A preliminary theoretical framework of microbial ecology

Abstract

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.