From genes to ecosystems in microbiology: modeling approaches and the importance of individuality

摘要: Models are important tools in microbial ecology. They can be used to advance understanding by helping interpret observations and test hypotheses, predict the effects of ecosystem management actions or a different climate. Over past decades, biological knowledge have advanced molecular particular gene level. However, ecology models changed less current challenge is make them utilize at genetic We review published that explicitly consider genes predictions population The grouped into three general approaches, i.e., metabolic flux, gene-centric agent-based. describe contrast these approaches applying hypothetical discuss their strengths weaknesses. An distinguishing feature how variation between individual cells (individuality) handled. In ecosystems, heterogeneity generated number mechanisms including stochastic interactions molecules (e.g., expression), deterministic cell division asymmetry, small-scale environmental heterogeneity, differential transport heterogeneous environment. This then amplified transferred other properties several mechanisms, nutrient uptake, metabolism growth, cycle asynchronicity age damage. For example, expression may lead uptake enzyme levels, which turn results intracellular levels. Individuality ecological consequences, labor, bet hedging, aging sub-optimality. Understanding importance individuality mechanism(s) underlying it for specific system question investigated essential selecting optimal modeling strategy.