scholarly journals Thermodynamic modelling of synthetic communities predicts minimum free energy requirements for sulfate reduction and methanogenesis

2019 ◽  
Author(s):  
Hadrien Delattre ◽  
Jing Chen ◽  
Matthew Wade ◽  
Orkun S Soyer
Keyword(s):  
Population Dynamics ◽  
Microbial Communities ◽  
Thermodynamic Model ◽  
Community Dynamics ◽  
Energy Requirement ◽  
Minimum Energy ◽  
Building Blocks ◽  
Thermodynamic Modelling ◽  
Energy Requirements ◽  
Experimental Population

ABSTRACTMicrobial communities are complex dynamical systems harbouring many species interacting together to implement higher-level functions. Among these higher-level functions, conversion of organic matter into simpler building blocks by microbial communities underpins biogeochemical cycles and animal and plant nutrition, and is exploited in biotechnology. A prerequisite to predicting the dynamics and stability of community-mediated metabolic conversions, is the development and calibration of appropriate mathematical models. Here, we present a generic, extendable thermodynamic model for community dynamics accounting explicitly for metabolic activities of composing microbes, system pH, and chemical exchanges. We calibrate a key parameter of this thermodynamic model, the minimum energy requirement associated with growth-supporting metabolic pathways, using experimental population dynamics data from synthetic communities composed of a sulfate reducer and two methanogens. Our findings show that accounting for thermodynamics is necessary in capturing experimental population dynamics of these synthetic communities that feature relevant species utilising low-energy growth pathways. Furthermore, they provide the first estimates for minimum energy requirements of methanogenesis and elaborates on previous estimates of lactate fermentation by sulfate reducers. The open-source nature of the developed model and demonstration of its use for estimating a key thermodynamic parameter should facilitate further thermodynamic modelling of microbial communities.

scholarly journals Thermodynamic modelling of synthetic communities predicts minimum free energy requirements for sulfate reduction and methanogenesis

2020 ◽  
Vol 17 (166) ◽  
pp. 20200053 ◽  
Author(s):  
Hadrien Delattre ◽  
Jing Chen ◽  
Matthew J. Wade ◽  
Orkun S. Soyer
Keyword(s):  
Population Dynamics ◽  
Microbial Communities ◽  
Thermodynamic Model ◽  
Community Dynamics ◽  
Energy Requirement ◽  
Minimum Energy ◽  
Building Blocks ◽  
Thermodynamic Modelling ◽  
Energy Requirements ◽  
Experimental Population

Microbial communities are complex dynamical systems harbouring many species interacting together to implement higher-level functions. Among these higher-level functions, conversion of organic matter into simpler building blocks by microbial communities underpins biogeochemical cycles and animal and plant nutrition, and is exploited in biotechnology. A prerequisite to predicting the dynamics and stability of community-mediated metabolic conversions is the development and calibration of appropriate mathematical models. Here, we present a generic, extendable thermodynamic model for community dynamics and calibrate a key parameter of this thermodynamic model, the minimum energy requirement associated with growth-supporting metabolic pathways, using experimental population dynamics data from synthetic communities composed of a sulfate reducer and two methanogens. Our findings show that accounting for thermodynamics is necessary in capturing the experimental population dynamics of these synthetic communities that feature relevant species using low energy growth pathways. Furthermore, they provide the first estimates for minimum energy requirements of methanogenesis (in the range of −30 kJ mol −1 ) and elaborate on previous estimates of lactate fermentation by sulfate reducers (in the range of −30 to −17 kJ mol −1 depending on the culture conditions). The open-source nature of the developed model and demonstration of its use for estimating a key thermodynamic parameter should facilitate further thermodynamic modelling of microbial communities.

scholarly journals Which games are growing bacterial populations playing?

2015 ◽  
Vol 12 (108) ◽  
pp. 20150121 ◽  
Author(s):  
Xiang-Yi Li ◽  
Cleo Pietschke ◽  
Sebastian Fraune ◽  
Philipp M. Altrock ◽  
Thomas C. G. Bosch ◽  
...  
Keyword(s):  
Game Theory ◽  
Population Dynamics ◽  
Microbial Communities ◽  
Evolutionary Game Theory ◽  
Community Dynamics ◽  
Growth Parameters ◽  
Evolutionary Game ◽  
Frequency Dependent

Microbial communities display complex population dynamics, both in frequency and absolute density. Evolutionary game theory provides a natural approach to analyse and model this complexity by studying the detailed interactions among players, including competition and conflict, cooperation and coexistence. Classic evolutionary game theory models typically assume constant population size, which often does not hold for microbial populations. Here, we explicitly take into account population growth with frequency-dependent growth parameters, as observed in our experimental system. We study the in vitro population dynamics of the two commensal bacteria ( Curvibacter sp. (AEP1.3) and Duganella sp. (C1.2)) that synergistically protect the metazoan host Hydra vulgaris (AEP) from fungal infection. The frequency-dependent, nonlinear growth rates observed in our experiments indicate that the interactions among bacteria in co-culture are beyond the simple case of direct competition or, equivalently, pairwise games. This is in agreement with the synergistic effect of anti-fungal activity observed in vivo . Our analysis provides new insight into the minimal degree of complexity needed to appropriately understand and predict coexistence or extinction events in this kind of microbial community dynamics. Our approach extends the understanding of microbial communities and points to novel experiments.

scholarly journals Constrained proteome allocation affects coexistence in models of competitive microbial communities

2020 ◽  
Author(s):  
Leonardo Pacciani-Mori ◽  
Samir Suweis ◽  
Amos Maritan ◽  
Andrea Giometto
Keyword(s):  
Population Dynamics ◽  
Microbial Community ◽  
Microbial Communities ◽  
Community Dynamics ◽  
Bacterial Strains ◽  
Theoretical Frameworks ◽  
Microbial Community Dynamics ◽  
Common Resource ◽  
Multiple Species ◽  
Consumer Resource

Microbial communities are ubiquitous and play crucial roles in many natural processes. Despite their importance for the environment, industry and human health, there are still many aspects of microbial community dynamics that we do not understand quantitatively. Recent experiments have shown that the metabolism of species in a community is intertwined with its composition, suggesting that properties at the intracellular level such as the allocation of cellular proteomic resources must be taken into account when describing microbial communities with a population dynamics approach. In this work we reconsider one of the theoretical frameworks most commonly used to model population dynamics in competitive ecosystems, MacArthur’s consumer-resource model, in light of experimental evidence showing how pro-teome allocation affects microbial growth. This new framework allows us to describe community dynamics at an intermediate level of complexity between classical consumer-resource models and biochemical models of microbial metabolism, accounting for temporally-varying proteome allocation subject to constraints on growth and protein synthesis in the presence of multiple resources, while preserving analytical insight into the dynamics of the system. We first show experimentally that proteome allocation needs to be accounted for to properly understand the dynamics of even the simplest microbial community, i.e. two bacterial strains competing for one common resource. We then study the model analytically and numerically to determine the conditions that allow multiple species to coexist in systems with arbitrary numbers of species and resources.

scholarly journals Longitudinal assessment of the bovine ocular bacterial community dynamics in calves

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Alison C. Bartenslager ◽  
Nirosh D. Althuge ◽  
John Dustin Loy ◽  
Matthew M. Hille ◽  
Matthew L. Spangler ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Community Dynamics ◽  
Bacterial Community Composition ◽  
Clinical Signs ◽  
Sampling Time ◽  
Experimental Population ◽  
Opportunistic Pathogens ◽  
Time Periods ◽  
Over Time

Abstract Background Infectious Bovine Keratoconjunctivitis (IBK), commonly known as pinkeye, is one of the most significant diseases of beef cattle. As such, IBK costs the US beef industry at least 150 million annually. However, strategies to prevent IBK are limited, with most cases resulting in treatment with antibiotics once the disease has developed. Longitudinal studies evaluating establishment of the ocular microbiota may identify critical risk periods for IBK outbreaks or changes in the microbiota that may predispose animals to IBK. Results In an attempt to characterize the establishment and colonization patterns of the bovine ocular microbiota, we conducted a longitudinal study consisting of 227 calves and evaluated the microbiota composition over time using amplicon sequence variants (ASVs) based on 16S rRNA sequencing data and culture-based approaches. Beef calves on trial consisted of both male (intact) and females. Breeds were composed of purebred Angus and composites with varying percentages of Simmental, Angus, and Red Angus breeds. Average age at the start of the trial was 65 days ±15.02 and all calves remained nursing on their dam until weaning (day 139 of the study). The trial consisted of 139 days with four sampling time points on day 0, 21, 41, and 139. The experimental population received three different vaccination treatments (autogenous, commercial (both inactivated bacteria), and adjuvant placebo), to assess the effectiveness of different vaccines for IBK prevention. A significant change in bacterial community composition was observed across time periods sampled compared to the baseline (p < 0.001). However, no treatment effect of vaccine was detected within the ocular bacterial community. The bacterial community composition with the greatest time span between sampling time periods (98d span) was most similar to the baseline sample collected, suggesting re-establishment of the ocular microbiota to baseline levels over time after perturbation. The effect of IgA levels on the microbial community was investigated in a subset of cattle within the study. However, no significant effect of IgA was observed. Significant changes in the ocular microbiota were identified when comparing communities pre- and post-clinical signs of IBK. Additionally, dynamic changes in opportunistic pathogens Moraxella spp. were observed and confirmed using culture based methods. Conclusions Our results indicate that the bovine ocular microbiota is well represented by opportunistic pathogens such as Moraxella and Mycoplasma. Furthermore, this study characterizes the diversity of the ocular microbiota in calves and demonstrates the plasticity of the ocular microbiota to change. Additionally, we demonstrate the ocular microbiome in calves is similar between the eyes and the perturbation of one eye results in similar changes in the other eye. We also demonstrate the bovine ocular microbiota is slow to recover post perturbation and as a result provide opportunistic pathogens a chance to establish within the eye leading to IBK and other diseases. Characterizing the dynamic nature of the ocular microbiota provides novel opportunities to develop potential probiotic intervention to reduce IBK outbreaks in cattle.

An equation, suitable for computer use, based on the ARC feeding system to determine the energy requirements of growing and fattening cattle

1972 ◽  
Vol 14 (1) ◽  
pp. 17-23 ◽  
Author(s):  
C. A. Zulberti ◽  
J. T. Reid
Keyword(s):  
Weight Gain ◽  
Computer Use ◽  
Agricultural Research ◽  
Energy Requirement ◽  
Metabolizable Energy ◽  
Energy Requirements ◽  
Energy Concentration ◽  
Feeding System ◽  
Agricultural Research Council ◽  
Forward Calculation

SUMMARYBased on the Agricultural Research Council's feeding system, equations were developed that allow the calculation of the metabolizable energy requirements for maintenance and weight gain by cattle, separately or combined. A general equation was developed for the straight-forward calculation of the total metabolizable energy requirements of growing and fattening cattle for any combination of body weight, rate of weight gain, age, level of muscular work, and metabolizable energy concentration of the diet. The estimates of energy requirement made by the use of this equation are in excellent agreement with those made by the Agricultural Research Council using an iterative method.In addition to avoiding the awkward iterative process, the equations proposed are readily adaptable to computer use.

Effects of Community Versus Single Strain Inoculants on the Biocontrol of Salmonella and Microbial Community Dynamics in Alfalfa Sprouts†

2005 ◽  
Vol 68 (1) ◽  
pp. 40-48 ◽  
Author(s):  
ANABELLE MATOS ◽  
JAY L. GARLAND
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Dynamics ◽  
Community Level ◽  
Microbial Consortia ◽  
Single Strain ◽  
Acridine Orange Staining ◽  
Physiological Profiles ◽  
Alfalfa Sprouts ◽  
Alfalfa Seeds

Potential biological control inoculants, Pseudomonas fluorescens 2-79 and microbial communities derived from market sprouts or laboratory-grown alfalfa sprouts, were introduced into alfalfa seeds with and without a Salmonella inoculum. We examined their ability to inhibit the growth of this foodborne pathogen and assess the relative effects of the inoculants on the alfalfa microbial community structure and function. Alfalfa seeds contaminated with a Salmonella cocktail were soaked for 2 h in bacterial suspensions from each inoculant tested. Inoculated alfalfa seeds were grown for 7 days and sampled during days 1, 3, and 7. At each sampling, alfalfa sprouts were sonicated for 7 min to recover microflora from the surface, and the resulting suspensions were diluted and plated on selective and nonselective media. Total bacterial counts were obtained using acridine orange staining, and the percentage culturability was calculated. Phenotypic potential of sprout-associated microbial communities inoculated with biocontrol treatments was assessed using community-level physiological profiles based on patterns of use of 95 separate carbon sources in Biolog plates. Community-level physiological profiles were also determined using oxygen-sensitive fluorophore in BD microtiter plates to examine functional patterns in these communities. No significant differences in total and mesophilic aerobe microbial cell density or microbial richness resulting from the introduction of inoculants on alfalfa seeds with and without Salmonella were observed. P. fluorescens 2-79 exhibited the greatest reduction in the growth of Salmonella early during alfalfa growth (4.22 log at day 1), while the market sprout inoculum had the reverse effect, resulting in a maximum log reduction (5.48) of Salmonella on day 7. Community-level physiological profiles analyses revealed that market sprout communities peaked higher and faster compared with the other inoculants tested. These results suggest that different modes of actions of single versus microbial consortia biocontrol treatments may be involved.

scholarly journals Energy Analysis in Combined Reforming of Propane

2013 ◽  
Vol 2013 ◽  
pp. 1-10
Author(s):  
K. Moon ◽  
Ganesh R. Kale
Keyword(s):  
Steam Reforming ◽  
Energy Requirement ◽  
Minimum Energy ◽  
Dry Reforming ◽  
Optimum Process ◽  
Methane Formation ◽  
Equilibrium Data ◽  
Process Operation ◽  
Gibbs Free Energy Minimization ◽  
Pure Steam

Combined (steam and CO2) reforming is one of the methods to produce syngas for different applications. An energy requirement analysis of steam reforming to dry reforming with intermediate steps of steam reduction and equivalent CO2addition to the feed fuel for syngas generation has been done to identify condition for optimum process operation. Thermodynamic equilibrium data for combined reforming was generated for temperature range of 400–1000°C at 1 bar pressure and combined oxidant (CO2+ H2O) stream to propane (fuel) ratio of 3, 6, and 9 by employing the Gibbs free energy minimization algorithm of HSC Chemistry software 5.1. Total energy requirement including preheating and reaction enthalpy calculations were done using the equilibrium product composition. Carbon and methane formation was significantly reduced in combined reforming than pure dry reforming, while the energy requirements were lower than pure steam reforming. Temperatures of minimum energy requirement were found in the data analysis of combined reforming which were optimum for the process.

scholarly journals Energy Requirement and Food Intake Behaviour in Young Adult Intact Male Cats with and without Predisposition to Overweight

2012 ◽  
Vol 2012 ◽  
pp. 1-6 ◽  
Author(s):  
Brigitta Wichert ◽  
Julia Trossen ◽  
Daniel Uebelhart ◽  
Marcel Wanner ◽  
Sonja Hartnack
Keyword(s):  
Body Weight ◽  
Food Intake ◽  
Dry Matter ◽  
Body Condition Score ◽  
Energy Requirement ◽  
Fat Free Mass ◽  
Energy Requirements ◽  
Intact Male ◽  
Feeding Station ◽  
Condition Score

Obesity is a common problem in cats. In the experimental cat family of the institute of animal nutrition besides a “normal” lean phenotype, cats with predisposition to an overweight phenotype are present. To investigate energy requirements and food intake behaviour of intact male cats of different phenotypes, six “normal” lean cats (GL) and six cats disposed to overweight (GO) were used. At the beginning of the experiment, all cats had an ideal body condition score of 5. To reach this the GO cats had to pass a weight-loss program. Energy requirements of the cats were determined using respiration chambers, whereas the amount and frequency of food intake was measured with a feeding station recording the data automatically. Energy requirement at weight constancy of the GO cats was even on fat-free mass (FFM) significantly (P=0.02) lower (162.6 kJ/kg FFM/d) than that of the “normal” lean cats (246 kJ/kg FFM/d). The GO cats also showed a higher food intake34.5±1.5 g dry matter/kg body weight0.67compared to the GL cats (24.0±2.1 g dry matter/kg body weight0.67)(P=0.001). In conclusion quantifiable differences in food intake and behaviour in cats predisposed to overweight compared to “normal” lean cats were found.

scholarly journals Quantifying the effect of genetic, environmental and individual demographic stochastic variability for population dynamics in Plantago lanceolata

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ulrich K. Steiner ◽  
Shripad Tuljapurkar ◽  
Deborah A. Roach
Keyword(s):  
Population Dynamics ◽  
Population Growth ◽  
Population Change ◽  
Adaptive Dynamics ◽  
Plantago Lanceolata ◽  
Environmental Parameters ◽  
Experimental Population ◽  
Stochastic Variation ◽  
Survival And Reproduction ◽  
Stochastic Events

AbstractSimple demographic events, the survival and reproduction of individuals, drive population dynamics. These demographic events are influenced by genetic and environmental parameters, and are the focus of many evolutionary and ecological investigations that aim to predict and understand population change. However, such a focus often neglects the stochastic events that individuals experience throughout their lives. These stochastic events also influence survival and reproduction and thereby evolutionary and ecological dynamics. Here, we illustrate the influence of such non-selective demographic variability on population dynamics using population projection models of an experimental population of Plantago lanceolata. Our analysis shows that the variability in survival and reproduction among individuals is largely due to demographic stochastic variation with only modest effects of differences in environment, genes, and their interaction. Common expectations of population growth, based on expected lifetime reproduction and generation time, can be misleading when demographic stochastic variation is large. Large demographic stochastic variation exhibited within genotypes can lower population growth and slow evolutionary adaptive dynamics. Our results accompany recent investigations that call for more focus on stochastic variation in fitness components, such as survival, reproduction, and functional traits, rather than dismissal of this variation as uninformative noise.

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