Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
ISME J. 2010 May;4(5):599-610. doi: 10.1038/ismej.2009.158. Epub 2010 Feb 18.
Similar to virtually all components of natural environments, microbial systems are inherently complex and dynamic. Advances in cultivation-independent molecular methods have provided a route to study microbial consortia in their natural surroundings and to begin resolving the community structure, dominant metabolic processes and inter-organism interactions. However, the utility of these methods generally scales inversely with community complexity. By applying genomics-enabled methods to the study of natural microbial communities with reduced levels of species richness, a relatively comprehensive understanding of the metabolic networks and evolutionary processes within these communities can be attained. In such well-defined model systems, it is also possible to link emergent ecological patterns to their molecular and evolutionary underpinnings, facilitating construction of predictive ecosystem models. In this study, we review over a decade of research on one such system-acid mine drainage biofilm communities. We discuss the value and limitations of tractable model microbial communities in developing molecular methods for microbial ecology and in uncovering principles that may explain behavior in more complex systems.
类似于自然环境的几乎所有组成部分，微生物系统本质上是复杂和动态的。非培养依赖性分子方法的进步为研究微生物群落在其自然环境中的情况提供了一条途径，并开始解决群落结构、主要代谢过程和生物间相互作用。然而，这些方法的效用通常与群落的复杂性成反比。通过将基因组学方法应用于具有较低物种丰富度的自然微生物群落的研究，可以相对全面地了解这些群落中的代谢网络和进化过程。在这些定义明确的模型系统中，也有可能将新兴的生态模式与其分子和进化基础联系起来，从而促进预测性生态系统模型的构建。在这项研究中，我们回顾了十年来对一个这样的系统——酸性矿山排水生物膜群落的研究。我们讨论了在开发微生物生态学的分子方法和揭示可能解释更复杂系统行为的原则方面，可处理的模型微生物群落的价值和局限性。
