From Genes to Ecosystems in Microbiology: Modeling Approaches and the Importance of Individuality
| العنوان: | From Genes to Ecosystems in Microbiology: Modeling Approaches and the Importance of Individuality |
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| المؤلفون: | Johan H. J. Leveau, Caroline M. Plugge, Weiwen Zhang, Clara Prats, Ferdi L. Hellweger, Jan-Ulrich Kreft |
| المساهمون: | Universitat Politècnica de Catalunya. Departament de Física, Universitat Politècnica de Catalunya. BIOCOM-SC - Grup de Biologia Computacional i Sistemes Complexos |
| المصدر: | Frontiers in microbiology, vol 8, iss NOV Frontiers in Microbiology, 8(NOV) UPCommons. Portal del coneixement obert de la UPC Universitat Politècnica de Catalunya (UPC) Recercat. Dipósit de la Recerca de Catalunya instname Frontiers in Microbiology 8 (2017) NOV Frontiers in Microbiology Frontiers in Microbiology, Vol 8 (2017) |
| بيانات النشر: | Frontiers Media SA, 2017. |
| سنة النشر: | 2017 |
| مصطلحات موضوعية: | 0301 basic medicine, individuality, Microbiology (medical), Environmental Science and Management, Population, lcsh:QR1-502, Individuality, Microbiologia, Review, Variation (game tree), Biology, microbial ecology, Microbiology, lcsh:Microbiology, Microbial ecology, 03 medical and health sciences, Microbiologie, Genetics, Enginyeria agroalimentària::Ciències de la terra i de la vida::Microbiologia [Àrees temàtiques de la UPC], Ecosystem, Single cell, education, Gene, 2. Zero hunger, education.field_of_study, WIMEK, gene-centric modeling, Mechanism (biology), Ecology, agent-based modeling, 15. Life on land, single cell, Gene-centric modeling, metabolic flux modeling, Genètica microbiana, 030104 developmental biology, 13. Climate action, Evolutionary biology, Agent-based modeling, Soil Sciences, Ecosystem management, Generic health relevance, Metabolic flux modeling, heterogeneity, Heterogeneity, Flux (metabolism), Microbial genetics |
| الوصف: | Models are important tools in microbial ecology. They can be used to advance understanding by helping to interpret observations and test hypotheses, and to predict the effects of ecosystem management actions or a different climate. Over the past decades, biological knowledge and ecosystem observations have advanced to the molecular and in particular gene level. However, microbial ecology models have changed less and a current challenge is to make them utilize the knowledge and observations at the genetic level. We review published models that explicitly consider genes and make predictions at the population or ecosystem level. The models can be grouped into three general approaches, i.e., metabolic flux, gene-centric and agent-based. We describe and contrast these approaches by applying them to a hypothetical ecosystem and discuss their strengths and weaknesses. An important distinguishing feature is how variation between individual cells (individuality) is handled. In microbial ecosystems, individual heterogeneity is generated by a number of mechanisms including stochastic interactions of molecules (e.g., gene expression), stochastic and deterministic cell division asymmetry, small-scale environmental heterogeneity, and differential transport in a heterogeneous environment. This heterogeneity can then be amplified and transferred to other cell properties by several mechanisms, including nutrient uptake, metabolism and growth, cell cycle asynchronicity and the effects of age and damage. For example, stochastic gene expression may lead to heterogeneity in nutrient uptake enzyme levels, which in turn results in heterogeneity in intracellular nutrient levels. Individuality can have important ecological consequences, including division of labor, bet hedging, aging and sub-optimality. Understanding the importance of individuality and the mechanism(s) underlying it for the specific microbial system and question investigated is essential for selecting the optimal modeling strategy. |
| وصف الملف: | application/pdf; application/octet-stream |
| اللغة: | English |
| تدمد: | 1664-302X |
| DOI: | 10.3389/fmicb.2017.02299 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6e305635e1a1ce2c63c0c85798ec0a3cTest |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....6e305635e1a1ce2c63c0c85798ec0a3c |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 1664302X |
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| DOI: | 10.3389/fmicb.2017.02299 |