Corrigendum: Modeled energetics of bacterial communities in ancient subzero brines

[This corrects the article DOI: 10.3389/fmicb.2023.1206641.].

Modeled energetics of bacterial communities in ancient subzero brines

Cryopeg brines are isolated volumes of hypersaline water in subzero permafrost. The cryopeg system at Utqiaġvik, Alaska, is estimated to date back to 40 ka BP or earlier, a remnant of a late Pleistocene Ocean. Surprisingly, the cryopeg brines contain high concentrations of organic carbon, including extracellular polysaccharides, and high densities of bacteria. How can these physiologically extreme, old, and geologically isolated systems support such an ecosystem? This study addresses this question by examining the energetics of the Utqiaġvik cryopeg brine ecosystem. Using literature-derived assumptions and new measurements on archived borehole materials, we first estimated the quantity of organic carbon when the system formed. We then considered two bacterial growth trajectories to calculate the lower and upper bounds of the cell-specific metabolic rate of these communities. These bounds represent the first community estimates of metabolic rate in a subzero hypersaline environment. To assess the plausibility of the different growth trajectories, we developed a model of the organic carbon cycle and applied it to three borehole scenarios. We also used dissolved inorganic carbon and nitrogen measurements to independently estimate the metabolic rate. The model reconstructs the growth trajectory of the microbial community and predicts the present-day cell density and organic carbon content. Model input included measured rates of the in-situ enzymatic conversion of particulate to dissolved organic carbon under subzero brine conditions. A sensitivity analysis of model parameters was performed, revealing an interplay between growth rate, cell-specific metabolic rate, and extracellular enzyme activity. This approach allowed us to identify plausible growth trajectories consistent with the observed bacterial densities in the cryopeg brines. We found that the cell-specific metabolic rate in this system is relatively high compared to marine sediments. We attribute this finding to the need to invest energy in the production of extracellular enzymes, for generating bioavailable carbon from particulate organic carbon, and the production of extracellular polysaccharides for cryoprotection and osmoprotection. These results may be relevant to other isolated systems in the polar regions of Earth and to possible ice-bound brines on worlds such as Europa, Enceladus, and Mars.

Gradually supply of isoamyl alcohol increases the isoamyl acetate production in solid-state fermentation

Nowadays, isoamyl acetate production is carried out by chemical synthesis with a recent interest in developing biological producing processes, mainly based on microorganisms in submerged fermentation. This work assayed producing isoamyl acetate through solid-state fermentation (SSF), feeding the precursor in the gas phase. Polyurethane foam functioned as the inert support to contain 20 ml of a solution of molasses (10% w/v, pH 5.0). The yeast Pichia fermentans was inoculated at 3 × 107 cells per gram of initial dry weight. The airstream to supply oxygen also served to supply the precursor. Slow supply was obtained using an isoamyl alcohol solution of 5 g l-1 in the bubbling columns and an air stream of 50 ml min-1. For fast supply, fermentations were aerated using 10 g l-1 and 100 ml min-1 for isoamyl alcohol solution and air stream, respectively. It demonstrated the feasibility of isoamyl acetate production in SSF. Moreover, the slow supply of the precursor increased isoamyl acetate production up to 390 mg l-1, which is 12.5 times higher than that obtained without precursor (32 mg l-1). On the other hand, fast supply caused an evident inhibition of the growth and production capacity of the yeast.

Strategies to manage barn feed supply to prolong and hold late finishing pigs during a supply chain disruption

The U.S. pork production system is sensitive to supply chain disruptions, including those that can create challenges of feed delivery and feed management during the event of a foreign animal disease outbreak. Therefore, the objective was to evaluate feeding strategies during a prolonged feed availability shortage in group-housed finishing pigs and assess the impacts on pig performance. A total of 1,407 mixed-sex pigs (92 ± 11 kg BW) were randomly allocated to one of five treatments across 60 pens (N = 12 pens per treatment, 22 pigs per pen) and were blocked by initial body weight (BW) within the replicate, over a 21-d test period. Treatments were fed for 14 d (P1), and thereafter all pens returned to ad libitum access to a standard commercial diet for 7 d (P2). Treatments included: 1) Pens fed ad libitum (CON); 2) Pens fed at 1.45X ME maintenance requirement daily of CON diet (1.45X); 3) Pens fed 2X ME maintenance requirement daily of CON diet (2X); 4) Tightened feeders to the lowest setting, fed ad libitum of CON diet (CF); and 5) whole corn kernels, fed ad libitum (WC). P1 and P2 BW and feed disappearance were recorded to calculate ADG, ADFI, and G:F. Data were analyzed with pen as the experimental unit and least-squares means values reported by treatment. Compared to CON, pens fed 1.45X, 2X, CF, and WC treatments had significantly reduced P1 ADG (1.09 vs. 0.02, 0.34, 0.72, 0.41 kg/d, respectively), ADFI (3.21 vs. 1.42, 1.90, 2.49, 2.40 kg/d, respectively) and G:F (P < 0.05). During P2, ADG and G:F were increased (P < 0.05) compared to CON across all treatments. However, ADFI increased only in the 2X, CF, and WC diet from the CON (P < 0.05). Overall (days 0 to 21), all strategies attenuated BW, ADG, and ADFI (P < 0.01) compared to CON. However, G:F was only reduced (P < 0.01) in 1.45X and WC, but not 2X and CF (P > 0.05) compared to CON. In conclusion, all strategies explored could extend feed budgets. Even though these strategies were successful, increased BW variability was reported with more restrictive strategies. Further, adverse pig behaviors and welfare implications needs to be considered in adopting any restrictive feeding strategy.

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.

An alternative resource allocation strategy in the chemolithoautotrophic archaeon Methanococcus maripaludis

Most microorganisms in nature spend the majority of time in a state of slow or zero growth and slow metabolism under limited energy or nutrient flux rather than growing at maximum rates. Yet, most of our knowledge has been derived from studies on fast-growing bacteria. Here, we systematically characterized the physiology of the methanogenic archaeon Methanococcus maripaludis during slow growth. M. maripaludis was grown in continuous culture under energy (formate)-limiting conditions at different dilution rates ranging from 0.09 to 0.002 h^-1, the latter corresponding to 1% of its maximum growth rate under laboratory conditions (0.23 h^-1). While the specific rate of methanogenesis correlated with growth rate as expected, the fraction of cellular energy used for maintenance increased and the maintenance energy per biomass decreased at slower growth. Notably, proteome allocation between catabolic and anabolic pathways was invariant with growth rate. Unexpectedly, cells maintained their maximum methanogenesis capacity over a wide range of growth rates, except for the lowest rates tested. Cell size, cellular DNA, RNA, and protein content as well as ribosome numbers also were largely invariant with growth rate. A reduced protein synthesis rate during slow growth was achieved by a reduction in ribosome activity rather than via the number of cellular ribosomes. Our data revealed a resource allocation strategy of a methanogenic archaeon during energy limitation that is fundamentally different from commonly studied versatile chemoheterotrophic bacteria such as E. coli.

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.

Fed-Batch Cultivations of Rhodospirillum rubrum Under Multiple Nutrient-Limited Growth Conditions on Syngas as a Novel Option to Produce Poly(3-Hydroxybutyrate) (PHB)

Syngas from gasified organic waste materials is a promising feedstock for the biotechnological synthesis of the bioplastic poly([R]-3-hydroxybutyrate) (PHB) with Rhodospirillum rubrum. In a first approach, growth studies were carried out with this strain in gas-tight serum vials. When syngas (40% CO, 40% H₂, 10% CO₂, and 10% N₂ v/v) was diluted with N₂ to 60%, a 4-fold higher biomass production was detected compared to samples grown on 100% syngas, thus indicating a growth inhibitory effect. The best performing syngas-mixture was then used for C-, C,N-, and C,P-limited fed-batch fermentations in a bioreactor with continuous syngas and acetate supply. It was found that C,P-limited PHB productivity was 5 times higher than for only C-limited growth and reached a maximal PHB content of 30% w/w. Surprisingly, growth and PHB production stopped when N, as a second nutrient, became growth-limiting. Finally, it was concluded that a minimal supply of 0.2 g CO g^-1 biomass h^-1 has to be guaranteed in order to cover the cellular maintenance energy.

Bioenergetic Controls on Microbial Ecophysiology in Marine Sediments

Marine sediments constitute one of the most energy-limited habitats on Earth, in which microorganisms persist over extraordinarily long timescales with very slow metabolisms. This habitat provides an ideal environment in which to study the energetic limits of life. However, the bioenergetic factors that can determine whether microorganisms will grow, lie dormant, or die, as well as the selective environmental pressures that determine energetic trade-offs between growth and maintenance activities, are not well understood. Numerical models will be pivotal in addressing these knowledge gaps. However, models rarely account for the variable physiological states of microorganisms and their demand for energy. Here, we review established modeling constructs for microbial growth rate, yield, maintenance, and physiological state, and then provide a new model that incorporates all of these factors. We discuss this new model in context with its future application to the marine subsurface. Understanding the factors that regulate cell death, physiological state changes, and the provenance of maintenance energy (i.e., endogenous versus exogenous metabolism), is crucial to the design of this model. Further, measurements of growth rate, growth yield, and basal metabolic activity will enable bioenergetic parameters to be better constrained. Last, biomass and biogeochemical rate measurements will enable model simulations to be validated. The insight provided from the development and application of new microbial modeling tools for marine sediments will undoubtedly advance the understanding of the minimum power required to support life, and the ecophysiological strategies that organisms utilize to cope under extreme energy limitation for extended periods of time.

Flux measurements and maintenance energy for carbon dioxide utilization by Methanococcus maripaludis

BACKGROUND

The rapidly growing mesophilic methanogen Methanococcus maripaludis S2 has a unique ability to consume both CO2 and N2, the main components of a flue gas, and produce methane with H2 as the electron donor. The existing literature lacks experimental measurements of CO2 and H2 uptake rates and CH4 production rates on M. maripaludis. Furthermore, it lacks estimates of maintenance energies for use with genome-scale models. In this paper, we performed batch culture experiments on M. maripaludis S2 using CO2 as the sole carbon substrate to quantify three key extracellular fluxes (CO2, H2, and CH4) along with specific growth rates. For precise computation of these fluxes from experimental measurements, we developed a systematic process simulation approach. Then, using an existing genome-scale model, we proposed an optimization procedure to estimate maintenance energy parameters: growth associated maintenance (GAM) and non-growth associated maintenance (NGAM).

RESULTS

The measured extracellular fluxes for M. maripaludis showed excellent agreement with in silico predictions from a validated genome-scale model (iMM518) for NGAM = 7.836 mmol/gDCW/h and GAM = 27.14 mmol/gDCW. M. maripaludis achieved a CO2 to CH4 conversion yield of 70-95 % and a growth yield of 3.549 ± 0.149 g DCW/mol CH4 during the exponential phase. The ATP gain of 0.35 molATP/molCH4 for M. maripaludis, computed using NGAM, is in the acceptable range of 0.3-0.7 mol ATP/molCH4 reported for methanogens. Interestingly, the uptake distribution of amino acids, quantified using iMM518, confirmed alanine to be the most preferred amino acids for growth and methanogenesis.

CONCLUSIONS

This is the first study to report experimental gas consumption and production rates for the growth of M. maripaludis on CO2 and H2 in minimal media. A systematic process simulation and optimization procedure was successfully developed to precisely quantify extracellular fluxes along with cell growth and maintenance energy parameters. Our growth yields, ATP gain, and energy parameters fall within acceptable ranges known in the literature for hydrogenotrophic methanogens.

Life cycle biological efficiency of mice divergently selected for heat loss

Divergent selection in mice for heat loss was conducted in 3 independent replicates creating a high maintenance, high heat loss (MH) and low maintenance, low heat loss (ML) line and unselected control (MC). Improvement in feed efficiency was observed in ML mice due to a reduced maintenance energy requirement but there was also a slight decline in reproductive performance, survivability, and lean content, particularly when compared to MC animals. The objective of this study was to model a life cycle scenario similar to a livestock production system and calculate total inputs and outputs to estimate overall biological efficiency of these lines and determine if reduced feed intake resulted in improved life cycle efficiency. Feed intake, reproductive performance, growth, and body composition were recorded on 21 mating pairs from each line × replicate combination, cohabitated at 7 wk of age and maintained for up to 1 yr unless culled. Proportion of animals at each parity was calculated from survival rates estimated from previous research when enforcing a maximum of 4, 8, or 12 allowed parities. This parity distribution was then combined with values from previous studies to calculate inputs and outputs of mating pairs and offspring produced in a single cycle at equilibrium. Offspring output was defined as kilograms of lean output of offspring at 49 d. Offspring input was defined as megacalories of energy intake for growing offspring from 21 to 49 d. Parent output was defined as kilograms of lean output of culled parents. Parent input was defined as megacalories of energy intake for mating pairs from weaning of one parity to weaning of the next. Offspring output was greatest in MC mice due to superior BW and numbers weaned, while output was lowest in ML mice due to smaller litter sizes and lean content. Parent output did not differ substantially between lines but was greatest in MH mice due to poorer survival rates resulting in more culled animals. Input was greatest in MH and lowest for ML mice for both offspring and parent pairs, consistent with previous results in these lines. Life cycle efficiency was similar in MC and ML mice, while MH mice were least efficient. Ultimately, superior output in MC mice slightly outweighed the lower inputs in ML animals resulting from decreased maintenance energy requirements. Therefore, selection to reduce maintenance energy requirements may be more useful in terminal crosses or in a selection index to reduce possible negative effects on output, especially reproductive performance.