中文摘要：

土壤微生物驱动着土壤中的物质循环和养分转化。在土壤学的研究中，长期将土壤作为一个黑箱系统来对待，对其中的生物组成及其参与的生化过程知之甚少。土壤中绝大部分微生物目前尚难以分离培养，因此基于传统的培养方法对于认识土壤微生物群落组成和功能有其局限性。宏基因组学直接从环境样品中提取全部微生物的DNA，或通过测序探究环境中微生物的群落结构和功能（序列驱动），或构建宏基因组文库，筛选新的基因或生物活性物质（功能驱动），克服了传统培养方法的缺陷，极大地丰富了对土壤微生物多样性及其功能的认知。本文在综述土壤宏基因组学基本流程的基础上，重点介绍了日益重要的第二代测序平台在土壤宏基因组学研究中的应用及其产生的海量数据的分析处理方法，并简要探讨了宏基因组学在土壤微生物生态学中的应用。最后，作者建议在国家层面上展开相关土壤宏基因组学研究，调查微生物群落及其变化，为生物资源开发、农业生产和环境保护作出应有的贡献。

英文摘要：

Soil microorganisms are a driving force in material recycling and nutrient transformation in soil. However, for a long time, soil has been treated as a “black box” system, wherein microbial diversity and biochemical processes they participate in soil remain to be explored. Since most of the soil microorganisms are still quite hard to be isolated for culture, traditional culture methods are quite limited in helping reveal compositions and functions of soil microbial communities. The metagenomic method is able to explore the structures and functions （sequence-driven approach） of soil microbial community and to screen bioactive materials and new genes （function-driven approach） through extracting all microbial DNAs direct from environment samples and then sequencing or constructing clone library, thus breaking through the bottleneck of the traditional methods and greatly enriching the knowledge about soil microbial biodiversity and functions. While reviewing main procedures of the metagenomic technique, the paper focuses on the introduction to application of the next-generation sequencing （NGS） technologies in metagenomic research and processing of the huge volume of data it may produce. The new processes on soil microbial ecology with the metagenomic technique is then discussed. And in the end, the authors propose that research projects on soil metagenomics projects should be launched at the national level to explore soil microorganism communities and their variation, so as to contribute to the causes of bioresource exploitation, agricultural production and environment protection.