Jia Zhongjun
State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
Wei Sheng Wu Xue Bao. 2011 Dec;51(12):1585-94.
Microbial communities are the engines that drive the global biogeochemical cycle of carbon and nitrogen essential for life on Earth. However, microorganisms have evolved as a result of complex interactions with other organisms and environments. Deciphering the metabolism of microorganisms at the community level in nature will be crucial for a better understanding of the mechanisms that lead to the enormous divergence of microbial ecophysiology. Due to the immense number of uncultivated microbial species and the complexity of microbial communities, delineating community metabolism proves a virtually insurmountable hurdle. By tracing the heavy isotope flow of key elements such as carbon and nitrogen, DNA-based stable isotope probing (DNA-SIP) can provide unequivocal evidence for substrate assimilation by microorganisms in complex environments. The essential prerequisite for a successful DNA-SIP is the identification, with confidence, of isotopically enriched 13C-DNA, of which the amount is generally too low to allow the direct measurement of 13C atom percent of nucleic acid. The methodological considerations for obtaining unambiguous DNA highly enriched in heavy isotope are presented with emphasis on next-generation sequencing technology and metagenomics.
微生物群落是驱动地球上生命所必需的碳和氮全球生物地球化学循环的引擎。然而，微生物是在与其他生物和环境的复杂相互作用中进化而来的。在群落水平上解析自然界中微生物的代谢对于更好地理解导致微生物生态生理学巨大差异的机制至关重要。由于未培养微生物种类数量庞大且微生物群落复杂，描绘群落代谢几乎是一个无法逾越的障碍。通过追踪碳和氮等关键元素的重同位素流，基于DNA的稳定同位素探测（DNA-SIP）可以为复杂环境中微生物的底物同化提供明确证据。成功进行DNA-SIP的基本前提是准确鉴定同位素富集的13C-DNA，其含量通常过低，无法直接测量核酸的13C原子百分比。本文重点介绍了利用下一代测序技术和宏基因组学获得高度富集重同位素的明确DNA的方法学考量。
