微生物生态学理论框架

微生物是生态系统的重要组成部分,直接或间接地参与所有的生态过程。微生物生态学是基于微生物群体的科学,利用微生物群体DNA/RNA等标志物,重点研究微生物群落构建、组成演变、多样性及其与环境的关系,在生态学理论的指导和反复模型拟合下由统计分析得出具有普遍意义的结论。其研究范围从基因尺度到全球尺度。分子生物学技术的发展,使人们可以直接从基因水平上考查其多样性,从而使得对微生物空间分布格局及其成因的深入研究成为可能。进而可以从方法学探讨微生物生物多样性、分布格局、影响机制及其对全球变化的响应等。在微生物生态学研究中,群落构建与演化、分布特征(含植物-微生物相互关系)、执行群体功能的机理(生物地球化学循环等)、对环境变化的响应与反馈机理是今后需要关注的重点领域。概述了微生物生态学的概念,并初步提出其理论框架,在对比宏观生态学基础理论和模型的基础上,分析微生物多样性的研究内容、研究方法和群落构建的理论机制,展望了今后研究的重点领域。

A preliminary theoretical framework of microbial ecology

Microorganisms are important parts of ecosystems, and are essential to virtually all ecological processes such as the material cycle and energy transformation. Microbial ecology is the ecology of microorganisms, especially the guilds/consortia or community, and their relationship with one another and with their environment. Using DNA/RNA as the biomarker from the gene to the global scale, the construction of communities, change in composition, diversity, and the relationship with the environment are investigated. Sampling designs, statistical evaluation of results, and modeling approaches are widely used in microbial ecology studies. The target is to reach universal conclusions through model fitting and ecological theoretical syntheses. However, microbial ecology is limited by the lack of conceptual and theoretical approaches. The rapid accumulation of molecular data is uncovering vast diversity, abundant uncultivated microbial groups, and novel microbial functions. This accumulation of data requires the application of theory to provide organization, structure, mechanistic insight, and, ultimately, predictive power that is of practical value, but the application of theory in microbial ecology is currently very limited where, paradoxically, it is required most. It is possible that microbial diversity can be measured at the gene level using molecular biological technology. After a brief historical introduction, microbial diversity and the function in ecosystem are reviewed, and ecological parameters and their measurement are then discussed. This work also provides insights into relevant methodologies for the characterization of microorganisms in the environment. Differences between micro-and macro-organisms when ecological theories are applied are also described. Microbial activities in biogeochemical cycling and applied aspects of microbial ecology could also be considered in future. We argue that the full potential of the ongoing revolution will not be realized if research is not directed and driven by theory, and that the generality of established ecological theory must be tested using microbial systems. Understanding the ecology of microorganisms is arguably one of the most compelling intellectual challenges facing contemporary ecology. Although worthy for its intellectual merits alone, developing such an understanding is essential to meet many of the major challenges facing human society today, such as the management of natural ecosystems and the mitigation of climate change. In addition to carbon fixation, the key metabolic processes of microorganisms (including nitrogen fixation, methane metabolism, and sulfur metabolism) collectively control global biogeochemical cycling. The studies in the theoretical field have primarily focused on terrestrial macro-organisms for a long time. The microbial ecosystem has been neglected, especially the construction of a theoretical framework. However, microorganisms drive the biogeochemical cycling of elements and participate in ecosystem process. Therefore, the construction of a theoretical framework is crucial to the proper development of this academic subject. In this paper, we briefly introduce the concepts and research approaches of microbial ecology, research units (guilds/consortia, community), and the theoretical framework. Furthermore, we compare the application of ecological theories in microbial, animal, and botanical communities. This paper introduces microbial guilds/consortia and communities and explores a preliminary theoretical framework to the microbial ecology field, extending and deepening our understanding of microbial ecology. We also predict developments in the field of microbial ecology.