The development of culture-independent strategies to study microbial diversity and function has led to a revolution in microbial ecology, enabling us to address fundamental questions about the distribution of microbes and their influence on Earth’s biogeochemical cycles. This article discusses some of the progress that scientists have made with the use of so-called “omic” techniques (metagenomics, metatranscriptomics, and metaproteomics) and the limitations and major challenges these approaches are currently facing. These ‘omic methods have been used to describe the taxonomic structure of microbial communities in different environments and to discover new genes and enzymes of industrial and medical interest. However, microbial community structure varies in different spatial and temporal scales and none of the ‘omic techniques are individually able to elucidate the complex aspects of microbial communities and ecosystems. In this article we highlight the importance of a spatiotemporal sampling design, together with a multilevel ‘omic approach and a community analysis strategy (association networks and modeling) to examine and predict interacting microbial communities and their impact on the environment.

中文翻译：

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超越基因组：微生物世界的社区级分析

研究微生物多样性和功能的独立培养策略的发展引发了微生物生态学的革命，使我们能够解决有关微生物分布及其对地球生物地球化学循环影响的基本问题。本文讨论了科学家使用所谓的“组学”技术（宏基因组学、宏转录组学和宏蛋白质组学）取得的一些进展，以及这些方法目前面临的局限性和主要挑战。这些“组学方法”已被用于描述不同环境中微生物群落的分类结构，并发现具有工业和医学意义的新基因和酶。然而，微生物群落结构在不同的空间和时间尺度上各不相同，并且没有一种组学技术能够单独阐明微生物群落和生态系统的复杂方面。在本文中，我们强调了时空抽样设计的重要性，以及多层次的“组学方法”和社区分析策略（关联网络和建模），以检查和预测相互作用的微生物群落及其对环境的影响。