环境DNA技术在地下生态学中的应用

Applied environmental DNA technology to study underground ecology

地下生态过程是生态系统结构、功能和过程研究中最不确定的因素。由于技术和方法的限制,作为"黑箱"的地下生态系统已经成为限制生态学发展的瓶颈,也是未来生态学发展的主要方向。环境DNA技术,是指从土壤等环境样品中直接提取DNA片段,然后通过DNA测序技术来定性或定量化目标生物,以确定目标生物在生态系统中的分布及功能特征。环境DNA技术已成功用于地下生态过程的研究。目前,环境DNA技术在土壤微生物多样性及其功能方面的研究相对成熟,克服了土壤微生物研究中不能培养的问题,可以有效地分析土壤微生物的群落组成、多样性及空间分布,尤其是宏基因组学技术的发展,使得微生物生态功能方面的研究成为可能;而且,环境DNA技术已经在土壤动物生态学的研究中得到了初步应用,可快速分析土壤动物的多样性及其分布特征,更有效地鉴定出未知的或稀少的物种,鉴定土壤动物类群的幅度较宽;部分研究者通过提取分析土壤中DNA片段信息对生态系统植物多样性及植物分类进行了研究,其结果比传统的植物分类及物种多样性测定更精确,改变了以往对植物群落物种多样性模式的理解。同时,环境DNA技术克服传统根系研究方法中需要洗根、分根、只能测定单物种根系的局限,降低根系研究中细根区分的误差,并探索性地用于细根生物量的研究。主要综述了基于环境DNA技术的分子生物学方法在土壤微生物多样性及功能、土壤动物多样性、地下植物多样性及根系生态等地下生态过程研究中的应用进展。环境DNA技术对于以土壤微生物、土壤动物及地下植物根系为主体的地下生态学过程的研究具有革命性意义,并展现出良好的应用前景。可以预期,分子生物学技术与传统的生态学研究相结合将成为未来地下生态学研究的一个发展趋势。

Ecological processes below ground have the least understood factors in ecosystem structure, functions, and processes. Due to technical and methodological limitations, the underground ecosystem ecology, as a ＂black box＂, has become a bottleneck in the development of modern ecology. With the recent development of new DNA methods, the underground ecological research is becoming a hot topic in ecology. Environmental DNA technology includes extraction of DNA fragments directly from environmental samples such as soil, qualitative and quantitative analyses of target organisms by DNA sequencing, and determination of the distribution and functional characteristics of target organisms in the ecosystem. The technology has been successfully applied to study underground ecological processes. Currently, environmental DNA technology is relatively established in the study of microbial diversity and function, and overcomes the long and unsolved issue that most soil microorganisms cannot be cultured. The environmental DNA technology can effectively analyze soil microbial community composition, diversity, and spatial distribution. Microbial function in underground ecological processes can be determined by metagenomics technology. This technology has also been applied to study soil animals; it can quickly analyze diversity and distribution of soil animals, more effectively identify unknown or rare species, and widen the magnitude of the soil fauna identification. Some studies on plant biodiversity and plant taxonomy have utilized extraction and analysis of DNA fragment information in soil. The results obtained by this technology have been more accurate than those obtained by traditional methods. The environmental DNA technology has changed our knowledge about the pattern of plant species diversity. Meanwhile, this technology can overcome the limitations in traditional studies of root systems by reducing the error in root identification, and it can be applied to analyze complex roots involving several species. The environmental DNA technology has also been used to estimate the fine root biomass. In this paper, we summarized the DNA-based molecular methods applied in the study of microbial diversity and function, soil animal diversity, underground plant diversity, roots ecology, and other underground ecological processes, and we believe that our results will provide new ideas and inspiration for studies on complex underground ecology. Environmental DNA technology will be revolutionary in identifying the underground ecosystem structure and function, especially in the ecological processes related to soil microorganisms, animals, plant diversity, and plant roots studies. Future work should focus on three research aspects： （1） ecological function of soil organisms, especially soil animals, by metagenomics technology; （2） application of environmental DNA technology in roots ecology, such as fine root biomass estimation, underground configuration of plant communities, distinguishing roots and rhizosphere, nutrient competition between plants and microbes in soil; and （3） scaling up, from small-scale observations and experiments to the prediction of large-scale patterns as a key to unravel the questions in molecular ecology. It is necessary to fully combine environmental DNA technology with the theory and methods of traditional ecology, especially in the studies of community ecology and ecosystem ecology. Environmental DNA technology has very broad application prospects in underground ecological research. Molecular biology techniques combined with traditional ecological methods will be the future trend of underground ecology.