Partial Formalization: An Approach for Critical Analysis of Definitions and Methods Used in Bulk Extraction-Based Molecular Microbial Ecology

Abstract

Partial formalization, which involves the development of deductive connections among statements, can be used to examine assumptions, definitions and related methodologies that are used in science. This approach has been applied to the study of nucleic acids recovered from natural microbial assemblages (NMA) by the use of bulk extraction. Six pools of bulk-extractable nucleic acids (BENA) are suggested to be present in a NMA: (pool 1) inactive microbes (abiotic-limited); (pool 2) inactive microbes (abiotic permissive, biotic-limited); (pool 3) dormant microbes (abiotic permissive, biotic-limited, but can become biotic permissive); (pool 4) in situ active microbes (the microbial community); (pool 5) viruses (virocells/virions/cryptic viral genomes); and (pool 6) extracellular nucleic acids including extracellular DNA (eDNA). Definitions for cells, the microbial community (in situ active cells), the rare biosphere, dormant cells (the microbial seed bank), viruses (virocells/virions/cryptic viral genomic), and diversity are presented, together with methodology suggested to allow their study. The word diversity will require at least 4 definitions, each involving a different methodology. These suggested definitions and methodologies should make it possible to make further advances in bulk extraction-based molecular microbial ecology.