure in determining the dynamics and thermodynamics of growth.

Characterizing the conditions for indefinite growth in open chemical reaction networks

The thermodynamic and dynamical conditions necessary to observe indefinite growth in homogeneous open chemical reaction networks (CRNs) satisfying mass action kinetics are presented in Srinivas et al. [Phys. Rev. Lett. 132, 268001 (2024)10.1103/PhysRevLett.132.268001]. Unimolecular CRNs can accumulate only equilibrium concentrations of species while multimolecular CRNs are needed to produce indefinite growth with nonequilibrium concentrations. Within multimolecular CRNs, pseudo-unimolecular CRNs produce nonequilibrium concentrations with zero efficiencies. Nonequilibrium growth with efficiencies greater than zero requires dynamically nonlinear CRNs. In this paper, we provide a detailed analysis supporting these results. Mathematical proofs are provided for growth in unimolecular and pseudo-unimolecular CRNs. For multimolecular CRNs, four models displaying very distinctive topological properties are extensively studied, both numerically and partly analytically.

Animal bioenergetics: Thermodynamic and kinetic analysis of growth and metabolism of Anguilla anguilla

Bioenergetics and biothermodynamics are valuable tools in research on growth and metabolic processes of a wide range of organisms, including viruses, bacteria, fungi, algae and plants, as is shown by the many publications on this topic in the literature. These studies provide insight into growth and metabolism of individual species, as well as interactions between species, like the virus-host interaction (infection) and virus-virus interaction (competition). However, this approach has not yet been applied to animal species. The universality of biothermodynamics and bioenergetics provides a good motive to apply them in analysis of animals. In this research, we made a bioenergetic, biothermodynamic and kinetic characterization for the first time for an animal species - Anguilla anguilla L. (European eel). We made a comparative analysis on yellow (young adult) and silver (mature adult) phases. Metabolic processes were modeled as chemical reactions with characteristic thermodynamic properties: enthalpy, entropy and Gibbs energy. Moreover, Gibbs energy explained growth rates, through phenomenological equations. This analysis of animal metabolism and growth explained metabolic properties of yellow and silver A. anguilla, including the bioenergetic aspect of life history. Moreover, we compared thermodynamic properties of A. anguilla with those of its main macromolecular components and other organisms. The thermodynamic properties were explained by the structural properties of organisms. This research extends the bioenergetic and biothermodynamic approaches to zoology, which should allow analysis of the energetic aspect of animal metabolic processes, interactions with their environment and interactions with other organisms. Furthermore, it connects the macroscopic perspective of zoology with the microscopic perspectives of biochemistry, bioenergetics and biothermodynamics. This will provide a basis for development of mechanistic models of animal growth and metabolism.

Microbial Pathway Thermodynamics: Stoichiometric Models Unveil Anabolic and Catabolic Processes

The biotechnological exploitation of microorganisms enables the use of metabolism for the production of economically valuable substances, such as drugs or food. It is, thus, unsurprising that the investigation of microbial metabolism and its regulation has been an active research field for many decades. As a result, several theories and techniques were developed that allow for the prediction of metabolic fluxes and yields as biotechnologically relevant output parameters. One important approach is to derive macrochemical equations that describe the overall metabolic conversion of an organism and basically treat microbial metabolism as a black box. The opposite approach is to include all known metabolic reactions of an organism to assemble a genome-scale metabolic model. Interestingly, both approaches are rather successful at characterizing and predicting the expected product yield. Over the years, macrochemical equations especially have been extensively characterized in terms of their thermodynamic properties. However, a common challenge when characterizing microbial metabolism by a single equation is to split this equation into two, describing the two modes of metabolism, anabolism and catabolism. Here, we present strategies to systematically identify separate equations for anabolism and catabolism. Based on metabolic models, we systematically identify all theoretically possible catabolic routes and determine their thermodynamic efficiency. We then show how anabolic routes can be derived, and we use these to approximate biomass yield. Finally, we challenge the view of metabolism as a linear energy converter, in which the free energy gradient of catabolism drives the anabolic reactions.

Respiration-driven methanotrophic growth of diverse marine methanogens

Anaerobic marine environments are the third largest producer of the greenhouse gas methane. The release to the atmosphere is prevented by anaerobic 'methanotrophic archaea (ANME) dependent on a symbiotic association with sulfate-reducing bacteria or direct reduction of metal oxides. Metagenomic analyses of ANME are consistent with a reverse methanogenesis pathway, although no wild-type isolates have been available for validation and biochemical investigation. Herein is reported the characterization of methanotrophic growth for the diverse marine methanogens Methanosarcina acetivorans C2A and Methanococcoides orientis sp. nov. Growth was dependent on reduction of either ferrihydrite or humic acids revealing a respiratory mode of energy conservation. Acetate and/or formate were end products. Reversal of the well-characterized methanogenic pathways is remarkably like the consensus pathways for uncultured ANME based on extensive metagenomic analyses.

Functional convergence in slow-growing microbial communities arises from thermodynamic constraints

The dynamics of microbial communities is complex, determined by competition for metabolic substrates and cross-feeding of byproducts. Species in the community grow by harvesting energy from chemical reactions that transform substrates to products. In many anoxic environments, these reactions are close to thermodynamic equilibrium and growth is slow. To understand the community structure in these energy-limited environments, we developed a microbial community consumer-resource model incorporating energetic and thermodynamic constraints on an interconnected metabolic network. The central element of the model is product inhibition, meaning that microbial growth may be limited not only by depletion of metabolic substrates but also by accumulation of products. We demonstrate that these additional constraints on microbial growth cause a convergence in the structure and function of the community metabolic network-independent of species composition and biochemical details-providing a possible explanation for convergence of community function despite taxonomic variation observed in many natural and industrial environments. Furthermore, we discovered that the structure of community metabolic network is governed by the thermodynamic principle of maximum free energy dissipation. Our results predict the decrease of functional convergence in faster growing communities, which we validate by analyzing experimental data from anaerobic digesters. Overall, the work demonstrates how universal thermodynamic principles may constrain community metabolism and explain observed functional convergence in microbial communities.

Comparing theoretical and practical biomass yields calls for revisiting thermodynamic growth models for electroactive microorganisms

Research on electroactive microorganisms (EAM) often focuses either on their physiology and the underlying mechanisms of extracellular electron transfer or on their application in microbial electrochemical technologies (MET). Thermodynamic understanding of energy conversions related to growth and activity of EAM has received only a little attention. In this study, we aimed to prove the hypothesized restricted energy harvest of EAM by determining biomass yields by monitoring growth of acetate-fed biofilms presumably enriched in Geobacter, using optical coherence tomography, at three anode potentials and four acetate concentrations. Experiments were concurrently simulated using a refined thermodynamic model for EAM. Neither clear correlations were observed between biomass yield and anode potential nor acetate concentration, albeit the statistical significances are limited, mainly due to the observed experimental variances. The experimental biomass yield based on acetate consumption (YX/ac = 37 ± 9 mgCODbiomass gCODac-1) was higher than estimated by modeling, indicating limitations of existing growth models to predict yields of EAM. In contrast, the modeled biomass yield based on catabolic energy harvest was higher than the biomass yield from experimental data (YX/cat = 25.9 ± 6.8 mgCODbiomass kJ-1), supporting restricted energy harvest of EAM and indicating a role of not considered energy sinks. This calls for an adjusted growth model for EAM, including, e.g., the microbial electrochemical Peltier heat to improve the understanding and modeling of their energy metabolism. Furthermore, the reported biomass yields are important parameters to design strategies for influencing the interactions between EAM and other microorganisms and allowing more realistic feasibility assessments of MET.

Bioenergetics of aerobic and anaerobic growth of Shewanella putrefaciens CN32

Shewanella putrefaciens is a model dissimilatory iron-reducing bacterium that can use Fe(III) and O2 as terminal electron acceptors. Consequently, it has the ability to influence both aerobic and anaerobic groundwater systems, making it an ideal microorganism for improving our understanding of facultative anaerobes with iron-based metabolism. In this work, we examine the bioenergetics of O2 and Fe(III) reduction coupled to lactate oxidation in Shewanella putrefaciens CN32. Bioenergetics were measured directly via isothermal calorimetry and by changes to the chemically defined growth medium. We performed these measurements from 25 to 36°C. Modeling metabolism with macrochemical equations allowed us to define a theoretical growth stoichiometry for the catabolic reaction of 1.00 O2:lactate and 1.33 Fe(III):lactate that was consistent with the observed ratios of O2:lactate (1.20 ± 0.23) and Fe(III):lactate (1.46 ± 0.15) consumption. Aerobic growth showed minimal variation with temperature and minimal variation in thermodynamic potentials of incubation. Fe(III)-based growth showed a strong temperature dependence. The Gibbs energy and enthalpy of incubation was minimized at ≥30°C. Energy partitioning modeling of Fe(III)-based calorimetric incubation data predicted that energy consumption for non-growth associate maintenance increases substantially above 30°C. This prediction agrees with the data at 33 and 35°C. These results suggest that the effects of temperature on Shewanella putrefaciens CN32 are metabolism dependent. Gibbs energy of incubation above 30°C was 3-5 times more exergonic with Fe(III)-based growth than with aerobic growth. We compared data gathered in this study with predictions of microbial growth based on standard-state conditions and based on the thermodynamic efficiency of microbial growth. Quantifying the growth requirements of Shewanella putrefaciens CN32 has advanced our understanding of the thermodynamic constraints of this dissimilatory iron-reducing bacterium.

Inferring Microbial Biomass Yield and Cell Weight Using Probabilistic Macrochemical Modeling

Growth rates and biomass yields are key descriptors used in microbiology studies to understand how microbial species respond to changes in the environment. Of these, biomass yield estimates are typically obtained using cell counts and measurements of the feed substrate. These quantities are perturbed with measurement noise however. Perhaps most crucially, estimating biomass from cell counts, as needed to assess yields, relies on an assumed cell weight. Noise and discrepancies on these assumptions can lead to significant changes in conclusions regarding the microbes' response. This article proposes a methodology to address these challenges using probabilistic macrochemical models of microbial growth. It is shown that a model can be developed to fully use the experimental data, relax assumptions and greatly improve robustness to a priori estimates of the cell weight, and provides uncertainty estimates of key parameters. This methodology is demonstrated in the context of a specific case study and the estimation characteristics are validated in several scenarios using synthetically generated microbial growth data.

Greater functional diversity and redundancy of coral endolithic microbiomes align with lower coral bleaching susceptibility

The skeleton of reef-building coral harbors diverse microbial communities that could compensate for metabolic deficiencies caused by the loss of algal endosymbionts, i.e., coral bleaching. However, it is unknown to what extent endolith taxonomic diversity and functional potential might contribute to thermal resilience. Here we exposed Goniastrea edwardsi and Porites lutea, two common reef-building corals from the central Red Sea to a 17-day long heat stress. Using hyperspectral imaging, marker gene/metagenomic sequencing, and NanoSIMS, we characterized their endolithic microbiomes together with ¹⁵N and ¹³C assimilation of two skeletal compartments: the endolithic band directly below the coral tissue and the deep skeleton. The bleaching-resistant G. edwardsi was associated with endolithic microbiomes of greater functional diversity and redundancy that exhibited lower N and C assimilation than endoliths in the bleaching-sensitive P. lutea. We propose that the lower endolithic primary productivity in G. edwardsi can be attributed to the dominance of chemolithotrophs. Lower primary production within the skeleton may prevent unbalanced nutrient fluxes to coral tissues under heat stress, thereby preserving nutrient-limiting conditions characteristic of a stable coral-algal symbiosis. Our findings link coral endolithic microbiome structure and function to bleaching susceptibility, providing new avenues for understanding and eventually mitigating reef loss.

Modeling a propionate-oxidizing syntrophic coculture using thermodynamic principles

A coculture of Syntrophobacter fumaroxidans and Methanospirillum hungatei was modeled using four biokinetic models, which only differed by the functions used to describe the growth yields (dynamic or constant) and the hydrogen inhibition function (noncompetitive or based on thermodynamics). First, a batch experiment was used to train the model and analyze the fitted parameters. Two fitting procedures were followed by minimizing the error on different indicators. Second, a chemostat experiment was used as a test data set to assess the predictive power of the models. Overall, the four models were able to accurately fit the train data set following both fitting procedures. However, some parameters fitted with the ADM1-like model differed significantly from values reported in the literature and were dependent on the fitting procedure. When applied to the test data set it systematically resulted in positive Gibbs free energy changes values for propionate oxidation, in contradiction with the second law of thermodynamics. On the opposite, the parameters fitted with model including both a thermodynamic-based inhibition function and a dynamic computation of growth yields were more consistent with values reported in the literature and repeatable whatever the fitting procedure. The results highlight the potential of implementing thermodynamic-based functions in biokinetic models.

Microbial maintenance energy quantified and modeled with microcalorimetry

Refining the energetic costs of cellular maintenance is essential for predicting microbial growth and survival in the environment. Here, we evaluate a simple batch culture method to quantify energy partitioning between growth and maintenance using microcalorimetry and thermodynamic modeling. The constants derived from the batch culture system were comparable to those that have been reported from meta-analyses of data derived from chemostat studies. The model accurately predicted temperature-dependent biomass yield and the upper temperature limit of growth for Desulfovibrio alaskensis G20, suggesting the method may have broad application. An Arrhenius temperature dependence for the specific energy consumption rate, inferred from substrate consumption and heat evolution, was observed over the entire viable temperature range. By combining this relationship for specific energy consumption rates and observed specific growth rates, the model describes an increase in nongrowth associated maintenance at higher temperatures and the corresponding decrease in energy available for growth. This analytical and thermodynamic formulation suggests that simply monitoring heat evolution in batch culture could be a useful complement to the recognized limitations of estimating maintenance using extrapolation to zero growth in chemostats.

Interacting Bioenergetic and Stoichiometric Controls on Microbial Growth

Microorganisms function as open systems that exchange matter and energy with their surrounding environment. Even though mass (carbon and nutrients) and energy exchanges are tightly linked, there is a lack of integrated approaches that combine these fluxes and explore how they jointly impact microbial growth. Such links are essential to predicting how the growth rate of microorganisms varies, especially when the stoichiometry of carbon- (C) and nitrogen (N)-uptake is not balanced. Here, we present a theoretical framework to quantify the microbial growth rate for conditions of C-, N-, and energy-(co-) limitations. We use this framework to show how the C:N ratio and the degree of reduction of the organic matter (OM), which is also the electron donor, availability of electron acceptors (EAs), and the different sources of N together control the microbial growth rate under C, nutrient, and energy-limited conditions. We show that the growth rate peaks at intermediate values of the degree of reduction of OM under oxic and C-limited conditions, but not under N-limited conditions. Under oxic conditions and with N-poor OM, the growth rate is higher when the inorganic N (N_Inorg)-source is ammonium compared to nitrate due to the additional energetic cost involved in nitrate reduction. Under anoxic conditions, when nitrate is both EA and N_Inorg-source, the growth rates of denitrifiers and microbes performing the dissimilatory nitrate reduction to ammonia (DNRA) are determined by both OM degree of reduction and nitrate-availability. Consistent with the data, DNRA is predicted to foster growth under extreme nitrate-limitation and with a reduced OM, whereas denitrifiers are favored as nitrate becomes more available and in the presence of oxidized OM. Furthermore, the growth rate is reduced when catabolism is coupled to low energy yielding EAs (e.g., sulfate) because of the low carbon use efficiency (CUE). However, the low CUE also decreases the nutrient demand for growth, thereby reducing N-limitation. We conclude that bioenergetics provides a useful conceptual framework for explaining growth rates under different metabolisms and multiple resource-limitations.

Catabolic protein degradation in marine sediments confined to distinct archaea

Metagenomic analysis has facilitated prediction of a variety of carbon utilization potentials by uncultivated archaea including degradation of protein, which is a wide-spread carbon polymer in marine sediments. However, the activity of detrital catabolic protein degradation is mostly unknown for the vast majority of archaea. Here, we show actively executed protein catabolism in three archaeal phyla (uncultivated Thermoplasmata, SG8-5; Bathyarchaeota subgroup 15; Lokiarchaeota subgroup 2c) by RNA- and lipid-stable isotope probing in incubations with different marine sediments. However, highly abundant potential protein degraders Thermoprofundales (MBG-D) and Lokiarchaeota subgroup 3 were not incorporating ¹³C-label from protein during incubations. Nonetheless, we found that the pathway for protein utilization was present in metagenome associated genomes (MAGs) of active and inactive archaea. This finding was supported by screening extracellular peptidases in 180 archaeal MAGs, which appeared to be widespread but not correlated to organisms actively executing this process in our incubations. Thus, our results have important implications: (i) multiple low-abundant archaeal groups are actually catabolic protein degraders; (ii) the functional role of widespread extracellular peptidases is not an optimal tool to identify protein catabolism, and (iii) catabolic degradation of sedimentary protein is not a common feature of the abundant archaeal community in temperate and permanently cold marine sediments.

Developmental energetics: Energy expenditure, budgets and metabolism during animal embryogenesis

Developing embryos are metabolically active, open systems that constantly exchange matter and energy with their environment. They function out of thermodynamic equilibrium and continuously use metabolic pathways to obtain energy from maternal nutrients, in order to fulfill the energetic requirements of growth and development. While an increasing number of studies highlight the role of metabolism in different developmental contexts, the physicochemical basis of embryogenesis, or how cellular processes use energy and matter to act together and transform a zygote into an adult organism, remains unknown. As we obtain a better understanding of metabolism, and benefit from current technology development, it is a promising time to revisit the energetic cost of development and how energetic principles may govern embryogenesis. Here, we review recent advances in methodology to measure and infer energetic parameters in developing embryos. We highlight a potential common pattern in embryonic energy expenditure and metabolic strategy across animal embryogenesis, and discuss challenges and open questions in developmental energetics.

The significance of the biomass subfraction of high-MW organic carbon for the microbial growth and maintenance potential of disinfectant-free drinking water produced from surface water

Drinking water must be sufficiently biostable to avoid excessive microbial and invertebrate growth in disinfectant-free distribution systems. The production of biologically stable drinking water is challenging for conventional surface water treatment plants using reservoirs as feed water due to the presence of slowly biodegradable particulate and high-molecular weight biopolymeric organic carbon (high-MW OC) which increases the Microbial Growth Potential (MGP) in the feed water and produced drinking water. The study presented here provides new insights in the relationship between high-MW OC and MGP for a full-scale surface water treatment plant. Controlled-conditions addition series experiments showed that MGP increases linearly with the high-MW OC concentration with a seasonally variable ratio. Laboratory filtration indicated that MGP is mainly attributable to the high-MW OC subfraction of >  0.12 µm particle size coinciding with microbial biomass. Intensive field monitoring revealed clear seasonal patterns in the plant's feed water and treated water levels of high-MW OC, biomass and MGP. These parameters reach maximum levels in the periods of high water temperature with the notable exception of the treated water's high-MW OC concentration which exhibits an opposite seasonal pattern (reflecting seasonally variable removal in the treatment). Moreover, the field monitoring showed that MGP correlates well with the concentrations of biodegradable biopolymeric OC and with microbial biomass measured as ATP (adenosine triphosphate) and cell counts, but not with the total high-MW OC concentration in the treated water. Theoretical estimations showed that the OC quantities present in and consumed by the microbial biomass are in the same order of magnitude as slowly biodegradable biopolymers. From these results it is concluded that specifically the microbial biomass-associated and biodegradable biopolymeric OC subfraction of the totally present high-MW OC is important for MGP. Finally, the MGP-assay results and theoretical calculations showed for the high-MW OC matrix that the microbial biomass' OC consumption for maintenance is significant vis-á-vis that for growth, and that stable and high levels of biomass are sustained in the treated water which may adversely affect biological stability in the distribution network.

Hydrothermal plumes as hotspots for deep-ocean heterotrophic microbial biomass production

Carbon budgets of hydrothermal plumes result from the balance between carbon sinks through plume chemoautotrophic processes and carbon release via microbial respiration. However, the lack of comprehensive analysis of the metabolic processes and biomass production rates hinders an accurate estimate of their contribution to the deep ocean carbon cycle. Here, we use a biogeochemical model to estimate the autotrophic and heterotrophic production rates of microbial communities in hydrothermal plumes and validate it with in situ data. We show how substrate limitation might prevent net chemolithoautotrophic production in hydrothermal plumes. Elevated prokaryotic heterotrophic production rates (up to 0.9 gCm^-2y^-1) compared to the surrounding seawater could lead to 0.05 GtCy^-1 of C-biomass produced through chemoorganotrophy within hydrothermal plumes, similar to the Particulate Organic Carbon (POC) export fluxes reported in the deep ocean. We conclude that hydrothermal plumes must be accounted for as significant deep sources of POC in ocean carbon budgets.

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.

Modeling of interspecies electron transfer in anaerobic microbial communities

Interspecies electron transfer (IET) is a key phenomenon in anaerobic ecosystems, which is traditionally modeled as hydrogen transfer. Recently discovered alternative mediated IET (MIET) or direct IET (DIET) offer exciting alternative mechanisms of microbial partnerships that could lead to new strategies for the improvement of biotechnologies. Here, we analyze mathematical modeling of DIET and MIET in anaerobic ecosystems. Bioenergetics approaches already enable the evaluation of different energy sharing scenarios between microorganisms and give interesting clues on redox mediators and on possible ways of driving microbial communities relying on IET. The modeling of DIET kinetics however is currently only in its infancy. Recent concepts introduced for the modeling of electroactive biofilms should be further exploited. Recent modeling examples confirms the potential of DIET to increase the IET rates compared to H₂-MIET, but also point out the need for additional characterizations of biological components supporting IET to improve predictions.

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.

Assessing the potential of purple phototrophic microbial community for nitrogen recycling from ammonia-rich medium and anaerobic digestate

Purple phototrophic bacteria (PPB) community, enriched from municipal wastewater, was characterized to assess their growth, tolerance, composition and potential for resource recovery from NH₄⁺-rich medium. Batch experiments were conducted in tissue culture flasks and glass bottles under anaerobic conditions with infra-red lights. PPBs showed remarkable tolerance to high concentrations of NH₄⁺-N and acetate. Below 1.5 g/L, growth was unaffected by NH₄⁺-N with optical density at 590 nm (OD₅₉₀) reaching 2.6-2.9, while they could tolerate 4.5 g/L NH₄⁺-N. Similarly, PPB growth was unaffected at acetate concentrations below 4 g/L and they could tolerate >20 g/L acetate. Taxonomic characterization showed that the community comprised of 37-52% PPBs (with 15-20% proteins) under different conditions, with Rhodobacter sp. over Rhodopseudomonas sp. dominating at higher NH₄⁺-N concentrations. PPBs showed growth and removal rates in anaerobic digestate and accumulated 26% proteins. These results indicated the potential of PPBs in resource recovery from NH₄⁺-rich wastewater.

Standard Thermodynamic Properties, Biosynthesis Rates, and the Driving Force of Growth of Five Agricultural Plants

Elemental composition of Gossypium hirsutum L. (cotton), Oryza sativa L. (Asian rice), Phaseolus vulgaris L. (common bean), Saccharum spp. L. (sugarcane), and Zea mays L. (corn) was used to calculate their empirical formulas (unit carbon formulas) and growth stoichiometry. The empirical formulas were used to find standard enthalpy of formation, standard molar entropy, standard Gibbs energy of formation, and standard molar heat capacity. A comparison was made between thermodynamic properties of live matter of the analyzed plants and other unicellular and multicellular organisms. Moreover, the growth process was analyzed through standard enthalpy, entropy, and Gibbs energy of biosynthesis. The average standard Gibbs energy of biosynthesis was found to be +463.0 kJ/C-mol. Thus, photosynthesis provides energy and carbon for plant growth. The average intercepted photosynthetic energy was found to be 15.5 MJ/C-mol for the analyzed plants. However, due to inefficiency, a great fraction of the intercepted photosynthetic energy cannot be used by plants. The average usable photosynthetic energy was found to be -2.3 MJ/C-mol. The average thermodynamic driving force for growth is -1.9 MJ/C-mol. Driving forces of growth of C3 and C4 plants were compared. It was found that C4 plants have a greater driving force of growth than C3 plants, which reflects the greater efficiency of C4 photosynthesis. The relationship between the driving force and growth rates was analyzed by determining phenomenological L coefficients. The determined phenomenological coefficients span two orders of magnitude, depending on plant species and environmental conditions. The L coefficient of P. vulgaris was found to be lower than that of other plants, due to additional energy requirements of nitrogen fixation.

Bioprocess intensification: Cases that (don't) work

Development of affordable and low carbon biobased manufacturing depends critically on strategies that reduce cost and emission profiles. This paper indicates that efforts around the reduction of capital costs by intensification of process equipment need to be carefully weighed against the inherently fast increasing financial and climate costs of driving forces used for the intensification. The fundamental relation between capital expenditures (CAPEX) and operational expenditures (OPEX) of intensified and non-intensified biobased processes and their financial and climatic impacts are emphasized and provisionally explored for a few industrial processes. General learnings flag the importance in particular of OPEX minimisation for sustainable bio-economic development.

A bioenergetic model to predict habitability, biomass and biosignatures in astrobiology and extreme conditions

In order to grow, reproduce and evolve life requires a supply of energy and nutrients. Astrobiology has the challenge of studying life on Earth in environments which are poorly characterized or extreme, usually both, and predicting the habitability of extraterrestrial environments. We have developed a general astrobiological model for assessing the energetic and nutrient availability of poorly characterized environments to predict their potential biological productivity. NutMEG (nutrients, maintenance, energy and growth) can be used to estimate how much biomass an environment could host, and how that life might affect the local chemistry. It requires only an overall catabolic reaction and some knowledge of the local environment to begin making estimations, with many more customizable parameters, such as microbial adaptation. In this study, the model was configured to replicate laboratory data on the growth of methanogens. It was used to predict the effect of temperature and energy/nutrient limitation on their microbial growth rates, total biomass levels, and total biosignature production in laboratory-like conditions to explore how it could be applied to astrobiological problems. As temperature rises from 280 to 330 K, NutMEG predicts exponential drops in final biomass ([Formula: see text]) and total methane production ([Formula: see text]) despite an increase in peak growth rates ([Formula: see text]) for a typical methanogen in ideal conditions. This is caused by the increasing cost of microbial maintenance diverting energy away from growth processes. Restricting energy and nutrients exacerbates this trend. With minimal assumptions NutMEG can reliably replicate microbial growth behaviour, but better understanding of the synthesis and maintenance costs life must overcome in different extremes is required to improve its results further. NutMEG can help us assess the theoretical habitability of extraterrestrial environments and predict potential biomass and biosignature production, for example on exoplanets using minimum input parameters to guide observations.

Comment on "A compilation and bioenergetic evaluation of syntrophic microbial growth yields in anaerobic digestion" by Patón, M. and Rodríguez, J. [Water Research 162 (2019), 516-517]

Recent efforts have focused on providing a systematic analysis of syntrophic microbial growth yields. These biokinetic parameters are key to developing an accurate mathematical description of the anaerobic digestion process. The agreement between experimentally determined growth yields and those obtained from bioenergetic estimations is therefore of great interest. Considering five important syntrophic groups, including acetoclastic and hydrogenotrophic methanogens, as well as propionate, butyrate and lactate oxidizers, previous findings suggest that measured and estimated growth yields were consistent only for acetoclastic methanogens. A re-analysis revealed that data are also consistent for lactate oxidizers and hydrogenotrophic methanogens, whereas the limited data available for propionate and butyrate oxidizers are unsupportive of firm conclusions. These results highlight pertinent challenges in the analysis of microbial syntrophy and encourage more accurate measurements of syntrophic microbial growth yields in the future.

Thermodynamic Limits and Optimality of Microbial Growth

Understanding microbial growth with the use of mathematical models has a long history that dates back to the pioneering work of Jacques Monod in the 1940s. Monod’s famous growth law expressed microbial growth rate as a simple function of the limiting nutrient concentration. However, to explain growth laws from underlying principles is extremely challenging. In the second half of the 20th century, numerous experimental approaches aimed at precisely measuring heat production during microbial growth to determine the entropy balance in a growing cell and to quantify the exported entropy. This has led to the development of thermodynamic theories of microbial growth, which have generated fundamental understanding and identified the principal limitations of the growth process. Although these approaches ignored metabolic details and instead considered microbial metabolism as a black box, modern theories heavily rely on genomic resources to describe and model metabolism in great detail to explain microbial growth. Interestingly, however, thermodynamic constraints are often included in modern modeling approaches only in a rather superficial fashion, and it appears that recent modeling approaches and classical theories are rather disconnected fields. To stimulate a closer interaction between these fields, we here review various theoretical approaches that aim at describing microbial growth based on thermodynamics and outline the resulting thermodynamic limits and optimality principles. We start with classical black box models of cellular growth, and continue with recent metabolic modeling approaches that include thermodynamics, before we place these models in the context of fundamental considerations based on non-equilibrium statistical mechanics. We conclude by identifying conceptual overlaps between the fields and suggest how the various types of theories and models can be integrated. We outline how concepts from one approach may help to inform or constrain another, and we demonstrate how genome-scale models can be used to infer key black box parameters, such as the energy of formation or the degree of reduction of biomass. Such integration will allow understanding to what extent microbes can be viewed as thermodynamic machines, and how close they operate to theoretical optima.

Hydrogenotrophic methanogens of the mammalian gut: Functionally similar, thermodynamically different-A modelling approach

Methanogenic archaea occupy a functionally important niche in the gut microbial ecosystem of mammals. Our purpose was to quantitatively characterize the dynamics of methanogenesis by integrating microbiology, thermodynamics and mathematical modelling. For that, in vitro growth experiments were performed with pure cultures of key methanogens from the human and ruminant gut, namely Methanobrevibacter smithii, Methanobrevibacter ruminantium and Methanobacterium formicium. Microcalorimetric experiments were performed to quantify the methanogenesis heat flux. We constructed an energetic-based mathematical model of methanogenesis. Our model captured efficiently the dynamics of methanogenesis with average concordance correlation coefficients of 0.95 for CO₂, 0.98 for H₂ and 0.97 for CH₄. Together, experimental data and model enabled us to quantify metabolism kinetics and energetic patterns that were specific and distinct for each species despite their use of analogous methane-producing pathways. Then, we tested in silico the interactions between these methanogens under an in vivo simulation scenario using a theoretical modelling exercise. In silico simulations suggest that the classical competitive exclusion principle is inapplicable to gut ecosystems and that kinetic information alone cannot explain gut ecological aspects such as microbial coexistence. We suggest that ecological models of gut ecosystems require the integration of microbial kinetics with nonlinear behaviours related to spatial and temporal variations taking place in mammalian guts. Our work provides novel information on the thermodynamics and dynamics of methanogens. This understanding will be useful to construct new gut models with enhanced prediction capabilities and could have practical applications for promoting gut health in mammals and mitigating ruminant methane emissions.

Amino Acid and Sugar Catabolism in the Marine Bacterium Phaeobacter inhibens DSM 17395 from an Energetic Viewpoint

Growth energetics and metabolic efficiency contribute to the lifestyle and habitat imprint of microorganisms. Roseobacters constitute one of the most abundant and successful marine bacterioplankton groups. Here, we reflect on the energetics and metabolic efficiency of Phaeobacter inhibens DSM 17395, a versatile heterotrophic roseobacter. Fourteen different substrates (five sugars and nine amino acids) and their degradation pathways were assessed for energetic efficiencies based on catabolic ATP yields, calculated from net formed ATP and reducing equivalents. The latter were converted into ATP by employing the most divergent coupling ratios (i.e., ions per ATP) currently known for F₁F_o ATP synthases in heterotrophic bacteria. The catabolic ATP yields of the pathways studied in P. inhibens differed ∼3-fold. The actual free energy costs for ATP synthesis were estimated at 81.6 kJ per mol ATP (3.3 ions per ATP) or 104.2 kJ per mol ATP (4.3 ions per ATP), yielding an average thermodynamic efficiency of ∼37.7% or ∼29.5%, respectively. Growth performance (rates, yields) and carbon assimilation efficiency were determined for P. inhibens growing in process-controlled bioreactors with 10 different single substrates (Glc, Man, N-acetylglucosamine [Nag], Phe, Trp, His, Lys, Thr, Val, or Leu) and with 2 defined substrate mixtures. The efficiencies of carbon assimilation into biomass ranged from ∼28% to 61%, with His/Trp and Thr/Leu yielding the lowest and highest levels. These efficiencies correlated with catabolic and ATP yields only to some extent. Substrate-specific metabolic demands and/or functions, as well as the compositions of the substrate mixtures, apparently affected the energetic costs of growth. These include energetic burdens associated with, e.g., slow growth, stress, and/or the production of tropodithietic acid.IMPORTANCE Heterotrophic members of the bacterioplankton serve the marine ecosystem by transforming organic matter, an activity that is governed by the bacterial growth efficiencies (BGEs) obtained under given environmental conditions. In marine ecology, the concept of BGE refers to the carbon assimilation efficiency within natural communities. The marine bacterium studied here, Phaeobacter inhibens DSM 17395, is a copiotrophic representative of the globally abundant Roseobacter group, and the 15 catabolic pathways investigated are widespread among these marine heterotrophs. Combining pathway-specific catabolic ATP yields with in-depth quantitative physiological data could (i) provide a new baseline for the study of growth energetics and efficiency in further Roseobacter group members and other copiotrophic marine bacteria in productive coastal ecosystems and (ii) contribute to a better understanding of the factors controlling BGE (including the additional energetic burden arising from widespread secondary-metabolite formation) based on laboratory studies with pure cultures.

INDISIM-Denitrification, an individual-based model for study the denitrification process

Denitrification is one of the key processes of the global nitrogen (N) cycle driven by bacteria. It has been widely known for more than 100 years as a process by which the biogeochemical N-cycle is balanced. To study this process, we develop an individual-based model called INDISIM-Denitrification. The model embeds a thermodynamic model for bacterial yield prediction inside the individual-based model INDISIM and is designed to simulate in aerobic and anaerobic conditions the cell growth kinetics of denitrifying bacteria. INDISIM-Denitrification simulates a bioreactor that contains a culture medium with succinate as a carbon source, ammonium as nitrogen source and various electron acceptors. To implement INDISIM-Denitrification, the individual-based model INDISIM was used to give sub-models for nutrient uptake, stirring and reproduction cycle. Using a thermodynamic approach, the denitrification pathway, cellular maintenance and individual mass degradation were modeled using microbial metabolic reactions. These equations are the basis of the sub-models for metabolic maintenance, individual mass synthesis and reducing internal cytotoxic products. The model was implemented in the open-access platform NetLogo. INDISIM-Denitrification is validated using a set of experimental data of two denitrifying bacteria in two different experimental conditions. This provides an interactive tool to study the denitrification process carried out by any denitrifying bacterium since INDISIM-Denitrification allows changes in the microbial empirical formula and in the energy-transfer-efficiency used to represent the metabolic pathways involved in the denitrification process. The simulator can be obtained from the authors on request.

Parameters Governing the Community Structure and Element Turnover in Kermadec Volcanic Ash and Hydrothermal Fluids as Monitored by Inorganic Electron Donor Consumption, Autotrophic CO2 Fixation and 16S Tags of the Transcriptome in Incubation Experiments

The microbial community composition and its functionality was assessed for hydrothermal fluids and volcanic ash sediments from Haungaroa and hydrothermal fluids from the Brothers volcano in the Kermadec island arc (New Zealand). The Haungaroa volcanic ash sediments were dominated by epsilonproteobacterial Sulfurovum sp. Ratios of electron donor consumption to CO₂ fixation from respective sediment incubations indicated that sulfide oxidation appeared to fuel autotrophic CO₂ fixation, coinciding with thermodynamic estimates predicting sulfide oxidation as the major energy source in the environment. Transcript analyses with the sulfide-supplemented sediment slurries demonstrated that Sulfurovum prevailed in the experiments as well. Hence, our sediment incubations appeared to simulate environmental conditions well suggesting that sulfide oxidation catalyzed by Sulfurovum members drive biomass synthesis in the volcanic ash sediments. For the Haungaroa fluids no inorganic electron donor and responsible microorganisms could be identified that clearly stimulated autotrophic CO₂ fixation. In the Brothers hydrothermal fluids Sulfurimonas (49%) and Hydrogenovibrio/Thiomicrospira (15%) species prevailed. Respective fluid incubations exhibited highest autotrophic CO₂ fixation if supplemented with iron(II) or hydrogen. Likewise catabolic energy calculations predicted primarily iron(II) but also hydrogen oxidation as major energy sources in the natural fluids. According to transcript analyses with material from the incubation experiments Thiomicrospira/Hydrogenovibrio species dominated, outcompeting Sulfurimonas. Given that experimental conditions likely only simulated environmental conditions that cause Thiomicrospira/Hydrogenovibrio but not Sulfurimonas to thrive, it remains unclear which environmental parameters determine Sulfurimonas’ dominance in the Brothers natural hydrothermal fluids.

The evolution and productivity of carbon fixation pathways in response to changes in oxygen concentration over geological time

The fixation of inorganic carbon species like CO₂ to more reduced organic forms is one of the most fundamental processes of life as we know it. Although several carbon fixation pathways are known to exist, on Earth today nearly all global carbon fixation is driven by the Calvin cycle in oxygenic photosynthetic plants, algae, and Cyanobacteria. At other times in Earth history, other organisms utilizing different carbon fixation pathways may have played relatively larger roles, with this balance shifting over geological time as the environmental context of life has changed and evolutionary innovations accumulated. Among the most dramatic changes that our planet and the biosphere have undergone are those surrounding the rise of O₂ in our atmosphere-first during the Great Oxygenation Event at ∼2.3 Ga, and perhaps again during Neoproterozoic or Paleozoic time. These oxygenation events likely represent major step changes in the tempo and mode of biological productivity as a result of the increased productivity of oxygenic photosynthesis and the introduction of O₂ into geochemical and biological systems, and likely involved shifts in the relative contribution of different carbon fixation pathways. Here, we review what is known from both the rock record and comparative biology about the evolution of carbon fixation pathways, their contributions to primary productivity through time, and their relationship to the evolving oxygenation state of the fluid Earth following the evolution and expansion of oxygenic photosynthesis.

A compilation and bioenergetic evaluation of syntrophic microbial growth yields in anaerobic digestion

A compilation and analysis of experimentally determined microbial growth yields for syntrophic volatile fatty acid (VFA), lactate oxidisers and methanogens in anaerobic digestion (AD) systems is presented. Only studies based on experimental determinations or sound model-to-data fitting that specifically address parameter identifiability, have been considered. The experimentally determined values are compared and discussed with estimations based on bioenergetic correlations. Only for acetoclastic methanogens the experimentally determined microbial yields appear in good consistency with bioenergetic estimations. For syntrophic microbial groups, the experimetal yield values reported appear much higher than those expected from the low amount of metabolic energy available. These large deviations imply either inaccuracy on the microbial biomass quantification methods or that the syntrophic interspecies electron transfer occurs under mechanisms, or hydrogen equivalent intermediate activities, much below those ever observed in methanogenic environments. In addition, the microbial growth yield values most widely adopted in AD model applications (those reported in the IWA Anaerobic Digestion Model No. 1 (ADM1)) are even higher than the experimental determinations from literature. It is therefore proposed that microbial growth yield values should be restricted by the maximum harvestable ATP calculated through a detailed bioenergetic pathway analysis. Model simulations with different parameter configurations for different yield sources (default ADM1, experimentally determined and bioenergetically estimated values) displayed low sensitivity of the simulations with respect to the yield values as long as the maximum specific microbial growth rate (μ_max) remain the same. This suggests that model calibrations could target the accuracy of μ_max maintaining the bioenergetic upper limit for microbial growth yields.

Integration of bioenergetics in the ADM1 and its impact on model predictions

In this work, the integration of dynamic bioenergetic calculations in the IWA Anaerobic Digestion Model No. 1 (ADM1) is presented. The impact of bioenergetics on kinetics was addressed via two different approaches: a thermodynamic-based inhibition function and variable microbial growth yields based on dynamic Gibbs free energy calculations. The dynamic bioenergetic calculations indicate that the standard ADM1 predicts positive reaction rates under thermodynamically unfeasible conditions. The dissolved hydrogen inhibition approach used in ADM1 is, however, deemed as adequate, offering the trade-off of not requiring dynamic bioenergetics computation despite the need of hydrogen inhibition parameters. Simulations of the model with bioenergetics showed the low amount of energy available in butyrate and propionate oxidation, suggesting that microbial growth on these substrates must be very limited or occur via alternative mechanisms rather than dissolved hydrogen.

Bioenergetics analysis of ammonia-oxidizing bacteria and the estimation of their maximum growth yield

The currently accepted biochemistry and bioenergetics of ammonia-oxidizing bacteria (AOB) show an inefficient metabolism: only 53.8% of the energy released when a mole of ammonia is oxidised and less than two of the electrons liberated can be directed to the autotrophic anabolism. However, paradoxically, AOB seem to thrive in challenging conditions: growing readily in virtually most aerobic environment, yet limited AOB exist in pure culture. In this study, a comprehensive model of the biochemistry of the metabolism of AOB is presented. Using bioenergetics calculations and selecting the minimum estimation for the energy dissipated in each of the metabolic steps, the model predicts the highest possible true yield of 0.16 gBio/gN and a yield of 0.13 gBio/gN when cellular maintenance is considered. Observed yields should always be lower than these values but the range of experimental values in literature vary between 0.04 and 0.45 gBio/gN. In this work, we discuss if this variance of observed values for AOB growth yield could be understood if other non-considered alternative energy sources are present in the biochemistry of AOB. We analyse how the predicted maximum growth yield of AOB changes considering co-metabolism, the use of hydroxylamine as a substrate, the abiotic oxidation of NO, energy harvesting in the monooxygenase enzyme or the use of organic carbon sources.

Multi-agent simulation regulated by microbe-oriented thermodynamics and kinetics equations for exploiting interspecies dynamics and evolution between methanogenesis, sulfidogenesis, hydrogenesis and exoelectrogenesis

Multi-agent simulation (MAS) regulated by microbe-oriented thermodynamics and kinetics equations were performed for exploiting the interspecies dynamics and evolution in anaerobic respiration and bioelectrochemical systems. A newly-defined kinetically thermodynamic parameter is recognized microbes as agents in various conditions, including electron donors and acceptors, temperature, pH, etc. For verification of the MAS, the treatment of synthetic wastewater containing glucose and acetate was evaluated in four 25°C laboratory-scale reactors with different electron acceptors and cathode materials that had potential for methanogenesis, hydrogenesis, sulfidogenesis and exoelectrogenesis. Within 1000 h operation, the reactors performance and microbial structures using 16S rRNA sequencing matched with the MAS, suggesting acetoclastic exoelectrogenesis predominance (Geobacter). After 2400 h, MAS observed the co-existence of acetoclastic methanogenesis and acetoclastic and propionate exoelectrogenesis, as was reported previously. Such microbial evolution from the short-term to long-term operation likely resulted from the glucose-driven propionate. The MAS developed is applicable in a wide range of complex engineering and natural ecosystems.

Engineering the Dark Food Chain

Meeting global food needs in the face of climate change and resource limitation requires innovative approaches to food production. Here, we explore incorporation of new dark food chains into human food systems, drawing inspiration from natural ecosystems, the history of single cell protein, and opportunities for new food production through wastewater treatment, microbial protein production, and aquaculture. The envisioned dark food chains rely upon chemoautotrophy in lieu of photosynthesis, with primary production based upon assimilation of CH₄ and CO₂ by methane- and hydrogen-oxidizing bacteria. The stoichiometry, kinetics, and thermodynamics of these bacteria are evaluated, and opportunities for recycling of carbon, nitrogen, and water are explored. Because these processes do not require light delivery, high volumetric productivities are possible; because they are exothermic, heat is available for downstream protein processing; because the feedstock gases are cheap, existing pipeline infrastructure could facilitate low-cost energy-efficient delivery in urban environments. Potential life-cycle benefits include: a protein alternative to fishmeal; partial decoupling of animal feed from human food; climate change mitigation due to decreased land use for agriculture; efficient local cycling of carbon and nutrients that offsets the need for energy-intensive fertilizers; and production of high value products, such as the prebiotic polyhydroxybutyrate.

Survival of the fewest: Microbial dormancy and maintenance in marine sediments through deep time

Microorganisms buried in marine sediments are known to endure starvation over geologic timescales. However, the mechanisms of how these microorganisms cope with prolonged energy limitation is unknown and therefore yet to be captured in a quantitative framework. Here, we present a novel mathematical model that considers (a) the physiological transitions between the active and dormant states of microorganisms, (b) the varying requirement for maintenance power between these phases, and (c) flexibility in the provenance (i.e., source) of energy from exogenous and endogenous catabolism. The model is applied to sediments underlying the oligotrophic South Pacific Gyre where microorganisms endure ultra-low fluxes of energy for tens of millions of years. Good fits between model simulations and measurements of cellular carbon and organic carbon concentrations are obtained and are interpreted as follows: (a) the unfavourable microbial habitat in South Pacific Gyre sediments triggers rapid mortality and a transition to dormancy; (b) there is minimal biomass growth, and organic carbon consumption is dominated by catabolism to support maintenance activities rather than new biomass synthesis; (c) the amount of organic carbon that microorganisms consume for maintenance activities is equivalent to approximately 2% of their carbon biomass per year; and (d) microorganisms must rely solely on exogenous rather than endogenous catabolism to persist in South Pacific Gyre sediments over long timescales. This leads us to the conclusion that under oligotrophic conditions, the fitness of an organism is determined by its ability to simply stay alive, rather than to grow. This modelling framework is designed to be flexible for application to other sites and habitats, and thus serves as a new quantitative tool for determining the habitability of and an ultimate limit for life in any environment.

Microbially Mediated Hydrogen Cycling in Deep-Sea Hydrothermal Vents

Deep-sea hydrothermal vents may provide one of the largest reservoirs on Earth for hydrogen-oxidizing microorganisms. Depending on the type of geological setting, hydrothermal environments can be considerably enriched in hydrogen (up to millimolar concentrations). As hot, reduced hydrothermal fluids ascend to the seafloor they mix with entrained cold, oxygenated seawater, forming thermal and chemical gradients along their fluid pathways. Consequently, in these thermally and chemically dynamic habitats biochemically distinct hydrogenases (adapted to various temperature regimes, oxygen and hydrogen concentrations) from physiologically and phylogenetically diverse Bacteria and Archaea can be expected. Hydrogen oxidation is one of the important inorganic energy sources in these habitats, capable of providing relatively large amounts of energy (237 kJ/mol H2) for driving ATP synthesis and autotrophic CO2 fixation. Therefore, hydrogen-oxidizing organisms play a key role in deep-sea hydrothermal vent ecosystems as they can be considerably involved in light-independent primary biomass production. So far, the specific role of hydrogen-utilizing microorganisms in deep-sea hydrothermal ecosystems has been investigated by isolating hydrogen-oxidizers, measuring hydrogen consumption (ex situ), studying hydrogenase gene distribution and more recently by analyzing metatranscriptomic and metaproteomic data. Here we summarize this available knowledge and discuss the advent of new techniques for the identification of novel hydrogen-uptake and -evolving enzymes from hydrothermal vent microorganisms.

Consistent microbial dynamics and functional community patterns derived from first principles

Microbial communities are key engines that drive earth's biogeochemical cycles. However, existing ecosystem models have only limited ability to predict microbial dynamics and require the calibration of multiple population-specific empirical equations. In contrast, we build on a new kinetic "Microbial Transition State" (MTS) theory of growth derived from first principles. We show how the theory coupled to simple mass and energy balance calculations provides a framework with intrinsically important qualitative properties to model microbial community dynamics. We first show how the theory can simultaneously account for the influence of all the resources needed for growth (electron donor, acceptor, and nutrients) while still producing consistent dynamics that fulfill the Liebig rule of a single limiting substrate. We also show consistent patterns of energy-dependent microbial successions in mixed culture without the need for calibration of population-specific parameters. We then show how this approach can be used to model a simplified activated sludge community. To this end, we compare MTS-derived dynamics with those of a widely used activated sludge model and show that similar growth yields and overall dynamics can be obtained using two parameters instead of twelve. This new kinetic theory of growth grounded by a set of generic physical principles parsimoniously gives rise to consistent microbial population and community dynamics, thereby paving the way for the development of a new class of more predictive microbial ecosystem models.

Linking Spectral Induced Polarization (SIP) and Subsurface Microbial Processes: Results from Sand Column Incubation Experiments

Geophysical techniques, such as spectral induced polarization (SIP), offer potentially powerful approaches for in situ monitoring of subsurface biogeochemistry. The successful implementation of these techniques as monitoring tools for reactive transport phenomena, however, requires the deconvolution of multiple contributions to measured signals. Here, we present SIP spectra and complementary biogeochemical data obtained in saturated columns packed with alternating layers of ferrihydrite-coated and pure quartz sand, and inoculated with Shewanella oneidensis supplemented with lactate and nitrate. A biomass-explicit diffusion-reaction model is fitted to the experimental biogeochemical data. Overall, the results highlight that (1) the temporal response of the measured imaginary conductivity peaks parallels the microbial growth and decay dynamics in the columns, and (2) SIP is sensitive to changes in microbial abundance and cell surface charging properties, even at relatively low cell densities (<10⁸ cells mL^-1). Relaxation times (τ) derived using the Cole-Cole model vary with the dominant electron accepting process, nitrate or ferric iron reduction. The observed range of τ values, 0.012-0.107 s, yields effective polarization diameters in the range 1-3 μm, that is, 2 orders of magnitude smaller than the smallest quartz grains in the columns, suggesting that polarization of the bacterial cells controls the observed chargeability and relaxation dynamics in the experiments.

Optimizing anaerobic growth rate and fermentation kinetics in Saccharomyces cerevisiae strains expressing Calvin-cycle enzymes for improved ethanol yield

BACKGROUND

Reduction or elimination of by-product formation is of immediate economic relevance in fermentation processes for industrial bioethanol production with the yeast Saccharomyces cerevisiae. Anaerobic cultures of wild-type S. cerevisiae require formation of glycerol to maintain the intracellular NADH/NAD+ balance. Previously, functional expression of the Calvin-cycle enzymes ribulose-1,5-bisphosphate carboxylase (RuBisCO) and phosphoribulokinase (PRK) in S. cerevisiae was shown to enable reoxidation of NADH with CO2 as electron acceptor. In slow-growing cultures, this engineering strategy strongly decreased the glycerol yield, while increasing the ethanol yield on sugar. The present study explores engineering strategies to improve rates of growth and alcoholic fermentation in yeast strains that functionally express RuBisCO and PRK, while maximizing the positive impact on the ethanol yield.

RESULTS

Multi-copy integration of a bacterial-RuBisCO expression cassette was combined with expression of the Escherichia coli GroEL/GroES chaperones and expression of PRK from the anaerobically inducible DAN1 promoter. In anaerobic, glucose-grown bioreactor batch cultures, the resulting S. cerevisiae strain showed a 31% lower glycerol yield and a 31% lower specific growth rate than a non-engineered reference strain. Growth of the engineered strain in anaerobic, glucose-limited chemostat cultures revealed a negative correlation between its specific growth rate and the contribution of the Calvin-cycle enzymes to redox homeostasis. Additional deletion of GPD2, which encodes an isoenzyme of NAD+-dependent glycerol-3-phosphate dehydrogenase, combined with overexpression of the structural genes for enzymes of the non-oxidative pentose-phosphate pathway, yielded a CO2-reducing strain that grew at the same rate as a non-engineered reference strain in anaerobic bioreactor batch cultures, while exhibiting a 86% lower glycerol yield and a 15% higher ethanol yield.

CONCLUSIONS

The metabolic engineering strategy presented here enables an almost complete elimination of glycerol production in anaerobic, glucose-grown batch cultures of S. cerevisiae, with an associated increase in ethanol yield, while retaining near wild-type growth rates and a capacity for glycerol formation under osmotic stress. Using current genome-editing techniques, the required genetic modifications can be introduced in one or a few transformations. Evaluation of this concept in industrial strains and conditions is therefore a realistic next step towards its implementation for improving the efficiency of first- and second-generation bioethanol production.

Prediction of the Formation of Biogenic Nonextractable Residues during Degradation of Environmental Chemicals from Biomass Yields

Degradation tests with radio or stable isotope labeled compounds enable the detection of the formation of nonextractable residues (NER). In PBT and vPvB assessment, remobilisable NER are considered as a potential risk while biogenic NER from incorporation of labeled carbon into microbial biomass are treated as degradation products. Relationships between yield, released CO₂ (as indicator of microbial activity and mineralization) and microbial growth can be used to estimate the formation of biogenic NER. We provide a new approach for calculation of potential substrate transformation to microbial biomass (theoretical yield) based on Gibbs free energy and microbially available electrons. We compare estimated theoretical yields of biotechnological substrates and of chemicals of environmental concern with experimentally determined yields for validation of the presented approach. A five-compartment dynamic model is applied to simulate experiments of ¹³C-labeled 2,4-D and ibuprofen turnover. The results show that bioNER increases with time, and that most bioNER originates from microbial proteins. Simulations with precalculated input data demonstrate that precalculation of yields reduces the number of fit parameters considerably, increases confidence in fitted kinetic data, and reduces the uncertainty of the simulation results.

Fine-tuning the P. pastoris iMT1026 genome-scale metabolic model for improved prediction of growth on methanol or glycerol as sole carbon sources

The methylotrophic yeast Pichia pastoris (Komagataella spp.) is widely used as cell factory for recombinant protein production. In the past recent years, important breakthroughs in the systems-level quantitative analysis of its physiology have been achieved. This wealth of information has allowed the development of genome-scale metabolic models, which make new approaches possible for host cell and bioprocess engineering. Nevertheless, the predictive accuracy of the previous consensus model required to be upgraded and validated with new experimental data sets for P. pastoris growing on glycerol or methanol as sole carbon sources, two of the most relevant substrates for this cell factory. In this study, we have characterized P. pastoris growing in chemostat cultures using glycerol or methanol as sole carbon sources over a wide range of growth rates, thereby providing physiological data on the effect of growth rate and culture conditions on biomass macromolecular and elemental composition. In addition, these data sets were used to improve the performance of the P. pastoris consensus genomic-scale metabolic model iMT1026. Thereupon, new experimentally determined bounds, including the representation of biomass composition for these growth conditions, have been incorporated. As a result, here, we present version 3 (v3.0) of the consensus P. pastoris genome-scale metabolic model as an update of the iMT1026 model. The v3.0 model was validated for growth on glycerol and methanol as sole carbon sources, demonstrating improved prediction capabilities over an extended substrate range including two biotechnologically relevant carbon sources.