Dataset Information

Individual Based Model Links Thermodynamics, Chemical Speciation and Environmental Conditions to Microbial Growth.

ABSTRACT: Individual based Models (IbM) must transition from research tools to engineering tools. To make the transition we must aspire to develop large, three dimensional and physically and biologically credible models. Biological credibility can be promoted by grounding, as far as possible, the biology in thermodynamics. Thermodynamic principles are known to have predictive power in microbial ecology. However, this in turn requires a model that incorporates pH and chemical speciation. Physical credibility implies plausible mechanics and a connection with the wider environment. Here, we propose a step toward that ideal by presenting an individual based model connecting thermodynamics, pH and chemical speciation and environmental conditions to microbial growth for 5·10⁵ individuals. We have showcased the model in two scenarios: a two functional group nitrification model and a three functional group anaerobic community. In the former, pH and connection to the environment had an important effect on the outcomes simulated. Whilst in the latter pH was less important but the spatial arrangements and community productivity (that is, methane production) were highly dependent on thermodynamic and reactor coupling. We conclude that if IbM are to attain their potential as tools to evaluate the emergent properties of engineered biological systems it will be necessary to combine the chemical, physical, mechanical and biological along the lines we have proposed. We have still fallen short of our ideals because we cannot (yet) calculate specific uptake rates and must develop the capacity for longer runs in larger models. However, we believe such advances are attainable. Ideally in a common, fast and modular platform. For future innovations in IbM will only be of use if they can be coupled with all the previous advances.

SUBMITTER: Gogulancea V

PROVIDER: S-EPMC6700366 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Individual Based Model Links Thermodynamics, Chemical Speciation and Environmental Conditions to Microbial Growth.

Gogulancea Valentina V González-Cabaleiro Rebeca R Li Bowen B Taniguchi Denis D Jayathilake Pahala Gedara PG Chen Jinju J Wilkinson Darren D Swailes David D McGough Andrew Stephen AS Zuliani Paolo P Ofiteru Irina Dana ID Curtis Thomas P TP

Frontiers in microbiology 20190813

Individual based Models (IbM) must transition from research tools to engineering tools. To make the transition we must aspire to develop large, three dimensional and physically and biologically credible models. Biological credibility can be promoted by grounding, as far as possible, the biology in thermodynamics. Thermodynamic principles are known to have predictive power in microbial ecology. However, this in turn requires a model that incorporates pH and chemical speciation. Physical credibili ...[more]

PMID: 31456784

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Project description:Metabolic theories in ecology interpret ecological patterns at different levels through the lens of metabolism, typically applying allometric power scaling laws to describe rates of energy use. This requires a sound theory for metabolism at the individual level. Commonly used mechanistic growth models lack some potentially important aspects and fail to accurately capture a growth pattern often observed in insects. Recently, a new model (MGM-the Maintenance-Growth Model) was developed for ontogenetic and post-mature growth, based on an energy balance that expresses growth as the net result of assimilation and metabolic costs for maintenance and feeding. The most important contributions of MGM are: 1) the division of maintenance costs into a non-negotiable and a negotiable part, potentially resulting in maintenance costs that increase faster than linearly with mass and are regulated in response to food restriction; 2) differentiated energy allocation strategies between sexes and 3) explicit description of costs for finding and processing food. MGM may also account for effects of body composition and type of growth at the cellular level. The model was here calibrated and evaluated using empirical data from an experiment on house crickets growing under ad libitum conditions. The procedure involved parameter estimations from the literature and collected data, using statistical models to account for individual variation in parameter values. It was found that ingestion rate cannot be generally described by a simple allometry, here requiring a more complex description after maturity. Neither could feeding costs be related to ingestion rate in a simplistic manner. By the unusual feature of maintenance costs increasing faster than linearly with body mass, MGM could well capture the differentiated growth patterns of male and female crickets. Some other mechanistic growth models have been able to provide good predictions of insect growth during early ontogeny, but MGM may accurately describe the trajectory until terminated growth.

Project description:Microbial heterotopic metabolism in the ocean is fueled by a supply of essential nutrients acquired via exoenzymes catalyzing depolymerization of high-molecular-weight compounds. Although the rates of activity for a variety of exoenzymes across various marine environments are well established, the factors regulating the production of these exoenzymes, and to some extent their correlation with microbial community composition, are less known. This study focuses on addressing these challenges using a mesocosm experiment that compared a natural seawater microbial community (control) and exposed (to oil) treatment. Exoenzyme activities for ?-glucosidase, leucine aminopeptidase (LAP), and lipase were significantly correlated with dissolved nutrient concentrations. We measured correlations between carbon- and nitrogen-acquiring enzymes (?-glucosidase/lipase versus LAP) and found that the correlation of carbon-acquiring enzymes varies with the chemical nature of the available primary carbon source. Notably, a strong correlation between particulate organic carbon and ?-glucosidase activity demonstrates their polysaccharide depolymerization in providing the carbon for microbial growth. Last, we show that exoenzyme activity patterns are not necessarily correlated with prokaryotic community composition, suggesting a redundancy of exoenzyme functions among the marine microbial community and substrate availability. This study provides foundational work for linking exoenzyme function with dissolved organic substrate and downstream processes in marine systems.IMPORTANCE Microbes release exoenzymes into the environment to break down complex organic matter and nutrients into simpler forms that can be assimilated and utilized, thereby addressing their cellular carbon, nitrogen, and phosphorus requirements. Despite its importance, the factors associated with the synthesis of exoenzymes are not clearly defined, especially for the marine environment. Here, we found that exoenzymes associated with nitrogen and phosphorus acquisition were strongly correlated with inorganic nutrient levels, while those associated with carbon acquisition depended on the type of organic carbon available. We also show a linear relationship between carbon- and nitrogen-acquiring exoenzymes and a strong correlation between microbial biomass and exoenzymes, highlighting their significance to microbial productivity. Last, we show that changes in microbial community composition are not strongly associated with changes in exoenzyme activity profiles, a finding which reveals a redundancy of exoenzyme activity functions among microbial community. These findings advance our understanding of previously unknown factors associated with exoenzyme production in the marine environment.

Dataset Information

Individual Based Model Links Thermodynamics, Chemical Speciation and Environmental Conditions to Microbial Growth.

Publications

Individual Based Model Links Thermodynamics, Chemical Speciation and Environmental Conditions to Microbial Growth.

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