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From Donald A. Klein

Title: Molecular microbial ecology and natural microbial assemblages: it’s time to reclaim the paradigm of the past, so we can move forward to the future.

A notion from the 1985-1986 period become a non-negotiable view of science, a paradigm based on an indefensible notion: any molecular sequence extracted from microbial assemblages by bulk extraction-based techniques represents a microbe that is part of the microbial community, contributes to microbial diversity, and plays a role in microbial ecology. Since that time, the bulk extraction-based recovery of nucleic acids from natural microbial assemblages has become the “gold standard” for characterization of microbial communities, microbial diversity, and microbial ecology. It is now time to reject this indefensible notion-based paradigm and replace it with the etymologically and ecologically defensible paradigm that was in place before the 1985-1986 period.
What is the basis of the pre-l985-l986 paradigm for the study of communities, diversity and ecology, that developed over many decades of macroecology? These words were defined in terms of the assessment of in situ active organisms. When microorganisms are studied, similar approaches are required, at the same level of resolution. To provide information on microbial communities, diversity and ecology, in terms of assessing active organisms, great skill and refined techniques, frequently linked to careful direct observation of microbes in situ or ex situ, are required, to be able to generate information that is relevant to the etymologically defensible use of these words.
The use of bulk extraction-based analyses of nucleic acids recovered from microbial assemblages, in contrast, it makes it possible for individuals using this approach to say that they are studying these phenomena (communities, diversity and microbial ecology) that involve the study of in situ active microbes, when in reality they are not - they are merely studying extracted nucleic acids for which they do not know their origin or significance.

This indefensible post 1985-1986 paradigm eventually will be recognized as an enduring scandal of the molecular biology era, that has wreaked great damage upon scientific thinking and literally generations of aspiring scientists. What is the greatest damage? The legitimization of the notion that one can draw a conclusion concerning the source of information ( in this case nucleic acids) when the source of the information (nucleic acids) is not known.
Perhaps it’s time to go back to Science 101 - we can only draw conclusions that the data allow us to draw. In this case, if we don’t know the source of the nucleic acids that have been recovered from natural microbial assemblages by bulk extraction-based techniques, we can draw no conclusions concerning their possible source. It’s time to use defensible definitions of community, diversity and ecology, available to us from macroecology, when using molecular techniques to study microorganisms present in natural microbial assemblages. It’s time to reclaim the paradigm of the past, so we can move forward to the future.

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