Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstrasse 15, Leipzig, Germany.
Appl Microbiol Biotechnol. 2012 May;94(4):851-73. doi: 10.1007/s00253-012-4025-0. Epub 2012 Apr 4.
Biodegradation of anthropogenic pollutants in shallow aquifers is an important microbial ecosystem service which is mainly brought about by indigenous anaerobic microorganisms. For the management of contaminated sites, risk assessment and control of natural attenuation, the assessment of in situ biodegradation and the underlying microbial processes is essential. The development of novel molecular methods, "omics" approaches, and high-throughput techniques has revealed new insight into complex microbial communities and their functions in anoxic environmental systems. This review summarizes recent advances in the application of molecular methods to study anaerobic microbial communities in contaminated terrestrial subsurface ecosystems. We focus on current approaches to analyze composition, dynamics, and functional diversity of subsurface communities, to link identity to activity and metabolic function, and to identify the ecophysiological role of not yet cultured microbes and syntrophic consortia. We discuss recent molecular surveys of contaminated sites from an ecological viewpoint regarding degrader ecotypes, abiotic factors shaping anaerobic communities, and biotic interactions underpinning the importance of microbial cooperation for microbial ecosystem services such as contaminant degradation.
在浅层含水层中生物降解人为污染物是一项重要的微生物生态系统服务，主要由本土的厌氧微生物带来。为了管理污染场地、进行自然衰减的风险评估和控制，评估原位生物降解和潜在的微生物过程是必不可少的。新型分子方法、“组学”方法和高通量技术的发展，揭示了在缺氧环境系统中复杂微生物群落及其功能的新见解。本文综述了分子方法在研究污染的陆地地下生态系统中厌氧微生物群落的应用方面的最新进展。我们重点介绍了当前分析地下群落组成、动态和功能多样性的方法，将身份与活性和代谢功能联系起来，并确定尚未培养的微生物和共生体的生态生理学作用。我们从生态角度讨论了污染场地的最新分子调查，涉及降解菌生态型、塑造厌氧群落的非生物因素以及支持微生物合作对微生物生态系统服务（如污染物降解）重要性的生物相互作用。
