School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen AB24 3UU, UK.
Philos Trans R Soc Lond B Biol Sci. 2020 May 11;375(1798):20190240. doi: 10.1098/rstb.2019.0240. Epub 2020 Mar 23.
Microbial ecology, the scientific study of interactions between natural microbial communities and their environments, has been facilitated by the application of molecular and 'omics'-based techniques that overcome some of the limitations of cultivation-based studies. This has increased emphasis on community ecology and 'microbiome' studies, but the majority address technical, rather than scientific challenges. Most are descriptive, do not address scientific aims or questions and are not designed to increase understanding or test hypotheses. The term 'hypothesis' is increasingly misused and critical testing of ideas or theory is restricted to a small minority of studies. This article discusses current microbial ecology research within the context of four approaches: description, induction, inference to the best explanation and deduction. The first three of these do not follow the established scientific method and are not based on scientific ecological questions. Observations are made and sometimes compared with published data, sometimes with attempts to explain findings in the context of existing ideas or hypotheses, but all lack objectivity and are biased by the observations made. By contrast, deductive studies address ecological questions and attempt to explain currently unexplained phenomena through the construction of hypotheses, from mechanism-based assumptions, that generate predictions that are then tested experimentally. Identification of key scientific questions, research driven by meaningful hypotheses and adoption of scientific method are essential for progress in microbial ecology, rather than the current emphasis on descriptive approaches that address only technical challenges. It is, therefore, imperative that we carefully consider and define the fundamental scientific questions that drive our own research and focus on ideas, concepts and hypotheses that can increase understanding, and only then consider which techniques are required for experimental testing. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.
微生物生态学是研究自然微生物群落与其环境之间相互作用的科学，它得益于分子和“组学”技术的应用，这些技术克服了培养研究的一些局限性。这增加了对群落生态学和“微生物组”研究的重视，但大多数研究都是针对技术问题，而不是科学问题。大多数研究是描述性的，没有解决科学目标或问题，也不是为了增加理解或检验假设而设计的。“假设”一词的使用越来越不当，批判性地检验思想或理论的研究仅限于少数研究。本文讨论了当前微生物生态学研究在以下四种方法的背景下的情况：描述、归纳、最佳解释推理和演绎。这前三种方法都不符合既定的科学方法，也不是基于科学的生态问题。人们进行观察，有时与已发表的数据进行比较，有时试图在现有思想或假设的背景下解释发现，但所有这些方法都缺乏客观性，并且受到观察结果的偏见。相比之下，演绎研究解决生态问题，并试图通过构建假设、基于机制的假设来解释当前无法解释的现象，这些假设产生预测，然后通过实验进行检验。确定关键的科学问题，以有意义的假设为驱动的研究，并采用科学方法，对于微生物生态学的进展至关重要，而不是当前强调仅解决技术挑战的描述性方法。因此，我们必须仔细考虑和定义推动我们自己研究的基本科学问题，关注能够增加理解的思想、概念和假设，然后再考虑需要哪些技术进行实验检验。本文是“微生物群落生态学的概念性挑战”主题特刊的一部分。
