TITLE:
Partial Formalization: An Approach for Critical Analysis of Definitions and Methods Used in Bulk Extraction-Based Molecular Microbial Ecology
AUTHORS:
Donald A. Klein
KEYWORDS:
Abiotic Envelope, Baas Becking, Biotic Envelope, Bulk Extraction, Cells, Community, Definitions, Dormancy, Methodology, Microbial Diversity, Microbial Seed Bank, Natural Microbial Assemblages, Partial Formalization, Rare Biosphere
JOURNAL NAME:
Open Journal of Ecology,
Vol.5 No.8,
August
25,
2015
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.